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Sample records for highly diverse adaptive

  1. High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population.

    Directory of Open Access Journals (Sweden)

    Adam L Bailey

    Full Text Available Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel members of the viral family Arteriviridae: simian hemorrhagic fever virus (SHFV-krc1 and SHFV-krc2, infecting a single wild red colobus (Procolobus rufomitratus tephrosceles in Kibale National Park, Uganda. Nearly nothing is known about the biological properties of SHFVs in nature, although the SHFV type strain, SHFV-LVR, has caused devastating outbreaks of viral hemorrhagic fever in captive macaques. Here we detected SHFV-krc1 and SHFV-krc2 in 40% and 47% of 60 wild red colobus tested, respectively. We found viral loads in excess of 10(6-10(7 RNA copies per milliliter of blood plasma for each of these viruses. SHFV-krc1 and SHFV-krc2 also showed high genetic diversity at both the inter- and intra-host levels. Analyses of synonymous and non-synonymous nucleotide diversity across viral genomes revealed patterns suggestive of positive selection in SHFV open reading frames (ORF 5 (SHFV-krc2 only and 7 (SHFV-krc1 and SHFV-krc2. Thus, these viruses share several important properties with some of the most rapidly evolving, emergent RNA viruses.

  2. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

    Directory of Open Access Journals (Sweden)

    Marie Touchon

    2009-01-01

    Full Text Available The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re- annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species, including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an

  3. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

    Science.gov (United States)

    Touchon, Marie; Hoede, Claire; Tenaillon, Olivier; Barbe, Valérie; Baeriswyl, Simon; Bidet, Philippe; Bingen, Edouard; Bonacorsi, Stéphane; Bouchier, Christiane; Bouvet, Odile; Calteau, Alexandra; Chiapello, Hélène; Clermont, Olivier; Cruveiller, Stéphane; Danchin, Antoine; Diard, Médéric; Dossat, Carole; Karoui, Meriem El; Frapy, Eric; Garry, Louis; Ghigo, Jean Marc; Gilles, Anne Marie; Johnson, James; Le Bouguénec, Chantal; Lescat, Mathilde; Mangenot, Sophie; Martinez-Jéhanne, Vanessa; Matic, Ivan; Nassif, Xavier; Oztas, Sophie; Petit, Marie Agnès; Pichon, Christophe; Rouy, Zoé; Ruf, Claude Saint; Schneider, Dominique; Tourret, Jérôme; Vacherie, Benoit; Vallenet, David; Médigue, Claudine; Rocha, Eduardo P C; Denamur, Erick

    2009-01-01

    The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.

  4. Intragenomic diversity and geographical adaptability of diploid ...

    African Journals Online (AJOL)

    SERVER

    2007-06-18

    Jun 18, 2007 ... indicates genomic differences among diploid G. herbaceum cultivars, which can be used in cotton hybridization programs in Iran or other countries. Key words: Gossypium herbaceum, Intragenomic diversity, Adaptability, Karyotype. INTRODUCTION. Variation in chromosome number and karyotype has.

  5. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.

    Science.gov (United States)

    Lachance, Joseph; Vernot, Benjamin; Elbers, Clara C; Ferwerda, Bart; Froment, Alain; Bodo, Jean-Marie; Lema, Godfrey; Fu, Wenqing; Nyambo, Thomas B; Rebbeck, Timothy R; Zhang, Kun; Akey, Joshua M; Tishkoff, Sarah A

    2012-08-03

    To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at > 60× coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

    Science.gov (United States)

    de Vries, Ronald P; Riley, Robert; Wiebenga, Ad; Aguilar-Osorio, Guillermo; Amillis, Sotiris; Uchima, Cristiane Akemi; Anderluh, Gregor; Asadollahi, Mojtaba; Askin, Marion; Barry, Kerrie; Battaglia, Evy; Bayram, Özgür; Benocci, Tiziano; Braus-Stromeyer, Susanna A; Caldana, Camila; Cánovas, David; Cerqueira, Gustavo C; Chen, Fusheng; Chen, Wanping; Choi, Cindy; Clum, Alicia; Dos Santos, Renato Augusto Corrêa; Damásio, André Ricardo de Lima; Diallinas, George; Emri, Tamás; Fekete, Erzsébet; Flipphi, Michel; Freyberg, Susanne; Gallo, Antonia; Gournas, Christos; Habgood, Rob; Hainaut, Matthieu; Harispe, María Laura; Henrissat, Bernard; Hildén, Kristiina S; Hope, Ryan; Hossain, Abeer; Karabika, Eugenia; Karaffa, Levente; Karányi, Zsolt; Kraševec, Nada; Kuo, Alan; Kusch, Harald; LaButti, Kurt; Lagendijk, Ellen L; Lapidus, Alla; Levasseur, Anthony; Lindquist, Erika; Lipzen, Anna; Logrieco, Antonio F; MacCabe, Andrew; Mäkelä, Miia R; Malavazi, Iran; Melin, Petter; Meyer, Vera; Mielnichuk, Natalia; Miskei, Márton; Molnár, Ákos P; Mulé, Giuseppina; Ngan, Chew Yee; Orejas, Margarita; Orosz, Erzsébet; Ouedraogo, Jean Paul; Overkamp, Karin M; Park, Hee-Soo; Perrone, Giancarlo; Piumi, Francois; Punt, Peter J; Ram, Arthur F J; Ramón, Ana; Rauscher, Stefan; Record, Eric; Riaño-Pachón, Diego Mauricio; Robert, Vincent; Röhrig, Julian; Ruller, Roberto; Salamov, Asaf; Salih, Nadhira S; Samson, Rob A; Sándor, Erzsébet; Sanguinetti, Manuel; Schütze, Tabea; Sepčić, Kristina; Shelest, Ekaterina; Sherlock, Gavin; Sophianopoulou, Vicky; Squina, Fabio M; Sun, Hui; Susca, Antonia; Todd, Richard B; Tsang, Adrian; Unkles, Shiela E; van de Wiele, Nathalie; van Rossen-Uffink, Diana; Oliveira, Juliana Velasco de Castro; Vesth, Tammi C; Visser, Jaap; Yu, Jae-Hyuk; Zhou, Miaomiao; Andersen, Mikael R; Archer, David B; Baker, Scott E; Benoit, Isabelle; Brakhage, Axel A; Braus, Gerhard H; Fischer, Reinhard; Frisvad, Jens C; Goldman, Gustavo H; Houbraken, Jos; Oakley, Berl; Pócsi, István; Scazzocchio, Claudio; Seiboth, Bernhard; vanKuyk, Patricia A; Wortman, Jennifer; Dyer, Paul S; Grigoriev, Igor V

    2017-02-14

    The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

  7. Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.

    Directory of Open Access Journals (Sweden)

    Steven Micheletti

    Full Text Available Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana that is found in habitats with both dark (lava and light colored (granite substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b. Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation.

  8. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians

    National Research Council Canada - National Science Library

    Yang, Xinwang; Wang, Ying; Zhang, Yue; Lee, Wen-Hui; Zhang, Yun

    2016-01-01

    .... wuchuanensis to elevated UV radiation was investigated. Compared with O. wuchuanensis, O. andersonii exhibited greater diversity and free radical scavenging potentiality of skin antioxidant peptides to cope with UV radiation...

  9. RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis (L.) Schrad: a unique source of germplasm highly adapted to drought and high-temperature stress.

    Science.gov (United States)

    Verma, Kumar Sambhav; Ul Haq, Shamshad; Kachhwaha, Sumita; Kothari, S L

    2017-10-01

    Citrullus colocynthis (L.) Schrad. (Cucurbitaceae) shows high levels of variation in fruit color, fruit stripe pattern, seed coat color, and size. Thirty-eight accessions of C. colocynthis plants from different parts of semi-arid Rajasthan were collected and genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 65 RAPD decamer primers, 50 primers produced 549 scorable bands of which 318 were polymorphic. Polymorphic banding patterns with the number of amplified fragments varied from 5 (OPA-08 and OPF-9) to 19 (OPT-20) in the molecular size range of 150-6000 bp. Percent polymorphism ranged from 22.2% (OPA-09) to 83.3% (OPE-12) with 55.14% polymorphism. Out of the 20 ISSR primers screened, 13 primers produced 166 amplification products, of which 99 were polymorphic. The number of bands amplified per primer varied between 9 (UBC-807, 802) and 16 (UBC-803, 812) with average band size between 250 and 4000 bp. Percent polymorphism ranged from 45.4% (UBC-815) to 73.3% (UBC-814) with 65.05% polymorphism. Dendrogram constructed on the basis of RAPD + ISSR polymorphism separated the accessions into four distinct clusters at 72% variation with Jaccard's similarity coefficient ranging from minimum 0.64 to 0.95. The matrices for RAPD and ISSR were also compared using Mantel's test and obtained correlation value (r = 0.7947). Discriminating power of RAPD and ISSR markers was assessed by calculating polymorphic information content, multiplex ratio, marker index, and resolving power. Approx. 50% RAPD and ISSR markers showed PIC value and heterozygosity (H) ≥ 0.50, indicating marker as informative. The primers that showed higher polymorphism had higher RP, MR, and MI values.

  10. Adaptive morphologies and guild structure in a high-diversity bivalve fauna from an early Campanian rocky shore, Ivö Klack (Sweden)

    DEFF Research Database (Denmark)

    Sørensen, Anne Mehlin; Surlyk, Finn; Jagt, John W. M.

    2012-01-01

    habitats. Study of the functional morphology of bivalve shells and comparison with extant relatives has resulted in a subdivision of the fauna into seven guilds and five habitats. The bivalve fauna represents a withinhabitat, time-averaged assemblage to which none of the species was introduced from......The bivalve fauna from a late early Campanian rocky shore at Ivö Klack (southern Sweden), comprises just over sixty species, a very high diversity in comparison to other Late Cretaceous and modern rocky shore bivalve assemblages. This high diversity is here considered to represent a reliable census...... of the fauna; only in part can it be explained by the cumulative effect of generations of bivalves inhabiting this coastal environment. The high density and diversity and the wide range of shell morphologies allow interpretation of different modes of life in this variable environment with many contrasting...

  11. [Phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, Artic].

    Science.gov (United States)

    Yu, Yong; Li, Hui-Rong; Chen, Bo; Zeng, Yin-Xin; He, Jian-Feng

    2006-04-01

    The phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'N - 81 degrees 12'N), Canadian Basin and Greenland sea Arctic, was investigated. A total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microL of each dilution ice-melt sample was spreaded onto the surface of Marine 2216 agar (DIFCO laboratories, Detroit, MI) and incubated for 2 to 6 weeks at 4 degrees C; ( ii ) bath culture and spread plate method: 1 mL of sample was added to 9mL of NSW (unamended natural seawater, 0.2 microm prefiltered and autoclaved) and incubated for 1 months at - 1 degrees C, then spread plate method was used to isolate bacterial strains from the pre-cultured samples; ( iii ) cold shock, bath culture and spread plate method: samples were exposed to - 20 degrees C for 24h, then bacterial strains isolated by bath culture and spread plate method under aerobic conditions. Nearly half of psychrophilic strains are isolated by using method iii . 16S rDNA nearly full-length sequence analysis reveal that psychrophilic strains fall in two phylogenetic divisions, gamma-proteobacteria (in the genera Colwellia, Marinobacter, Shewanella, Thalassomonas, Glaciecola, Marinomonas and Pseudoalteromonas) and Cytophaga-Flexibacter-Bacteroides (in the genera Flavobacterium and Psychroflexus). Nine of bacterial isolates (BSi20007, BSi20497, BSi20517, BSi20537, BSi20170, BSi20001, BSi20002, BSi20675 and BSi20101) quite likely represent novel species (16S rDNA sequence similarity below 97%). One of strains (BSi20002) from Canadian Basin shows 100% sequence similarity to the Antarctic Weddell sea ice isolate Marinobacter sp. ANT8277, suggesting bacteria may have a bipolar distribution at the species level. AF283859 sequences were submitted to the BLAST search program of the National Center for Biotechnology Information website (NCBI, http://www. ncbi. nlm.nih. gov). Twenty sequences

  12. The statistics of genetic diversity in rapidly adapting populations.

    Science.gov (United States)

    Desai, Michael

    2013-03-01

    Evolutionary adaptation is driven by the accumulation of beneficial mutations, but the sequence-level dynamics of this process are poorly understood. The traditional view is that adaptation is dominated by rare beneficial ``driver'' mutations that occur sporadically and then rapidly increase in frequency until they fix (a ``selective sweep''). Yet in microbial populations, multiple beneficial mutations are often present simultaneously. Selection cannot act on each mutation independently, but only on linked combinations. This means that the fate of any mutation depends on a complex interplay between its own fitness effect, the genomic background in which it arises, and the rest of the sequence variation in the population. The balance between these factors determines which mutations fix, the patterns of sequence diversity within populations, and the degree to which evolution in replicate populations will follow parallel (or divergent) trajectories at the sequence level. Earlier work has uncovered signatures of these effects, but the dynamics of genomic sequence evolution in adapting microbial populations have not yet been directly observed. In this talk, I will describe how full-genome whole-population sequencing can be used to provide a detailed view of these dynamics at high temporal resolution over 1000 generations in 40 adapting Saccharomyces cerevisiaepopulations. This data shows how patterns of sequence evolution are driven by a balance between chance interference and hitchhiking effects, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favors parallel solutions in replicate populations.

  13. Defining the landscape of adaptive genetic diversity.

    Science.gov (United States)

    Eckert, Andrew J; Dyer, Rodney J

    2012-06-01

    Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). © 2012 Blackwell Publishing Ltd.

  14. Stress-mediated adaptive response leading to genetic diversity and instability in metabolite contents of high medicinal value: an overview on Podophyllum hexandrum.

    Science.gov (United States)

    Gupta, Manju Lata; Dutta, Ajaswrata

    2011-12-01

    Podophyllum hexandrum, known for its diversified clinical importance particularly for antineoplastic activity and valuable source for biological protection against high doses of radiation, has its unique position in the plant kingdom. Detailed understanding of mechanism and opportunity of chemical manipulations has amplified the scope of its bioactivity. Podophyllotoxin, the major active principle of this plant, has passed through various structural deviations with the basic aim of making the end product clinically more effective with minimal toxicity. However, over exploitation and limited growth has categorized this plant under endangered species. Depending upon the geographical variations, different species and subspecies of this plant have been explored. Morphological variations and quantitative differences in active principles are the major concern of its unstable medicinal value in whole and semifractionated preparations. The current review has addressed the issues related to the genetic diversity of P. hexandrum, extrinsic and intrinsic stresses responsible for its diversified nature, chemical modifications to enhance its multitasking bioactivity, and efforts for its cultivation and production of important metabolites to avoid collection of wild species due to its critically endangered nature.

  15. Joint adaptive modulation and diversity combining with feedback error compensation

    KAUST Repository

    Choi, Seyeong

    2009-11-01

    This letter investigates the effect of feedback error on the performance of the joint adaptive modulation and diversity combining (AMDC) scheme which was previously studied with an assumption of error-free feedback channels. We also propose to utilize adaptive diversity to compensate for the performance degradation due to feedback error. We accurately quantify the performance of the joint AMDC scheme in the presence of feedback error, in terms of the average number of combined paths, the average spectral efficiency, and the average bit error rate. Selected numerical examples are presented and discussed to illustrate the effectiveness of the proposed feedback error compensation strategy with adaptive combining. It is observed that the proposed compensation strategy can offer considerable error performance improvement with little loss in processing power and spectral efficiency in comparison with the no compensation case. Copyright © 2009 IEEE.

  16. Adapting populations in space: clonal interference and genetic diversity

    Science.gov (United States)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  17. Measuring high-altitude adaptation.

    Science.gov (United States)

    Moore, Lorna G

    2017-11-01

    High altitudes (>8,000 ft or 2,500 m) provide an experiment of nature for measuring adaptation and the physiological processes involved. Studies conducted over the past ~25 years in Andeans, Tibetans, and, less often, Ethiopians show varied but distinct O2 transport traits from those of acclimatized newcomers, providing indirect evidence for genetic adaptation to high altitude. Short-term (acclimatization, developmental) and long-term (genetic) responses to high altitude exhibit a temporal gradient such that, although all influence O2 content, the latter also improve O2 delivery and metabolism. Much has been learned concerning the underlying physiological processes, but additional studies are needed on the regulation of blood flow and O2 utilization. Direct evidence of genetic adaptation comes from single-nucleotide polymorphism (SNP)-based genome scans and whole genome sequencing studies that have identified gene regions acted upon by natural selection. Efforts have begun to understand the connections between the two with Andean studies on the genetic factors raising uterine blood flow, fetal growth, and susceptibility to Chronic Mountain Sickness and Tibetan studies on genes serving to lower hemoglobin and pulmonary arterial pressure. Critical for future studies will be the selection of phenotypes with demonstrable effects on reproductive success, the calculation of actual fitness costs, and greater inclusion of women among the subjects being studied. The well-characterized nature of the O2 transport system, the presence of multiple long-resident populations, and relevance for understanding hypoxic disorders in all persons underscore the importance of understanding how evolutionary adaptation to high altitude has occurred.NEW & NOTEWORTHY Variation in O2 transport characteristics among Andean, Tibetan, and, when available, Ethiopian high-altitude residents supports the existence of genetic adaptations that improve the distribution of blood flow to vital organs

  18. Making it personal: Diversity and deliberation in climate adaptation planning

    Directory of Open Access Journals (Sweden)

    Roopali Phadke

    2015-01-01

    Full Text Available The vulnerabilities and health burdens of climate change fall disproportionately upon lower income communities and communities of color. Yet the very groups who are most affected by climate change impacts are least likely to be involved in climate adaptation discussions. These communities face critical barriers to involvement including historical disenfranchisement, as well as a sense that climate change is distant and not personally relevant. Boundary organizations are increasingly playing an important role in bringing science to bear on policy decision-making with respect to climate change adaptation, an issue fraught with political and ideological tensions. Our project aimed to engage underrepresented communities in climate change adaptation decision-making using a neighborhood consensus conference model developed and tested in several diverse districts of Saint Paul, Minnesota. Our partnership, a “linked chain” of boundary organizations, devised a neighborhood consensus conference model to present best-available climate data as tangible, place-based scenarios. In so doing, we made climate change “personal” for those who remain outside of climate change planning discourses and opened an opportunity for them to assess their community’s vulnerabilities and communicate their priorities for public investment. Our neighborhood-based model built trust and social capital with local residents and allowed us to bring new voices into conversations around climate change adaptation concerns and priorities. We believe this work will have a long term impact on local climate adaptation planning decisions.

  19. Diversity and adaptive evolution of Saccharomyces wine yeast: a review.

    Science.gov (United States)

    Marsit, Souhir; Dequin, Sylvie

    2015-11-01

    Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. © FEMS 2015.

  20. Diversity and adaptive evolution of Saccharomyces wine yeast: a review

    Science.gov (United States)

    Marsit, Souhir; Dequin, Sylvie

    2015-01-01

    Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. PMID:26205244

  1. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  2. The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress.

    Directory of Open Access Journals (Sweden)

    Dilara Ally

    Full Text Available Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially.We serially transferred bacteriophage populations growing at high temperatures (40°C on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved.Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide evidence that some substitutions exclude each other.

  3. Power adaptation for joint switched diversity and adaptive modulation schemes in spectrum sharing systems

    KAUST Repository

    Bouida, Zied

    2012-09-01

    Under the scenario of an underlay cognitive radio network, we propose in this paper an adaptive scheme using transmit power adaptation, switched transmit diversity, and adaptive modulation in order to improve the performance of existing switching efficient schemes (SES) and bandwidth efficient schemes (BES). Taking advantage of the channel reciprocity principle, we assume that the channel state information (CSI) of the interference link is available to the secondary transmitter. This information is then used by the secondary transmitter to adapt its transmit power, modulation constellation size, and used transmit branch. The goal of this joint adaptation is to minimize the average number of switched branches and the average system delay given the fading channel conditions, the required error rate performance, and a peak interference constraint to the primary receiver. We analyze the proposed scheme in terms of the average number of branch switching, average delay, and we provide a closed-form expression of the average bit error rate (BER). We demonstrate through numerical examples that the proposed scheme provides a compromise between the SES and the BES schemes. © 2012 IEEE.

  4. Adaptation of problem-solving treatment for prevention of depression among low-income, culturally diverse mothers.

    Science.gov (United States)

    Feinberg, Emily; Stein, Rachel; Diaz-Linhart, Yaminette; Egbert, Lucia; Beardslee, William; Hegel, Mark T; Silverstein, Michael

    2012-01-01

    Adapting evidence-based interventions to be more accessible and culturally sensitive to the needs of diverse populations is a potential strategy to address disparities in mental health care. We adapted an evidence-based depression-treatment strategy, Problem-Solving Treatment, to prevent depression among low-income mothers with vulnerable children. Intervention adaptations spanned 3 domains: (1) the intervention's new prevention focus, (2) conducting a parent-focused intervention in venues oriented to children; and (3) cultural competency. The feasibility of adaptations was assessed through 2 pilot-randomized trials (n = 93), which demonstrated high participant adherence, satisfaction, and retention, demonstrating the feasibility of our adaptations.

  5. Evolution of adaptive diversity and genetic connectivity in Arctic charr (Salvelinus alpinus) in Iceland

    Science.gov (United States)

    Kapralova, K H; Morrissey, M B; Kristjánsson, B K; Ólafsdóttir, G Á; Snorrason, S S; Ferguson, M M

    2011-01-01

    The ecological theory of adaptive radiation predicts that the evolution of phenotypic diversity within species is generated by divergent natural selection arising from different environments and competition between species. Genetic connectivity among populations is likely also to have an important role in both the origin and maintenance of adaptive genetic diversity. Our goal was to evaluate the potential roles of genetic connectivity and natural selection in the maintenance of adaptive phenotypic differences among morphs of Arctic charr, Salvelinus alpinus, in Iceland. At a large spatial scale, we tested the predictive power of geographic structure and phenotypic variation for patterns of neutral genetic variation among populations throughout Iceland. At a smaller scale, we evaluated the genetic differentiation between two morphs in Lake Thingvallavatn relative to historically explicit, coalescent-based null models of the evolutionary history of these lineages. At the large spatial scale, populations are highly differentiated, but weakly structured, both geographically and with respect to patterns of phenotypic variation. At the intralacustrine scale, we observe modest genetic differentiation between two morphs, but this level of differentiation is nonetheless consistent with strong reproductive isolation throughout the Holocene. Rather than a result of the homogenizing effect of gene flow in a system at migration-drift equilibrium, the modest level of genetic differentiation could equally be a result of slow neutral divergence by drift in large populations. We conclude that contemporary and recent patterns of restricted gene flow have been highly conducive to the evolution and maintenance of adaptive genetic variation in Icelandic Arctic charr. PMID:21224880

  6. High rate of adaptive evolution in two widespread European pines.

    Science.gov (United States)

    Grivet, Delphine; Avia, Komlan; Vaattovaara, Aleksia; Eckert, Andrew J; Neale, David B; Savolainen, Outi; González-Martínez, Santiago C

    2017-11-07

    Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the Distribution of Fitness Effects (DFE), were similar across species, and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not differentially affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  7. A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence

    NARCIS (Netherlands)

    Etienne, Rampal S.; Haegeman, Bart

    2012-01-01

    In this article we propose a new framework for studying adaptive radiations in the context of diversity-dependent diversification. Diversity dependence causes diversification to decelerate at the end of an adaptive radiation but also plays a key role in the initial pulse of diversification. In

  8. High-Order Adaptive Galerkin Methods

    NARCIS (Netherlands)

    Canuto, C.; Nochetto, R.H.; Stevenson, R.; Verani, M.; Kirby, R.M.; Berzins, M.; Hesthaven, J.S.

    2015-01-01

    We design adaptive high-order Galerkin methods for the solution of linear elliptic problems and study their performance. We first consider adaptive Fourier-Galerkin methods and Legendre-Galerkin methods, which offer unlimited approximation power only restricted by solution and data regularity. Their

  9. General and craniofacial development are complex adaptive processes influenced by diversity.

    Science.gov (United States)

    Brook, A H; O'Donnell, M Brook; Hone, A; Hart, E; Hughes, T E; Smith, R N; Townsend, G C

    2014-06-01

    Complex systems are present in such diverse areas as social systems, economies, ecosystems and biology and, therefore, are highly relevant to dental research, education and practice. A Complex Adaptive System in biological development is a dynamic process in which, from interacting components at a lower level, higher level phenomena and structures emerge. Diversity makes substantial contributions to the performance of complex adaptive systems. It enhances the robustness of the process, allowing multiple responses to external stimuli as well as internal changes. From diversity comes variation in outcome and the possibility of major change; outliers in the distribution enhance the tipping points. The development of the dentition is a valuable, accessible model with extensive and reliable databases for investigating the role of complex adaptive systems in craniofacial and general development. The general characteristics of such systems are seen during tooth development: self-organization; bottom-up emergence; multitasking; self-adaptation; variation; tipping points; critical phases; and robustness. Dental findings are compatible with the Random Network Model, the Threshold Model and also with the Scale Free Network Model which has a Power Law distribution. In addition, dental development shows the characteristics of Modularity and Clustering to form Hierarchical Networks. The interactions between the genes (nodes) demonstrate Small World phenomena, Subgraph Motifs and Gene Regulatory Networks. Genetic mechanisms are involved in the creation and evolution of variation during development. The genetic factors interact with epigenetic and environmental factors at the molecular level and form complex networks within the cells. From these interactions emerge the higher level tissues, tooth germs and mineralized teeth. Approaching development in this way allows investigation of why there can be variations in phenotypes from identical genotypes; the phenotype is the outcome

  10. Pulmonary Adaptation to High Altitude.

    Science.gov (United States)

    1983-08-12

    T.I. Musch, and J.A. Dempsey. Central- peripheral chemoreceptor interaction in the awake CSF-perfused goat. J. Appl. Physiol. (accepted for...of obtaining limb and respiratory muscles. Assays are cur- rently being done for fiber type, oxidative capacity (citrase synthase activity ) and high...hypoxia. III. Mechanism of Periodic Breathing in Hypoxia Sleep--Humans A. We have now completed our study and analysis of the role of chemoreceptor stimuli

  11. Perspectives on Highly Adaptive or Morphing Aircraft

    Science.gov (United States)

    McGowan, Anna-Maria R.; Vicroy, Dan D.; Busan, Ronald C.; Hahn, Andrew S.

    2009-01-01

    The ability to adapt to different flight conditions has been fundamental to aircraft design since the Wright Brothers first flight. Over a hundred years later, unconventional aircraft adaptability, often called aircraft morphing has become a topic of considerable renewed interest. In the past two decades, this interest has been largely fuelled by advancements in multi-functional or smart materials and structures. However, highly adaptive or morphing aircraft is certainly a cross-discipline challenge that stimulates a wide range of design possibilities. This paper will review some of the history of morphing aircraft including recent research programs and discuss some perspectives on this work.

  12. Adaptive Transmission with Mixed Band-AMC and Diversity Modes for Multiuser OFDMA

    Science.gov (United States)

    Sim, Sung Bo; Kim, Yun Hee; Kim, Kwang Soon

    In this letter, we propose an adaptive transmission method for an OFDMA system supporting both band-AMC and diversity modes in a frame, simultaneously. In the proposed method, users are classified into the two groups preferring the band-AMC mode or the diversity mode based on their channel parameters. Then the BS performs resource allocation to maximize the throughput. It is observed that the proposed adaptive transmission method can reduce the feedback overhead with negligible performance loss.

  13. Ecologically-Relevant Maps of Landforms and Physiographic Diversity for Climate Adaptation Planning.

    Science.gov (United States)

    Theobald, David M; Harrison-Atlas, Dylan; Monahan, William B; Albano, Christine M

    2015-01-01

    Key to understanding the implications of climate and land use change on biodiversity and natural resources is to incorporate the physiographic platform on which changes in ecological systems unfold. Here, we advance a detailed classification and high-resolution map of physiography, built by combining landforms and lithology (soil parent material) at multiple spatial scales. We used only relatively static abiotic variables (i.e., excluded climatic and biotic factors) to prevent confounding current ecological patterns and processes with enduring landscape features, and to make the physiographic classification more interpretable for climate adaptation planning. We generated novel spatial databases for 15 landform and 269 physiographic types across the conterminous United States of America. We examined their potential use by natural resource managers by placing them within a contemporary climate change adaptation framework, and found our physiographic databases could play key roles in four of seven general adaptation strategies. We also calculated correlations with common empirical measures of biodiversity to examine the degree to which the physiographic setting explains various aspects of current biodiversity patterns. Additionally, we evaluated the relationship between landform diversity and measures of climate change to explore how changes may unfold across a geophysical template. We found landform types are particularly sensitive to spatial scale, and so we recommend using high-resolution datasets when possible, as well as generating metrics using multiple neighborhood sizes to both minimize and characterize potential unknown biases. We illustrate how our work can inform current strategies for climate change adaptation. The analytical framework and classification of landforms and parent material are easily extendable to other geographies and may be used to promote climate change adaptation in other settings.

  14. Extremophilic adaptations and biotechnological applications in diverse environments

    Directory of Open Access Journals (Sweden)

    Brendan P. Burns

    2016-07-01

    Full Text Available Extremophiles are organisms that tolerate and thrive in the most extreme and challenging conditions to life. As a result of these extreme environmental insults extremophiles have developed a number of interesting adaptations to cellular membranes, proteins and extracellular metabolites. These uniquely adapted biological molecules and systems already have roles in a number of biotechnological fields. In this review we give a brief overview of a number of different extreme environments and the potential for biotechnological innovation from the microbes which inhabit them.

  15. Joint switched transmit diversity and adaptive modulation in spectrum sharing systems

    KAUST Repository

    Qaraqe, Khalid A.

    2011-01-01

    Under the scenario of an underlay cognitive radio network, we propose in this paper an adaptive scheme using switched transmit diversity and adaptive modulation in order to minimize the average number of switched branches at the secondary transmitter while increasing the capacity of the secondary link. The proposed switching efficient scheme (SES) uses the scan and wait (SWC) combining technique where a transmission occurs only when a branch with an acceptable performance is found, otherwise data is buffered. In our scheme, the modulation constellation size and the used transmit branch are determined to achieve the highest spectral efficiency with a minimum processing power, given the fading channel conditions, the required error rate performance, and a peak interference constraint to the primary receiver. Selected numerical examples show that the SES scheme minimizes the average number of switched branches for the average and the high secondary signal-to-noise ratio range. This improvement comes at the expense of a small delay introduced by the SWC technique. For reference, we also compare the performance of the SES scheme to the selection diversity scheme (SDS) where the best branch verifying the modulation mode and the interference constraint is always selected. © 2011 ICST.

  16. Habitat diversity and adaptation to environmental stress in encysted ...

    Indian Academy of Sciences (India)

    Unknown

    adaptation implicated in the ecological success of Artemia is p26, a small heat shock protein that previous evi- dence indicates ... summarize recently published work on thermal tolerance and stress protein levels in embryos from the San. Francisco Bay ...... encouraged my participation in it and related projects at the Artemia ...

  17. A unified framework for diversity gradients : The adaptive trait continuum

    NARCIS (Netherlands)

    Carnicer, Jofre; Stefanescu, Constanti; Vila, Roger; Dinca, Vlad; Font, Xavier; Penuelas, Josep

    Aim Adaptive trait continua are axes of covariation observed in multivariate trait data for a given taxonomic group. These continua quantify and summarize life-history variation at the inter-specific level in multi-specific assemblages. Here we examine whether trait continua can provide a useful

  18. Habitat diversity and adaptation to environmental stress in encysted ...

    Indian Academy of Sciences (India)

    2004-10-27

    Oct 27, 2004 ... Encysted embryos (cysts) of the brine shrimp, Artemia, provide excellent opportunities for the study of biochemical and biophysical adaptation to extremes of environmental stress in animals. Among other virtues, this organism is found in a wide variety of hypersaline habitats, ranging from deserts, to tropics, ...

  19. The role of viral population diversity in adaptation of bovine coronavirus to new host environments.

    Directory of Open Access Journals (Sweden)

    Monica K Borucki

    Full Text Available The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing and 38,000×(Illumina. The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were "selected" from a pre-existing pool rather than through de novo mutation and subsequent population fixation.

  20. Diverse Roles of Inhibitor of Differentiation 2 in Adaptive Immunity

    Directory of Open Access Journals (Sweden)

    Lucille Rankin

    2011-01-01

    Full Text Available The helix-loop-helix (HLH transcription factor inhibitor of DNA binding 2 (Id2 has been implicated as a regulator of hematopoiesis and embryonic development. While its role in early lymphopoiesis has been well characterized, new roles in adaptive immune responses have recently been uncovered opening exciting new directions for investigation. In the innate immune system, Id2 is required for the development of mature natural killer (NK cells, lymphoid tissue-inducer (LTi cells, and the recently identified interleukin (IL-22 secreting nonconventional innate lymphocytes found in the gut. In addition, Id2 has been implicated in the development of specific dendritic cell (DC subsets, decisions determining the formation of αβ and γδ T-cell development, NK T-cell behaviour, and in the maintenance of effector and memory CD8+ T cells in peripheral tissues. Here, we review the current understanding of the role of Id2 in lymphopoiesis and in the development of the adaptive immune response required for maintaining immune homeostasis and immune protection.

  1. Ancient homology underlies adaptive mimetic diversity across butterflies

    Science.gov (United States)

    Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

    2014-01-01

    Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

  2. Diverse seed banks favour adaptation of microalgal populations to future climate conditions.

    Science.gov (United States)

    Kremp, Anke; Oja, Johanna; LeTortorec, Anniina H; Hakanen, Päivi; Tahvanainen, Pia; Tuimala, Jarno; Suikkanen, Sanna

    2016-02-01

    Selection of suitable genotypes from diverse seed banks may help phytoplankton populations to cope with environmental changes. This study examines whether the high genotypic diversity found in the Baltic cyst pool of the toxic dinoflagellate Alexandrium ostenfeldii is coupled to phenotypic variability that could aid short-term adaptation. Growth rates, cellular toxicities and bioluminescence of 34 genetically different clones isolated from cyst beds of four Baltic bloom sites were determined in batch culture experiments along temperature and salinity gradients covering present and future conditions in the Baltic Sea. For all parameters a significant effect of genotype on the response to temperature and salinity changes was identified. General or site-specific effects of the two factors remained minor. Clones thriving at future conditions were different from the best performing at present conditions, suggesting that genotypic shifts may be expected in the future. Increased proportions of highly potent saxitoxin were observed as a plastic response to temperature increase, indicating a potential for higher toxicity of future blooms. The observed standing variation in Baltic seed banks of A. ostenfeldii suggests that the population is likely to persist under environmental change. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  3. The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

    Energy Technology Data Exchange (ETDEWEB)

    Sunderam, Vaidy S.

    2012-03-20

    The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept of a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.

  4. Genome architecture enables local adaptation of Atlantic cod despite high connectivity

    DEFF Research Database (Denmark)

    Barth, Julia M I; Berg, Paul R; Jonsson, Per R.

    2017-01-01

    Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species......-nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless...... in the rearranged region. Our study provides new insights into the potential of local adaptation in high gene flow species within fine geographical scales and highlights the importance of genome architecture in analyses of ecological adaptation. This article is protected by copyright. All rights reserved....

  5. Joint multiuser switched diversity and adaptive modulation schemes for spectrum sharing systems

    KAUST Repository

    Qaraqe, Marwa

    2012-12-01

    In this paper, we develop multiuser access schemes for spectrum sharing systems whereby secondary users are allowed to share the spectrum with primary users under the condition that the interference observed at the primary receiver is below a predetermined threshold. In particular, we devise two schemes for selecting a user among those that satisfy the interference constraint and achieve an acceptable signal-to-noise ratio level. The first scheme selects the user that reports the best channel quality. In order to alleviate the high feedback load associated with the first scheme, we develop a second scheme based on the concept of switched diversity where the base station scans the users in a sequential manner until an acceptable user is found. In addition to these two selection schemes, we consider two power adaptive settings at the secondary users based on the amount of interference available at the secondary transmitter. In the On/Off power setting, users are allowed to transmit based on whether the interference constraint is met or not, while in the full power adaptive setting, the users are allowed to vary their transmission power to satisfy the interference constraint. Finally, we present numerical results for our proposed algorithms where we show the trade-off between the average spectral efficiency and average feedback load for both schemes. © 2012 IEEE.

  6. Performance analysis of joint diversity combining, adaptive modulation, and power control schemes

    KAUST Repository

    Qaraqe, Khalid A.

    2011-01-01

    Adaptive modulation and diversity combining represent very important adaptive solutions for future generations of wireless communication systems. Indeed, in order to improve the performance and the efficiency of these systems, these two techniques have been recently used jointly in new schemes named joint adaptive modulation and diversity combining (JAMDC) schemes. Considering the problem of finding low hardware complexity, bandwidth-efficient, and processing-power efficient transmission schemes for a downlink scenario and capitalizing on some of these recently proposed JAMDC schemes, we propose and analyze in this paper three joint adaptive modulation, diversity combining, and power control (JAMDCPC) schemes where a constant-power variable-rate adaptive modulation technique is used with an adaptive diversity combining scheme and a common power control process. More specifically, the modulation constellation size, the number of combined diversity paths, and the needed power level are jointly determined to achieve the highest spectral efficiency with the lowest possible processing power consumption quantified in terms of the average number of combined paths, given the fading channel conditions and the required bit error rate (BER) performance. In this paper, the performance of these three JAMDCPC schemes is analyzed in terms of their spectral efficiency, processing power consumption, and error-rate performance. Selected numerical examples show that these schemes considerably increase the spectral efficiency of the existing JAMDC schemes with a slight increase in the average number of combined paths for the low signal-to-noise ratio range while maintaining compliance with the BER performance and a low radiated power which yields to a substantial decrease in interference to co-existing users and systems. © 2011 IEEE.

  7. Diverse microbial species survive high ammonia concentrations

    Science.gov (United States)

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  8. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production.

    Science.gov (United States)

    Peris, David; Moriarty, Ryan V; Alexander, William G; Baker, EmilyClare; Sylvester, Kayla; Sardi, Maria; Langdon, Quinn K; Libkind, Diego; Wang, Qi-Ming; Bai, Feng-Yan; Leducq, Jean-Baptiste; Charron, Guillaume; Landry, Christian R; Sampaio, José Paulo; Gonçalves, Paula; Hyma, Katie E; Fay, Justin C; Sato, Trey K; Hittinger, Chris Todd

    2017-01-01

    Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to

  9. Parent Cultural Adaptation and Child Functioning in Culturally Diverse, Urban Families of Preschoolers

    Science.gov (United States)

    Calzada, Esther J.; Brotman, Laurie Miller; Huang, Keng-Yen; Bat-Chava, Yael; Kingston, Sharon

    2008-01-01

    Parent cultural adaptation and preschool behavioral and socioemotional functioning were examined in a community sample of urban families from diverse cultural backgrounds. Participants were 130 families of children (mean age = 4.1 years) attending eight public Pre-Kindergarten programs in urban communities. Parents completed a measure of cultural…

  10. Diversity and adaptations of deep-sea microorganisms

    Digital Repository Service at National Institute of Oceanography (India)

    Raghukumar, C.

    directly in to sterile plastic bags to avoid any aerial contaminants. The sediments were diluted with malt extract broth and pressurized to desired pressure in a pressure vessel and incubated in a refigerator at 4-5oC on board the research vessel. Fungi...-sea yeasts in gas permeable plastic bags for cultivation under high pressure and a fluorocarbon liquid (FC-77) as hydraulic fluid (Lorenz and Molitoris, 1997). Raghukumar et al. (1992) germinated conidia of the fungus Aspergillus restrictus isolated from...

  11. Valuing the Recreational Benefits of Wetland Adaptation to Climate Change: A Trade-off Between Species' Abundance and Diversity

    Science.gov (United States)

    Faccioli, Michela; Riera Font, Antoni; Torres Figuerola, Catalina M.

    2015-03-01

    Climate change will further exacerbate wetland deterioration, especially in the Mediterranean region. On the one side, it will accelerate the decline in the populations and species of plants and animals, this resulting in an impoverishment of biological abundance. On the other one, it will also promote biotic homogenization, resulting in a loss of species' diversity. In this context, different climate change adaptation policies can be designed: those oriented to recovering species' abundance and those aimed at restoring species' diversity. Based on the awareness that knowledge about visitors' preferences is crucial to better inform policy makers and secure wetlands' public use and conservation, this paper assesses the recreational benefits of different adaptation options through a choice experiment study carried out in S'Albufera wetland (Mallorca). Results show that visitors display positive preferences for an increase in both species' abundance and diversity, although they assign a higher value to the latter, thus suggesting a higher social acceptability of policies pursuing wetlands' differentiation. This finding acquires special relevance not only for adaptation management in wetlands but also for tourism planning, as most visitors to S'Albufera are tourists. Thus, given the growing competition to attract visitors and the increasing demand for high environmental quality and unique experiences, promoting wetlands' differentiation could be a good strategy to gain competitive advantage over other wetland areas and tourism destinations.

  12. From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation.

    Science.gov (United States)

    Moen, Daniel; Morlon, Hélène

    2014-05-01

    What explains why some groups of organisms, like birds, are so species rich? And what explains their extraordinary ecological diversity, ranging from large, flightless birds to small migratory species that fly thousand of kilometers every year? These and similar questions have spurred great interest in adaptive radiation, the diversification of ecological traits in a rapidly speciating group of organisms. Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil record, rigorous attempts to identify adaptive radiation in the fossil record are still uncommon. Moreover, most studies of adaptive radiation concern groups that are less than 50 million years old. Thus, it is unclear how important adaptive radiation is over temporal scales that span much larger portions of the history of life. In this issue, Benson et al. test the idea of a "deep-time" adaptive radiation in dinosaurs, compiling and using one of the most comprehensive phylogenetic and body-size datasets for fossils. Using recent phylogenetic statistical methods, they find that in most clades of dinosaurs there is a strong signal of an "early burst" in body-size evolution, a predicted pattern of adaptive radiation in which rapid trait evolution happens early in a group's history and then slows down. They also find that body-size evolution did not slow down in the lineage leading to birds, hinting at why birds survived to the present day and diversified. This paper represents one of the most convincing attempts at understanding deep-time adaptive radiations.

  13. Adaptation and diversity along an altitudinal gradient in Ethiopian barley (Hordeum vulgare L. landraces revealed by molecular analysis

    Directory of Open Access Journals (Sweden)

    Bitocchi Elena

    2010-06-01

    Full Text Available Abstract Background Among the cereal crops, barley is the species with the greatest adaptability to a wide range of environments. To determine the level and structure of genetic diversity in barley (Hordeum vulgare L. landraces from the central highlands of Ethiopia, we have examined the molecular variation at seven nuclear microsatellite loci. Results A total of 106 landrace populations were sampled in the two growing seasons (Meher and Belg; the long and short rainy seasons, respectively, across three districts (Ankober, Mojanawadera and Tarmaber, and within each district along an altitudinal gradient (from 1,798 to 3,324 m a.s.l. Overall, although significant, the divergence (e.g. FST is very low between seasons and geographical districts, while it is high between different classes of altitude. Selection for adaptation to different altitudes appears to be the main factor that has determined the observed clinal variation, along with population-size effects. Conclusions Our data show that barley landraces from Ethiopia are constituted by highly variable local populations (farmer's fields that have large within-population diversity. These landraces are also shown to be locally adapted, with the major driving force that has shaped their population structure being consistent with selection for adaptation along an altitudinal gradient. Overall, our study highlights the potential of such landraces as a source of useful alleles. Furthermore, these landraces also represent an ideal system to study the processes of adaptation and for the identification of genes and genomic regions that have adaptive roles in crop species.

  14. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes.

    Science.gov (United States)

    Dwivedi, Sangam L; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

    2017-01-01

    There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and

  15. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

    Directory of Open Access Journals (Sweden)

    Sangam L. Dwivedi

    2017-08-01

    Full Text Available There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection

  16. Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology.

    Directory of Open Access Journals (Sweden)

    David T Kysela

    2016-10-01

    Full Text Available The modern age of metagenomics has delivered unprecedented volumes of data describing the genetic and metabolic diversity of bacterial communities, but it has failed to provide information about coincident cellular morphologies. Much like metabolic and biosynthetic capabilities, morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain. In this essay, we discuss the diversity of bacterial morphology and its implications for understanding both the mechanistic and the adaptive basis of morphogenesis. We consider how best to leverage genomic data and recent experimental developments in order to advance our understanding of bacterial shape and its functional importance.

  17. Drought-adaptation potential in Fagus sylvatica: linking moisture availability with genetic diversity and dendrochronology.

    Directory of Open Access Journals (Sweden)

    Andrea R Pluess

    Full Text Available BACKGROUND: Microevolution is essential for species persistence especially under anticipated climate change scenarios. Species distribution projection models suggested that the dominant tree species of lowland forests in Switzerland, European beech (Fagus sylvatica L., might disappear from most areas due to expected longer dry periods. However, if genotypes at the moisture boundary of the species climatic envelope are adapted to lower moisture availability, they can serve as seed source for the continuation of beech forests under changing climates. METHODOLOGY/PRINCIPAL FINDINGS: With an AFLP genome scan approach, we studied neutral and potentially adaptive genetic variation in Fagus sylvatica in three regions containing a dry and a mesic site each (n(ind. = 241, n(markers = 517. We linked this dataset with dendrochronological growth measures and local moisture availabilities based on precipitation and soil characteristics. Genetic diversity decreased slightly at dry sites. Overall genetic differentiation was low (F(st = 0.028 and Bayesian cluster analysis grouped all populations together suggesting high (historical gene flow. The Bayesian outlier analyses indicated 13 markers with three markers differing between all dry and mesic sites and the others between the contrasting sites within individual regions. A total of 41 markers, including seven outlier loci, changed their frequency with local moisture availability. Tree height and median basal growth increments were reduced at dry sites, but marker presence/absence was not related to dendrochronological characteristics. CONCLUSION AND THEIR SIGNIFICANCE: The outlier alleles and the makers with changing frequencies in relation to moisture availability indicate microevolutionary processes occurring within short geographic distances. The general genetic similarity among sites suggests that 'preadaptive' genes can easily spread across the landscape. Yet, due to the long live span of

  18. Drought-adaptation potential in Fagus sylvatica: linking moisture availability with genetic diversity and dendrochronology.

    Science.gov (United States)

    Pluess, Andrea R; Weber, Pascale

    2012-01-01

    Microevolution is essential for species persistence especially under anticipated climate change scenarios. Species distribution projection models suggested that the dominant tree species of lowland forests in Switzerland, European beech (Fagus sylvatica L.), might disappear from most areas due to expected longer dry periods. However, if genotypes at the moisture boundary of the species climatic envelope are adapted to lower moisture availability, they can serve as seed source for the continuation of beech forests under changing climates. With an AFLP genome scan approach, we studied neutral and potentially adaptive genetic variation in Fagus sylvatica in three regions containing a dry and a mesic site each (n(ind.) = 241, n(markers) = 517). We linked this dataset with dendrochronological growth measures and local moisture availabilities based on precipitation and soil characteristics. Genetic diversity decreased slightly at dry sites. Overall genetic differentiation was low (F(st) = 0.028) and Bayesian cluster analysis grouped all populations together suggesting high (historical) gene flow. The Bayesian outlier analyses indicated 13 markers with three markers differing between all dry and mesic sites and the others between the contrasting sites within individual regions. A total of 41 markers, including seven outlier loci, changed their frequency with local moisture availability. Tree height and median basal growth increments were reduced at dry sites, but marker presence/absence was not related to dendrochronological characteristics. CONCLUSION AND THEIR SIGNIFICANCE: The outlier alleles and the makers with changing frequencies in relation to moisture availability indicate microevolutionary processes occurring within short geographic distances. The general genetic similarity among sites suggests that 'preadaptive' genes can easily spread across the landscape. Yet, due to the long live span of trees, fostering saplings originating from dry sites and

  19. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

    Science.gov (United States)

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

    2016-07-05

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

  20. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    DEFF Research Database (Denmark)

    Thøgersen, Juliane Charlotte; Mørup, Morten; Pedersen, Søren Damkiær

    2013-01-01

    expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates....... This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. CONCLUSIONS: Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering...

  1. Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos.

    Science.gov (United States)

    Gillingham, Mark A F; Béchet, Arnaud; Courtiol, Alexandre; Rendón-Martos, Manuel; Amat, Juan A; Samraoui, Boudjéma; Onmuş, Ortaç; Sommer, Simone; Cézilly, Frank

    2017-02-20

    Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity

  2. Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction.

    Science.gov (United States)

    Sánchez-Quinto, Federico; Lalueza-Fox, Carles

    2015-01-19

    Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations-including morphological and behavioural traits-as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's-and our very own-evolutionary history. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  3. Adaptation of teleosts to very high salinity

    DEFF Research Database (Denmark)

    Laverty, Gary; Skadhauge, Erik

    2012-01-01

    with intestinal water absorption and with the properties of the gill epithelium. While there is much that is still not completely understood, recent work has begun to look at these adaptations at the cellular and molecular level. As with seawater osmoregulation, fish adapting to hypersaline conditions generally......A number of species of euryhaline teleosts have the remarkable ability to adapt and survive in environments of extreme salinity, up to two or even three times the osmolality of seawater. This review looks at some of the literature describing the adaptive changes that occur, primarily...... in several species. Adaptive changes in the gill epithelium are also critical in this process, allowing for secretion of absorbed NaCl from the extracellular fluids. Most notably there are important changes in the numbers and size of mitochondrion-rich (MR) cells, the sites of active secretion of Cl...

  4. High Resolution Observations using Adaptive Optics: Achievements ...

    Indian Academy of Sciences (India)

    AURA) under co-operative agreement with National Science Foundation (NSF). ... usually enhanced using post-processing techniques: speckle reconstruction, phase- diversity, or long-exposure point spread deconvolution with or without frame ...

  5. From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation.

    Directory of Open Access Journals (Sweden)

    Daniel Moen

    2014-05-01

    Full Text Available What explains why some groups of organisms, like birds, are so species rich? And what explains their extraordinary ecological diversity, ranging from large, flightless birds to small migratory species that fly thousand of kilometers every year? These and similar questions have spurred great interest in adaptive radiation, the diversification of ecological traits in a rapidly speciating group of organisms. Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil record, rigorous attempts to identify adaptive radiation in the fossil record are still uncommon. Moreover, most studies of adaptive radiation concern groups that are less than 50 million years old. Thus, it is unclear how important adaptive radiation is over temporal scales that span much larger portions of the history of life. In this issue, Benson et al. test the idea of a "deep-time" adaptive radiation in dinosaurs, compiling and using one of the most comprehensive phylogenetic and body-size datasets for fossils. Using recent phylogenetic statistical methods, they find that in most clades of dinosaurs there is a strong signal of an "early burst" in body-size evolution, a predicted pattern of adaptive radiation in which rapid trait evolution happens early in a group's history and then slows down. They also find that body-size evolution did not slow down in the lineage leading to birds, hinting at why birds survived to the present day and diversified. This paper represents one of the most convincing attempts at understanding deep-time adaptive radiations.

  6. Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities.

    Science.gov (United States)

    Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernandez, Domingo; Mouillot, David

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules.

  7. Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows

    NARCIS (Netherlands)

    Hook, S.E.; Steele, M.A.; Northwood, K.S.; Dijkstra, J.; France, J.; Wright, A.G.; McBride, B.W.

    2011-01-01

    Subacute ruminal acidosis (SARA) is characterized by ruminal pH depression and microbial perturbation. The impact of SARA adaptation and recovery on rumen bacterial density and diversity was investigated following high-grain feeding. Four ruminally cannulated dairy cows were fed a hay diet,

  8. Utilizing forest tree genetic diversity for an adaptation of forest to climate change

    Science.gov (United States)

    Schueler, Silvio; Lackner, Magdalena; Chakraborty, Debojyoti

    2017-04-01

    Since climate conditions are considered to be major determinants of tree species' distribution ranges and drivers of local adaptation, anthropogenic climate change (CC) is expected to modify the distribution of tree species, tree species diversity and the forest ecosystems connected to these species. The expected speed of environmental change is significantly larger than the natural migration and adaptation capacity of trees and makes spontaneous adjustment of forest ecosystems improbable. Planting alternative tree species and utilizing the tree species' intrinsic adaptive capacity are considered to be the most promising adaptation strategy. Each year about 900 million seedlings of the major tree species are being planted in Central Europe. At present, the utilization of forest reproductive material is mainly restricted to nationally defined ecoregions (seed/provenance zones), but when seedlings planted today become adult, they might be maladapted, as the climate conditions within ecoregions changed significantly. In the cooperation project SUSTREE, we develop transnational delineation models for forest seed transfer and genetic conservation based on species distribution models and available intra-specific climate-response function. These models are being connected to national registers of forest reproductive material in order support nursery and forest managers by selecting the appropriate seedling material for future plantations. In the long-term, European and national policies as well as regional recommendations for provenances use need to adapted to consider the challenges of climate change.

  9. Cultural Adaptation and Implementation of Family Evidence-Based Interventions with Diverse Populations.

    Science.gov (United States)

    Kumpfer, Karol; Magalhães, Catia; Xie, Jing

    2017-08-01

    Family evidence-based interventions (FEBIs) are effective in creating lasting improvements and preventing children's behavioral health problems, even in genetically at-risk children. Most FEBIs, however, were designed for English-speaking families. Consequently, providers have difficulty engaging non-English-speaking populations in their own country or in other countries where the content, language, and recruitment methods of the FEBIs do not reflect their culture. The practical solution has been to culturally adapt existing FEBIs. Research suggests this can increase family engagement by about 40 %. This article covers background, theory, and research on FEBIs and the need to engage more diverse families. Steps for culturally adapting FEBIs with fidelity are presented based on our own and local implementers' experiences in 36 countries with the Strengthening Families Program. These steps, also previously recommended by a United Nations Office on Drugs and Crime panel of experts in family skills interventions, include: (1) creating a cultural advisory group, (2) assessing specific needs of cultural subgroups, (3) language translation, (4) hiring implementers from the culture, (5) developing culturally adapted training systems, (6) making cultural adaptations cautiously during repeated delivery, (7) continuous implementation quality and outcome evaluation to assure effectiveness in comparison with the original FEBI, (8) developing local and international dissemination partnerships, and (9) securing funding support for sustainability. Future efficacy trials should compare existing FEBIs to culturally adapted versions to determine comparative cost effectiveness.

  10. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice.

    Science.gov (United States)

    Song, Xianwei; Cao, Xiaofeng

    2017-04-01

    Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Algal MIPs, high diversity and conserved motifs

    Directory of Open Access Journals (Sweden)

    Johanson Urban

    2011-04-01

    Full Text Available Abstract Background Major intrinsic proteins (MIPs also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in terrestrial plants but little is known about their evolutionary history. In an attempt to investigate the origin of the plant MIP subfamilies, genomes of chlorophyte algae, the sister group of charophyte algae and land plants, were searched for MIP encoding genes. Results A total of 22 MIPs were identified in the nine analysed genomes and phylogenetic analyses classified them into seven subfamilies. Two of these, Plasma membrane Intrinsic Proteins (PIPs and GlpF-like Intrinsic Proteins (GIPs, are also present in land plants and divergence dating support a common origin of these algal and land plant MIPs, predating the evolution of terrestrial plants. The subfamilies unique to algae were named MIPA to MIPE to facilitate the use of a common nomenclature for plant MIPs reflecting phylogenetically stable groups. All of the investigated genomes contained at least one MIP gene but only a few species encoded MIPs belonging to more than one subfamily. Conclusions Our results suggest that at least two of the seven subfamilies found in land plants were present already in an algal ancestor. The total variation of MIPs and the number of different subfamilies in chlorophyte algae is likely to be even higher than that found in land plants. Our analyses indicate that genetic exchanges between several of the algal subfamilies have occurred. The PIP1 and PIP2 groups and the Ca2+ gating appear to be specific to land plants whereas the pH gating is a more ancient characteristic shared by all PIPs. Further studies are needed to discern the function of the algal specific subfamilies MIPA-E and to fully understand the evolutionary relationship of algal and terrestrial plant MIPs.

  12. Development of adaptive resonator techniques for high-power lasers

    Energy Technology Data Exchange (ETDEWEB)

    An, J; Brase, J; Carrano, C; Dane, C B; Flath, L; Fochs, S; Hurd, R; Kartz, M; Sawvel, R

    1999-07-12

    The design of an adaptive wavefront control system for a high-power Nd:Glass laser will be presented. Features of this system include: an unstable resonator in confocal configuration, a multi-module slab amplifier, and real-time intracavity adaptive phase control using deformable mirrors and high-speed wavefront sensors. Experimental results demonstrate the adaptive correction of an aberrated passive resonator (no gain).

  13. Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans

    Science.gov (United States)

    Sattath, Shmuel; Elyashiv, Eyal; Kolodny, Oren; Rinott, Yosef; Sella, Guy

    2011-01-01

    In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence—in particular, conclusions about the rate and strength of beneficial substitutions—remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot), and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3%) that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis of adaptation

  14. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Directory of Open Access Journals (Sweden)

    Shmuel Sattath

    2011-02-01

    Full Text Available In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot, and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3% that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis

  15. Multiuser Diversity with Adaptive Modulation in Non-Identically Distributed Nakagami Fading Environments

    KAUST Repository

    Rao, Anlei

    2012-09-08

    In this paper, we analyze the performance of adaptive modulation with single-cell multiuser scheduling over independent but not identical distributed (i.n.i.d.) Nakagami fading channels. Closed-form expressions are derived for the average channel capacity, spectral efficiency, and bit-error-rate (BER) for both constant-power variable-rate and variable-power variable-rate uncoded/coded M-ary quadrature amplitude modulation (M-QAM) schemes. We also study the impact of time delay on the average BER of adaptive M-QAM. Selected numerical results show that the multiuser diversity brings a considerably better performance even over i.n.i.d. fading environments.

  16. A Unified Approach to High-Gain Adaptive Controllers

    Directory of Open Access Journals (Sweden)

    Ian A. Gravagne

    2009-01-01

    Full Text Available It has been known for some time that proportional output feedback will stabilize MIMO, minimum-phase, linear time-invariant systems if the feedback gain is sufficiently large. High-gain adaptive controllers achieve stability by automatically driving up the feedback gain monotonically. More recently, it was demonstrated that sample-and-hold implementations of the high-gain adaptive controller also require adaptation of the sampling rate. In this paper, we use recent advances in the mathematical field of dynamic equations on time scales to unify and generalize the discrete and continuous versions of the high-gain adaptive controller. We prove the stability of high-gain adaptive controllers on a wide class of time scales.

  17. Genome architecture enables local adaptation of Atlantic cod despite high connectivity.

    Science.gov (United States)

    Barth, Julia M I; Berg, Paul R; Jonsson, Per R; Bonanomi, Sara; Corell, Hanna; Hemmer-Hansen, Jakob; Jakobsen, Kjetill S; Johannesson, Kerstin; Jorde, Per Erik; Knutsen, Halvor; Moksnes, Per-Olav; Star, Bastiaan; Stenseth, Nils Chr; Svedäng, Henrik; Jentoft, Sissel; André, Carl

    2017-09-01

    Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless, we also find evidence for discrete fjord populations that are genetically differentiated from offshore populations, indicative of local adaptation, the degree of which appears to be influenced by connectivity. Analyses of the genomic architecture reveal a significant overrepresentation of a large ~5 Mb chromosomal rearrangement in fjord cod, previously proposed to comprise genes critical for the survival at low salinities. This suggests that despite considerable connectivity with offshore populations, local adaptation to fjord environments may be enabled by suppression of recombination in the rearranged region. Our study provides new insights into the potential of local adaptation in high gene flow species within fine geographical scales and highlights the importance of genome architecture in analyses of ecological adaptation. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  18. Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes.

    Science.gov (United States)

    Colombo, M; Damerau, M; Hanel, R; Salzburger, W; Matschiner, M

    2015-02-01

    According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation. © 2014 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

  19. High Efficiency Lighting with Integrated Adaptive Control (HELIAC) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed project is the continued development of the High Efficiency Lighting with Integrated Adaptive Control (HELIAC) system. Solar radiation is not a viable...

  20. High Efficiency Lighting with Integrated Adaptive Control (HELIAC) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovation of the proposed project is the development of High Efficiency Lighting with Integrated Adaptive Control (HELIAC) systems to drive plant growth. Solar...

  1. High-altitude adaptations in vertebrate hemoglobins

    DEFF Research Database (Denmark)

    Weber, Roy E.

    2007-01-01

    Vertebrates at high altitude are subjected to hypoxic conditions that challenge aerobic metabolism. O2 transport from the respiratory surfaces to tissues requires matching between the O2 loading and unloading tensions and theO2-affinity of blood, which is an integrated function of hemoglobin......, birds and ectothermic vertebrates at high altitude....

  2. Novice high school science teachers: Lesson plan adaptations

    Science.gov (United States)

    Scharon, Aracelis Janelle

    The Next Generation Science Standards (NRC, 2013) positions teachers as responsible for necessary decision making about how their intended science lesson plan content supports continuous student science learning. Teachers interact with their instructional lesson plans in dynamic and constructive ways. Adapting lesson plans is complex. This process of adapting lesson plans may play an important role in affording and constraining teachers' actions and students' learning (Brown, 2009). This study explored how five novice chemistry teachers (under 4 years of total teaching experience) at five Midwestern high schools adapted or retained their honors chemistry instructional lesson plans, and what associated contextual factors influenced their decisions. Using a case study design, this study was conducted during the fall semester of 2013 when teachers were focusing on introductory chemistry topics. Three frameworks (pedagogical content knowledge (PCK), teacher decision making, and pedagogical discontentment and self-efficacy) were used to investigate the relationships between teacher adaptations, contextual factors and decision making. The outcome of this study was the identification of 15 types of adaptations and 17 relevant contextual factors. Contextual factors were categorized by factors that relate to students or the teacher. Adaptations were categorized into three overarching types of adaptations: adapting the activity presented during the lesson, adapting the levels of support to assist students with the lesson plan content, and adapting the lesson plan to create another iteration of the same lesson plan that supports the next class. Lesson plan adaptations and contextual factors are discussed in the context of research on teacher decision making and lesson plan adaptations.

  3. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes.

    Science.gov (United States)

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-11-11

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome.Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs.Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular

  4. Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth.

    Science.gov (United States)

    Brown, Alastair; Thatje, Sven

    2014-05-01

    Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal

  5. Human factors recommendations for highly automated driving in the EU project AdaptIVe

    OpenAIRE

    Dziennus, Marc

    2016-01-01

    Due to technical developments our cars become more and more intelligent and are able to take over an increasing amount of driving tasks leading its way to highly automated and autonomous driving. The EU Project AdaptIVe develops innovative automation functionalities for highway, urban and parking scenarios with focus of the changing role of the driver in automated vehicles. The more we automate vehicles, the more important human machine interaction becomes. Derived from literature and conduct...

  6. Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows.

    Science.gov (United States)

    Hook, Sarah E; Steele, Michael A; Northwood, Korinne S; Dijkstra, Jan; France, James; Wright, André-Denis G; McBride, Brian W

    2011-11-01

    Subacute ruminal acidosis (SARA) is characterized by ruminal pH depression and microbial perturbation. The impact of SARA adaptation and recovery on rumen bacterial density and diversity was investigated following high-grain feeding. Four ruminally cannulated dairy cows were fed a hay diet, transitioned to a 65% grain diet for 3 weeks, and returned to the hay diet for 3 weeks. Rumen fluid, rumen solids, and feces were sampled during weeks 0 (hay), 1 and 3 (high grain), and 4 and 6 (hay). SARA was diagnosed during week 1, with a pH below 5.6 for 4.6±1.4 h. Bacterial density was significantly lower in the rumen solids with high grain (P=0.047). Rumen fluid clone libraries from weeks 0, 3, and 6 were assessed at the 98% level and 154 operational taxonomic units were resolved. Week 3 diversity significantly differed from week 0, and community structure differed from weeks 0 and 6 (P<0.0001). Clones belonging to the phylum Firmicutes predominated. Compared with the hay diet, the high-grain diet contained clones from Selenomonas ruminantium and Succiniclasticum ruminis, but lacked Eubacterium spp. SARA adaptation was found to significantly alter bacterial density, diversity, and community structure, warranting further investigation into the role bacteria play in SARA adaptation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  7. Ortholog identification in genera of high genetic diversity and evolution

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Frisvad, Jens Christian

    In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...... genome annotations, gene or protein evolutions or defining functional features in individual species and groups....

  8. Human impacts flatten rainforest-savanna gradient and reduce adaptive diversity in a rainforest bird.

    Directory of Open Access Journals (Sweden)

    Adam H Freedman

    Full Text Available Ecological gradients have long been recognized as important regions for diversification and speciation. However, little attention has been paid to the evolutionary consequences or conservation implications of human activities that fundamentally change the environmental features of such gradients. Here we show that recent deforestation in West Africa has homogenized the rainforest-savanna gradient, causing a loss of adaptive phenotypic diversity in a common rainforest bird, the little greenbul (Andropadus virens. Previously, this species was shown to exhibit morphological and song divergence along this gradient in Central Africa. Using satellite-based estimates of forest cover, recent morphological data, and historical data from museum specimens collected prior to widespread deforestation, we show that the gradient has become shallower in West Africa and that A. virens populations there have lost morphological variation in traits important to fitness. In contrast, we find no loss of morphological variation in Central Africa where there has been less deforestation and gradients have remained more intact. While rainforest deforestation is a leading cause of species extinction, the potential of deforestation to flatten gradients and inhibit rainforest diversification has not been previously recognized. More deforestation will likely lead to further flattening of the gradient and loss of diversity, and may limit the ability of species to persist under future environmental conditions.

  9. Giving Context to the Physician Competency Reference Set: Adapting to the Needs of Diverse Populations.

    Science.gov (United States)

    Eckstrand, Kristen L; Potter, Jennifer; Bayer, Carey Roth; Englander, Robert

    2016-07-01

    Delineating the requisite competencies of a 21st-century physician is the first step in the paradigm shift to competency-based medical education. Over the past two decades, more than 150 lists of competencies have emerged. In a synthesis of these lists, the Physician Competency Reference Set (PCRS) provided a unifying framework of competencies that define the general physician. The PCRS is not context or population specific; however, competently caring for certain underrepresented populations or specific medical conditions can require more specific context. Previously developed competency lists describing care for these populations have been disconnected from an overarching competency framework, limiting their uptake. To address this gap, the Association of American Medical Colleges Advisory Committee on Sexual Orientation, Gender Identity, and Sex Development adapted the PCRS by adding context- and content-specific qualifying statements to existing PCRS competencies to better meet the needs of diverse patient populations. This Article describes the committee's process in developing these qualifiers of competence. To facilitate widespread adoption of the contextualized competencies in U.S. medical schools, the committee used an established competency framework to develop qualifiers of competence to improve the health of individuals who are lesbian, gay, bisexual, transgender; gender nonconforming; or born with differences in sexual development. This process can be applied to other underrepresented populations or medical conditions, ensuring that relevant topics are included in medical education and, ultimately, health care outcomes are improved for all patients inclusive of diversity, background, and ability.

  10. Analyses between Reproductive Behaviour, Genetic Diversity and Pythium Responsiveness in Zingiber spp. reveal an adaptive significance for hemiclonality

    Directory of Open Access Journals (Sweden)

    Geethu Elizabath Thomas

    2016-12-01

    Full Text Available AbstractMode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet. However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behaviour on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behaviour, amplified fragment length polymorphism (AFLP diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale. Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behaviour. The populations inhabiting forest understory were large and

  11. Diversity and cold adaptation of microorganisms isolated from the Schirmacher Oasis, Antarctica

    Science.gov (United States)

    Mojib, Nazia; Bej, Asim K.; Hoover, Richard

    2008-08-01

    We have investigated the feasibility of the PCR amplification of the 16S rRNA genes from eubacteria and Archea on samples collected on Whatman FTA filters from Schirmacher Oasis for the study of culture-independent analysis of the microbial diversity. Both conventional PCR and real-time TaqmaTM PCR successfully amplified the targeted genes. A number of diverse groups of psychrotolerant microorganisms with various pigments have been isolated when cultured on agar medium. 16S rRNA gene analysis of these isolates helped us to identify closest taxonomic genus Pseudomonas, Frigoribacterium, Arthrobacter, Flavobacterium, and Janthinobacterium. It is possible that the pigments play protective role from solar UV radiation, which is prevalent in Antarctic continent especially during Austral summer months. Study of the expression of cold adaptive protein CapB and ice-binding protein IBP using western blots showed positive detection of both or either of these proteins in 6 out of 8 isolates. Since the CapB and IBP protein structure greatly varies in microorganisms, it is possible that the 2 isolates with negative results could have a different class of these proteins. The expression of the CapB and the IBP in these isolates suggest that these proteins are essential for the survival in the Antarctic cold and subzero temperatures and protect themselves from freeze-damage. The current study provided sufficient data to further investigate the rich and diverse biota of psychrotolerant extremophiles in the Antarctic Schirmacher Oasis using both culture-independent and culture-based approaches; and understand the mechanisms of cold tolerance.

  12. Cohabitation promotes high diversity of clownfishes in the Coral Triangle.

    Science.gov (United States)

    Camp, Emma F; Hobbs, Jean-Paul A; De Brauwer, Maarten; Dumbrell, Alex J; Smith, David J

    2016-03-30

    Global marine biodiversity peaks within the Coral Triangle, and understanding how such high diversity is maintained is a central question in marine ecology. We investigated broad-scale patterns in the diversity of clownfishes and their host sea anemones by conducting 981 belt-transects at 20 locations throughout the Indo-Pacific. Of the 1508 clownfishes encountered, 377 fish occurred in interspecific cohabiting groups and cohabitation was almost entirely restricted to the Coral Triangle. Neither the diversity nor density of host anemone or clownfish species alone influenced rates of interspecific cohabitation. Rather cohabitation occurred in areas where the number of clownfish species exceeds the number of host anemone species. In the Coral Triangle, cohabiting individuals were observed to finely partition their host anemone, with the subordinate species inhabiting the periphery. Furthermore, aggression did not increase in interspecific cohabiting groups, instead dominant species were accepting of subordinate species. Various combinations of clownfish species were observed cohabiting (independent of body size, phylogenetic relatedness, evolutionary age, dentition, level of specialization) in a range of anemone species, thereby ensuring that each clownfish species had dominant reproductive individuals in some cohabiting groups. Clownfishes are obligate commensals, thus cohabitation is an important process in maintaining biodiversity in high diversity systems because it supports the persistence of many species when host availability is limiting. Cohabitation is a likely explanation for high species richness in other obligate commensals within the Coral Triangle, and highlights the importance of protecting these habitats in order to conserve unique marine biodiversity. © 2016 The Author(s).

  13. High genetic diversity of Jatropha curcas assessed by ISSR.

    Science.gov (United States)

    Díaz, B G; Argollo, D M; Franco, M C; Nucci, S M; Siqueira, W J; de Laat, D M; Colombo, C A

    2017-05-31

    Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.

  14. [Hemoglobin and testosterone: importance on high altitude acclimatization and adaptation].

    Science.gov (United States)

    Gonzales, Gustavo F

    2011-03-01

    The different types of response mechanisms that the organism uses when exposed to hypoxia include accommodation, acclimatization and adaptation. Accommodation is the initial response to acute exposure to high altitude hypoxia and is characterized by an increase in ventilation and heart rate. Acclimatization is observed in individuals temporarily exposed to high altitude, and to some extent, it enables them to tolerate the high altitudes. In this phase, erythropoiesis is increased, resulting in higher hemoglobin and hematocrit levels to improve oxygen delivery capacity. Adaptation is the process of natural acclimatization where genetical variations and acclimatization play a role in allowing subjects to live without any difficulties at high altitudes. Testosterone is a hormone that regulates erythropoiesis and ventilation and could be associated to the processes of acclimatization and adaptation to high altitude. Excessive erythrocytosis, which leads to chronic mountain sickness, is caused by low arterial oxygen saturation, ventilatory inefficiency and reduced ventilatory response to hypoxia. Testosterone increases during acute exposure to high altitude and also in natives at high altitude with excessive erythrocytosis. Results of current research allow us to conclude that increase in serum testosterone and hemoglobin is adequate for acclimatization, as they improve oxygen transport, but not for high altitude adaptation, since high serum testosterone levels are associated to excessive erythrocytosis.

  15. The yak genome and adaptation to life at high altitude

    DEFF Research Database (Denmark)

    Qiu, Qiang; Zhang, Guojie; Ma, Tao

    2012-01-01

    Domestic yaks (Bos grunniens) provide meat and other necessities for Tibetans living at high altitude on the Qinghai-Tibetan Plateau and in adjacent regions. Comparison between yak and the closely related low-altitude cattle (Bos taurus) is informative in studying animal adaptation to high altitude...... of protein domains involved in sensing the extracellular environment and hypoxic stress. Positively selected and rapidly evolving genes in the yak lineage are also found to be significantly enriched in functional categories and pathways related to hypoxia and nutrition metabolism. These findings may have...... important implications for understanding adaptation to high altitude in other animal species and for hypoxia-related diseases in humans....

  16. Solar multi-conjugate adaptive optics based on high order ground layer adaptive optics and low order high altitude correction.

    Science.gov (United States)

    Zhang, Lanqiang; Guo, Youming; Rao, Changhui

    2017-02-20

    Multi-conjugate adaptive optics (MCAO) is the most promising technique currently developed to enlarge the corrected field of view of adaptive optics for astronomy. In this paper, we propose a new configuration of solar MCAO based on high order ground layer adaptive optics and low order high altitude correction, which result in a homogeneous correction effect in the whole field of view. An individual high order multiple direction Shack-Hartmann wavefront sensor is employed in the configuration to detect the ground layer turbulence for low altitude correction. Furthermore, the other low order multiple direction Shack-Hartmann wavefront sensor supplies the wavefront information caused by high layers' turbulence through atmospheric tomography for high altitude correction. Simulation results based on the system design at the 1-meter New Vacuum Solar Telescope show that the correction uniform of the new scheme is obviously improved compared to conventional solar MCAO configuration.

  17. Highly adaptive tests for group differences in brain functional connectivity

    Directory of Open Access Journals (Sweden)

    Junghi Kim

    2015-01-01

    The proposed tests combine statistical evidence against a null hypothesis from multiple sources across a range of plausible tuning parameter values reflecting uncertainty with the unknown truth. These highly adaptive tests are not only easy to use, but also high-powered robustly across various scenarios. The usage and advantages of these novel tests are demonstrated on an Alzheimer's disease dataset and simulated data.

  18. Evolution of highly diverse forms of behavior in molluscs.

    Science.gov (United States)

    Hochner, Binyamin; Glanzman, David L

    2016-10-24

    Members of the phylum Mollusca demonstrate the animal kingdom's tremendous diversity of body morphology, size and complexity of the nervous system, as well as diversity of behavioral repertoires, ranging from very simple to highly flexible. Molluscs include Solenogastres, with their worm-like bodies and behavior (see phylogenetic tree; Figure 1); Bivalvia (mussels and clams), protected by shells and practically immobile; and the cephalopods, such as the octopus, cuttlefish and squid. The latter are strange-looking animals with nervous systems comprising up to half a billion neurons, which mediate the complex behaviors that characterize these freely moving, highly visual predators. Molluscs are undoubtedly special - their extraordinary evolutionary advance somehow managed to sidestep the acquisition of the rigid skeleton that appears essential to the evolution of other 'successful' phyla: the exoskeleton in ecdysozoan invertebrates and the internal skeleton in Deuterostomia, including vertebrates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

    Science.gov (United States)

    Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

    2014-01-01

    The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

  20. [Agrobacterium rubi strains from blueberry plants are highly diverse].

    Science.gov (United States)

    Abrahamovich, Eliana; López, Ana C; Alippi, Adriana M

    2014-01-01

    The diversity of a collection of Agrobacterium rubi strains isolated from blueberries from different regions of Argentina was studied by conventional microbiological tests and molecular techniques. Results from biochemical and physiological reactions, as well as from rep-PCR and RFLP analysis of PCR-amplified 23S rDNA showed high phenotypic and genotypic intraspecific variation. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

  1. Dynamics of adaptation at high luminances : Adaptation is faster after luminance decrements than after luminance increments

    NARCIS (Netherlands)

    Poot, L.; Snippe, H.P.; Hateren, J.H. van

    As is well known, dark adaption in the human visual system is much slower than is recovery from darkness. We show that at high photopic luminances the situation is exactly opposite. First, we study detection thresholds for a small light flash, at various delays from decrement and increment steps in

  2. Macro-evolutionary studies of cultural diversity: a review of empirical studies of cultural transmission and cultural adaptation

    Science.gov (United States)

    Mace, Ruth; Jordan, Fiona M.

    2011-01-01

    A growing body of theoretical and empirical research has examined cultural transmission and adaptive cultural behaviour at the individual, within-group level. However, relatively few studies have tried to examine proximate transmission or test ultimate adaptive hypotheses about behavioural or cultural diversity at a between-societies macro-level. In both the history of anthropology and in present-day work, a common approach to examining adaptive behaviour at the macro-level has been through correlating various cultural traits with features of ecology. We discuss some difficulties with simple ecological associations, and then review cultural phylogenetic studies that have attempted to go beyond correlations to understand the underlying cultural evolutionary processes. We conclude with an example of a phylogenetically controlled approach to understanding proximate transmission pathways in Austronesian cultural diversity. PMID:21199844

  3. Macro-evolutionary studies of cultural diversity: a review of empirical studies of cultural transmission and cultural adaptation.

    Science.gov (United States)

    Mace, Ruth; Jordan, Fiona M

    2011-02-12

    A growing body of theoretical and empirical research has examined cultural transmission and adaptive cultural behaviour at the individual, within-group level. However, relatively few studies have tried to examine proximate transmission or test ultimate adaptive hypotheses about behavioural or cultural diversity at a between-societies macro-level. In both the history of anthropology and in present-day work, a common approach to examining adaptive behaviour at the macro-level has been through correlating various cultural traits with features of ecology. We discuss some difficulties with simple ecological associations, and then review cultural phylogenetic studies that have attempted to go beyond correlations to understand the underlying cultural evolutionary processes. We conclude with an example of a phylogenetically controlled approach to understanding proximate transmission pathways in Austronesian cultural diversity.

  4. High and distinct range-edge genetic diversity despite local bottlenecks.

    Directory of Open Access Journals (Sweden)

    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  5. Evolutionary adaptation to high altitude: a view from in utero

    Science.gov (United States)

    Julian, Colleen Glyde; Wilson, Megan J.; Moore, Lorna G.

    2010-01-01

    A primary focus within biological anthropology has been to elucidate the processes of evolutionary adaptation. A. Roberto Frisancho helped move anthropology towards more mechanistic explanations of human adaptation by drawing attention to the importance of the functional relevance of human variation. Using the natural laboratory of high altitude, he and others asked whether the unique physiology of indigenous high-altitude residents was the result of acclimatization, developmental plasticity and/or genetic adaptation in response to the high-altitude environment. We approach the question of human adaptation to high altitude from a somewhat unique vantage point; namely, by examining physiological characteristics – pregnancy and pregnancy outcome -- that are most closely associated with reproductive fitness. Here we review the potent example of high-altitude native population’s resistance to hypoxia-associated reductions in birth weight, which is often associated with higher infant morbidity and mortality at high altitude. With the exception of two recent publications, these comparative birth weight studies have utilized surnames, self-identification and/or linguistic characteristics to assess ancestry, and none have linked ‘advantageous’ phenotypes to specific genetic variations. Recent advancements in genetic and statistical tools have enabled us to assess individual ancestry with higher resolution, identify the genetic basis of complex phenotypes and to infer the effect of natural selection on specific gene regions. Using these technologies our studies are now directed to determine the genetic variations that underlie the mechanisms by which high-altitude ancestry protects fetal growth and, in turn, to further our understanding of evolutionary processes involved in human adaptation to high altitude. PMID:19367578

  6. Evolutionary adaptation to high altitude: a view from in utero.

    Science.gov (United States)

    Julian, Colleen Glyde; Wilson, Megan J; Moore, Lorna G

    2009-01-01

    A primary focus within biological anthropology has been to elucidate the processes of evolutionary adaptation. Frisancho helped to move anthropology towards more mechanistic explanations of human adaptation by drawing attention to the importance of the functional relevance of human variation. Using the natural laboratory of high altitude, he and others asked whether the unique physiology of indigenous high-altitude residents was the result of acclimatization, developmental plasticity, and/or genetic adaptation in response to the high-altitude environment. We approach the question of human adaptation to high altitude from a somewhat unique vantage point; namely, by examining physiological characteristics-pregnancy and pregnancy outcome-which are closely associated with reproductive fitness. Here we review the potent example of high-altitude native population's resistance to hypoxia-associated reductions in birth weight, which is often associated with higher infant morbidity and mortality at high altitude. With the exception of two recent publications, these comparative birth weight studies have utilized surnames, self-identification, and/or linguistic characteristics to assess ancestry, and none have linked 'advantageous' phenotypes to specific genetic variations. Recent advancements in genetic and statistical tools have enabled us to assess individual ancestry with higher resolution, identify the genetic basis of complex phenotypes and to infer the effect of natural selection on specific gene regions. Using these technologies our studies are now directed to determine the genetic variations that underlie the mechanisms by which high-altitude ancestry protects fetal growth and, in turn, to further our understanding of evolutionary processes involved in human adaptation to high altitude.

  7. Hemoglobin and testosterone: importance on high altitude acclimatization and adaptation

    OpenAIRE

    Gonzales, Gustavo F.; Jefe de la Unidad de Reproducción, Instituto de Investigaciones de la Altura y Jefe del Laboratorio de Endocrinología y Reproducción, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia. Doctor en Medicina y Doctor en Ciencias. Especialista en Endocrinología.

    2011-01-01

    The different types of response mechanisms that the organism uses when exposed to hypoxia include accommodation, acclimatization and adaptation. Accommodation is the initial response to acute exposure to high altitude hypoxia and is characterized by an increase in ventilation and heart rate. Acclimatization is observed in individuals temporarily exposed to high altitude, and to some extent, it enables them to tolerate the high altitudes. In this phase, erythropoiesis is increased, resulti...

  8. Determination of a Screening Metric for High Diversity DNA Libraries.

    Directory of Open Access Journals (Sweden)

    Nicholas J Guido

    Full Text Available The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

  9. Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin.

    Science.gov (United States)

    Mousavi-Derazmahalleh, Mahsa; Bayer, Philipp E; Nevado, Bruno; Hurgobin, Bhavna; Filatov, Dmitry; Kilian, Andrzej; Kamphuis, Lars G; Singh, Karam B; Berger, Jens D; Hane, James K; Edwards, David; Erskine, William; Nelson, Matthew N

    2018-01-20

    This first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East-West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables. Most grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.

  10. High Diversity of Fungi in Air Particulate Matter

    Science.gov (United States)

    Fröhlich-Nowoisky, J.; Despres, V. R.; Pöschl, U.

    2009-04-01

    Fungal spores account for large proportions of air particulate matter, and they influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, hardly known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse and more human pathogens and allergens in the respirable fine particle fraction (fungi to primary biogenic aerosols in the atmosphere: wet and dry discharged spores, carbohydrates, and inorganic ions, Atmospheric Chemistry and Physics, 7, 4569-4588, 2007. Fröhlich-Nowoisky, J. Despres, V.R., Pöschl, U.: High diversity of fungi in air particulate matter, Proceedings of the National Academy of Sciences, submitted, 2008.

  11. Genetic adaptation to high altitude in the Ethiopian highlands.

    Science.gov (United States)

    Scheinfeldt, Laura B; Soi, Sameer; Thompson, Simon; Ranciaro, Alessia; Woldemeskel, Dawit; Beggs, William; Lambert, Charla; Jarvis, Joseph P; Abate, Dawit; Belay, Gurja; Tishkoff, Sarah A

    2012-01-20

    Genomic analysis of high-altitude populations residing in the Andes and Tibet has revealed several candidate loci for involvement in high-altitude adaptation, a subset of which have also been shown to be associated with hemoglobin levels, including EPAS1, EGLN1, and PPARA, which play a role in the HIF-1 pathway. Here, we have extended this work to high- and low-altitude populations living in Ethiopia, for which we have measured hemoglobin levels. We genotyped the Illumina 1M SNP array and employed several genome-wide scans for selection and targeted association with hemoglobin levels to identify genes that play a role in adaptation to high altitude. We have identified a set of candidate genes for positive selection in our high-altitude population sample, demonstrated significantly different hemoglobin levels between high- and low-altitude Ethiopians and have identified a subset of candidate genes for selection, several of which also show suggestive associations with hemoglobin levels. We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia.

  12. Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

    Science.gov (United States)

    Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

    2015-01-01

    This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

  13. Andean and Tibetan patterns of adaptation to high altitude.

    Science.gov (United States)

    Bigham, Abigail W; Wilson, Megan J; Julian, Colleen G; Kiyamu, Melisa; Vargas, Enrique; Leon-Velarde, Fabiola; Rivera-Chira, Maria; Rodriquez, Carmelo; Browne, Vaughn A; Parra, Esteban; Brutsaert, Tom D; Moore, Lorna G; Shriver, Mark D

    2013-01-01

    High-altitude hypoxia, or decreased oxygen levels caused by low barometric pressure, challenges the ability of humans to live and reproduce. Despite these challenges, human populations have lived on the Andean Altiplano and the Tibetan Plateau for millennia and exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. We and others have identified natural selection candidate genes and gene regions for these adaptations using dense genome scan data. One gene previously known to be important in cellular oxygen sensing, egl nine homolog 1 (EGLN1), shows evidence of positive selection in both Tibetans and Andeans. Interestingly, the pattern of variation for this gene differs between the two populations. Continued research among Tibetan populations has identified statistical associations between hemoglobin concentration and single nucleotide polymorphism (SNP) genotype at EGLN1 and a second gene, endothelial PAS domain protein 1 (EPAS1). To measure for the effects of EGLN1 and EPAS1 altitude genotypes on hemoglobin concentration among Andean highlanders, we performed a multiple linear regression analysis of 10 candidate SNPs in or near these two genes. Our analysis did not identify significant associations between EPAS1 or EGLN1 SNP genotypes and hemoglobin concentration in Andeans. These results contribute to our understanding of the unique set of adaptations developed in different highland groups to the hypoxia of high altitude. Overall, the results provide key insights into the patterns of genetic adaptation to high altitude in Andean and Tibetan populations. Copyright © 2013 Wiley Periodicals, Inc.

  14. Adaptation of microorganisms and their transport systems to high temperatures

    NARCIS (Netherlands)

    Tolner, B; Poolman, B.; Konings, W.N

    1997-01-01

    Growth of Bacteria and Archaea has been observed at temperatures up to 95 and 110 degrees C, respectively. These thermophiles are adapted to environments of high temperature by changes in the membrane lipid composition, higher thermostabilities of the (membrane) proteins, higher turnover rates of

  15. Rare species support vulnerable functions in high-diversity ecosystems.

    Directory of Open Access Journals (Sweden)

    David Mouillot

    Full Text Available Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees, we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by

  16. Impact of co-channel interference on the performance of adaptive non-ideal generalized transmit diversity

    KAUST Repository

    Radaydeh, Redha Mahmoud Mesleh

    2010-09-01

    The impact of co-channel interference and nonideal estimation of the desired user channel state information (CSI) on the performance of an adaptive threshold-based generalized transmit diversity for low-complexity multiple-input single-output configuration is investigated. The adaptation to channel conditions is assumed to be based on the desired user CSI, and the number of active transmit antennas is adjusted accordingly to guarantee predetermined target performance. To facilitate comparisons between different adaptation schemes, new analytical results for the statistics of combined signal-to-interference-plus-noise ratio (SINR) are derived, which can be applied for different fading conditions of interfering signals. Selected numerical results are presented to validate the analytical development and to compare the outage performance of the considered adaptation schemes. © 2010 IEEE.

  17. Adaptive Sampling for High Throughput Data Using Similarity Measures

    Energy Technology Data Exchange (ETDEWEB)

    Bulaevskaya, V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sales, A. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-05-06

    The need for adaptive sampling arises in the context of high throughput data because the rates of data arrival are many orders of magnitude larger than the rates at which they can be analyzed. A very fast decision must therefore be made regarding the value of each incoming observation and its inclusion in the analysis. In this report we discuss one approach to adaptive sampling, based on the new data point’s similarity to the other data points being considered for inclusion. We present preliminary results for one real and one synthetic data set.

  18. Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

    Directory of Open Access Journals (Sweden)

    Yasir Mehmood

    2017-06-01

    Full Text Available The Australian Ascochyta rabiei (Pass. Labr. (syn. Phoma rabiei population has low genotypic diversity with only one mating type detected to date, potentially precluding substantial evolution through recombination. However, a large diversity in aggressiveness exists. In an effort to better understand the risk from selective adaptation to currently used resistance sources and chemical control strategies, the population was examined in detail. For this, a total of 598 isolates were quasi-hierarchically sampled between 2013 and 2015 across all major Australian chickpea growing regions and commonly grown host genotypes. Although a large number of haplotypes were identified (66 through short sequence repeat (SSR genotyping, overall low gene diversity (Hexp = 0.066 and genotypic diversity (D = 0.57 was detected. Almost 70% of the isolates assessed were of a single dominant haplotype (ARH01. Disease screening on a differential host set, including three commonly deployed resistance sources, revealed distinct aggressiveness among the isolates, with 17% of all isolates identified as highly aggressive. Almost 75% of these were of the ARH01 haplotype. A similar pattern was observed at the host level, with 46% of all isolates collected from the commonly grown host genotype Genesis090 (classified as “resistant” during the term of collection identified as highly aggressive. Of these, 63% belonged to the ARH01 haplotype. In conclusion, the ARH01 haplotype represents a significant risk to the Australian chickpea industry, being not only widely adapted to the diverse agro-geographical environments of the Australian chickpea growing regions, but also containing a disproportionately large number of aggressive isolates, indicating fitness to survive and replicate on the best resistance sources in the Australian germplasm.

  19. High-order adaptive methods for parabolic systems

    Science.gov (United States)

    Adjerid, S.; Flaherty, J. E.; Moore, P. K.; Wang, Y. J.

    1992-11-01

    We consider the adaptive solution of parabolic partial differential systems in one and two space dimensions by finite element procedures that automatically refine and coarsen computational meshes, vary the degree of the piecewise polynomial basis and, in one dimension, move the computational mesh. Two-dimensional meshes of triangular, quadrilateral, or a mixture of triangular and quadrilateral elements are generated using a finite quadtree procedure that is also used for data management. A posteriori estimates, used to control adaptive enrichment, are generated from the hierarchical polynomial basis. Temporal integration, within a method-of-lines framework, uses either backward difference methods or a variant of the singly implicit Runge-Kutta (SIRK) methods. A high-level user interface facilitates use of the adaptive software.

  20. De novo assembly of highly diverse viral populations

    Directory of Open Access Journals (Sweden)

    Yang Xiao

    2012-09-01

    Full Text Available Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

  1. De novo assembly of highly diverse viral populations.

    Science.gov (United States)

    Yang, Xiao; Charlebois, Patrick; Gnerre, Sante; Coole, Matthew G; Lennon, Niall J; Levin, Joshua Z; Qu, James; Ryan, Elizabeth M; Zody, Michael C; Henn, Matthew R

    2012-09-13

    Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

  2. Diversion assumptions for high-powered research reactors

    Energy Technology Data Exchange (ETDEWEB)

    Binford, F.T.

    1984-01-01

    This study deals with diversion assumptions for high-powered research reactors -- specifically, MTR fuel; pool- or tank-type research reactors with light-water moderator; and water, beryllium, or graphite reflectors, and which have a power level of 25 MW(t) or more. The objective is to provide assistance to the IAEA in documentation of criteria and inspection observables related to undeclared plutonium production in the reactors described above, including: criteria for undeclared plutonium production, necessary design information for implementation of these criteria, verification guidelines including neutron physics and heat transfer, and safeguards measures to facilitate the detection of undeclared plutonium production at large research reactors.

  3. Adaptation and survival of plants in high stress habitats via fungal endophyte conferred stress tolerance

    Science.gov (United States)

    Rodriguez, Rusty J.; Woodward, Claire; Redman, Regina S.

    2010-01-01

    From the Arctic to the Antarctic, plants thrive in diverse habitats that impose different levels of adaptive pressures depending on the type and degree of biotic and abiotic stresses inherent to each habitat (Stevens, 1989). At any particular location, the abundance and distribution of individual plant species vary tremendously and is theorized to be based on the ability to tolerate a wide range of edaphic conditions and habitat-specific stresses (Pianka, 1966). The ability of individual plant species to thrive in diverse habitats is commonly referred to as phenotypic plasticity and is thought to involve adaptations based on changes in the plant genome (Givnish, 2002; Pan et al., 2006; Robe and Griffiths, 2000; Schurr et al., 2006). Habitats that impose high levels of abiotic stress are typically colonized with fewer plant species compared to habitats imposing low levels of stress. Moreover, high stress habitats have decreased levels of plant abundance compared to low stress habitats even though these habitats may occur in close proximity to one another (Perelman et al., 2007). This is particularly interesting because all plants are known to perceive, transmit signals, and respond to abiotic stresses such as drought, heat, and salinity (Bartels and Sunkar, 2005; Bohnert et al., 1995). Although there has been extensive research performed to determine the genetic, molecular, and physiological bases of how plants respond to and tolerate stress, the nature of plant adaptation to high stress habitats remains unresolved (Leone et al., 2003; Maggio et al., 2003; Tuberosa et al., 2003). However, recent evidence indicates that a ubiquitous aspect of plant biology (fungal symbiosis) is involved in the adaptation and survival of at least some plants in high stress habitats (Rodriguez et al., 2008).

  4. Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards.

    Science.gov (United States)

    Ren, Tiantian; Kahrl, Ariel F; Wu, Martin; Cox, Robert M

    2016-10-01

    Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species. © 2016 John Wiley & Sons Ltd.

  5. Phenotypic diversity in autosomal-dominant cone-rod dystrophy elucidated by adaptive optics retinal imaging.

    Science.gov (United States)

    Song, Hongxin; Rossi, Ethan A; Stone, Edwin; Latchney, Lisa; Williams, David; Dubra, Alfredo; Chung, Mina

    2018-01-01

    Several genes causing autosomal-dominant cone-rod dystrophy (AD-CRD) have been identified. However, the mechanisms by which genetic mutations lead to cellular loss in human disease remain poorly understood. Here we combine genotyping with high-resolution adaptive optics retinal imaging to elucidate the retinal phenotype at a cellular level in patients with AD-CRD harbouring a defect in the GUCA1A gene. Nine affected members of a four-generation AD-CRD pedigree and three unaffected first-degree relatives underwent clinical examinations including visual acuity, fundus examination, Goldmann perimetry, spectral domain optical coherence tomography and electroretinography. Genome-wide scan followed by bidirectional sequencing was performed on all affected participants. High-resolution imaging using a custom adaptive optics scanning light ophthalmoscope (AOSLO) was performed for selected participants. Clinical evaluations showed a range of disease severity from normal fundus appearance in teenaged patients to pronounced macular atrophy in older patients. Molecular genetic testing showed a mutation in in GUCA1A segregating with disease. AOSLO imaging revealed that of the two teenage patients with mild disease, one had severe disruption of the photoreceptor mosaic while the other had a normal cone mosaic. AOSLO imaging demonstrated variability in the pattern of cone and rod cell loss between two teenage cousins with early AD-CRD, who had similar clinical features and had the identical disease-causing mutation in GUCA1A . This finding suggests that a mutation in GUCA1A does not lead to the same degree of AD-CRD in all patients. Modifying factors may mitigate or augment disease severity, leading to different retinal cellular phenotypes. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  6. Adaptive optics with pupil tracking for high resolution retinal imaging.

    Science.gov (United States)

    Sahin, Betul; Lamory, Barbara; Levecq, Xavier; Harms, Fabrice; Dainty, Chris

    2012-02-01

    Adaptive optics, when integrated into retinal imaging systems, compensates for rapidly changing ocular aberrations in real time and results in improved high resolution images that reveal the photoreceptor mosaic. Imaging the retina at high resolution has numerous potential medical applications, and yet for the development of commercial products that can be used in the clinic, the complexity and high cost of the present research systems have to be addressed. We present a new method to control the deformable mirror in real time based on pupil tracking measurements which uses the default camera for the alignment of the eye in the retinal imaging system and requires no extra cost or hardware. We also present the first experiments done with a compact adaptive optics flood illumination fundus camera where it was possible to compensate for the higher order aberrations of a moving model eye and in vivo in real time based on pupil tracking measurements, without the real time contribution of a wavefront sensor. As an outcome of this research, we showed that pupil tracking can be effectively used as a low cost and practical adaptive optics tool for high resolution retinal imaging because eye movements constitute an important part of the ocular wavefront dynamics.

  7. Understanding Students' Precollege Experiences with Racial Diversity: The High School as Microsystem

    Science.gov (United States)

    Park, Julie J.; Chang, Stephanie H.

    2015-01-01

    Few qualitative studies consider how high school experiences affect readiness for diversity engagement in college. Using data from an ethnographic case study, three central trends (student experiences within homogeneous high schools, racial divisions within diverse high schools, and students who attended diverse high schools but had little…

  8. Population differentiation and genetic diversity of Trichophyton rubrum as revealed by highly discriminatory microsatellites.

    Science.gov (United States)

    Gong, Jie; Wu, Weiwei; Ran, MengLong; Wang, Xiaowen; Liu, Wei; Wan, Zhe; Yao, Limin; Li, Ruoyu

    2016-10-01

    Little is known regarding the population information of Trichophyton rubrum due to a lack of strains with clear sampling information and molecular markers with high discriminatory power. In the present study, we developed a set of microsatellite markers that have a cumulative discriminatory power was 0.993. Using these microsatellites loci, 243 strains T. rubrum that had clear sampling information were analysed. Three genetic diversity indices (Shannon's Information Index, Nei's unbiased gene diversity and allelic richness) were shown to be related to the human population size of the sampling city rather than mean annual temperature or humidity. Population structure analyses revealed that T. rubrum can be separated into two clusters. AMOVA results indicated that genetic variation was more significant between these two clusters than among geographical populations. Our work is the first to reveal population information of T. rubrum using highly discriminatory molecular markers, and suggest that T. rubrum populations in cities with larger population size might have better adaptability due to higher genetic diversity under selective pressures (such as antifungal agents). Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

    Science.gov (United States)

    Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

    2014-05-19

    The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Genetic adaptation to high altitude in the Ethiopian highlands

    OpenAIRE

    Scheinfeldt, Laura B.; Soi, Sameer; Thompson, Simon; Ranciaro, Alessia; Woldemeskel, Dawit; Beggs, William; Lambert, Charla; Jarvis, Joseph P.; Abate, Dawit; Belay, Gurja; Tishkoff, Sarah A.

    2012-01-01

    Background Genomic analysis of high-altitude populations residing in the Andes and Tibet has revealed several candidate loci for involvement in high-altitude adaptation, a subset of which have also been shown to be associated with hemoglobin levels, including EPAS1, EGLN1, and PPARA, which play a role in the HIF-1 pathway. Here, we have extended this work to high- and low-altitude populations living in Ethiopia, for which we have measured hemoglobin levels. We genotyped the Illumina 1M SNP ar...

  11. Predator diversity and abundance provide little support for the enemies hypothesis in forests of high tree diversity.

    Directory of Open Access Journals (Sweden)

    Andreas Schuldt

    Full Text Available Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity--and thus information on the relevance of experimental findings--for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25-69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis--derived from studies in less diverse ecosystems--of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species

  12. Digital control of high performance aircraft using adaptive estimation techniques

    Science.gov (United States)

    Van Landingham, H. F.; Moose, R. L.

    1977-01-01

    In this paper, an adaptive signal processing algorithm is joined with gain-scheduling for controlling the dynamics of high performance aircraft. A technique is presented for a reduced-order model (the longitudinal dynamics) of a high performance STOL aircraft. The actual controller views the nonlinear behavior of the aircraft as equivalent to a randomly switching sequence of linear models taken from a preliminary piecewise-linear fit of the system nonlinearities. The adaptive nature of the estimator is necessary to select the proper sequence of linear models along the flight trajectory. Nonlinear behavior is approximated by effective switching of the linear models at random times, with durations reflecting aircraft motion in response to pilot commands.

  13. The genetic architecture of adaptations to high altitude in Ethiopia

    OpenAIRE

    Gorka Alkorta-Aranburu; Beall, Cynthia M.; Witonsky, David B.; Amha Gebremedhin; Pritchard, Jonathan K.; Anna Di Rienzo

    2012-01-01

    Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic gro...

  14. Genome architecture enables local adaptation of Atlantic cod despite high connectivity

    DEFF Research Database (Denmark)

    Barth, Julia M I; Berg, Paul R; Jonsson, Per R.

    2017-01-01

    characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single......-nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless...... Mb chromosomal rearrangement in fjord cod, previously proposed to comprise genes critical for the survival at low salinities. This suggests that despite considerable connectivity with offshore populations, local adaptation to fjord environments may be enabled by suppression of recombination...

  15. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities.

    Science.gov (United States)

    Aylward, Frank O; McDonald, Bradon R; Adams, Sandra M; Valenzuela, Alejandra; Schmidt, Rebeccah A; Goodwin, Lynne A; Woyke, Tanja; Currie, Cameron R; Suen, Garret; Poulsen, Michael

    2013-06-01

    Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.

  16. High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2

    Directory of Open Access Journals (Sweden)

    Hellberg Michael E

    2010-05-01

    Full Text Available Abstract Background Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching. Results In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus, a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella possess proteins structurally similar to tachylectin-2. Conclusions Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1 part of Oculina's innate immunity repertoire, and 2 evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change.

  17. Legionella species diversity and dynamics from surface reservoir to tap water: from cold adaptation to thermophily.

    Science.gov (United States)

    Lesnik, René; Brettar, Ingrid; Höfle, Manfred G

    2016-05-01

    Water samples of the Drinking Water Supply System (DWSS) of the city of Braunschweig were analysed for its Legionella species composition using genus-specific PCR amplicons and single-strand conformation polymorphism (SSCP) fingerprint analyses based on 16S rRNA genes. These analyses comprised the whole supply chain including raw water, treatment process and large-scale storage, and a seasonal study of finished drinking water sampled monthly from cold and hot tap water. Treatment of raw water had a major impact on Legionella species by reducing their diversity and abundances. The Legionella species composition of the tap water was highly distinct from that of both source waters. In cold water, 8-14 different phylotypes of Legionella (PTLs) were observed per sample with relative abundances ranging from >1% to 53%. In hot water, L. pneumophila was present during all seasons at high relative abundances (8-40%) accompanied by 5-14 other PTLs of which 6 PTLs were in common with cold water. This thermophilic Legionella community, including L. pneumophila, was able to grow in the hot water above 50 °C. Such thermophilic Legionella populations are of general relevance for drinking water management and public health, but also for the ecology and evolution of the genus Legionella.

  18. Fungal endophytes in above-ground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts

    OpenAIRE

    Massimo, Nicholas C.; Nandi Devan, MM; Arendt, Kayla R.; Wilch, Margaret H.; Riddle, Jakob M.; Furr, Susan H.; Steen, Cole; U?Ren, Jana M.; Sandberg, Dustin C.; Arnold, A. Elizabeth

    2015-01-01

    In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in above-ground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fun...

  19. Predator Diversity and Abundance Provide Little Support for the Enemies Hypothesis in Forests of High Tree Diversity

    Science.gov (United States)

    Schuldt, Andreas; Both, Sabine; Bruelheide, Helge; Härdtle, Werner; Schmid, Bernhard; Zhou, Hongzhang; Assmann, Thorsten

    2011-01-01

    Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity—and thus information on the relevance of experimental findings—for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25–69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes) of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis—derived from studies in less diverse ecosystems—of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species-rich forest

  20. High diversity of genogroup I picobirnaviruses in mammals

    Directory of Open Access Journals (Sweden)

    Patrick CY Woo

    2016-11-01

    Full Text Available In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs were positive by RT-PCR targeting the partial RdRp gene in specimens from 5 cattle, 6 monkeys, 17 horses, 9 pigs, 1 rabbit, 1 dog and 12 California sea lions, with 11, 9, 23, 17, 1, 1 and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4 to 89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segments 1 (viral loads 1.7×104 to 5.9×106/ml and 15 segments 2 (viral loads 4.1×103 to 1.3×106/ml of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1 to C4. In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1 to R9. In four sea lions, PBVs were detected in two different years, with the same segment 1 clade (C3 present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.

  1. High diversity at PRDM9 in chimpanzees and bonobos.

    Science.gov (United States)

    Groeneveld, Linn Fenna; Atencia, Rebeca; Garriga, Rosa M; Vigilant, Linda

    2012-01-01

    The PRDM9 locus in mammals has increasingly attracted research attention due to its role in mediating chromosomal recombination and possible involvement in hybrid sterility and hence speciation processes. The aim of this study was to characterize sequence variation at the PRDM9 locus in a sample of our closest living relatives, the chimpanzees and bonobos. PRDM9 contains a highly variable and repetitive zinc finger array. We amplified this domain using long-range PCR and determined the DNA sequences using conventional Sanger sequencing. From 17 chimpanzees representing three subspecies and five bonobos we obtained a total of 12 alleles differing at the nucleotide level. Based on a data set consisting of our data and recently published Pan PRDM9 sequences, we found that at the subspecies level, diversity levels did not differ among chimpanzee subspecies or between chimpanzee subspecies and bonobos. In contrast, the sample of chimpanzees harbors significantly more diversity at PRDM9 than samples of humans. Pan PRDM9 shows signs of rapid evolution including no alleles or ZnFs in common with humans as well as signals of positive selection in the residues responsible for DNA binding. The high number of alleles specific to the genus Pan, signs of positive selection in the DNA binding residues, and reported lack of conservation of recombination hotspots between chimpanzees and humans suggest that PRDM9 could be active in hotspot recruitment in the genus Pan. Chimpanzees and bonobos are considered separate species and do not have overlapping ranges in the wild, making the presence of shared alleles at the amino acid level between the chimpanzee and bonobo species interesting in view of the hypothesis that PRDM9 plays a universal role in interspecific hybrid sterility.

  2. High diversity at PRDM9 in chimpanzees and bonobos.

    Directory of Open Access Journals (Sweden)

    Linn Fenna Groeneveld

    Full Text Available BACKGROUND: The PRDM9 locus in mammals has increasingly attracted research attention due to its role in mediating chromosomal recombination and possible involvement in hybrid sterility and hence speciation processes. The aim of this study was to characterize sequence variation at the PRDM9 locus in a sample of our closest living relatives, the chimpanzees and bonobos. METHODOLOGY/PRINCIPAL FINDINGS: PRDM9 contains a highly variable and repetitive zinc finger array. We amplified this domain using long-range PCR and determined the DNA sequences using conventional Sanger sequencing. From 17 chimpanzees representing three subspecies and five bonobos we obtained a total of 12 alleles differing at the nucleotide level. Based on a data set consisting of our data and recently published Pan PRDM9 sequences, we found that at the subspecies level, diversity levels did not differ among chimpanzee subspecies or between chimpanzee subspecies and bonobos. In contrast, the sample of chimpanzees harbors significantly more diversity at PRDM9 than samples of humans. Pan PRDM9 shows signs of rapid evolution including no alleles or ZnFs in common with humans as well as signals of positive selection in the residues responsible for DNA binding. CONCLUSIONS AND SIGNIFICANCE: The high number of alleles specific to the genus Pan, signs of positive selection in the DNA binding residues, and reported lack of conservation of recombination hotspots between chimpanzees and humans suggest that PRDM9 could be active in hotspot recruitment in the genus Pan. Chimpanzees and bonobos are considered separate species and do not have overlapping ranges in the wild, making the presence of shared alleles at the amino acid level between the chimpanzee and bonobo species interesting in view of the hypothesis that PRDM9 plays a universal role in interspecific hybrid sterility.

  3. The genetic architecture of adaptations to high altitude in Ethiopia.

    Science.gov (United States)

    Alkorta-Aranburu, Gorka; Beall, Cynthia M; Witonsky, David B; Gebremedhin, Amha; Pritchard, Jonathan K; Di Rienzo, Anna

    2012-01-01

    Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control and DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

  4. Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers.

    Science.gov (United States)

    Edea, Zewdu; Dessie, Tadelle; Dadi, Hailu; Do, Kyoung-Tag; Kim, Kwan-Suk

    2017-01-01

    Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin-i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered

  5. Enhanced Wort Fermentation withDe NovoLager Hybrids Adapted to High-Ethanol Environments.

    Science.gov (United States)

    Krogerus, Kristoffer; Holmström, Sami; Gibson, Brian

    2018-02-15

    Interspecific hybridization is a valuable tool for developing and improving brewing yeast in a number of industry-relevant aspects. However, the genomes of newly formed hybrids can be unstable. Here, we exploited this trait by adapting four brewing yeast strains, three of which were de novo interspecific lager hybrids with different ploidy levels, to high ethanol concentrations in an attempt to generate variant strains with improved fermentation performance in high-gravity wort. Through a batch fermentation-based adaptation process and selection based on a two-step screening process, we obtained eight variant strains which we compared to the wild-type strains in 2-liter-scale wort fermentations replicating industrial conditions. The results revealed that the adapted variants outperformed the strains from which they were derived, and the majority also possessed several desirable brewing-relevant traits, such as increased ester formation and ethanol tolerance, as well as decreased diacetyl formation. The variants obtained from the polyploid hybrids appeared to show greater improvements in fermentation performance than those derived from diploid strains. Interestingly, it was not only the hybrid strains, but also the Saccharomyces cerevisiae parent strain, that appeared to adapt and showed considerable changes in genome size. Genome sequencing and ploidy analysis revealed that changes had occurred at both the chromosome and single nucleotide levels in all variants. Our study demonstrates the possibility of improving de novo lager yeast hybrids through adaptive evolution by generating stable and superior variants that possess traits relevant to industrial lager beer fermentation. IMPORTANCE Recent studies have shown that hybridization is a valuable tool for creating new and diverse strains of lager yeast. Adaptive evolution is another strain development tool that can be applied in order to improve upon desirable traits. Here, we apply adaptive evolution to newly

  6. Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

    Science.gov (United States)

    Sánchez-Quinto, Federico; Lalueza-Fox, Carles

    2015-01-01

    Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations—including morphological and behavioural traits—as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's—and our very own—evolutionary history. PMID:25487326

  7. Adaptive optics high resolution spectroscopy: present status and future direction

    Energy Technology Data Exchange (ETDEWEB)

    Alcock, C; Angel, R; Ciarlo, D; Fugate, R O; Ge, J; Kuzmenko, P; Lloyd-Hart, M; Macintosh, B; Najita, J; Woolf, N

    1999-07-27

    High resolution spectroscopy experiments with visible adaptive optics (AO) telescopes at Starfire Optical Range and Mt. Wilson have demonstrated that spectral resolution can be routinely improved by a factor of - 10 over the seeing-limited case with no extra light losses at visible wavelengths. With large CCDs now available, a very wide wavelength range can be covered in a single exposure. In the near future, most large ground-based telescopes will be equipped with powerful A0 systems. Most of these systems are aimed primarily at diffraction-limited operation in the near IR. An exciting new opportunity will thus open up for high resolution IR spectroscopy. Immersion echelle gratings with much coarser grooves being developed by us at LLNL will play a critical role in achieving high spectral resolution with a compact and low cost IR cryogenically cooled spectrograph and simultaneous large wavelength coverage on relatively small IR detectors. We have constructed a new A0 optimized spectrograph at Steward Observatory to provide R = 200,000 in the optical, which is being commissioned at the Starfire Optical Range 3.5m telescope. We have completed the optical design of the LLNL IR Immersion Spectrograph (LISPEC) to take advantage of improved silicon etching technology. Key words: adaptive optics, spectroscopy, high resolution, immersion gratings

  8. Lineage Diversity and Size Disparity in Musteloidea: Testing Patterns of Adaptive Radiation Using Molecular and Fossil-Based Methods.

    Science.gov (United States)

    Law, Chris J; Slater, Graham J; Mehta, Rita S

    2018-01-01

    Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods. The species diversity and equally impressive ecological and phenotypic diversity found across Musteloidea is often attributed to two adaptive radiations coinciding with two major climate events, the Eocene-Oligocene transition and the Mid-Miocene Climate Transition. Here, we compiled a novel time-scaled phylogeny for 88% of extant musteloids and used it as a framework for testing the predictions of adaptive radiation hypotheses with respect to rates of lineage diversification and phenotypic evolution. Contrary to expectations, we found no evidence for rapid bursts of lineage diversification at the origin of Musteloidea, and further analyses of lineage diversification rates using molecular and fossil-based methods did not find associations between rates of lineage diversification and the Eocene-Oligocene transition or Mid-Miocene Climate Transition as previously hypothesized. Rather, we found support for decoupled diversification dynamics driven by increased clade carrying capacity in the branches leading to a subclade of elongate mustelids. Supporting decoupled diversification dynamics between the subclade of elongate mustelids and the ancestral musteloid regime is our finding of increased rates of body length evolution, but not body mass evolution, within the decoupled mustelid subclade. The lack of correspondence in rates of body mass and length evolution suggest that phenotypic evolutionary rates under a single

  9. An adaptive finite element method for high speed flows

    Science.gov (United States)

    Peraire, J.; Morgan, K.; Peiro, J.; Zienkiewicz, O. C.

    1987-01-01

    The solution of the equations of compressible high speed flow, on unstructured triangular grids in 2D and tetrahedral grids in 3D, is considered. Solution methods based upon both Taylor-Galerkin and Runge-Kutta time-stepping techniques are presented and the incorporation of the ideas of flux corrected transport (FCT) is discussed. These methods are combined with an adaptive mesh regeneration procedure and are employed in the solution of several examples, consisting of Euler flows in both 2D and 3D and Navier-Stokes flows in 2D.

  10. Scientific Knowledge and Knowledge Needs in Climate Adaptation Policy: A Case Study of Diverse Mountain Regions

    Directory of Open Access Journals (Sweden)

    Veruska Muccione

    2016-08-01

    Full Text Available Mountain ecosystems around the world are recognized to be among the most vulnerable to the impacts of climate change. The need to develop sound adaptation strategies in these areas is growing. Knowledge from the natural sciences has an important role to play in the development of adaptation strategies. However, the extent of and gaps in such knowledge have not been systematically investigated for mountain areas. This paper analyzes the status of knowledge from natural science disciplines and research needs relevant to the national and subnational climate adaptation policies of 1 US state (Washington and 7 countries (Austria, Bhutan, Colombia, Germany, Nepal, Peru, and Switzerland, in particular the elements of those policies focused on mountain areas. In addition, we asked key individuals involved in drafting those policies to answer a short questionnaire. We found that research needs mainly concern impact and vulnerability assessments at regional and local levels, integrated assessments, and improved climate and socioeconomic data. These needs are often related to the challenges to data coverage and model performance in mountainous areas. In these areas, the base data are often riddled with gaps and uncertainties, making it particularly difficult to formulate adaptation strategies. In countries where data coverage is less of an issue, there is a tendency to explore quantitative forms of impact and vulnerability assessments. We highlight how the knowledge embedded in natural science disciplines is not always useful to address complex vulnerabilities in coupled human and natural systems and briefly refer to alternative pathways to adaptation in the form of no-regret, flexible, and adaptive management solutions. Finally, in recognition of the trans- and interdisciplinary nature of climate change adaptation, we raise the question of which knowledge production paradigms are best able to deliver sustainable adaptations to growing environmental

  11. Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation.

    Science.gov (United States)

    Zhang, Hangxiao; Luo, Qibin; Sun, Jing; Liu, Fei; Wu, Gang; Yu, Jun; Wang, Weiwei

    2013-05-01

    Brine shrimps, Artemia (Crustacea, Anostraca), inhabit hypersaline environments and have a broad geographical distribution from sea level to high plateaus. Artemia therefore possess significant genetic diversity, which gives them their outstanding adaptability. To understand this remarkable plasticity, we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia, A. franciscana. We compared the ratio of the rate of nonsynonymous (Ka) and synonymous (Ks) substitutions (Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of A. franciscana with either A. tibetiana or A. urmiana and that atp6 had the highest Ka/Ks ratio between A. tibetiana and A. urmiana. Atp6 may have experienced strong selective pressure for high-altitude adaptation because although A. tibetiana and A. urmiana are closely related they live at different altitudes. We identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial genomes. We propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

  12. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    Science.gov (United States)

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.

  13. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Steeves Buckland

    Full Text Available Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko, is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA markers in 13 subpopulations to: (i assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii estimate effective population sizes and migration rates of subpopulations; and (iii examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable

  14. DISPERSAL AS A MECHANISM LIMITING DIVERSITY OF HIGH LATITUDES

    Science.gov (United States)

    The pervasiveness acress taxa, space, and time of the latitudinal gradient in species diversity is conventionally thought to suggest a common cause that is not yet identified. Conventionally, the cause of the gradient is thought to originate in the tropics where diversity is hig...

  15. Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites.

    Science.gov (United States)

    Toneatti, Diego M; Albarracín, Virginia H; Flores, Maria R; Polerecky, Lubos; Farías, María E

    2017-01-01

    At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H2S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5-7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.

  16. The Strengths of High-Achieving Black High School Students in a Racially Diverse Setting

    Science.gov (United States)

    Marsh, Kris; Chaney, Cassandra; Jones, Derrick

    2012-01-01

    Robert Hill (1972) identified strengths of Black families: strong kinship bonds, strong work orientation, adaptability of family roles, high achievement orientation, and religious orientation. Some suggest these strengths sustain the physical, emotional, social, and spiritual needs of Blacks. This study used narratives and survey data from a…

  17. High diversity of methanotrophic bacteria in geothermal soils affected by high methane fluxes

    Science.gov (United States)

    D'Alessandro, Walter; Gagliano, Antonina Lisa; Quatrini, Paola; Parello, Francesco

    2014-05-01

    enrichment cultures. The isolates showed a wide range of tolerance to pH (3.5 - 8) and temperatures (18 - 45°C), and an average methane oxidation rate of 450 ppm/h. A larger diversity of proteobacterial and verrucomicrobial methanotrophs was detected by the amplification of the methane mono-oxygenase gene pmoA. This study demonstrates the coexistence of both the methanotrophic phyla Verrucomicrobia and Proteobacteria in the same geothermal site. The presence of proteobacterial methanotrophs was quite unexpected because they are generally considered not adapted to live in such harsh environments. Their presence at Favara Grande could be explained by not so low soil pH values (> 5) of this specific geothermal site and by the high methane availability. Such species could have found their niches in the shallowest part of the soils, were the temperatures are not so high, thriving on the abundant upraising methane. Understanding the ecology of methanotrophy in geothermal sites will increase our knowledge of their role in methane emissions to the atmosphere.

  18. Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle.

    Science.gov (United States)

    Bragina, Anastasia; Berg, Christian; Cardinale, Massimiliano; Shcherbakov, Andrey; Chebotar, Vladimir; Berg, Gabriele

    2012-04-01

    Knowledge about Sphagnum-associated microbial communities, their structure and their origin is important to understand and maintain climate-relevant Sphagnum-dominated bog ecosystems. We studied bacterial communities of two cosmopolitan Sphagnum species, which are well adapted to different abiotic parameters (Sphagnum magellanicum, which are strongly acidic and ombrotrophic, and Sphagnum fallax, which are weakly acidic and mesotrophic), in three Alpine bogs in Austria by a multifaceted approach. Great differences between bacterial fingerprints of both Sphagna were found independently from the site. This remarkable specificity was confirmed by a cloning and a deep sequencing approach. Besides the common Alphaproteobacteria, we found a discriminative spectrum of bacteria; although Gammaproteobacteria dominated S. magellanicum, S. fallax was mainly colonised by Verrucomicrobia and Planctomycetes. Using this information for fluorescent in situ hybridisation analyses, corresponding colonisation patterns for Alphaproteobacteria and Planctomycetes were detected. Bacterial colonies were found in high abundances inside the dead big hyalocytes, but they were always connected with the living chlorocytes. Using multivariate statistical analysis, the abiotic factors nutrient richness and pH were identified to modulate the composition of Sphagnum-specific bacterial communities. Interestingly, we found that the immense bacterial diversity was transferred via the sporophyte to the gametophyte, which can explain the high specificity of Sphagnum-associated bacteria over long distances. In contrast to higher plants, which acquire their bacteria mainly from the environment, mosses as the phylogenetically oldest land plants maintain their bacterial diversity within the whole lifecycle.

  19. Bacterial diversity and their adaptations in the shallow water hydrothermal vent at D. Joao de Castro Seamount (DJCS), Azores, Portugal

    Digital Repository Service at National Institute of Oceanography (India)

    Mohandass, C.; Rajasabapathy, R.; Ravindran, C.; Colaco, A.; Santos, R.S.; Meena, R.M.

    of the Biosphere, 15: 327–345. Bolton D.J., Kelly C.T. & Fogarty W.M. 1997. Purification and characterization of the α-amylase of Bacillus flavothermus. Enzyme and Microbial Technology, 20: 340–343. Cardigos F., Colaco A., Dando P.R., Avila S.P., Sarradin P.... Biol. Mar., vol.53; 2012; 65-76 Bacterial diversity and their adaptations in the shallow water hydrothermal vent at D. João de Castro Seamount (DJCS), Azores, Portugal Chellandi MOHANDASS 1 , Raju RAJASABAPATHY 1 , Chinnarajan RAVINDRAN 1 , Ana...

  20. The genetic architecture of adaptations to high altitude in Ethiopia.

    Directory of Open Access Journals (Sweden)

    Gorka Alkorta-Aranburu

    Full Text Available Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control and DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

  1. A New, Adaptable, Optical High-Resolution 3-Axis Sensor

    Directory of Open Access Journals (Sweden)

    Niels Buchhold

    2017-01-01

    Full Text Available This article presents a new optical, multi-functional, high-resolution 3-axis sensor which serves to navigate and can, for example, replace standard joysticks in medical devices such as electric wheelchairs, surgical robots or medical diagnosis devices. A light source, e.g., a laser diode, is affixed to a movable axis and projects a random geometric shape on an image sensor (CMOS or CCD. The downstream microcontroller’s software identifies the geometric shape’s center, distortion and size, and then calculates x, y, and z coordinates, which can be processed in attached devices. Depending on the image sensor in use (e.g., 6.41 megapixels, the 3-axis sensor features a resolution of 1544 digits from right to left and 1038 digits up and down. Through interpolation, these values rise by a factor of 100. A unique feature is the exact reproducibility (deflection to coordinates and its precise ability to return to its neutral position. Moreover, optical signal processing provides a high level of protection against electromagnetic and radio frequency interference. The sensor is adaptive and adjustable to fit a user’s range of motion (stroke and force. This recommendation aims to optimize sensor systems such as joysticks in medical devices in terms of safety, ease of use, and adaptability.

  2. Loss and recovery of genetic diversity in adapting populations of HIV.

    Directory of Open Access Journals (Sweden)

    Pleuni S Pennings

    2014-01-01

    Full Text Available The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence data, we make four observations that shed a light on the underlying processes and allow us to infer the short-term effective population size of the viral population in a patient. Our first observation is that the evolution of drug resistance usually occurs by the fixation of one drug-resistance mutation at a time, as opposed to several changes simultaneously. Second, we find that these fixation events are accompanied by a reduction in genetic diversity in the region surrounding the fixed drug-resistance mutation, due to the hitchhiking effect. Third, we observe that the fixation of drug-resistance mutations involves both hard and soft selective sweeps. In a hard sweep, a resistance mutation arises in a single viral particle and drives all linked mutations with it when it spreads in the viral population, which dramatically reduces genetic diversity. On the other hand, in a soft sweep, a resistance mutation occurs multiple times on different genetic backgrounds, and the reduction of diversity is weak. Using the frequency of occurrence of hard and soft sweeps we estimate the effective population size of HIV to be 1.5 x 10(5 (95% confidence interval [0.8 x 10(5,4.8 x 10(5]. This number is much lower than the actual number of infected cells, but much larger than previous population size estimates based on synonymous diversity. We propose several explanations for the observed discrepancies. Finally, our fourth observation is that genetic diversity at non-synonymous sites recovers to its pre-fixation value within 18 months, whereas diversity at synonymous sites remains depressed after this time period. These results improve our understanding of HIV evolution and have potential implications for treatment strategies.

  3. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

    Science.gov (United States)

    Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R

    2013-06-01

    Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow. © 2012 John Wiley & Sons Ltd.

  4. Robust adaptive cruise control of high speed trains.

    Science.gov (United States)

    Faieghi, Mohammadreza; Jalali, Aliakbar; Mashhadi, Seyed Kamal-e-ddin Mousavi

    2014-03-01

    The cruise control problem of high speed trains in the presence of unknown parameters and external disturbances is considered. In particular a Lyapunov-based robust adaptive controller is presented to achieve asymptotic tracking and disturbance rejection. The system under consideration is nonlinear, MIMO and non-minimum phase. To deal with the limitations arising from the unstable zero-dynamics we do an output redefinition such that the zero-dynamics with respect to new outputs becomes stable. Rigorous stability analyses are presented which establish the boundedness of all the internal states and simultaneously asymptotic stability of the tracking error dynamics. The results are presented for two common configurations of high speed trains, i.e. the DD and PPD designs, based on the multi-body model and are verified by several numerical simulations. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

  5. Early Parental Adaptation, Prenatal Distress, and High-Risk Pregnancy.

    Science.gov (United States)

    Dollberg, Daphna G; Rozenfeld, Tamir; Kupfermincz, Michael

    2016-09-01

    To examine the examined the effects of high risk pregnancy and prenatal distress on parental postnatal adaptation. A sample of 111 expecting parents, consisting of 32 high risk pregnancy (HRP) mothers and 21 spouses and 36 matched low risk pregnancy (LRP) mothers and 22 spouses completed reports of depression symptoms (BDI) and pregnancy related concerns prenatally. At three months postpartum, parent-infant direct observations and reports of parenting alliance (PAI), stress (PSI-SF), satisfaction and efficacy (PSOC) were gathered. Data was analyzed with GLM multivariate analyses and the actor-partner interdependence model. Parents' prenatal BDI predicted postnatal parental stress. BDI and concerns predicted postnatal satisfaction, but only for mothers. Mother's concerns predicted low maternal and high paternal parenting alliance. Partner effect was found so that high concerns predicted high reports of parenting alliance by spouse. Mean-group differences were found between HRP and LRP during parent-infant observations, so that HRP parents displayed lower sensitivity and reciprocity. Prenatal distress, and to some degree high risk pregnancy, are risk factors that may interfere with the early formation of parent-infant relationship. Clinical implications of these findings are presented. © The Author 2016. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. High bacterial diversity in epilithic biofilms of oligotrophic mountain lakes.

    Science.gov (United States)

    Bartrons, Mireia; Catalan, Jordi; Casamayor, Emilio O

    2012-11-01

    Benthic microbial biofilms attached to rocks (epilithic) are major sites of carbon cycling and can dominate ecosystem primary production in oligotrophic lakes. We studied the bacterial community composition of littoral epilithic biofilms in five connected oligotrophic high mountain lakes located at different altitudes by genetic fingerprinting and clone libraries of the 16S rRNA gene. Different intra-lake samples were analyzed, and consistent changes in community structure (chlorophyll a and organic matter contents, and bacterial community composition) were observed along the altitudinal gradient, particularly related with the location of the lake above or below the treeline. Epilithic biofilm genetic fingerprints were both more diverse among lakes than within lakes and significantly different between montane (below the tree line) and alpine lakes (above the tree line). The genetic richness in the epilithic biofilm was much higher than in the plankton of the same lacustrine area studied in previous works, with significantly idiosyncratic phylogenetic composition (specifically distinct from lake plankton or mountain soils). Data suggest the coexistence of aerobic, anaerobic, phototrophic, and chemotrophic microorganisms in the biofilm, Bacteroidetes and Cyanobacteria being the most important bacterial taxa, followed by Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Chlorobi, Planctomycetes, and Verrucomicrobia. The degree of novelty was especially high for epilithic Bacteroidetes, and up to 50 % of the sequences formed monophyletic clusters distantly related to any previously reported sequence. More than 35 % of the total sequences matched at <95 % identity to any previously reported 16S rRNA gene, indicating that alpine epilithic biofilms are unexplored habitats that contain a substantial degree of novelty within a short geographical distance. Further research is needed to determine whether these communities are involved in more biogeochemical pathways than

  7. High functional diversity stimulates diversification in experimental microbial communities

    NARCIS (Netherlands)

    Jousset, Alexandre|info:eu-repo/dai/nl/370632656; Eisenhauer, Nico; Merker, Monika; Mouquet, Nicolas; Scheu, Stefan

    There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can

  8. Adapting to global change in a diverse landscape: the Kruger to Canyons Biosphere Reserve

    CSIR Research Space (South Africa)

    Davis, C

    2010-04-01

    Full Text Available This study will draw on the findings of a significant amount of research that has already taken place in the area. There is a keen desire amongst diverse stakeholders to access global change information (for example, the use of such information...

  9. Highly task-related diversity vs. less task-related diversity among university staff

    DEFF Research Database (Denmark)

    Lauring, Jakob; Selmer, Jan

    2013-01-01

    As only very few large-scale studies have investigated multi-cultural university staff and as none of these studies have dealt with diversity and group processes, this survey was directed toward staffs in 16 science departments from three large universities in Denmark. Results based on the response...

  10. Adaptation and Assimilation: US Business Responses to Linguistic Diversity in the Workplace.

    Science.gov (United States)

    Dicker, Susan J.

    1998-01-01

    Provides a historical overview of attitudes toward immigrants and their languages in the United States, gives an update of the Official English movement, and analyzes recent articles in business-related journals. Discussion centers on how businesses have adapted to a multilingual workforce and on the connection between the Official English…

  11. Curricular Adaptations: Accommodating the Instructional Needs of Diverse Learners in the Context of General Education.

    Science.gov (United States)

    Udvari-Solner, Alice

    This manual offers definitions, techniques, and strategies to generate curricular adaptations to meet the needs of students with a range of intellectual abilities, and thereby increase the practice of inclusive schooling in which all children learn together and multiplicity of learning styles is valued. First, an in-depth definition of…

  12. Phytoplasma adapt to the diverse environments of their plant and insect hosts by altering gene expression

    DEFF Research Database (Denmark)

    Makarova, Olga; MacLean, Allyson M.; Nicolaisen, Mogens

    2015-01-01

    Phytoplasmas are intracellular insect-transmitted phytopathogenic bacteria with small genomes. To understand how Aster Yellows phytoplasma strain witches' broom (AY-WB) adapts to their hosts, we performed qRT-PCR analysis of 179 in silico functionally annotated AY-WB genes that are likely to have...

  13. Making Sense of Adaptations: Resilience in High-Risk Work

    OpenAIRE

    Rankin, Amy

    2017-01-01

    To cope with variations, disturbances, and unexpected events in complex socio-technical systems people are required to continuously adapt to the changing environment, sometimes in novel and innovative ways. This thesis investigates adaptive performance in complex work settings across domains, with a focus on examining what enables and disables successful adaptations, and how contextual factors shape performance. Examples of adaptive performance studies include a crisis command team dealing wi...

  14. Criteria for psychological adaptation to high-altitude hypoxia.

    Science.gov (United States)

    Bonnon, M; Noël-Jorand, M C; Therme, P

    1999-08-01

    The purpose of this study was to test an ascent program for ideal psychological adaptation to high altitudes. A psychological approach was used to test a model describing a gradual step-by-step ascent. Seven subjects spent nine days between 3,500 m and 4,400 m altitude, followed by eight days climbing 500 m each day from 3,500 m to 5,400 m. They performed a cognitive-motor task three times, once under normoxia, once under acute hypoxia, and once under chronic hypoxic conditions. Durations for these subjects were compared with those obtained by a control group tested under normoxia. Subjects' emotional state was assessed by analyzing their remarks during an interview conducted at 5,400 m and by calculating from the answers given to the three questions, a mood index for each subject. Analysis showed that the performances of both groups improved on the second and third administrations of the test. There was, however, no interaction between the group and the time of administration. Mood indexes indicated that the majority of the subjects had no trouble in adapting to the situation and few cognitive or emotional disturbances were observed. These findings may be attributed to the ascent being well designed and planned thereby preventing various possible forms of mountain sickness and other pathologies from developing in the subjects.

  15. Adaptive metal mirror for high-power CO2 lasers

    Science.gov (United States)

    Jarosch, Uwe-Klaus

    1996-08-01

    Spherical mirrors with a variable radius of curvature are used inside laser resonators as well as in the beam path between the laser and the workpiece. Commercially-available systems use piezoelectric actuators, or the pressure of the coolant, to deform the mirror surface. In both cases, the actuator and the cooling system influence each other. This interaction is avoided through the integration of the cooling system with the flexible mirror membrane. A multi- channel design leads to an optimized cooling effect, which is necessary for high power applications. The contour of the variable metal mirror depends on the mounting between the membrane and the mirror body and on the distribution of forces. Four cases of deformation can be distinguished for a circular elastic membrane. The realization of an adaptive metal mirror requires a technical compromise to be made. A mechanical construction is presented which combines an elastic hinge with the inlet and outlet of the coolant. For the deformation of the mirror membranes two actuators with different character of deformation are used. The superposition of the two deformations results in smaller deviations from the spherical surface shape than can be achieved using a single actuator. DC proportional magnets have been introduced as cheap and rigid actuators. The use of this adaptive mirror, either in a low pressure atmosphere of a gas laser resonator, or in an extra-cavity beam path is made possible through the use of a ventilation system.

  16. Teaching Mathematical Biology in High School Using Adapted Primary Literature

    Science.gov (United States)

    Norris, Stephen P.; Stelnicki, Nathan; de Vries, Gerda

    2012-01-01

    The study compared the effect of two adaptations of a scientific article on students' comprehension and use of scientific inquiry skills. One adaptation preserved as much as possible the canonical form of the original article (APL, Adapted Primary Literature) and the other was written in a more narrative mode typical of secondary literature (SL).…

  17. AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species.

    Science.gov (United States)

    de Witte, Lucienne C; Armbruster, Georg F J; Gielly, Ludovic; Taberlet, Pierre; Stöcklin, Jürg

    2012-03-01

    We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic-alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left-skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long-lived clonal plants in arctic-alpine ecosystems can persist, despite considerable climatic change. © 2011 Blackwell Publishing Ltd.

  18. Staphylococcus aureus from the German general population is highly diverse.

    Science.gov (United States)

    Becker, Karsten; Schaumburg, Frieder; Fegeler, Christian; Friedrich, Alexander W; Köck, Robin

    2017-01-01

    This prospective cohort study evaluates colonization dynamics and molecular characteristics of methicillin-susceptible and - resistant Staphylococcus aureus (MSSA/MRSA) in a German general population. Nasal swabs of 1878 non-hospitalized adults were screened for S. aureus. Participants were screened thrice in intervals of 6-8 months. Isolates were characterized by spa and agr typing, mecA and mecC possession, respectively, and PCRs targeting virulence factors. 40.9% of all participants carried S. aureus at least once while 0.7% of the participants carried MRSA (mainly spa t011). MSSA isolates (n=1359) were associated with 331 different spa types; t084 (7.7%), t091 (6.1%) and t012 (71, 5.2%) were predominant. Of 206 participants carrying S. aureus at all three sampling time points, 14.1% carried the same spa type continuously; 5.3% carried different spa types with similar repeat patterns, but 80.6% carried S. aureus with unrelated spa types. MSSA isolates frequently harboured genes encoding enterotoxins (sec: 16.6%, seg: 63.1%, sei: 64.5%) and toxic shock syndrome toxin (tst: 17.5%), but rarely Panton-Valentine leukocidin (lukS-PV/lukF-PV: 0.2%). MSSA colonizing human nares in the community are clonally highly diverse. Among those constantly carrying S. aureus, clonal lineages changed over time. The proportion of persistent S. aureus carriers was lower than reported elsewhere. Copyright © 2016 Elsevier GmbH. All rights reserved.

  19. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities

    DEFF Research Database (Denmark)

    Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.

    2013-01-01

    versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs......Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic...... compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides...

  20. The Adaptability of Life on Earth and the Diversity of Planetary Habitats.

    Science.gov (United States)

    Schulze-Makuch, Dirk; Airo, Alessandro; Schirmack, Janosch

    2017-01-01

    The evolutionary adaptability of life to extreme environments is astounding given that all life on Earth is based on the same fundamental biochemistry. The range of some physicochemical parameters on Earth exceeds the ability of life to adapt, but stays within the limits of life for other parameters. Certain environmental conditions such as low water availability in hyperarid deserts on Earth seem to be close to the limit of biological activity. A much wider range of environmental parameters is observed on planetary bodies within our Solar System such as Mars or Titan, and presumably even larger outside of our Solar System. Here we review the adaptability of life as we know it, especially regarding temperature, pressure, and water activity. We use then this knowledge to outline the range of possible habitable environments for alien planets and moons and distinguish between a variety of planetary environment types. Some of these types are present in our Solar System, others are hypothetical. Our schematic categorization of alien habitats is limited to life as we know it, particularly regarding to the use of solvent (water) and energy source (light and chemical compounds).

  1. The Adaptability of Life on Earth and the Diversity of Planetary Habitats

    Directory of Open Access Journals (Sweden)

    Dirk Schulze-Makuch

    2017-10-01

    Full Text Available The evolutionary adaptability of life to extreme environments is astounding given that all life on Earth is based on the same fundamental biochemistry. The range of some physicochemical parameters on Earth exceeds the ability of life to adapt, but stays within the limits of life for other parameters. Certain environmental conditions such as low water availability in hyperarid deserts on Earth seem to be close to the limit of biological activity. A much wider range of environmental parameters is observed on planetary bodies within our Solar System such as Mars or Titan, and presumably even larger outside of our Solar System. Here we review the adaptability of life as we know it, especially regarding temperature, pressure, and water activity. We use then this knowledge to outline the range of possible habitable environments for alien planets and moons and distinguish between a variety of planetary environment types. Some of these types are present in our Solar System, others are hypothetical. Our schematic categorization of alien habitats is limited to life as we know it, particularly regarding to the use of solvent (water and energy source (light and chemical compounds.

  2. Allelic combinations of soybean maturity Loci E1, E2, E3 and E4 result in diversity of maturity and adaptation to different latitudes.

    Science.gov (United States)

    Jiang, Bingjun; Nan, Haiyang; Gao, Youfei; Tang, Lili; Yue, Yanlei; Lu, Sijia; Ma, Liming; Cao, Dong; Sun, Shi; Wang, Jialin; Wu, Cunxiang; Yuan, Xiaohui; Hou, Wensheng; Kong, Fanjiang; Han, Tianfu; Liu, Baohui

    2014-01-01

    Soybean cultivars are extremely diverse in time to flowering and maturation as a result of various photoperiod sensitivities. The underlying molecular genetic mechanism is not fully clear, however, four maturity loci E1, E2, E3 and E4 have been molecularly identified. In this report, cultivars were selected with various photoperiod sensitivities from different ecological zones, which covered almost all maturity groups (MG) from MG 000 to MG VIII and MG X adapted from latitude N 18° to N 53°. They were planted in the field under natural daylength condition (ND) in Beijing, China or in pots under different photoperiod treatments. Maturity-related traits were then investigated. The four E maturity loci were genotyped at the molecular level. Our results suggested that these four E genes have different impacts on maturity and their allelic variations and combinations determine the diversification of soybean maturity and adaptation to different latitudes. The genetic mechanisms underlying photoperiod sensitivity and adaptation in wild soybean seemed unique from those in cultivated soybean. The allelic combinations and functional molecular markers for the four E loci will significantly assist molecular breeding towards high productivity.

  3. SANParks, people and adaptive management: Understanding a diverse field of practice during changing times

    Directory of Open Access Journals (Sweden)

    Louise K. Swemmer

    2011-05-01

    Full Text Available Biodiversity conservation is often measurable and achievable and has been reasonably successful within the boundaries of national parks. However, the concept of parks providing tangible benefits and hence being seen as ‘valuable’ to the majority of the nation has been more difficult to define, measure and, importantly, deliver on. This function has traditionally fallen under what is currently known as the People and Conservation Department, which has a rich history in South African National Parks (SANParks of change and adaptive learning in terms of defining core functions and associated management strategies, spanning from its original inception as the Information Services Department over 80 years ago. Learning from and in some cases, adapting to change, is evident throughout this broad scale national evolution of the department, from an initial focus on information sharing and education in the 1930s, to what we see today. This includes the primary focus areas of cultural resource management and indigenous knowledge, community relations, environmental education, awareness, youth outreach, interpretation and training. At a more local, park scale, there is a current drive to formalise the adaptive management and learning process for the people component of protected areas through the alignment of relevant project, programme and park objectives with those at a corporate or national level. Associated with this is an attempt to further align the associated monitoring, evaluation and reporting processes, thereby completing the formal adaptive management loops in order to facilitate and stimulate co-learning within and between relevant responsible departments within the organisation.Conservation implications: Benefit sharing through biodiversity conservation has been shown to be crucial for the long-term success of protected areas, but the practicalities of implementing this are thwart with challenges. Despite this, SANParks is attempting to

  4. Microsatellite genotyping reveals high genetic diversity but low ...

    African Journals Online (AJOL)

    JMwacharos

    2016-03-16

    Mar 16, 2016 ... Genetic diversity and structure of goats within an early ... due to their recognized features and characteristics. The ... Genomic DNA was extracted from whole blood using. DNeasy® Blood and Tissue Kit (Qiagen GmbH, Germany). DNA concentration and purity were assessed using the BioPhotometer.

  5. Resilience in High Risk Work : Analysing Adaptive Performance

    OpenAIRE

    Rankin, Amy

    2013-01-01

    In today’s complexsocio-technical systems it is not possible to foresee and prepare for allfuture events. To cope with the intricacy and coupling between people,technical systems and the dynamic environment people are required tocontinuously adapt. To design resilient systems a deepened understanding ofwhat supports and enables adaptive performance is needed. In this thesis two studiesare presented that investigate how adaptive abilities can be identified andanalysed in complex work settings ...

  6. North-South Differentiation and a Region of High Diversity in European Wolves (Canis lupus)

    Science.gov (United States)

    Stronen, Astrid V.; Jędrzejewska, Bogumiła; Pertoldi, Cino; Demontis, Ditte; Randi, Ettore; Niedziałkowska, Magdalena; Pilot, Małgorzata; Sidorovich, Vadim E.; Dykyy, Ihor; Kusak, Josip; Tsingarska, Elena; Kojola, Ilpo; Karamanlidis, Alexandros A.; Ornicans, Aivars; Lobkov, Vladimir A.; Dumenko, Vitalii; Czarnomska, Sylwia D.

    2013-01-01

    European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part. PMID:24146871

  7. North-South differentiation and a region of high diversity in European wolves (Canis lupus).

    Science.gov (United States)

    Stronen, Astrid V; Jędrzejewska, Bogumiła; Pertoldi, Cino; Demontis, Ditte; Randi, Ettore; Niedziałkowska, Magdalena; Pilot, Małgorzata; Sidorovich, Vadim E; Dykyy, Ihor; Kusak, Josip; Tsingarska, Elena; Kojola, Ilpo; Karamanlidis, Alexandros A; Ornicans, Aivars; Lobkov, Vladimir A; Dumenko, Vitalii; Czarnomska, Sylwia D

    2013-01-01

    European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part.

  8. North-South differentiation and a region of high diversity in European wolves (Canis lupus.

    Directory of Open Access Journals (Sweden)

    Astrid V Stronen

    Full Text Available European wolves (Canis lupus show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part.

  9. Shared Genetic Signals of Hypoxia Adaptation in Drosophila and in High-Altitude Human Populations

    Science.gov (United States)

    Jha, Aashish R.; Zhou, Dan; Brown, Christopher D.; Kreitman, Martin; Haddad, Gabriel G.; White, Kevin P.

    2016-01-01

    The ability to withstand low oxygen (hypoxia tolerance) is a polygenic and mechanistically conserved trait that has important implications for both human health and evolution. However, little is known about the diversity of genetic mechanisms involved in hypoxia adaptation in evolving populations. We used experimental evolution and whole-genome sequencing in Drosophila melanogaster to investigate the role of natural variation in adaptation to hypoxia. Using a generalized linear mixed model we identified significant allele frequency differences between three independently evolved hypoxia-tolerant populations and normoxic control populations for approximately 3,800 single nucleotide polymorphisms. Around 50% of these variants are clustered in 66 distinct genomic regions. These regions contain genes that are differentially expressed between hypoxia-tolerant and normoxic populations and several of the differentially expressed genes are associated with metabolic processes. Additional genes associated with respiratory and open tracheal system development also show evidence of directional selection. RNAi-mediated knockdown of several candidate genes’ expression significantly enhanced survival in severe hypoxia. Using genomewide single nucleotide polymorphism data from four high-altitude human populations—Sherpas, Tibetans, Ethiopians, and Andeans, we found that several human orthologs of the genes under selection in flies are also likely under positive selection in all four high-altitude human populations. Thus, our results indicate that selection for hypoxia tolerance can act on standing genetic variation in similar genes and pathways present in organisms diverged by hundreds of millions of years. PMID:26576852

  10. An adaptable architecture for patient cohort identification from diverse data sources.

    Science.gov (United States)

    Bache, Richard; Miles, Simon; Taweel, Adel

    2013-12-01

    We define and validate an architecture for systems that identify patient cohorts for clinical trials from multiple heterogeneous data sources. This architecture has an explicit query model capable of supporting temporal reasoning and expressing eligibility criteria independently of the representation of the data used to evaluate them. The architecture has the key feature that queries defined according to the query model are both pre and post-processed and this is used to address both structural and semantic heterogeneity. The process of extracting the relevant clinical facts is separated from the process of reasoning about them. A specific instance of the query model is then defined and implemented. We show that the specific instance of the query model has wide applicability. We then describe how it is used to access three diverse data warehouses to determine patient counts. Although the proposed architecture requires greater effort to implement the query model than would be the case for using just SQL and accessing a data-based management system directly, this effort is justified because it supports both temporal reasoning and heterogeneous data sources. The query model only needs to be implemented once no matter how many data sources are accessed. Each additional source requires only the implementation of a lightweight adaptor. The architecture has been used to implement a specific query model that can express complex eligibility criteria and access three diverse data warehouses thus demonstrating the feasibility of this approach in dealing with temporal reasoning and data heterogeneity.

  11. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.

    2017-01-17

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  12. Microorganisms under high pressure--adaptation, growth and biotechnological potential.

    Science.gov (United States)

    Mota, Maria J; Lopes, Rita P; Delgadillo, Ivonne; Saraiva, Jorge A

    2013-12-01

    Hydrostatic pressure is a well-known physical parameter which is now considered an important variable of life, since organisms have the ability to adapt to pressure changes, by the development of resistance against this variable. In the past decades a huge interest in high hydrostatic pressure (HHP) technology is increasingly emerging among food and biosciences researchers. Microbial specific stress responses to HHP are currently being investigated, through the evaluation of pressure effects on biomolecules, cell structure, metabolic behavior, growth and viability. The knowledge development in this field allows a better comprehension of pressure resistance mechanisms acquired at sub-lethal pressures. In addition, new applications of HHP could arise from these studies, particularly in what concerns to biotechnology. For instance, the modulation of microbial metabolic pathways, as a response to different pressure conditions, may lead to the production of novel compounds with potential biotechnological and industrial applications. Considering pressure as an extreme life condition, this review intends to present the main findings so far reported in the scientific literature, focusing on microorganisms with the ability to withstand and to grow in high pressure conditions, whether they have innated or acquired resistance, and show the potential of the application of HHP technology for microbial biotechnology. © 2013.

  13. Polysaccharide utilization locus and CAZYme genome repertoires reveal diverse ecological adaptation of Prevotella species.

    Science.gov (United States)

    Accetto, Tomaž; Avguštin, Gorazd

    2015-10-01

    The results of metagenomic studies have clearly established that bacteria of the genus Prevotella represent one of the important groups found in the oral cavity and large intestine of man, and they also dominate the rumen. They belong to the Bacteroidetes, a phylum well-known for its polysaccharide degrading potential that stems from the outer membrane-localized enzyme/binding protein complexes encoded in polysaccharide utilization loci (PULs). Dozens of Prevotella species have been described, primarily from the oral cavity, and many of them occur simultaneously at the same sites, but research on their ecological adaptation has been neglected. Therefore, in this study, the repertoires of PULs and carbohydrate acting enzymes (CAZYmes) found in Prevotella genomes were analyzed and it was concluded that the Prevotella species were widely heterogeneous in this respect and displayed several distinct adaptations with regard to the number, source and nature of the substrates apparently preferred for growth. Copyright © 2015 Elsevier GmbH. All rights reserved.

  14. Novel Genetic Diversity Through Somatic Mutations: Fuel for Adaptation of Reef Corals?

    Directory of Open Access Journals (Sweden)

    Emily J. Howells

    2011-08-01

    Full Text Available Adaptation of reef corals to climate change is an issue of much debate, and often viewed as too slow a process to be of relevance over decadal time scales. This notion is based on the long sexual generation times typical for some coral species. However, the importance of somatic mutations during asexual reproduction and growth on evolution and adaptation (i.e., cell lineage selection is rarely considered. Here we review the existing literature on cell lineage selection and show that the scope for somatic mutations to arise in the coral animal and associated Symbiodinium is large. For example, we estimate that ~100 million somatic mutations can arise within a branching Acropora coral colony of average size. Similarly, the large population sizes and rapid turn-over times of in hospite Symbiodinium likely result in considerable numbers of somatic mutations. While the fate of new mutations depends on many factors, including ploidy level and force and direction of selection, we argue that they likely play a key role in the evolution of reef corals.

  15. Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life.

    Science.gov (United States)

    Tong, Chao; Fei, Tian; Zhang, Cunfang; Zhao, Kai

    2017-03-09

    Understanding the genetic basis of adaptation to high altitude life is of paramount importance for preserving and managing genetic diversity in highland animals. This objective has been addressed mainly in terrestrial fauna but rarely in aquatic animals. Tibetan Schizothoracinae fish is the ideal model system in evolutionary biology, carrying key insights into evolutionary genetics of speciation and adaptation at high altitude. Gymnocypris przewalskii is the newly formed Schizothoracinae fish species in the Tibetan Plateau, inhabits chronic cold, extreme saline and alkaline aquatic environment in Lake Qinghai, thus evolving the unique genomic signatures to adapt extremely severe environments. To characterize its genomic features, we assembled de novo transcriptome of G. przewalskii from Lake Qinghai. Intriguingly, by comparative genomic analyses of G. przewalskii and 8 other fish species, we identified potential expansions in gene families related to energy metabolism, transport and developmental functions, possibly underlying the adaptation to these environmental stresses. Through comprehensive molecular evolution analyses, we found that sets of genes controlling mitochondrion, ion homoeostasis, acid-base balance and innate immunity show significant signals of positive selection. Compared to previous studies on highland fishes, we failed to identify any positively selected genes related to hypoxia response. Our findings provide comprehensive insights into the genetic basis of teleost fish that underlie their adaptation to extreme high altitude aquatic life on the Tibetan Plateau.

  16. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

    Directory of Open Access Journals (Sweden)

    Craig W. Herbold

    2015-07-01

    Full Text Available High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse and high quality sets of amplicon sequence data for modern studies in microbial ecology.

  17. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...... misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan-and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity...

  18. Climate Change Impacts and Adaptation on Water Resources and Agricultural Diversity of the Upper Rio Grande Watershed

    Science.gov (United States)

    Rouhi Rad, M.; Hurd, B. H.

    2012-12-01

    Climate change can alter the balance of the water resources systems. It can both change the amount and the timing of the streamflow available in a basin and the amount of water consumed at the end point due to higher temperatures. These changes in the supply and demand sides can result in a different allocation of water and different price for water in basin scale based on economic principles. In a previous study Hurd and Coonrod (2012) modeled the impacts of climate change on the water related economic activities of the Rio Grande. In their study they assumed an aggregated benefit function for the agricultural sector. In another study on the Rio Grande Brinegar and Ward (2009) modeled the agricultural diversity of the Rio Grande within the framework of a hydro-economic model. This study builds upon and extends the previous studies by developing a model that can more carefully assess the role of adaptation in agriculture. Specially, the current study adds quadratic production functions for each crop. These production functions add a major benefit to the modeling of the hydro-economic system, namely that of adding diversity and expanded resolution to the agricultural sector. Using this production function the model includes both land and water as independent variables in the agricultural sector and, therefore this extension of the model has more flexibility to represent adaptive responses to climatic changes by including the capacity to change the crop mix and acreages as well as the water applied i.e. the capacity to deficit irrigate. The results of this study show that the agricultural sector can lose nearly a third of its water and more than 30% of its net economic benefits as a result of possible climate changes. It also shows as the climate become drier and population grows then economic forces will encourage agriculture to move towards more beneficial crops and reduce total acreage and in some cases applied water.

  19. Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality.

    Science.gov (United States)

    Thomas, Geethu E; Geetha, Kiran A; Augustine, Lesly; Mamiyil, Sabu; Thomas, George

    2016-01-01

    Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller's ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller's ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically diverse

  20. Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

    Science.gov (United States)

    Thomas, Geethu E.; Geetha, Kiran A.; Augustine, Lesly; Mamiyil, Sabu; Thomas, George

    2016-01-01

    Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically

  1. Adaptive slope compensation for high bandwidth digital current mode controller

    DEFF Research Database (Denmark)

    Taeed, Fazel; Nymand, Morten

    2015-01-01

    An adaptive slope compensation method for digital current mode control of dc-dc converters is proposed in this paper. The compensation slope is used for stabilizing the inner current loop in peak current mode control. In this method, the compensation slope is adapted with the variations...... in converter duty cycle. The adaptive slope compensation provides optimum controller operation in term of bandwidth over wide range of operating points. In this paper operation principle of the controller is discussed. The proposed controller is implemented in an FPGA to control a 100 W buck converter...

  2. Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars.

    Science.gov (United States)

    Pallotta, Margaret; Schnurbusch, Thorsten; Hayes, Julie; Hay, Alison; Baumann, Ute; Paull, Jeff; Langridge, Peter; Sutton, Tim

    2014-10-02

    Environmental constraints severely restrict crop yields in most production environments, and expanding the use of variation will underpin future progress in breeding. In semi-arid environments boron toxicity constrains productivity, and genetic improvement is the only effective strategy for addressing the problem. Wheat breeders have sought and used available genetic diversity from landraces to maintain yield in these environments; however, the identity of the genes at the major tolerance loci was unknown. Here we describe the identification of near-identical, root-specific boron transporter genes underlying the two major-effect quantitative trait loci for boron tolerance in wheat, Bo1 and Bo4 (ref. 2). We show that tolerance to a high concentration of boron is associated with multiple genomic changes including tetraploid introgression, dispersed gene duplication, and variation in gene structure and transcript level. An allelic series was identified from a panel of bread and durum wheat cultivars and landraces originating from diverse agronomic zones. Our results demonstrate that, during selection, breeders have matched functionally different boron tolerance alleles to specific environments. The characterization of boron tolerance in wheat illustrates the power of the new wheat genomic resources to define key adaptive processes that have underpinned crop improvement.

  3. Hybrid Adaptive Ray-Moment Method (HARM2): A highly parallel method for radiation hydrodynamics on adaptive grids

    Science.gov (United States)

    Rosen, A. L.; Krumholz, M. R.; Oishi, J. S.; Lee, A. T.; Klein, R. I.

    2017-02-01

    We present a highly-parallel multi-frequency hybrid radiation hydrodynamics algorithm that combines a spatially-adaptive long characteristics method for the radiation field from point sources with a moment method that handles the diffuse radiation field produced by a volume-filling fluid. Our Hybrid Adaptive Ray-Moment Method (HARM2) operates on patch-based adaptive grids, is compatible with asynchronous time stepping, and works with any moment method. In comparison to previous long characteristics methods, we have greatly improved the parallel performance of the adaptive long-characteristics method by developing a new completely asynchronous and non-blocking communication algorithm. As a result of this improvement, our implementation achieves near-perfect scaling up to O (103) processors on distributed memory machines. We present a series of tests to demonstrate the accuracy and performance of the method.

  4. High Spatial Resolution shape Sensing for Adaptive Aerospace Vehicles Project

    Data.gov (United States)

    National Aeronautics and Space Administration — It is accepted that adaptive aerospace vehicles whose flight avionic systems are reconfigurable are needed to respond to changing flight parameters, vehicle system...

  5. High-intensity kayak performance after adaptation to intermittent hypoxia.

    Science.gov (United States)

    Bonetti, Darrell L; Hopkins, Will G; Kilding, Andrew E

    2006-09-01

    Live-high train-low altitude training produces worthwhile gains in performance for endurance athletes, but the benefits of adaptation to various forms of artificial altitude are less clear. To quantify the effects of intermittent hypoxic exposure on kayak performance. In a crossover design with a 6-week washout, we randomized 10 subelite male sprint kayak paddlers to hypoxia or control groups for 3 weeks (5 days/week) of intermittent hypoxic exposure using a nitrogen-filtration device. Each day's exposure consisted of alternately breathing hypoxic and ambient air for 5 minutes each over 1 hour. Performance tests were an incremental step test to estimate peak power, maximal oxygen uptake, exercise economy, and lactate threshold; a 500-m time trial; and 5 x 100-m sprints. All tests were performed on a wind-braked kayak ergometer 7 and 3 days pretreatment and 3 and 10 days posttreatment. Hemoglobin concentration was measured at 1 day pretreatment, 5 and 10 days during treatment, and 3 days after treatment. Relative to control, at 3 days posttreatment the hypoxia group showed the following increases: peak power 6.8% (90% confidence limits, + or - 5.2%), mean repeat sprint power 8.3% (+ or - 6.7%), and hemoglobin concentration 3.6% (+ or - 3.2%). Changes in lactate threshold, mean 500-m power, maximal oxygen uptake, and exercise economy were unclear. Large effects for peak power and mean sprint speed were still present 10 days posthypoxia. These effects of intermittent hypoxic exposure should enhance performance in kayak racing. The effects might be mediated via changes in oxygen transport.

  6. High local genetic diversity of canine parvovirus from Ecuador.

    Science.gov (United States)

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Yellowstone Lake: high-energy geochemistry and rich bacterial diversity.

    Science.gov (United States)

    Clingenpeel, Scott; Macur, Richard E; Kan, Jinjun; Inskeep, William P; Lovalvo, Dave; Varley, John; Mathur, Eric; Nealson, Kenneth; Gorby, Yuri; Jiang, Hongchen; LaFracois, Toben; McDermott, Timothy R

    2011-08-01

    Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H(2)S, CH(4), CO(2) and H(2), although CH(4) and H(2) levels were also significant throughout the lake. Pyrosequencing and near full-length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size-fractionated by sequentially filtering through 20-µm-, 3.0-µm-, 0.8-µm- and 0.1-µm-pore-size filters, with the >0.1 to <0.8 µm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α- and β-Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α-Proteobacteria clade tightly linked with freshwater SAR11-like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97-100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  8. Highly Adaptive Primary Mirror Having Embedded Actuators, Sensors, and Neural Control Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Xinetics has demonstrated the technology required to fabricate a self-compensating highly adaptive silicon carbide primary mirror system having embedded actuators,...

  9. Terrestrial adaptation of green algae Klebsormidium and Zygnema (Charophyta) involves diversity in photosynthetic traits but not in CO2 acquisition.

    Science.gov (United States)

    Pierangelini, Mattia; Ryšánek, David; Lang, Ingeborg; Adlassnig, Wolfram; Holzinger, Andreas

    2017-11-01

    The basal streptophyte Klebsormidium and the advanced Zygnema show adaptation to terrestrialization. Differences are found in photoprotection and resistance to short-term light changes, but not in CO 2 acquisition. Streptophyte green algae colonized land about 450-500 million years ago giving origin to terrestrial plants. We aim to understand how their physiological adaptations are linked to the ecological conditions (light, water and CO2) characterizing modern terrestrial habitats. A new Klebsormidium isolate from a strongly acidic environment of a former copper mine (Schwarzwand, Austria) is investigated, in comparison to Klebsormidium cf. flaccidum and Zygnema sp. We show that these genera possess different photosynthetic traits and water requirements. Particularly, the Klebsormidium species displayed a higher photoprotection capacity, concluded from non-photochemical quenching (NPQ) and higher tolerance to high light intensity than Zygnema. However, Klebsormidium suffered from photoinhibition when the light intensity in the environment increased rapidly, indicating that NPQ is involved in photoprotection against strong and stable irradiance. Klebsormidium was also highly resistant to cellular water loss (dehydration) under low light. On the other hand, exposure to relatively high light intensity during dehydration caused a harmful over-reduction of the electron transport chain, leading to PSII damages and impairing the ability to recover after rehydration. Thus, we suggest that dehydration is a selective force shaping the adaptation of this species towards low light. Contrary to the photosynthetic characteristics, the inorganic carbon (C i ) acquisition was equivalent between Klebsormidium and Zygnema. Despite their different habitats and restriction to hydro-terrestrial environment, the three organisms showed similar use of CO2 and HCO3- as source of Ci for photosynthesis, pointing out a similar adaptation of their CO2-concentrating mechanisms to terrestrial

  10. Sequencing of 50 human exomes reveals adaptation to high altitude

    DEFF Research Database (Denmark)

    Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia

    2010-01-01

    represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency......Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which...... difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus...

  11. Prokaryotic diversity pattern in high-altitude ecosystems of the Chilean Altiplano

    Science.gov (United States)

    Demergasso, Cecilia; Dorador, Cristina; Meneses, Daniela; Blamey, Jenny; Cabrol, Nathalie; Escudero, Lorena; Chong, Guillermo

    2010-06-01

    The Chilean Altiplano is the westernmost part of a large volcanic-sedimentary plateau in the central Andes. High solar irradiance and rapid increase of temperature have contributed to make it a hot spot of global climatic change. In this study, we describe microbial diversity in the summit lake of the Simba volcano (5,870 m) and the evaporitic basins of Salar de Aguas Calientes (4,200 m) and Laguna Lejía (4,325 m) using both culture and culture-independent methods. The results obtained were analyzed together with available information from related environments to describe the traits of the microbial community driven by main environmental factors. Isolated cultures exhibit high resistance to all three types of UV radiation, further supporting the adaptation of microorganisms to the high altitude environment. The microbial community structures at Salar de Aguas Calientes and Laguna Lejía are similar to those from other saline systems and cold environments where Bacteroidetes is the major bacterial group. The abundance of sequences related to alphaproteobacteria and methanogenic populations likely reflects the importance of aerobic anoxigenic phothosynthesis and the cycling of one-carbon compounds in the high altitude lake ecosystems. Geochemistry and microbial communities at Simba as well as those reported in the Licancabur summit lake provide evidence for sulfur-rich environments but under different conditions. Those differences between neighboring mountain lake ecosystems highlight the effect of volcanic activity on microbial communities. The hypothetical ecosystem model described in this work provides a clue to follow the microbial community responses to geophysical environment coupled with rapid climate change.

  12. PHYSICAL ADAPTATION OF CHILDREN TO LIFE AT HIGH-ALTITUDE

    NARCIS (Netherlands)

    DEMEER, K; HEYMANS, HSA; ZIJLSTRA, WG

    Children permanently exposed to hypoxia at altitudes of > 3000 m above sea level show a phenotypical form of adaptation. Under these environmental conditions, oxygen uptake in the lungs is enhanced by increases in ventilation, lung compliance, and pulmonary diffusion. Lung and thorax volumes in

  13. Performance analysis of joint multi-branch switched diversity and adaptive modulation schemes for spectrum sharing systems

    KAUST Repository

    Bouida, Zied

    2012-12-01

    Under the scenario of an underlay cognitive radio network, we propose in this paper two adaptive schemes using switched transmit diversity and adaptive modulation in order to increase the spectral efficiency of the secondary link and maintain a desired performance for the primary link. The proposed switching efficient scheme (SES) and bandwidth efficient scheme (BES) use the scan and wait combining technique (SWC) where a transmission occurs only when a branch with an acceptable performance is found, otherwise data is buffered. In these schemes, the modulation constellation size and the used transmit branch are determined to minimize the average number of switched branches and to achieve the highest spectral efficiency given the fading channel conditions, the required error rate performance, and a peak interference constraint to the primary receiver (PR). For delay-sensitive applications, we also propose two variations of the SES and BES schemes using power control (SES-PC and BES-PC) where the secondary transmitter (ST) starts sending data using a nominal power level which is selected in order to minimize the average delay introduced by the SWC technique. We demonstrate through numerical examples that the BES scheme increases the capacity of the secondary link when compared to the SES scheme. This spectral efficiency improvement comes at the expense of an increased average number of switched branches and thus an increased average delay. We also show that the SES-PC and the BES-PC schemes minimize the average delay while satisfying the same spectral efficiency as the SES and BES schemes, respectively. © 2012 IEEE.

  14. Extensive Genomic Diversity among Bovine-Adapted Staphylococcus aureus: Evidence for a Genomic Rearrangement within CC97.

    Directory of Open Access Journals (Sweden)

    Kathleen E Budd

    Full Text Available Staphylococcus aureus is an important pathogen associated with both human and veterinary disease and is a common cause of bovine mastitis. Genomic heterogeneity exists between S. aureus strains and has been implicated in the adaptation of specific strains to colonise particular mammalian hosts. Knowledge of the factors required for host specificity and virulence is important for understanding the pathogenesis and management of S. aureus mastitis. In this study, a panel of mastitis-associated S. aureus isolates (n = 126 was tested for resistance to antibiotics commonly used to treat mastitis. Over half of the isolates (52% demonstrated resistance to penicillin and ampicillin but all were susceptible to the other antibiotics tested. S. aureus isolates were further examined for their clonal diversity by Multi-Locus Sequence Typing (MLST. In total, 18 different sequence types (STs were identified and eBURST analysis demonstrated that the majority of isolates grouped into clonal complexes CC97, CC151 or sequence type (ST 136. Analysis of the role of recombination events in determining S. aureus population structure determined that ST diversification through nucleotide substitutions were more likely to be due to recombination compared to point mutation, with regions of the genome possibly acting as recombination hotspots. DNA microarray analysis revealed a large number of differences amongst S. aureus STs in their variable genome content, including genes associated with capsule and biofilm formation and adhesion factors. Finally, evidence for a genomic arrangement was observed within isolates from CC97 with the ST71-like subgroup showing evidence of an IS431 insertion element having replaced approximately 30 kb of DNA including the ica operon and histidine biosynthesis genes, resulting in histidine auxotrophy. This genomic rearrangement may be responsible for the diversification of ST71 into an emerging bovine adapted subgroup.

  15. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography.

    Directory of Open Access Journals (Sweden)

    Ruth Hershberg

    2008-12-01

    Full Text Available Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC. However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

  16. Adapting generalization tools to physiographic diversity for the united states national hydrography dataset

    Science.gov (United States)

    Buttenfield, B.P.; Stanislawski, L.V.; Brewer, C.A.

    2011-01-01

    This paper reports on generalization and data modeling to create reduced scale versions of the National Hydrographic Dataset (NHD) for dissemination through The National Map, the primary data delivery portal for USGS. Our approach distinguishes local differences in physiographic factors, to demonstrate that knowledge about varying terrain (mountainous, hilly or flat) and varying climate (dry or humid) can support decisions about algorithms, parameters, and processing sequences to create generalized, smaller scale data versions which preserve distinct hydrographic patterns in these regions. We work with multiple subbasins of the NHD that provide a range of terrain and climate characteristics. Specifically tailored generalization sequences are used to create simplified versions of the high resolution data, which was compiled for 1:24,000 scale mapping. Results are evaluated cartographically and metrically against a medium resolution benchmark version compiled for 1:100,000, developing coefficients of linear and areal correspondence.

  17. Neutrophilic iron oxidizers adapted to highly oxic environments

    DEFF Research Database (Denmark)

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen

    carbon) while oxygen (O2) is the electron acceptor provided during the aeration process. Numerous previous studies have described neutrophilic iron oxidizers as a bacterial guild with a special niche preference, especially the transition zone between aerobic and anoxic regions, where abiotic chemical...... oxidation of iron would be retarded. For that reason, no attempts have been documented to describe the density and diversity of iron oxidizing bacteria (FeOB) in oxic neutrophilic environments. Under low temperatures (5 to 10°C) conditions, as typically found in groundwater, extremely low rates of chemical...... iron oxidation (t1/2: 315min.) have been documented. This assumed slow chemical oxidation of Fe2 + in rapid sand filters may allow certain bacteria to oxidize iron concurrently with the ongoing slow chemical oxidation. Hence, we aimed to investigate the abundance, diversity, and spatial distribution...

  18. RAPD discloses high molecular diversity of Mycobacterium tuberculosis from Michoacan, Mexico.

    Science.gov (United States)

    Guill N-Nepita, A L; Vazquez-Marrufo, G; Blanco-Guillot, F T; Figueroa-Aguilar, G A; Vazquez-Garciduenas, M S

    2013-10-01

    Random amplified polymorphism DNA (RAPD) is an easy, inexpensive technique for the characterization of pathogens in low-income countries. In this study we used RAPD to assess the genetic diversity of a small collection of isolates of mycobacteria from the Mexican state of Michoacan. In contrast with the low annual tuberculosis incidence in Michoacan relative to the national average, we found a high molecular diversity value suggesting high population diversity of M. tuberculosis in the studied region. Our findings justify further typing efforts with other molecular tools such as MIRU-VNTR and spoligotyping.

  19. Diversity and cold adaptation of culturable endophytic fungi from bryophytes in the Fildes Region, King George Island, maritime Antarctica.

    Science.gov (United States)

    Zhang, Tao; Zhang, Yu-Qin; Liu, Hong-Yu; Wei, Yu-Zhen; Li, Hai-Long; Su, Jing; Zhao, Li-Xun; Yu, Li-Yan

    2013-04-01

    Endophytic fungi associated with three bryophyte species in the Fildes Region, King George Island, maritime Antarctica, that is, the liverwort Barbilophozia hatcheri, the mosses Chorisodontium aciphyllum and Sanionia uncinata, were studied by culture-dependent method. A total of 128 endophytic fungi were isolated from 1329 tissue segments of 14 samples. The colonization rate of endophytic fungi in three bryophytes species were 12.3%, 12.1%, and 8.7%, respectively. These isolates were identified to 21 taxa, with 15 Ascomycota, 5 Basidiomycota, and 1 unidentified fungus, based on morphological characteristics and sequence analyses of ITS region and D1/D2 domain. The dominant fungal endophyte was Hyaloscyphaceae sp. in B. hatcheri, Rhizoscyphus sp. in C. aciphyllum, and one unidentified fungus in S. uncinata; and their relative frequencies were 33.3%, 32.1%, and 80.0%, respectively. Furthermore, different Shannon-Weiner diversity indices (0.91-1.99) for endophytic fungi and low endophytic fungal composition similarities (0.19-0.40) were found in three bryophyte species. Growth temperature tests indicated that 21 taxa belong to psychrophiles (9), psychrotrophs (11), and mesophile (1). The results herein demonstrate that the Antarctic bryophytes are an interesting source of fungal endophytes and the endophytic fungal composition is different among the bryophyte species, and suggest that these fungal endophytes are adapted to cold stress in Antarctica. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  20. Adaptive Optics Technology for High-Resolution Retinal Imaging

    Science.gov (United States)

    Lombardo, Marco; Serrao, Sebastiano; Devaney, Nicholas; Parravano, Mariacristina; Lombardo, Giuseppe

    2013-01-01

    Adaptive optics (AO) is a technology used to improve the performance of optical systems by reducing the effects of optical aberrations. The direct visualization of the photoreceptor cells, capillaries and nerve fiber bundles represents the major benefit of adding AO to retinal imaging. Adaptive optics is opening a new frontier for clinical research in ophthalmology, providing new information on the early pathological changes of the retinal microstructures in various retinal diseases. We have reviewed AO technology for retinal imaging, providing information on the core components of an AO retinal camera. The most commonly used wavefront sensing and correcting elements are discussed. Furthermore, we discuss current applications of AO imaging to a population of healthy adults and to the most frequent causes of blindness, including diabetic retinopathy, age-related macular degeneration and glaucoma. We conclude our work with a discussion on future clinical prospects for AO retinal imaging. PMID:23271600

  1. Biodiversity for multifunctional grasslands: equal productivity in high-diversity low-input and low-diversity high-input systems

    Directory of Open Access Journals (Sweden)

    A. Weigelt

    2009-08-01

    Full Text Available Modern grassland management seeks to provide many ecosystem services and experimental studies in resource-poor grasslands have shown a positive relationship between plant species richness and a variety of ecosystem functions. Thus, increasing species richness might help to enhance multifunctionality in managed grasslands if the relationship between species richness and ecosystem functioning is equally valid in high-input grassland systems.

    We tested the relative effects of low-input to high-input management intensities and low to high plant species richness. Using a combination of mowing frequencies (1, 2 or 4 cuts per season and fertilisation levels (0, 100 and 200 kg N ha−1 a−1, we studied the productivity of 78 experimental grassland communities of increasing plant species richness (1, 2, 4, 8 or 16 species with 1 to 4 functional groups in two successive years.

    Our results showed that in both years higher diversity was more effective in increasing productivity than higher management intensity: the 16-species mixtures had a surplus of 449 g m−2 y−1 in 2006 and 492 g m−2 y−1 in 2007 over the monoculture yields whereas the high-input management resulted in only 315 g m−2 y−1 higher productivity in 2006 and 440 g m−2 y−1 in 2007 than the low-input management. In addition, high-diversity low-input grassland communities had similar productivity as low-diversity high-input communities. The slopes of the biodiversity – productivity relationships significantly increased with increasing levels of management intensity in both years.

    We conclude that the biological mechanisms leading to enhanced biomass production in diverse grassland communities are as effective for productivity as a combination of several agricultural measures. Our results demonstrate that high-diversity low-input grassland

  2. Limnology and cyanobacterial diversity of high altitude lakes of ...

    Indian Academy of Sciences (India)

    2014-07-08

    Jul 8, 2014 ... inventory of Indian Space Research Organisation (2011), a total of 272 high altitude lakes covering an area of 617 ha are present in Himachal Pradesh ...... diatoms flora of four lakes and ponds from the Windmill Islands,. East Antarctica. Antarct. Sci. 13 410–419. Sabbe K, Hodgson DA, Verleyen E, Taton A, ...

  3. Limnology and cyanobacterial diversity of high altitude lakes of ...

    Indian Academy of Sciences (India)

    The second group, including Gloeocapsopsis pleurocapsoides, Leptolyngbya antarctica, L. frigida, Pseudanabaena frigida and N. spongiaeforme, occurred in oligotrophic water with high pH and low temperature. The distribution of third group of Cyanobium parvum, Synechocystis pevalekii, L. benthonica, L. foveolarum, ...

  4. Low genetic diversity and high genetic differentiation among ...

    African Journals Online (AJOL)

    Possible reasons for the high population genetic differentiation and the low levels of genetic variation within populations are inbreeding and genetic drift. Of a total of 26 known populations, 14 are now extinct, five during the course of this study. Action to prevent complete extinction of the species is therefore urgent.

  5. Effects of Crowding and Attention on High-Levels of Motion Processing and Motion Adaptation

    Science.gov (United States)

    Pavan, Andrea; Greenlee, Mark W.

    2015-01-01

    The motion after-effect (MAE) persists in crowding conditions, i.e., when the adaptation direction cannot be reliably perceived. The MAE originating from complex moving patterns spreads into non-adapted sectors of a multi-sector adapting display (i.e., phantom MAE). In the present study we used global rotating patterns to measure the strength of the conventional and phantom MAEs in crowded and non-crowded conditions, and when attention was directed to the adapting stimulus and when it was diverted away from the adapting stimulus. The results show that: (i) the phantom MAE is weaker than the conventional MAE, for both non-crowded and crowded conditions, and when attention was focused on the adapting stimulus and when it was diverted from it, (ii) conventional and phantom MAEs in the crowded condition are weaker than in the non-crowded condition. Analysis conducted to assess the effect of crowding on high-level of motion adaptation suggests that crowding is likely to affect the awareness of the adapting stimulus rather than degrading its sensory representation, (iii) for high-level of motion processing the attentional manipulation does not affect the strength of either conventional or phantom MAEs, neither in the non-crowded nor in the crowded conditions. These results suggest that high-level MAEs do not depend on attention and that at high-level of motion adaptation the effects of crowding are not modulated by attention. PMID:25615577

  6. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes

    DEFF Research Database (Denmark)

    Barnes, Christopher James; Maldonado Goyzueta, Carla Brenda; Frøslev, Tobias Guldberg

    2016-01-01

    in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography...... in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß......-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of -0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 % and 7.2 % of community...

  7. Ecosystems with mutually exclusive interactions self-organize to a state of high diversity.

    Science.gov (United States)

    Mathiesen, Joachim; Mitarai, Namiko; Sneppen, Kim; Trusina, Ala

    2011-10-28

    Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general unknown. Using lichen communities as an example, we propose a model for the evolution of mutually excluding organisms that compete for space. We suggest that chainlike or cyclic invasions open for creation of spatially separated subpopulations that subsequently can lead to increased diversity. In contrast to its nonspatial counterpart, our model predicts robust coexistence of a large number of species. It is demonstrated that large species diversity can be obtained on evolutionary time scales, provided that interactions between species have spatial constraints. In particular, a phase transition to a sustainable state of high diversity is identified.

  8. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  9. Diverse response of tomato fruit explants to high temperature

    Directory of Open Access Journals (Sweden)

    Zofia Starck

    2014-01-01

    Full Text Available Tomato explants (fruit with a pedicel and a piece of peduncle, with fruit growth stimulated by treating the flowers with NOA + GA3 (NG-series were used as a model system for studying the effect of high temperature on C-sucrose uptake, its distribution and Ca retranslocation. Two cultivars with contrasting responses to high temperature were compared. In sensitive cv. Roma heat stress during 22h (40oC for 10h and 30oC for 12h, drastically depressed the uptake of 14C-sucrose coinciding with diminished fruit 14C-supply. It also decreased the specific activity of soluble acid invertase and the calcium content. All these strong negative responses to high temperature were markedly reduced in the NG-treated series involving remobilization of Ca to the fruits and a higher stability of the invertase activity. This indicates the indirect role of flower treatment with NG in addaptation to heat stress. In tolerant cv. Robin even higher temperatures (42oC for 10h and 34oC for 12h were not stressful. They did not affect the 14C-sucrose uptake and stimulated 14C-supply to the fruit. Increased specific activity of acid invertase and a higher calcium content were also recorded but only in the control explants. In contrast to cv. Roma elevated temperature was slightly stressful for cv. Robin explants of NG-series. The differences in response of both cultivar explants to elevated temperature, based on unequal fruit supply with 14C-sucrose, seem to be causaly connected with two factors: the invertase activity being more or less sensitive to the heat stress, the ability to translocate Ca to the heated fruits.

  10. High resolution observations using adaptive optics: Achievements and future needs

    Science.gov (United States)

    Sankarasubramanian, K.; Rimmele, T.

    2008-06-01

    Over the last few years, several interesting observations were obtained with the help of solar Adaptive Optics (AO). In this paper, few observations made using the solar AO are enlightened and briefly discussed. A list of disadvantages with the current AO system are presented. With telescopes larger than 1.5 m expected during the next decade, there is a need to develop the existing AO technologies for large aperture telescopes. Some aspects of this development are highlighted. Finally, the recent AO developments in India are also presented.

  11. High Schools, Race, and America's Future: What Students Can Teach Us about Morality, Diversity, and Community

    Science.gov (United States)

    Blum, Lawrence

    2012-01-01

    In "High Schools, Race, and America's Future", Lawrence Blum offers a lively account of a rigorous high school course on race and racism. Set in a racially, ethnically, and economically diverse high school, the book chronicles students' engagement with one another, with a rich and challenging academic curriculum, and with questions that relate…

  12. Understanding Resilience in Diverse, Talented Students in an Urban High School

    Science.gov (United States)

    Reis, Sally M.; Colbert, Robert D.; Hebert, Thomas P.

    2005-01-01

    This article summarizes findings from a 3-year study of 35 economically disadvantaged, ethnically diverse, academically talented high school students who either achieved or underachieved in their urban high school. In particular, the resilience of these two groups of high ability students is explored. Comparative case study and ethnographic…

  13. Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity.

    Science.gov (United States)

    Klaedtke, Stephanie M; Caproni, Leonardo; Klauck, Julia; de la Grandville, Paul; Dutartre, Martin; Stassart, Pierre M; Chable, Véronique; Negri, Valeria; Raggi, Lorenzo

    2017-02-28

    Recognizing both the stakes of traditional European common bean diversity and the role farmers' and gardeners' networks play in maintaining this diversity, the present study examines the role that local adaptation plays for the management of common bean diversity in situ. To the purpose, four historical bean varieties and one modern control were multiplied on two organic farms for three growing seasons. The fifteen resulting populations, the initial ones and two populations of each variety obtained after the three years of multiplication, were then grown in a common garden. Twenty-two Simple Sequence Repeat (SSR) markers and 13 phenotypic traits were assessed. In total, 68.2% of tested markers were polymorphic and a total of 66 different alleles were identified. FST analysis showed that the genetic composition of two varieties multiplied in different environments changed. At the phenotypic level, differences were observed in flowering date and leaf length. Results indicate that three years of multiplication suffice for local adaptation to occur. The spatial dynamics of genetic and phenotypic bean diversity imply that the maintenance of diversity should be considered at the scale of the network, rather than individual farms and gardens. The microevolution of bean populations within networks of gardens and farms emerges as a research perspective.

  14. The Factors Contribute to Career Adaptability of High-School Students

    Science.gov (United States)

    Karacan-Ozdemir, Nurten; Yerin Guneri, Oya

    2017-01-01

    Purpose: Regarded as an important means of career development, preparation, and transition, career adaptability is a lifelong skill that can enable individuals to overcome 21st-century work--life requirements and challenges. This study aims to investigate the factors contributing career adaptability of high-school students, which pose beneficial…

  15. Genetic analyses of adaptation of barley to low and high input ...

    African Journals Online (AJOL)

    Chromosomes 1, 3 and 4 were found harbouring QTLs affecting many agronomic traits. The QTL on chromosome 3 (region of the denso mutant allele) showed adaptation to high and intermediate environments and the QTL on chromosome 1 showed adaptation to the intermediate and low input environments. The QTL on ...

  16. Associations between Conceptual Reasoning, Problem Solving, and Adaptive Ability in High-Functioning Autism

    Science.gov (United States)

    Williams, Diane L.; Mazefsky, Carla A.; Walker, Jon D.; Minshew, Nancy J.; Goldstein, Gerald

    2014-01-01

    Abstract thinking is generally highly correlated with problem-solving ability which is predictive of better adaptive functioning. Measures of conceptual reasoning, an ecologically-valid laboratory measure of problem-solving, and a report measure of adaptive functioning in the natural environment, were administered to children and adults with and…

  17. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

    KAUST Repository

    Perdigão, João

    2014-11-18

    Background Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades. Results In the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM). The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation. Conclusions Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

  18. High resolution adaptive imaging of a single atom

    CERN Document Server

    Wong-Campos, J D; Neyenhuis, B; Mizrahi, J; Monroe, C

    2015-01-01

    We report the optical imaging of a single atom with nanometer resolution using an adaptive optical alignment technique that is applicable to general optical microscopy. By decomposing the image of a single laser-cooled atom, we identify and correct optical aberrations in the system and realize an atomic position sensitivity of $\\approx$ 0.5 nm/$\\sqrt{\\text{Hz}}$ with a minimum uncertainty of 1.7 nm, allowing the direct imaging of atomic motion. This is the highest position sensitivity ever measured for an isolated atom, and opens up the possibility of performing out-of-focus 3D particle tracking, imaging of atoms in 3D optical lattices or sensing forces at the yoctonewton (10$^{-24}$ N) scale.

  19. High diversity in cretaceous ichthyosaurs from Europe prior to their extinction.

    Directory of Open Access Journals (Sweden)

    Valentin Fischer

    Full Text Available BACKGROUND: Ichthyosaurs are reptiles that inhabited the marine realm during most of the Mesozoic. Their Cretaceous representatives have traditionally been considered as the last survivors of a group declining since the Jurassic. Recently, however, an unexpected diversity has been described in Upper Jurassic-Lower Cretaceous deposits, but is widely spread across time and space, giving small clues on the adaptive potential and ecosystem control of the last ichthyosaurs. The famous but little studied English Gault Formation and 'greensands' deposits (the Upper Greensand Formation and the Cambridge Greensand Member of the Lower Chalk Formation offer an unprecedented opportunity to investigate this topic, containing thousands of ichthyosaur remains spanning the Early-Late Cretaceous boundary. METHODOLOGY/PRINCIPAL FINDINGS: To assess the diversity of the ichthyosaur assemblage from these sedimentary bodies, we recognized morphotypes within each type of bones. We grouped these morphotypes together, when possible, by using articulated specimens from the same formations and from new localities in the Vocontian Basin (France; a revised taxonomic scheme is proposed. We recognize the following taxa in the 'greensands': the platypterygiines 'Platypterygius' sp. and Sisteronia seeleyi gen. et sp. nov., indeterminate ophthalmosaurines and the rare incertae sedis Cetarthrosaurus walkeri. The taxonomic diversity of late Albian ichthyosaurs now matches that of older, well-known intervals such as the Toarcian or the Tithonian. Contrasting tooth shapes and wear patterns suggest that these ichthyosaurs colonized three distinct feeding guilds, despite the presence of numerous plesiosaur taxa. CONCLUSION/SIGNIFICANCE: Western Europe was a diversity hot-spot for ichthyosaurs a few million years prior to their final extinction. By contrast, the low diversity in Australia and U.S.A. suggests strong geographical disparities in the diversity pattern of Albian

  20. High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi.

    Science.gov (United States)

    Sánchez-Ramírez, Santiago; Etienne, Rampal S; Moncalvo, Jean-Marc

    2015-08-01

    Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity buildup, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well-recognized pattern describing a decline in species richness from the equator polewards. Recent macroecological studies in ectomycorrhizal (EM) fungi have shown that their LDG is shifted, peaking at temperate rather than tropical latitudes. Here we investigate this phenomenon from a macroevolutionary perspective, focusing on a well-sampled group of edible EM mushrooms from the genus Amanita-the Caesar's mushrooms, which follow similar diversity patterns. Our approach consisted in applying a suite of models including (1) nontrait-dependent time-varying diversification (Bayesian analysis of macroevolutionary mixtures [BAMM]), (2) continuous trait-dependent diversification (quantitative-state speciation and extinction [QuaSSE]), and (3) diversity-dependent diversification. In short, results give strong support for high speciation rates at temperate latitudes (BAMM and QuaSSE). We also find some evidence for different diversity-dependence thresholds in "temperate" and "tropical" subclades, and little differences in diversity due to extinction. We conclude that our analyses on the Caesar's mushrooms give further evidence of a temperate-peaking LDG in EM fungi, highlighting the importance and the implications of macroevolutionary processes in explaining diversity gradients in microorganisms. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  1. CMOS continuous-time adaptive equalizers for high-speed serial links

    CERN Document Server

    Gimeno Gasca, Cecilia; Aldea Chagoyen, Concepción

    2015-01-01

    This book introduces readers to the design of adaptive equalization solutions integrated in standard CMOS technology for high-speed serial links. Since continuous-time equalizers offer various advantages as an alternative to discrete-time equalizers at multi-gigabit rates, this book provides a detailed description of continuous-time adaptive equalizers design - both at transistor and system levels-, their main characteristics and performances. The authors begin with a complete review and analysis of the state of the art of equalizers for wireline applications, describing why they are necessary, their types, and their main applications. Next, theoretical fundamentals of continuous-time adaptive equalizers are explored. Then, new structures are proposed to implement the different building blocks of the adaptive equalizer: line equalizer, loop-filters, power comparator, etc.  The authors demonstrate the design of a complete low-power, low-voltage, high-speed, continuous-time adaptive equalizer. Finally, a cost-...

  2. Awareness of Consequence of High School Students on Loss of Bio-Diversity

    Science.gov (United States)

    Kasot, Nazim; Özbas, Serap

    2015-01-01

    The aim of this study is to assess the egoistic, altruistic and biospheric awareness of the consequence of high school students regarding the loss of bio-diversity, then comparing the results on the basis of some independent variables (gender, class and family income). The research data were collected from 884 ninth and tenth grade high school…

  3. Language Proficiency and Cross-cultural Adaptation as Part of Cross-cultural Communication Competence : A Study of an Ethnically Diverse Team in a Multinational Company in Sweden

    OpenAIRE

    Farah, Deqa; Vuniqi, Valentina

    2012-01-01

    Purpose: Our purpose is to study how language proficiency and cross-cultural adaptation affect ethnically diverse teams in their cross-cultural communication competence. Methodology: The data was collected through six interviews of team members working in a product development project in a multinational company. The interviews were conducted in March of 2012. The data analysis followed an interpretative thematic analysis inspired by Boyatzis (1998). To analyze the data we have utilized some s...

  4. Are High Carbon Stocks in Agroforests and Forest Associated with High Plant Species Diversity?

    OpenAIRE

    Natalia, Depi; Arisoesilaningsih, Endang; Hairiah, Kurniatun

    2017-01-01

    Conserving plant diversity and retaining terrestrial carbon stocks are targets for environmental policy and appear to be generally compatible. However, detailed information on the way both respond to agroforestry management is lacking. Rubber and fruit tree agroforestry systems combine planted trees and trees that are tolerated or actively managed that derived from natural vegetation. The research aimed to evaluate plant species diversity, vegetation structure, and C stock in rubber agrofores...

  5. Promoting High-Quality Cancer Care and Equity Through Disciplinary Diversity in Team Composition.

    Science.gov (United States)

    Parsons, Susan K; Fineberg, Iris C; Lin, Mingqian; Singer, Marybeth; Tang, May; Erban, John K

    2016-11-01

    Disciplinary diversity in team composition is a valuable vehicle for oncology care teams to provide high-quality, person-centered comprehensive care. Such diversity facilitates care that effectively addresses the complex needs (biologic, psychosocial, and spiritual) of the whole person. The concept of professional or disciplinary diversity centers on differences in function, education, and culture, reflecting variety and heterogeneity in the perspectives of team members contributing to care. Thorough understanding of the skills, knowledge, and education related to each team member's professional or lay expertise is critical for members to be able to optimize the team's potential. Furthermore, respect and appreciation for differences and similarities across disciplinary cultures allow team members to create a positive collaboration dynamic that maintains a focus on the care of the person with cancer. We present a case study of one oncology team's provision of care to the patient, a Chinese immigrant woman with breast cancer. The case illuminates the strengths and challenges of disciplinary diversity in team composition in assessing and addressing potential barriers to care. Coordinated sharing of information among the varied team members facilitated understanding and care planning focused on the patient's concerns, needs, and strengths. Importantly, collaboration across the disciplinarily diverse set of team members facilitated high-quality oncology care and promoted equity in access to the full range of care options, including enrollment on a National Cancer Institute-sponsored clinical trial. Further implications of disciplinary diversity in oncology care teams are considered for both clinical practice and research.

  6. A novel high-throughput drip-flow system to grow autotrophic biofilms of contrasting diversities

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen

    . Thus, thicker biofilms are likely to host greater diversity. A system with 40 replicates has been constructed using flow-through polypropylene columns housing a defined number of single-sized glass beads supported by a stainless steel mesh. Biofilms consisting primarily of ammonia oxidizing and nitrite...... are often ill controlled and thus likely to be poorly reproducible. The purpose of this work is to develop a high-throughput continuous-flow system for growing replicate microbial biofilms of varying, but controlled, average thickness and associated community diversity. With these replicate biofilms......, the effect of community composition and diversity on various ecological processes can then be rigorously examined. We hypothesize that the increased loading, resulting in thicker biofilms, will decrease the drift in the community and impose limited environmental filtering by providing more diverse niches...

  7. High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin.

    Science.gov (United States)

    Wang, Jianan; Fernández-Pavía, Sylvia P; Larsen, Meredith M; Garay-Serrano, Edith; Gregorio-Cipriano, Rosario; Rodríguez-Alvarado, Gerardo; Grünwald, Niklaus J; Goss, Erica M

    2017-02-01

    Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their centre of origin and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the centre of origin and diversity of P. infestans and migration events out of Mexico have enormously impacted disease dynamics in North America and Europe. The debate over the origin of the pathogen, and population studies of P. infestans in Mexico, has focused on the Toluca Valley, whereas neighbouring regions have been little studied. We examined the population structure of P. infestans across central Mexico, including samples from Michoacán, Tlaxcala and Toluca. We found high levels of diversity consistent with sexual reproduction in Michoacán and Tlaxcala and population subdivision that was strongly associated with geographic region. We determined that population structure in central Mexico has contributed to diversity in introduced populations based on relatedness of U.S. clonal lineages to Mexican isolates from different regions. Our results suggest that P. infestans exists as a metapopulation in central Mexico, and this population structure could be contributing to the repeated re-emergence of P. infestans in the United States and elsewhere. © 2016 John Wiley & Sons Ltd.

  8. High genotypic diversity found among population of Phytophthora infestans collected in Estonia.

    Science.gov (United States)

    Runno-Paurson, Eve; Kiiker, Riinu; Joutsjoki, Tiina; Hannukkala, Asko

    2016-03-01

    Potato late blight, caused by the oomycete pathogen Phytophthora infestans, is one of the most important diseases of potato worldwide. This is the first study characterising Estonian P. infestans population using the SSR marker genotyping method. 70 P. infestans isolates collected during the growing season in 2004 from eight potato fields in three different regions of Estonia were characterised with nine polymorphic SSR markers. A1 and A2 mating type isolates were detected from every studied field indicating the high potential for sexual reproduction, which raises the genotypic diversity in P. infestans population. Results revealed highly diverse P. infestans population in Estonia resembling the Northern European populations. Most of the multilocus genotypes were detected only once among the collected isolates. Subpopulations collected from different geographical regions of Estonia showed no differentiation from each other but instead formed one highly diverse group. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  9. High altitude genetic adaptation in Tibetans: no role of increased hemoglobin-oxygen affinity

    OpenAIRE

    Tashi, Tsewang; Feng, Tang; Koul, Parvaiz; Amaru, Ricardo; Hussey, Dottie; Lorenzo, Felipe R.; Rili, Ge; Prchal, Josef T.

    2014-01-01

    High altitude exerts selective evolutionary pressure primarily due to its hypoxic environment, resulting in multiple adaptive responses. High hemoglobin-oxygen affinity is postulated to be one such adaptive change, which has been reported in Sherpas of the Himalayas. Tibetans have lived on the Qinghai-Tibetan plateau for thousands of years and have developed unique phenotypes, such as protection from polycythemia which has been linked to PDH2 mutation, resulting in downregulation of HIF pathw...

  10. Adaptive RF Transient Reduction for HIGH Intensity Beams with Gaps

    CERN Document Server

    Tückmantel, Joachim

    2006-01-01

    When a high-intensity beam with bunch-trains and gaps passes a cavity with a high-gain vector feedback enforcing a constant voltage, large transients appear, stressing the RF high power hardware and increasing the trip rate. By modulating the cavity voltage with a varying periodic waveform (set-function), the RF power can be made constant while still preserving the high feedback gain. The average cavity voltage is conserved but bunches have to settle at slightly shifted positions. A method is derived to obtain this set-function in practice while making no assumptions or measurements of the beam or RF parameters. Adiabatic iterations are made including the whole machine as an analog computing device, using all parameters as they are. A computer simulation shows the success of the method.

  11. Assessment of the Lebanese grapevine germplasm reveals a substantial diversity and a high potential for selection

    Directory of Open Access Journals (Sweden)

    Chalak Lamis

    2016-01-01

    Full Text Available Lebanon is illustrious for the cultivation of grapevine since the old antiquity. Grapevine is well adapted to the agroclimatic conditions of the country which makes it one of the major element of the Lebanese agriculture. Nevertheless germplasm assessment has attributed limited interest to grapevine while genetic resources have not been exploited before despite their potential in adaptation to environmental changes. In this study we assess the diversity of traditional grapevine accessions growing in different production areas in Lebanon. A total of 35 accessions belonging to 22 vernacular names were evaluated using 33 leaf and fruit traits previously developed by OIV. An important variability was revealed among the accessions studied based on grape and grain characteristics. The most discriminant traits were grape and grain weight, dimensions, form, and skin color; leaf size, form, color, lobes number, depth of petiole sinus. Hierarchical clustering analysis showed five main clusters, each regrouping accessions of different named varieties and different agro-climatic areas. An intra-varietal variability is also suspected. Although preliminary, our results indicate a potential of genetic diversity within the Lebanese grape germplasm that should be further investigated in order to understand their performance and to evaluate them in selection programs.

  12. High nutrient availability reduces the diversity and stability of the equine caecal microbiota

    Directory of Open Access Journals (Sweden)

    Naja C. K. Hansen

    2015-08-01

    Full Text Available Background: It is well known that nutrient availability can alter the gut microbiota composition, while the effect on diversity and temporal stability remains largely unknown. Methods: Here we address the equine caecal microbiota temporal stability, diversity, and functionality in response to diets with different levels of nutrient availability. Hay (low and slower nutrient availability versus a mixture of hay and whole oats (high and more rapid nutrient availability were used as experimental diets. Results: We found major effects on the microbiota despite that the caecal pH was far from sub-clinical acidosis. We found that the low nutrient availability diet was associated with a higher level of both diversity and temporal stability of the caecal microbiota than the high nutrient availability diet. These observations concur with general ecological theories, suggesting a stabilising effect of biological diversity and that high nutrient availability has a destabilising effect through reduced diversity. Conclusion: Nutrient availability does not only change the composition but also the ecology of the caecal microbiota.

  13. Psychosocial Adaptation and Depressive Manifestations in High-Risk Pregnant Women: Implications for Clinical Practice.

    Science.gov (United States)

    Fiskin, Gamze; Kaydirak, Meltem Mecdi; Oskay, Umran Yesiltepe

    2017-02-01

    High-risk pregnancy research has focused primarily on psychological well-being. The aim is to determine psychosocial adaptation and depression levels of pregnant women who were admitted to hospital with diagnosis of high-risk pregnancy. This study was descriptive. Sampling was composed of 122 high-risk pregnant women who were hospitalized in the perinatology service of Istanbul University Medical School, Department of Obstetrics and Gynecology between January 1, 2014, and May 31, 2014, and met the study criteria. The Pregnant Introduction Form, Psychosocial Adjustment of Illness Scale-Self Report, and CES Depression Scale were used. Of high-risk pregnant women, 47% were found to have a poor level of psychosocial adaptation and 57% presented with depressive symptoms. There were statistically significant difference found between the levels of psychosocial adaptation and status of depressive manifestations. The difference between the average scores increased as the adaptation levels weaken and the pregnant women with a poor level of psychosocial adaptation showed more depressive manifestations. The results of this study indicate that, depending on the high-risk pregnancy status, pregnant women experience difficulty in adaptation to their current status and pregnant women with a poor level of psychosocial adaptation showed more depressive manifestations. Nurses should deliver care in high-risk pregnancies with the awareness of physiological needs as well the psychosocial needs of pregnant women, and information meetings should be held in order to increase the psychosocial support of their families and decrease their tendency toward depression. Nursing initiatives should be developed with further studies for the psychosocial adaptation of high-risk pregnancy and reduction of the depressive manifestations. © 2016 Sigma Theta Tau International.

  14. Adaptation of an epilithic ecosystem to harsh high altitude environment

    Science.gov (United States)

    de La Torre Noetzel, R.; Horneck, G.; García Sancho, L.; Scherer, K.; Facius, R.; Urlings, T.; Rettberg, P.; Reina, M.; Pintado, A.

    2003-04-01

    Epilithic ecosystems in high mountains are exposed to an extreme microclimate characterized by intense solar UV radiation, high temperature fluctuations and high aridity. Using the epilithic ecosystem Rhizocarpon geographicum, the most abundant lichen at the Plataforma de Gredos (Sierra de Gredos, Central Spain, 1.895 m a.s.l.) as model system, we have investigated whether the cortex protects the photobiont against impacts by this extreme environment. The UV radiation climate was measured optoelectronically as well by use of the biological dosimeter DLR-Biofilm, and the microclimate (temperature, relative humidity, PAR) by a microclimatic station (Squirrel, U.K.). The photosynthetic activity of the lichens was periodically determined by use of a photosynthesis yield analyser MINI PAM. Using lichen samples with- and without cortex during different periods of a growing season, showed a substantial protection by the cortex against environmental stress conditions, especially at summer solstice. Solar UV radiation and desiccation exerted the most damaging effects in lichens without cortex. Because of the high resistance of the intact lichen against the harsh high altitude climate, R. geographicum has been selected as test system for survival studies in space to be performed during the upcoming BIOPAN mission of ESA.

  15. A high-throughput multiplex method adapted for GMO detection.

    Science.gov (United States)

    Chaouachi, Maher; Chupeau, Gaëlle; Berard, Aurélie; McKhann, Heather; Romaniuk, Marcel; Giancola, Sandra; Laval, Valérie; Bertheau, Yves; Brunel, Dominique

    2008-12-24

    A high-throughput multiplex assay for the detection of genetically modified organisms (GMO) was developed on the basis of the existing SNPlex method designed for SNP genotyping. This SNPlex assay allows the simultaneous detection of up to 48 short DNA sequences (approximately 70 bp; "signature sequences") from taxa endogenous reference genes, from GMO constructions, screening targets, construct-specific, and event-specific targets, and finally from donor organisms. This assay avoids certain shortcomings of multiplex PCR-based methods already in widespread use for GMO detection. The assay demonstrated high specificity and sensitivity. The results suggest that this assay is reliable, flexible, and cost- and time-effective for high-throughput GMO detection.

  16. Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

    Science.gov (United States)

    Coelho, G R C; Brondani, C; Hoffmann, L V; Valdisser, P A M R; Borba, T C O; Mendonça, J A; Rodrigues, L A; de Menezes, I P P

    2017-09-21

    The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

  17. Development and Testing of Adaptive HF (High Frequency) Radio Techniques

    Science.gov (United States)

    1984-10-01

    December 1980). 2. HFDM : AN/USQ-83(XH-1)(V), The High Frequency Digital Modem, Opera- tion and Maintenance Manual, Sylvania Systems Group, Needham Heights...the HF digital modem ( HFDM ) 2 that per- mits implementing of different modulaticn formats simply by changing the program code. The sounding signal can

  18. Adapting high-rate anaerobic treatment to Middle East conditions

    NARCIS (Netherlands)

    Mahmoud, N.A.; Zeeman, G.; Lier, van J.B.

    2008-01-01

    High-rate anaerobic technologies offer cost-effective solutions for sewage treatment in the Middle East and Palestine in particular. The sewage characteristics in Palestine are quite different from the values elsewhere and show solids contents of more than 1000 mg chemical oxygen demand (COD)ss/L

  19. Virulence comparisons of high-temperature-adapted Heterorhabditis bacteriophora, Steinernema feltiae and S. carpocapsae

    Directory of Open Access Journals (Sweden)

    Susurluk I. A.

    2015-06-01

    Full Text Available Entomopathogenic nematodes (EPNs are environmentally safe alternative control agents. Nematodes in the Heterorhabditidae and Steinernematidae families are widely used in biological control frameworks, especially for soil-inhabiting insect pests. In this experiment, Heterorhabditis bacteriophora (Poinar, 1976, Steinernema feltiae (Filipjev, 1934 and S. carpocapsae (Weiser, 1955 adapted at high temperature were assessed in order to detect differences in virulence between adapted and non-adapted populations. All species were exposed to 38 °C for 2 h. After this treatment, live infective juveniles (IJs were used to infect to last instar Galleria mellonella (Linnaeus, 1758. larvae at the following doses: 1, 2, 3, 4 and 5 IJs/larva. The LD50 and LD90 were obtained for these species. Non-adapted populations of the nematode species were used as controls for this experiment. The results indicated that differences in S. feltiae and S. carpocapsae virulence between the adapted and non-adapted populations were significant; no significant difference was observed between the adapted and non-adapted H. bacteriophora populations.

  20. Exploiting peer group concept for adaptive and highly available services

    CERN Document Server

    Jan, M A; Fraz, M M; Ali, A; Ali, Arshad; Fraz, Mohammad Moazam; Jan, Muhammad Asif; Zahid, Fahd Ali

    2003-01-01

    This paper presents a prototype for redundant, highly available and fault tolerant peer to peer framework for data management. Peer to peer computing is gaining importance due to its flexible organization, lack of central authority, distribution of functionality to participating nodes and ability to utilize unused computational resources. Emergence of GRID computing has provided much needed infrastructure and administrative domain for peer to peer computing. The components of this framework exploit peer group concept to scope service and information search, arrange services and information in a coherent manner, provide selective redundancy and ensure availability in face of failure and high load conditions. A prototype system has been implemented using JXTA peer to peer technology and XML is used for service description and interfaces, allowing peers to communicate with services implemented in various platforms including web services and JINI services. It utilizes code mobility to achieve role interchange amo...

  1. Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates.

    Science.gov (United States)

    Storz, Jay F; Scott, Graham R; Cheviron, Zachary A

    2010-12-15

    High-altitude environments provide ideal testing grounds for investigations of mechanism and process in physiological adaptation. In vertebrates, much of our understanding of the acclimatization response to high-altitude hypoxia derives from studies of animal species that are native to lowland environments. Such studies can indicate whether phenotypic plasticity will generally facilitate or impede adaptation to high altitude. Here, we review general mechanisms of physiological acclimatization and genetic adaptation to high-altitude hypoxia in birds and mammals. We evaluate whether the acclimatization response to environmental hypoxia can be regarded generally as a mechanism of adaptive phenotypic plasticity, or whether it might sometimes represent a misdirected response that acts as a hindrance to genetic adaptation. In cases in which the acclimatization response to hypoxia is maladaptive, selection will favor an attenuation of the induced phenotypic change. This can result in a form of cryptic adaptive evolution in which phenotypic similarity between high- and low-altitude populations is attributable to directional selection on genetically based trait variation that offsets environmentally induced changes. The blunted erythropoietic and pulmonary vasoconstriction responses to hypoxia in Tibetan humans and numerous high-altitude birds and mammals provide possible examples of this phenomenon. When lowland animals colonize high-altitude environments, adaptive phenotypic plasticity can mitigate the costs of selection, thereby enhancing prospects for population establishment and persistence. By contrast, maladaptive plasticity has the opposite effect. Thus, insights into the acclimatization response of lowland animals to high-altitude hypoxia can provide a basis for predicting how altitudinal range limits might shift in response to climate change.

  2. Adaptive Process Management in Highly Dynamic and Pervasive Scenarios

    Directory of Open Access Journals (Sweden)

    Massimiliano de Leoni

    2009-06-01

    Full Text Available Process Management Systems (PMSs are currently more and more used as a supporting tool for cooperative processes in pervasive and highly dynamic situations, such as emergency situations, pervasive healthcare or domotics/home automation. But in all such situations, designed processes can be easily invalidated since the execution environment may change continuously due to frequent unforeseeable events. This paper aims at illustrating the theoretical framework and the concrete implementation of SmartPM, a PMS that features a set of sound and complete techniques to automatically cope with unplanned exceptions. PMS SmartPM is based on a general framework which adopts the Situation Calculus and Indigolog.

  3. Disclosure Experiences of Urban, Ethnically Diverse LGBT High School Students: Implications for School Personnel

    Science.gov (United States)

    Varjas, Kris; Kiperman, Sarah; Meyers, Joel

    2016-01-01

    Disclosure of sexual orientation and/or gender identity is a milestone event for lesbian, gay, bisexual, or transgender (LGBT) youth and can have both positive and negative mental health consequences. Twenty-nine urban, ethnically diverse LGBT high school students participated in face-to-face, in-depth interviews. Qualitative results revealed two…

  4. Individuals and the variation needed for high species diversity in forest trees

    Science.gov (United States)

    James S. Clark

    2010-01-01

    In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for...

  5. iPad Deployment in a Diverse Urban High School: A Formative Experiment

    Science.gov (United States)

    Frey, Nancy; Fisher, Douglas; Lapp, Diane

    2015-01-01

    We explore the use of iPads in a diverse urban high school and the ways in which teachers and students were supported to integrate these tools into their instruction. We provided 4 English teachers with 20 iPads with little or no professional development about how to integrate them into their instruction. Using a formative experiment design, we…

  6. Comment on "Carbon-negative biofuels from low-input high-diversity grassland biomass".

    Science.gov (United States)

    Russelle, Michael P; Morey, R Vance; Baker, John M; Porter, Paul M; Jung, Hans-Joachim G

    2007-06-15

    Tilman et al. (Reports, 8 December 2006, p. 1598) argued that low-input high-diversity grasslands can provide a substantial proportion of global energy needs. We contend that their conclusions are not substantiated by their experimental protocol. The authors understated the management inputs required to establish prairies, extrapolated globally from site-specific results, and presented potentially misleading energy accounting.

  7. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    DEFF Research Database (Denmark)

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica

    2016-01-01

    of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential...

  8. High genetic diversity in the coat protein and 3'untranslated regions ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences; Volume 28; Issue 5. High genetic diversity in the coat protein and 3' untranslated regions among geographical isolates of Cardamom mosaic virus from south India. T Jacob T Jebasingh M N Venugopal R Usha. Articles Volume 28 Issue 5 September 2003 pp 589-595 ...

  9. Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)

    Science.gov (United States)

    Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

  10. High-demand jobs: age-related diversity in work ability?

    NARCIS (Netherlands)

    Sluiter, Judith K.

    2006-01-01

    High-demand jobs include 'specific' job demands that are not preventable with state of the art ergonomics knowledge and may overburden the bodily capacities, safety or health of workers. An interesting question is whether the age of the worker is an important factor in explanations of diversity in

  11. Adaptations to speed endurance training in highly trained soccer players

    DEFF Research Database (Denmark)

    Nyberg, Michael Permin; Fiorenza, Matteo; Lund, Anders

    2016-01-01

    PURPOSE: The present study examined whether a period of additional speed endurance training would improve intense intermittent exercise performance in highly trained soccer players during the season and whether the training changed aerobic metabolism and the level of oxidative enzymes in type I...... and II muscle fibers. METHODS: During the last nine weeks of the season, thirteen semi-professional soccer players performed additional speed endurance training sessions consisting of 2-3 sets of 8 - 10 repetitions of 30 m sprints with 10 s of passive recovery (SET). Before and after SET, subjects......-Yo Intermittent Recovery Test level 1 (YYIRT-1) was performed and a muscle biopsy was obtained at rest. RESULTS: YYIRT-1 performance was 11.6±6.4% (mean±SD) better (2803±330 vs. 3127±383 m, P

  12. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity.

    Science.gov (United States)

    Granados-Cifuentes, Camila; Bellantuono, Anthony J; Ridgway, Tyrone; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

    2013-04-08

    Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the

  13. Single Image Super-Resolution via Adaptive High-Dimensional Non-Local Total Variation and Adaptive Geometric Feature.

    Science.gov (United States)

    Ren, Chao; He, Xiaohai; Nguyen, Truong Q

    2017-01-01

    Single image super-resolution (SR) is very important in many computer vision systems. However, as a highly ill-posed problem, its performance mainly relies on the prior knowledge. Among these priors, the non-local total variation (NLTV) prior is very popular and has been thoroughly studied in recent years. Nevertheless, technical challenges remain. Because NLTV only exploits a fixed non-shifted target patch in the patch search process, a lack of similar patches is inevitable in some cases. Thus, the non-local similarity cannot be fully characterized, and the effectiveness of NLTV cannot be ensured. Based on the motivation that more accurate non-local similar patches can be found by using shifted target patches, a novel multishifted similar-patch search (MSPS) strategy is proposed. With this strategy, NLTV is extended as a newly proposed super-high-dimensional NLTV (SHNLTV) prior to fully exploit the underlying non-local similarity. However, as SHNLTV is very high-dimensional, applying it directly to SR is very difficult. To solve this problem, a novel statistics-based dimension reduction strategy is proposed and then applied to SHNLTV. Thus, SHNLTV becomes a more computationally effective prior that we call adaptive high-dimensional non-local total variation (AHNLTV). In AHNLTV, a novel joint weight strategy that fully exploits the potential of the MSPS-based non-local similarity is proposed. To further boost the performance of AHNLTV, the adaptive geometric duality (AGD) prior is also incorporated. Finally, an efficient split Bregman iteration-based algorithm is developed to solve the AHNLTV-AGD-driven minimization problem. Extensive experiments validate the proposed method achieves better results than many state-of-the-art SR methods in terms of both objective and subjective qualities.

  14. Plant diversity on high elevation islands – drivers of species richness and endemism

    Directory of Open Access Journals (Sweden)

    Severin D.H. Irl

    2016-10-01

    Full Text Available High elevation islands elicit fascination because of their large array of endemic species and strong environmental gradients. First, I define a high elevation island according to geographic and environmental characteristics. Then, within this high elevation island framework, I address local disturbance effects on plant distribution, drivers of diversity and endemism on the island scale, and global patterns of treeline elevation and climate change. Locally, introduced herbivores have strong negative effects on the summit scrub of my model island La Palma (Canary Islands, while roads have unexpected positive effects on endemics. On the island scale, topography and climate drive diversity and endemism. Hotspots of endemicity are found in summit regions – a general pattern on high elevation islands. The global pattern of treeline elevation behaves quite differently on islands than on the mainland. A thorough literature review and climate projections suggest that climate change will profoundly affect oceanic island floras.

  15. Development and Validation of a Behavioural Index for Adaptation to High Summer Temperatures among Urban Dwellers

    Science.gov (United States)

    Valois, Pierre; Caron, Maxime; Carrier, Marie-Pier; Morin, Alexandre J. S.; Renaud, Jean-Sébastien; Jacob, Johann; Gosselin, Pierre

    2017-01-01

    One of the consequences of climate change is the growing number of extreme weather events, including heat waves, which have substantial impacts on the health of populations. From a public health standpoint, it is vital to ensure that people can adapt to high heat, particularly in cities where heat islands abound. Identifying indicators to include in a parsimonious index would help better differentiate individuals who adapt well to heat from those who do not adapt as well. This study aimed at developing and validating a summer heat adaptation index for residents of the 10 largest cities in the province of Québec, Canada. A sample of 2000 adults in 2015 and 1030 adults in 2016 completed a telephone questionnaire addressing their adoption (or non-adoption) of behaviours recommended by public health agencies to protect themselves during periods of high temperature, and their perceptions of how high summer heat affects their mental and physical health. Item analysis, confirmatory factor analysis, multiple correspondence analysis, measurement invariance analyses and criterion-validity analyses were used to develop a 12-behaviour heat adaptation index for distinguishing between individuals who adapt well to high temperatures and those who do not adapt as well. The results indicated that the measurement and the factor structure of the index were invariant (equivalent) across the two independent samples of participants who completed the questionnaire at different times one year apart, an important prerequisite for unambiguous interpretation of index scores across groups and over time. The results also showed that individuals who perceived more adverse effects on their physical or mental health adopted more preventive behaviours during periods of high temperatures and humidity conditions compared to those who felt lesser or no effects. This study thus presents support for the validity of the index that could be used in future studies to monitor preventive behaviours

  16. Development and Validation of a Behavioural Index for Adaptation to High Summer Temperatures among Urban Dwellers.

    Science.gov (United States)

    Valois, Pierre; Talbot, Denis; Caron, Maxime; Carrier, Marie-Pier; Morin, Alexandre J S; Renaud, Jean-Sébastien; Jacob, Johann; Gosselin, Pierre

    2017-07-21

    One of the consequences of climate change is the growing number of extreme weather events, including heat waves, which have substantial impacts on the health of populations. From a public health standpoint, it is vital to ensure that people can adapt to high heat, particularly in cities where heat islands abound. Identifying indicators to include in a parsimonious index would help better differentiate individuals who adapt well to heat from those who do not adapt as well. This study aimed at developing and validating a summer heat adaptation index for residents of the 10 largest cities in the province of Québec, Canada. A sample of 2000 adults in 2015 and 1030 adults in 2016 completed a telephone questionnaire addressing their adoption (or non-adoption) of behaviours recommended by public health agencies to protect themselves during periods of high temperature, and their perceptions of how high summer heat affects their mental and physical health. Item analysis, confirmatory factor analysis, multiple correspondence analysis, measurement invariance analyses and criterion-validity analyses were used to develop a 12-behaviour heat adaptation index for distinguishing between individuals who adapt well to high temperatures and those who do not adapt as well. The results indicated that the measurement and the factor structure of the index were invariant (equivalent) across the two independent samples of participants who completed the questionnaire at different times one year apart, an important prerequisite for unambiguous interpretation of index scores across groups and over time. The results also showed that individuals who perceived more adverse effects on their physical or mental health adopted more preventive behaviours during periods of high temperatures and humidity conditions compared to those who felt lesser or no effects. This study thus presents support for the validity of the index that could be used in future studies to monitor preventive behaviours

  17. High endemism and stem density distinguish New Caledonian from other high-diversity rainforests in the Southwest Pacific.

    Science.gov (United States)

    Ibanez, Thomas; Blanchard, E; Hequet, V; Keppel, G; Laidlaw, M; Pouteau, R; Vandrot, H; Birnbaum, P

    2017-10-25

    The biodiversity hotspot of New Caledonia is globally renowned for the diversity and endemism of its flora. New Caledonia's tropical rainforests have been reported to have higher stem densities, higher concentrations of relictual lineages and higher endemism than other rainforests. This study investigates whether these aspects differ in New Caledonian rainforests compared to other high-diversity rainforests in the Southwest Pacific. Plants (with a diameter at breast height ≥10 cm) were surveyed in nine 1-ha rainforest plots across the main island of New Caledonia and compared with 14 1-ha plots in high-diversity rainforests of the Southwest Pacific (in Australia, Fiji, Papua New Guinea and the Solomon Islands). This facilitated a comparison of stem densities, taxonomic composition and diversity, and species turnover among plots and countries. The study inventoried 11 280 stems belonging to 335 species (93 species ha-1 on average) in New Caledonia. In comparison with other rainforests in the Southwest Pacific, New Caledonian rainforests exhibited higher stem density (1253 stems ha-1 on average) including abundant palms and tree ferns, with the high abundance of the latter being unparalleled outside New Caledonia. In all plots, the density of relictual species was ≥10 % for both stems and species, with no discernible differences among countries. Species endemism, reaching 89 % on average, was significantly higher in New Caledonia. Overall, species turnover increased with geographical distance, but not among New Caledonian plots. High stem density, high endemism and a high abundance of tree ferns with stem diameters ≥10 cm are therefore unique characteristics of New Caledonian rainforests. High endemism and high spatial species turnover imply that the current system consisting of a few protected areas is inadequate, and that the spatial distribution of plant species needs to be considered to adequately protect the exceptional flora of New Caledonian rainforests.

  18. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance.

    Science.gov (United States)

    Schou, Mads F; Loeschcke, Volker; Bechsgaard, Jesper; Schlötterer, Christian; Kristensen, Torsten N

    2017-12-01

    The effective population size (Ne ) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on Ne , with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between Ne and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long-term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X-chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X-chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations. © 2017 John Wiley & Sons Ltd.

  19. Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts.

    Science.gov (United States)

    Massimo, Nicholas C; Nandi Devan, M M; Arendt, Kayla R; Wilch, Margaret H; Riddle, Jakob M; Furr, Susan H; Steen, Cole; U'Ren, Jana M; Sandberg, Dustin C; Arnold, A Elizabeth

    2015-07-01

    In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in aboveground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on nonsucculent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity, and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert-plant communities and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.

  20. Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

    DEFF Research Database (Denmark)

    Gresham, D.; Usaite, Renata; Germann, S.M.

    2010-01-01

    To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications and delet......To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications....... Extrachromosomal DNA circles (GAP1(circle)) contain GAP1, the replication origin ARS1116, and a single hybrid LTR derived from recombination between the two flanking LTRs. Formation of the GAP1(circle) is associated with deletion of chromosomal GAP1 (gap1 Delta) and production of a single hybrid LTR at the GAP1...

  1. High-altitude adaptation of Tibetan chicken from MT-COI and ATP-6 perspective.

    Science.gov (United States)

    Zhao, Xiaoling; Wu, Nan; Zhu, Qing; Gaur, Uma; Gu, Ting; Li, Diyan

    2016-09-01

    The problem of hypoxia adaptation in high altitudes is an unsolved brainteaser in the field of life sciences. As one of the best chicken breeds with adaptability to highland environment, the Tibetan chicken, is genetically different from lowland chicken breeds. In order to gain a better understanding of the mechanism of hypoxic adaptability in high altitude, in the present study, we focused on the MT-COI together with ATP-6 gene to explore the regulatory mechanisms for hypoxia adaptability in Tibet chicken. Here, we sequenced MT-COI of 29 Tibetan chickens and 30 Chinese domestic chickens and ATP-6 gene of 28 Tibetan chickens and 29 Chinese domestic chickens. In MT-COI gene, 9 single nucleotide polymorphisms (SNPs) were detected though none of these was a missense mutation, confirming the fact that MT-COI gene is a largely conservative sequence. In ATP-6 gene, 6 single nucleotide polymorphisms (SNPs) were detected and we found a missense mutation (m.9441G > A) in the ATP-6 gene of Tibetan chicken resulting in an amino acid substitution. Due to the critical role of ATP-6 gene in the proton translocation and energy metabolism, we speculated the possibility of this mutation playing an important role in easier energy conversion and metabolism in Tibetan chickens than Chinese domestic chickens so as to better adapt to the harsh environment of the high-altitude areas. The Median-joining profile also suggested that haplotype Ha2 has the ancestral position to the other haplotypes and has significant relationship with high-altitude adaptation in ATP-6 gene. Therefore, we considered that the polymorphism (m.9441G > A) in the ATP-6 gene may affect the specific functions of ATP-6 enzyme relating to high-altitude adaptation of Tibetan chicken and MT-COI gene is a largely conservative sequence.

  2. L1 Adaptive Manoeuvring Control of Unmanned High-speed Water Craft

    DEFF Research Database (Denmark)

    Svendsen, Casper H.; Holck, Niels Ole; Galeazzi, Roberto

    2012-01-01

    This work addresses the issue of designing an adaptive robust control system to govern the steering of a high speed unmanned personal watercraft (PWC) maintaining equal performance across the craft’s envelope of operation. The maneuvering dynamics of a high speed PWC is presented and a strong...

  3. Assessment of genetic diversity among barley cultivars and breeding lines adapted to the US Pacific Northwest, and its implications in breeding barley for imidazolinone-resistance.

    Directory of Open Access Journals (Sweden)

    Sachin Rustgi

    Full Text Available Extensive application of imidazolinone (IMI herbicides had a significant impact on barley productivity contributing to a continuous decline in its acreage over the last two decades. A possible solution to this problem is to transfer IMI-resistance from a recently characterized mutation in the 'Bob' barley AHAS (acetohydroxy acid synthase gene to other food, feed and malting barley cultivars. We focused our efforts on transferring IMI-resistance to barley varieties adapted to the US Pacific Northwest (PNW, since it comprises ∼23% (335,000 ha of the US agricultural land under barley production. To effectively breed for IMI-resistance, we studied the genetic diversity among 13 two-rowed spring barley cultivars/breeding-lines from the PNW using 61 microsatellite markers, and selected six barley genotypes that showed medium to high genetic dissimilarity with the 'Bob' AHAS mutant. The six selected genotypes were used to make 29-53 crosses with the AHAS mutant and a range of 358-471 F1 seeds were obtained. To make informed selection for the recovery of the recipient parent genome, the genetic location of the AHAS gene was determined and its genetic nature assessed. Large F2 populations ranging in size from 2158-2846 individuals were evaluated for herbicide resistance and seedling vigor. Based on the results, F3 lines from the six most vigorous F2 genotypes per cross combination were evaluated for their genetic background. A range of 20%-90% recovery of the recipient parent genome for the carrier chromosome was observed. An effort was made to determine the critical dose of herbicide to distinguish between heterozygotes and homozygotes for the mutant allele. Results suggested that the mutant can survive up to the 10× field recommended dose of herbicide, and the 8× and 10× herbicide doses can distinguish between the two AHAS mutant genotypes. Finally, implications of this research in sustaining barley productivity in the PNW are discussed.

  4. Cranial biomechanics underpins high sauropod diversity in resource-poor environments.

    Science.gov (United States)

    Button, David J; Rayfield, Emily J; Barrett, Paul M

    2014-11-22

    High megaherbivore species richness is documented in both fossil and contemporary ecosystems despite their high individual energy requirements. An extreme example of this is the Late Jurassic Morrison Formation, which was dominated by sauropod dinosaurs, the largest known terrestrial vertebrates. High sauropod diversity within the resource-limited Morrison is paradoxical, but might be explicable through sophisticated resource partitioning. This hypothesis was tested through finite-element analysis of the crania of the Morrison taxa Camarasaurus and Diplodocus. Results demonstrate divergent specialization, with Camarasaurus capable of exerting and accommodating greater bite forces than Diplodocus, permitting consumption of harder food items. Analysis of craniodental biomechanical characters taken from 35 sauropod taxa demonstrates a functional dichotomy in terms of bite force, cranial robustness and occlusal relationships yielding two polyphyletic functional 'grades'. Morrison taxa are widely distributed within and between these two morphotypes, reflecting distinctive foraging specializations that formed a biomechanical basis for niche partitioning between them. This partitioning, coupled with benefits associated with large body size, would have enabled the high sauropod diversities present in the Morrison Formation. Further, this provides insight into the mechanisms responsible for supporting the high diversities of large megaherbivores observed in other Mesozoic and Cenozoic communities, particularly those occurring in resource-limited environments.

  5. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake.

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, Jana; Knudsen, Rune; Kuhn, Jesper A; Henriksen, Eirik H; Siwertsson, Anna; Shaw, Jenny C; Kuris, Armand M; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D; Kostadinova, Aneta

    2017-05-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages) and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages. Copyright © 2017 Australian Society for Parasitology. All rights reserved.

  6. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  7. Diverse Drought Spatiotemporal Trends, Diverse Etic-Emic Perceptions and Knowledge: Implications for Adaptive Capacity and Resource Management for Indigenous Maasai-Pastoralism in the Rangelands of Kenya

    Directory of Open Access Journals (Sweden)

    Margaret Mwangi

    2016-04-01

    hazard is perceived, communicated, and characterized; hence, ceteris paribus, alongside its spatiotemporal distribution, shapes the nature of the adaptive capacity of and resource management in Maasai-pastoralism. Studies that anticipate enhancing the drought-adaptive capacity of the Maasai should account for cross-scale social and biophysical factors, their processes, and interactions; they must engage the affected inhabitants, and utilize and integrate multiple data sources and approaches. These necessities become more crucial for informing adaptation under the present spatiotemporal distribution of drought as well as in relation to the projected increase in occurrence and intensity of this climatic hazard as the climate continues to change, and as pressures from socioeconomic globalization persistently proliferate into the Maasai’s social and biophysical landscapes.

  8. High-Resolution Adaptive Optics Test-Bed for Vision Science

    Energy Technology Data Exchange (ETDEWEB)

    Wilks, S C; Thomspon, C A; Olivier, S S; Bauman, B J; Barnes, T; Werner, J S

    2001-09-27

    We discuss the design and implementation of a low-cost, high-resolution adaptive optics test-bed for vision research. It is well known that high-order aberrations in the human eye reduce optical resolution and limit visual acuity. However, the effects of aberration-free eyesight on vision are only now beginning to be studied using adaptive optics to sense and correct the aberrations in the eye. We are developing a high-resolution adaptive optics system for this purpose using a Hamamatsu Parallel Aligned Nematic Liquid Crystal Spatial Light Modulator. Phase-wrapping is used to extend the effective stroke of the device, and the wavefront sensing and wavefront correction are done at different wavelengths. Issues associated with these techniques will be discussed.

  9. A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus

    Directory of Open Access Journals (Sweden)

    Quintela Maria

    2008-12-01

    Full Text Available Abstract Background There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10-3 and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (πt was between 1.30 × 10-4 and 7.66 × 10-3 (average πt = 2.72 × 10-3 ± 2.06 × 10-3 and silent nucleotide diversity varied between 4.20 × 10-4and 2.76 × 10-2 (average πS = 9.22 × 10-3 ± 7.43 × 10-4. The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10-3 (average πa = 5.08 × 10-4 ± 7.43 × 103, which suggest that purifying selection is strong in these genes. FST values based on synonymous SNP's varied between -5.60 × 10-4 and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of FST = 0.03 (95% CI: 0.006 – 0.057 over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low

  10. Genetic diversity of dispersed seeds is highly variable among leks of the long-wattled umbrellabird

    Science.gov (United States)

    Ottewell, Kym; Browne, Luke; Cabrera, Domingo; Olivo, Jorge; Karubian, Jordan

    2018-01-01

    Frugivorous animals frequently generate clumped distributions of seeds away from source trees, but genetic consequences of this phenomenon remain poorly resolved. Seed dispersal of the palm Oenocarpus bataua by long-wattled umbrellabirds Cephalopterus penduliger generates high seed densities in leks (i.e., multi-male display sites), providing a suitable venue to investigate how dispersal by this frugivore may influence seed source diversity and genetic structure at local and landscape levels. We found moderate levels of maternal seed source diversity in primary seed rain across five leks in northwest Ecuador (unweighted mean alpha diversity α = 9.52, weighted mean αr = 3.52), with considerable variation among leks (αr range: 1.81-24.55). Qualitatively similar findings were obtained for allelic diversity and heterozygosity. Higher densities of O. bataua adults around leks were associated with higher values of αr and heterozygosity (non-significant trends) and allelic diversity (significant correlation). Seed source overlap between different leks was not common but did occur at low frequency, providing evidence for long-distance seed dispersal by umbrellabirds into leks. Our findings are consistent with the idea that seed pool diversity within leks may be shaped by the interaction between density of local trees, which can vary considerably between leks, and umbrellabird foraging ecology, particularly a lack of territorial defense of fruiting trees. Taken as a whole, this work adds to our growing appreciation of the ways resource distribution and associated frugivore foraging behaviors mechanistically shape seed dispersal outcomes and the distribution of plant genotypes across the landscape.

  11. EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda

    Science.gov (United States)

    Aggarwal, Shilpi; Negi, Sapna; Jha, Pankaj; Singh, Prashant K.; Stobdan, Tsering; Pasha, M. A. Qadar; Ghosh, Saurabh; Agrawal, Anurag; Prasher, Bhavana; Mukerji, Mitali; Brahmachari, S. K.; Majumder, P. P.; Mukerji, M.; Habib, S.; Dash, D.; Ray, K.; Bahl, S.; Singh, L.; Sharma, A.; Roychoudhury, S.; Chandak, G. R.; Thangaraj, K.; Parmar, D.; Sengupta, S.; Bharadwaj, D.; Rath, S. K.; Singh, J.; Jha, G. N.; Virdi, K.; Rao, V. R.; Sinha, S.; Singh, A.; Mitra, A. K.; Mishra, S. K.; Pasha, Q.; Sivasubbu, S.; Pandey, R.; Baral, A.; Singh, P. K.; Sharma, A.; Kumar, J.; Stobdan, T.; Bhasin, Y.; Chauhan, C.; Hussain, A.; Sundaramoorthy, E.; Singh, S. P.; Bandyopadhyay, A.; Dasgupta, K.; Reddy, A. K.; Spurgeon, C. J.; Idris, M. M.; Khanna, V.; Dhawan, A.; Anand, M.; Shankar, R.; Bharti, R. S.; Singh, M.; Singh, A. P.; Khan, A. J.; Shah, P. P.; Pant, A. B.; Kaur, R.; Bisht, K. K.; Kumar, A.; Rajamanickam, V.; Wilson, E.; Thangadurai, A.; Jha, P. K.; Maulik, M.; Makhija, N.; Rahim, A.; Sharma, S.; Chopra, R.; Rana, P.; Chidambaram, M.; Maitra, A.; Chawla, R.; Soni, S.; Khurana, P.; Khan, M. N.; Sutar, S. D.; Tuteja, A.; Narayansamy, K.; Shukla, R.; Prakash, S.; Mahurkar, S.; Mani, K. Radha; Hemavathi, J.; Bhaskar, S.; Khanna, P.; Ramalakshmi, G. S.; Tripathi, S. M.; Thakur, N.; Ghosh, B.; Kukreti, R.; Madan, T.; Verma, R.; Sudheer, G.; Mahajan, A.; Chavali, S.; Tabassum, R.; Grover, S.; Gupta, M.; Batra, J.; Kumar, A.; Nejatizadeh, A.; Vaid, M.; Das, S. K.; Sharma, S.; Sharma, M.; Chatterjee, R.; Paul, J. A.; Srivastava, P.; Rajput, C.; Mittal, U.; Singh, M.; Hariharan, M.; Das, S.; Chaudhuri, K.; Sengupta, M.; Acharya, M.; Bhattacharyya, A.; Saha, A.; Biswas, A.; Chaki, M.; Gupta, A.; Mukherjee, S.; Mookherjee, S.; Chattopadhyay, I.; Banerjee, T.; Chakravorty, M.; Misra, C.; Monadal, G.; Sengupta, S.; Dutta, De. D.; Bajaj, S.; Deb, I.; Banerjee, A.; Chowdhury, R.; Banerjee, D.; Kumar, D.; Das, S. R.; Tiwari, S.; Bharadwaj, A.; Khanna, S.; Ahmed, I.; Parveen, S.; Singh, N.; Dasgupta, D.; Bisht, S. S.; Rajput, R.; Ghosh, B.; Kumar, N.; Chaurasia, A.; Abraham, J. K.; Sinha, A.; Scaria, V.; Sethi, T. P.; Mandal, A. K.; Mukhopadhyay, A.

    2010-01-01

    It is being realized that identification of subgroups within normal controls corresponding to contrasting disease susceptibility is likely to lead to more effective predictive marker discovery. We have previously used the Ayurvedic concept of Prakriti, which relates to phenotypic differences in normal individuals, including response to external environment as well as susceptibility to diseases, to explore molecular differences between three contrasting Prakriti types: Vata, Pitta, and Kapha. EGLN1 was one among 251 differentially expressed genes between the Prakriti types. In the present study, we report a link between high-altitude adaptation and common variations rs479200 (C/T) and rs480902 (T/C) in the EGLN1 gene. Furthermore, the TT genotype of rs479200, which was more frequent in Kapha types and correlated with higher expression of EGLN1, was associated with patients suffering from high-altitude pulmonary edema, whereas it was present at a significantly lower frequency in Pitta and nearly absent in natives of high altitude. Analysis of Human Genome Diversity Panel-Centre d’Etude du Polymorphisme Humain (HGDP-CEPH) and Indian Genome Variation Consortium panels showed that disparate genetic lineages at high altitudes share the same ancestral allele (T) of rs480902 that is overrepresented in Pitta and positively correlated with altitude globally (P < 0.001), including in India. Thus, EGLN1 polymorphisms are associated with high-altitude adaptation, and a genotype rare in highlanders but overrepresented in a subgroup of normal lowlanders discernable by Ayurveda may confer increased risk for high-altitude pulmonary edema. PMID:20956315

  12. Adaptation potential of naturally ventilated barns to high temperature extremes: The OptiBarn project

    Science.gov (United States)

    Menz, Christoph

    2016-04-01

    Climate change interferes with various aspects of the socio-economic system. One important aspect is its influence on animal husbandry, especially dairy faming. Dairy cows are usually kept in naturally ventilated barns (NVBs) which are particular vulnerable to extreme events due to their low adaptation capabilities. An effective adaptation to high outdoor temperatures for example, is only possible under certain wind and humidity conditions. High temperature extremes are expected to increase in number and strength under climate change. To assess the impact of this change on NVBs and dairy cows also the changes in wind and humidity needs to be considered. Hence we need to consider the multivariate structure of future temperature extremes. The OptiBarn project aims to develop sustainable adaptation strategies for dairy housings under climate change for Europe, by considering the multivariate structure of high temperature extremes. In a first step we identify various multivariate high temperature extremes for three core regions in Europe. With respect to dairy cows in NVBs we will focus on the wind and humidity field during high temperature events. In a second step we will use the CORDEX-EUR-11 ensemble to evaluate the capability of the RCMs to model such events and assess their future change potential. By transferring the outdoor conditions to indoor climate and animal wellbeing the results of this assessment can be used to develop technical, architectural and animal specific adaptation strategies for high temperature extremes.

  13. High level of genetic diversity among the selected accessions of tea (Camellia sinensis) from abandoned tea gardens in western Himalaya.

    Science.gov (United States)

    Karthigeyan, S; Rajkumar, S; Sharma, R K; Gulati, Ashu; Sud, R K; Ahuja, P S

    2008-12-01

    To revive cultivation of the tea unique to the western Himalayan region, it is important to evaluate the seed-derived bushes available in the area's abandoned gardens. This study used quantitative leaf characters, catechin content, and AFLP markers to assess these China cultivar type bushes. Compared with other China cultivar germplasm, these accessions showed a higher level of diversity among themselves. Among the quantitative morphological characters, leaf length is important in distinguishing the accessions studied, with a high loading value in the principal component analysis. The catechins and AFLP markers displayed the genetic makeup of the accessions. Other than total catechins, the trihydroxylated catechins showed a high loading value in differentiating the accessions. The genetic control of the ratio of dihydroxylated and trihydroxylated catechins is found to be based on a correlation with AFLP markers. The genetic similarity between Kangra Asha and Kangra Jat suggests that Kangra Jat must be descended from Kangra Asha. Kangra Jat is well adapted to local environmental conditions, as is evident from its high catechin content.

  14. Unexpected high diversity of galling insects in the Amazonian upper canopy: the savanna out there.

    Directory of Open Access Journals (Sweden)

    Genimar R Julião

    Full Text Available A relatively large number of studies reassert the strong relationship between galling insect diversity and extreme hydric and thermal status in some habitats, and an overall pattern of a greater number of galling species in the understory of scleromorphic vegetation. We compared galling insect diversity in the forest canopy and its relationship with tree richness among upland terra firme, várzea, and igapó floodplains in Amazonia, Brazil. The soils of these forest types have highly different hydric and nutritional status. Overall, we examined the upper layer of 1,091 tree crowns. Galling species richness and abundance were higher in terra firme forests compared to várzea and igapó forests. GLM-ANCOVA models revealed that the number of tree species sampled in each forest type was determinant in the gall-forming insect diversity. The ratio between galling insect richness and number of tree species sampled (GIR/TSS ratio was higher in the terra firme forest and in seasonally flooded igapó, while the várzea presented the lowest GIR/TSS ratio. In this study, we recorded unprecedented values of galling species diversity and abundance per sampling point. The GIR/TSS ratio from várzea was approximately 2.5 times higher than the highest value of this ratio ever reported in the literature. Based on this fact, we ascertained that várzea and igapó floodplain forests (with lower GIA and GIR, together with the speciose terra firme galling community emerge as the gall diversity apex landscape among all biogeographic regions already investigated. Contrary to expectation, our results also support the "harsh environment hypothesis", and unveil the Amazonian upper canopy as similar to Mediterranean vegetation habitats, hygrothermically stressed environments with leaf temperature at lethal limits and high levels of leaf sclerophylly.

  15. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    Full Text Available This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs. Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.

  16. Functional diversity and environmental services in landscapes in moor and high Andean forest Boyacá

    Directory of Open Access Journals (Sweden)

    Aracely Burgos

    2012-10-01

    Full Text Available Understanding how functional diversity operates to provide environmental services in the various landscapes ecosystem, is crucial to maintain the welfare of the people who depend on them. This review aims to address: 1. Overview of functional diversity and state of research in the páramo and forest altondino of Boyacá. 2. The loan provides environmental services functional diversity boyacense population, which has a high percentage rural (49% for both lives immersed in these landscapes, facing their importance in environmental and public policy decisions. 3. The description of the modeling of the landscape as a determinant, largely on the structure of ecological communities, functioning and ecosystem services. This is formulated with the aim of reversing the focus of research so far has been aimed at quantification studies of local diversity, to effects involving landscape modeling functional biodiversity, this approach to be critical for the development of joint solutions for the sake of the future of biodiversity and ecosystem services management

  17. High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains.

    Science.gov (United States)

    Kammerlander, Barbara; Breiner, Hans-Werner; Filker, Sabine; Sommaruga, Ruben; Sonntag, Bettina; Stoeck, Thorsten

    2015-04-01

    We analyzed the genetic diversity (V4 region of the 18S rRNA) of planktonic microbial eukaryotes in four high mountain lakes including two remote biogeographic regions (the Himalayan mountains and the European Alps) and distinct habitat types (clear and glacier-fed turbid lakes). The recorded high genetic diversity in these lakes was far beyond of what is described from high mountain lake plankton. In total, we detected representatives from 66 families with the main taxon groups being Alveolata (55.0% OTUs 97%, operational taxonomic units), Stramenopiles (34.0% OTUs 97%), Cryptophyta (4.0% OTUs 97%), Chloroplastida (3.6% OTUs 97%) and Fungi (1.7% OTUs 97%). Centrohelida, Choanomonada, Rhizaria, Katablepharidae and Telonema were represented by <1% OTUs 97%. Himalayan lakes harbored a higher plankton diversity compared to the Alpine lakes (Shannon index). Community structures were significantly different between lake types and biogeographic regions (Fisher exact test, P < 0.01). Network analysis revealed that more families of the Chloroplastida (10 vs 5) and the Stramenopiles (14 vs 8) were found in the Himalayan lakes than in the Alpine lakes and none of the fungal families was shared between them. Biogeographic aspects as well as ecological factors such as water turbidity may structure the microbial eukaryote plankton communities in such remote lakes. © FEMS 2015.

  18. The Double ABCX Model of Adaptation in Racially Diverse Families with a School-Age Child with Autism

    Science.gov (United States)

    Manning, Margaret M.; Wainwright, Laurel; Bennett, Jillian

    2011-01-01

    In this study, the Double ABCX model of family adaptation was used to explore the impact of severity of autism symptoms, behavior problems, social support, religious coping, and reframing, on outcomes related to family functioning and parental distress. The sample included self-report measures collected from 195 families raising school-age…

  19. When can refuges mediate the genetic effects of fire regimes? A simulation study of the effects of topography and weather on neutral and adaptive genetic diversity in fire-prone landscapes.

    Science.gov (United States)

    Banks, Sam C; Davies, Ian D; Cary, Geoffrey J

    2017-10-01

    Understanding how landscape heterogeneity mediates the effects of fire on biodiversity is increasingly important under global changes in fire regimes. We used a simulation experiment to investigate how fire regimes interact with topography and weather to shape neutral and selection-driven genetic diversity under alternative dispersal scenarios, and to explore the conditions under which microrefuges can maintain genetic diversity of populations exposed to recurrent fire. Spatial heterogeneity in simulated fire frequency occurred in topographically complex landscapes, with fire refuges and fire-prone "hotspots" apparent. Interannual weather variability reduced the effect of topography on fire patterns, with refuges less apparent under high weather variability. Neutral genetic diversity was correlated with long-term fire frequency under spatially heterogeneous fire regimes, being higher in fire refuges than fire-prone areas, except under high dispersal or low fire severity (low mortality). This generated different spatial genetic structures in fire-prone and fire-refuge components of the landscape, despite similar dispersal. In contrast, genetic diversity was only associated with time since the most recent fire in flat landscapes without predictable refuges and hotspots. Genetic effects of selection driven by fire-related conditions depended on selection pressure, migration distance and spatial heterogeneity in fire regimes. Allele frequencies at a locus conferring higher fitness under successional environmental conditions followed a pattern of "temporal adaptation" to contemporary conditions under strong selection pressure and high migration. However, selected allele frequencies were correlated with spatial variation in long-term mean fire frequency (relating to environmental predictability) under weak dispersal, low selection pressure and strong spatial heterogeneity in fire regimes. © 2017 John Wiley & Sons Ltd.

  20. West Nile Virus: Using Adapted Primary Literature in Mathematical Biology to Teach Scientific and Mathematical Reasoning in High School

    Science.gov (United States)

    Norris, Stephen P.; Macnab, John S.; Wonham, Marjorie; de Vries, Gerda

    2009-01-01

    This paper promotes the use of adapted primary literature as a curriculum and instruction innovation for use in high school. Adapted primary literature is useful for promoting an understanding of scientific and mathematical reasoning and argument and for introducing modern science into the schools. We describe a prototype adapted from a published…

  1. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    Science.gov (United States)

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  2. High-demand jobs: age-related diversity in work ability?

    Science.gov (United States)

    Sluiter, Judith K

    2006-07-01

    High-demand jobs include 'specific' job demands that are not preventable with state of the art ergonomics knowledge and may overburden the bodily capacities, safety or health of workers. An interesting question is whether the age of the worker is an important factor in explanations of diversity in work ability in the context of high-demand jobs. In this paper, the work ability of ageing workers is addressed according to aspects of diversity in specific job demands and the research methods that are needed to shed light upon the relevant associated questions. From the international literature, a body of evidence was elicited concerning rates of chronological ageing in distinct bodily systems and functions. Intra-age-cohort differences in capacities and work ability, however, require (not yet existing) valid estimates of functional age or biological age indices for the specific populations of workers in high-demand jobs. Many studies have drawn on the highly demanding work of fire-fighters, ambulance workers, police officers, medical specialists, pilots/astronauts and submarine officers. Specific job demands in these jobs can be physical, mental or psychosocial in origin but may cause combined task-level loadings. Therefore, the assessment of single demands probably will not reveal enough relevant information about work ability in high-demand jobs and there will be a call for more integrated measures. Existing studies have used a variety of methodologies to address parts of the issue: task analyses for quantifying physical work demands, observations of psychological and physiological parameters, measures of psychosocial work demands and health complaints. Specific details about the work ability of ageing workers in high-demand jobs are scarce. In general, specific demands are more likely to overtax the capacities of older workers than those of younger workers in high-demand jobs, implying greater repercussions for health, although these effects also vary considerably

  3. Adaptive testing for association between two random vectors in moderate to high dimensions.

    Science.gov (United States)

    Xu, Zhiyuan; Xu, Gongjun; Pan, Wei

    2017-11-01

    Testing for association between two random vectors is a common and important task in many fields, however, existing tests, such as Escoufier's RV test, are suitable only for low-dimensional data, not for high-dimensional data. In moderate to high dimensions, it is necessary to consider sparse signals, which are often expected with only a few, but not many, variables associated with each other. We generalize the RV test to moderate-to-high dimensions. The key idea is to data adaptively weight each variable pair based on its empirical association. As the consequence, the proposed test is adaptive, alleviating the effects of noise accumulation in high-dimensional data, and thus maintaining the power for both dense and sparse alternative hypotheses. We show the connections between the proposed test with several existing tests, such as a generalized estimating equations-based adaptive test, multivariate kernel machine regression (KMR), and kernel distance methods. Furthermore, we modify the proposed adaptive test so that it can be powerful for nonlinear or nonmonotonic associations. We use both real data and simulated data to demonstrate the advantages and usefulness of the proposed new test. The new test is freely available in R package aSPC on CRAN at https://cran.r-project.org/web/packages/aSPC/index.html and https://github.com/jasonzyx/aSPC. © 2017 WILEY PERIODICALS, INC.

  4. Structural Equation Modeling for Studying Adaptation of the Students with Disabilities in Inclusive Junior High Schools

    Science.gov (United States)

    Chen, Li Ju

    2014-01-01

    This research explored the factors of the adaptation for the children with disabilities studying in inclusive junior high schools. The subjects were recruited from the Special Needs Education Longitudinal Study of Taiwan. The result of the Confirmatory Factor Analyses reflects that there are two, three and five observed variables included in the…

  5. Focal-plane wavefront sensing with high-order adaptive optics systems

    NARCIS (Netherlands)

    Korkiakoski, V.; Keller, C.U.; Doelman, N.J.; Kenworthy, M.; Otten, G.; Verhaegen, M.

    2014-01-01

    We investigate methods to calibrate the non-common path aberrations at an adaptive optics system having a wavefront-correcting device working with an extremely high resolution (larger than 150x150 correcting elements). We use focal-plane images collected successively, the corresponding

  6. Large adaptive deformable membrane mirror with high actuator density: design and first prototypes

    NARCIS (Netherlands)

    Hamelinck, R.; Rosielle, N.; Steinbuch, M.; Doelman, N.J.

    2005-01-01

    A large adaptive deformable mirror with high actuator density is presented. The DM consists of a thin continuous membrane which acts as the correcting element. A grid of low voltage electro-magnetical push-pull actuators, - located in an actuator plate -, impose out-of-plane displacements in the

  7. Avoidant Attachment Style Indicates Job Adaptation of People with High Functional Autistic Spectrum Disorders

    Science.gov (United States)

    Yokotani, Kenji

    2011-01-01

    The aim of the present study was to investigate whether or not the avoidant attachment style indicates job adaptation of people with High Functional Autistic Spectrum Disorders (HFASD). HFASD are groups of developmental disorders characterized by impairment of social interaction and normal level of intelligence. Twenty-two people with HFASD…

  8. Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

    KAUST Repository

    Amer, Ranya A.

    2015-02-01

    Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

  9. Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    Ranya A. Amer

    2015-01-01

    Full Text Available Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt. Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

  10. Multiplicity and diversity of Plasmodium vivax infections in a highly endemic region in Papua New Guinea.

    Directory of Open Access Journals (Sweden)

    Cristian Koepfli

    2011-12-01

    Full Text Available Plasmodium vivax is highly endemic in the lowlands of Papua New Guinea and accounts for a large proportion of the malaria cases in children less than 5 years of age. We collected 2117 blood samples at 2-monthly intervals from a cohort of 268 children aged 1 to 4.5 years and estimated the diversity and multiplicity of P. vivax infection. All P. vivax clones were genotyped using the merozoite surface protein 1 F3 fragment (msp1F3 and the microsatellite MS16 as molecular markers. High diversity was observed with msp1F3 (H(E = 88.1% and MS16 (H(E = 97.8%. Of the 1162 P. vivax positive samples, 74% harbored multi-clone infections with a mean multiplicity of 2.7 (IQR = 1-3. The multiplicity of P. vivax infection increased slightly with age (P = 0.02, with the strongest increase in very young children. Intensified efforts to control malaria can benefit from knowledge of the diversity and MOI both for assessing the endemic situation and monitoring the effects of interventions.

  11. Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

    Science.gov (United States)

    Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

    2015-10-01

    This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic.

  12. Research of Smart Grid Cyber Architecture and Standards Deployment with High Adaptability for Security Monitoring

    DEFF Research Database (Denmark)

    Hu, Rui; Hu, Weihao; Chen, Zhe

    2015-01-01

    . It is significant to develop a security monitoring system. This paper discussed the cyber architecture of smart grid with high adaptability for security monitoring. An adaptable structure with Demilitarized Zone (DMZ) is proposed. Focusing on this network structure, the rational utilization of standards...... huge losses. Although OpenADR specificationsprovide continuous, secure and reliable two-way communications in application level defined in ISO model, which is also an open architecture for security is adopted by it and no specific or proprietary technologies is restricted to OpenADR itself...

  13. Importance of Diversity in the Oral Microbiota including Candida Species Revealed by High-Throughput Technologies

    Directory of Open Access Journals (Sweden)

    Tamaki Cho

    2014-01-01

    Full Text Available Taking advantage of high-throughput technologies, deep sequencing of the human microbiome has revealed commensal bacteria independent of the ability to culture them. The composition of the commensal microbiome is dependent on bacterial diversity and the state of the host regulated by the immune system. Candida species are well known as components of the commensal oral microbiota. Candida species frequently colonize and develop biofilms on medical devices like dentures and catheters. Therefore, Candida biofilm on dentures leads to a decrease in the bacterial diversity and then to a change in the composition of the oral microbiota. A disturbance in the balance between commensal bacteria and the host immune system results in a switch from a healthy state to a diseased state even in the limited oral niche.

  14. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

    Science.gov (United States)

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  15. The Effect of Mutual Coupling on a High Altitude Platform Diversity System Using Compact Antenna Arrays

    Directory of Open Access Journals (Sweden)

    Tommy Hult

    2010-01-01

    Full Text Available We analyze the destructive effects of mutual coupling and spatial correlation between the separate antenna elements on a combined diversity system consisting of multiple HAPs (High-Altitude Platforms employing various compact MIMO (Multiple-Input Multiple-Output antenna array configurations, in order to enhance the mutual information in HAP communication links. In addition, we assess the influence of the separation angle between HAPs on system performance, and determine the optimal separation angles that maximize the total mutual information of the system for various compact MIMO antennas. Simulation results show that although the mutual information is degraded by mutual coupling and spatial correlation, the proposed HAP diversity system still provides better performance compared to a nondiversity system for all tested scenarios.

  16. High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall.

    Science.gov (United States)

    Schmitt-Kopplin, Philippe; Gabelica, Zelimir; Gougeon, Régis D; Fekete, Agnes; Kanawati, Basem; Harir, Mourad; Gebefuegi, Istvan; Eckel, Gerhard; Hertkorn, Norbert

    2010-02-16

    Numerous descriptions of organic molecules present in the Murchison meteorite have improved our understanding of the early interstellar chemistry that operated at or just before the birth of our solar system. However, all molecular analyses were so far targeted toward selected classes of compounds with a particular emphasis on biologically active components in the context of prebiotic chemistry. Here we demonstrate that a nontargeted ultrahigh-resolution molecular analysis of the solvent-accessible organic fraction of Murchison extracted under mild conditions allows one to extend its indigenous chemical diversity to tens of thousands of different molecular compositions and likely millions of diverse structures. This molecular complexity, which provides hints on heteroatoms chronological assembly, suggests that the extraterrestrial chemodiversity is high compared to terrestrial relevant biological- and biogeochemical-driven chemical space.

  17. Specific and diversive curiosity and depression in junior high school students of divorced and nondivorced parents.

    Science.gov (United States)

    Kerr, J; Beer, J

    1992-08-01

    124 junior high school students (Grades 5 to 8) from a small school district in north central Kansas completed the Beck Depression Scale, the Maze test, and the Which-to-Discuss test. Background information, such as age, sex, grade, and marital status of parents, were also collected. There were no significant differences between boys and girls of divorced and nondivorced parents or across grades for scores on the Which-to-Discuss (specific curiosity) and depression, but boys scored significantly higher on the Maze test (diversive curiosity). No differences were noted between the students of divorced and nondivorced parents or across grades. Scores on Which-to-Discuss test and Maze test were not significantly correlated, but scores on one Maze test and depression correlated positively and significantly. When these students scored as more depressed, although in the normal range, they tended to score higher on diversive curiosity.

  18. Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.

    Science.gov (United States)

    Gollner, Sabine; Stuckas, Heiko; Kihara, Terue C; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

    2016-01-01

    Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid

  19. Waveform Design and Diversity for Advanced Space-Time Adaptive Processing and Multiple Input Multiple Output Systems

    Science.gov (United States)

    2012-08-01

    and P.-C. Ching, “Quasi-Maximum-Likelihood Multiuser Detection Using Semi-Definite Relaxation With Application to Synchronous CDMA ”, IEEE Transactions...86] J.C. Liberti Jr. and T.S. Rappaport, “Analytical results for capacity im- provements in CDMA ,” IEEE Transaction on Vehicular Technology, Vol. 43...no. 3, pp. 680 - 690, Aug. 1994. [87] S. Anderson, M. Millnert, M. Viberg, and B. Wahlberg, “An adaptive ar- ray for mobile communication systems

  20. Identifying areas of high herpetofauna diversity that are threatened by planned infrastructure projects in Spain.

    Science.gov (United States)

    Benayas, José M Rey; Montaña, Enrique De La; Belliure, Josabel; Eekhout, Xavier R

    2006-05-01

    A major task related to conservation is to predict if planned infrastructure projects are likely to threaten biodiversity. In this study we investigated the potential impact of planned infrastructure in Spain on amphibian and reptile species, two highly vulnerable groups given their limited dispersal and current situation of population decline. We used distribution data of both groups to identify areas of high herpetofauna diversity, and compared the locations of these areas with the locations of the planned road, high-speed train railway and water reservoir network. Four criteria were used for this identification: species richness, rarity, vulnerability, and a combined index of the three criteria. From a total of 1441 cells of 20 x 20 km, areas of high diversity were defined as those cells whose ranked values for the different criteria included either all species or all threatened species. The combined index provided the smallest number of cells needed to retain all threatened species (1.7 and 2.6% of the cells for amphibian and reptile species, respectively). Coincidences between these high diversity areas and cells including planned infrastructures-denominated 'alert planning units'-were 35.4% for amphibians and 31.2% for reptiles. Mitigation of the potential impacts would include actions such as barriers to animal access to roads and railways and ecoducts under these constructions. Our approach provides conservation authorities information that can be used to make decisions on habitat protection. A technique that identifies threats to herpetofauna before they occur is also likely to improve the chance of herpetofauna being protected.

  1. High altitude genetic adaptation in Tibetans: no role of increased hemoglobin-oxygen affinity.

    Science.gov (United States)

    Tashi, Tsewang; Feng, Tang; Koul, Parvaiz; Amaru, Ricardo; Hussey, Dottie; Lorenzo, Felipe R; RiLi, Ge; Prchal, Josef T

    2014-01-01

    High altitude exerts selective evolutionary pressure primarily due to its hypoxic environment, resulting in multiple adaptive responses. High hemoglobin-oxygen affinity is postulated to be one such adaptive change, which has been reported in Sherpas of the Himalayas. Tibetans have lived on the Qinghai-Tibetan plateau for thousands of years and have developed unique phenotypes, such as protection from polycythemia which has been linked to PDH2 mutation, resulting in the downregulation of the HIF pathway. In order to see if Tibetans also developed high hemoglobin-oxygen affinity as a part of their genetic adaptation, we conducted this study assessing hemoglobin-oxygen affinity and their fetal hemoglobin levels in Tibetan subjects from 3 different altitudes. We found normal hemoglobin-oxygen affinity in all subjects, fetal hemoglobin levels were normal in all except one and no hemoglobin variants in any of the subjects. We conclude that increased hemoglobin-oxygen affinity or increased fetal hemoglobin are not adaptive phenotypes of the Tibetan highlanders. Published by Elsevier Inc.

  2. Supporting Common Core-Driven Curriculum Adaptations for High School Algebra

    OpenAIRE

    Johnson, Raymond; Leary, Heather; Penuel, William R.

    2016-01-01

    The adoption of the Common Core State Standards for Mathematics (CCSSM) has created a need for many teachers and school districts to adapt their current curricular materials. Using the methods of design-based implementation research (Penuel et al., 2011), this project partnered with high school algebra teachers, district curriculum staff, and university researchers to support teachers in the selection and use of high-quality mathematical tasks. This participatory design process yielded a set ...

  3. [Phospholipids and structural modification of tissues and cell membranes for adaptation in high altitude mountains].

    Science.gov (United States)

    Iakovlev, V M; Vishnevskiĭ, A A; Shanazarov, A S

    2012-01-01

    The nature of the impact of physical factors of high altitudes (3200 m) on the lipids of tissues and membranes of animals was researched. It was established that the adaptation process in Wistar rats was followed by peroxide degradation and subsequent modification of the phospholipids' structure of tissues and microsomal membranes. Adaptive phospholipids reconstruction takes place in microsomal membranes in the tissues of the lungs, brain, liver and skeletal muscles. Together with this, the amount of phosphatidylinositol and phosphatidic acid accumulates, indicating that the hydrolysis of phosphatidylinositol-4, 5 biphosphate to diacylglycerol and secondary messenger--inositol triphosphate, occurs. A decrease in temperature adaptation (+10 degrees C) leads to a more noticeable shift in peroxide oxidation of lipids, phospholipid structure in the tissues and membranes rather than adaptation in thermoneutral conditions (+30 degrees C). Modification of lipid composition of tissues and cell membranes in the highlands obviously increases the adaptive capabilities of cells of the whole body: physical performance and resistance to hypoxia increases in animals.

  4. Local adaptation in Trinidadian guppies alters stream ecosystem structure at landscape scales despite high environmental variability

    Science.gov (United States)

    Simon, Troy N.; Bassar, Ronald D.; Binderup, Andrew J.; Flecker, Alex S.; Freeman, Mary C.; Gilliam, James F.; Marshall, Michael C.; Thomas, Steve A.; Travis, Joseph; Reznick, David N.; Pringle, Catherine M.

    2017-01-01

    While previous studies have shown that evolutionary divergence alters ecological processes in small-scale experiments, a major challenge is to assess whether such evolutionary effects are important in natural ecosystems at larger spatial scales. At the landscape scale, across eight streams in the Caroni drainage, we found that the presence of locally adapted populations of guppies (Poecilia reticulata) is associated with reduced algal biomass and increased invertebrate biomass, while the opposite trends were true in streams with experimentally introduced populations of non-locally adapted guppies. Exclusion experiments conducted in two separate reaches of a single stream showed that guppies with locally adapted phenotypes significantly reduced algae with no effect on invertebrates, while non-adapted guppies had no effect on algae but significantly reduced invertebrates. These divergent effects of phenotype on stream ecosystems are comparable in strength to the effects of abiotic factors (e.g., light) known to be important drivers of ecosystem condition. They also corroborate the results of previous experiments conducted in artificial streams. Our results demonstrate that local adaptation can produce phenotypes with significantly different effects in natural ecosystems at a landscape scale, within a tropical watershed, despite high variability in abiotic factors: five of the seven physical and chemical parameters measured across the eight study streams varied by more than one order of magnitude. Our findings suggest that ecosystem structure is, in part, an evolutionary product and not simply an ecological pattern.

  5. A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition.

    Science.gov (United States)

    Li, Wei; Wang, Mengmeng; Bian, Xiaomeng; Guo, Jiajia; Cai, Lei

    2016-01-01

    The intertidal region is one of the most dynamic environments in the biosphere, which potentially supports vast biodiversity. Fungi have been found to play important roles in marine ecosystems, e.g., as parasites or symbionts of plants and animals, and as decomposers of organic materials. The fungal diversity in intertidal region, however, remains poorly understood. In this study, sediment samples from various intertidal habitats of Chinese seas were collected and investigated for determination of fungal community and spatial distribution. Through ribosomal RNA internal transcribed spacer-2 (ITS2) metabarcoding, a high-level fungal diversity was revealed, as represented by 6,013 OTUs that spanned six phyla, 23 classes, 84 orders and 526 genera. The presence of typical decomposers (e.g., Corollospora in Ascomycota and Lepiota in Basidiomycota) and pathogens (e.g., Olpidium in Chytriomycota, Actinomucor in Zygomycota and unidentified Rozellomycota spp.), and even mycorrhizal fungi (e.g., Glomus in Glomeromycota) indicated a complicated origin of intertidal fungi. Interestingly, a small proportion of sequences were classified to obligate marine fungi (e.g., Corollospora, Lignincola, Remispora, Sigmoidea). Our data also showed that the East China Sea significantly differed from other regions in terms of species richness and community composition, indicating a profound effect of the huge discharge of the Yangtze River. No significant difference in fungal communities was detected, however, among habitat types (i.e., aquaculture, dock, plant, river mouth and tourism). These observations raise further questions on adaptation of these members to environments and the ecological functions they probably perform.

  6. A highly adaptive magnetorheological fluid robotic leg for efficient terrestrial locomotion

    Science.gov (United States)

    Jiang, Nan; Sun, Shuaishuai; Ouyang, Yiming; Xu, Min; Li, Weihua; Zhang, Shiwu

    2016-09-01

    To survive in nature, animals adjust the characteristics of their legs or fins to adapt the motion to their environment. Inspired by the locomotion of animals, a study on the tunable stiffness and damping of a leg will help in the development of intelligent locomotion robots. In this paper we report on the development and experiment of a novel and simple robotic leg that can be adapted to the environment via a smart magnetorheological fluid (MRF). The robotic leg consists of a rotation MRF damper, a torsional spring, a ‘foot’ and a ‘leg’. The curved part of the ‘foot’ makes contact with the grounds while the other end is linked to an outer cylinder of the MRF damper with an inelastic cable. The variable force arm rising from the MRF damper and the torsional spring can help the leg adapt to a changing environment. The characteristics of the MRF damper have been investigated and a model is built to describe its mechanical features when different currents are applied to the MRF damper. A test on a linear dynamic test instrument has been conducted to verify the accuracy of the model. The robotic leg is installed in a locomotion platform to investigate the speed of its locomotion and the cost of the transport; the result demonstrated the feasibility and adaptability of the leg when walking on hard terrain. Its simple structure, high adaptability, and easy control of the MRF leg helped in the design and development of a high performance field robot that can adapt to various environments.

  7. Adaptation to Life in the High Andes: Nocturnal Oxyhemoglobin Saturation in Early Development.

    Science.gov (United States)

    Hill, Catherine Mary; Baya, Ana; Gavlak, Johanna; Carroll, Annette; Heathcote, Kate; Dimitriou, Dagmara; L'Esperance, Veline; Webster, Rebecca; Holloway, John; Virues-Ortega, Javier; Kirkham, Fenella Jane; Bucks, Romola Starr; Hogan, Alexandra Marie

    2016-05-01

    Physiological adaptation to high altitude hypoxia may be impaired in Andeans with significant European ancestry. The respiratory 'burden' of sleep may challenge adaptation, leading to relative nocturnal hypoxia. Developmental aspects of sleep-related breathing in high-altitude native children have not previously been reported. We aimed to determine the influence of development on diurnal-nocturnal oxyhemoglobin differences in children living at high altitude. This was a cross-sectional, observational study. Seventy-five healthy Bolivian children aged 6 mo to 17 y, native to low altitude (500 m), moderate high altitude (2,500 m), and high altitude (3,700 m) were recruited. Daytime resting pulse oximetry was compared to overnight recordings using Masimo radical oximeters. Genetic ancestry was determined from DNA samples. Children had mixed European/Amerindian ancestry, with no significant differences between altitudes. Sixty-two participants had ≥ 5 h of nocturnal, artifact-free data. As predicted, diurnal mean oxyhemoglobin saturation decreased across altitudes (infants and children, both P childhood, with no further change during adolescence. Physiological adaptation to high-altitude living in native Andeans is unlikely to compensate for the significant differences we observed between diurnal and nocturnal oxyhemoglobin saturation, most marked in infancy. This vulnerability to sleep-related hypoxia in early childhood has potential lifespan implications. Future studies should characterize the sleep- related respiratory physiology underpinning our observations. © 2016 Associated Professional Sleep Societies, LLC.

  8. Physiological Adaptations to Hypoxic vs. Normoxic Training during Intermittent Living High.

    Science.gov (United States)

    De Smet, Stefan; van Herpt, Paul; D'Hulst, Gommaar; Van Thienen, Ruud; Van Leemputte, Marc; Hespel, Peter

    2017-01-01

    In the setting of "living high," it is unclear whether high-intensity interval training (HIIT) should be performed "low" or "high" to stimulate muscular and performance adaptations. Therefore, 10 physically active males participated in a 5-week "live high-train low or high" program (TR), whilst eight subjects were not engaged in any altitude or training intervention (CON). Five days per week (~15.5 h per day), TR was exposed to normobaric hypoxia simulating progressively increasing altitude of ~2,000-3,250 m. Three times per week, TR performed HIIT, administered as unilateral knee-extension training, with one leg in normobaric hypoxia (~4,300 m; TR HYP ) and with the other leg in normoxia (TR NOR ). "Living high" elicited a consistent elevation in serum erythropoietin concentrations which adequately predicted the increase in hemoglobin mass ( r = 0.78, P 0.05). Muscle oxygenation during training was lower in TR HYP vs. TR NOR ( P 0.05). In conclusion, muscular and performance adaptations were largely similar following normoxic vs. hypoxic HIIT. However, hypoxic HIIT stimulated adaptations in isometric strength and muscle perfusion during intermittent sprinting.

  9. The last polar dinosaurs: high diversity of latest Cretaceous arctic dinosaurs in Russia.

    Science.gov (United States)

    Godefroit, Pascal; Golovneva, Lina; Shchepetov, Sergei; Garcia, Géraldine; Alekseev, Pavel

    2009-04-01

    A latest Cretaceous (68 to 65 million years ago) vertebrate microfossil assemblage discovered at Kakanaut in northeastern Russia reveals that dinosaurs were still highly diversified in Arctic regions just before the Cretaceous-Tertiary mass extinction event. Dinosaur eggshell fragments, belonging to hadrosaurids and non-avian theropods, indicate that at least several latest Cretaceous dinosaur taxa could reproduce in polar region and were probably year-round residents of high latitudes. Palaeobotanical data suggest that these polar dinosaurs lived in a temperate climate (mean annual temperature about 10 degrees C), but the climate was apparently too cold for amphibians and ectothermic reptiles. The high diversity of Late Maastrichtian dinosaurs in high latitudes, where ectotherms are absent, strongly questions hypotheses according to which dinosaur extinction was a result of temperature decline, caused or not by the Chicxulub impact.

  10. Novel and highly diverse fungal endophytes in soybean revealed by the consortium of two different techniques.

    Science.gov (United States)

    de Souza Leite, Tiago; Cnossen-Fassoni, Andréia; Pereira, Olinto Liparini; Mizubuti, Eduardo Seiti Gomide; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2013-02-01

    Fungal endophytes were isolated from the leaves of soybean cultivars in Brazil using two different isolation techniques - fragment plating and the innovative dilution-to-extinction culturing - to increase the species richness, frequency of isolates and diversity. A total of 241 morphospecies were obtained corresponding to 62 taxa that were identified by analysis of the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). The Phylum Ascomycota predominated, representing 99% and 95.2% of isolates in the Monsoy and Conquista cultivars, respectively, whereas the Phylum Basidiomycota represented 1% and 4.8% of isolates, respectively. The genera Ampelomyces, Annulohypoxylon, Guignardia, Leptospora, Magnaporthe, Ophiognomonia, Paraconiothyrium, Phaeosphaeriopsis, Rhodotorula, Sporobolomyces, and Xylaria for the first time were isolated from soybean; this suggests that soybean harbours novel and highly diverse fungi. The yeasts genera Rhodotorula and Sporobolomyces (subphylum Pucciniomycotina) represent the Phylum Basidiomycota. The species richness was greater when both isolation techniques were used. The diversity of fungal endophytes was similar in both cultivars when the same isolation technique was used except for Hill's index, N1. The use of ITS region sequences allowed the isolates to be grouped according to Order, Class and Phylum. Ampelomyces, Chaetomium, and Phoma glomerata are endophytic species that may play potential roles in the biological control of soybean pathogens. This study is one of the first to apply extinction-culturing to isolate fungal endophytes in plant leaves, thus contributing to the development and improvement of this technique for future studies.

  11. [Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

    Science.gov (United States)

    Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

    2015-07-01

    To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

  12. A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity.

    Science.gov (United States)

    Ren, Yi; Palusiak, Agata; Wang, Wei; Wang, Yi; Li, Xiao; Wei, Huiting; Kong, Qingke; Rozalski, Antoni; Yao, Zhi; Wang, Quan

    2016-01-01

    Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, causing cystitis, pyelonephritis, and renal failure. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTIs. Accurate and rapid discrimination of UPEC lineages is useful for epidemiological surveillance. Fimbriae are necessary for the adherence of UPEC strains to host uroepithelia, and seem to be abundant and diverse in UPEC strains. By analyzing all the possible fimbrial operons in UPEC strains, we found that closely related strains had similar types of chaperone-usher fimbriae, and the diversity of fimbrial genes was higher than that of multilocus sequence typing (MLST) genes. A typing assay based on the polymorphism of four gene sequences (three fimbrial genes and one housekeeping gene) and the diversity of fimbriae present was developed. By comparison with the MLST, whole-genome sequence (WGS) and fumC/fimH typing methods, this was shown to be accurate and have high resolution, and it was also relatively inexpensive and easy to perform. The assay can supply more discriminatory information for UPEC lineages, and have the potential to be applied in epidemiological surveillance of UPEC isolates.

  13. AfroDb: a select highly potent and diverse natural product library from African medicinal plants.

    Directory of Open Access Journals (Sweden)

    Fidele Ntie-Kang

    Full Text Available Computer-aided drug design (CADD often involves virtual screening (VS of large compound datasets and the availability of such is vital for drug discovery protocols. We assess the bioactivity and "drug-likeness" of a relatively small but structurally diverse dataset (containing >1,000 compounds from African medicinal plants, which have been tested and proven a wide range of biological activities. The geographical regions of collection of the medicinal plants cover the entire continent of Africa, based on data from literature sources and information from traditional healers. For each isolated compound, the three dimensional (3D structure has been used to calculate physico-chemical properties used in the prediction of oral bioavailability on the basis of Lipinski's "Rule of Five". A comparative analysis has been carried out with the "drug-like", "lead-like", and "fragment-like" subsets, as well as with the Dictionary of Natural Products. A diversity analysis has been carried out in comparison with the ChemBridge diverse database. Furthermore, descriptors related to absorption, distribution, metabolism, excretion and toxicity (ADMET have been used to predict the pharmacokinetic profile of the compounds within the dataset. Our results prove that drug discovery, beginning with natural products from the African flora, could be highly promising. The 3D structures are available and could be useful for virtual screening and natural product lead generation programs.

  14. MHC variability supports dog domestication from a large number of wolves: high diversity in Asia.

    Science.gov (United States)

    Niskanen, A K; Hagström, E; Lohi, H; Ruokonen, M; Esparza-Salas, R; Aspi, J; Savolainen, P

    2013-01-01

    The process of dog domestication is still somewhat unresolved. Earlier studies indicate that domestic dogs from all over the world have a common origin in Asia. So far, major histocompatibility complex (MHC) diversity has not been studied in detail in Asian dogs, although high levels of genetic diversity are expected at the domestication locality. We sequenced the second exon of the canine MHC gene DLA-DRB1 from 128 Asian dogs and compared our data with a previously published large data set of MHC alleles, mostly from European dogs. Our results show that Asian dogs have a higher MHC diversity than European dogs. We also estimated that there is only a small probability that new alleles have arisen by mutation since domestication. Based on the assumption that all of the currently known 102 DLA-DRB1 alleles come from the founding wolf population, we simulated the number of founding wolf individuals. Our simulations indicate an effective population size of at least 500 founding wolves, suggesting that the founding wolf population was large or that backcrossing has taken place.

  15. High-resolution retinal imaging using adaptive optics and Fourier-domain optical coherence tomography

    Science.gov (United States)

    Olivier, Scot S.; Werner, John S.; Zawadzki, Robert J.; Laut, Sophie P.; Jones, Steven M.

    2010-09-07

    This invention permits retinal images to be acquired at high speed and with unprecedented resolution in three dimensions (4.times.4.times.6 .mu.m). The instrument achieves high lateral resolution by using adaptive optics to correct optical aberrations of the human eye in real time. High axial resolution and high speed are made possible by the use of Fourier-domain optical coherence tomography. Using this system, we have demonstrated the ability to image microscopic blood vessels and the cone photoreceptor mosaic.

  16. Rate-adaptive BCH coding for Slepian-Wolf coding of highly correlated sources

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Salmistraro, Matteo; Larsen, Knud J.

    2012-01-01

    This paper considers using BCH codes for distributed source coding using feedback. The focus is on coding using short block lengths for a binary source, X, having a high correlation between each symbol to be coded and a side information, Y, such that the marginal probability of each symbol, Xi in X......, given Y is highly skewed. In the analysis, noiseless feedback and noiseless communication are assumed. A rate-adaptive BCH code is presented and applied to distributed source coding. Simulation results for a fixed error probability show that rate-adaptive BCH achieves better performance than LDPCA (Low......-Density Parity-Check Accumulate) codes for high correlation between source symbols and the side information....

  17. Natural Selection on Genes Related to Cardiovascular Health in High-Altitude Adapted Andeans.

    Science.gov (United States)

    Crawford, Jacob E; Amaru, Ricardo; Song, Jihyun; Julian, Colleen G; Racimo, Fernando; Cheng, Jade Yu; Guo, Xiuqing; Yao, Jie; Ambale-Venkatesh, Bharath; Lima, João A; Rotter, Jerome I; Stehlik, Josef; Moore, Lorna G; Prchal, Josef T; Nielsen, Rasmus

    2017-11-02

    The increase in red blood cell mass (polycythemia) due to the reduced oxygen availability (hypoxia) of residence at high altitude or other conditions is generally thought to be beneficial in terms of increasing tissue oxygen supply. However, the extreme polycythemia and accompanying increased mortality due to heart failure in chronic mountain sickness most likely reduces fitness. Tibetan highlanders have adapted to high altitude, possibly in part via the selection of genetic variants associated with reduced polycythemic response to hypoxia. In contrast, high-altitude-adapted Quechua- and Aymara-speaking inhabitants of the Andean Altiplano are not protected from high-altitude polycythemia in the same way, yet they exhibit other adaptive features for which the genetic underpinnings remain obscure. Here, we used whole-genome sequencing to scan high-altitude Andeans for signals of selection. The genes showing the strongest evidence of selection-including BRINP3, NOS2, and TBX5-are associated with cardiovascular development and function but are not in the response-to-hypoxia pathway. Using association mapping, we demonstrated that the haplotypes under selection are associated with phenotypic variations related to cardiovascular health. We hypothesize that selection in response to hypoxia in Andeans could have vascular effects and could serve to mitigate the deleterious effects of polycythemia rather than reduce polycythemia itself. Copyright © 2017. Published by Elsevier Inc.

  18. THE ABUNDANCE, DIVERSITY AND METABOLIC FOOTPRINT OF SOIL NEMATODES IS HIGHEST IN HIGH ELEVATION ALPINE GRASSLANDS

    Directory of Open Access Journals (Sweden)

    Alan Kergunteuil

    2016-07-01

    Full Text Available Nematodes are key components of soil biodiversity and represent valuable bio-indicators of soil food webs. Numerous community indices have been developed in order to track variations in soil ecosystem processes, but their use is mainly restricted to anthropogenic stresses. In this study, we propose to expand the use of nematodes’ derived ecological indices in order to shed light on variations of soil food webs in natural systems distributed along elevation gradients. For this purpose, we aimed at determining how elevation affects the community structure and the trophic diversity by studying the abundance, the composition and the functional diversity of nematode communities. Nematode communities were sampled every 200 m across five transects that span about 2000 m in elevation in the Alps. To understand the underlying ecological parameters driving these patterns we studied both abiotic factors (soil properties and biotic factors (trophic links, relationships with plant diversity. We found that (1 nematode abundance increases with elevation of lowland forests and alpine meadows; (2 differences in nematodes communities rely on habitat-specific functional diversity (e.g. tolerance to harsh environments, colonizer/persister status while most trophic groups are ubiquitous; and (3 the metabolic footprint of the complete nematode community increases with elevation. We thus conclude that the contribution of soil dwelling nematodes to belowground ecosystem processes, including carbon and energy flow, is stronger at high elevation. The resulting cascading effects on the soil food web structure are discussed from an ecosystem functioning perspective. Overall, this study highlights the importance of nematodes in soil ecosystems and brings insights in their enhanced role along ecological gradients.

  19. Neuropsychological presentation and adaptive skills in high-functioning adolescents with visual impairment: A preliminary investigation.

    Science.gov (United States)

    Greenaway, R; Pring, L; Schepers, A; Isaacs, D P; Dale, N J

    2017-01-01

    Studies in infants and young children with congenital visual impairment (VI) have indicated early developmental vulnerabilities, conversely research with older children and adults have highlighted areas of cognitive strength. A minimal amount is known, however, about the possible combination of strengths and weaknesses in adolescence, and this present study therefore aims to explore the neuropsychological presentation and adaptive behavior profile in high-functioning adolescents with congenital VI. Participants completed a battery of commonly used neuropsychological measures assessing memory, executive function, and attention. The measures utilized focused on auditory neuropsychological function, because only subtests that could be completed with auditory administration were suitable for this sample. Parents completed standardized measures of adaptive behavior, executive function, and social communication. Compared to aged-based norms for normal sight, adolescents with VI demonstrated strengths in aspects of working memory and verbal memory. Furthermore, performance across the neuropsychological battery was within or above the average range for the majority of the sample. In contrast, parent-report measures indicated areas of weakness in adaptive functioning, social communication, and behavioral executive functioning. Overall, this study provides preliminary evidence that relative to fully sighted peers, high-functioning adolescents with VI present with an uneven profile of cognitive and adaptive skills, which has important implications for assessment and intervention.

  20. A constrained Delaunay discretization method for adaptively meshing highly discontinuous geological media

    Science.gov (United States)

    Wang, Yang; Ma, Guowei; Ren, Feng; Li, Tuo

    2017-12-01

    A constrained Delaunay discretization method is developed to generate high-quality doubly adaptive meshes of highly discontinuous geological media. Complex features such as three-dimensional discrete fracture networks (DFNs), tunnels, shafts, slopes, boreholes, water curtains, and drainage systems are taken into account in the mesh generation. The constrained Delaunay triangulation method is used to create adaptive triangular elements on planar fractures. Persson's algorithm (Persson, 2005), based on an analogy between triangular elements and spring networks, is enriched to automatically discretize a planar fracture into mesh points with varying density and smooth-quality gradient. The triangulated planar fractures are treated as planar straight-line graphs (PSLGs) to construct piecewise-linear complex (PLC) for constrained Delaunay tetrahedralization. This guarantees the doubly adaptive characteristic of the resulted mesh: the mesh is adaptive not only along fractures but also in space. The quality of elements is compared with the results from an existing method. It is verified that the present method can generate smoother elements and a better distribution of element aspect ratios. Two numerical simulations are implemented to demonstrate that the present method can be applied to various simulations of complex geological media that contain a large number of discontinuities.

  1. Classroom Management Strategies of Highly Effective Teachers in Diverse Middle Schools: Be Strict and Calm, Not Mean

    Science.gov (United States)

    McGregor, Katheryne L.

    2012-01-01

    This qualitative research study investigated and identified the classroom management strategies of 12 highly effective middle school teachers who served diverse student populations at two different school sites. In addition, this research explored the beliefs and experiences of 305 diverse middle school students regarding their experiences with…

  2. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm.

    Science.gov (United States)

    Jollivet, Didier; Mary, Jean; Gagnière, Nicolas; Tanguy, Arnaud; Fontanillas, Eric; Boutet, Isabelle; Hourdez, Stéphane; Segurens, Béatrice; Weissenbach, Jean; Poch, Olivier; Lecompte, Odile

    2012-01-01

    Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively 'high' temperatures and thus a novelty in thermophilic

  3. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm.

    Directory of Open Access Journals (Sweden)

    Didier Jollivet

    Full Text Available Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively 'high' temperatures and thus a novelty

  4. A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

    Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

  5. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  6. Phylogenetic analysis reveals positive correlations between adaptations to diverse hosts in a group of pathogen-like herbivores.

    Science.gov (United States)

    Peterson, Daniel A; Hardy, Nate B; Morse, Geoffrey E; Stocks, Ian C; Okusu, Akiko; Normark, Benjamin B

    2015-10-01

    A jack of all trades can be master of none-this intuitive idea underlies most theoretical models of host-use evolution in plant-feeding insects, yet empirical support for trade-offs in performance on distinct host plants is weak. Trade-offs may influence the long-term evolution of host use while being difficult to detect in extant populations, but host-use evolution may also be driven by adaptations for generalism. Here we used host-use data from insect collection records to parameterize a phylogenetic model of host-use evolution in armored scale insects, a large family of plant-feeding insects with a simple, pathogen-like life history. We found that a model incorporating positive correlations between evolutionary changes in host performance best fit the observed patterns of diaspidid presence and absence on nearly all focal host taxa, suggesting that adaptations to particular hosts also enhance performance on other hosts. In contrast to the widely invoked trade-off model, we advocate a "toolbox" model of host-use evolution in which armored scale insects accumulate a set of independent genetic tools, each of which is under selection for a single function but may be useful on multiple hosts. © 2015 The Author(s).

  7. Diversion assumptions for high-powered research reactors. ISPO C-50 Phase 1

    Energy Technology Data Exchange (ETDEWEB)

    Binford, F.T.

    1984-01-01

    This study deals with diversion assumptions for high-powered research reactors -- specifically, MTR fuel; pool- or tank-type research reactors with light-water moderator; and water, beryllium, or graphite reflectors, and which have a power level of 25 MW(t) or more. The objective is to provide assistance to the IAEA in documentation of criteria and inspection observables related to undeclared plutonium production in the reactors described above, including: criteria for undeclared plutonium production, necessary design information for implementation of these criteria, verification guidelines including neutron physics and heat transfer, and safeguards measures to facilitate the detection of undeclared plutonium production at large research reactors.

  8. Characterization of the Prokaryotic Diversity in Cold Saline Perennial Springs of the Canadian High Arctic▿

    OpenAIRE

    Perreault, Nancy N.; Andersen, Dale T.; Pollard, Wayne H.; Greer, Charles W.; Whyte, Lyle G.

    2007-01-01

    The springs at Gypsum Hill and Colour Peak on Axel Heiberg Island in the Canadian Arctic originate from deep salt aquifers and are among the few known examples of cold springs in thick permafrost on Earth. The springs discharge cold anoxic brines (7.5 to 15.8% salts), with a mean oxidoreduction potential of −325 mV, and contain high concentrations of sulfate and sulfide. We surveyed the microbial diversity in the sediments of seven springs by denaturing gradient gel electrophoresis (DGGE) and...

  9. Does the globally invasive marine angiosperm, Halophila stipulacea, have high genetic diversity or unique mutations?

    Science.gov (United States)

    Chiquillo, K.; Campese, L.; Barber, P. H.; Willette, D. A.

    2016-02-01

    Seagrasses are important primary producers in many marine ecosystems, and support a wide diversity of marine life. However, invasive seagrasses like Halophila stipulacea can have pronounced negative impacts on an ecosystem by displacing native seagrasses and changing the community composition of the reef. Endemic to the Red Sea, Persian Gulf and Indian Ocean, Halophila stipulacea has become invasive in the Mediterranean and Caribbean Seas, presumably as a result of the opening of the Suez Canal and international ship traffic. However, it is unclear why this marine angiosperm has become invasive in parts of its range and not others. It is hypothesized that invasive forms may have evolved rapidly in response to natural selection in new and novel environments. Alternatively, genetic variation of introduced populations may be uniquely suited to thrive in regions where it is invasive. In this study, we use RAD next-generation sequencing to screen thousands of SNPs to investigate the genetic basis of adaptation in both native and invasive populations. We test whether genes under selection in the native range are the same as in the invasive range, or whether new genes have arisen with the invasion of each marine basin. The comparison of SNP frequencies unique among basins and environmental variables will aid in predicting new areas of invasion, assisting in improved management strategies to combat this invasive seagrass.

  10. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  11. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    Science.gov (United States)

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  12. Assessment of adaptation measures to high-mountain risks in Switzerland under climate uncertainties

    Science.gov (United States)

    Muccione, Veruska; Lontzek, Thomas; Huggel, Christian; Ott, Philipp; Salzmann, Nadine

    2015-04-01

    The economic evaluation of different adaptation options is important to support policy-makers that need to set priorities in the decision-making process. However, the decision-making process faces considerable uncertainties regarding current and projected climate impacts. First, physical climate and related impact systems are highly complex and not fully understood. Second, the further we look into the future, the more important the emission pathways become, with effects on the frequency and severity of climate impacts. Decision on adaptation measures taken today and in the future must be able to adequately consider the uncertainties originating from the different sources. Decisions are not taken in a vacuum but always in the context of specific social, economic, institutional and political conditions. Decision finding processes strongly depend on the socio-political system and usually have evolved over some time. Finding and taking decisions in the respective socio-political and economic context multiplies the uncertainty challenge. Our presumption is that a sound assessment of the different adaptation options in Switzerland under uncertainty necessitates formulating and solving a dynamic, stochastic optimization problem. Economic optimization models in the field of climate change are not new. Typically, such models are applied for global-scale studies but barely for local-scale problems. In this analysis, we considered the case of the Guttannen-Grimsel Valley, situated in the Swiss Bernese Alps. The alpine community has been affected by high-magnitude, high-frequency debris flows that started in 2009 and were historically unprecendented. They were related to thaw of permafrost in the rock slopes of Ritzlihorn and repeated rock fall events that accumulated at the debris fan and formed a sediment source for debris flows and were transported downvalley. An important transit road, a trans-European gas pipeline and settlements were severely affected and partly

  13. High-speed adaptive optics line scan confocal retinal imaging for human eye.

    Science.gov (United States)

    Lu, Jing; Gu, Boyu; Wang, Xiaolin; Zhang, Yuhua

    2017-01-01

    Continuous and rapid eye movement causes significant intraframe distortion in adaptive optics high resolution retinal imaging. To minimize this artifact, we developed a high speed adaptive optics line scan confocal retinal imaging system. A high speed line camera was employed to acquire retinal image and custom adaptive optics was developed to compensate the wave aberration of the human eye's optics. The spatial resolution and signal to noise ratio were assessed in model eye and in living human eye. The improvement of imaging fidelity was estimated by reduction of intra-frame distortion of retinal images acquired in the living human eyes with frame rates at 30 frames/second (FPS), 100 FPS, and 200 FPS. The device produced retinal image with cellular level resolution at 200 FPS with a digitization of 512×512 pixels/frame in the living human eye. Cone photoreceptors in the central fovea and rod photoreceptors near the fovea were resolved in three human subjects in normal chorioretinal health. Compared with retinal images acquired at 30 FPS, the intra-frame distortion in images taken at 200 FPS was reduced by 50.9% to 79.7%. We demonstrated the feasibility of acquiring high resolution retinal images in the living human eye at a speed that minimizes retinal motion artifact. This device may facilitate research involving subjects with nystagmus or unsteady fixation due to central vision loss.

  14. High Dynamic Range adaptive ΔΣ-based Focal Plane Array architecture

    KAUST Repository

    Yao, Shun

    2012-10-16

    In this paper, an Adaptive Delta-Sigma based architecture for High Dynamic Range (HDR) Focal Plane Arrays is presented. The noise shaping effect of the Delta-Sigma modulation in the low end, and the distortion noise induced in the high end of Photo-diode current were analyzed in detail. The proposed architecture can extend the DR for about 20N log2 dB at the high end of Photo-diode current with an N bit Up-Down counter. At the low end, it can compensate for the larger readout noise by employing Extended Counting. The Adaptive Delta-Sigma architecture employing a 4-bit Up-Down counter achieved about 160dB in the DR, with a Peak SNR (PSNR) of 80dB at the high end. Compared to the other HDR architectures, the Adaptive Delta-Sigma based architecture provides the widest DR with the best SNR performance in the extended range.

  15. Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen

    Directory of Open Access Journals (Sweden)

    Takishita Kiyotaka

    2012-02-01

    Full Text Available Abstract Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes. Reviewers This article was reviewed by Eric Bapteste and Eugene Koonin.

  16. High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone

    Directory of Open Access Journals (Sweden)

    Dafae Foday

    2008-06-01

    Full Text Available Abstract Background Among tuberculosis (TB high incidence regions, Sub-Saharan Africa is particularly affected with approx. 1.6 million new cases every year. Besides this dramatic situation, data on the diversity of Mycobacterium tuberculosis complex (MTBC strains causing this epidemic in this area are only sparsely available. Here we analyzed the population structure of strains from Sierra Leone with a special focus on the prevalence of M. africanum. Results A total of 97 strains isolated from smear positive cases registered for re-treatment in the Western Area and Kenema districts in years 2003/2004 were investigated by susceptibility testing (first line drugs and molecular typing (IS6110 fingerprinting, spoligotyping, and MIRU-VNTR typing. Among the strains analyzed, 32 were resistant to isoniazid, and 11 were multidrug resistant (at least resistant to isoniazid and rifampin. The population diversity was high with two previously described M. africanum lineages (West African-1, n = 6; West African-2, n = 17 and seven M. tuberculosis lineages (Haarlem, n = 14; LAM, n = 15; EAI, n = 4; Beijing, n = 4; S-type, n = 4, X-type, n = 1; Cameroon, n = 4. Furthermore, two new M. tuberculosis genotypes Sierra Leone-1 (n = 7 and -2 (n = 10 were found. Strain classification according to a 7 bp deletion in pks1/15 revealed that the majority of M. tuberculosis strains belonged to the Euro American lineage (66 out of 74. Conclusion Resistance rates in Sierra Leone have reached an alarming level. The population structure of MTBC strains shows an intriguing diversity raising the question of possible consequences for TB epidemic and for the introduction of new diagnostic tests or treatment strategies in West Africa.

  17. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

    Directory of Open Access Journals (Sweden)

    Lukasz eDziewit

    2015-03-01

    Full Text Available The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland. It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m Lubin mine were taken and twenty bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e. they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.

  18. Seed arrival and ecological filters interact to assemble high-diversity plant communities.

    Science.gov (United States)

    Myers, Jonathan A; Harms, Kyle E

    2011-03-01

    Two prominent mechanisms proposed to structure biodiversity are niche-based ecological filtering and chance arrival of propagules from the species pool. Seed arrival is hypothesized to play a particularly strong role in high-diversity plant communities with large potential species pools and many rare species, but few studies have explored how seed arrival and local ecological filters interactively assemble species-rich communities in space and time. We experimentally manipulated seed arrival and multiple ecological filters in high-diversity, herbaceous-dominated groundcover communities in longleaf pine savannas, which contain the highest small-scale species richness in North America (up to > 40 species/m2). We tested three hypotheses: (1) local communities constitute relatively open-membership assemblages, in which increased seed arrival from the species pool strongly increases species richness; (2) ecological filters imposed by local fire intensity and soil moisture influence recruitment and richness of immigrating species; and (3) ecological filters increase similarity in the composition of immigrating species. In a two-year factorial field experiment, we manipulated local fire intensity by increasing pre-fire fuel loads, soil moisture using rain shelters and irrigation, and seed arrival by adding seeds from the local species pool. Seed arrival increased species richness regardless of fire intensity and soil moisture but interacted with both ecological filters to influence community assembly. High-intensity fire decreased richness of resident species, suggesting an important abiotic filter. In contrast, high-intensity fire increased recruitment and richness of immigrating species, presumably by decreasing effects of other ecological filters (competition and resource limitation) in postfire environments. Drought decreased recruitment and richness of immigrating species, whereas wet soil conditions increased recruitment but decreased or had little effect on

  19. Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae).

    Science.gov (United States)

    Zhou, Dangwei; Zhou, Jie; Meng, Lihua; Wang, Qingbiao; Xie, He; Guan, Yucheng; Ma, Zeyang; Zhong, Yang; Chen, Fan; Liu, Jianquan

    2009-07-15

    Plants have evolved diverse adaptive mechanisms that enable them to tolerate abiotic stresses, to varying degrees, and such stresses may have strongly influenced evolutionary changes at levels ranging from molecular to morphological. Previous studies on these phenomena have focused on the adaptive evolution of stress-related orthologous genes in specific lineages. However, heterogenetic evolution of the paralogous genes following duplication has only been examined in a very limited number of stress-response gene families. The COR15 gene encodes a low molecular weight protein that plays an important role in protecting plants from cold stresses. Although two different copies of this gene have been found in the model species, Arabidopsis thaliana, evolutionary patterns of this small gene family in plants have not been previously explored. In this study, we cloned COR15-like sequences and performed evolutionary analyses of these sequences (including those previously reported) in the highly cold-tolerant Draba lineage and related lineages of Brassicaceae. Our phylogenetic analyses indicate that all COR15-like sequences clustered into four clades that corresponded well to the morphological lineages. Gene conversions were found to have probably occurred before/during the divergence of Brassica and Draba lineage. However, repeated, independent duplications of this gene have occurred in different lineages of Brassicaceae. Further comparisons of all sequences suggest that there have been significant inter-lineage differences in evolutionary rates between the duplicated and original genes. We assessed the likelihood that the differences between two well-supported gene subfamilies that appear to have originated from a single duplication, COR15a and COR15b, within the Draba lineage have been driven by adaptive evolution. Comparisons of their non-synonymous/synonymous substitution ratios and rates of predicted amino acid changes indicate that these two gene groups are evolving

  20. High-Level Synthesis of DSP Applications Using Adaptive Negative Cycle Detection

    Directory of Open Access Journals (Sweden)

    Nitin Chandrachoodan

    2002-09-01

    Full Text Available The problem of detecting negative weight cycles in a graph is examined in the context of the dynamic graph structures that arise in the process of high level synthesis (HLS. The concept of adaptive negative cycle detection is introduced, in which a graph changes over time and negative cycle detection needs to be done periodically, but not necessarily after every individual change. We present an algorithm for this problem, based on a novel extension of the well-known Bellman-Ford algorithm that allows us to adapt existing cycle information to the modified graph, and show by experiments that our algorithm significantly outperforms previous incremental approaches for dynamic graphs. In terms of applications, the adaptive technique leads to a very fast implementation of Lawlers algorithm for the computation of the maximum cycle mean (MCM of a graph, especially for a certain form of sparse graph. Such sparseness often occurs in practical circuits and systems, as demonstrated, for example, by the ISCAS 89/93 benchmarks. The application of the adaptive technique to design-space exploration (synthesis is also demonstrated by developing automated search techniques for scheduling iterative data-flow graphs.

  1. Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.

    Science.gov (United States)

    Cai, Qingle; Qian, Xiaoju; Lang, Yongshan; Luo, Yadan; Xu, Jiaohui; Pan, Shengkai; Hui, Yuanyuan; Gou, Caiyun; Cai, Yue; Hao, Meirong; Zhao, Jinyang; Wang, Songbo; Wang, Zhaobao; Zhang, Xinming; He, Rongjun; Liu, Jinchao; Luo, Longhai; Li, Yingrui; Wang, Jun

    2013-03-28

    The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial. Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions. Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.

  2. Adaptive Modulation for DFIG and STATCOM With High-Voltage Direct Current Transmission.

    Science.gov (United States)

    Tang, Yufei; He, Haibo; Ni, Zhen; Wen, Jinyu; Huang, Tingwen

    2016-08-01

    This paper develops an adaptive modulation approach for power system control based on the approximate/adaptive dynamic programming method, namely, the goal representation heuristic dynamic programming (GrHDP). In particular, we focus on the fault recovery problem of a doubly fed induction generator (DFIG)-based wind farm and a static synchronous compensator (STATCOM) with high-voltage direct current (HVDC) transmission. In this design, the online GrHDP-based controller provides three adaptive supplementary control signals to the DFIG controller, STATCOM controller, and HVDC rectifier controller, respectively. The mechanism is to observe the system states and their derivatives and then provides supplementary control to the plant according to the utility function. With the GrHDP design, the controller can adaptively develop an internal goal representation signal according to the observed power system states, therefore, to achieve more effective learning and modulating. Our control approach is validated on a wind power integrated benchmark system with two areas connected by HVDC transmission lines. Compared with the classical direct HDP and proportional integral control, our GrHDP approach demonstrates the improved transient stability under system faults. Moreover, experiments under different system operating conditions with signal transmission delays are also carried out to further verify the effectiveness and robustness of the proposed approach.

  3. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Directory of Open Access Journals (Sweden)

    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  4. Importance of riparian remnants for frog species diversity in a highly fragmented rainforest

    Science.gov (United States)

    Rodríguez-Mendoza, Clara; Pineda, Eduardo

    2010-01-01

    Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest. PMID:20554561

  5. High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei.

    Science.gov (United States)

    Woo, Patrick C Y; Tam, Emily W T; Chong, Ken T K; Cai, James J; Tung, Edward T K; Ngan, Antonio H Y; Lau, Susanna K P; Yuen, Kwok-Yung

    2010-09-01

    Despite the unique phenotypic properties and clinical importance of Penicillium marneffei, the polyketide synthase genes in its genome have never been characterized. Twenty-three putative polyketide synthase genes and two putative polyketide synthase nonribosomal peptide-synthase hybrid genes were identified in the P. marneffei genome, a diversity much higher than found in other pathogenic thermal dimorphic fungi, such as Histoplasma capsulatum (one polyketide synthase gene) and Coccidioides immitis (10 polyketide synthase genes). These genes were evenly distributed on the phylogenetic tree with polyketide synthase genes of Aspergillus and other fungi, indicating that the high diversity was not a result of lineage-specific gene expansion through recent gene duplication. The melanin-biosynthesis gene cluster had gene order and orientations identical to those in the Talaromyces stipitatus (a teleomorph of Penicillium emmonsii) genome. Phylogenetically, all six genes of the melanin-biosynthesis gene cluster in P. marneffei were also most closely related to those in T. stipitatus, with high bootstrap supports. The polyketide synthase gene of the melanin-biosynthesis gene cluster (alb1) in P. marneffei was knocked down, which was accompanied by loss of melanin pigment production and reduced ornamentation in conidia. The survival of mice challenged with the alb1 knockdown mutant was significantly better than those challenged with wild-type P. marneffei (P melanin-biosynthesis gene cluster contributed to virulence through decreased susceptibility to killing by hydrogen peroxide. © 2010 The Authors Journal compilation © 2010 FEBS.

  6. High levels of diversity characterize mandrill (Mandrillus sphinx) Mhc-DRB sequences.

    Science.gov (United States)

    Abbott, Kristin M; Wickings, E Jean; Knapp, Leslie A

    2006-08-01

    The major histocompatibility complex (MHC) is highly polymorphic in most primate species studied thus far. The rhesus macaque (Macaca mulatta) has been studied extensively and the Mhc-DRB region demonstrates variability similar to humans. The extent of MHC diversity is relatively unknown for other Old World monkeys (OWM), especially among genera other than Macaca. A molecular survey of the Mhc-DRB region in mandrills (Mandrillus sphinx) revealed extensive variability, suggesting that other OWMs may also possess high levels of Mhc-DRB polymorphism. In the present study, 33 Mhc-DRB loci were identified from only 13 animals. Eleven were wild-born and presumed to be unrelated and two were captive-born twins. Two to seven different sequences were identified for each individual, suggesting that some mandrills may have as many as four Mhc-DRB loci on a single haplotype. From these sequences, representatives of at least six Mhc-DRB loci or lineages were identified. As observed in other primates, some new lineages may have arisen through the process of gene conversion. These findings indicate that mandrills have Mhc-DRB diversity not unlike rhesus macaques and humans.

  7. High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales.

    Science.gov (United States)

    Healy, R A; Smith, M E; Bonito, G M; Pfister, D H; Ge, Z-W; Guevara, G G; Williams, G; Stafford, K; Kumar, L; Lee, T; Hobart, C; Trappe, J; Vilgalys, R; McLaughlin, D J

    2013-03-01

    Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in Argentina, Chile, China, Mexico and the USA between 2009 and 2012. We collated spore mat ITS sequences with 105 fruit body and 47 EcM root sequences to generate operational taxonomic units (OTUs). Phylogenetic inferences were made through analyses of both molecular data sets. A total of 48 OTUs from spore mats represented six independent EcM Pezizales lineages and included truffles and cup fungi. Three clades of seven OTUs have no known meiospore stage. Mitospores failed to germinate on sterile media, or form ectomycorrhizas on Quercus, Pinus and Populus seedlings, consistent with a hypothesized role of spermatia. The broad geographic range, high frequency and phylogenetic diversity of spore mats produced by EcM Pezizales suggests that a mitospore stage is important for many species in this group in terms of mating, reproduction and/or dispersal. © 2012 Blackwell Publishing Ltd.

  8. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

    KAUST Repository

    Pearman, John K.

    2015-11-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  9. Physiological Adaptations to Hypoxic vs. Normoxic Training during Intermittent Living High

    Science.gov (United States)

    De Smet, Stefan; van Herpt, Paul; D'Hulst, Gommaar; Van Thienen, Ruud; Van Leemputte, Marc; Hespel, Peter

    2017-01-01

    In the setting of “living high,” it is unclear whether high-intensity interval training (HIIT) should be performed “low” or “high” to stimulate muscular and performance adaptations. Therefore, 10 physically active males participated in a 5-week “live high-train low or high” program (TR), whilst eight subjects were not engaged in any altitude or training intervention (CON). Five days per week (~15.5 h per day), TR was exposed to normobaric hypoxia simulating progressively increasing altitude of ~2,000–3,250 m. Three times per week, TR performed HIIT, administered as unilateral knee-extension training, with one leg in normobaric hypoxia (~4,300 m; TRHYP) and with the other leg in normoxia (TRNOR). “Living high” elicited a consistent elevation in serum erythropoietin concentrations which adequately predicted the increase in hemoglobin mass (r = 0.78, P 0.05). Muscle oxygenation during training was lower in TRHYP vs. TRNOR (P 0.05). In conclusion, muscular and performance adaptations were largely similar following normoxic vs. hypoxic HIIT. However, hypoxic HIIT stimulated adaptations in isometric strength and muscle perfusion during intermittent sprinting. PMID:28620311

  10. Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations.

    Science.gov (United States)

    Huerta-Sánchez, Emilia; Degiorgio, Michael; Pagani, Luca; Tarekegn, Ayele; Ekong, Rosemary; Antao, Tiago; Cardona, Alexia; Montgomery, Hugh E; Cavalleri, Gianpiero L; Robbins, Peter A; Weale, Michael E; Bradman, Neil; Bekele, Endashaw; Kivisild, Toomas; Tyler-Smith, Chris; Nielsen, Rasmus

    2013-08-01

    The Tibetan and Andean Plateaus and Ethiopian highlands are the largest regions to have long-term high-altitude residents. Such populations are exposed to lower barometric pressures and hence atmospheric partial pressures of oxygen. Such "hypobaric hypoxia" may limit physical functional capacity, reproductive health, and even survival. As such, selection of genetic variants advantageous to hypoxic adaptation is likely to have occurred. Identifying signatures of such selection is likely to help understanding of hypoxic adaptive processes. Here, we seek evidence of such positive selection using five Ethiopian populations, three of which are from high-altitude areas in Ethiopia. As these populations may have been recipients of Eurasian gene flow, we correct for this admixture. Using single-nucleotide polymorphism genotype data from multiple populations, we find the strongest signal of selection in BHLHE41 (also known as DEC2 or SHARP1). Remarkably, a major role of this gene is regulation of the same hypoxia response pathway on which selection has most strikingly been observed in both Tibetan and Andean populations. Because it is also an important player in the circadian rhythm pathway, BHLHE41 might also provide insights into the mechanisms underlying the recognized impacts of hypoxia on the circadian clock. These results support the view that Ethiopian, Andean, and Tibetan populations living at high altitude have adapted to hypoxia differently, with convergent evolution affecting different genes from the same pathway.

  11. Processes discriminating adaptive and maladaptive Internet use among European adolescents highly engaged online.

    Science.gov (United States)

    Tzavela, Eleni C; Karakitsou, Chryssoula; Dreier, Michael; Mavromati, Foteini; Wölfling, Klaus; Halapi, Eva; Macarie, George; Wójcik, Szymon; Veldhuis, Lydian; Tsitsika, Artemis K

    2015-04-01

    Today adolescents are highly engaged online. Contrary to common concern, not all highly engaged adolescents develop maladaptive patterns of internet use. The present qualitative study explored the experiences, patterns and impact of use of 124 adolescents (M(age) = 16.0) reporting signs of internet addictive behaviors. The focus was to discern adaptive and maladaptive use patterns, which promote or interfere with adolescents' development, respectively. Semi-structured individual interviews were conducted in seven European countries (Greece, Spain, Poland, Germany, Romania, Netherlands and Iceland) and qualitatively analyzed using grounded theory. Considerable variability emerged in the way adolescents satisfied their personal needs online and offline, in the experienced impact from high online engagement and functional value ascribed to the internet, and in the self-regulatory processes underlying use. Variability in these discriminating processes was linked to adaptive or maladaptive adolescent internet use patterns. The emerged processes can provide direction for designing prevention and intervention programs promoting adaptive use. Copyright © 2014 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

  12. Selection for wide adaptability and high phenotypic stability of Brazilian soybean genotypes.

    Science.gov (United States)

    Oliveira, V M; Hamawaki, O T; Nogueira, A O; Sousa, L B; Santos, F M; Hamawaki, R L

    2016-03-31

    Advances in genetic enhancement techniques have led to an increase in soybean production. Thus, soybean is currently one the most economically important cultured species worldwide. The objectives of the present study were to study the interaction of soybean genotypes per environment in terms of grain productivity and to evaluate their phenotypic adaptability and stability, with the final aim of selecting lineages with high productivity, wide adaptability, and high stability. Seven soybean genotypes, consisting of five lineages developed by the soybean genetic enhancement program of the Universidade Federal de Uberlândia (Brazil) and two controls, were evaluated during several annual cycles in seven different environments. A randomized complete block design (RCBD) with three replicates was adopted in each site. This study followed the methodology proposed by Eberhart and Russel and Lin and Binns, with modifications by Carneiro, and the AMMI (additive main effects and multiplicative interaction model) analysis. The average productivity of soybean cultivars in the trials was 2739.26 kg/ha. The L01V13 genotype and the UFUS Guarani cultivar had wide adaptation according to the methodology proposed by Eberhart and Russel and Lin and Binns, with modifications by Carneiro. When analyzed with the AMMI model, the UFUS Guarani cultivar showed high stability. In general, the methodologies studied are complementary and, when used together, increase the reliability of the classification, providing support for the use of specific soybean cultivars in different environments.

  13. Inspiring science achievement: a mixed methods examination of the practices and characteristics of successful science programs in diverse high schools

    Science.gov (United States)

    Scogin, Stephen C.; Cavlazoglu, Baki; LeBlanc, Jennifer; Stuessy, Carol L.

    2017-08-01

    While the achievement gap in science exists in the US, research associated with our investigation reveals some high school science programs serving diverse student bodies are successfully closing the gap. Using a mixed methods approach, we identified and investigated ten high schools in a large Southwestern state that fit the definition of "highly successful, highly diverse". By conducting interviews with science liaisons associated with each school and reviewing the literature, we developed a rubric identifying specific characteristics associated with successful science programs. These characteristics and practices included setting high expectations for students, providing extensive teacher support for student learning, and utilizing student-centered pedagogy. We used the rubric to assess the successful high school science programs and compare them to other high school science programs in the state (i.e., less successful and less diverse high school science programs). Highly successful, highly diverse schools were very different in their approach to science education when compared to the other programs. The findings from this study will help schools with diverse students to strengthen hiring practices, enhance teacher support mechanisms, and develop student-focused strategies in the classroom that increase science achievement.

  14. Unexpectedly high genetic diversity and divergence among populations of the apomictic Neotropical tree Miconia albicans.

    Science.gov (United States)

    Dias, A C C; Serra, A C; Sampaio, D S; Borba, E L; Bonetti, A M; Oliveira, P E

    2017-10-25

    Since tropical trees often have long generation times and relatively small reproductive populations, breeding systems and genetic variation are important for population viability and have consequences for conservation. Miconia albicans is an obligate, diplosporous, apomictic species widespread in the Brazilian Cerrado, the savanna areas in central Brazil and elsewhere in the Neotropics. The genetic variability would be, theoretically, low within these male-sterile and possibly clonal populations, although some variation would be expected due to recombination during restitutional meiosis. We used ISSR markers to assess genetic diversity of M. albicans and to compare with other tropical trees, including invasive species of Melastomataceae. A total of 120 individuals from six populations were analysed using ten ISSR primers, which produced 153 fully reproducible fragments. The populations of M. albicans presented mean Shannon's information index (I) of 0.244 and expected heterozygosity (H e ) of 0.168. Only two pairs of apparently clonal trees were identified, and genetic diversity was relatively high. A hierarchical amova for all ISSR datasets showed that 74% of the variance was found among populations, while only 26% of the variance was found within populations of this species. Multivariate and Bayesian analyses indicated marked separation between the studied populations. The genetic diversity generated by restitutional meiosis, polyploidy and possibly other genome changes may explain the morpho-physiological plasticity and the ability of these plants to differentiate and occupy such a wide territory and different environmental conditions. Producing enormous amounts of bird-dispersed fruits, M. albicans possess weedy potential that may rival other Melastomataceae alien invaders. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  15. Genetic basis for high population diversity in Protea-associated Knoxdaviesia.

    Science.gov (United States)

    Aylward, Janneke; Steenkamp, Emma T; Dreyer, Léanne L; Roets, Francois; Wingfield, Michael J; Wingfield, Brenda D

    2016-11-01

    Sexual reproduction is necessary to generate genetic diversity and, in ascomycete fungi, this process is controlled by a mating type (MAT) locus with two complementary idiomorphs. Knoxdaviesia capensis and K. proteae (Sordariomycetes; Microascales; Gondwanamycetaceae) are host-specific saprophytic fungi that show high population diversity within their Protea plant hosts in the Cape Floristic Region of South Africa. We hypothesise that this diversity is the result of outcrossing driven by a heterothallic mating system and sought to describe the MAT1 loci of both species. The available genome assembly of each isolate contained only one of the MAT1 idiomorphs necessary for sexual reproduction, implying that both species are heterothallic. Idiomorph segregation during meiosis, a 1:1 ratio of idiomorphs in natural populations and mating experiments also supported heterothallism as a sexual strategy. Long-range PCR and shot-gun sequencing to identify the opposite idiomorph in each species revealed no sequence similarity between MAT1-1 and MAT1-2 idiomorphs, but the homologous idiomorphs between the species were almost identical. The MAT1-1 idiomorph contained the characteristic MAT1-1-1 and MAT1-1-2 genes, whereas the MAT1-2 idiomorph consisted of the genes MAT1-2-7 and MAT1-2-1. This gene content was similar to that of the three species in the Ceratocystidaceae (Microascales) with characterized MAT loci. The Knoxdaviesia MAT1-2-7 protein contained and alpha domain and predicted intron, which suggests that this gene arose from MAT1-1-1 during a recombination event. In contrast to the Ceratocystidaceae species, Knoxdaviesia conformed to the ancestral Sordariomycete arrangement of flanking genes and is, therefore, a closer reflection of the structure of this locus in the Microascalean ancestor. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in Musa.

    Science.gov (United States)

    Risterucci, Ange-Marie; Hippolyte, Isabelle; Perrier, Xavier; Xia, Ling; Caig, Vanessa; Evers, Margaret; Huttner, Eric; Kilian, Andrzej; Glaszmann, Jean-Christophe

    2009-10-01

    Diversity Arrays Technology (DArT) is a DNA hybridisation-based molecular marker technique that can detect simultaneously variation at numerous genomic loci without sequence information. This efficiency makes it a potential tool for a quick and powerful assessment of the structure of germplasm collections. This article demonstrates the usefulness of DArT markers for genetic diversity analyses of Musa spp. genotypes. We developed four complexity reduction methods to generate DArT genomic representations and we tested their performance using 48 reference Musa genotypes. For these four complexity reduction methods, DArT markers displayed high polymorphism information content. We selected the two methods which generated the most polymorphic genomic representations (PstI/BstNI 16.8%, PstI/TaqI 16.1%) to analyze a panel of 168 Musa genotypes from two of the most important field collections of Musa in the world: Cirad (Neufchateau, Guadeloupe), and IITA (Ibadan, Nigeria). Since most edible cultivars are derived from two wild species, Musa acuminata (A genome) and Musa balbisiana (B genome), the study is restricted mostly to accessions of these two species and those derived from them. The genomic origin of the markers can help resolving the pedigree of valuable genotypes of unknown origin. A total of 836 markers were identified and used for genotyping. Ten percent of them were specific to the A genome and enabled targeting this genome portion in relatedness analysis among diverse ploidy constitutions. DArT markers revealed genetic relationships among Musa genotype consistent with those provided by the other markers technologies, but at a significantly higher resolution and speed and reduced cost.

  17. Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes.

    Science.gov (United States)

    Porter, Stephanie S; Faber-Hammond, Joshua J; Friesen, Maren L

    2018-01-01

    Exotic, invasive plants and animals can wreak havoc on ecosystems by displacing natives and altering environmental conditions. However, much less is known about the identities or evolutionary dynamics of the symbiotic microbes that accompany invasive species. Most leguminous plants rely upon symbiotic rhizobium bacteria to fix nitrogen and are incapable of colonizing areas devoid of compatible rhizobia. We compare the genomes of symbiotic rhizobia in a portion of the legume's invaded range with those of the rhizobium symbionts from across the legume's native range. We show that in an area of California the legume Medicago polymorpha has invaded, its Ensifer medicae symbionts: (i) exhibit genome-wide patterns of relatedness that together with historical evidence support host-symbiont co-invasion from Europe into California, (ii) exhibit population genomic patterns consistent with the introduction of the majority of deep diversity from the native range, rather than a genetic bottleneck during colonization of California and (iii) harbor a large set of accessory genes uniquely enriched in binding functions, which could play a role in habitat invasion. Examining microbial symbiont genome dynamics during biological invasions is critical for assessing host-symbiont co-invasions whereby microbial symbiont range expansion underlies plant and animal invasions. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Photosynthetic performance in Antarctic lichens with different growth forms reflect the diversity of lichenized algal adaptation to microhabitats

    Directory of Open Access Journals (Sweden)

    Cao Shunan

    2015-06-01

    Full Text Available Lichens, as typical obligate associations between lichenized fungi and their photosynthetic partners, are dominant in Antarctica. Three Antarctic lichens, Ochrolechia frigida, Umbilicaria antarctica, and Usnea aurantiacoatra with different growth forms, were sampled nearby the Great Wall Station, King George Island. Molecular data revealed that the photosynthetic algae in these three lichens were Trebouxia jamesii. The net photo− synthesis (Pn of three individuals from these species, together with environmental factors such as light and temperature, were recorded by CO2 gas exchange measurements using a CI−340 portable photosynthetic system in situ. Differences between T(leaf (the temperature of the thalli and T(air (the air temperature for these lichens were not consistent, which reflected that environment and the growth form of thalli could affect T(leaf significantly. Strong irradiation was expected to have adverse effects on Pn of Ochrolechia frigida and Umbilicaria antarctica whose thalli spread flat; but this photoinhibition had little effect on Usnea aurantiacoatra with exuberant tufted thallus. These results indicated that photosynthetic activity in lichens was affected by the growth forms of thalli besides microhabitat factors. One species of lichenized alga could exhibit diversified types of photosynthetic behavior when it was associated with various lichenized fungi in different microhabitats. It will be helpful for understanding how lichens are able to adapt to and colonize in extreme environments.

  19. [Adaptive mechanisms and behavioural recommendations: playing football in heat, cold and high altitude conditions].

    Science.gov (United States)

    Born, D-P; Hoppe, M W; Lindner, N; Freiwald, J; Holmberg, H-C; Sperlich, B

    2014-03-01

    Football is played worldwide and players often have to cope with hot and cold temperatures as well as high altitude conditions. The upcoming and past world championships in Brazil, Qatar and South Africa illustrate the necessity for behavioural strategies and adaptation to extreme environmental conditions. When playing football in the heat or cold, special clothing, hydration and nutritional and acclimatisation strategies are vital for high-level performance. When playing at high altitude, the reduced oxygen partial pressure impairs endurance performance and alters the technical and tactical requirements. Special high-altitude adaptation and preparation strategies are essential for football teams based at sea-level in order to perform well and compete successfully. Therefore, the aim of the underlying review is: 1) to highlight the difficulties and needs of football teams competing in extreme environmental conditions, 2) to summarise the thermoregulatory, physiological, neuronal and psychological mechanism, and 3) to provide recommendations for coping with extreme environmental conditions in order to perform at a high level when playing football in the heat, cold and at high altitude. © Georg Thieme Verlag KG Stuttgart · New York.

  20. Cognitive, adaptive, and psychosocial differences between high ability youth with and without autism spectrum disorder.

    Science.gov (United States)

    Doobay, Alissa F; Foley-Nicpon, Megan; Ali, Saba R; Assouline, Susan G

    2014-08-01

    Research on Autism Spectrum Disorder (ASD) is thriving; however, scant empirical research has investigated how ASD manifests in high ability youth. Further research is necessary to accurately differentiate high ability students with ASD from those without the disorder, and thus decrease the risk of misdiagnosis. The purpose of the present study is to provide an empirical account of the intellectual, adaptive, and psychosocial functioning of high ability youth with and without ASD utilizing a group study design. Forty youth with high cognitive ability and ASD and a control group of 41 youth with high cognitive ability and no psychological diagnosis were included in the study. In comparison to the control group, the ASD group showed poorer functioning on measures of processing speed, adaptive skills, and broad psychological functioning, as perceived by parents and teachers. These findings have significant implications for diagnosing ASD among those with high ability, and the development of related psychological and educational interventions to address talent domains and areas of concern.

  1. Adaptation of the Long-Lived Monocarpic Perennial Saxifraga longifolia to High Altitude.

    Science.gov (United States)

    Munné-Bosch, Sergi; Cotado, Alba; Morales, Melanie; Fleta-Soriano, Eva; Villellas, Jesús; Garcia, Maria B

    2016-10-01

    Global change is exerting a major effect on plant communities, altering their potential capacity for adaptation. Here, we aimed at unveiling mechanisms of adaptation to high altitude in an endemic long-lived monocarpic, Saxifraga longifolia, by combining demographic and physiological approaches. Plants from three altitudes (570, 1100, and 2100 m above sea level [a.s.l.]) were investigated in terms of leaf water and pigment contents, and activation of stress defense mechanisms. The influence of plant size on physiological performance and mortality was also investigated. Levels of photoprotective molecules (α-tocopherol, carotenoids, and anthocyanins) increased in response to high altitude (1100 relative to 570 m a.s.l.), which was paralleled by reduced soil and leaf water contents and increased ABA levels. The more demanding effect of high altitude on photoprotection was, however, partly abolished at very high altitudes (2100 m a.s.l.) due to improved soil water contents, with the exception of α-tocopherol accumulation. α-Tocopherol levels increased progressively at increasing altitudes, which paralleled with reductions in lipid peroxidation, thus suggesting plants from the highest altitude effectively withstood high light stress. Furthermore, mortality of juveniles was highest at the intermediate population, suggesting that drought stress was the main environmental driver of mortality of juveniles in this rocky plant species. Population structure and vital rates in the high population evidenced lower recruitment and mortality in juveniles, activation of clonal growth, and absence of plant size-dependent mortality. We conclude that, despite S. longifolia has evolved complex mechanisms of adaptation to altitude at the cellular, whole-plant and population levels, drought events may drive increased mortality in the framework of global change. © 2016 American Society of Plant Biologists. All Rights Reserved.

  2. Milk at altitude: Human milk macronutrient composition in a high-altitude adapted population of Tibetans.

    Science.gov (United States)

    Quinn, Elizabeth A; Diki Bista, Kesang; Childs, Geoff

    2016-02-01

    The physiological challenges of high altitude have led to population-specific patterns of adaptation. These include alterations to child growth and reproduction, including lactation. However, while breastfeeding has been investigated, nothing is known about milk composition in high altitude adapted populations. Here, we investigate milk macronutrient composition, volume, and energy in a sample of 82 Tibetans living at high and low altitude in rural villages (Nubri Valley, Nepal) and at low altitude in Kathmandu, Nepal. Milk samples were collected in the morning using hand expression, frozen, and assayed for fat, protein, and total sugars. Reproductive histories and health recalls were also collected. Milk fat averaged 5.2 ±2.0 g/100 mL, milk sugar 7.37 ± 0.49 g/100 mL, and milk protein 1.26 ± 0.35 g/100 mL for a mean energy density of 81.4 ± 17.4 kcal/100 mL. There were no associations between altitude of residence and milk composition; however, overall milk fat was high compared to reference populations. Within the three groups, milk fat was positively associated with infant age (B = 0.103; p milk sugar was significantly and inversely associated with maternal parity and triceps skinfold thickness. Milk fat, and consequently milk energy, may be increased in high-altitude adapted Tibetans when compared to populations living at low altitude. The association between milk fat and maternal adiposity suggests that milk composition may be sensitive to maternal adiposity in this sample, likely reflecting increased metabolic costs of producing a high-fat milk. © 2015 Wiley Periodicals, Inc.

  3. Robust Adaptation Research in High Mountains: Integrating the Scientific, Social, and Ecological Dimensions of Glacio-Hydrological Change

    Directory of Open Access Journals (Sweden)

    Graham McDowell

    2017-09-01

    Full Text Available Climate-related changes in glacierized watersheds are widely documented, stimulating adaptive responses among the 370 million people living in glacier-influenced watersheds as well as aquatic and riparian ecosystems. The situation denotes important interdependencies between science, society, and ecosystems, yet integrative approaches to the study of adaptation to such changes remain scarce in both the mountain- and non-mountain-focused adaptation scholarship. Using the example of glacio-hydrological change, it is argued here that this analytical limitation impedes the identification, development, and implementation of “successful” adaptations. In response, the paper introduces three guiding principles for robust adaptation research in glaciated mountain regions. Principle 1: Adaptation research should integrate detailed analyses of watershed-specific glaciological and hydro-meteorological conditions; glacio-hydrological changes are context-specific and therefore cannot be assumed to follow idealized trajectories of “peak water”. Principle 2: Adaptation research should consider the complex interplay between glacio-hydrological changes and socio-economic, cultural, and political conditions; responses to environmental changes are non-deterministic and therefore not deducible from hydrological changes alone. Principle 3: Adaptation research should be attentive to interdependencies, feedbacks, and tradeoffs between human and ecological responses to glacio-hydrological change; research that does not evaluate these socio-ecological dynamics may lead to maladaptive adaptation plans. These principles call attention to the linked scientific, social, and ecological dimensions of adaptation, and offer a point of departure for future climate change adaptation research in high mountains.

  4. Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8 locus.

    Directory of Open Access Journals (Sweden)

    Sophie Bouchet

    Full Text Available The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the ZCN8 gene, which is the closest maize homologue to Arabidopsis major flowering time (FT gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of Vgt2 QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide

  5. Academic Motivation Scale: adaptation and psychometric analyses for high school and college students.

    Science.gov (United States)

    Stover, Juliana Beatriz; de la Iglesia, Guadalupe; Boubeta, Antonio Rial; Liporace, Mercedes Fernández

    2012-01-01

    The Academic Motivation Scale (AMS), supported in Self-Determination Theory, has been applied in recent decades as well in high school as in college education. Although several versions in Spanish are available, the underlying linguistic and cultural differences raise important issues when they are applied to Latin-American population. Consequently an adapted version of the AMS was developed, and its construct validity was analyzed in Argentine students. Results obtained on a sample that included 723 students from Buenos Aires (393 high school and 330 college students) verified adequate psychometric properties in this new version, solving some controversies regarded to its dimensionality.

  6. Adapting high-level language programs for parallel processing using data flow

    Science.gov (United States)

    Standley, Hilda M.

    1988-01-01

    EASY-FLOW, a very high-level data flow language, is introduced for the purpose of adapting programs written in a conventional high-level language to a parallel environment. The level of parallelism provided is of the large-grained variety in which parallel activities take place between subprograms or processes. A program written in EASY-FLOW is a set of subprogram calls as units, structured by iteration, branching, and distribution constructs. A data flow graph may be deduced from an EASY-FLOW program.

  7. The Effect of Different High-Intensity Periodization Models on Endurance Adaptations

    OpenAIRE

    Sylta, Øystein; Tønnessen, Espen; Hammarström, Daniel; Danielsen, Jørgen; Skovereng, Knut; Ravn, Troels; Rønnestad, Bent; Sandbakk, Øyvind; Seiler, Stephen

    2016-01-01

    Purpose: This study aimed to compare the effects of three different high-intensity training (HIT) models, balanced for total load but differing in training plan progression, on endurance adaptations. Methods: Sixty-three cyclists (peak oxygen uptake (V˙O2peak) 61.3 ± 5.8 mL·kg−1·min−1) were randomized to three training groups and instructed to follow a 12-wk training program consisting of 24 interval sessions, a high volume of low-intensity training, and laboratory testing. The increasing...

  8. Soil biota suppress positive plant diversity effects on productivity at high but not low soil fertility

    NARCIS (Netherlands)

    Luo, Shan; Deyn, De Gerlinde B.; Jiang, B.; Yu, Shixiao

    2017-01-01

    Plant community productivity commonly increases with increasing plant diversity, which is explained by complementarity among plant species in resource utilization (complementarity effect), or by selection of particularly productive plant species in diverse plant communities (selection effect).

  9. The molecular basis of high-altitude adaptation in deer mice.

    Directory of Open Access Journals (Sweden)

    Jay F Storz

    2007-03-01

    Full Text Available Elucidating genetic mechanisms of adaptation is a goal of central importance in evolutionary biology, yet few empirical studies have succeeded in documenting causal links between molecular variation and organismal fitness in natural populations. Here we report a population genetic analysis of a two-locus alpha-globin polymorphism that underlies physiological adaptation to high-altitude hypoxia in natural populations of deer mice, Peromyscus maniculatus. This system provides a rare opportunity to examine the molecular underpinnings of fitness-related variation in protein function that can be related to a well-defined selection pressure. We surveyed DNA sequence variation in the duplicated alpha-globin genes of P. maniculatus from high- and low-altitude localities (i to identify the specific mutations that may be responsible for the divergent fine-tuning of hemoglobin function and (ii to test whether the genes exhibit the expected signature of diversifying selection between populations that inhabit different elevational zones. Results demonstrate that functionally distinct protein alleles are maintained as a long-term balanced polymorphism and that adaptive modifications of hemoglobin function are produced by the independent or joint effects of five amino acid mutations that modulate oxygen-binding affinity.

  10. Serum testosterone levels and excessive erythrocytosis during the process of adaptation to high altitudes

    Science.gov (United States)

    Gonzales, Gustavo F

    2013-01-01

    Populations living at high altitudes (HAs), particularly in the Peruvian Andes, are characterized by a mixture of subjects with erythrocytosis (16 g dl−121 g dl−1). Elevated haemoglobin values (EE) are associated with chronic mountain sickness, a condition reflecting the lack of adaptation to HA. According to current data, native men from regions of HA are not adequately adapted to live at such altitudes if they have elevated serum testosterone levels. This seems to be due to an increased conversion of dehydroepiandrosterone sulphate (DHEAS) to testosterone. Men with erythrocytosis at HAs show higher serum androstenedione levels and a lower testosterone/androstenedione ratio than men with EE, suggesting reduced 17beta-hydroxysteroid dehydrogenase (17beta-HSD) activity. Lower 17beta-HSD activity via Δ4-steroid production in men with erythrocytosis at HA may protect against elevated serum testosterone levels, thus preventing EE. The higher conversion of DHEAS to testosterone in subjects with EE indicates increased 17beta-HSD activity via the Δ5-pathway. Currently, there are various situations in which people live (human biodiversity) with low or high haemoglobin levels at HA. Antiquity could be an important adaptation component for life at HA, and testosterone seems to participate in this process. PMID:23524530

  11. Reconfigurable and adaptive photonic networks for high-performance computing systems.

    Science.gov (United States)

    Kodi, Avinash; Louri, Ahmed

    2009-08-01

    As feature sizes decrease to the submicrometer regime and clock rates increase to the multigigahertz range, the limited bandwidth at higher bit rates and longer communication distances in electrical interconnects will create a major bandwidth imbalance in future high-performance computing (HPC) systems. We explore the application of an optoelectronic interconnect for the design of flexible, high-bandwidth, reconfigurable and adaptive interconnection architectures for chip-to-chip and board-to-board HPC systems. Reconfigurability is realized by interconnecting arrays of optical transmitters, and adaptivity is implemented by a dynamic bandwidth reallocation (DBR) technique that balances the load on each communication channel. We evaluate a DBR technique, the lockstep (LS) protocol, that monitors traffic intensities, reallocates bandwidth, and adapts to changes in communication patterns. We incorporate this DBR technique into a detailed discrete-event network simulator to evaluate the performance for uniform, nonuniform, and permutation communication patterns. Simulation results indicate that, without reconfiguration techniques being applied, optical based system architecture shows better performance than electrical interconnects for uniform and nonuniform patterns; with reconfiguration techniques being applied, the dynamically reconfigurable optoelectronic interconnect provides much better performance for all communication patterns. Based on the performance study, the reconfigured architecture shows 30%-50% increased throughput and 50%-75% reduced network latency compared with HPC electrical networks.

  12. The QoE implications of ultra-high definition video adaptation strategies

    Science.gov (United States)

    Nightingale, James; Awobuluyi, Olatunde; Wang, Qi; Alcaraz-Calero, Jose M.; Grecos, Christos

    2016-04-01

    As the capabilities of high-end consumer devices increase, streaming and playback of Ultra-High Definition (UHD) is set to become commonplace. The move to these new, higher resolution, video services is one of the main factors contributing to the predicted continuation of growth in video related traffic in the Internet. This massive increases in bandwidth requirement, even when mitigated by the use of new video compression standards such as H.265, will place an ever-increasing burden on network service providers. This will be especially true in mobile environments where users have come to expect ubiquitous access to content. Consequently, delivering UHD and Full UHD (FUHD) video content is one of the key drivers for future Fifth Generation (5G) mobile networks. One often voiced, but as yet unanswered question, is whether users of mobile devices with modest screen sizes (e.g. smartphones or smaller tablet) will actually benefit from consuming the much higher bandwidth required to watch online UHD video, in terms of an improved user experience. In this paper, we use scalable H.265 encoded video streams to conduct a subjective evaluation of the impact on a user's perception of video quality across a comprehensive range of adaptation strategies, covering each of the three adaptation domains, for UHD and FUHD video. The results of our subjective study provide insightful and useful indications of which methods of adapting UHD and FUHD streams have the least impact on user's perceived QoE. In particular, it was observed that, in over 70% of cases, users were unable to distinguish between full HD (1080p) and UHD (4K) videos when they were unaware of which version was being shown to them. Our results from this evaluation can be used to provide adaptation rule sets that will facilitate fast, QoE aware in-network adaptation of video streams in support of realtime adaptation objectives. Undoubtedly they will also promote discussion around how network service providers manage

  13. A parallel nonlinear adaptive enhancement algorithm for low- or high-intensity color images

    Science.gov (United States)

    Zhou, Zhigang; Sang, Nong; Hu, Xinrong

    2014-12-01

    This article addresses the problem of color image enhancement for images with low or high intensity and poor contrast (LIPC or HIPC). A parallel nonlinear adaptive enhancement (PNAE) algorithm using information from local neighborhood is presented to resolve the problem in parallel. The PNAE algorithm consists of three steps. First, a red-green-blue (RGB) color image is converted to an intensity image, then an adaptive intensity adjustment with local contrast enhancement is parallelly performed, and finally, colors are restored. The PNAE algorithm can be adjusted to control the level of enhancement on the overall lightness and the contrast achieved at the output separately. Most of the parameters used in PNAE are robust for LIPC and HIPC color image enhancement. Experimental results show that PNAE outperforms two popular methods in both computational efficiency and overall content preservation of image while improving local contrast for LIPC and HIPC image enhancement.

  14. High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

    Directory of Open Access Journals (Sweden)

    Hector Fernando Arocha-Garza

    2017-05-01

    shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

  15. High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis.

    Science.gov (United States)

    Arocha-Garza, Hector Fernando; Canales-Del Castillo, Ricardo; Eguiarte, Luis E; Souza, Valeria; De la Torre-Zavala, Susana

    2017-01-01

    isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

  16. High recombination frequency creates genotypic diversity in colonies of the leaf-cutting ant Acromyrmex echinatior

    DEFF Research Database (Denmark)

    Sirviö, A.; Gadau, J.; Rueppell, O.

    2006-01-01

    Honeybees are known to have genetically diverse colonies because queens mate with many males and the recombination rate is extremely high. Genetic diversity among social insect workers has been hypothesized to improve general performance of large and complex colonies, but this idea has not been...... tested in other social insects. Here, we present a linkage map and an estimate of the recombination rate for Acromyrmex echinatior, a leaf-cutting ant that resembles the honeybee in having multiple mating of queens and colonies of approximately the same size. A map of 145 AFLP markers in 22 linkage...... groups yielded a total recombinational size of 2076 cM and an inferred recombination rate of 161 kb cM-1 (or 6.2 cM Mb-1). This estimate is lower than in the honeybee but, as far as the mapping criteria can be compared, higher than in any other insect mapped so far. Earlier studies on A. echinatior have...

  17. Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)

    Science.gov (United States)

    Peters, Jeffrey L.; Sonsthagen, Sarah A.; Lavretsky, Philip; Rezsutek, Michael; Johnson, William P.; McCracken, Kevin G.

    2014-01-01

    Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (Ne). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks (Anas fulvigula) and geographically widespread mallards (A. platyrhynchos), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated Ne of mottled ducks to 33 % of the equilibrium Ne and yielded an estimated Ne consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.

  18. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

    Directory of Open Access Journals (Sweden)

    Jiali Wang

    Full Text Available Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene of the planktonic microbial eukaryotes (nano- and picoeukaryotes in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%, whereas Stramenopiles (26.65% and Alveolates (10.84% are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%, whereas less represented in other hypersaline lakes such as Gahai (0.50% and Xiaochaidan (1.15%. Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  19. Differences in genetic diversity in Holstein cattle with high and low genetic merit

    NARCIS (Netherlands)

    Engelsma, K.A.; Veerkamp, R.F.; Calus, M.P.L.; Windig, J.J.

    2010-01-01

    Evaluations of genetic diversity in Holstein cattle based on pedigree data, indicate a decrease in genetic diversity in Holstein cattle, because of a lower effective population size and a higher relatedness compared to other cattle breeds. However, pedigree based diversity reflects only the overall

  20. An Adaptive ANOVA-based PCKF for High-Dimensional Nonlinear Inverse Modeling

    Energy Technology Data Exchange (ETDEWEB)

    LI, Weixuan; Lin, Guang; Zhang, Dongxiao

    2014-02-01

    The probabilistic collocation-based Kalman filter (PCKF) is a recently developed approach for solving inverse problems. It resembles the ensemble Kalman filter (EnKF) in every aspect—except that it represents and propagates model uncertainty by polynomial chaos expansion (PCE) instead of an ensemble of model realizations. Previous studies have shown PCKF is a more efficient alternative to EnKF for many data assimilation problems. However, the accuracy and efficiency of PCKF depends on an appropriate truncation of the PCE series. Having more polynomial chaos bases in the expansion helps to capture uncertainty more accurately but increases computational cost. Bases selection is particularly important for high-dimensional stochastic problems because the number of polynomial chaos bases required to represent model uncertainty grows dramatically as the number of input parameters (random dimensions) increases. In classic PCKF algorithms, the PCE bases are pre-set based on users’ experience. Also, for sequential data assimilation problems, the bases kept in PCE expression remain unchanged in different Kalman filter loops, which could limit the accuracy and computational efficiency of classic PCKF algorithms. To address this issue, we present a new algorithm that adaptively selects PCE bases for different problems and automatically adjusts the number of bases in different Kalman filter loops. The algorithm is based on adaptive functional ANOVA (analysis of variance) decomposition, which approximates a high-dimensional function with the summation of a set of low-dimensional functions. Thus, instead of expanding the original model into PCE, we implement the PCE expansion on these low-dimensional functions, which is much less costly. We also propose a new adaptive criterion for ANOVA that is more suited for solving inverse problems. The new algorithm is tested with different examples and demonstrated great effectiveness in comparison with non-adaptive PCKF and En

  1. An adaptive ANOVA-based PCKF for high-dimensional nonlinear inverse modeling

    Energy Technology Data Exchange (ETDEWEB)

    Li, Weixuan, E-mail: weixuan.li@usc.edu [Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA 90089 (United States); Lin, Guang, E-mail: guang.lin@pnnl.gov [Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Zhang, Dongxiao, E-mail: dxz@pku.edu.cn [Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871 (China)

    2014-02-01

    The probabilistic collocation-based Kalman filter (PCKF) is a recently developed approach for solving inverse problems. It resembles the ensemble Kalman filter (EnKF) in every aspect—except that it represents and propagates model uncertainty by polynomial chaos expansion (PCE) instead of an ensemble of model realizations. Previous studies have shown PCKF is a more efficient alternative to EnKF for many data assimilation problems. However, the accuracy and efficiency of PCKF depends on an appropriate truncation of the PCE series. Having more polynomial chaos basis functions in the expansion helps to capture uncertainty more accurately but increases computational cost. Selection of basis functions is particularly important for high-dimensional stochastic problems because the number of polynomial chaos basis functions required to represent model uncertainty grows dramatically as the number of input parameters (random dimensions) increases. In classic PCKF algorithms, the PCE basis functions are pre-set based on users' experience. Also, for sequential data assimilation problems, the basis functions kept in PCE expression remain unchanged in different Kalman filter loops, which could limit the accuracy and computational efficiency of classic PCKF algorithms. To address this issue, we present a new algorithm that adaptively selects PCE basis functions for different problems and automatically adjusts the number of basis functions in different Kalman filter loops. The algorithm is based on adaptive functional ANOVA (analysis of variance) decomposition, which approximates a high-dimensional function with the summation of a set of low-dimensional functions. Thus, instead of expanding the original model into PCE, we implement the PCE expansion on these low-dimensional functions, which is much less costly. We also propose a new adaptive criterion for ANOVA that is more suited for solving inverse problems. The new algorithm was tested with different examples and

  2. Race and Academic Achievement in Racially Diverse High Schools: Opportunity and Stratification.

    Science.gov (United States)

    Muller, Chandra; Riegle-Crumb, Catherine; Schiller, Kathryn S; Wilkinson, Lindsey; Frank, Kenneth A

    2010-04-01

    BACKGROUND/CONTEXT: Brown v Board of Education fundamentally changed our nation's schools, yet we know surprisingly little about how and whether they provide equality of educational opportunity. Although substantial evidence suggests that African American and Latino students who attend these schools face fewer learning opportunities than their White counterparts, until now, it has been impossible to examine this using a representative sample because of lack of data. PURPOSE/OBJECTIVE/RESEARCH QUESTION/FOCUS OF STUDY: This study uses newly available data to investigate whether racially diverse high schools offer equality of educational opportunity to students from different racial and ethnic groups. This is examined by measuring the relative representation of minority students in advanced math classes at the beginning of high school and estimating whether and how this opportunity structure limits the level of achievement attained by African American and Latino students by the end of high school. SETTING: This study uses data from the Adolescent Health and Academic Achievement Study (AHAA) and its partner study, the National Longitudinal Study of Adolescent Health (Add Health), a stratified, nationally representative study of students in U.S. high schools first surveyed in 1994-1995. POPULATION/PARTICIPANTS/SUBJECTS: Two samples of racially diverse high schools were used in the analysis: one with African Americans, Whites, and Asians (26 schools with 3,149 students), and the other with Latinos, Whites, and Asians (22 schools with 2,775 students). RESEARCH DESIGN: Quantitative analyses first assess how high schools vary in the extent to which minority students are underrepresented in advanced sophomore math classes. Hierarchical multilevel modeling is then used to estimate whether racial-ethnic differences in representation in advanced math have an impact on African American and Latino students' achievement by the end of high school, relative to the Whites and Asians

  3. Predictors of individual adaptation to high-volume or high-intensity endurance training in recreational endurance runners.

    Science.gov (United States)

    Vesterinen, V; Häkkinen, K; Laine, T; Hynynen, E; Mikkola, J; Nummela, A

    2016-08-01

    The aim of this study was to investigate factors that can predict individual adaptation to high-volume or high-intensity endurance training. After the first 8-week preparation period, 37 recreational endurance runners were matched into the high-volume training group (HVT) and high-intensity training group (HIT). During the next 8-week training period, HVT increased their running training volume and HIT increased training intensity. Endurance performance characteristics, heart rate variability (HRV), and serum hormone concentrations were measured before and after the training periods. While HIT improved peak treadmill running speed (RSpeak ) 3.1 ± 2.8% (P endurance training in recreational runners. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. New Tools For Understanding Microbial Diversity Using High-throughput Sequence Data

    Science.gov (United States)

    Knight, R.; Hamady, M.; Liu, Z.; Lozupone, C.

    2007-12-01

    High-throughput sequencing techniques such as 454 are straining the limits of tools traditionally used to build trees, choose OTUs, and perform other essential sequencing tasks. We have developed a workflow for phylogenetic analysis of large-scale sequence data sets that combines existing tools, such as the Arb phylogeny package and the NAST multiple sequence alignment tool, with new methods for choosing and clustering OTUs and for performing phylogenetic community analysis with UniFrac. This talk discusses the cyberinfrastructure we are developing to support the human microbiome project, and the application of these workflows to analyze very large data sets that contrast the gut microbiota with a range of physical environments. These tools will ultimately help to define core and peripheral microbiomes in a range of environments, and will allow us to understand the physical and biotic factors that contribute most to differences in microbial diversity.

  5. Impacts of comprehensive reading instruction on diverse outcomes of low- and high-achieving readers.

    Science.gov (United States)

    Guthrie, John T; McRae, Angela; Coddington, Cassandra S; Lutz Klauda, Susan; Wigfield, Allan; Barbosa, Pedro

    2009-01-01

    Low-achieving readers in Grade 5 often lack comprehension strategies, domain knowledge, word recognition skills, fluency, and motivation to read. Students with such multiple reading needs seem likely to benefit from instruction that supports each of these reading processes. The authors tested this expectation experimentally by comparing the effects of Concept-Oriented Reading Instruction (CORI) with traditional instruction (TI) on several outcomes in a 12-week intervention for low achievers and high achievers. Low achievers in the CORI group were afforded explicit instruction, leveled texts, and motivation support. Compared with TI students, CORI students scored higher on posttest measures of word recognition speed, reading comprehension on the Gates-MacGinitie Reading Test, and ecological knowledge. CORI was equally effective for lower achievers and higher achievers. Explicitly supporting multiple aspects of reading simultaneously appeared to benefit diverse learners on a range of reading outcomes.

  6. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

    Science.gov (United States)

    Boyle, Alan P; Song, Lingyun; Lee, Bum-Kyu; London, Darin; Keefe, Damian; Birney, Ewan; Iyer, Vishwanath R; Crawford, Gregory E; Furey, Terrence S

    2011-03-01

    Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find that footprints for specific transcription factors correlate with ChIP-seq enrichment and can accurately identify functional versus nonfunctional transcription factor motifs. We also find that footprints reveal a unique evolutionary conservation pattern that differentiates functional footprinted bases from surrounding DNA. Finally, detailed analysis of CTCF footprints suggests multiple modes of binding and a novel DNA binding motif upstream of the primary binding site.

  7. Genes associated to lactose metabolism illustrate the high diversity of Carnobacterium maltaromaticum

    DEFF Research Database (Denmark)

    Iskandar, Christelle F.; Cailliez-Grimal, Catherine; Rahman, Abdur

    2016-01-01

    , III and IV. These data suggest that these genes evolved thanks to horizontal transfer, genetic duplication and translocation. We hypothesize that the lac and gal genes evolved in C. maltaromaticum according to a complex scenario that mirrors the high population diversity....... genomic analysis revealed that the species C. maltaromaticum exhibits genes related to the Leloir and the tagatose-6-phosphate (Tagatose-6P) pathways. More precisely, strains can bear genes related to one or both pathways and several strains apparently do not contain homologs related to these pathways....... Analysis at the population scale revealed that the Tagatose-6P and the Leloir encoding genes are disseminated in multiple phylogenetic lineages of C. maltaromaticum: genes of the Tagatose-6P pathway are present in the lineages I, II and III, and genes of the Leloir pathway are present in the lineages I...

  8. Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing.

    Science.gov (United States)

    Sun, Zhihong; Liu, Wenjun; Bao, Qiuhua; Zhang, Jiachao; Hou, Qiangchuan; Kwok, Laiyu; Sun, Tiansong; Zhang, Heping

    2014-10-01

    This is the first study on the bacterial and fungal community diversity in 17 tarag samples (naturally fermented dairy products) through a metagenomic approach involving high-throughput pyrosequencing. Our results revealed the presence of a total of 47 bacterial and 43 fungal genera in all tarag samples, in which Lactobacillus and Galactomyces were the predominant genera of bacteria and fungi, respectively. The number of some microbial genera, such as Lactococcus, Acetobacter, Saccharomyces, Trichosporon, and Kluyveromyces, among others, was found to vary between different samples. Altogether, our results showed that the microbial flora in different samples may be stratified by geographic region. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  9. What does impacted look like? High diversity and abundance of epibiota in modified estuaries.

    Science.gov (United States)

    Clark, Graeme F; Kelaher, Brendan P; Dafforn, Katherine A; Coleman, Melinda A; Knott, Nathan A; Marzinelli, Ezequiel M; Johnston, Emma L

    2015-01-01

    Ecosystems modified by human activities are generally predicted to be biologically impoverished. However, much pollution impact theory stems from laboratory or small-scale field studies, and few studies replicate at the level of estuary. Furthermore, assessments are often based on sediment contamination and infauna, and impacts to epibiota (sessile invertebrates and algae) are seldom considered. We surveyed epibiota in six estuaries in south-east Australia. Half the estuaries were relatively pristine, and half were subject to internationally high levels of contamination, urbanisation, and industrialisation. Contrary to predictions, epibiota in modified estuaries had greater coverage and were similarly diverse as those in unmodified estuaries. Change in epibiota community structure was linearly correlated with sediment-bound copper, and the tubeworm Hydroides elegans showed a strong positive correlation with sediment metals. Stressors such as metal contamination can reduce biodiversity and productivity, but others such as nutrient enrichment and resource provision may obscure signals of impact. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. High resolution crop growth simulation for identification of potential adaptation strategies under climate change

    Science.gov (United States)

    Kim, K. S.; Yoo, B. H.

    2016-12-01

    Impact assessment of climate change on crop production would facilitate planning of adaptation strategies. Because socio-environmental conditions would differ by local areas, it would be advantageous to assess potential adaptation measures at a specific area. The objectives of this study was to develop a crop growth simulation system at a very high spatial resolution, e.g., 30 m, and to assess different adaptation options including shift of planting date and use of different cultivars. The Decision Support System for Agrotechnology Transfer (DSSAT) model was used to predict yields of soybean and maize in Korea. Gridded data for climate and soil were used to prepare input data for the DSSAT model. Weather input data were prepared at the resolution of 30 m using bilinear interpolation from gridded climate scenario data. Those climate data were obtained from Korean Meteorology Administration. Spatial resolution of temperature and precipitation was 1 km whereas that of solar radiation was 12.5 km. Soil series data at the 30 m resolution were obtained from the soil database operated by Rural Development Administration, Korea. The SOL file, which is a soil input file for the DSSAT model was prepared using physical and chemical properties of a given soil series, which were available from the soil database. Crop yields were predicted by potential adaptation options based on planting date and cultivar. For example, 10 planting dates and three cultivars were used to identify ideal management options for climate change adaptation. In prediction of maize yield, combination of 20 planting dates and two cultivars was used as management options. Predicted crop yields differed by site even within a relatively small region. For example, the maximum of average yields for 2001-2010 seasons differed by sites In a county of which areas is 520 km2 (Fig. 1). There was also spatial variation in the ideal management option in the region (Fig. 2). These results suggested that local

  11. The Althoff-Radtke Test Adapted for High Chromium Cast Iron

    Directory of Open Access Journals (Sweden)

    Kopyciński D.

    2016-12-01

    Full Text Available The paper presents results of the possibility of adapting the Althoff-Radtke test for High Chromium Cast Iron. The Althoff-Radtke test is a clump attempt used for steel. The Althoff-Radtke test has four different lengths of clamp which qualifies it as a test to quantitatively take into account different kinds of shrinkage ΔL. The length of the slot of the cracked corner and the length of each staple (50 - 350 mm are the parameters tendency to cast cracks. Castings of white cast iron have a high tendency to hot cracking due to the large range of solidification temperatures, unfavorable kinetics parameters of shrinkage, and especially a lack of expansion before shrinkage. Shrinkage of high chromium white cast iron is similar to the shrinkage of cast steel, and is approximately 2%. Therefore it is important to test susceptibility to hot cracks. Research was carried out under industrial conditions. Four melts were performed, one of the initial chemical composition and the other three modified by different amounts of Fe-Ti, respectively, 0.25%, 0.5% and 0.75% Fe-Ti. The propensity for hot cracking was based on the observation of the dark surface in the corner of the sample. The study shows that the Althoff-Radtke test can be adapted to determine the tendency for hot cracking of high chromium cast iron. It should however be noted that the test results cannot be compared with those for other alloys.

  12. Low-intensity agricultural landscapes in Transylvania support high butterfly diversity: implications for conservation.

    Science.gov (United States)

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  13. High Genetic Diversity among Stenotrophomonas maltophilia Strains Despite Their Originating at a Single Hospital

    Science.gov (United States)

    Valdezate, Sylvia; Vindel, Ana; Martín-Dávila, Pilar; Del Saz, Begoña Sánchez; Baquero, Fernando; Cantón, Rafael

    2004-01-01

    The levels of genetic relatedness of 139 Stenotrophomonas maltophilia strains recovered from 105 hospitalized non-cystic fibrosis patients (51% from medical wards, 35% from intensive care units, and 14% from surgical wards) and 7 environmental sources in the same hospital setting during a 4-year period were typed by the pulsed-field gel electrophoresis (PFGE) technique. A total of 99 well-defined distinct XbaI PFGE patterns were identified (Simpson's discrimination index, 0.996). The dendrogram showed a Dice similarity coefficient ranging from 28 to 80%. Two major clusters (I and II), three minor clusters (III, IV, and V), and two independent branches were observed when using a 36% Dice coefficient, indicating a high diversity of genetic relatedness. It is of note that 84% of strains were grouped within two major clonal lineages. No special cluster gathering was found among strains belonging to the same sample type specimen, patients' infection or colonization status, and ward of precedence. Despite this fact, three different clones (A, B, and C) recovered from respiratory samples from six, three, and two patients, respectively, and two clones, D and E, in two bacteremic patients each, were identified. Isolation of an S. maltophilia strain belonging to the clone A profile in a bronchoscope demonstrated a common source from this clone. This study revealed a high genetic diversity of S. maltophilia isolates despite their origin from a single hospital, which may be related to the wide environmental distribution of this pathogen. However, few clones could be transmitted among different patients, yielding outbreak situations. PMID:14766838

  14. Low-intensity agricultural landscapes in Transylvania support high butterfly diversity: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Jacqueline Loos

    Full Text Available European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation

  15. High-throughput genotyping for species identification and diversity assessment in germplasm collections.

    Science.gov (United States)

    Mason, Annaliese S; Zhang, Jing; Tollenaere, Reece; Vasquez Teuber, Paula; Dalton-Morgan, Jessica; Hu, Liyong; Yan, Guijun; Edwards, David; Redden, Robert; Batley, Jacqueline

    2015-09-01

    Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers. © 2015 John Wiley & Sons Ltd.

  16. AN ADAPTIVE MORPHOLOGICAL MEAN FILTER FOR VERY HIGH-RESOLUTION REMOTE SENSING IMAGE PROCESSING

    Directory of Open Access Journals (Sweden)

    Z. Lv

    2017-09-01

    Full Text Available Very high resolution (VHR remote sensing imagery can reveal the ground object in greater detail, depicting their color, shape, size and structure. However, VHR also leads much original noise in spectra, and this original noise may reduce the reliability of the classification’s result. This paper presents an Adaptive Morphological Mean Filter (AMMF for smoothing the original noise of VHR imagery and improving the classification’s performance. AMMF is a shape-adaptive filter which is constructed by detecting gradually the spectral similarity between a kernel-anchored pixel and its contextual pixels through an extension-detector with 8-neighbouring pixels, and the spectral value of the kernel-anchored pixel is instead by the mean of group pixels within the adaptive region. The classification maps based on the AMMF are compared with the classification of VHR images based on the homologous filter processing, such as Mean Filter (MF and Median Filter(MedF. The experimental results suggest the following: 1 VHR image processed using AMMF can not only preserve the detail information among inter-classes but also smooth the noise within intra-class; 2 The proposed AMMF processing can improve the classification’s performance of VHR image, and it obtains a better visual performance and accuracy while comparing with MF and MedF.

  17. Nonlinear Adaptive Power-Level Control for Modular High Temperature Gas-Cooled Reactors

    Science.gov (United States)

    Dong, Zhe

    2013-04-01

    After the Fukushima nuclear accident, much more attention has to be drawn on the safety issues. The improvement of safety has already become the focus of the developing trend of the nuclear energy systems. Due to the inherent safety feature and the potential economic competitiveness, the modular high temperature gas-cooled reactor (MHTGR) has been seen as the central part of the next generation of nuclear plant (NGNP). Power-level control is one of the key techniques that guarantee the safe, stable and efficient operation for nuclear reactors. Since the MHTGR dynamics has the features of strong nonlinearity and uncertainty, in order to improve the operation performance, it is meaningful to develop the nonlinear adaptive power-level control law for the MHTGR. Based on using the natural dynamic features beneficial to system stabilization, a novel nonlinear adaptive power-level control is given for the MHTGR in this paper. It is theoretically proved that this newly-built controller does not only provide globally asymptotic closed-loop stability but is also adaptive to the system uncertainty. This control law is then applied to the power-level regulation of the pebble-bed MHTGR of the HTR-PM power plant. Numerical simulation results show the feasibility of this control law and the relationship between the performance and controller parameters.

  18. Mixed models for selection of Jatropha progenies with high adaptability and yield stability in Brazilian regions.

    Science.gov (United States)

    Teodoro, P E; Bhering, L L; Costa, R D; Rocha, R B; Laviola, B G

    2016-08-19

    The aim of this study was to estimate genetic parameters via mixed models and simultaneously to select Jatropha progenies grown in three regions of Brazil that meet high adaptability and stability. From a previous phenotypic selection, three progeny tests were installed in 2008 in the municipalities of Planaltina-DF (Midwest), Nova Porteirinha-MG (Southeast), and Pelotas-RS (South). We evaluated 18 families of half-sib in a randomized block design with three replications. Genetic parameters were estimated using restricted maximum likelihood/best linear unbiased prediction. Selection was based on the harmonic mean of the relative performance of genetic values method in three strategies considering: 1) performance in each environment (with interaction effect); 2) performance in each environment (with interaction effect); and 3) simultaneous selection for grain yield, stability and adaptability. Accuracy obtained (91%) reveals excellent experimental quality and consequently safety and credibility in the selection of superior progenies for grain yield. The gain with the selection of the best five progenies was more than 20%, regardless of the selection strategy. Thus, based on the three selection strategies used in this study, the progenies 4, 11, and 3 (selected in all environments and the mean environment and by adaptability and phenotypic stability methods) are the most suitable for growing in the three regions evaluated.

  19. Complexity control algorithm based on adaptive mode selection for interframe coding in high efficiency video coding

    Science.gov (United States)

    Chen, Gang; Yang, Bing; Zhang, Xiaoyun; Gao, Zhiyong

    2017-07-01

    The latest high efficiency video coding (HEVC) standard significantly increases the encoding complexity for improving its coding efficiency. Due to the limited computational capability of handheld devices, complexity constrained video coding has drawn great attention in recent years. A complexity control algorithm based on adaptive mode selection is proposed for interframe coding in HEVC. Considering the direct proportionality between encoding time and computational complexity, the computational complexity is measured in terms of encoding time. First, complexity is mapped to a target in terms of prediction modes. Then, an adaptive mode selection algorithm is proposed for the mode decision process. Specifically, the optimal mode combination scheme that is chosen through offline statistics is developed at low complexity. If the complexity budget has not been used up, an adaptive mode sorting method is employed to further improve coding efficiency. The experimental results show that the proposed algorithm achieves a very large complexity control range (as low as 10%) for the HEVC encoder while maintaining good rate-distortion performance. For the lowdelayP condition, compared with the direct resource allocation method and the state-of-the-art method, an average gain of 0.63 and 0.17 dB in BDPSNR is observed for 18 sequences when the target complexity is around 40%.

  20. Adaptive Behavior Ratings Correlate with Symptomatology and IQ among Individuals with High-Functioning Autism Spectrum Disorders

    Science.gov (United States)

    Kenworthy, Lauren; Case, Laura; Harms, Madeline B.; Martin, Alex; Wallace, Gregory L.

    2010-01-01

    Caregiver report on the Adaptive Behavior Assessment System-II (ABAS) for 40 high-functioning individuals with Autism Spectrum Disorders (ASD) and 30 typically developing (TD) individuals matched for age, IQ, and sex ratio revealed global adaptive behavior deficits in ASD, with social skills impairments particularly prominent. Within the ASD…

  1. An Integrative Genomic Island Affects the Adaptations of Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii to High Temperature and High Hydrostatic Pressure

    Directory of Open Access Journals (Sweden)

    Zhen Li

    2016-11-01

    Full Text Available Deep-sea hydrothermal vent environments are characterized by high hydrostatic pressure and sharp temperature and chemical gradients. Horizontal gene transfer is thought to play an important role in the microbial adaptation to such an extreme environment. In this study, a 21.4-kb DNA fragment was identified as a genomic island, designated PYG1, in the genomic sequence of the piezophilic hyperthermophile Pyrococcus yayanosii. According to the sequence alignment and functional annotation, the genes in PYG1 could tentatively be divided into five modules, with functions related to mobility, DNA repair, metabolic processes and the toxin-antitoxin system. Integrase can mediate the site-specific integration and excision of PYG1 in the chromosome of P. yayanosii A1. Gene replacement of PYG1 with a SimR cassette was successful. The growth of the mutant strain ∆PYG1 was compared with its parent strain P. yayanosii A2 under various stress conditions, including different pH, salinity, temperature and hydrostatic pressure. The ∆PYG1 mutant strain showed reduced growth when grown at 100 °C, while the biomass of ∆PYG1 increased significantly when cultured at 80 MPa. Differential expression of the genes in module Ⅲ of PYG1 was observed under different temperature and pressure conditions. This study demonstrates the first example of an archaeal integrative genomic island that could affect the adaptation of the hyperthermophilic piezophile P. yayanosii to high temperature and high hydrostatic pressure.

  2. Physiological Adaptations to Hypoxic vs. Normoxic Training during Intermittent Living High

    Directory of Open Access Journals (Sweden)

    Stefan De Smet

    2017-05-01

    Full Text Available In the setting of “living high,” it is unclear whether high-intensity interval training (HIIT should be performed “low” or “high” to stimulate muscular and performance adaptations. Therefore, 10 physically active males participated in a 5-week “live high-train low or high” program (TR, whilst eight subjects were not engaged in any altitude or training intervention (CON. Five days per week (~15.5 h per day, TR was exposed to normobaric hypoxia simulating progressively increasing altitude of ~2,000–3,250 m. Three times per week, TR performed HIIT, administered as unilateral knee-extension training, with one leg in normobaric hypoxia (~4,300 m; TRHYP and with the other leg in normoxia (TRNOR. “Living high” elicited a consistent elevation in serum erythropoietin concentrations which adequately predicted the increase in hemoglobin mass (r = 0.78, P < 0.05; TR: +2.6%, P < 0.05; CON: −0.7%, P > 0.05. Muscle oxygenation during training was lower in TRHYP vs. TRNOR (P < 0.05. Muscle homogenate buffering capacity and pH-regulating protein abundance were similar between pretest and posttest. Oscillations in muscle blood volume during repeated sprints, as estimated by oscillations in NIRS-derived tHb, increased from pretest to posttest in TRHYP (~80%, P < 0.01 but not in TRNOR (~50%, P = 0.08. Muscle capillarity (~15% as well as repeated-sprint ability (~8% and 3-min maximal performance (~10–15% increased similarly in both legs (P < 0.05. Maximal isometric strength increased in TRHYP (~8%, P < 0.05 but not in TRNOR (~4%, P > 0.05. In conclusion, muscular and performance adaptations were largely similar following normoxic vs. hypoxic HIIT. However, hypoxic HIIT stimulated adaptations in isometric strength and muscle perfusion during intermittent sprinting.

  3. High-resolution nanotransfer printing applicable to diverse surfaces via interface-targeted adhesion switching

    Science.gov (United States)

    Jeong, Jae Won; Yang, Se Ryeun; Hur, Yoon Hyung; Kim, Seong Wan; Baek, Kwang Min; Yim, Soonmin; Jang, Hyun-Ik; Park, Jae Hong; Lee, Seung Yong; Park, Chong-Ook; Jung, Yeon Sik

    2014-11-01

    Nanotransfer printing technology offers outstanding simplicity and throughput in the fabrication of transistors, metamaterials, epidermal sensors and other emerging devices. Nevertheless, the development of a large-area sub-50 nm nanotransfer printing process has been hindered by fundamental reliability issues in the replication of high-resolution templates and in the release of generated nanostructures. Here we present a solvent-assisted nanotransfer printing technique based on high-fidelity replication of sub-20 nm patterns using a dual-functional bilayer polymer thin film. For uniform and fast release of nanostructures on diverse receiver surfaces, interface-specific adhesion control is realized by employing a polydimethylsiloxane gel pad as a solvent-emitting transfer medium, providing unusual printing capability even on biological surfaces such as human skin and fruit peels. Based on this principle, we also demonstrate reliable printing of high-density metallic nanostructures for non-destructive and rapid surface-enhanced Raman spectroscopy analyses and for hydrogen detection sensors with excellent responsiveness.

  4. High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

    Science.gov (United States)

    Ng, Terry Fei Fan; Marine, Rachel; Wang, Chunlin; Simmonds, Peter; Kapusinszky, Beatrix; Bodhidatta, Ladaporn; Oderinde, Bamidele Soji; Wommack, K. Eric

    2012-01-01

    Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high-throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, 90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses. PMID:22933275

  5. Discrete-time adaptive backstepping nonlinear control via high-order neural networks.

    Science.gov (United States)

    Alanis, Alma Y; Sanchez, Edgar N; Loukianov, Alexander G

    2007-07-01

    This paper deals with adaptive tracking for discrete-time multiple-input-multiple-output (MIMO) nonlinear systems in presence of bounded disturbances. In this paper, a high-order neural network (HONN) structure is used to approximate a control law designed by the backstepping technique, applied to a block strict feedback form (BSFF). This paper also includes the respective stability analysis, on the basis of the Lyapunov approach, for the whole controlled system, including the extended Kalman filter (EKF)-based NN learning algorithm. Applicability of the scheme is illustrated via simulation for a discrete-time nonlinear model of an electric induction motor.

  6. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption

    Directory of Open Access Journals (Sweden)

    Hu Quanjun

    2012-11-01

    Full Text Available Abstract Background The yak (Bos grunniens is a long-haired bovine that lives at high altitudes and is an important source of milk, meat, fiber and fuel. The recent sequencing, assembly and annotation of its genome are expected to further our understanding of the means by which it has adapted to life at high altitudes and its ecologically important traits. Description The Yak Genome Database (YGD is an internet-based resource that provides access to genomic sequence data and predicted functional information concerning the genes and proteins of Bos grunniens. The curated data stored in the YGD includes genome sequences, predicted genes and associated annotations, non-coding RNA sequences, transposable elements, single nucleotide variants, and three-way whole-genome alignments between human, cattle and yak. YGD offers useful searching and data mining tools, including the ability to search for genes by name or using function keywords as well as GBrowse genome browsers and/or BLAST servers, which can be used to visualize genome regions and identify similar sequences. Sequence data from the YGD can also be downloaded to perform local searches. Conclusions A new yak genome database (YGD has been developed to facilitate studies on high-altitude adaption and bovine genomics. The database will be continuously updated to incorporate new information such as transcriptome data and population resequencing data. The YGD can be accessed at http://me.lzu.edu.cn/yak.

  7. Adaptation, acclimation, and assembly: How optimality principles govern the scaling of form, function, and diversity of ecosystem function in the light of climate change.

    Science.gov (United States)

    Enquist, B. J.

    2016-12-01

    The link between variation in species-specific traits - due to acclimation, adaptation, and how ecological communities assemble in time and space - and larger scale ecosystem processes is an important focus for global change research. Understanding such linkages requires synthesis of evolutionary, biogeograpahic, and biogeochemical approaches. Recent observations reveal several paradoxical patterns across ecosystems. Optimality principles provide a novel framework for generating numerous predictions for how ecosystems have and will reorganize and respond to climate change. Tropical elevation gradients are natural laboratories to assess how changing climate can ramify to influence tropical forest diversity and ecosystem functioning. We tested several new predictions from trait- and metabolic scaling theories by assessing the covariation between climate, traits, biomass and gross and net primary productivity (GPP and NPP) across tropical forest plots spanning elevation gradients. We measured multiple leaf physiological, morphological, and stoichiometric traits linked to variation in tree growth. Consistent with theory, observed decreases in NPP and GPP with temperature were best predicted by forest biomass, and scaled allometrically as predicted by theory but the effect of temperature was much less, characterized by a kinetic response much lower ( 0.1eV) than predicted ( 0.65eV). This is likely due to an observed exponential increase in the mean community leaf P:N ratio and photosynthetic nutrient use efficiency with decreases in temperature. Our results are consistent with predictions from Trait Driver Theory, where adaptive/acclamatory shifts in plant traits compensate for the kinetic effects of temperature on tree growth. Further, most of the traits measured showed significantly skewed trait distributions consistent with recent observations that observed shifts in species composition. The development of trait-based scaling theory provides a robust basis to predict

  8. Adaptive Partitioning Algorithms for Optimized State Replication of Highly Available Services

    DEFF Research Database (Denmark)

    Matthiesen, Erling Vestergaard; Renier, Thibault; Bozinovski, Marjan

    2005-01-01

    in an ad-hoc setting where the application will have to adapt to highly fluctuating network parameters. By knowing the characteristics of the network, the servers can be partitioned in an efficient manner, thereby increasing consistency. Subset division algorithms that take the characteristics......In order to provide highly available, stateful services it is often necessary to setup several servers that actively provide the service, while performing dynamic state-replication between them. As the number of servers increases, scalability issues arise because of the large amount of state...... sharing messages. In this paper, methods are provided to reduce the amount of state sharing messages, while reserving high availability, scalability, and consistency. To reduce the amount of state update messages, the servers are divided into subsets of servers. The stateful services could be running...

  9. High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

    KAUST Repository

    Michoud, Gregoire

    2016-06-02

    Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and Clustered Regularly Interspaced Short Palindromic Repeats sequences associated with Cellular apoptosis susceptibility proteins.

  10. Helicobacter pylori adaptation in vivo in response to a high-salt diet.

    Science.gov (United States)

    Loh, John T; Gaddy, Jennifer A; Algood, Holly M Scott; Gaudieri, Silvana; Mallal, Simon; Cover, Timothy L

    2015-12-01

    Helicobacter pylori exhibits a high level of intraspecies genetic diversity. In this study, we investigated whether the diversification of H. pylori is influenced by the composition of the diet. Specifically, we investigated the effect of a high-salt diet (a known risk factor for gastric adenocarcinoma) on H. pylori diversification within a host. We analyzed H. pylori strains isolated from Mongolian gerbils fed either a high-salt diet or a regular diet for 4 months by proteomic and whole-genome sequencing methods. Compared to the input strain and output strains from animals fed a regular diet, the output strains from animals fed a high-salt diet produced higher levels of proteins involved in iron acquisition and oxidative-stress resistance. Several of these changes were attributable to a nonsynonymous mutation in fur (fur-R88H). Further experiments indicated that this mutation conferred increased resistance to high-salt conditions and oxidative stress. We propose a model in which a high-salt diet leads to high levels of gastric inflammation and associated oxidative stress in H. pylori-infected animals and that these conditions, along with the high intraluminal concentrations of sodium chloride, lead to selection of H. pylori strains that are most fit for growth in this environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  11. Diversification of the monoterpene synthase gene family (TPSb) in Protium, a highly diverse genus of tropical trees.

    Science.gov (United States)

    Zapata, Felipe; Fine, Paul V A

    2013-09-01

    Plant monoterpenes are a diverse class of secondary metabolites mediating biotic and abiotic interactions with direct effects on plant fitness. To evaluate the hypothesis that monoterpene diversity is related to functional diversification after gene duplication, we reconstructed the evolutionary history of monoterpene synthases (TPSb)--the genes underlying monoterpene synthesis--in Protium, a taxonomically and chemically diverse genus of tropical trees. We isolated multiple copies of TPSb genes from chemically divergent Protium species, reconstructed the phylogeny of this gene family, used maximum-likelihood estimation of selection coefficients, and inferred residues evolving under positive selection. We found evidence for one ancient and multiple more recent duplication events giving rise to three, and potentially five, copies of TPSb genes currently present in Protium. There was evidence for adaptive evolution in one copy with a positively selected residue likely involved in protein folding and product specificity. All other copies were inferred to be evolving under a combination of stabilizing and/or relaxed selection. Although gene copy number is consistent with the extensive phenotypic diversity in monoterpenes shown in Protium, selection analyses suggest that not all copies are undergoing divergent selection consistent with a coevolutionary arms race with enemies, but instead may be under stabilizing and relaxed selection consistent with signaling or physiological stress functionality. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. High photobiont diversity in the common European soil crust lichen Psora decipiens.

    Science.gov (United States)

    Ruprecht, Ulrike; Brunauer, Georg; Türk, Roman

    2014-01-01

    The genetic diversity of green algal photobionts (chlorobionts) in soil crust forming lichens was studied as part of the SCIN-project (Soil Crust InterNational). A total of 64 lichen samples were collected from four different sites along latitudinal and altitudinal gradients in Europe (Tabernas/Spain; Hochtor-Großglockner/Austria; Gynge Alvar/Sweden; Ruine Homburg/Germany). The dominant lichen species at all four sites was Psora decipiens, often occurring with Buellia elegans, Fulgensia bracteata, F. fulgens and Peltigera rufescens. Genetic identification of chlorobionts was carried out using the nuclear marker (nrITS) and a chloroplast marker (psbL-J). We found P. decipiens to be associated with several different species of Trebouxia and Asterochloris, although previously described to only have Asterochloris sp. The phylogenetic analyses revealed a high chlorobiont diversity with 12 well supported clades, including Trebouxia asymmetrica, T. jamesii, T. impressa and other, as yet taxonomically unidentified clades (Trebouxia sp. URa1-4, T. sp. URa6, T. sp. URa7-13). Additionally, five clades of Asterochloris were identified (A. magna, A. sp. URa14 -17). Most of the chlorobiont species appeared to be cosmopolitan, but five clades were unevenly distributed between the sampling sites with only Trebouxia being found in the warm and dry Spanish habitats and combinations of Trebouxia and Asterochloris in the cooler and more humid habitats. The wide range of chlorobiont species might contribute to the observed domination of P. decipiens at all four research sites of the SCIN project which range from a desert in Spain to an alpine site in the Alps of Austria.

  13. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Yanying Zhang

    2017-10-01

    Full Text Available Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

  14. Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges.

    Science.gov (United States)

    Ribes, Marta; Dziallas, Claudia; Coma, Rafel; Riemann, Lasse

    2015-09-01

    Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (nifH) and measured N2 fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories. nifH genes were found in all LMA species and sporadically in one HMA species, and about half of the nifH gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission. (15)N2-enriched incubations showed that N2 fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of (15)N to (14)N in sponge tissue indicated that N2 fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Collaboratively Adaptive Vibration Sensing System for High-fidelity Monitoring of Structural Responses Induced by Pedestrians

    Directory of Open Access Journals (Sweden)

    Shijia Pan

    2017-05-01

    Full Text Available This paper presents a collaboratively adaptive vibration monitoring system that captures high-fidelity structural vibration signals induced by pedestrians. These signals can be used for various human activities’ monitoring by inferring information about the impact sources, such as pedestrian footsteps, door opening and closing, and dragging objects. Such applications often require high-fidelity (high resolution and low distortion signals. Traditionally, expensive high resolution and high dynamic range sensors are adopted to ensure sufficient resolution. However, for sensing systems that use low-cost sensing devices, the resolution and dynamic range are often limited; hence this type of sensing methods is not well explored ubiquitously. We propose a low-cost sensing system that utilizes (1 a heuristic model of the investigating excitations and (2 shared information through networked devices to adapt hardware configurations and obtain high-fidelity structural vibration signals. To further explain the system, we use indoor pedestrian footstep sensing through ambient structural vibration as an example to demonstrate the system performance. We evaluate the application with three metrics that measure the signal quality from different aspects: the sufficient resolution rate to present signal resolution improvement without clipping, the clipping rate to measure the distortion of the footstep signal, and the signal magnitude to quantify the detailed resolution of the detected footstep signal. In experiments conducted in a school building, our system demonstrated up to 2× increase on the sufficient resolution rate and 2× less error rate when used to locate the pedestrians as they walk along the hallway, compared to a fixed sensing setting.

  16. Depth and breadth: Bridging the gap between scientific inquiry and high-stakes testing with diverse junior high school students

    Science.gov (United States)

    Kang, Jee Sun Emily

    This study explored how inquiry-based teaching and learning processes occurred in two teachers' diverse 8th grade Physical Science classrooms in a Program Improvement junior high school within the context of high-stakes standardized testing. Instructors for the courses examined included not only the two 8th grade science teachers, but also graduate fellows from a nearby university. Research was drawn from inquiry-based instruction in science education, the achievement gap, and the high stakes testing movement, as well as situated learning theory to understand how opportunities for inquiry were negotiated within the diverse classroom context. Transcripts of taped class sessions; student work samples; interviews of teachers and students; and scores from the California Standards Test in science were collected and analyzed. Findings indicated that the teachers provided structured inquiry in order to support their students in learning about forces and to prepare them for the standardized test. Teachers also supported students in generating evidence-based explanations, connecting inquiry-based investigations with content on forces, proficiently using science vocabulary, and connecting concepts about forces to their daily lives. Findings from classroom data revealed constraints to student learning: students' limited language proficiency, peer counter culture, and limited time. Supports were evidenced as well: graduate fellows' support during investigations, teachers' guided questioning, standardized test preparation, literacy support, and home-school connections. There was no statistical difference in achievement on the Forces Unit test or science standardized test between classes with graduate fellows and without fellows. There was also no statistical difference in student performance between the two teachers' classrooms, even though their teaching styles were very different. However, there was a strong correlation between students' achievement on the chapter test and

  17. Diagnostic criteria of high-altitude de-adaptation for high-altitude migrants returning to the plains: a multicenter, randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Qi-quan ZHOU

    2012-02-01

    Full Text Available Objective  To investigate the diagnostic method of high-altitude de-adaptation and constitute the diagnostic criteria of high-altitude de-adaptation for people returning to the plains from high-altitude. Methods  Epidemiological survey and clinical multicenter randomized controlled studies were used to determine/perform blood picture, routine urine analysis, routine stool examination, myocardial enzymes, liver and kidney functions, nerve function, sex hormone, microalbuminuria, ECG, echocardiography, pulmonary function tests, and so on, in 3011 subjects after they returned to the plains from high-altitude. The diagnostic criteria of high-altitude de-adaptation were formulated by a comparative analysis of the obtained data with those of healthy subjects living in the same area, altitude, and age. The regularity and characteristics of high-altitude de-adaptation syndrome were found and diagnostic criteria for high-altitude de-adaptation was established based on the results. Results  The investigative results showed that the incidence of high-altitude de-adaptation syndrome was found in 84.36% of population returning to the plains from high-altitude. About 60% of them were considered to have mild reactions, 30% medium, and only 10% were severe. The lower the altitude they returned to, the longer the duration of stay in highland, and the heavier the labor they engaged in high altitude, the higher the incidence rate of high-altitude de-adaptation syndrome was. Patients with high-altitude de-adaptation syndrome exhibited hematological abnormality and abnormal ventricular function, especially the right ventricular diastolic function after returning for 1 year to 5 years. Long-term hypoxia exposure often caused obvious change in cardiac morphology with left and right ventricular hypertrophy, particularly the right ventricle. In addition, low blood pressure and low pulse pressure were found at times. Microalbuminuria was found in some high-altitude de-adaptation

  18. Confronting the "Acid Test": Educators' Perspectives on Expanding Access to Advanced Placement at a Diverse Florida High School

    Science.gov (United States)

    Rowland, M. Lance; Shircliffe, Barbara J.

    2016-01-01

    This study examines educators' perspectives on accountability mandates designed to expand access to the College Board's Advanced Placement (AP) classes to traditionally underserved students at a diverse suburban high school in Florida, Palm Crest High School. Consistent with Elmore (1979), district and site-based administrators focused on the…

  19. High-throughput heterogeneous integration of diverse nanomaterials on a single chip for sensing applications.

    Directory of Open Access Journals (Sweden)

    Samuel MacNaughton

    Full Text Available There is a large variety of nanomaterials each with unique electronic, optical and sensing properties. However, there is currently no paradigm for integration of different nanomaterials on a single chip in a low-cost high-throughput manner. We present a high throughput integration approach based on spatially controlled dielectrophoresis executed sequentially for each nanomaterial type to realize a scalable array of individually addressable assemblies of graphene, carbon nanotubes, metal oxide nanowires and conductive polymers on a single chip. This is a first time where such a diversity of nanomaterials has been assembled on the same layer in a single chip. The resolution of assembly can range from mesoscale to microscale and is limited only by the size and spacing of the underlying electrodes on chip used for assembly. While many applications are possible, the utility of such an array is demonstrated with an example application of a chemical sensor array for detection of volatile organic compounds below parts-per-million sensitivity.

  20. Endohedral Metallofullerene as Molecular High Spin Qubit: Diverse Rabi Cycles in Gd2@C79N.

    Science.gov (United States)

    Hu, Ziqi; Dong, Bo-Wei; Liu, Zheng; Liu, Jun-Jie; Su, Jie; Yu, Changcheng; Xiong, Jin; Shi, Di-Er; Wang, Yuanyuan; Wang, Bing-Wu; Ardavan, Arzhang; Shi, Zujin; Jiang, Shang-Da; Gao, Song

    2018-01-24

    An anisotropic high-spin qubit with long coherence time could scale the quantum system up. It has been proposed that Grover's algorithm can be implemented in such systems. Dimetallic aza[80]fullerenes M 2 @C 79 N (M = Y or Gd) possess an unpaired electron located between two metal ions, offering an opportunity to manipulate spin(s) protected in the cage for quantum information processing. Herein, we report the crystallographic determination of Gd 2 @C 79 N for the first time. This molecular magnet with a collective high-spin ground state (S = 15/2) generated by strong magnetic coupling (J Gd-Rad = 350 ± 20 cm -1 ) has been unambiguously validated by magnetic susceptibility experiments. Gd 2 @C 79 N has quantum coherence and diverse Rabi cycles, allowing arbitrary superposition state manipulation between each adjacent level. The phase memory time reaches 5 μs at 5 K by dynamic decoupling. This molecule fulfills the requirements of Grover's searching algorithm proposed by Leuenberger and Loss.

  1. Tropical Refuges with Exceptionally High Phylogenetic Diversity Reveal Contrasting Phylogenetic Structures

    Directory of Open Access Journals (Sweden)

    Lara Pugliesi

    2015-01-01

    Full Text Available Loss of phylogenetic diversity (PD has gained increasing attention in conservation biology. However, PD is not equally distributed in a phylogeny and can be better assessed when species relatedness (phylogenetic structure: PS is also considered. Here, we investigate PD and PS in two refuges of biodiversity in northeastern Brazil: the Bahia Costal Forest (BCF in the Atlantic Forest domain and Chapada Diamantina (CD in the Caatinga domain. We used geographic data of 205 species at two spatial scales and a chronogram of Apocynaceae based on matK sequences to estimate PD and PS. Our results show an exceptionally high PD in both refuges, overdispersed in BCF and clustered in CD, although this difference is less evident or absent for recent relationships, especially at a smaller spatial scale. Overall, PS suggests long-term competitive exclusion under climatic stability, currently balanced by habitat filtering, in BCF, and biome conservatism and limited dispersal leading to in situ diversification and high density of microendemics in CD. The phylogenetically clustered flora in CD, also threatened by climate changes, are naturally more vulnerable than BCF. Therefore, while in situ conservation may ensure protection of biodiversity in BCF, emergency ex situ conservation is strongly recommended in CD.

  2. High Genetic Diversity of Measles Virus, World Health Organization European Region, 2005–2006

    Science.gov (United States)

    Brown, Kevin E.; Jin, Li; Santibanez, Sabine; Shulga, Sergey V.; Aboudy, Yair; Demchyshyna, Irina V.; Djemileva, Sultana; Echevarria, Juan E.; Featherstone, David F.; Hukic, Mirsada; Johansen, Kari; Litwinska, Bogumila; Lopareva, Elena; Lupulescu, Emilia; Mentis, Andreas; Mihneva, Zefira; Mosquera, Maria M.; Muscat, Mark; Naumova, M.A.; Nedeljkovic, Jasminka; Nekrasova, Ljubov S.; Magurano, Fabio; Fortuna, Claudia; Rebelo de Andrade, Helena; Richard, Jean-Luc; Robo, Alma; Rota, Paul A.; Samoilovich, Elena O.; Sarv, Inna; Semeiko, Galina V.; Shugayev, Nazim; Utegenova, Elmira S.; van Binnendijk, Rob; Vinner, Lasse; Waku-Kouomou, Diane; Wild, T. Fabian; Brown, David W.G.; Mankertz, Annette; Muller, Claude P.; Mulders, Mick N.

    2008-01-01

    During 2005–2006, nine measles virus (MV) genotypes were identified throughout the World Health Organization European Region. All major epidemics were associated with genotypes D4, D6, and B3. Other genotypes (B2, D5, D8, D9, G2, and H1) were only found in limited numbers of cases after importation from other continents. The genetic diversity of endemic D6 strains was low; genotypes C2 and D7, circulating in Europe until recent years, were no longer identified. The transmission chains of several indigenous MV strains may thus have been interrupted by enhanced vaccination. However, multiple importations from Africa and Asia and virus introduction into highly mobile and unvaccinated communities caused a massive spread of D4 and B3 strains throughout much of the region. Thus, despite the reduction of endemic MV circulation, importation of MV from other continents caused prolonged circulation and large outbreaks after their introduction into unvaccinated and highly mobile communities. PMID:18258089

  3. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

    Science.gov (United States)

    Tu, Zong-cai; Wang, Xiao-lan

    2016-01-01

    Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food. PMID:27992473

  4. Retrocyte Display® technology: generation and screening of a high diversity cellular antibody library.

    Science.gov (United States)

    Breous-Nystrom, Ekaterina; Schultze, Kornelia; Meier, Marco; Flueck, Lukas; Holzer, Christina; Boll, Melanie; Seibert, Volker; Schuster, Andrea; Blanusa, Milan; Schaefer, Verena; Grawunder, Ulf; Martin-Parras, Luis; van Dijk, Marc A

    2014-01-01

    Over the last nearly three decades in vitro display technologies have played an important role in the discovery and optimization of antibodies and other proteins for therapeutic applications. Here we describe the use of retroviral expression technology for the display of full-length IgG on B lineage cells in vitro with a hallmark of a tight and stable genotype to phenotype coupling. We describe the creation of a high-diversity (>1.0E09 different heavy- and light-chain combinations) cell displayed fully human antibody library from healthy donor-derived heavy- and light-chain gene libraries, and demonstrate the recovery of high affinity target-specific antibodies from this library by staining of cells with a labeled target antigen and their magnetic- and flow cytometry-based cell sorting. The present technology represents a further evolution in the discovery of full-length, fully human antibodies using mammalian display, and is termed Retrocyte Display® (Retroviral B lymphocyte Display). Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Adaptability and stability of corn hybrids grown for high grain yield

    Directory of Open Access Journals (Sweden)

    Paulo Roberto da Silva

    2014-04-01

    Full Text Available The objective of the present study was to evaluate the adaptability and stability of corn hybrids for grain yield in environments with high crop management standards. Ten corn hybrids were evaluated for grain yield in 48 environments, consisting of 12 locations over a period of four years inSouth Brazil. A complete experimental, random block design with two repetitions was used. Adaptability and stability were analyzed according to the bi-segmented discontinuous model with measurement errors in the variables. The behavior of hybrids was studied as a function of the average yield in the inferior and/or superior environments, the estimates of the parameters of the equation, and the quality of the fit. The 30F36 hybrid behaved better in the superior environments and it is indicated for farmers who adopt the highest technological standards for crop management, whereas the 30F53 hybrid was classified as close to ideal; that is, it is indicated for cultivation under various environmental conditions. The 30R50 and 32R48 hybrids are appropriate only for average environments. There is a very good phenotypic stability in simple hybrids associated with high potential yield.

  6. Interferometric adaptive optics for high power laser pointing, wave-front control and phasing

    Energy Technology Data Exchange (ETDEWEB)

    Baker, K L; Stappaerts, E A; Homoelle, D C; Henesian, M A; Bliss, E S; Siders, C W; Barty, C J

    2009-01-21

    Implementing the capability to perform fast ignition experiments, as well as, radiography experiments on the National Ignition Facility (NIF) places stringent requirements on the control of each of the beam's pointing and overall wavefront quality. One quad of the NIF beams, 4 beam pairs, will be utilized for these experiments and hydrodynamic and particle-in-cell simulations indicate that for the fast ignition experiments, these beams will be required to deliver 50% (4.0 kJ) of their total energy (7.96 kJ) within a 40 {micro}m diameter spot at the end of a fast ignition cone target. This requirement implies a stringent pointing and overall phase conjugation error budget on the adaptive optics system used to correct these beam lines. The overall encircled energy requirement is more readily met by phasing of the beams in pairs but still requires high Strehl ratios, Sr, and rms tip/tilt errors of approximately one {micro}rad. To accomplish this task we have designed an interferometric adaptive optics system capable of beam pointing, high Strehl ratio and beam phasing with a single pixilated MEMS deformable mirror and interferometric wave-front sensor. We present the design of a testbed used to evaluate the performance of this wave-front sensor below along with simulations of its expected performance level.

  7. High-Contrast Imaging using Adaptive Optics for Extrasolar Planet Detection

    Energy Technology Data Exchange (ETDEWEB)

    Evans, Julia Wilhelmsen [Univ. of California, Davis, CA (United States)

    2006-01-01

    Direct imaging of extrasolar planets is an important, but challenging, next step in planetary science. Most planets identified to date have been detected indirectly--not by emitted or reflected light but through the effect of the planet on the parent star. For example, radial velocity techniques measure the doppler shift in the spectrum of the star produced by the presence of a planet. Indirect techniques only probe about 15% of the orbital parameter space of our solar system. Direct methods would probe new parameter space, and the detected light can be analyzed spectroscopically, providing new information about detected planets. High contrast adaptive optics systems, also known as Extreme Adaptive Optics (ExAO), will require contrasts of between 10-6 and 10-7 at angles of 4-24 λ/D on an 8-m class telescope to image young Jupiter-like planets still warm with the heat of formation. Contrast is defined as the intensity ratio of the dark wings of the image, where a planet might be, to the bright core of the star. Such instruments will be technically challenging, requiring high order adaptive optics with > 2000 actuators and improved diffraction suppression. Contrast is ultimately limited by residual static wavefront errors, so an extrasolar planet imager will require wavefront control with an accuracy of better than 1 nm rms within the low- to mid-spatial frequency range. Laboratory demonstrations are critical to instrument development. The ExAO testbed at the Laboratory for Adaptive Optics was designed with low wavefront error and precision optical metrology, which is used to explore contrast limits and develop the technology needed for an extrasolar planet imager. A state-of-the-art, 1024-actuator micro-electrical-mechanical-systems (MEMS) deformable mirror was installed and characterized to provide active wavefront control and test this novel technology. I present 6.5 x 10-8 contrast measurements with a prolate shaped pupil and

  8. High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

    NARCIS (Netherlands)

    Sánchez-Ramírez, Santiago; Etienne, Rampal S; Moncalvo, Jean-Marc

    2015-01-01

    Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity build-up, namely speciation and extinction. The general latitudinal diversity

  9. High Prevalence of Diverse Insertion Sequences within the rRNA Operons of Mycoplasma bovis.

    Science.gov (United States)

    Amram, Eytan; Borovok, Ilya; Nachum-Biala, Yaarit; Ayling, Roger; Lerner, Uri; Harrus, Shimon; Lysnyansky, Inna

    2016-11-01

    Insertion sequences (ISs) are widespread in the genome of Mycoplasma bovis strain PG45, but no ISs were identified within its two tandemly positioned rRNA operons (rrn1 and rrn2). However, characterization of the rrn locus in 70 M. bovis isolates revealed the presence of ISs related to the ISMbov1 (IS30 family) and ISMbov4 (IS4 family) isomers in 35 isolates. ISs were inserted into intergenic region 1 (IGR-1) or IGR-3, which are the putative promoter regions of rrn1 and rrn2, respectively, and into IGR-5, located downstream of the rrl2 gene. Seven different configurations (A to G) of the rrn locus with respect to ISs were identified, including those in five annotated genomes. The transcriptional start site for the single rrn operon in M. bovis strain 88127 was mapped within IGR-1, 60 bp upstream of the rrs gene. Notably, only 1 nucleotide separated the direct repeat (DR) for ISMbov1 and the promoter -35 element in configuration D, while in configuration F, the -35 motif was a part of the ISMbov1 DR. Relative quantitative real-time (qRT) PCR analysis and growth rate comparisons detected a significant increase (P operons that did not have ISs. A high prevalence of IS elements within or close to the M. bovis rrn operon-promoter region may reflect their important role in regulation of both ribosome synthesis and function. Data presented in this study show a high prevalence of diverse ISs within the M. bovis rrn locus resulting in intraspecies variability and diversity. Such abundance of IS elements near or within the rrn locus may offer a selective advantage to M. bovis Moreover, the fact that expression of the rrs genes as well as the number of viable cells increased in the group of strains with IS element insertion within a putative promoter -35 sequence (configuration F) in comparison to that in strains with one or two rrn operons that do not have ISs may serve as a basis for understanding the possible role of M. bovis IS elements in fundamental biological processes

  10. Academic Motivation Scale: adaptation and psychometric analyses for high school and college students

    Directory of Open Access Journals (Sweden)

    Stover JB

    2012-07-01

    Full Text Available Juliana Beatriz Stover,1 Guadalupe de la Iglesia,1 Antonio Ria,l Boubeta,2 Mercedes Fernández Liporace11Buenos Aires University and National Research Council (CONICET, Buenos Aires, Argentina; 2Santiago de Compostela University, Santiago de Compostela, SpainAbstract: The Academic Motivation Scale (AMS, supported in Self-Determination Theory, has been applied in recent decades as well in high school as in college education. Although several versions in Spanish are available, the underlying linguistic and cultural differences raise important issues when they are applied to Latin-American population. Consequently an adapted version of the AMS was developed, and its construct validity was analyzed in Argentine students. Results obtained on a sample that included 723 students from Buenos Aires (393 high school and 330 college students verified adequate psychometric properties in this new version, solving some controversies regarded to its dimensionality.Keywords: Academic Motivation, self-determination, confirmatory factor analysis, internal consistency

  11. Screening tomato genotypes for adaptation to high temperature in West Africa

    DEFF Research Database (Denmark)

    Kugblenu, Yvonne O.; Danso, Eric Oppong; Ofori, Kwadjo

    2013-01-01

    Tomato is an important vegetable widely grown in the tropics due to its nutritional value and financial benefits for farmers. In Ghana, there is an undersupply caused by production ceasing entirely from October to May due to high temperatures. Heat stress has been reported to cause excessive flower...... drop leading to drastic reduction in yield; however, genotypic differences in heat tolerance exist in tomato. A greenhouse experiment was conducted to screen 19 different tomato genotypes for their tolerance to heat stress. The genotypes were selected because they were the commercial varieties widely...... available to farmers. The average day and night temperatures recorded were 33.8°C and 25.9°C, respectively. Cultivars were evaluated for heat adaptation traits such as flower drop and number of fruits. There were highly significant differences between the genotypes for numbers of fruits per plant, ranging...

  12. Adaptive Backstepping Control Based on Floating Offshore High Temperature Superconductor Generator for Wind Turbines

    Directory of Open Access Journals (Sweden)

    Feng Yang

    2014-01-01

    Full Text Available With the rapid development of offshore wind power, the doubly fed induction generator and permanent magnet synchronous generator cannot meet the increasing request of power capacity. Therefore, superconducting generator should be used instead of the traditional motor, which can improve generator efficiency, reduce the weight of wind turbines, and increase system reliability. This paper mainly focuses on nonlinear control in the offshore wind power system which is consisted of a wind turbine and a high temperature superconductor generator. The proposed control approach is based on the adaptive backstepping method. Its main purpose is to regulate the rotor speed and generator voltage, therefore, achieving the maximum power point tracking (MPPT, improving the efficiency of a wind turbine, and then enhancing the system’s stability and robustness under large disturbances. The control approach can ensure high precision of generator speed tracking, which is confirmed in both the theoretical analysis and numerical simulation.

  13. High speed and adaptable error correction for megabit/s rate quantum key distribution.

    Science.gov (United States)

    Dixon, A R; Sato, H

    2014-12-02

    Quantum Key Distribution is moving from its theoretical foundation of unconditional security to rapidly approaching real world installations. A significant part of this move is the orders of magnitude increases in the rate at which secure key bits are distributed. However, these advances have mostly been confined to the physical hardware stage of QKD, with software post-processing often being unable to support the high raw bit rates. In a complete implementation this leads to a bottleneck limiting the final secure key rate of the system unnecessarily. Here we report details of equally high rate error correction which is further adaptable to maximise the secure key rate under a range of different operating conditions. The error correction is implemented both in CPU and GPU using a bi-directional LDPC approach and can provide 90-94% of the ideal secure key rate over all fibre distances from 0-80 km.

  14. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

    Science.gov (United States)

    Martinez, N.; Michoud, G.; Cario, A.; Ollivier, J.; Franzetti, B.; Jebbar, M.; Oger, P.; Peters, J.

    2016-09-01

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.

  15. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

    KAUST Repository

    Martinez, N.

    2016-09-06

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.

  16. Genetic variants in EPAS1 contribute to adaptation to high-altitude hypoxia in Sherpas.

    Directory of Open Access Journals (Sweden)

    Masayuki Hanaoka

    Full Text Available Sherpas comprise a population of Tibetan ancestry in the Himalayan region that is renowned for its mountaineering prowess. The very small amount of available genetic information for Sherpas is insufficient to explain their physiological ability to adapt to high-altitude hypoxia. Recent genetic evidence has indicated that natural selection on the endothelial PAS domain protein 1 (EPAS1 gene was occurred in the Tibetan population during their occupation in the Tibetan Plateau for millennia. Tibetan-specific variations in EPAS1 may regulate the physiological responses to high-altitude hypoxia via a hypoxia-inducible transcription factor pathway. We examined three significant tag single-nucleotide polymorphisms (SNPs, rs13419896, rs4953354, and rs4953388 in the EPAS1 gene in Sherpas, and compared these variants with Tibetan highlanders on the Tibetan Plateau as well as with non-Sherpa lowlanders. We found that Sherpas and Tibetans on the Tibetan Plateau exhibit similar patterns in three EPAS1 significant tag SNPs, but these patterns are the reverse of those in non-Sherpa lowlanders. The three SNPs were in strong linkage in Sherpas, but in weak linkage in non-Sherpas. Importantly, the haplotype structured by the Sherpa-dominant alleles was present in Sherpas but rarely present in non-Sherpas. Surprisingly, the average level of serum erythropoietin in Sherpas at 3440 m was equal to that in non-Sherpas at 1300 m, indicating a resistant response of erythropoietin to high-altitude hypoxia in Sherpas. These observations strongly suggest that EPAS1 is under selection for adaptation to the high-altitude life of Tibetan populations, including Sherpas. Understanding of the mechanism of hypoxia tolerance in Tibetans is expected to provide lights to the therapeutic solutions of some hypoxia-related human diseases, such as cardiovascular disease and cancer.

  17. Influence of dark phase restricted high fat feeding on myocardial adaptation in mice.

    Science.gov (United States)

    Tsai, Ju-Yun; Villegas-Montoya, Carolina; Boland, Brandon B; Blasier, Zachary; Egbejimi, Oluwaseun; Gonzalez, Raquel; Kueht, Michael; McElfresh, Tracy A; Brewer, Rachel A; Chandler, Margaret P; Bray, Molly S; Young, Martin E

    2013-02-01

    Prolonged high fat feeding is associated with myocardial contractile dysfunction in rodents. However, epidemiological data do not necessarily support the concept that fat-enriched diets adversely affect cardiac function in humans. When fed in an ad libitum manner, laboratory rodents consume chow throughout the day. In contrast, humans typically consume food only during the awake phase. Discrepancies between rodent and human feeding behaviors led us to hypothesize that the time of day at which dietary lipids are consumed significantly influences myocardial adaptation. In order to better mimic feeding behavior in humans, mice were fed (either a control or high fat diet) only during the 12-hour dark phase (i.e., no food was provided during the light phase). We report that compared to dark phase restricted control diet fed mice, mice fed a high fat diet during the dark phase exhibit: 1) essentially normal body weight gain and energy balance; 2) increased fatty acid oxidation at whole body, as well as skeletal and cardiac muscle (in the presence of insulin and/or at high workloads) levels; 3) induction of fatty acid responsive genes, including genes promoting triglyceride turnover in the heart; 4) no evidence of cardiac hypertrophy; and 5) persistence/improvement of myocardial contractile function, as assessed ex vivo. These data are consistent with the hypothesis that ingestion of dietary fat only during the more active/awake period allows adequate metabolic adaptation, thereby preserving myocardial contractile function. This article is part of a Special Issue entitled "Focus on cardiac metabolism". Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. High-Altitude Airborne Platform Characterisation of Adaptive Optic Corrected Ground Based Laser

    Science.gov (United States)

    Bennet, F.; Petkovic, M.; Sheard, B.; Greene, B.

    Adaptive optics can be used for more than astronomical imaging with large telescopes. The Research School of Astronomy and Astrophysics (RSAA) and the Space Environment Management Research Centre (SERC) at the Mount Stromlo Observatory in Canberra, Australia, have been developing adaptive optics (AO) for space environment management. Turbulence in the atmosphere causes optical signals to become degraded during propagation, which reduces the effective aperture of your transmitting or receiving telescope. An AO system measures and corrects for the turbulence in the atmosphere, allowing for greater resolution of optical signals. AO can be used to correct a laser beam propagating from the ground into space, or high-altitude airborne platform. The AO system performance depends heavily on the chosen site and system design. In order to properly design and implement a cost-effective AO system to propagate a laser into orbit, we propose using high-altitude platforms to measure AO system performance directly as a precursor in-orbit measurements. SERC plan on demonstrating remote manoeuvre of an orbiting object using photon pressure from an AO corrected high power ground based laser. The manoeuvre target will be a suitable piece of debris, or a dedicated satellite mission which is instrumented and tracked to measure the applied photon pressure and resulting orbit perturbation. High-altitude airborne platforms such as weather balloons or UAVs enable us to efficiently de-risk elements of this program by validating our numerical simulations of AO system performance with actual measurements. We are then able to confidently move towards in-orbit measurement of an AO corrected ground based laser, and remote manoeuvre with photon pressure. We present simulations along with experimental results for the development of array detectors which can be used to directly measure AO system performance.

  19. Adolescents Misperceive and Are Influenced By High Status Peers' Health Risk, Deviant, and Adaptive Behavior

    Science.gov (United States)

    Helms, Sarah W.; Choukas-Bradley, Sophia; Widman, Laura; Giletta, Matteo; Cohen, Geoffrey L.; Prinstein, Mitchell J.

    2015-01-01

    Most peer influence research examines socialization between adolescents and their best friends. Yet, adolescents also are influenced by popular peers, perhaps due to misperceptions of social norms. This research examined the extent to which out-group and in-group adolescents misperceive the frequencies of peers' deviant, health risk, and adaptive behaviors in different reputation-based peer crowds (Study 1) and the prospective associations between perceptions of high status peers' and adolescents' own substance use over 2.5 years (Study 2). Study 1 examined 235 adolescents' reported deviant (vandalism, theft), health risk (substance use, sexual risk), and adaptive (exercise, studying) behavior, and their perceptions of Jocks', Populars', Burnouts', and Brains' engagement in the same behaviors. Peer nominations identified adolescents in each peer crowd. Jocks and Populars were rated as higher status than Brains and Burnouts. Results indicated that peer crowd stereotypes are caricatures. Misperceptions of high status crowds were dramatic, but for many behaviors, no differences between Populars'/Jocks' and others' actual reported behaviors were revealed. Study 2 assessed 166 adolescents' substance use and their perceptions of popular peers' (i.e., peers high in peer perceived popularity) substance use. Parallel process latent growth analyses revealed that higher perceptions of popular peers' substance use in Grade 9 (intercept) significantly predicted steeper increases in adolescents' own substance use from Grade 9 to 11 (slope). Results from both studies, utilizing different methods, offer evidence to suggest that adolescents misperceive high status peers' risk behaviors, and these misperceptions may predict adolescents' own risk behavior engagement. PMID:25365121

  20. Theropod fauna from southern Australia indicates high polar diversity and climate-driven dinosaur provinciality.

    Science.gov (United States)

    Benson, Roger B J; Rich, Thomas H; Vickers-Rich, Patricia; Hall, Mike

    2012-01-01

    The Early Cretaceous fauna of Victoria, Australia, provides unique data on the composition of high latitude southern hemisphere dinosaurs. We describe and review theropod dinosaur postcranial remains from the Aptian-Albian Otway and Strzelecki groups, based on at least 37 isolated bones, and more than 90 teeth from the Flat Rocks locality. Several specimens of medium- and large-bodied individuals (estimated up to ~8.5 metres long) represent allosauroids. Tyrannosauroids are represented by elements indicating medium body sizes (~3 metres long), likely including the holotype femur of Timimus hermani, and a single cervical vertebra represents a juvenile spinosaurid. Single specimens representing medium- and small-bodied theropods may be referrable to Ceratosauria, Ornithomimosauria, a basal coelurosaur, and at least three taxa within Maniraptora. Thus, nine theropod taxa may have been present. Alternatively, four distinct dorsal vertebrae indicate a minimum of four taxa. However, because most taxa are known from single bones, it is likely that small-bodied theropod diversity remains underestimated. The high abundance of allosauroids and basal coelurosaurs (including tyrannosauroids and possibly ornithomimosaurs), and the relative rarity of ceratosaurs, is strikingly dissimilar to penecontemporaneous dinosaur faunas of Africa and South America, which represent an arid, lower-latitude biome. Similarities between dinosaur faunas of Victoria and the northern continents concern the proportional representatation of higher clades, and may result from the prevailing temperate-polar climate of Australia, especially at high latitudes in Victoria, which is similar to the predominant warm-temperate climate of Laurasia, but distinct from the arid climate zone that covered extensive areas of Gondwana. Most dinosaur groups probably attained a near-cosmopolitan distribution in the Jurassic, prior to fragmentation of the Pangaean supercontinent, and some aspects of the hallmark

  1. Theropod Fauna from Southern Australia Indicates High Polar Diversity and Climate-Driven Dinosaur Provinciality

    Science.gov (United States)

    Benson, Roger B. J.; Rich, Thomas H.; Vickers-Rich, Patricia; Hall, Mike

    2012-01-01

    The Early Cretaceous fauna of Victoria, Australia, provides unique data on the composition of high latitude southern hemisphere dinosaurs. We describe and review theropod dinosaur postcranial remains from the Aptian–Albian Otway and Strzelecki groups, based on at least 37 isolated bones, and more than 90 teeth from the Flat Rocks locality. Several specimens of medium- and large-bodied individuals (estimated up to ∼8.5 metres long) represent allosauroids. Tyrannosauroids are represented by elements indicating medium body sizes (∼3 metres long), likely including the holotype femur of Timimus hermani, and a single cervical vertebra represents a juvenile spinosaurid. Single specimens representing medium- and small-bodied theropods may be referrable to Ceratosauria, Ornithomimosauria, a basal coelurosaur, and at least three taxa within Maniraptora. Thus, nine theropod taxa may have been present. Alternatively, four distinct dorsal vertebrae indicate a minimum of four taxa. However, because most taxa are known from single bones, it is likely that small-bodied theropod diversity remains underestimated. The high abundance of allosauroids and basal coelurosaurs (including tyrannosauroids and possibly ornithomimosaurs), and the relative rarity of ceratosaurs, is strikingly dissimilar to penecontemporaneous dinosaur faunas of Africa and South America, which represent an arid, lower-latitude biome. Similarities between dinosaur faunas of Victoria and the northern continents concern the proportional representatation of higher clades, and may result from the prevailing temperate–polar climate of Australia, especially at high latitudes in Victoria, which is similar to the predominant warm–temperate climate of Laurasia, but distinct from the arid climate zone that covered extensive areas of Gondwana. Most dinosaur groups probably attained a near-cosmopolitan distribution in the Jurassic, prior to fragmentation of the Pangaean supercontinent, and some aspects of the

  2. High-Throughput, Adaptive FFT Architecture for FPGA-Based Spaceborne Data Processors

    Science.gov (United States)

    NguyenKobayashi, Kayla; Zheng, Jason X.; He, Yutao; Shah, Biren N.

    2011-01-01

    Exponential growth in microelectronics technology such as field-programmable gate arrays (FPGAs) has enabled high-performance spaceborne instruments with increasing onboard data processing capabilities. As a commonly used digital signal processing (DSP) building block, fast Fourier transform (FFT) has been of great interest in onboard data processing applications, which needs to strike a reasonable balance between high-performance (throughput, block size, etc.) and low resource usage (power, silicon footprint, etc.). It is also desirable to be designed so that a single design can be reused and adapted into instruments with different requirements. The Multi-Pass Wide Kernel FFT (MPWK-FFT) architecture was developed, in which the high-throughput benefits of the parallel FFT structure and the low resource usage of Singleton s single butterfly method is exploited. The result is a wide-kernel, multipass, adaptive FFT architecture. The 32K-point MPWK-FFT architecture includes 32 radix-2 butterflies, 64 FIFOs to store the real inputs, 64 FIFOs to store the imaginary inputs, complex twiddle factor storage, and FIFO logic to route the outputs to the correct FIFO. The inputs are stored in sequential fashion into the FIFOs, and the outputs of each butterfly are sequentially written first into the even FIFO, then the odd FIFO. Because of the order of the outputs written into the FIFOs, the depth of the even FIFOs, which are 768 each, are 1.5 times larger than the odd FIFOs, which are 512 each. The total memory needed for data storage, assuming that each sample is 36 bits, is 2.95 Mbits. The twiddle factors are stored in internal ROM inside the FPGA for fast access time. The total memory size to store the twiddle factors is 589.9Kbits. This FFT structure combines the benefits of high throughput from the parallel FFT kernels and low resource usage from the multi-pass FFT kernels with desired adaptability. Space instrument missions that need onboard FFT capabilities such as the

  3. High occurrence and unusual serotype diversity of non-typhoidal Salmonella in non-clinical niches, Angola.

    Science.gov (United States)

    Antunes, P; Campos, J; Mourão, J; Ribeiro, T G; Novais, C; Peixe, L

    2017-04-01

    Non-typhoidal Salmonella is an important burden, particularly in developing countries of the African region. We report for the first time in Angola, a sub-Saharan African country with commercial/travel relationships with Europe, an unexpectedly high occurrence of Salmonella (n = 12/63, 19%) from a high diversity of sources, particularly farm and wild animals. The detection of diverse serotypes (n = 12), involving putative new S. enterica subsp. salamae serotypes, is also of note, reinforcing the need for a comprehensive surveillance in Angola critical to identify animal/food/environmental sources of salmonellosis with impact on animal health, local people, tourists and exported products.

  4. Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique.

    Science.gov (United States)

    Purahong, Witoon; Pietsch, Katherina A; Lentendu, Guillaume; Schöps, Ricardo; Bruelheide, Helge; Wirth, Christian; Buscot, François; Wubet, Tesfaye

    2017-01-01

    The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics ( Schima superba and Pinus massoniana ) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima . The two deadwood species differed significantly in WIF OTU richness ( Pinus > Schima ) and community composition ( P forest. Furthermore, by comparing our results to results from temperate and boreal forests we contribute to a better understanding of patterns of WIF communities across different biomes and geographic locations.

  5. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  6. Invited Article: Polarization diversity and modulation for high-speed optical communications: architectures and capacity

    Science.gov (United States)

    Shieh, William; Khodakarami, Hamid; Che, Di

    2016-07-01

    Polarization is one of the fundamental properties of optical waves. To cope with the exponential growth of the Internet traffic, optical communications has advanced by leaps and bounds within the last decade. For the first time, the polarization domain has been extensively explored for high-speed optical communications. In this paper, we discuss the general principle of polarization modulation in both Jones and Stokes spaces. We show that there is no linear optical device capable of transforming an arbitrary input polarization into one that is orthogonal to itself. This excludes the receiver self-polarization diversity architecture by splitting the signal into two branches, and then transferring one of the branches into orthogonal polarization. We next propose a novel Stokes vector (SV) detection architecture using four single-ended photodiodes (PD) that can recover a full set of SV. We then derive a closed-form expression for the information capacity of different SV detection architectures and compare the capacity of our proposed architectures with that of intensity-modulated directly-detected (IM/DD) method. We next study the 3-PD SV detection architecture where a subset of SV is detected, and devise a novel modulation algorithm that can achieve 2-dimensional modulation with the 3-PD detection. By using cost-effective SV receivers, polarization modulation and multiplexing offers a powerful solution for short-reach optical networks where the wavelength domain is quickly exhausted.

  7. Changes in microbial diversity of brined green asparagus upon treatment with high hydrostatic pressure.

    Science.gov (United States)

    Toledo Del Árbol, Julia; Pérez Pulido, Rubén; La Storia, Antonietta; Grande Burgos, Maria José; Lucas, Rosario; Ercolini, Danilo; Gálvez, Antonio

    2016-01-04

    The application of high hydrostatic pressure (HHP, 600MPa, 8 min) on brined green asparagus and the changes in bacterial diversity after treatments and during storage at 4 °C (30 days) or 22 °C (10 days) were studied. HHP treatments reduced viable cell counts by 3.6 log cycles. The residual surviving population did not increase during storage at 4 °C. However, bacterial counts significantly increased at 22 °C by day 3, leading to rapid spoilage. The microbiota of green asparagus was composed mainly by Proteobacteria (mainly Pantoea and Pseudomonas), followed by Firmicutes (mainly Lactococcus and Enterococcus) and to a less extent Bacteroidetes and Actinobacteria. During chill storage of untreated asparagus, the relative abundance of Proteobacteria as well as Enterococcus and Lactococcus decreased while Lactobacillus increased. During storage of untreated asparagus at 22 °C, the abundance of Bacteroidetes decreased while Proteobacteria increased during late storage. The HHP treatment determined a reduction of the Proteobacteria both early after treatment and during chill storage. In the HHP treated samples stored at 22 °C, the relative abundance of Pseudomonas rapidly decreased at day 1, with an increase of Bacteroidetes. This was followed by a marked increase in Enterobacteriaceae (Escherichia) simultaneously with increase in viable counts and spoilage. Results from the study indicate that the effect of HHP treatments on the viability ofmicrobial populations in foods also has an impact on the dynamics of microbial populations during the storage of the treated foods.

  8. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

    Science.gov (United States)

    Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez; Stahl-Hennig, Christiane; Sumida, Noriyuki; Persson, Mats A. A.; Martin, Marcel; Hedestam, Gunilla B. Karlsson

    2016-12-01

    Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool.

  9. High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean.

    Science.gov (United States)

    Xu, Wei; Pang, Ka-Lai; Luo, Zhu-Hua

    2014-11-01

    Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.

  10. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies

    Science.gov (United States)

    Van Blarcom, Thomas; Melton, Zea; Cheung, Wai Ling; Wagstrom, Chris; McDonough, Dan; Valle Oseguera, Cendy; Ding, Sheng; Rossi, Andrea; Potluri, Shobha; Sundar, Purnima; Sirota, Marina; Yan, Yu; Jones, Jeffrey; Roe-Zurz, Zygy; Srivatsa Srinivasan, Surabhi; Zhai, Wenwu; Pons, Jaume; Rajpal, Arvind; Chaparro-Riggers, Javier

    2018-01-01

    ABSTRACT The commercial success of bispecific antibodies generally has been hindered by the complexities associated with generating appropriate molecules for both research scale and large scale manufacturing purposes. Bispecific IgG (BsIgG) based on two antibodies that use an identical common light chain can be combined with a minimal set of Fc mutations to drive heavy chain heterodimerization in order to address these challenges. However, the facile generation of common light chain antibodies with properties similar to traditional monoclonal antibodies has not been demonstrated and they have only been used sparingly. Here, we describe the design of a synthetic human antibody library based on common light chains to generate antibodies with biochemical and biophysical properties that are indistinguishable to traditional therapeutic monoclonal antibodies. We used this library to generate diverse panels of well-behaved, high affinity antibodies toward a variety of epitopes across multiple antigens, including mouse 4-1BB, a therapeutically important T cell costimulatory receptor. Over 200 BsIgG toward 4-1BB were generated using an automated purification method we developed that enables milligram-scale production of BsIgG. This approach allowed us to identify antibodies with a wide range of agonistic activity that are being used to further investigate the therapeutic potential of antibodies targeting one or more epitopes of 4-1BB. PMID:29227213

  11. Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity

    Science.gov (United States)

    Marietou, Angeliki

    2014-01-01

    Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure. PMID:25063663

  12. High Prevalence and Genotypic Diversity of the Human Papillomavirus in Amazonian Women, Brazil

    Directory of Open Access Journals (Sweden)

    Danielle Albuquerque Pires Rocha

    2013-01-01

    Full Text Available The aim of this study was to determine the prevalence of human papillomavirus (HPV in a women population living within the state of Amazonas, Brazil, and to determine the viral genotypes found. The study included 361 sexually active women over 18 years of age. We performed the Pap test and the molecular diagnosis for HPV DNA using polymerase chain reaction (PCR. The amplicons obtained were sequenced in automatic sequencer for genotyping. The presence of HPV DNA was found in 29.1% (105 of the women. Only 321 women presented satisfactory slides for cytological diagnosis, 97.9% (314 had normal cytology (negative for cancer, and 2.1% (7 had abnormal cytology (4 ASCUS, 1 LSIL, and 2 HSIL. The types more frequently found were HPV 16 (58.1% and HPV 58 (20.0%. Additionally, we found more 13 types of HPV. Compared with previous studies in Brazil, our data confirmed a high prevalence and genotypic diversity of HPV in Brazilian women.

  13. Effects of high hydrostatic pressure on coastal bacterial community abundance and diversity.

    Science.gov (United States)

    Marietou, Angeliki; Bartlett, Douglas H

    2014-10-01

    Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  14. Application of Zernike polynomials towards accelerated adaptive focusing of transcranial high intensity focused ultrasound.

    Science.gov (United States)

    Kaye, Elena A; Hertzberg, Yoni; Marx, Michael; Werner, Beat; Navon, Gil; Levoy, Marc; Pauly, Kim Butts

    2012-10-01

    To study the phase aberrations produced by human skulls during transcranial magnetic resonance imaging guided focused ultrasound surgery (MRgFUS), to demonstrate the potential of Zernike polynomials (ZPs) to accelerate the adaptive focusing process, and to investigate the benefits of using phase corrections obtained in previous studies to provide the initial guess for correction of a new data set. The five phase aberration data sets, analyzed here, were calculated based on preoperative computerized tomography (CT) images of the head obtained during previous transcranial MRgFUS treatments performed using a clinical prototype hemispherical transducer. The noniterative adaptive focusing algorithm [Larrat et al., "MR-guided adaptive focusing of ultrasound," IEEE Trans. Ultrason. Ferroelectr. Freq. Control 57(8), 1734-1747 (2010)] was modified by replacing Hadamard encoding with Zernike encoding. The algorithm was tested in simulations to correct the patients' phase aberrations. MR acoustic radiation force imaging (MR-ARFI) was used to visualize the effect of the phase aberration correction on the focusing of a hemispherical transducer. In addition, two methods for constructing initial phase correction estimate based on previous patient's data were investigated. The benefits of the initial estimates in the Zernike-based algorithm were analyzed by measuring their effect on the ultrasound intensity at the focus and on the number of ZP modes necessary to achieve 90% of the intensity of the nonaberrated case. Covariance of the pairs of the phase aberrations data sets showed high correlation between aberration data of several patients and suggested that subgroups can be based on level of correlation. Simulation of the Zernike-based algorithm demonstrated the overall greater correction effectiveness of the low modes of ZPs. The focal intensity achieves 90% of nonaberrated intensity using fewer than 170 modes of ZPs. The initial estimates based on using the average of the

  15. Neural adaptations after short-term wingate-based high-intensity interval training

    Science.gov (United States)

    Vera-Ibañez, Antonio; Colomer-Poveda, David; Romero-Arenas, Salvador; Viñuela-García, Manuel; Márquez, Gonzalo

    2017-01-01

    Objectives: