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Sample records for generates rich diversity

  1. Generational diversity.

    Science.gov (United States)

    Kramer, Linda W

    2010-01-01

    Generational diversity has proven challenges for nurse leaders, and generational values may influence ideas about work and career planning. This article discusses generational gaps, influencing factors and support, and the various generational groups present in today's workplace as well as the consequences of need addressing these issues. The article ends with a discussion of possible solutions.

  2. Diversity and Generation X.

    Science.gov (United States)

    Davis, S K

    2001-09-01

    Managing Generation X (1965-1980) to be of better service to patients and organizations is a challenge for nurse managers. This article provides action scenarios that assist in understanding diversity and generations.

  3. A Rich Morphological Diversity of Biosaline Drying Patterns Is Generated by Different Bacterial Species, Different Salts and Concentrations: Astrobiological Implications

    Science.gov (United States)

    Gómez Gómez, José María; Medina, Jesús; Rull, Fernando

    2016-07-01

    Biosaline formations (BSFs) are complex self-organized biomineral patterns formed by "hibernating" bacteria as the biofilm that contains them dries out. They were initially described in drying biofilms of Escherichia coli cells + NaCl. Due to their intricate 3-D morphology and anhydrobiosis, these biomineralogical structures are of great interest in astrobiology. Here we report experimental data obtained with various alkali halide salts (NaF, NaCl, NaBr, LiCl, KCl, CsCl) on BSF formation with E. coli and Bacillus subtilis bacteria at two saline concentrations: 9 and 18 mg/mL. Our results indicate that, except for LiCl, which is inactive, all the salts assayed are active during BSF formation and capable of promoting the generation of distinctive drying patterns at each salt concentration. Remarkably, the BSFs produced by these two bacterial species produce characteristic architectural hallmarks as the BSF dries. The potential biogenicity of these biosaline drying patterns is studied, and the astrobiological implications of these findings are discussed.

  4. Utilizing the rich resources of a diverse workplace.

    Science.gov (United States)

    Miller, E K

    1993-01-01

    The dynamic and ever-increasing diversity of the U.S. workforce challenges those in executive management to utilize human resources in a manner that maximizes those resources and produces optimal results. A diverse organization is itself laden with rich resources of human capital waiting to be tapped in creative ways. In order to be competitive and remain so, physician executives in today's market must engage in the management of diversity on a continuous basis.

  5. Species richness and morphological diversity of passerine birds.

    Science.gov (United States)

    Ricklefs, Robert E

    2012-09-01

    The relationship between species richness and the occupation of niche space can provide insight into the processes that shape patterns of biodiversity. For example, if species interactions constrained coexistence, one might expect tendencies toward even spacing within niche space and positive relationships between diversity and total niche volume. I use morphological diversity of passerine birds as a proxy for diet, foraging maneuvers, and foraging substrates and examine the morphological space occupied by regional and local passerine avifaunas. Although independently diversified regional faunas exhibit convergent morphology, species are clustered rather than evenly distributed, the volume of the morphological space is weakly related to number of species per taxonomic family, and morphological volume is unrelated to number of species within both regional avifaunas and local assemblages. These results seemingly contradict patterns expected when species interactions constrain regional or local diversity, and they suggest a larger role for diversification, extinction, and dispersal limitation in shaping species richness.

  6. Generational diversity: teaching and learning approaches.

    Science.gov (United States)

    Johnson, Susan A; Romanello, Mary L

    2005-01-01

    Nursing students represent multiple generations--Baby Boomers, Generation X, and now the Millennials. Each generation has its own set of values, ideas, ethics, beliefs, and learning styles. The authors describe the context, characteristics, and learning styles of each generation and provide suggestions for enhanced teaching and learning across multiple generations. Using generational diversity as a teaching tool in the classroom is also discussed.

  7. Tardigrades of Alaska: distribution patterns, diversity and species richness

    Directory of Open Access Journals (Sweden)

    Carl Johansson

    2013-05-01

    Full Text Available During the summer of 2010, a biotic survey of tardigrades was conducted along a latitudinal transect in central Alaska from the Kenai Peninsula, via Fairbanks and the Arctic Circle to the coastal plain. Work was centred at the Toolik and Bonanza Creek Long Term Ecological Research Network sites and supplemented by opportunistic collections from the Kenai Peninsula and Anchorage areas. The 235 samples collected at 20 sites over 10 degrees of latitude yielded 1463 tardigrades representing two classes, three orders, 10 families, 23 genera and 73 species from 142 positive samples. A total of 50 species are new to Alaska, increasing the state's known species richness to 84. Several environmental metrics, such as pH, substrate, elevation, location and habitat were measured, recorded and analysed along the latitudinal gradient. Contrary to expectations, pH did not appear to be a predictor of tardigrade abundance or distribution. Density and species richness were relatively consistent across sites. However, the assemblages were highly variable within and between sites at only 14–20% similarity. We detected no correlation between species diversity and latitudinal or environmental gradients, though this may be affected by a high (59.9% occurrence of single-species samples (containing individuals of only one species. Estimates of species richness were calculated for Alaska (118 and the Arctic (172. Our efforts increased the number of known species in Alaska to 84, and those results led us to question the validity of the estimate numbers.

  8. Traditional cheeses: rich and diverse microbiota with associated benefits.

    Science.gov (United States)

    Montel, Marie-Christine; Buchin, Solange; Mallet, Adrien; Delbes-Paus, Céline; Vuitton, Dominique A; Desmasures, Nathalie; Berthier, Françoise

    2014-05-02

    The risks and benefits of traditional cheeses, mainly raw milk cheeses, are rarely set out objectively, whence the recurrent confused debate over their pros and cons. This review starts by emphasizing the particularities of the microbiota in traditional cheeses. It then describes the sensory, hygiene, and possible health benefits associated with traditional cheeses. The microbial diversity underlying the benefits of raw milk cheese depends on both the milk microbiota and on traditional practices, including inoculation practices. Traditional know-how from farming to cheese processing helps to maintain both the richness of the microbiota in individual cheeses and the diversity between cheeses throughout processing. All in all more than 400 species of lactic acid bacteria, Gram and catalase-positive bacteria, Gram-negative bacteria, yeasts and moulds have been detected in raw milk. This biodiversity decreases in cheese cores, where a small number of lactic acid bacteria species are numerically dominant, but persists on the cheese surfaces, which harbour numerous species of bacteria, yeasts and moulds. Diversity between cheeses is due particularly to wide variations in the dynamics of the same species in different cheeses. Flavour is more intense and rich in raw milk cheeses than in processed ones. This is mainly because an abundant native microbiota can express in raw milk cheeses, which is not the case in cheeses made from pasteurized or microfiltered milk. Compared to commercial strains, indigenous lactic acid bacteria isolated from milk/cheese, and surface bacteria and yeasts isolated from traditional brines, were associated with more complex volatile profiles and higher scores for some sensorial attributes. The ability of traditional cheeses to combat pathogens is related more to native antipathogenic strains or microbial consortia than to natural non-microbial inhibitor(s) from milk. Quite different native microbiota can protect against Listeria monocytogenes in

  9. Advances in generating functional diversity for directed protein evolution.

    Science.gov (United States)

    Shivange, Amol V; Marienhagen, Jan; Mundhada, Hemanshu; Schenk, Alexander; Schwaneberg, Ulrich

    2009-02-01

    Despite advances in screening technologies, only a very small fraction of theoretical protein sequence can be sampled in directed evolution experiments. At the current state of random mutagenesis technologies mutation frequencies have often been adjusted to values that cause a limited number of amino acid changes (often one to four amino acid changes per protein). For harvesting the power of directed evolution algorithms it is therefore important that generated mutant libraries are rich in diversity and enriched in active population. Insufficient knowledge about protein traits, mutational robustness of protein folds and technological limitations in diversity generating methods are main challenges for managing the complexity of protein sequence space. This review covers computational and experimental advances for high quality mutant library generation that have been achieved in the past two years.

  10. Tree diversity promotes functional dissimilarity and maintains functional richness despite species loss in predator assemblages.

    Science.gov (United States)

    Schuldt, Andreas; Bruelheide, Helge; Durka, Walter; Michalski, Stefan G; Purschke, Oliver; Assmann, Thorsten

    2014-02-01

    The effects of species loss on ecosystems depend on the community's functional diversity (FD). However, how FD responds to environmental changes is poorly understood. This applies particularly to higher trophic levels, which regulate many ecosystem processes and are strongly affected by human-induced environmental changes. We analyzed how functional richness (FRic), evenness (FEve), and divergence (FDiv) of important generalist predators-epigeic spiders-are affected by changes in woody plant species richness, plant phylogenetic diversity, and stand age in highly diverse subtropical forests in China. FEve and FDiv of spiders increased with plant richness and stand age. FRic remained on a constant level despite decreasing spider species richness with increasing plant species richness. Plant phylogenetic diversity had no consistent effect on spider FD. The results contrast with the negative effect of diversity on spider species richness and suggest that functional redundancy among spiders decreased with increasing plant richness through non-random species loss. Moreover, increasing functional dissimilarity within spider assemblages with increasing plant richness indicates that the abundance distribution of predators in functional trait space affects ecological functions independent of predator species richness or the available trait space. While plant diversity is generally hypothesized to positively affect predators, our results only support this hypothesis for FD-and here particularly for trait distributions within the overall functional trait space-and not for patterns in species richness. Understanding the way predator assemblages affect ecosystem functions in such highly diverse, natural ecosystems thus requires explicit consideration of FD and its relationship with species richness.

  11. Cascade effects of crop species richness on the diversity of pest insects and their natural enemies.

    Science.gov (United States)

    Shi, PeiJian; Hui, Cang; Men, XingYuan; Zhao, ZiHua; Ouyang, Fang; Ge, Feng; Jin, XianShi; Cao, HaiFeng; Li, B Larry

    2014-07-01

    Understanding how plant species richness influences the diversity of herbivorous and predatory/parasitic arthropods is central to community ecology. We explore the effects of crop species richness on the diversity of pest insects and their natural enemies. Using data from a four-year experiment with five levels of crop species richness, we found that crop species richness significantly affected the pest species richness, but there were no significant effects on richness of the pests' natural enemies. In contrast, the species richness of pest insects significantly affected their natural enemies. These findings suggest a cascade effect where trophic interactions are strong between adjacent trophic levels, while the interactions between connected but nonadjacent trophic levels are weakened by the intermediate trophic level. High crop species richness resulted in a more stable arthropod community compared with communities in monoculture crops. Our results highlight the complicated cross-trophic interactions and the crucial role of crop diversity in the food webs of agro-ecosystems.

  12. Oxygen rich gas generator design and performance analysis

    Science.gov (United States)

    Gloyer, P. W.; Knuth, W. H.; Crawford, R. A.

    1993-01-01

    The present oxygen-rich combustion research investigates oxygen gas generator concepts. The theoretical and modeling aspects of a selected concept are presented, together with a refined concept resulting from the findings of the study. This investigation examined a counter-flow gas generator design for O2/H2 mass ratios of 100-200, featuring a near-stoichiometric combustion zone followed by downstream mixing. The critical technologies required to develop a performance model are analyzed and include the following: (1) oxygen flow boiling; (2) two-phase oxygen flow heat transfer; (3) film-cooling in the combustion zone; (4) oxygen-rich combustion with hydrogen; and (5) mixing and dilution.

  13. Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

    Directory of Open Access Journals (Sweden)

    Penelope K Lindeque

    Full Text Available BACKGROUND: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. METHODOLOGY/PRINCIPLE FINDINGS: Plankton net hauls (200 µm were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. CONCLUSIONS: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may

  14. Diversity and richness of benthic insects in three cold desert spring-streams

    Energy Technology Data Exchange (ETDEWEB)

    Gaines, W.L.; Cushing, C.E. [Pacific Northwest Lab., Richland, WA (United States)

    1993-05-01

    The authors examined species diversity and richness in three cold desert spring-streams, and showed that species diversity was similar and species richness was lower than in similar-size streams from other and or semi-arid regions. Species diversity in the spring-streams increased with increasing stream size and substratum diversity, but declined as distance increased from the nearest large source. However, this latter relationship is difficult to quantify because the nearest large source was the Columbia River, or one of its reservoirs, that has environmental conditions very different from those found in the study streams. It is more likely that the main source of colonizers for the spring-streams studied were other nearby small springs that could provide sources or stepping stone habitats for colonizers. Species diversity declined after winter spates, and the low species diversity and richness values appear to be greatly influenced by these events.

  15. Microbial Diversity of Impact-Generated Habitats

    Science.gov (United States)

    Pontefract, Alexandra; Osinski, Gordon R.; Cockell, Charles S.; Southam, Gordon; McCausland, Phil J. A.; Umoh, Joseph; Holdsworth, David W.

    2016-10-01

    Impact-generated lithologies have recently been identified as viable and important microbial habitats, especially within cold and arid regions such as the polar deserts on Earth. These unique habitats provide protection from environmental stressors, such as freeze-thaw events, desiccation, and UV radiation, and act to trap aerially deposited detritus within the fissures and pore spaces, providing necessary nutrients for endoliths. This study provides the first culture-independent analysis of the microbial community structure within impact-generated lithologies in a Mars analog environment, involving the analysis of 44,534 16S rRNA sequences from an assemblage of 21 rock samples that comprises three shock metamorphism categories. We find that species diversity increases (H = 2.4-4.6) with exposure to higher shock pressures, which leads to the development of three distinct populations. In each population, Actinobacteria were the most abundant (41%, 65%, and 59%), and the dominant phototrophic taxa came from the Chloroflexi. Calculated porosity (a function of shock metamorphism) for these samples correlates (R2 = 0.62) with inverse Simpson indices, accounting for overlap in populations in the higher shock levels. The results of our study show that microbial diversity is tied to the amount of porosity in the target substrate (as a function of shock metamorphism), resulting in the formation of distinct microbial populations.

  16. 富油凹陷不同洼陷烃源岩的热演化及生烃特征差异性%DIVERSITY IN THE THERMAL EVOLUTION AND HYDROCARBON GENERATION OF SOURCE SOCKS IN DIFFERENT SUB-DEPRESSIONS OF RICH OIL DEPRESSION

    Institute of Scientific and Technical Information of China (English)

    蒋有录; 卓勤功; 谈玉明; 鲁雪松

    2009-01-01

    Every rich oil depression in the Bohai Bay Basin generally consists of several sub-depressions which are commonly independent hydrocarbon-generating centers. Due to the differences in sedimentary-burial history of these sub-depressions, there are obvious differences in thermal evolution and hydrocarbon generation of source rocks between different sub-depressions and their different structural positions. Taking the main source rocks of Paleogene Shahejie Formation in Dongpu Depression and Dongying Depression of the Bohai Bay Basin for example, the article demonstrated a comparative analysis in the thermal history and hydrocarbon generation history of source rock between major sub-depressions in two depressions, and the control effects on the reservoir formation and distribution were illustrated in detail. The result shows that, in rich oil depression which consists of several hydrocarbon generation sub-depressions , the source rock in the most deep buried sub-depression adjacent to fault in steep slop is the best, which is widely distributed with high thermal evolution degree, great hydrocarbon generation potential and rich resources. Because of the distinction of the conditions of source rock and burial-thermal history, the hydrocarbon-generating cha-racteristics of source rock in different members of the same strata series and different structural positions in the same sub-depression show relatively large diversity. There are obvious diversities in hydrocarbon generation of source rock in different rich oil depressions.%渤海湾盆地富油凹陷通常发育多个生烃洼陷,每个洼陷往往为相对独立的生烃中心;由于沉积埋藏史的差异,不同洼陷及其不同构造部位烃源岩的热演化和生烃特征存在明显差异.以渤海湾盆地东濮凹陷和东营凹陷古近系沙河街组主要烃源岩系为例,对比分析了两凹陷中主要生烃洼陷烃源岩的热演化及生烃史特征,并探讨了其对油气藏形成及分布的

  17. Predicting coral species richness: the effect of input variables, diversity and scale.

    Science.gov (United States)

    Richards, Zoe T; Hobbs, Jean-Paul A

    2014-01-01

    Coral reefs are facing a biodiversity crisis due to increasing human impacts, consequently, one third of reef-building corals have an elevated risk of extinction. Logistic challenges prevent broad-scale species-level monitoring of hard corals; hence it has become critical that effective proxy indicators of species richness are established. This study tests how accurately three potential proxy indicators (generic richness on belt transects, generic richness on point-intercept transects and percent live hard coral cover on point-intercept transects) predict coral species richness at three different locations and two analytical scales. Generic richness (measured on a belt transect) was found to be the most effective predictor variable, with significant positive linear relationships across locations and scales. Percent live hard coral cover consistently performed poorly as an indicator of coral species richness. This study advances the practical framework for optimizing coral reef monitoring programs and empirically demonstrates that generic richness offers an effective way to predict coral species richness with a moderate level of precision. While the accuracy of species richness estimates will decrease in communities dominated by species-rich genera (e.g. Acropora), generic richness provides a useful measure of phylogenetic diversity and incorporating this metric into monitoring programs will increase the likelihood that changes in coral species diversity can be detected.

  18. Predicting coral species richness: the effect of input variables, diversity and scale.

    Directory of Open Access Journals (Sweden)

    Zoe T Richards

    Full Text Available Coral reefs are facing a biodiversity crisis due to increasing human impacts, consequently, one third of reef-building corals have an elevated risk of extinction. Logistic challenges prevent broad-scale species-level monitoring of hard corals; hence it has become critical that effective proxy indicators of species richness are established. This study tests how accurately three potential proxy indicators (generic richness on belt transects, generic richness on point-intercept transects and percent live hard coral cover on point-intercept transects predict coral species richness at three different locations and two analytical scales. Generic richness (measured on a belt transect was found to be the most effective predictor variable, with significant positive linear relationships across locations and scales. Percent live hard coral cover consistently performed poorly as an indicator of coral species richness. This study advances the practical framework for optimizing coral reef monitoring programs and empirically demonstrates that generic richness offers an effective way to predict coral species richness with a moderate level of precision. While the accuracy of species richness estimates will decrease in communities dominated by species-rich genera (e.g. Acropora, generic richness provides a useful measure of phylogenetic diversity and incorporating this metric into monitoring programs will increase the likelihood that changes in coral species diversity can be detected.

  19. 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.

  20. Functional diversity supports the physiological tolerance hypothesis for plant species richness along climatic gradients

    Science.gov (United States)

    Spasojevic, Marko J.; Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman

    2013-01-01

    1. The physiological tolerance hypothesis proposes that plant species richness is highest in warm and/or wet climates because a wider range of functional strategies can persist under such conditions. Functional diversity metrics, combined with statistical modeling, offer new ways to test whether diversity-environment relationships are consistent with this hypothesis. 2. In a classic study by R. H. Whittaker (1960), herb species richness declined from mesic (cool, moist, northerly) slopes to xeric (hot, dry, southerly) slopes. Building on this dataset, we measured four plant functional traits (plant height, specific leaf area, leaf water content and foliar C:N) and used them to calculate three functional diversity metrics (functional richness, evenness, and dispersion). We then used a structural equation model to ask if ‘functional diversity’ (modeled as the joint responses of richness, evenness, and dispersion) could explain the observed relationship of topographic climate gradients to species richness. We then repeated our model examining the functional diversity of each of the four traits individually. 3. Consistent with the physiological tolerance hypothesis, we found that functional diversity was higher in more favorable climatic conditions (mesic slopes), and that multivariate functional diversity mediated the relationship of the topographic climate gradient to plant species richness. We found similar patterns for models focusing on individual trait functional diversity of leaf water content and foliar C:N. 4. Synthesis. Our results provide trait-based support for the physiological tolerance hypothesis, suggesting that benign climates support more species because they allow for a wider range of functional strategies.

  1. The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards.

    Science.gov (United States)

    Russo, Laura; Park, Mia; Gibbs, Jason; Danforth, Bryan

    2015-09-01

    Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years. We used species rarefaction analyses to test for the completeness of sampling and the relationship between species richness and sampling effort, orchard size, and percent agriculture in the surrounding landscape. We performed more than 190 h of sampling, collecting 11,219 specimens representing 104 species. Despite the sampling intensity, we captured <75% of expected species richness at more than half of the sites. For most of these, the variation in bee community composition between years was greater than among sites. Species richness was influenced by percent agriculture, orchard size, and sampling effort, but we found no factors explaining the difference between observed and expected species richness. Competition between honeybees and wild bees did not appear to be a factor, as we found no correlation between honeybee and wild bee abundance. Our study shows that the pollinator fauna of agroecosystems can be diverse and challenging to thoroughly sample. We demonstrate that there is high temporal variation in community composition and that sites vary widely in the sampling effort required to fully describe their diversity. In order to maximize pollination services provided by wild bee species, we must first accurately estimate species richness. For researchers interested in providing this estimate, we recommend multiyear studies and rarefaction analyses to quantify the gap between observed and expected species richness.

  2. Spider Silk: From Protein-Rich Gland Fluids to Diverse Biopolymer Fibers

    Science.gov (United States)

    2016-01-06

    AFRL-AFOSR-VA-TR-2016-0036 Spider Silk : From Protein-rich Gland Fluids to Diverse Biopolymer Fibers Gregory Holland ARIZONA STATE UNIVERSITY 660 S...3.  DATES COVERED (From - To)      01-12-2013 to 30-11-2015 4.  TITLE AND SUBTITLE Spider Silk : From Protein-rich Gland Fluids to Diverse Biopolymer...research is to elucidate the interactions, mechanisms and biochemistry of the spider silk producing process at the molecular level. Our primary focus is to

  3. Food plant diversity as broad-Scale Determinant of Avian Frugivore Richness

    DEFF Research Database (Denmark)

    Kissling, W. Daniel; Rahbek, Carsten; Böhning-Gaese, Katrin

    2007-01-01

    The causes of variation in animal species richness at large spatial scales are intensively debated. Here, we examine whether the diversity of food plants, contemporary climate and energy, or habitat heterogeneity determine species richness patterns of avian frugivores across sub-Saharan Africa...... from niche assembly mechanisms (e.g. coevolutionary adaptations to fruit size, fruit colour or vertical stratification of fruit presentation) or, alternatively, from stochastic speciation-extinction processes. In any case, the close relationship between species richness of Ficus and avian frugivores...... suggests that figs are keystone resources for animal consumers, even at continental scales....

  4. Intermediate pond sizes contain the highest density, richness, and diversity of pond-breeding amphibians.

    Directory of Open Access Journals (Sweden)

    Raymond D Semlitsch

    Full Text Available We present data on amphibian density, species richness, and diversity from a 7140-ha area consisting of 200 ponds in the Midwestern U.S. that represents most of the possible lentic aquatic breeding habitats common in this region. Our study includes all possible breeding sites with natural and anthropogenic disturbance processes that can be missing from studies where sampling intensity is low, sample area is small, or partial disturbance gradients are sampled. We tested whether pond area was a significant predictor of density, species richness, and diversity of amphibians and if values peaked at intermediate pond areas. We found that in all cases a quadratic model fit our data significantly better than a linear model. Because small ponds have a high probability of pond drying and large ponds have a high probability of fish colonization and accumulation of invertebrate predators, drying and predation may be two mechanisms driving the peak of density and diversity towards intermediate values of pond size. We also found that not all intermediate sized ponds produced many larvae; in fact, some had low amphibian density, richness, and diversity. Further analyses of the subset of ponds represented in the peak of the area distribution showed that fish, hydroperiod, invertebrate density, and canopy are additional factors that drive density, richness and diversity of ponds up or down, when extremely small or large ponds are eliminated. Our results indicate that fishless ponds at intermediate sizes are more diverse, produce more larvae, and have greater potential to recruit juveniles into adult populations of most species sampled. Further, hylid and chorus frogs are found predictably more often in ephemeral ponds whereas bullfrogs, green frogs, and cricket frogs are found most often in permanent ponds with fish. Our data increase understanding of what factors structure and maintain amphibian diversity across large landscapes.

  5. Intermediate pond sizes contain the highest density, richness, and diversity of pond-breeding amphibians.

    Science.gov (United States)

    Semlitsch, Raymond D; Peterman, William E; Anderson, Thomas L; Drake, Dana L; Ousterhout, Brittany H

    2015-01-01

    We present data on amphibian density, species richness, and diversity from a 7140-ha area consisting of 200 ponds in the Midwestern U.S. that represents most of the possible lentic aquatic breeding habitats common in this region. Our study includes all possible breeding sites with natural and anthropogenic disturbance processes that can be missing from studies where sampling intensity is low, sample area is small, or partial disturbance gradients are sampled. We tested whether pond area was a significant predictor of density, species richness, and diversity of amphibians and if values peaked at intermediate pond areas. We found that in all cases a quadratic model fit our data significantly better than a linear model. Because small ponds have a high probability of pond drying and large ponds have a high probability of fish colonization and accumulation of invertebrate predators, drying and predation may be two mechanisms driving the peak of density and diversity towards intermediate values of pond size. We also found that not all intermediate sized ponds produced many larvae; in fact, some had low amphibian density, richness, and diversity. Further analyses of the subset of ponds represented in the peak of the area distribution showed that fish, hydroperiod, invertebrate density, and canopy are additional factors that drive density, richness and diversity of ponds up or down, when extremely small or large ponds are eliminated. Our results indicate that fishless ponds at intermediate sizes are more diverse, produce more larvae, and have greater potential to recruit juveniles into adult populations of most species sampled. Further, hylid and chorus frogs are found predictably more often in ephemeral ponds whereas bullfrogs, green frogs, and cricket frogs are found most often in permanent ponds with fish. Our data increase understanding of what factors structure and maintain amphibian diversity across large landscapes.

  6. Diversity Generation in Evolving Microbial Populations

    DEFF Research Database (Denmark)

    Markussen, Trine

    in relation to chronic infection is a major concern as high population diversity has been predicted to result in survival and persistence of the infecting microbe. Therefore, understanding within-host dynamics and population diversification is necessary for optimal diagnosis and therapeutic treatment. Chronic...... diversity has been documented in contemporary respiratory specimens, it is less clear to what extent within-patient diversity contributes to the overall population structure and whether the population is geographically or homogeneously distributed throughout the airways. The focus of this thesis has been...... to get a better understanding of how bacterial populations adapt to new, complex and heterogeneous environments with multiple selective pressures over long periods, and to analyse diversification during this adaptation. Using the P. aeruginosa chronic infection as a model system, and by combining...

  7. Functional-diversity indices can be driven by methodological choices and species richness.

    Science.gov (United States)

    Poos, Mark S; Walker, Steven C; Jackson, Donald A

    2009-02-01

    Functional diversity is an important concept in community ecology because it captures information on functional traits absent in measures of species diversity. One popular method of measuring functional diversity is the dendrogram-based method, FD. To calculate FD, a variety of methodological choices are required, and it has been debated about whether biological conclusions are sensitive to such choices. We studied the probability that conclusions regarding FD were sensitive, and that patterns in sensitivity were related to alpha and beta components of species richness. We developed a randomization procedure that iteratively calculated FD by assigning species into two assemblages and calculating the probability that the community with higher FD varied across methods. We found evidence of sensitivity in all five communities we examined, ranging from a probability of sensitivity of 0 (no sensitivity) to 0.976 (almost completely sensitive). Variations in these probabilities were driven by differences in alpha diversity between assemblages and not by beta diversity. Importantly, FD was most sensitive when it was most useful (i.e., when differences in alpha diversity were low). We demonstrate that trends in functional-diversity analyses can be largely driven by methodological choices or species richness, rather than functional trait information alone.

  8. Plant species richness drives the density and diversity of Collembola in temperate grassland

    Science.gov (United States)

    Sabais, Alexander C. W.; Scheu, Stefan; Eisenhauer, Nico

    2011-05-01

    Declining biodiversity is one of the most important aspects of anthropogenic global change phenomena, but the implications of plant species loss for soil decomposers are little understood. We used the experimental grassland community of the Jena Experiment to assess the response of density and diversity of Collembola to varying plant species richness, plant functional group richness and plant functional group identity. We sampled the experimental plots in spring and autumn four years after establishment of the experimental plant communities. Collembola density and diversity significantly increased with plant species and plant functional group richness highlighting the importance of the singular hypothesis for soil invertebrates. Generally, grasses and legumes beneficially affected Collembola density and diversity, whereas effects of small herbs usually were detrimental. These impacts were largely consistent in spring and autumn. By contrast, in the presence of small herbs the density of hemiedaphic Collembola and the diversity of Isotomidae increased in spring whereas they decreased in autumn. Beneficial impacts of plant diversity as well as those of grasses and legumes were likely due to increased root and microbial biomass, and elevated quantity and quality of plant residues serving as food resources for Collembola. By contrast, beneficial impacts of small herbs in spring probably reflect differences in microclimatic conditions, and detrimental effects in autumn likely were due to low quantity and quality of resources. The results point to an intimate relationship between plants and the diversity of belowground biota, even at small spatial scales, contrasting the findings of previous studies. The pronounced response of soil animals in the present study was presumably due to the fact that plant communities had established over several years. As decomposer invertebrates significantly impact plant performance, changes in soil biota density and diversity are likely

  9. Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness

    Directory of Open Access Journals (Sweden)

    Shaw Kerry L

    2010-07-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC libraries and expressed sequence tag (EST libraries. Results 288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs. Conclusion The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physical and structural constraints, such as slippage of DNA replication machinery, that may generate increased allelic diversity in AT-rich sequence motifs. Although in silico approaches work well for SSR locus identification in both EST and BAC libraries, BAC library sequence and AT-rich repeat motifs are generally superior SSR development resources for most applications.

  10. Richness and diversity of helminth communities in tropical freshwater fishes: Empirical evidence

    Science.gov (United States)

    Choudhury, A.; Dick, T.A.

    2000-01-01

    Aim: Published information on the richness and diversity of helminth parasite communities in tropical freshwater fishes is reviewed in response to expectations of species-rich parasite communities in tropical regions. Location: Areas covered include the tropics and some subtropical areas. In addition, the north temperate area of the nearctic zone is included for comparison. Methods: Data from 159 communities in 118 species of tropical freshwater fish, summarized from 46 published studies, were used for this review. Parasite community descriptors used in the analyses included component community richness and calculated mean species richness. Data from 130 communities in 47 species of nearctic north temperate freshwater fish were summarized from 31 studies and used for comparison. Results: The component helminth communities of many tropical freshwater fish are species-poor, and considerable proportions of fish from certain parts of the tropics, e.g. West African drainages, are uninfected or lightly infected. Mean helminth species richness was low and equaled or exceeded 2.0 in only 22 of 114 communities. No single group of helminths was identified as a dominant component of the fauna and species composition was variable among and within broader geographical areas. The richest enteric helminth assemblages were found in mochokid and clariid catfish with a mixed carnivorous diet, whereas algal feeders, herbivores and detritivores generally had species-poor gut helminth communities. Comparisons indicated that certain areas in the north temperate region had higher helminth species richness in fishes than areas in the tropics. Main conclusions: Expectations of high species richness in helminth communities of tropical freshwater fishes are not fulfilled by the data. Direct comparisons of infracommunities and component communities in host species across widely separated phylogenetic and geographical lines are inappropriate. Examination of latitudinal differences in richness

  11. Richness and diversity of sand flies (Diptera, Psychodidae) in an Atlantic rainforest reserve in southeastern Brazil.

    Science.gov (United States)

    Pinto, Israel Souza; Dos Santos, Claudiney Biral; Ferreira, Adelson Luiz; Falqueto, Aloísio

    2010-12-01

    Our objective was to study and evaluate the richness and diversity of Phlebotominae fauna in the Duas Bocas Biological Reserve (DBBR) in the state of Espírito Santo, in southeastern Brazil. Sand fly collections were carried out during four consecutive nights each month between August 2007 and July 2008 at DBBR by using CDC automatic light traps and an illuminated Shannon trap. Specific richness (S) and Shannon diversity index (H) was calculated for each trap. We collected 18,868 sand flies belonging to 29 species and 13 genera. Nyssomyia yuilli yuilli was the most abundant species followed by Psychodopygus ayrozai, Ps. hirsutus, Psathyromyia pascalei, and Ps. matosi. We recorded Brumptomyia cardosoi, Br. troglodytes, and Ps. geniculatus for the first time in the state of Espírito Santo. We discuss the differences in diversity and richness of the sand flies in both traps and in relation to other Brazilian localities and biomes. We also discuss the possibility of wild transmission of Leishmania in the DBBR and the influence of the sand fly species in leishmaniasis transmission to the adjacent areas of the reserve.

  12. (macro- Evolutionary ecology of parasite diversity: From determinants of parasite species richness to host diversification

    Directory of Open Access Journals (Sweden)

    Serge Morand

    2015-04-01

    Full Text Available The present review summarized the factors or determinants that may explain parasite diversity among host species and the consequences of this parasite diversity on the evolution of host-life history traits. As host–parasite interactions are asymmetrical exploited–exploiter relationships, ecological and epidemiological theories produce hypotheses to find the potential determinants of parasite species richness, while life-history theory helps for testing potential consequences on parasite diversity on the evolution of hosts. This review referred only to studies that have specifically controlled or took into account phylogenetic information illustrated with parasites of mammals. Several points needing more investigation were identified with a special emphasis to develop the metabolic theory of epidemiology.

  13. Butterfly species richness and diversity in the Trishna Wildlife Sanctuary in South Asia.

    Science.gov (United States)

    Majumder, Joydeb; Lodh, Rahul; Agarwala, B K

    2013-01-01

    Several wildlife sanctuaries in the world are home to the surviving populations of many endemic species. Trishna wildlife sanctuary in northeast India is protected by law, and is home to the last surviving populations of Asian bison (Bos gorus Smith), spectacle monkey (Trachypithecus phayrie Blyth), capped langur (Trachypithecus pileatus Blyth), slow loris (Nycticebus coucang Boddaert), wild cat (Felis chaus Schreber), and wild boars (Sus scrofa L.), among many other animals and plants. The sanctuary was explored for species richness and diversity of butterflies. A six-month-long study revealed the occurrence of 59 butterfly species that included 21 unique species and 9 species listed in the threatened category. The mixed moist deciduous mature forest of the sanctuary harbored greater species richness and species diversity (39 species under 31 genera) than other parts of the sanctuary, which is comprised of regenerated secondary mixed deciduous forest (37 species under 32 genera), degraded forests (32 species under 28 genera), and open grassland with patches of plantations and artificial lakes (24 species under 17 genera). The majority of these species showed a distribution range throughout the Indo-Malayan region and Australasia tropics, and eight species were distributed in the eastern parts of South Asia, including one species, Labadea martha (F.), which is distributed in the eastern Himalayas alone. Estimator Chao 2 provided the best-predicted value of species richness. The steep slope of the species accumulation curve suggested the occurrence of a large number of rare species, and a prolonged gentle slope suggested a higher species richness at a higher sample abundance. The species composition of vegetation-rich habitats showed high similarity in comparison to vegetation-poor habitats.

  14. Butterfly Species Richness and Diversity in the Trishna Wildlife Sanctuary in South Asia

    Science.gov (United States)

    Majumder, Joydeb; Lodh, Rahul; Agarwala, B. K.

    2013-01-01

    Several wildlife sanctuaries in the world are home to the surviving populations of many endemic species. Trishna wildlife sanctuary in northeast India is protected by law, and is home to the last surviving populations of Asian bison (Bos gorus Smith), spectacle monkey (Trachypithecus phayrie Blyth), capped langur (Trachypithecus pileatus Blyth), slow loris (Nycticebus coucang Boddaert), wild cat (Felis chaus Schreber), and wild boars (Sus scrofa L.), among many other animals and plants. The sanctuary was explored for species richness and diversity of butterflies. A six-month-long study revealed the occurrence of 59 butterfly species that included 21 unique species and 9 species listed in the threatened category. The mixed moist deciduous mature forest of the sanctuary harbored greater species richness and species diversity (39 species under 31 genera) than other parts of the sanctuary, which is comprised of regenerated secondary mixed deciduous forest (37 species under 32 genera), degraded forests (32 species under 28 genera), and open grassland with patches of plantations and artificial lakes (24 species under 17 genera). The majority of these species showed a distribution range throughout the Indo-Malayan region and Australasia tropics, and eight species were distributed in the eastern parts of South Asia, including one species, Labadea martha (F.), which is distributed in the eastern Himalayas alone. Estimator Chao 2 provided the best-predicted value of species richness. The steep slope of the species accumulation curve suggested the occurrence of a large number of rare species, and a prolonged gentle slope suggested a higher species richness at a higher sample abundance. The species composition of vegetation-rich habitats showed high similarity in comparison to vegetation-poor habitats. PMID:24219624

  15. Generational diversity: what nurse managers need to know.

    Science.gov (United States)

    Hendricks, Joyce M; Cope, Vicki C

    2013-03-01

    This article presents a discussion of generational differences and their impact on the nursing workforce and how this impact affects the work environment. The global nursing workforce represents four generations of nurses. This generational diversity frames attitudes, beliefs, work habits and expectations associated with the role of the nurse in the provision of care and in the way the nurse manages their day-to-day activities. An electronic search of MEDLINE, PubMed and Cinahl databases was performed using the words generational diversity, nurse managers and workforce. The search was limited to 2000-2012. Generational differences present challenges to contemporary nurse managers working in a healthcare environment which is complex and dynamic, in terms of managing nurses who think and behave in a different way because of disparate core personal and generational values, namely, the three Cs of communication, commitment and compensation. An acceptance of generational diversity in the workplace allows a richer scope for practice as the experiences and knowledge of each generation in the nursing environment creates an environment of acceptance and harmony facilitating retention of nurses. Acknowledgement of generational characteristics provides the nurse manager with strategies which focus on mentoring and motivation; communication, the increased use of technology and the ethics of nursing, to bridge the gap between generations of nurses and to increase nursing workforce cohesion. © 2012 Blackwell Publishing Ltd.

  16. Organic, integrated and conventional management in apple orchards: effect on plant species composition, richness and diversity

    Directory of Open Access Journals (Sweden)

    Zdeňka Lososová

    2011-01-01

    Full Text Available The study was conducted to assess the effect of conventional, integrated and organic management on differences in plant species composition, richness and diversity. The plants were studied in triads of orchards situated in three regions of the Czech Republic. Data about species occurrences were collected on 15 permanent plots in the tree rows and 15 plots between tree rows in each of the apple orchards during 2009. A total of 201 vascular plant species (127 native species, 65 archaeophytes, and 9 neophytes were found. Management type and also different regional conditions had a significant effect on plant species composition and on diversity parameters of orchard spontaneous vegetation. Species richness and species pool was significantly higher in the organic orchards than in the differently managed orchards. Management type had significant effect on proportions of archaeophytes, and also neophytes in apple orchards. The results showed that a change from conventional to integrated and organic management in apple orchards lead to higher plant species diversity and to changes in plant species composition.

  17. Vector species richness increases haemorrhagic disease prevalence through functional diversity modulating the duration of seasonal transmission.

    Science.gov (United States)

    Park, Andrew W; Cleveland, Christopher A; Dallas, Tad A; Corn, Joseph L

    2016-06-01

    Although many parasites are transmitted between hosts by a suite of arthropod vectors, the impact of vector biodiversity on parasite transmission is poorly understood. Positive relationships between host infection prevalence and vector species richness (SR) may operate through multiple mechanisms, including (i) increased vector abundance, (ii) a sampling effect in which species of high vectorial capacity are more likely to occur in species-rich communities, and (iii) functional diversity whereby communities comprised species with distinct phenologies may extend the duration of seasonal transmission. Teasing such mechanisms apart is impeded by a lack of appropriate data, yet could highlight a neglected role for functional diversity in parasite transmission. We used statistical modelling of extensive host, vector and microparasite data to test the hypothesis that functional diversity leading to longer seasonal transmission explained variable levels of disease in a wildlife population. We additionally developed a simple transmission model to guide our expectation of how an increased transmission season translates to infection prevalence. Our study demonstrates that vector SR is associated with increased levels of disease reporting, but not via increases in vector abundance or via a sampling effect. Rather, the relationship operates by extending the length of seasonal transmission, in line with theoretical predictions.

  18. Entamoeba dispar: genetic diversity of Iranian isolates based on serine-rich Entamoeba dispar protein gene.

    Science.gov (United States)

    Haghighi, A; Rasti, S; Nazemalhosseini Mojarad, E; Kazemi, B; Bandehpour, M; Nochi, Z; Hooshyar, H; Rezaian, M

    2008-12-01

    The nucleotide sequences of Serine-Rich Entamoeba histolytica Protein (SREHP) gene have already exhibited stable and significant polymorphism in the gene studies. Serine-rich protein is also present and polymorphic in Entamoeba dispar which called SREDP. The polymorphism of the Serine-Rich Entamoeba dispar Protein (SREDP) gene among 8 isolates obtained from Iranian cyst carriers were analyzed by a nested PCR-RFLP followed by sequencing of the PCR products. From those isolates, six distinct DNA patterns were observed after PCR-RFLP of the nested PCR, whereas sequencing showed 8 different patterns among the isolates. The results demonstrate an extensive genetic variability among Iranian E. dispar isolates. The repeat-containing region of the SREDP was found extensively polymorphic in size, number and order of repeat units. Genetic diversity of Iranian E. dispar isolates based on the SREDP was more polymorphic in comparison of Serine-Rich Entamoeba histolytica Protein (SREHP) of the E. histolytica isolates as well as were different from a few known SREDP genes.

  19. The regional species richness and genetic diversity of Arctic vegetation reflect both past glaciations and current climate

    DEFF Research Database (Denmark)

    Stewart, L.; Alsos, Inger G.; Bay, Christian

    2016-01-01

    species richness of the vascular plant flora of 21 floristic provinces and examined local species richness in 6215 vegetation plots distributed across the Arctic. We assessed levels of genetic diversity inferred from amplified fragment length polymorphism variation across populations of 23 common Arctic......, it will most probably also exhibit lags in response to current and future climate change. Our results also suggest that local species richness at the plot scale is more determined by local habitat factors...

  20. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

    Directory of Open Access Journals (Sweden)

    Félix Marie-Anne

    2013-01-01

    Full Text Available Abstract Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and

  1. Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes.

    Science.gov (United States)

    Forget, N L; Murdock, S A; Juniper, S K

    2010-12-01

    Seafloor iron oxide deposits are a common feature of submarine hydrothermal systems. Morphological study of these deposits has led investigators to suggest a microbiological role in their formation, through the oxidation of reduced Fe in hydrothermal fluids. Fe-oxidizing bacteria, including the recently described Zetaproteobacteria, have been isolated from a few of these deposits but generally little is known about the microbial diversity associated with this habitat. In this study, we characterized bacterial diversity in two Fe oxide samples collected on the seafloor of Volcanoes 1 and 19 on the South Tonga Arc. We were particularly interested in confirming the presence of Zetaproteobacteria at these two sites and in documenting the diversity of groups other than Fe oxidizers. Our results (small subunit rRNA gene sequence data) showed a surprisingly high bacterial diversity, with 150 operational taxonomic units belonging to 19 distinct taxonomic groups. Both samples were dominated by Zetaproteobacteria Fe oxidizers. This group was most abundant at Volcano 1, where sediments were richer in Fe and contained more crystalline forms of Fe oxides. Other groups of bacteria found at these two sites include known S- and a few N-metabolizing bacteria, all ubiquitous in marine environments. The low similarity of our clones with the GenBank database suggests that new species and perhaps new families were recovered. The results of this study suggest that Fe-rich hydrothermal sediments, while dominated by Fe oxidizers, can be exploited by a variety of autotrophic and heterotrophic micro-organisms.

  2. Population expansion and individual age affect endoparasite richness and diversity in a recolonising large carnivore population

    Science.gov (United States)

    Lesniak, Ines; Heckmann, Ilja; Heitlinger, Emanuel; Szentiks, Claudia A.; Nowak, Carsten; Harms, Verena; Jarausch, Anne; Reinhardt, Ilka; Kluth, Gesa; Hofer, Heribert; Krone, Oliver

    2017-01-01

    The recent recolonisation of the Central European lowland (CEL) by the grey wolf (Canis lupus) provides an excellent opportunity to study the effect of founder events on endoparasite diversity. Which role do prey and predator populations play in the re-establishment of endoparasite life cycles? Which intrinsic and extrinsic factors control individual endoparasite diversity in an expanding host population? In 53 individually known CEL wolves sampled in Germany, we revealed a community of four cestode, eight nematode, one trematode and 12 potential Sarcocystis species through molecular genetic techniques. Infections with zoonotic Echinococcus multilocularis, Trichinella britovi and T. spiralis occurred as single cases. Per capita endoparasite species richness and diversity significantly increased with population size and changed with age, whereas sex, microsatellite heterozygosity, and geographic origin had no effect. Tapeworm abundance (Taenia spp.) was significantly higher in immigrants than natives. Metacestode prevalence was slightly higher in ungulates from wolf territories than from control areas elsewhere. Even though alternative canid definitive hosts might also play a role within the investigated parasite life cycles, our findings indicate that (1) immigrated wolves increase parasite diversity in German packs, and (2) prevalence of wolf-associated parasites had declined during wolf absence and has now risen during recolonisation. PMID:28128348

  3. Population expansion and individual age affect endoparasite richness and diversity in a recolonising large carnivore population

    Science.gov (United States)

    Lesniak, Ines; Heckmann, Ilja; Heitlinger, Emanuel; Szentiks, Claudia A.; Nowak, Carsten; Harms, Verena; Jarausch, Anne; Reinhardt, Ilka; Kluth, Gesa; Hofer, Heribert; Krone, Oliver

    2017-01-01

    The recent recolonisation of the Central European lowland (CEL) by the grey wolf (Canis lupus) provides an excellent opportunity to study the effect of founder events on endoparasite diversity. Which role do prey and predator populations play in the re-establishment of endoparasite life cycles? Which intrinsic and extrinsic factors control individual endoparasite diversity in an expanding host population? In 53 individually known CEL wolves sampled in Germany, we revealed a community of four cestode, eight nematode, one trematode and 12 potential Sarcocystis species through molecular genetic techniques. Infections with zoonotic Echinococcus multilocularis, Trichinella britovi and T. spiralis occurred as single cases. Per capita endoparasite species richness and diversity significantly increased with population size and changed with age, whereas sex, microsatellite heterozygosity, and geographic origin had no effect. Tapeworm abundance (Taenia spp.) was significantly higher in immigrants than natives. Metacestode prevalence was slightly higher in ungulates from wolf territories than from control areas elsewhere. Even though alternative canid definitive hosts might also play a role within the investigated parasite life cycles, our findings indicate that (1) immigrated wolves increase parasite diversity in German packs, and (2) prevalence of wolf-associated parasites had declined during wolf absence and has now risen during recolonisation.

  4. Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa

    Science.gov (United States)

    Champagne, Juilette; Paine, C. E. Timothy; Schoolmaster, Donald; Stejskal, Robert; Volařík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

    2016-01-01

    Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory.

  5. Richness and Diversity in Dust Stormborne Biomes at the Southeast Mediterranean

    Science.gov (United States)

    Katra, Itzhak; Arotsker, Luba; Krasnov, Helena; Zaritsky, Arieh; Kushmaro, Ariel; Ben-Dov, Eitan

    2014-06-01

    Dust storms include particulate matter that is transported over land and sea with biota that could impact downwind ecosystems. In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared. The bio-assemblages in the collected dust samples were affiliated with scores of different taxa. Distinct patterns of richness and diversity of the two events were influenced by the origins of the air masses: Ev13 was rich with reads affiliated to Betaproteobacteria and Embryophyta, consistent with a European origin. Ev12, originated in north-Africa, contained significantly more of the Actinobacteria and fungi, without conifers. The abundance of bacterial and eukaryotic reads demonstrates dissemination of biological material in dust that may impose health hazards of pathogens and allergens, and influence vegetation migration throughout the world.

  6. Richness and diversity in dust stormborne biomes at the southeast mediterranean.

    Science.gov (United States)

    Katra, Itzhak; Arotsker, Luba; Krasnov, Helena; Zaritsky, Arieh; Kushmaro, Ariel; Ben-Dov, Eitan

    2014-06-12

    Dust storms include particulate matter that is transported over land and sea with biota that could impact downwind ecosystems. In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared. The bio-assemblages in the collected dust samples were affiliated with scores of different taxa. Distinct patterns of richness and diversity of the two events were influenced by the origins of the air masses: Ev13 was rich with reads affiliated to Betaproteobacteria and Embryophyta, consistent with a European origin. Ev12, originated in north-Africa, contained significantly more of the Actinobacteria and fungi, without conifers. The abundance of bacterial and eukaryotic reads demonstrates dissemination of biological material in dust that may impose health hazards of pathogens and allergens, and influence vegetation migration throughout the world.

  7. Richness, diversity, and similarity of arthropod prey consumed by a community of Hawaiian forest birds.

    Science.gov (United States)

    Banko, Paul C.; Peck, Robert W.; Brinck, Kevin W.; Leonard, David L.

    2015-01-01

    We evaluated the diet richness, diversity, and similarity of a community of seven endemic and two introduced passerine birds by analyzing the composition of arthropod prey in fecal samples collected during 1994–1998 at Hakalau Forest National Wildlife Refuge, Hawai‘i Island. Most prey fragments were identified to order, but we also distinguished among morpho-species of Lepidoptera based on the shape of larval (caterpillar) mandibles for higher resolution of this important prey type. Diets were compared among feeding specialists, generalists, and “intermediate” species and among introduced and three endangered Hawaiian honeycreeper (Fringillidae) species. Lepidoptera (moths), especially the larval (caterpillar) stage, comprised the greatest proportion of prey in samples of all bird species except for the introduced Japanese white-eye (Zosterops japonicus; JAWE). Araneae (spiders) was the most abundant order in JAWE samples and the second most abundant order for most other species. The two specialist honeycreepers ranked lowest in the richness and diversity of arthropod orders, but only the ‘akiapōlā‘au (Hemignathus munroi, AKIP) was significantly lower than the three generalist or intermediate honeycreeper species. The diversity of arthropod orders was significantly lower for the three endangered honeycreeper species compared to the two introduced species. No significant differences were observed among the five honeycreepers with respect to the arthropod orders they consumed. The use of arthropod orders taken by endangered honeycreepers and introduced species was significantly different in all paired comparisons except for JAWE and ‘ākepa (Loxops coccineus; AKEP). In terms of richness and diversity of caterpillar morpho-species in the diet, only the specialist, AKEP, was significantly lower than all three generalist and intermediate species. Both AKEP and AKIP consumed a significantly different diet of caterpillar morpho-species compared to at least

  8. Tree Species Richness, Diversity, and Vegetation Index for Federal Capital Territory, Abuja, Nigeria

    Directory of Open Access Journals (Sweden)

    Aladesanmi D Agbelade

    2017-01-01

    Full Text Available This study was conducted to investigate the tree species richness and diversity of urban and periurban areas of the Federal Capital Territory (FCT, Abuja, Nigeria, and produce Normalized Difference Vegetation Index (NDVI for the territory. Data were collected from urban (Abuja city and periurban (Lugbe areas of the FCT using both semistructured questionnaire and inventory of tree species within green areas. In the study location, all trees with diameter at breast height (dbh ≥ 10 cm were identified; their dbh was measured and frequency was taken. The NDVI was calculated in ArcGIS 10.3 environment using standard formula. A cumulative total of twenty-nine (29 families were encountered within the FCT, with 27 occurring in Abuja city (urban centre and 12 in Lugbe (periurban centre of the FCT. The results of Shannon-Wiener diversity index (H′ for the two centres are 3.56 and 2.24 while Shannon’s maximum diversity index (Hmax is 6.54 (Abuja city and 5.36 (Lugbe for the urban (Abuja city and periurban (Lugbe areas of the Federal Capital Territory (FCT. The result of tree species evenness (Shannon’s equitability (EH index in urban and periurban centres was 0.54 and 0.42, respectively. The study provided baseline information on urban and periurban forests in the FCT of Nigeria, which can be used for the development of tree species database of the territory.

  9. Effects of Different Grazing Management Methods on Plant Species Diversity and Richness in the Steppe Rangeland of Saveh, Iran

    Directory of Open Access Journals (Sweden)

    S. Zarekia

    2014-03-01

    Full Text Available Livestock grazing is a common human-induced activity with direct and indirect effects even on the ecosystems of protected areas. The present study analyzed the effects of different grazing management methods on species diversity and richness in the steppe rangelands of Saveh, Iran. Data were collected from sixty 2×2 m plots within the areas of three, four-years protected range management projects. Margalef’s and Menhinick's indices, Simpson and Shannon-Weiner indices, and Pielou's index were used to evaluate plant species richness, diversity, and evenness, respectively. All data analyses were performed in PAST and SPSS. According to the mean values obtained for Shannon-Weiner index, Nemati rangeland (with rest-rotation grazing system and moderate grazing intensity and Shirali Baglou rangeland (with continuous grazing throughout the year and high grazing intensity had high species diversity with no significant differences among them. However, Chagneh rangeland (with continuous grazing for six months and fairly high grazing intensity had the lowest diversity. Low values of diversity indices indicated low species diversity in steppe rangelands. Moreover, Shirali Baglou rangeland had the highest species richness compared to the other sites. In the other three rangelands, both species richness and diversity decreased with increasing the grazing intensity. Despite poor range conditions in Shirali Baglou rangeland, intensive livestock grazing and the consequent rise in invasive species increased species abundance and hence, resulting in species richness and diversity in the area. Although over-grazing throughout the year can promote plant species richness through increasing annual species, consequent soil degradation and instability of rangeland ecosystem can be expected.

  10. Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Herath, Lasantha; Møldrup, Per;

    2016-01-01

    no spatial autocorrelation was observed for them. Fungal Shannon diversity slightly increased from south to north, with spatial autocorrelation for distances larger than 100 m. The ratio of clay to organic carbon (n) was found to be the best predictor of bacterial richness and diversity indices. Neither...... organic carbon nor clay content was significantly correlated with fungal richness and diversity indices. For soil structural parameters, soil water retention in the pF range 5–6.8 (parameter B) was significantly correlated with both bacterial and fungal Shannon diversities. Amount of macropores (> 30 μm......) and total porosity (ϕ) were only significantly correlated with fungal Shannon diversity. These results suggest that variation in microbial communities is not random but strongly related with variations in organic carbon, clay content, and soil water characteristics at the field scale....

  11. An Antifungal Combination Matrix Identifies a Rich Pool of Adjuvant Molecules that Enhance Drug Activity against Diverse Fungal Pathogens

    Directory of Open Access Journals (Sweden)

    Nicole Robbins

    2015-11-01

    Full Text Available There is an urgent need to identify new treatments for fungal infections. By combining sub-lethal concentrations of the known antifungals fluconazole, caspofungin, amphotericin B, terbinafine, benomyl, and cyprodinil with ∼3,600 compounds in diverse fungal species, we generated a deep reservoir of chemical-chemical interactions termed the Antifungal Combinations Matrix (ACM. Follow-up susceptibility testing against a fluconazole-resistant isolate of C. albicans unveiled ACM combinations capable of potentiating fluconazole in this clinical strain. We used chemical genetics to elucidate the mode of action of the antimycobacterial drug clofazimine, a compound with unreported antifungal activity that synergized with several antifungals. Clofazimine induces a cell membrane stress for which the Pkc1 signaling pathway is required for tolerance. Additional tests against additional fungal pathogens, including Aspergillus fumigatus, highlighted that clofazimine exhibits efficacy as a combination agent against multiple fungi. Thus, the ACM is a rich reservoir of chemical combinations with therapeutic potential against diverse fungal pathogens.

  12. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

    Directory of Open Access Journals (Sweden)

    Delavat François

    2012-09-01

    Full Text Available Abstract Background Acid Mine Drainages (AMDs are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III oxidation, cellulose degradation and cobalamine biosynthesis. Results Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness. Conclusions This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected

  13. Generative models of rich clubs in Hebbian neuronal networks and large-scale human brain networks.

    Science.gov (United States)

    Vértes, Petra E; Alexander-Bloch, Aaron; Bullmore, Edward T

    2014-10-05

    Rich clubs arise when nodes that are 'rich' in connections also form an elite, densely connected 'club'. In brain networks, rich clubs incur high physical connection costs but also appear to be especially valuable to brain function. However, little is known about the selection pressures that drive their formation. Here, we take two complementary approaches to this question: firstly we show, using generative modelling, that the emergence of rich clubs in large-scale human brain networks can be driven by an economic trade-off between connection costs and a second, competing topological term. Secondly we show, using simulated neural networks, that Hebbian learning rules also drive the emergence of rich clubs at the microscopic level, and that the prominence of these features increases with learning time. These results suggest that Hebbian learning may provide a neuronal mechanism for the selection of complex features such as rich clubs. The neural networks that we investigate are explicitly Hebbian, and we argue that the topological term in our model of large-scale brain connectivity may represent an analogous connection rule. This putative link between learning and rich clubs is also consistent with predictions that integrative aspects of brain network organization are especially important for adaptive behaviour.

  14. Contributions of Dryland Forest (Caatinga) to Species Composition, Richness and Diversity of Drosophilidae.

    Science.gov (United States)

    Oliveira, G F; Rohde, C; Garcia, A C L; Montes, M A; Valente, V L S

    2016-10-01

    In this study, semi-arid environments were tested to see if they support insect diversity. This was evaluated through the structure of the composition of assemblies of drosophilids in three conservation units placed in three different ecoregions in the dryland forests, Caatinga. This is a unique biome in northeast Brazil, comprising approximately 10% of the country. Species richness was investigated over 2 years during a prolonged drought, considered the worst affliction the Caatinga ecosystem had experienced in the last 50 years. Alpha diversity indices and the ecological similarity between the samples were calculated to determine how the environments drive the composition of Drosophilidae in such semi-arid places. A total of 7352 specimens were sampled. They were classified into 20 species belonging to four genera: Drosophila, Rhinoleucophenga, Scaptodrosophila, and Zaprionus. Drosophila nebulosa Sturtevant (44.5%) and Drosophila cardini Sturtevant (12.5%) were the most abundant species. The occurrences and abundances of all the species differed greatly between sites. These results and other ecological analyses indicate that although placed in the same biome, there are great variability in the drosophilid species and abundance among the three protected and conserved dryland environments.

  15. Comparing CDRH3 diversity captured from secondary lymphoid organs for the generation of recombinant human antibodies.

    Science.gov (United States)

    Venet, Sophie; Kosco-Vilbois, Marie; Fischer, Nicolas

    2013-01-01

    The plasticity of natural immunoglobulin repertoires can be exploited for the generation of phage display libraries. Secondary lymphoid organs, such as the spleen and the lymph nodes, constitute interesting sources of diversity because they are rich in B cells, part of which can be affinity matured. These organs, however, differ in their anatomical structure, reflecting the different fluids they drain, which affects the B cell repertoires. The CDRH3 repertoires from these organs, extracted from naïve or immunized mice, were compared in the context of phage display libraries using human antibody framework families. Deep sequencing analysis revealed that all libraries displayed different CDRH3 repertoires, but the one derived from lymph nodes of naïve mice was the most diverse. Library performance was assessed by in vitro selection. For both organs, immunization increased substantially the frequency of molecules able to bind to the immunogen. The library derived from lymph nodes from naïve mice, however, was the most effective in generating diverse and high affinity candidates. These results illustrate that the use of a biased CDRH3 repertoire increases the performance of libraries, but reduces the clonal diversity, which may be detrimental for certain strategies.

  16. Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia.

    Science.gov (United States)

    Li, Rong; Kraft, Nathan J B; Yu, Haiying; Li, Heng

    2015-12-01

    One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning. © 2015 Society for Conservation Biology.

  17. Octave-spanning supercontinuum generation in a silicon-rich nitride waveguide

    DEFF Research Database (Denmark)

    Liu, Xing; Pu, Minhao; Zhou, Binbin;

    2016-01-01

    We experimentally show octave-spanning supercontinuum generation in a nonstoichiometric silicon-rich nitride waveguide when pumped by femtosecond pulses from an erbium fiber laser. The pulse energy and bandwidth are comparable to results achieved in stoichiometric silicon nitride waveguides...... the pump in the telecom band....

  18. How To Manage the Emerging Generational Divide in the Contemporary Knowledge-Rich Workplace.

    Science.gov (United States)

    Novicevic, Milorad M.; Buckley, M. Ronald

    2001-01-01

    Addresses the manager's dilemmas and options in resolving emerging latent intergenerational conflict in the contemporary knowledge-rich workplace. Topics include a theoretical framework for generational divide management; the polarization in task requirements; social and environmental factors; differences in employee needs and expectations; and…

  19. Duality and Topological Mass Generation in Diverse Dimensions

    CERN Document Server

    Wotzasek, C

    2004-01-01

    We shall discuss issues of duality and topological mass generation in diverse dimensions. Particular emphasis will be given to the mass generation mechanism from interference between self and anti self-dual components, as disclosed by the soldering formalism. This is a gauge embedding procedure derived from an old algorithm of second-class constraint conversion used by the author to approach anomalous gauge theories. The problem of classification of the electromagnetic duality groups, both massless and massive, that is closely related will be discussed. Particular attention will be paid to a new approach to duality based on the soldering embedding to tackle the problem of mass generation by topological mechanisms in arbitrary dimensions including the couplings to dynamical matter, nonlinear cases and nonabelian symmetries.

  20. On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions

    Energy Technology Data Exchange (ETDEWEB)

    Hurlbert, Allen H.; Stegen, James C.

    2014-12-02

    Many processes have been put forward to explain the latitudinal gradient in species richness. Here, we use a simulation model to examine four of the most common hypotheses and identify patterns that might be diagnostic of those four hypotheses. The hypotheses examined include (1) tropical niche conservatism, or the idea that the tropics are more diverse because a tropical clade origin has allowed more time for diversification in the tropics and has resulted in few species adapted to extra-tropical climates. (2) The productivity, or energetic constraints, hypothesis suggests that species richness is limited by the amount of biologically available energy in a region. (3) The tropical stability hypothesis argues that major climatic fluctuations and glacial cycles in extratropical regions have led to greater extinction rates and less opportunity for specialization relative to the tropics. (4) Finally, the speciation rates hypothesis suggests that the latitudinal richness gradient arises from a parallel gradient in rates of speciation. We found that tropical niche conservatism can be distinguished from the other three scenarios by phylogenies which are more balanced than expected, no relationship between mean root distance and richness across regions, and a homogeneous rate of speciation across clades and through time. The energy gradient, speciation gradient, and disturbance gradient scenarios all exhibited phylogenies which were more imbalanced than expected, showed a negative relationship between mean root distance and richness, and diversity-dependence of speciation rate estimates through time. Using Bayesian Analysis of Macroevolutionary Mixtures on the simulated phylogenies, we found that the relationship between speciation rates and latitude could distinguish among these three scenarios. We emphasize the importance of considering multiple hypotheses and focusing on diagnostic predictions instead of predictions that are consistent with more than one hypothesis.

  1. Species richness and traits predict overyielding in stem growth in an early-successional tree diversity experiment.

    Science.gov (United States)

    Grossman, Jake J; Cavender-Bares, Jeannine; Hobbie, Sarah E; Reich, Peter B; Montgomery, Rebecca A

    2017-07-20

    Over the last two decades, empirical work has established that higher biodiversity can lead to greater primary productivity; however, the importance of different aspects of biodiversity in contributing to such relationships is rarely elucidated. We assessed the relative importance of species richness, phylogenetic diversity, functional diversity, and identity of neighbors for stem growth three years after seedling establishment in a tree diversity experiment in eastern Minnesota. Generally, we found that community-weighted means of key functional traits (including mycorrhizal association, leaf nitrogen and calcium, and waterlogging tolerance) as well as species richness were strong, independent predictors of stem biomass growth. More phylogenetically diverse communities did not consistently produce more biomass than expected, and the trait values or diversity of individual functional traits better predicted biomass production than did a multidimensional functional diversity metric. Furthermore, functional traits and species richness best predicted growth at the whole-plot level (12 m(2) ), whereas neighborhood composition best predicted growth at the focal tree level (0.25 m(2) ). The observed effects of biodiversity on growth appear strongly driven by positive complementary effects rather than by species-specific selection effects, suggesting that synergistic species' interactions rather than the influence of a few important species may drive overyielding. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  2. Macroparasite community of the Eurasian red squirrel (Sciurus vulgaris): poor species richness and diversity.

    Science.gov (United States)

    Romeo, Claudia; Pisanu, Benoît; Ferrari, Nicola; Basset, Franck; Tillon, Laurent; Wauters, Lucas A; Martinoli, Adriano; Saino, Nicola; Chapuis, Jean-Louis

    2013-10-01

    The Eurasian red squirrel (Sciurus vulgaris) is the only naturally occurring tree squirrel throughout its range. We aim at improving current knowledge on its macroparasite fauna, expecting that it will have a poor parasite diversity because in species that have no sympatric congeners parasite richness should be lower than in hosts sharing their range with several closely related species, where host-switching events and lateral transmission are promoted. We examined gastro-intestinal helminth and ectoparasite communities (excluding mites) of, respectively, 147 and 311 red squirrel roadkills collected in four biogeographic regions in Italy and France. As expected, the macroparasite fauna was poor: we found five species of nematodes and some unidentified cestodes, three fleas, two sucking lice and two hard ticks. The helminth community was dominated by a single species, the oxyurid Trypanoxyuris (Rodentoxyuris) sciuri (prevalence, 87%; mean abundance, 373 ± 65 worms/host). Its abundance varied among seasons and biogeographic regions and increased with body mass in male hosts while decreased in females. The most prevalent ectoparasites were the flea Ceratophyllus (Monopsyllus) sciurorum (28%), whose presence was affected by season, and the generalist tick Ixodes (Ixodes) ricinus that was found only in France (34%). All the other helminths and arthropod species were rare, with prevalence below 10%. However, the first record of Strongyloides robustus, a common nematode of North American Eastern grey squirrels (S. carolinensis), in two red squirrels living in areas where this alien species co-inhabits, deserves further attention, since low parasite richness could result in native red squirrels being particularly vulnerable to parasite spillover.

  3. Platelet-rich fibrin: Evolution of a second-generation platelet concentrate

    Directory of Open Access Journals (Sweden)

    Sunitha Raja V

    2008-01-01

    Full Text Available Platelet-rich plasma (PRP is a platelet concentrate that has been used widely to accelerate soft-tissue and hard-tissue healing. The preparation of PRP has been described by several authors. Platelet-rich fibrin (PRF was first described by Choukroun et al. in France. It has been referred to as a second-generation platelet concentrate, which has been shown to have several advantages over traditionally prepared PRP. Its chief advantages include ease of preparation and lack of biochemical handling of blood, which makes this preparation strictly autologous. This article describes the evolution of this novel platelet concentrate, referred to as PRF.

  4. Rich and rare—First insights into species diversity and abundance of Antarctic abyssal Gastropoda (Mollusca)

    Science.gov (United States)

    Schwabe, Enrico; Michael Bohn, Jens; Engl, Winfried; Linse, Katrin; Schrödl, Michael

    2007-08-01

    The abyssal depths of the polar oceans are thought to be low in diversity compared with the shallower polar shelves and temperate and tropical deep-sea basins. Our recent study on the gastropod fauna of the deep Southern Ocean gives evidence of the existence of a rich gastropod assemblage at abyssal depths. During the ANDEEP I and II expeditions to the southern Drake Passage, Northwestern Weddell Sea, and South Sandwich Trench, gastropods were collected by bottom and Agassiz trawls, epibenthic sledge, and multicorer, at 40 stations in depths between 127 and 5194 m. On the whole, 473 specimens, corresponding to 93 species of 36 families, were obtained. Of those, 414 specimens were caught below 750 m depth and refer to 84 (90%) benthic species of 32 (89%) families. Most families were represented by a single species only. The numerically dominant families were Skeneidae and Buccinidae (with 10 and 11 species, respectively), Eulimidae and Trochidae (with 9 species each), and Turridae (6 species). Thirty-Seven benthic deep-sea species (44%) were represented by a single specimen, and another 20 species (24%) were found at a single station, suggesting that more than two thirds of Antarctic deep-sea gastropod species are very rare or have a very scattered distribution. Of the 27 species occurring at two or more deep-sea stations, 14 were collected with different gear. Approximately half of the deep-water species are new to science or have been recently described. The present investigation increases the total number of recorded benthic Antarctic deep-sea gastropods (below 750 m) from 115 to 177. The previously known depth ranges have been extended, often considerably, for 31 species. The collected deep-sea gastropods comprise both eurybathic shelf species (29%) and apparently true deep-sea species (58%); some of the latter may belong to a so far unknown Antarctic abyssal fauna. Geographical ranges of the collected Antarctic benthic deep-sea gastropod species appear limited

  5. Microbial diversity of the hypersaline and lithium-rich Salar de Uyuni, Bolivia.

    Science.gov (United States)

    Haferburg, Götz; Gröning, Janosch A D; Schmidt, Nadja; Kummer, Nicolai-Alexeji; Erquicia, Juan Carlos; Schlömann, Michael

    2017-06-01

    Salar de Uyuni, situated in the Southwest of the Bolivian Altiplano, is the largest salt flat on Earth. Brines of this athalassohaline hypersaline environment are rich in lithium and boron. Due to the ever- increasing commodity demand, the industrial exploitation of brines for metal recovery from the world's biggest lithium reservoir is likely to increase substantially in the near future. Studies on the composition of halophilic microbial communities in brines of the salar have not been published yet. Here we report for the first time on the prokaryotic diversity of four brine habitats across the salar. The brine is characterized by salinity values between 132 and 177 PSU, slightly acidic to near-neutral pH and lithium and boron concentrations of up to 2.0 and 1.4g/L, respectively. Community analysis was performed after sequencing the V3-V4 region of the 16S rRNA genes employing the Illumina MiSeq technology. The mothur software package was used for sequence processing and data analysis. Metagenomic analysis revealed the occurrence of an exclusively archaeal community comprising 26 halobacterial genera including only recently identified genera like Halapricum, Halorubellus and Salinarchaeum. Despite the high diversity of the halobacteria-dominated community in sample P3 (Shannon-Weaver index H'=3.12 at 3% OTU cutoff) almost 40% of the Halobacteriaceae-assigned sequences could not be classified on the genus level under stringent filtering conditions. Even if the limited taxonomic resolution of the V3-V4 region for halobacteria is considered, it seems likely to discover new, hitherto undescribed genera of the family halobacteriaceae in this particular habitat of Salar de Uyuni in future. Copyright © 2017 Elsevier GmbH. All rights reserved.

  6. Octave-spanning supercontinuum generation in a silicon-rich nitride waveguide

    CERN Document Server

    Liu, Xing; Zhou, Binbin; Krückel, Clemens J; Fülöp, Attila; Torres-Company, Victor; Bache, Morten

    2016-01-01

    We experimentally show octave-spanning supercontinuum generation in a non-stoichiometric silicon-rich nitride waveguide when pumped by femtosecond pulses from an erbium fiber laser. The pulse energy and bandwidth are comparable to results achieved in stoichiometric silicon nitride waveguides, but our material platform is simpler to manufacture. We also observe wave-breaking supercontinuum generation by using orthogonal pumping in the same waveguide. Additional analysis reveals that the waveguide height is a powerful tuning parameter for generating mid-infrared dispersive waves while keeping the pump in the telecom band.

  7. Species richness and diversity in different functional groups across environmental stress gradients : a model for marine rocky shores

    NARCIS (Netherlands)

    Scrosati, Ricardo A.; van Genne, Barbara; Heaven, Christine S.; Watt, Cortney A.

    2011-01-01

    We present a model predicting how the species richness and diversity within benthic functional groups should vary across the full environmental stress gradient across which a regional biota from marine rocky shores can occur. Built upon previous models, our model makes predictions for sessile specie

  8. Impact of Text-Mining and Imitating Strategies on Lexical Richness, Lexical Diversity and General Success in Second Language Writing

    Science.gov (United States)

    Çepni, Sevcan Bayraktar; Demirel, Elif Tokdemir

    2016-01-01

    This study aimed to find out the impact of "text mining and imitating" strategies on lexical richness, lexical diversity and general success of students in their compositions in second language writing. The participants were 98 students studying their first year in Karadeniz Technical University in English Language and Literature…

  9. Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats.

    Science.gov (United States)

    Hiiesalu, Indrek; Bahram, Mohammad; Tedersoo, Leho

    2017-09-01

    Fungi have important roles as decomposers, mycorrhizal root symbionts and pathogens in forest ecosystems, but there is limited information about their diversity and composition at the landscape scale. This work aimed to disentangle the factors underlying fungal richness and composition along the landscape-scale moisture, organic matter and productivity gradients. Using high-throughput sequencing, we identified soil fungi from 54 low-productivity Pinus sylvestris-dominated plots across three study areas in Estonia and determined the main predictors of fungal richness based on edaphic, floristic and spatial variables. Fungal richness displayed unimodal relationship with organic matter and deduced soil moisture. Plant richness and productivity constituted the key predictors for taxonomic richness of functional guilds. Composition of fungi and the main ectomycorrhizal fungal lineages and hyphal exploration types was segregated by moisture availability and soil nitrogen. We conclude that plant productivity and diversity determine the richness and proportion of most functional groups of soil fungi in low-productive pine forests on a landscape scale. Adjacent stands of pine forest may differ greatly in the dominance of functional guilds that have marked effects on soil carbon and nitrogen cycling in these forest ecosystems. © 2017 John Wiley & Sons Ltd.

  10. Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Gowda Cholenahalli LL

    2008-10-01

    Full Text Available Abstract Background Plant genetic resources (PGR are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA, 117 in South and South East Asia (SSEA, and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53% than kabuli (46%, while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78% of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents

  11. Effect of the invader Boccardia proboscidea (Polychaeta: Spionidae) on richness, diversity and structure of SW Atlantic epilithic intertidal community.

    Science.gov (United States)

    Elías, Rodolfo; Jaubet, María L; Llanos, Elizabeth N; Sanchez, María A; Rivero, María S; Garaffo, Griselda V; Sandrini-Neto, Leonardo

    2015-02-28

    In Mar del Plata (Argentine, SW Atlantic), a large seaside resort, the sewage discharges impact the littoral ecosystem. The invader polychaete Boccardia proboscidea has developed reefs since spring of 2008. The effect of this species on the richness, diversity and structure of epilithic intertidal community was assessed through an MBACI design in both sewage-impacted and reference sites, and Before/After the invasion. The presence of reefs of B. proboscidea since spring 2008 has caused a significant reduction of total individuals, total taxa and diversity in sewage-impacted sites regarding the reference ones. The species analyzed showed a high variable response because patterns were dominated by small-scale variability. Occasional peaks in abundance were observed on a single sampling site and time and a large variation among replicates. The associated fauna, formerly rich and diverse in impacted sites, shows a tendency to disappear as the ecosystem engineer Brachidontes rodriguezii is replaced by monocultures of B. proboscidea.

  12. Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India

    Directory of Open Access Journals (Sweden)

    Devanita eGhosh

    2014-11-01

    Full Text Available High arsenic (As concentration in groundwater has affected human health, particularly in South-East Asia putting millions of people at risk. Biogeochemical cycling of As carried out by different bacterial groups are suggested to control the As fluxes in aquifers. A functional diversity approach in link with As precipitation was adopted to study bacterial community structures and their variation within the As contaminated Bengal Delta Plain (BDP aquifers of India. Groundwater samples collected from two shallow aquifers in Karimpur II (West Bengal, India, during years 2010 and 2011, were investigated to trace the effects of inter-annual variability in precipitation on community structure and diversity of bacterial assemblages. The study focused on amplification, clone library generation and sequencing of the arsenite oxidase large sub-unit gene aioA and 16S rRNA marker, with respect to changes in elemental concentrations. New set of primers were designed to amplify the aioA gene as a phylogenetic marker to study taxonomically diverse arsenite oxidizing bacterial groups in these aquifers. Overall narrow distribution of bacterial communities based on aioA and 16S rRNA sequences observed was due to poor nutrient status and anoxic conditions in these As contaminated aquifers. Proteobacteria was the dominant phylum detected, within which Acidovorax, Hydrogenophaga, Albidiferax, Bosea and Polymorphum were the major arsenite oxidizing bacterial genera. The structure of bacterial assemblages including those of arsenite oxidizing bacteria were affected by an increase in major elemental concentrations (e.g., As, iron, sulfur, and silica within two sampling sessions, which was supported by PCA analysis. One of the significant findings of this study is detection of novel lineages of 16S rRNA-like bacterial sequences indicating presence of indigenous bacterial communities across both wells of BDP that can play important role in biogeochemical cycling of

  13. Frog species richness, composition and beta-diversity in coastal Brazilian restinga habitats.

    Science.gov (United States)

    Rocha, C F D; Hatano, F H; Vrcibradic, D; Van Sluys, M

    2008-02-01

    We studied the species richness and composition of frogs in 10 restinga habitats (sand dune environments dominated by herbaceous and shrubby vegetation) along approximately 1500 km of coastal areas of three Brazilian States: Rio de Janeiro (Grumari, Maricá, Massambaba, Jurubatiba and Grussaí), Espírito Santo (Praia das Neves and Setiba) and Bahia (Prado and Trancoso). We estimated beta-diversity and similarity among areas and related these parameters to geographic distance between areas. All areas were surveyed with a similar sampling procedure. We found 28 frog species belonging to the families Hylidae, Microhylidae, Leptodactylidae and Bufonidae. Frogs in restingas were in general nocturnal with no strictly diurnal species. The richest restinga was Praia das Neves (13 species), followed by Grussaí and Trancoso (eight species in each). The commonest species in the restingas was Scinax alter (found in eight restingas), followed by Aparasphenodon brunoi (seven areas). Our data shows that richness and composition of frog communities vary consistently along the eastern Brazilian coast and, in part, the rate of species turnover is affected by the distance among areas. Geographic distance explained approximately 12% of species turnover in restingas and about 9.5% of similarity among frog assemblages. Although geographic distance somewhat affects frog assemblages, other factors (e.g. historical factors, disturbances) seem to be also involved in explaining present frog assemblage composition in each area and species turnover among areas. The frog fauna along restinga habitats was significantly nested (matrix community temperature = 26.13 degrees; p = 0.007). Our data also showed that the most hospitable restinga was Praia das Neves and indicated that this area should be protected as a conservation unit. Frog assemblage of each area seems to partially represent a nested subset of the original assemblage, although we should not ignore the importance of historical

  14. Frog species richness, composition and beta-diversity in coastal Brazilian restinga habitats

    Directory of Open Access Journals (Sweden)

    CFD. Rocha

    Full Text Available We studied the species richness and composition of frogs in 10 restinga habitats (sand dune environments dominated by herbaceous and shrubby vegetation along approximately 1500 km of coastal areas of three Brazilian States: Rio de Janeiro (Grumari, Maricá, Massambaba, Jurubatiba and Grussaí, Espírito Santo (Praia das Neves and Setiba and Bahia (Prado and Trancoso. We estimated beta-diversity and similarity among areas and related these parameters to geographic distance between areas. All areas were surveyed with a similar sampling procedure. We found 28 frog species belonging to the families Hylidae, Microhylidae, Leptodactylidae and Bufonidae. Frogs in restingas were in general nocturnal with no strictly diurnal species. The richest restinga was Praia das Neves (13 species, followed by Grussaí and Trancoso (eight species in each. The commonest species in the restingas was Scinax alter (found in eight restingas, followed by Aparasphenodon brunoi (seven areas. Our data shows that richness and composition of frog communities vary consistently along the eastern Brazilian coast and, in part, the rate of species turnover is affected by the distance among areas. Geographic distance explained approximately 12% of species turnover in restingas and about 9.5% of similarity among frog assemblages. Although geographic distance somewhat affects frog assemblages, other factors (e.g. historical factors, disturbances seem to be also involved in explaining present frog assemblage composition in each area and species turnover among areas. The frog fauna along restinga habitats was significantly nested (matrix community temperature = 26.13°; p = 0.007. Our data also showed that the most hospitable restinga was Praia das Neves and indicated that this area should be protected as a conservation unit. Frog assemblage of each area seems to partially represent a nested subset of the original assemblage, although we should not ignore the importance of historical

  15. Generation of diversity in Streptococcus mutans genes demonstrated by MLST.

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    Thuy Do

    Full Text Available Streptococcus mutans, consisting of serotypes c, e, f and k, is an oral aciduric organism associated with the initiation and progression of dental caries. A total of 135 independent Streptococcus mutans strains from caries-free and caries-active subjects isolated from various geographical locations were examined in two versions of an MLST scheme consisting of either 6 housekeeping genes [accC (acetyl-CoA carboxylase biotin carboxylase subunit, gki (glucokinase, lepA (GTP-binding protein, recP (transketolase, sodA (superoxide dismutase, and tyrS (tyrosyl-tRNA synthetase] or the housekeeping genes supplemented with 2 extracellular putative virulence genes [gtfB (glucosyltransferase B and spaP (surface protein antigen I/II] to increase sequence type diversity. The number of alleles found varied between 20 (lepA and 37 (spaP. Overall, 121 sequence types (STs were defined using the housekeeping genes alone and 122 with all genes. However pi, nucleotide diversity per site, was low for all loci being in the range 0.019-0.007. The virulence genes exhibited the greatest nucleotide diversity and the recombination/mutation ratio was 0.67 [95% confidence interval 0.3-1.15] compared to 8.3 [95% confidence interval 5.0-14.5] for the 6 concatenated housekeeping genes alone. The ML trees generated for individual MLST loci were significantly incongruent and not significantly different from random trees. Analysis using ClonalFrame indicated that the majority of isolates were singletons and no evidence for a clonal structure or evidence to support serotype c strains as the ancestral S. mutans strain was apparent. There was also no evidence of a geographical distribution of individual isolates or that particular isolate clusters were associated with caries. The overall low sequence diversity suggests that S. mutans is a newly emerged species which has not accumulated large numbers of mutations but those that have occurred have been shuffled as a consequence of

  16. Generation of diversity in Streptococcus mutans genes demonstrated by MLST.

    Science.gov (United States)

    Do, Thuy; Gilbert, Steven C; Clark, Douglas; Ali, Farida; Fatturi Parolo, Clarissa C; Maltz, Marisa; Russell, Roy R; Holbrook, Peter; Wade, William G; Beighton, David

    2010-02-05

    Streptococcus mutans, consisting of serotypes c, e, f and k, is an oral aciduric organism associated with the initiation and progression of dental caries. A total of 135 independent Streptococcus mutans strains from caries-free and caries-active subjects isolated from various geographical locations were examined in two versions of an MLST scheme consisting of either 6 housekeeping genes [accC (acetyl-CoA carboxylase biotin carboxylase subunit), gki (glucokinase), lepA (GTP-binding protein), recP (transketolase), sodA (superoxide dismutase), and tyrS (tyrosyl-tRNA synthetase)] or the housekeeping genes supplemented with 2 extracellular putative virulence genes [gtfB (glucosyltransferase B) and spaP (surface protein antigen I/II)] to increase sequence type diversity. The number of alleles found varied between 20 (lepA) and 37 (spaP). Overall, 121 sequence types (STs) were defined using the housekeeping genes alone and 122 with all genes. However pi, nucleotide diversity per site, was low for all loci being in the range 0.019-0.007. The virulence genes exhibited the greatest nucleotide diversity and the recombination/mutation ratio was 0.67 [95% confidence interval 0.3-1.15] compared to 8.3 [95% confidence interval 5.0-14.5] for the 6 concatenated housekeeping genes alone. The ML trees generated for individual MLST loci were significantly incongruent and not significantly different from random trees. Analysis using ClonalFrame indicated that the majority of isolates were singletons and no evidence for a clonal structure or evidence to support serotype c strains as the ancestral S. mutans strain was apparent. There was also no evidence of a geographical distribution of individual isolates or that particular isolate clusters were associated with caries. The overall low sequence diversity suggests that S. mutans is a newly emerged species which has not accumulated large numbers of mutations but those that have occurred have been shuffled as a consequence of intra

  17. Diversity patterns in Iberian Calathus (Coleoptera, Carabidae: Harpalinae): species turnover shows a story overlooked by species richness.

    Science.gov (United States)

    Gañán, Israel; Baselga, Andrés; Novoa, Francisco

    2008-12-01

    We assessed the relationships between diversity patterns of Iberian Calathus and current environmental gradients or broad-scale spatial constraints, using 50-km grid cells as sampling units. We assessed the completeness of the inventories using nonparametric estimators to avoid spurious results based on sampling biases. We modeled species richness and beta diversity, using spatial position, and 23 topographical, climatic, and geological variables as predictors in regression and constrained analysis of principal coordinates modeling. Geographical situation does not seem to affect Calathus species richness, because no spatial pattern was detected. The environmental variables only explained 23% of the variation in richness. Spatial and environmental predictors explained a large part of the variation in species composition (58%). The fraction shared by both groups of variables was relatively large, but the pure effect of each model was still important. Our results show that it is necessary to assess the completeness of inventories to avoid drawing false conclusions. Also, Iberian Calathus represent a clear example of the need for combined analyses of species richness and beta diversity patterns, because the lack of patterns in the former does not imply the invariance of biotic communities.

  18. Influence of fire history and soil properties on plant species richness and functional diversity in a neotropical savanna

    Directory of Open Access Journals (Sweden)

    Danilo Muniz Silva

    2013-09-01

    Full Text Available Differences in plant species richness and composition are associated with soil properties and disturbances such as fire, which can therefore be key determinants of species occurrence in savanna plant communities. We measured species richness, using nine plant functional traits and abundance to calculate three functional diversity indices. We then used model selection analyses to select the best model for predicting functional diversity and richness based on soil variables at sites with three different fire frequencies. We also calculated the community-weighted mean of each trait and used ordination to examine how traits changed across fire frequencies. We found higher species richness and functional dispersion at sites that were more fertile and where fire was frequent, and the opposite at such sites where fire was infrequent. However, soil properties influenced functional evenness and divergence only where fire was infrequent, with higher values where soils were poorer. Fire can change functional traits directly by hindering development of plants and indirectly by altering competition. Different fire frequencies lead to different plant-soil relationships, which can affect the functioning of tropical savanna communities. Functional diversity components and functional identity of the communities are both affected by fire frequency and soil conditions.

  19. Generation of diverse neural cell types through direct conversion

    Institute of Scientific and Technical Information of China (English)

    Gayle; F; Petersen; Padraig; M; Strappe

    2016-01-01

    A characteristic of neurological disorders is the loss of critical populations of cells that the body is unable to replace,thus there has been much interest in identifying methods of generating clinically relevant numbers of cells to replace those that have been damaged or lost.The process of neural direct conversion,in which cells of one lineage are converted into cells of a neural lineage without first inducing pluripotency,shows great potential,with evidence of the generation of a range of functional neural cell types both in vitro and in vivo,through viral and non-viral delivery of exogenous factors,as well as chemical induction methods.Induced neural cells have been proposed as an attractive alternative to neural cells derived from embryonic or induced pluripotent stem cells,with prospective roles in the investigation of neurological disorders,including neurodegenerative disease modelling,drug screening,and cellular replacement for regenerative medicine applications,however further investigations into improving the efficacy and safety of these methods need to be performed before neural direct conversion becomes a clinically viable option.In this review,we describe the generation of diverse neural cell types via direct conversion of somatic cells,with comparison against stem cell-based approaches,as well as discussion of their potential research and clinical applications.

  20. Microbiology of sugar-rich environments: diversity, ecology and system constraints.

    Science.gov (United States)

    Lievens, Bart; Hallsworth, John E; Pozo, Maria I; Belgacem, Zouhaier Ben; Stevenson, Andrew; Willems, Kris A; Jacquemyn, Hans

    2015-02-01

    Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  1. Deconstructing responses of dragonfly species richness to area, nutrients, water plant diversity and forestry.

    Science.gov (United States)

    Honkanen, Merja; Sorjanen, Aili-Maria; Mönkkönen, Mikko

    2011-06-01

    Understanding large-scale variation in species richness in relation to area, energy, habitat heterogeneity and anthropogenic disturbance has been a major task in ecology. Ultimately, variation in species richness results from variation in individual species occupancies. We studied whether the individual species occupancy patterns are determined by the same candidate factors as total species richness. We sampled 26 boreal forest ponds for dragonflies (Odonata) and studied the effects of shoreline length, water vascular plant species density (WVPSD), availability of nutrients, intensity of forestry, amount of Sphagnum peat cover and pH on dragonfly species richness and individual dragonfly species. WVPSD and pH had a strong positive effect on species richness. Removal of six dragonfly species experiencing strongest responses to WVPSD cancelled the relationship between species richness and WVPSD. By contrast, removal of nine least observed species did not affect the relationship between WVPSD and species richness. Thus, our results showed that relatively common species responding strongly to WVPSD shaped the observed species richness pattern whereas the effect of least observed, often rare, species was negligible. Also, our results support the view that, despite of the great impact of energy on species richness at large spatial scales, habitat heterogeneity can still have an effect on species richness in smaller scales, even overriding the effects of area.

  2. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen.

    Directory of Open Access Journals (Sweden)

    Derrick E Fouts

    Full Text Available A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1-V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84% found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4-99.9% of OTUs represented by more than one read, using Good's coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.

  3. Organic richness and gas generation potential of Permian Barren Measures from Raniganj field, West Bengal, India

    Indian Academy of Sciences (India)

    Annapurna Boruah; S Ganapathi

    2015-07-01

    The organic geochemistry of shales in terms of its organic richness, hydrocarbon source potential, thermal maturity, depositional environment, etc., are essential stipulations for shale gas resources assessment. In this study, a total of 32 core samples of Permian Barren Measures from four boreholes in Raniganj field of Damodar Basin were analysed to evaluate their gas generation potential using Rock–Eval pyrolysis techniques. Petrographic analysis brings out the lithofacies of Barren Measures as carbonaceous silty shale, iron rich claystone and sand-shale intercalation. The total organic content (TOC) of the shale units of Barren Measures ranges from 3.75 to 20.9 wt%, whereas hydrogen index (HI) ranges from 58.45 to 125.34 mg HC/g TOC. Present study suggests early to late maturated (0.6–1%) organic matters in Barren Measures with gas prone type III kerogen. The study analysed the effect of burial history on the preservation and maturation of organic matters. The organic richness, kerogen type, thermal maturity and petrographic properties of Barren Measures signify fair to excellent gas generation potential.

  4. The exceptionally rich coordination chemistry generated by Schiff-base ligands derived from o-vanillin.

    Science.gov (United States)

    Andruh, Marius

    2015-10-14

    Ortho-vanillin became very popular in coordination chemistry because of its Schiff bases, which generate a rich variety of complexes, ranging from oligonuclear species to coordination polymers. Some of these organic molecules are particularly useful in metallosupramolecular chemistry for assembling homo- and heterometallic helicates. The Schiff bases obtained using aminoalcohols open the door to the synthesis of homo- and heterometallic clusters with various nuclearities and surprising topologies of the metal centers. Several relevant structural types are reviewed. The heterobinuclear 3d-3d' and 3d-4f complexes are valuable building-blocks for the synthesis of heterotrimetallic systems. Beyond the richness of this chemistry, the complexes obtained from o-vanillin-based Schiff ligands show interesting properties: magnetism, luminescence, chirality, catalysis, cytotoxicity, and ferroelectricity. This paper reviews recent data that illustrate a very fertile and dynamic research field in coordination chemistry and materials science.

  5. Richness and diversity of Leguminosae in an altitudinal gradient in the tropical semi-arid zone of Brazil

    Institute of Scientific and Technical Information of China (English)

    Jacira R.LIMA; Vidal F.MANSANO; Francisca S.ARA(U)JO

    2012-01-01

    Many studies are based on the premise that,on a local scale,diversity is the result of ecological processes,whereas on a regional scale factors such as the topography,geology,hydrology,and historical and evolutionary events would influence this control.The Baturité Mountain Range (Ceará state),located in the Brazilian semi-arid zone,is considered an area of extreme importance for conservation with its vegetation varying with the altitude and slope (windward vs.leeward).On the windward (wet) slope,rainforest dominates,whereas the leeward (dry) slope is dominated by seasonal forests and thorny woodland.The aim of this study was to contribute to the knowledge of the patterns of richness and diversity of the family Leguminosae on a local scale (Baturité Mountain Range) as well as a regional scale (northeastern Brazil).The two slopes present quite distinct floras.The dry slope presents higher richness and diversity indices for Leguminosae than the wet slope.The highest diversity of Leguminosae in the dry areas did not corroborate the ideas of other studies carried out in neotropical forests (total flora) that the higher species richness was predicted for wet areas.The present study indicates that the historical and evolutionary processes influence the diversity patterns on a local scale (Baturité Mountain Range),as well as on a regional scale (Brazilian semi-arid).Our results reinforce the uniqueness of each portion of this area and its importance for conservation.

  6. Application of the generator coordinate method to neutron-rich Se and Ge isotopes

    Science.gov (United States)

    Higashiyama, Koji; Yoshinaga, Naotaka

    2014-03-01

    The quantum-number projected generator coordinate method (GCM) is applied to the neutron-rich Se and Ge isotopes, where the monopole and quadrupole pairing plus quadrupole-quadrupole interaction is employed as an effective interaction. The energy spectra obtained by the GCM are compared to both the shell model results and the experimental data. The GCM reproduces well the energy levels of high-spin states as well as the low-lying states. The structure of the low-lying collective states is analyzed through the GCM wave functions.

  7. Application of the generator coordinate method to neutron-rich Se and Ge isotopes

    Directory of Open Access Journals (Sweden)

    Higashiyama Koji

    2014-03-01

    Full Text Available The quantum-number projected generator coordinate method (GCM is applied to the neutron-rich Se and Ge isotopes, where the monopole and quadrupole pairing plus quadrupole-quadrupole interaction is employed as an effective interaction. The energy spectra obtained by the GCM are compared to both the shell model results and the experimental data. The GCM reproduces well the energy levels of high-spin states as well as the low-lying states. The structure of the low-lying collective states is analyzed through the GCM wave functions.

  8. Functional diversity among seed dispersal kernels generated by carnivorous mammals.

    Science.gov (United States)

    González-Varo, Juan P; López-Bao, José V; Guitián, José

    2013-05-01

    1. Knowledge of the spatial scale of the dispersal service provided by important seed dispersers (i.e. common and/or keystone species) is essential to our understanding of their role on plant ecology, ecosystem functioning and, ultimately, biodiversity conservation. 2. Carnivores are the main mammalian frugivores and seed dispersers in temperate climate regions. However, information on the seed dispersal distances they generate is still very limited. We focused on two common temperate carnivores differing in body size and spatial ecology - red fox (Vulpes vulpes) and European pine marten (Martes martes) - for evaluating possible functional diversity in their seed dispersal kernels. 3. We measured dispersal distances using colour-coded seed mimics embedded in experimental fruits that were offered to the carnivores in feeding stations (simulating source trees). The exclusive colour code of each simulated tree allowed us to assign the exact origin of seed mimics found later in carnivore faeces. We further designed an explicit sampling strategy aiming to detect the longest dispersal events; as far we know, the most robust sampling scheme followed for tracking carnivore-dispersed seeds. 4. We found a marked functional heterogeneity among both species in their seed dispersal kernels according to their home range size: multimodality and long-distance dispersal in the case of the fox and unimodality and short-distance dispersal in the case of the marten (maximum distances = 2846 and 1233 m, respectively). As a consequence, emergent kernels at the guild level (overall and in two different years) were highly dependent on the relative contribution of each carnivore species. 5. Our results provide the first empirical evidence of functional diversity among seed dispersal kernels generated by carnivorous mammals. Moreover, they illustrate for the first time how seed dispersal kernels strongly depend on the relative contribution of different disperser species, thus on the

  9. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis.

    Science.gov (United States)

    Dachapak, Sujinna; Somta, Prakit; Poonchaivilaisak, Supalak; Yimram, Tarika; Srinives, Peerasak

    2017-04-01

    Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

  10. Patterns of species richness and diversity of insects associated with cucurbit fruits in the southern part of Cameroon.

    Science.gov (United States)

    Mokam, Didi Gaëlle; Djiéto-Lordon, Champlain; Bilong Bilong, Charles-Félix

    2014-01-01

    Patterns of species diversity and community structure of insects associated with fruits of domesticated cucurbits were investigated from January 2009 to 2011 in three localities from two agroecological zones in the southern part of Cameroon. Rarefaction curves combined with nonparametric estimators of species richness were used to extrapolate species richness beyond our own data. Sampling efforts of over 92% were reached in each of the three study localities. Data collected revealed a total of 66 insect morphospecies belonging to 37 families and five orders, identified from a set of 57,510 insects. The orders Diptera (especially Tephritidae and Lonchaeidae) and Hymenoptera (mainly Braconidae and Eulophidae) were the most important, in terms of both abundance and species richness on the one hand, and effects on agronomic performance on the other. Values for both the species diversity (Shannon and Simpson) and the species richness indices (Margalef and Berger-Parker) calculated showed that the insect communities were species-rich but dominated, all to a similar extent, by five main species (including four fruit fly species and one parasitoid). Species abundance distributions in these communities ranged from the Zipf-Mandelbrot to Mandelbrot models. The communities are structured as tritrophic networks, including cucurbit fruits, fruit-feeding species (fruit flies) and carnivorous species (parasitoids). Within the guild of the parasitoids, about 30% of species, despite their low abundance, may potentially be of use in biological control of important pests. Our field data contribute in important ways to basic knowledge of biodiversity patterns in agrosystems and constitute baseline data for the planned implementation of biological control in Integrated Pest Management. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

  11. Free tyrosine and tyrosine-rich peptide-dependent superoxide generation catalyzed by a copper-binding, threonine-rich neurotoxic peptide derived from prion protein

    Directory of Open Access Journals (Sweden)

    Ken Yokawa, Tomoko Kagenishi, Kaishi Goto, Tomonori Kawano

    2009-01-01

    Full Text Available Previously, generation of superoxide anion (O2•- catalyzed by Cu-binding peptides derived from human prion protein (model sequence for helical Cu-binding motif VNITKQHTVTTTT was most active in the presence of catecholamines and related aromatic monoamines such as phenylethylamine and tyramine, has been reported [Kawano, T., Int J Biol Sci 2007; 3: 57-63]. The peptide sequence (corresponding to helix 2 tested here is known as threonine-rich neurotoxic peptide. In the present article, the redox behaviors of aromatic monoamines, 20 amino acids and prion-derived tyrosine-rich peptide sequences were compared as putative targets of the oxidative reactions mediated with the threonine-rich prion-peptide. For detection of O2•-, an O2•--specific chemiluminescence probe, Cypridina luciferin analog was used. We found that an aromatic amino acid, tyrosine (structurally similar to tyramine behaves as one of the best substrates for the O2•- generating reaction (conversion from hydrogen peroxide catalyzed by Cu-bound prion helical peptide. Data suggested that phenolic moiety is required to be an active substrate while the presence of neither carboxyl group nor amino group was necessarily required. In addition to the action of free tyrosine, effect of two tyrosine-rich peptide sequences YYR and DYEDRYYRENMHR found in human prion corresponding to the tyrosine-rich region was tested as putative substrates for the threonine-rich neurotoxic peptide. YYR motif (found twice in the Y-rich region showed 2- to 3-fold higher activity compared to free tyrosine. Comparison of Y-rich sequence consisted of 13 amino acids and its Y-to-F substitution mutant sequence revealed that the tyrosine-residues on Y-rich peptide derived from prion may contribute to the higher production of O2•-. These data suggest that the tyrosine residues on prion molecules could be additional targets of the prion-mediated reactions through intra- or inter-molecular interactions. Lastly

  12. Free tyrosine and tyrosine-rich peptide-dependent superoxide generation catalyzed by a copper-binding, threonine-rich neurotoxic peptide derived from prion protein.

    Science.gov (United States)

    Yokawa, Ken; Kagenishi, Tomoko; Goto, Kaishi; Kawano, Tomonori

    2009-01-01

    Previously, generation of superoxide anion (O(2)(*-)) catalyzed by Cu-binding peptides derived from human prion protein (model sequence for helical Cu-binding motif VNITKQHTVTTTT was most active) in the presence of catecholamines and related aromatic monoamines such as phenylethylamine and tyramine, has been reported [Kawano, T., Int J Biol Sci 2007; 3: 57-63]. The peptide sequence (corresponding to helix 2) tested here is known as threonine-rich neurotoxic peptide. In the present article, the redox behaviors of aromatic monoamines, 20 amino acids and prion-derived tyrosine-rich peptide sequences were compared as putative targets of the oxidative reactions mediated with the threonine-rich prion-peptide. For detection of O(2)(*-), an O(2)(*-)-specific chemiluminescence probe, Cypridina luciferin analog was used. We found that an aromatic amino acid, tyrosine (structurally similar to tyramine) behaves as one of the best substrates for the O(2)(*-) generating reaction (conversion from hydrogen peroxide) catalyzed by Cu-bound prion helical peptide. Data suggested that phenolic moiety is required to be an active substrate while the presence of neither carboxyl group nor amino group was necessarily required. In addition to the action of free tyrosine, effect of two tyrosine-rich peptide sequences YYR and DYEDRYYRENMHR found in human prion corresponding to the tyrosine-rich region was tested as putative substrates for the threonine-rich neurotoxic peptide. YYR motif (found twice in the Y-rich region) showed 2- to 3-fold higher activity compared to free tyrosine. Comparison of Y-rich sequence consisted of 13 amino acids and its Y-to-F substitution mutant sequence revealed that the tyrosine-residues on Y-rich peptide derived from prion may contribute to the higher production of O(2)(*-). These data suggest that the tyrosine residues on prion molecules could be additional targets of the prion-mediated reactions through intra- or inter-molecular interactions. Lastly, possible

  13. Ecological Diversity in South American Mammals: Their Geographical Distribution Shows Variable Associations with Phylogenetic Diversity and Does Not Follow the Latitudinal Richness Gradient.

    Science.gov (United States)

    Fergnani, Paula Nilda; Ruggiero, Adriana

    2015-01-01

    The extent to which the latitudinal gradient in species richness may be paralleled by a similar gradient of increasing functional or phylogenetic diversity is a matter of controversy. We evaluated whether taxonomic richness (TR) is informative in terms of ecological diversity (ED, an approximation to functional diversity) and phylogenetic diversity (AvPD) using data on 531 mammal species representing South American old autochthonous (marsupials, xenarthrans), mid-Cenozoic immigrants (hystricognaths, primates) and newcomers (carnivorans, artiodactyls). If closely related species are ecologically more similar than distantly related species, AvPD will be a strong predictor of ED; however, lower ED than predicted from AvPD may be due to species retaining most of their ancestral characters, suggesting niche conservatism. This pattern could occur in tropical rainforests for taxa of tropical affinity (old autochthonous and mid-Cenozoic immigrants) and in open and arid habitats for newcomers. In contrast, higher ED than expected from AvPD could occur, possibly in association with niche evolution, in arid and open habitats for taxa of tropical affinity and in forested habitats for newcomers. We found that TR was a poor predictor of ED and AvPD. After controlling for TR, there was considerable variability in the extent to which AvPD accounted for ED. Taxa of tropical affinity did not support the prediction of ED deficit within tropical rainforests, rather, they showed a mosaic of regions with an excess of ED interspersed with zones of ED deficit within the tropics; newcomers showed ED deficit in arid and open regions. Some taxa of tropical affinity showed excess of ED in tropical desert areas (hystricognaths) or temperate semideserts (xenarthrans); newcomers showed excess of ED at cold-temperate latitudes in the Northern Hemisphere. This result suggests that extreme climatic conditions at both temperate and tropical latitudes may have promoted niche evolution in mammals.

  14. Ecological Diversity in South American Mammals: Their Geographical Distribution Shows Variable Associations with Phylogenetic Diversity and Does Not Follow the Latitudinal Richness Gradient.

    Directory of Open Access Journals (Sweden)

    Paula Nilda Fergnani

    Full Text Available The extent to which the latitudinal gradient in species richness may be paralleled by a similar gradient of increasing functional or phylogenetic diversity is a matter of controversy. We evaluated whether taxonomic richness (TR is informative in terms of ecological diversity (ED, an approximation to functional diversity and phylogenetic diversity (AvPD using data on 531 mammal species representing South American old autochthonous (marsupials, xenarthrans, mid-Cenozoic immigrants (hystricognaths, primates and newcomers (carnivorans, artiodactyls. If closely related species are ecologically more similar than distantly related species, AvPD will be a strong predictor of ED; however, lower ED than predicted from AvPD may be due to species retaining most of their ancestral characters, suggesting niche conservatism. This pattern could occur in tropical rainforests for taxa of tropical affinity (old autochthonous and mid-Cenozoic immigrants and in open and arid habitats for newcomers. In contrast, higher ED than expected from AvPD could occur, possibly in association with niche evolution, in arid and open habitats for taxa of tropical affinity and in forested habitats for newcomers. We found that TR was a poor predictor of ED and AvPD. After controlling for TR, there was considerable variability in the extent to which AvPD accounted for ED. Taxa of tropical affinity did not support the prediction of ED deficit within tropical rainforests, rather, they showed a mosaic of regions with an excess of ED interspersed with zones of ED deficit within the tropics; newcomers showed ED deficit in arid and open regions. Some taxa of tropical affinity showed excess of ED in tropical desert areas (hystricognaths or temperate semideserts (xenarthrans; newcomers showed excess of ED at cold-temperate latitudes in the Northern Hemisphere. This result suggests that extreme climatic conditions at both temperate and tropical latitudes may have promoted niche evolution in

  15. Post-fire salvage logging alters species composition and reduces cover, richness, and diversity in Mediterranean plant communities.

    Science.gov (United States)

    Leverkus, Alexandro B; Lorite, Juan; Navarro, Francisco B; Sánchez-Cañete, Enrique P; Castro, Jorge

    2014-01-15

    An intense debate exists on the effects of post-fire salvage logging on plant community regeneration, but scant data are available derived from experimental studies. We analyzed the effects of salvage logging on plant community regeneration in terms of species richness, diversity, cover, and composition by experimentally managing a burnt forest on a Mediterranean mountain (Sierra Nevada, S Spain). In each of three plots located at different elevations, three replicates of three treatments were implemented seven months after the fire, differing in the degree of intervention: "Non-Intervention" (all trees left standing), "Partial Cut plus Lopping" (felling 90% of the trees, cutting the main branches, and leaving all the biomass in situ), and "Salvage Logging" (felling and piling the logs, and masticating the woody debris). Plant composition in each treatment was monitored two years after the fire in linear point transects. Post-fire salvage logging was associated with reduced species richness, Shannon diversity, and total plant cover. Moreover, salvaged sites hosted different species assemblages and 25% lower cover of seeder species (but equal cover of resprouters) compared to the other treatments. Cover of trees and shrubs was also lowest in Salvage Logging, which could suggest a potential slow-down of forest regeneration. Most of these results were consistent among the three plots despite plots hosting different plant communities. Concluding, our study suggests that salvage logging may reduce species richness and diversity, as well as the recruitment of woody species, which could delay the natural regeneration of the ecosystem. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Effects of logging and recovery process on avian richness and diversity in hill dipterocarp tropical rainforest-Malaysia.

    Science.gov (United States)

    Husin, Mohamed Zakaria; Rajpar, Muhammad Nawaz

    2015-01-01

    The effects of logging and recovery process on avian richness and diversity was compared in recently logged and thirty year post-harvested hill dipterocarp tropical rainforest, using mist-netting method. Atotal of 803 bird individuals representing 86 bird species and 29 families (i.e., 37.90% from recently logged forest and 62.10% from thirty year post-harvested forest) were captured from October 2010 to September, 2012. Twenty one bird species were commonly captured from both types of forests, 37 bird species were caught only in thirty year post-harvested forest and 28 bird species were caught only from recently logged forest. Arachnothera longirostra--Little Spiderhunter, Malacopteron magnum--Rufous-crowned Babbler, Alophoixus phaeocephalus -Yellow-bellied Bulbul and Meiglyptes tukki--Buff-necked Woodpecker were the most abundant four bird species in the thirty year post-harvested forest. On the contrary, seven bird species, i.e., Trichastoma rostratum - White-chested Babbler, Lacedo pulchella - Banded Kingfisher, Picus miniaceus--Banded Woodpecker, Enicurus ruficapillus - Chestnut-naped Forktail, Anthreptes simplex--Plain Sunbird, Muscicapella hodgsoni--Pygmy Blue Flycatcher and Otus rufescens--Reddish Scope Owl were considered as the rarest (i.e., each represented only 0.12%). Likewise, A. longirostra, Pycnonotus eythropthalmos - Spectacled Bulbul, P. simplex--Cream-vented Bulbul and Merops viridis--Blue-throated Bee-eater were the most dominant and Copsychus malabaricus--White-rumped Shama Eurylaimus javanicus--Banded Broadbill /xos malaccensis - Streaked Bulbul and Harpactes diardii--Diard's Trogon (each 0.12%) were the rarest bird species in recently logged forest. CAP analysis indicated that avian species in thirty year post-harvested forest were more diverse and evenly distributed than recently logged forest. However, recently logged forest was rich in bird species than thirty year post- harvested forest. The results revealed that logging and retrieval

  17. Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing

    OpenAIRE

    Alexander, Alana; Steel, Debbie; Slikas, Beth; Hoekzema, Kendra; Carraher, Colm; Parks, Matthew; Cronn, Richard; Baker, C. Scott

    2012-01-01

    Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 45...

  18. Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected.

    Science.gov (United States)

    Xing, Yaowu; Onstein, Renske E; Carter, Richard J; Stadler, Tanja; Peter Linder, H

    2014-10-01

    The magnitude and extent of global change during the Cenozoic is remarkable, yet the impacts of these global changes on the biodiversity and evolutionary dynamics of species diversification remain poorly understood. To investigate this question, we combine paleontological and neontological data for the angiosperm order Fagales, an ecologically important clade of about 1370 species of trees with an exceptional fossil record. We show differences in patterns of accumulation of generic diversity, species richness, and turnover rates for Fagales. Generic diversity evolved rapidly since the Late Cretaceous and peaked during the Eocene or Oligocene. Turnover rates were high during periods of extreme global climate change, but relatively low when the climate remained stable. Species richness accumulated gradually throughout the Cenozoic, possibly at an accelerated pace after the Middle Miocene. Species diversification occurred in new environments: Quercoids radiating in Oligocene subtropical seasonally arid habitats, Casuarinaceae in Australian pyrophytic biomes, and Betula in Late Neogene holarctic habitats. These radiations were counterbalanced by regional extinctions in Late Neogene mesic warm-temperate forests. Thus, the overall diversification at species level is linked to regional radiations of clades with appropriate ecologies exploiting newly available habitats.

  19. Contribution of different mesohabitats to the maintenance of fish richness and diversity in the lower Preto River

    Directory of Open Access Journals (Sweden)

    Jaquelini Oliveira Zeni

    2015-07-01

    Full Text Available The presence of different mesohabitats in freshwater systems can support higher local and regional fish richness. Thus, their suppression by dam-building represents a real threat to aquatic biodiversity. Our aims were: (1 to survey the fish fauna in two different mesohabitats in lower Preto River: a riffle indirectly threatened by dam-building and a run with different physical structure; and (2 to analyze and compare the fish community structure in these different mesohabitats. Six samplings were made during one year in two reaches (R1 and R2. We conducted a ‘one way’ ANOSIM to assess the differences in fish community structure between R1 and R2. Fifty-three species were recorded, with the occurrence of Aphyocheirodon hemigrammus and Myleus tiete, two Brazilian threatened species. The highest richness was observed in R2. Nevertheless, diversity and evenness were significantly higher in R1. Rheophilic species were more common and restricted to R1 and species typical of lentic environments were predominant in R2. Fish community structure was different between R1 and R2 (R = 1, p = 0.02. Our results demonstrated that mesohabitats mosaic through rivers can contribute to the maintenance of a diverse fish assemblage.

  20. Species Richness and Functional Trait Diversity for Plants in Southern California's Green Infrastructure along a Climate Gradient

    Science.gov (United States)

    Rochford, M. E.; Ibsen, P.; Jenerette, D.

    2016-12-01

    Green infrastructure (GI) is greenery planted to absorb rainwater into the earth as an alternative to grey infrastructure, like storm drains. Not only does GI prevent flooding, but it also performs a number of ecosystem services, including increasing biodiversity, because it allows water to cycle through the environment naturally. Increased biodiversity in plant communities is said to help purify the air and improve the health and resilience of the plants themselves. I want to investigate these claims about GI's benefits by studying types of GI with slightly different functions. This will answer the questions 1) Are different types of green infrastructure's plant communities equally biodiverse in terms of functional trait diversity and species richness? 2) How does functional trait diversity and species richness differ along a temperature gradient in Southern California? To compare biodiversity, I must survey four different types of GI, urban parks, riparian zones, detention basins, and bioswales, in three cities in distinct climate regions. Detention basins are reservoirs lined with vegetation that collect water until it is absorbed into the soil. Bioswales are vegetated gutters that filter out pollutants in storm water. Unlike retention basins, they also add aesthetic value to an area. Even though parks are mainly for recreation and beatification rather than storm water management, they have plenty of permeable surface to absorb storm water. The types of GI that have high levels of interaction with humans should also have higher levels of maintenance. The results should follow the homogenization hypothesis and demonstrate that, regardless of climate, species richness should not differ much between highly maintained areas, like parks, in different cities. Otherwise, in GI that is not as manicured, species richness should be significantly different between cities and the different types of GI. Because types of GI selected vary in expected levels of human

  1. Generation of copper rich metallic phases from waste printed circuit boards

    Energy Technology Data Exchange (ETDEWEB)

    Cayumil, R. [Centre for Sustainable Materials Research and Technology (SMaRT), School of Materials Science and Engineering, The University of New South Wales, Sydney, NSW 2052 (Australia); Khanna, R., E-mail: ritakhanna@unsw.edu.au [Centre for Sustainable Materials Research and Technology (SMaRT), School of Materials Science and Engineering, The University of New South Wales, Sydney, NSW 2052 (Australia); Ikram-Ul-Haq, M.; Rajarao, R. [Centre for Sustainable Materials Research and Technology (SMaRT), School of Materials Science and Engineering, The University of New South Wales, Sydney, NSW 2052 (Australia); Hill, A. [CSIRO Process Science and Engineering, Clayton, Melbourne, VIC 3168 (Australia); Sahajwalla, V. [Centre for Sustainable Materials Research and Technology (SMaRT), School of Materials Science and Engineering, The University of New South Wales, Sydney, NSW 2052 (Australia)

    2014-10-15

    Highlights: • Recycling and material recovery from waste printed circuit boards is very complex. • Thermoset polymers, ceramics and metals are present simultaneously in waste PCBs. • Heat treatment of PCBs was carried out at 1150 °C under inert conditions. • Various metallic phases could be segregated out as copper based metallic droplets. • Carbon and ceramics residues can be further recycled in a range of applications. - Abstract: The rapid consumption and obsolescence of electronics have resulted in e-waste being one of the fastest growing waste streams worldwide. Printed circuit boards (PCBs) are among the most complex e-waste, containing significant quantities of hazardous and toxic materials leading to high levels of pollution if landfilled or processed inappropriately. However, PCBs are also an important resource of metals including copper, tin, lead and precious metals; their recycling is appealing especially as the concentration of these metals in PCBs is considerably higher than in their ores. This article is focused on a novel approach to recover copper rich phases from waste PCBs. Crushed PCBs were heat treated at 1150 °C under argon gas flowing at 1 L/min into a horizontal tube furnace. Samples were placed into an alumina crucible and positioned in the cold zone of the furnace for 5 min to avoid thermal shock, and then pushed into the hot zone, with specimens exposed to high temperatures for 10 and 20 min. After treatment, residues were pulled back to the cold zone and kept there for 5 min to avoid thermal cracking and re-oxidation. This process resulted in the generation of a metallic phase in the form of droplets and a carbonaceous residue. The metallic phase was formed of copper-rich red droplets and tin-rich white droplets along with the presence of several precious metals. The carbonaceous residue was found to consist of slag and ∼30% carbon. The process conditions led to the segregation of hazardous lead and tin clusters in the

  2. Generation of copper rich metallic phases from waste printed circuit boards.

    Science.gov (United States)

    Cayumil, R; Khanna, R; Ikram-Ul-Haq, M; Rajarao, R; Hill, A; Sahajwalla, V

    2014-10-01

    The rapid consumption and obsolescence of electronics have resulted in e-waste being one of the fastest growing waste streams worldwide. Printed circuit boards (PCBs) are among the most complex e-waste, containing significant quantities of hazardous and toxic materials leading to high levels of pollution if landfilled or processed inappropriately. However, PCBs are also an important resource of metals including copper, tin, lead and precious metals; their recycling is appealing especially as the concentration of these metals in PCBs is considerably higher than in their ores. This article is focused on a novel approach to recover copper rich phases from waste PCBs. Crushed PCBs were heat treated at 1150°C under argon gas flowing at 1L/min into a horizontal tube furnace. Samples were placed into an alumina crucible and positioned in the cold zone of the furnace for 5 min to avoid thermal shock, and then pushed into the hot zone, with specimens exposed to high temperatures for 10 and 20 min. After treatment, residues were pulled back to the cold zone and kept there for 5 min to avoid thermal cracking and re-oxidation. This process resulted in the generation of a metallic phase in the form of droplets and a carbonaceous residue. The metallic phase was formed of copper-rich red droplets and tin-rich white droplets along with the presence of several precious metals. The carbonaceous residue was found to consist of slag and ∼30% carbon. The process conditions led to the segregation of hazardous lead and tin clusters in the metallic phase. The heat treatment temperature was chosen to be above the melting point of copper; molten copper helped to concentrate metallic constituents and their separation from the carbonaceous residue and the slag. Inert atmosphere prevented the re-oxidation of metals and the loss of carbon in the gaseous fraction. Recycling e-waste is expected to lead to enhanced metal recovery, conserving natural resources and providing an environmentally

  3. COMPETENCY MODELS AND THE GENERATIONAL DIVERSITY OF A COMPANY WORKFORCE

    National Research Council Canada - National Science Library

    Malgorzata Baran; Monika Klos

    2014-01-01

      This paper aims to present an analysis of employee competencies across different generations, placing emphasis on their attitudes towards the labour market and future perspective concerning work...

  4. Preliminary observations of voluminous ice-rich and water-rich lahars generated during the 2009 eruption of Redoubt, Alaska

    Science.gov (United States)

    Waythomas, Christopher F.; Pierson, Thomas C.; Major, Jon J.; Scott, William E.

    2012-01-01

    Redoubt Volcano in south-central Alaska began erupting on March 15, 2009, and by April 4, 2009, had produced at least 20 explosive events that generated plumes of ash and lahars. The 3,108-m high, snow- and -ice-clad stratovolcano has an ice-filled summit crater that is breached to the north. The volcano supports about 4 km3 of ice and snow and about 1 km3 of this makes up the Drift glacier on the northern side of the volcano. Explosive eruptions between March 22 and April 4, which included the destruction of at least two lava domes, triggered significant lahars in the Drift River valley on March 23 and April 4 and several smaller lahars between March 24 and March 31. High-flow marks, character of deposits, areas of inundation, and estimates of flow velocity revealed that the lahars on March 23 and April 4 were the largest of the eruption. In the 2-km-wide upper Drift River valley, average flow depths were about 3–5 m. Average peak-flow velocities were likely between 10 and 15 ms-1, and peak discharges were on the order of 104–105 m3s-1. The area inundated by lahars on March 23 was at least 100 km2 and on April 4 about 125 km2. The lahars emplaced on March 23 and April 4 had volumes on the order of 107–108 m3 and were similar in size to the largest lahar of the 1989–90 eruption. The March 23 lahars were primarily flowing slurries of snow and ice entrained from the Drift glacier and seasonal snow and tabular blocks of river ice from the Drift River valley. Only a single, undifferentiated deposit up to 5 m thick was found and contained about 80–95 percent of poorly sorted, massive to imbricate assemblages of snow and ice. The deposit was frozen soon after it was emplaced and later eroded and buried by the April 4 lahar. The lahar of April 4, in contrast, was primarily a hyperconcentrated flow, as interpreted from 1- to 6-m thick deposits of massive to horizontally stratified sand-to-fine-gravel. Rock material in the April 4 lahar deposit is predominantly

  5. Community ecology of the Middle Miocene primates of La Venta, Colombia: the relationship between ecological diversity, divergence time, and phylogenetic richness.

    Science.gov (United States)

    Wheeler, Brandon C

    2010-04-01

    It has been suggested that the degree of ecological diversity that characterizes a primate community correlates positively with both its phylogenetic richness and the time since the members of that community diverged (Fleagle and Reed in Primate communities. Cambridge University Press, New York, pp 92-115, 1999). It is therefore questionable whether or not a community with a relatively recent divergence time but high phylogenetic richness would be as ecologically variable as a community with similar phylogenetic richness but a more distant divergence time. To address this question, the ecological diversity of a fossil primate community from La Venta, Colombia, a Middle Miocene platyrrhine community with phylogenetic diversity comparable with extant platyrrhine communities but a relatively short time since divergence, was compared with that of modern Neotropical primate communities. Shearing quotients and molar lengths, which together are reliable indicators of diet, for both fossil and extant species were plotted against each other to describe the dietary ''ecospace'' occupied by each community. Community diversity was calculated as the area of the minimum convex polygon encompassing all community members. The diversity of the fossil community was then compared with that of extant communities to test whether the fossil community was less diverse than extant communities while taking phylogenetic richness into account. Results indicate that the La Ventan community was not significantly less ecologically diverse than modern communities, supporting the idea that ecological diversification occurred along with phylogenetic diversification early in platyrrhine evolution.

  6. Voluminous ice-rich and water-rich lahars generated during the 2009 eruption of Redoubt Volcano, Alaska

    Science.gov (United States)

    Waythomas, Christopher F.; Pierson, Thomas C.; Major, Jon J.; Scott, William E.

    2013-06-01

    Redoubt Volcano in south-central Alaska began erupting on March 15, 2009, and by April 4, 2009, had produced at least 20 explosive events that generated multiple plumes of ash and numerous lahars. The 3108-m-high, snow- and ice-clad stratovolcano has an ice-filled summit crater that is breached to the north. The volcano supports about 4 km3 of ice and snow and about 1 km3 of this makes up the Drift glacier on the north side of the volcano. Explosive eruptions between March 23 and April 4, which included the destruction of at least two lava domes, triggered significant lahars in the Drift River valley on March 23 and April 4, and several smaller lahars between March 24 and March 31. Mud-line high-water marks, character of deposits, areas of inundation, and estimates of flow velocity revealed that the lahars on March 23 and April 4 were the largest of the eruption. In the 2-km-wide upper Drift River valley, average flow depths were at least 2-5 m. Average peak-flow velocities were likely between 10 and 15 ms- 1, and peak discharges were on the order of 104-105 m3 s- 1. The area inundated by lahars on March 23 was at least 100 km2 and on April 4 about 125 km2. Two substantial lahars emplaced on March 23 and one on April 4 had volumes on the order of 107-108 m3 and were similar in size to the largest lahar of the 1989-90 eruption. The two principal March 23 lahars were primarily flowing slurries of snow and ice derived from Drift glacier and the Drift River valley where seasonal snow and tabular blocks of river ice were entrained and incorporated into the lahars. Despite morphologic evidence of two lahars, only a single deposit up to 5 m thick was found in most places and it contained about 80-95% of poorly sorted, massive to imbricate assemblages of snow and ice clasts. The deposit was frozen soon after it was emplaced and later eroded and buried by the April 4 lahar. The lahar of April 4, in contrast, was primarily a hyperconcentrated flow, as interpreted from 1- to

  7. The roots of diversity: below ground species richness and rooting distributions in a tropical forest revealed by DNA barcodes and inverse modeling.

    Directory of Open Access Journals (Sweden)

    F Andrew Jones

    Full Text Available BACKGROUND: Plants interact with each other, nutrients, and microbial communities in soils through extensive root networks. Understanding these below ground interactions has been difficult in natural systems, particularly those with high plant species diversity where morphological identification of fine roots is difficult. We combine DNA-based root identification with a DNA barcode database and above ground stem locations in a floristically diverse lowland tropical wet forest on Barro Colorado Island, Panama, where all trees and lianas >1 cm diameter have been mapped to investigate richness patterns below ground and model rooting distributions. METHODOLOGY/PRINCIPAL FINDINGS: DNA barcode loci, particularly the cpDNA locus trnH-psba, can be used to identify fine and small coarse roots to species. We recovered 33 species of roots from 117 fragments sequenced from 12 soil cores. Despite limited sampling, we recovered a high proportion of the known species in the focal hectare, representing approximately 14% of the measured woody plant richness. This high value is emphasized by the fact that we would need to sample on average 13 m(2 at the seedling layer and 45 m(2 for woody plants >1 cm diameter to obtain the same number of species above ground. Results from inverse models parameterized with the locations and sizes of adults and the species identifications of roots and sampling locations indicates a high potential for distal underground interactions among plants. CONCLUSIONS: DNA barcoding techniques coupled with modeling approaches should be broadly applicable to studying root distributions in any mapped vegetation plot. We discuss the implications of our results and outline how second-generation sequencing technology and environmental sampling can be combined to increase our understanding of how root distributions influence the potential for plant interactions in natural ecosystems.

  8. Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil.

    Science.gov (United States)

    García-Salamanca, Adela; Molina-Henares, M Antonia; van Dillewijn, Pieter; Solano, Jennifer; Pizarro-Tobías, Paloma; Roca, Amalia; Duque, Estrella; Ramos, Juan L

    2013-01-01

    Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH 8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common.

  9. Protecting and Expanding the Richness and Diversity of Life, An Ethic for Astrobiology Research and Space Exploration

    Science.gov (United States)

    Randolph, Richard O.; McKay, Chris P.

    2011-01-01

    The ongoing search for life on other worlds and the prospects of eventual human exploration of the Moon and Mars indicate the need for new ethical guidelines to direct our actions as we search and how we respond if we discover microbial life on other worlds. Here we review how life on other worlds presents a novel question in environmental ethics. We propose a principle of protecting and expanding the richness and diversity of life as the basis of an ethic for astrobiology research and space exploration. There are immediate implications for the operational policies governing how we conduct the search for life on Mars and how we plan for human exploration throughout the Solar System.

  10. Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin.

    Science.gov (United States)

    Russ, Lina; Kartal, Boran; Op den Camp, Huub J M; Sollai, Martina; Le Bruchec, Julie; Caprais, Jean-Claude; Godfroy, Anne; Sinninghe Damsté, Jaap S; Jetten, Mike S M

    2013-01-01

    Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox) bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA). All clones retrieved were closely associated to the "Candidatus Scalindua" genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II). Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5'-phosphosulfate (APS) reductase (aprA). Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as sulfate-reducers.

  11. Trematodes of the Great Barrier Reef, Australia: emerging patterns of diversity and richness in coral reef fishes.

    Science.gov (United States)

    Cribb, Thomas H; Bott, Nathan J; Bray, Rodney A; McNamara, Marissa K A; Miller, Terrence L; Nolan, Mathew J; Cutmore, Scott C

    2014-10-15

    The Great Barrier Reef holds the richest array of marine life found anywhere in Australia, including a diverse and fascinating parasite fauna. Members of one group, the trematodes, occur as sexually mature adult worms in almost all Great Barrier Reef bony fish species. Although the first reports of these parasites were made 100 years ago, the fauna has been studied systematically for only the last 25 years. When the fauna was last reviewed in 1994 there were 94 species known from the Great Barrier Reef and it was predicted that there might be 2,270 in total. There are now 326 species reported for the region, suggesting that we are in a much improved position to make an accurate prediction of true trematode richness. Here we review the current state of knowledge of the fauna and the ways in which our understanding of this fascinating group is changing. Our best estimate of the true richness is now a range, 1,100-1,800 species. However there remains considerable scope for even these figures to be incorrect given that fewer than one-third of the fish species of the region have been examined for trematodes. Our goal is a comprehensive characterisation of this fauna, and we outline what work needs to be done to achieve this and discuss whether this goal is practically achievable or philosophically justifiable.

  12. Loktak Lake, Manipur, northeast India: a Ramsar site with rich rotifer (Rotifera: Eurotatoria diversity and its meta-analysis

    Directory of Open Access Journals (Sweden)

    Bhushan Kumar Sharma

    2016-04-01

    Full Text Available A total of 162 species (S of Rotifera belonging to 40 genera and 20 families examined from Loktak Lake, an important floodplain lake of northeast India (NEI that is one of the richest assemblages of the taxon known from the Indian sub-region. It merits biodiversity value as ~40.0% and ~62.0% of species recorded from India and NEI, respectively. One species is new to India, 23 species are new to Manipur and 14 species are new to Loktak basin. Biogeographically interesting elements included three Australasian, five Oriental, ten palaeotropical and one cosmo-subtropical species. Lecanidae > Lepadellidae > Brachionidae > Trichocercidae collectively comprised 65.4% of S; Lecane > Lepadella > Trichocerca are diverse genera; and paucity of Brachionus spp. is distinct. Loktak Rotifera indicated importance of cosmopolitan, the littoral-periphytonic and small-sized species, and ‘tropical character’. ANOVA recorded significant variations of the rotifer richness amongst three sampling sites of Loktak during June 2010–May 2012 survey. The richness followed osscillaring monthly variations and indicated lack of significant influence of any individual abioitic parameter at all three stations.

  13. Phosphate Solubilizing Ability and Phylogenetic Diversity of Bacteria from P-Rich Soils Around Dianchi Lake Drainage Area of China

    Institute of Scientific and Technical Information of China (English)

    YANG Pei-Xiang; YANG Fa-Xiang; MA Li; CHEN Ming-Hui; XI Jia-Qin; HE Feng; DUAN Chang-Qun; MO Ming-He; FANG Dun-Huang; DUAN Yan-Qing

    2012-01-01

    The phylogenetic diversity of phosphate solubilizing bacteria (PSB) distributed in P-rich soils in the Dianchi Lake drainage area of China was characterized,and the tricalcium phosphate (TCP) solubilizing activities of isolated PSB were determined.Among 1328 bacteria isolated from 100 P-rich soil samples,377 isolates (28.39% of the total) that exhibited TCP solubilization activity were taken as PSB.These PSB showed different abilities to solubilize TCP,with the concentrations of solubilized P in bacterial cultures varying from 33.48 to 69.63 mg L -1.A total of 123 PSB isolates,with relatively high TCP solubilization activity (> 54.00mg L-1),were submitted for restriction fragment length polymorphism (RFLP) analysis,which revealed 32 unique RFLP patterns.Based on these patterns,62 representative isolates,one to three from each RFLP pattern,were selected for 16S rRNA sequencing Phylogenetic analysis placed the 123 PSB into three bacterial phyla,namely proteobacteria,Actinobacteria and Firrnicutes.Members of proteobacteria were the dominant PSB,where 107 isolates represented by 26 RFLP patterns were associated with the genera of Burkholdema,Pseudomonas,Acinetobacter,Enterobacter,Pantoea,Serratia,Klebsiella,Leclercia,Raoultella and Cedecea.Firmicutes were the subdominant group,in which 13 isolates were affiliated with the genera of Bacillus and Brevibacterium.The remaining 3 isolates were identified as three species of the genus Arthrobacter.This research extends the knowledge on PSB in P-rich soils and broadens the spectrum of PSB for the development of environmentally friendly biophosphate fertilizers.

  14. Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity.

    Science.gov (United States)

    Giam, Xingli; Scheffers, Brett R; Sodhi, Navjot S; Wilcove, David S; Ceballos, Gerardo; Ehrlich, Paul R

    2012-01-01

    In the last few decades, there has been a remarkable discovery of new species of plants, invertebrates and vertebrates, in what have been called the new age of discovery. However, owing to anthropogenic impacts such as habitat conversion, many of the still unknown species may go extinct before being scientifically documented (i.e. 'crypto-extinctions'). Here, by applying a mathematical model of species descriptions which accounts for taxonomic effort, we show that even after 250 years of taxonomic classification, about 3050 amphibians and at least 160 land mammal species remain to be discovered and described. These values represent, respectively, 33 and 3 per cent of the current species total for amphibians and land mammals. We found that tropical moist forests of the Neotropics, Afrotropics and Indomalaya probably harbour the greatest numbers of undescribed species. Tropical forests with minimal anthropogenic disturbance are predicted to have larger proportions of undescribed species. However, the protected area coverage is low in many of these key biomes. Moreover, undescribed species are likely to be at a greater risk of extinction compared with known species because of small geographical ranges among other factors. By highlighting the key areas of undescribed species diversity, our study provides a starting template to rapidly document these species and protect them through better habitat management.

  15. Richness and diversity of helminth species in eels from a hypersaline coastal lagoon, Mar Menor, south-east Spain.

    Science.gov (United States)

    Mayo-Hernández, E; Peñalver, J; García-Ayala, A; Serrano, E; Muñoz, P; Ruiz de Ybáñez, R

    2015-05-01

    The composition and diversity of parasite communities and intestinal components, as well as infra-community structure, were assessed in eels Anguilla anguilla, from Mar Menor, a permanent Mediterranean hypersaline coastal lagoon. Data were used to determine whether this helminth community differs in composition and structure from that of eels in lagoons with lower salinity regimes and higher freshwater inputs. A total prevalence of 93% was detected. Specifically, parasites were identified as Deropristis inflata, Bucephalus anguillae, Contracaecum sp., Anguillicoloides crassus and two plerocercoid larvae belonging to the order Proteocephalidae, the marine species representing 91% of the isolated helminths. In the total community, digenetic trematodes were the dominant group of helminths, and D. inflata, an eel specialist, dominated both the component community and the infra-community. Richness and diversity were low but similar to those reported in other saline lagoons, and maximum species per eel did not exceed four. At the infra-community level, higher abundance than in other brackish or marine Mediterranean environments was detected. The findings provide further evidence of the similarity in composition and structure of helminth communities in eels from various Mediterranean coastal lagoons. Moreover, salinity-dependent specificities are well supported and reflect the life history of individual eels.

  16. Diversity of squalene-hopene cyclases in a tropical carbonate-rich environment

    Science.gov (United States)

    Leavitt, W. D.; Pearson, A.

    2007-12-01

    Hopanoids are isoprenoid lipids which derive primarily from bacteria and are ubiquitous in contemporary Earth surface environments. In the geologic record, hopanes found in sedimentary rocks are used as proxies to help decipher ancient biological communities. However, in contrast to the ubiquity of these lipid products, biosynthesis of hopanoids appears to be a relatively rare physiological trait among bacteria in complex environmental communities. We have recently estimated that fewer than one in ten bacterial cells in soils and fewer than one in twenty bacterial cells in the ocean contains the gene squalene-hopene cyclase (sqhC) [1]. Biosynthesis of hopanoids is rarer in natural communities than it is among species that have been propagated in pure culture [2]. Here we continue our previous work to survey the phylogeny and diversity of hopanoid producers using culture-independent methods. In particular, genes affiliated with known cyanobacterial sequences were not detected in the contemporary environments analyzed previously [1]. One possible explanation is that hopanoid-producing strains of cyanobacteria are regionally localized. It has been suggested that throughout the long-term sedimentary record there is a correlation between 2-methylhopanoid index (a putative indicator of cyanobacterial biomass) and the global prevalence of shallow carbonate platform environments [3], and in previous work we did not analyze any such environments. To address this question we surveyed a land-sea gradient across the Bahamian island of San Salvador. Samples were taken from upland soil, a hypersaline lake, a tidal creek, and the shallow open ocean. The data are remarkably similar to our previous results: environmental sqhCs average triterpenes in Prokaryotes. J. Gen. Microbiol. 130, 1137-1150. [3] Summons, RE (personal communication).

  17. Different Effects of Shrubs and Trees on Seed Bank Richness and Diversity in the Understory Soil (Case Study: Kerman Province, Sharbabak

    Directory of Open Access Journals (Sweden)

    2014-03-01

    Full Text Available This study aimed to investigate the effect of canopy trees and shrubs: Pistacia atlantica, Amygdalus scoparia, Amygdalus eburnean on the species diversity and richness of soil seed bank. Ten individuals of each species were selected and one quadrate was established in and outside of crown canopy of each species. In each plot, soil samples were collected from 0-5 and 5-10 cm depths. GLM was applied to assess the effect of woody species, canopy cover, and depth of sampling on the characteristics of soil seed bank. The paired t-test was used to compare the diversity and richness of soil seed banks beneath and outside the canopy. The results showed that the highest species richness of soil seed bank was related to Pistacia atlantica, 0.24, which was significantly higher than the average species richness of soil seed banks in other species Amygdalus scoparia, Amygdalus eburnea with 0.10 and 0.14, respectively. Pistacia atlantica had the highest species diversity with 0.65 compared to the two other species Amygdalus scoparia and Amygdalus eburnean with 0.48, 0.53, respectively. Paired t-test results showed that canopy of woody species significantly increased soil seed bank diversity and richness beneath their canopy. Our results indicated that canopy of tree and shrub species in arid region affected positively on soil seed bank preservation.

  18. Spatial Complexity, Resilience, and Policy Diversity: Fishing on Lake-rich Landscapes

    Directory of Open Access Journals (Sweden)

    Stephen R. Carpenter

    2004-06-01

    Full Text Available The dynamics of and policies governing spatially coupled social-ecological mosaics are considered for the case of fisheries in a lake district. A microeconomic model of households addresses agent decisions at three hierarchic levels: (1 selection of the lake district from among a larger set of alternative places to live or visit, (2 selection of a base location within the lake district, and (3 selection of a portfolio of ecosystem services to use. Ecosystem services are represented by dynamics of fish production subject to multiple stable domains and trophic cascades. Policy calculations show that optimal policies will be highly heterogeneous in space and fluid in time. The diversity of possible outcomes is illustrated by simulations for a hypothetical lake district based loosely on the Northern Highlands of the State of Wisconsin. Lake districts are frequently managed as if lakes were independent, similar, endogenously regulating systems. Our findings contradict that view. One-size-fits-all (OSFA policies erode ecological and social resilience. If regulations are too stringent, social resilience declines because of the potential rewards of overharvesting. If regulations are too lax, ecological resilience is diminished by overharvesting in some lakes. In either case, local collapses of fish populations evoke spatial shifts of angling effort that can lead to serial collapses in neighboring fisheries and degraded fisheries in most or all of the lakes. Under OSFA management, the natural resources of the entire landscape become more vulnerable to transformation because of changes in, e.g., human population, the demand for resources, or fish harvesting technology. Multiplicity of management regimes can increase the ecological resilience, social resilience, and inclusive value of a spatially heterogeneous social-ecological system. Because of the complex interactions of mobile people and multistable ecosystems, management regimes must also be flexible

  19. Clay-to-carbon ratio controls the effect of herbicide application on soil bacterial richness and diversity in a loamy field

    DEFF Research Database (Denmark)

    Herath, Lasantha; Møldrup, Per; de Jonge, Lis Wollesen

    2017-01-01

    application and increasing after glyphosate application. This indicated that the specific chemical nature of individual herbicides affected bacterial communities. This study reinforced the importance of including soil physical and chemical characteristics to explain the influence of pesticides....... Glyphosate and bentazon were used to evaluate the herbicidal effect on bacterial community under different conditions created by clay and OC gradients in a loamy field. Metabarcoding by highthroughput sequencing of bacterial rDNA was used to estimate bacterial richness and diversity using OTUs, abundance......-based coverage (ACE), Shannon diversity index, and phylogenetic diversity. In general, bacterial richness and diversity increased after bentazon application and decreased after glyphosate application. There was no significant effect for field locations with Dexter n (the ratio between clay and OC) values below 4...

  20. Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic.

    Science.gov (United States)

    Timling, I; Walker, D A; Nusbaum, C; Lennon, N J; Taylor, D L

    2014-07-01

    Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs - nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds.

  1. Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin

    Directory of Open Access Journals (Sweden)

    Lina eRuss

    2013-08-01

    Full Text Available Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA. All clones retrieved were closely associated to the ‘Candidatus Scalindua’ genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II. Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5’-phosphosulfate (APS reductase (aprA. Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as

  2. Archaeal and bacterial diversity in an arsenic-rich shallow-sea hydrothermal system undergoing phase separation

    Directory of Open Access Journals (Sweden)

    Roy Edward Price

    2013-07-01

    Full Text Available Phase separation is a ubiquitous process in seafloor hydrothermal vents, creating a large range of salinities. Toxic elements (e.g., arsenic partition into the vapor phase, and thus can be enriched in both high and low salinity fluids. However, investigations of microbial diversity at sites associated with phase separation are rare. We evaluated prokaryotic diversity in arsenic-rich shallow-sea vents off Milos Island (Greece by comparative analysis of 16S rRNA clone sequences from two vent sites with similar pH and temperature but marked differences in salinity. Clone sequences were also obtained for aioA-like functional genes (AFGs. Bacteria in the surface sediments (0 to 1.5 cm at the high salinity site consisted of mainly Epsilonproteobacteria (Arcobacter sp., which transitioned to almost exclusively Firmicutes (Bacillus sp. at ~10 cm depth. However, the low salinity site consisted of Bacteroidetes (Flavobacteria in the surface and Epsilonproteobacteria (Arcobacter sp. at ~10 cm depth. Archaea in the high salinity surface sediments were dominated by the orders Archaeoglobales and Thermococcales, transitioning to Thermoproteales and Desulfurococcales (Staphylothermus sp. in the deeper sediments. In contrast, the low salinity site was dominated by Thermoplasmatales in the surface and Thermoproteales at depth. Similarities in gas and redox chemistry suggest that salinity and/or arsenic concentrations may select for microbial communities that can tolerate these parameters. Many of the archaeal 16S rRNA sequences contained inserts, possibly introns, including members of the Euryarchaeota. Clones containing AFGs affiliated with either Alpha- or Betaproteobacteria, although most were only distantly related to published representatives. Most clones (89% originated from the deeper layer of the low salinity, highest arsenic site. This is the only sample with overlap in 16S rRNA data, suggesting arsenotrophy as an important metabolism in similar

  3. Tree species richness, diversity, and regeneration status in different oak (Quercus spp. dominated forests of Garhwal Himalaya, India

    Directory of Open Access Journals (Sweden)

    Sushma Singh

    2016-09-01

    Full Text Available Himalayan forests are dominated by different species of oaks (Quercus spp. at different altitudes. These oaks are intimately linked with hill agriculture as they protect soil fertility, watershed, and local biodiversity. They also play an important role in maintaining ecosystem stability. This work was carried out to study the diversity and regeneration status of some oak forests in Garhwal Himalaya, India. A total of 18 tree species belonging to 16 genera and 12 families were reported from the study area. Species richness varied for trees (4–7, saplings (3–10, and seedlings (2–6. Seedling and sapling densities (Ind/ha varied between 1,376 Ind/ha and 9,600 Ind/ha and 167 Ind/ha and 1,296 Ind/ha, respectively. Species diversity varied from 1.27 to 1.86 (trees, from 0.93 to 3.18 (saplings, and from 0.68 to 2.26 (seedlings. Total basal area (m2/ha of trees and saplings was 2.2–87.07 m2/ha and 0.20–2.24 m2/ha, respectively, whereas that of seedlings varied from 299 cm2/ha to 8,177 cm2/ha. Maximum tree species (20–80% had “good” regeneration. Quercus floribunda, the dominant tree species in the study area, showed “poor” regeneration, which is a matter of concern, and therefore, proper management and conservation strategies need to be developed for maintenance and sustainability of this oak species along with other tree species that show poor or no regeneration.

  4. Can parasites be indicators of free-living diversity? Relationships between species richness and the abundance of larval trematodes and of local benthos and fishes.

    Science.gov (United States)

    Hechinger, Ryan F; Lafferty, Kevin D; Huspeni, Todd C; Brooks, Andrew J; Kuris, Armand M

    2007-02-01

    Measuring biodiversity is difficult. This has led to efforts to seek taxa whose species richness correlates with the species richness of other taxa. Such indicator taxa could then reduce the time and cost of assessing the biodiversity of the more extensive community. The search for species richness correlations has yielded mixed results, however. This may be primarily because of the lack of functional relationships between the taxa studied. Trematode parasites are highly promising bioindicators. Diverse assemblages of larval trematode parasites are easily sampled in intermediate host snails. Through their life cycles these parasites are functionally coupled with the surrounding free-living diversity of vertebrate and invertebrate animals. It has been shown that larval trematodes in snails correlate positively with bird diversity and abundance. Here, we explore whether trematodes also correlate with standard measures of fishes, and large and small benthos, for 32 sites in three wetlands. We found associations between trematodes and benthic communities that were not consistent across wetlands. The associations were, however, consistently positive for large benthic species richness and density. Some of the contrasting associations between trematode and benthos may be explained by negative associations between large and small benthos. We found no associations with fish communities (probably because of the inadequacy of standard "snapshot" sampling methods for highly mobile fishes). The results support further exploration of trematodes as bioindicators of diversity and abundance of animal communities.

  5. Investigation of the microbial diversity of an extremely acidic, metal-rich water body (Lake Robule, Bor, Serbia

    Directory of Open Access Journals (Sweden)

    Stanković Srđan

    2014-01-01

    Full Text Available An investigation of the microbial diversity of the extremely acidic, metal-rich Lake Robule was carried out using culture-dependant and culture-independent (T-RFLP methods, and the ability of indigenous bacteria from the lake water to leach copper from a mineral concentrate was tested. T-RFLP analysis revealed that the dominant bacteria in lake water samples were the obligate heterotroph Acidiphilium cryptum (~50% of total bacteria and the iron-oxidizing autotroph Leptospirillum ferrooxidans (~40% The iron/sulfur-oxidizing autotroph Acidithiobacillus ferrooxidans had been reported to be the most abundant bacteria in the lake in an earlier study by other authors, but it was not detected in the present study using T-RFLP. Although it was isolated on solid media and detected in enrichment (bioleaching cultures. The presence of the two bacterial species detected by T-RFLP (L. ferrooxidans and A. cryptum was also confirmed by cultivation on solid media. The presence and relative abundance of bacteria inhabiting Lake Robule was explained by the physiological characteristics of the bacteria and the physico-chemical characteristics of the lake water. [Projekat Ministarstva nauke Republike Srbije, br. 176016 i br.173048

  6. Future high energy physics experiments using RICH detectors: The next generation

    Energy Technology Data Exchange (ETDEWEB)

    Ratcliff, B.N.

    1995-08-01

    This report describes some features of the new detectors now being constructed for use in high energy physics experiments that utilize RICH counters as a central element. The scope of this discussion is limited only to experiments which have been formally approved for construction as follows: (1) BaBar at PEP-II, which contains a quartz radiator DIRC counter; (2) CLEO III at the CESR upgrade, which utilizes a LiF/TEA Fast RICH; and (3) HERA-B at HERA, which uses a gas radiator RICH with either a TMAE- or a CsI-based photon detector. These experiments have much in common; all emphasize B-physics, run at the luminosity frontier, and plan to take first data either in 1998 or 1999. This review begins with a discussion of the physics goals and experimental context, and then explore the designs which have been chosen to confront the experimental issues. Particular emphasis is placed on the design and expected performance of the RICH detectors in these systems. Due to space limitations, only a few of the recent R and D results not covered elsewhere at the conference can be presented.

  7. Comparison of Plant Diversity and Stand Characteristics in Alnus subcordata C.A.Mey and Taxodium distichum (L. L.C. Rich

    Directory of Open Access Journals (Sweden)

    Masoud Tabari

    2011-12-01

    Full Text Available Stand characteristics and understory plant diversity were investigated in low-drained man-made stands of Alnus subcordata C.A.Mey and Taxodium distichum (L L.C. Rich. The trees were planted with distances of 3 × 3 m and 4 × 4 m in northern Iran. In these stands, herbaceous and woody species were counted in plots of 20 × 20 m. Then, indexes of richness, H/ diversity, J/ equitability and Jaccard similarity (JI, tree growths, cover crown percentage, and litter layer thickness of each stand were assessed following 17 years after planting. The results revealed that the greatest diameter at breast height (D.B.H and stem height were observed in Alnus 4 × 4 m. By contrast, crown cover percentage and litter thicknesses were greater in Taxodium stands. Species richness, H/ diversity and J/ equitability indexes, Jaccard similarity (JI of Alnus stands were greater than those of Taxodium stands. In reality, small and light canopy of Alnus is the main reason that the solar radiation can penetrate easily to forest ground and affect understory plant diversity. Alnus as a native tree species, due to greater growth attributes and higher diversity indices in their stands are proposed for plantations in such low-drained sites of northern Iran.

  8. In vivo recombination as a tool to generate molecular diversity in phage antibody libraries.

    Science.gov (United States)

    Sblattero, D; Lou, J; Marzari, R; Bradbury, A

    2001-06-01

    The creation of diversity in populations of polypeptides has become an important tool in the derivation of polypeptides with useful characteristics. This requires efficient methods to create diversity coupled with methods to select polypeptides with desired properties. In this review we describe the use of in vivo recombination as a powerful way to generate diversity. The novel principles for the recombination process and several applications of this process for the creation of phage antibody libraries are described. The advantage and disadvantages are discussed and possible future exploitation presented.

  9. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Niko eBeerenwinkel

    2012-09-01

    Full Text Available Many viruses, including the clinically relevant RNA viruses HIV and HCV, exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different next-generation sequencing platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of next-generation sequencing to estimate viral diversity.

  10. Understanding Generational Diversity: Strategic Human Resource Management and Development across the Generational "Divide"

    Science.gov (United States)

    Amayah, Angela Titi; Gedro, Julie

    2014-01-01

    There are more generations in today's workforce than ever before, which has the possibility to create challenges for Human Resource professionals. The purpose of this article is to interrogate existing stereotypes and generalities about the characteristics of different generations with respect to the workplace, and to offer suggestions for…

  11. Understanding Generational Diversity: Strategic Human Resource Management and Development across the Generational "Divide"

    Science.gov (United States)

    Amayah, Angela Titi; Gedro, Julie

    2014-01-01

    There are more generations in today's workforce than ever before, which has the possibility to create challenges for Human Resource professionals. The purpose of this article is to interrogate existing stereotypes and generalities about the characteristics of different generations with respect to the workplace, and to offer suggestions for…

  12. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing.

    Science.gov (United States)

    Alexander, Alana; Steel, Debbie; Slikas, Beth; Hoekzema, Kendra; Carraher, Colm; Parks, Matthew; Cronn, Richard; Baker, C Scott

    2013-01-01

    Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity.

  13. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater

    Science.gov (United States)

    Applegate, Olin; Li, Xunde; Kliegman, Joseph I.; Langelier, Charles; Atwill, Edward R.; Harter, Thomas; DeRisi, Joseph L.

    2017-01-01

    Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite

  14. Platelet-rich fibrin (PRF): a second-generation platelet concentrate. Part II: platelet-related biologic features.

    Science.gov (United States)

    Dohan, David M; Choukroun, Joseph; Diss, Antoine; Dohan, Steve L; Dohan, Anthony J J; Mouhyi, Jaafar; Gogly, Bruno

    2006-03-01

    Platelet-rich fibrin (PRF) belongs to a new generation of platelet concentrates, with simplified processing and without biochemical blood handling. In this second article, we investigate the platelet-associated features of this biomaterial. During PRF processing by centrifugation, platelets are activated and their massive degranulation implies a very significant cytokine release. Concentrated platelet-rich plasma platelet cytokines have already been quantified in many technologic configurations. To carry out a comparative study, we therefore undertook to quantify PDGF-BB, TGFbeta-1, and IGF-I within PPP (platelet-poor plasma) supernatant and PRF clot exudate serum. These initial analyses revealed that slow fibrin polymerization during PRF processing leads to the intrinsic incorporation of platelet cytokines and glycanic chains in the fibrin meshes. This result would imply that PRF, unlike the other platelet concentrates, would be able to progressively release cytokines during fibrin matrix remodeling; such a mechanism might explain the clinically observed healing properties of PRF.

  15. Glyphosate–rich air samples induce IL–33, TSLP and generate IL–13 dependent airway inflammation

    Science.gov (United States)

    Kumar, Sudhir; Khodoun, Marat; Kettleson, Eric M.; McKnight, Christopher; Reponen, Tiina; Grinshpun, Sergey A.; Adhikari, Atin

    2014-01-01

    Several low weight molecules have often been implicated in the induction of occupational asthma. Glyphosate, a small molecule herbicide, is widely used in the world. There is a controversy regarding a role of glyphosate in developing asthma and rhinitis among farmers, the mechanism of which is unexplored. The aim of this study was to explore the mechanisms of glyphosate induced pulmonary pathology by utilizing murine models and real environmental samples. C57BL/6, TLR4−/−, and IL-13−/− mice inhaled extracts of glyphosate-rich air samples collected on farms during spraying of herbicides or inhaled different doses of glyphosate and ovalbumin. The cellular response, humoral response, and lung function of exposed mice were evaluated. Exposure to glyphosate-rich air samples as well as glyphosate alone to the lungs increased: eosinophil and neutrophil counts, mast cell degranulation, and production of IL-33, TSLP, IL-13, and IL-5. In contrast, in vivo systemic IL-4 production was not increased. Co-administration of ovalbumin with glyphosate did not substantially change the inflammatory immune response. However, IL-13-deficiency resulted in diminished inflammatory response but did not have a significant effect on airway resistance upon methacholine challenge after 7 or 21 days of glyphosate exposure. Glyphosate-rich farm air samples as well as glyphosate alone were found to induce pulmonary IL-13-dependent inflammation and promote Th2 type cytokines, but not IL-4 for glyphosate alone. This study, for the first time, provides evidence for the mechanism of glyphosate-induced occupational lung disease. PMID:25172162

  16. Glyphosate-rich air samples induce IL-33, TSLP and generate IL-13 dependent airway inflammation.

    Science.gov (United States)

    Kumar, Sudhir; Khodoun, Marat; Kettleson, Eric M; McKnight, Christopher; Reponen, Tiina; Grinshpun, Sergey A; Adhikari, Atin

    2014-11-01

    Several low weight molecules have often been implicated in the induction of occupational asthma. Glyphosate, a small molecule herbicide, is widely used in the world. There is a controversy regarding a role of glyphosate in developing asthma and rhinitis among farmers, the mechanism of which is unexplored. The aim of this study was to explore the mechanisms of glyphosate induced pulmonary pathology by utilizing murine models and real environmental samples. C57BL/6, TLR4-/-, and IL-13-/- mice inhaled extracts of glyphosate-rich air samples collected on farms during spraying of herbicides or inhaled different doses of glyphosate and ovalbumin. The cellular response, humoral response, and lung function of exposed mice were evaluated. Exposure to glyphosate-rich air samples as well as glyphosate alone to the lungs increased: eosinophil and neutrophil counts, mast cell degranulation, and production of IL-33, TSLP, IL-13, and IL-5. In contrast, in vivo systemic IL-4 production was not increased. Co-administration of ovalbumin with glyphosate did not substantially change the inflammatory immune response. However, IL-13-deficiency resulted in diminished inflammatory response but did not have a significant effect on airway resistance upon methacholine challenge after 7 or 21 days of glyphosate exposure. Glyphosate-rich farm air samples as well as glyphosate alone were found to induce pulmonary IL-13-dependent inflammation and promote Th2 type cytokines, but not IL-4 for glyphosate alone. This study, for the first time, provides evidence for the mechanism of glyphosate-induced occupational lung disease.

  17. Measuring the diversity of the human microbiota with targeted next-generation sequencing.

    Science.gov (United States)

    Finotello, Francesca; Mastrorilli, Eleonora; Di Camillo, Barbara

    2016-12-26

    The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples. However, diversity is not a determined physical quantity for which a consensus definition and unit of measure have been established, and several diversity indices are currently available. Furthermore, they were originally developed for macroecology and their robustness to the possible bias introduced by sequencing has not been characterized so far. To assist the reader with the selection and interpretation of diversity measures, we review a panel of broadly used indices, describing their mathematical formulations, purposes and properties, and characterize their behaviour and criticalities in dependence of the data features using simulated data as ground truth. In addition, we make available an R package, DiversitySeq, which implements in a unified framework the full panel of diversity indices and a simulator of 16S-seq data, and thus represents a valuable resource for the analysis of diversity from NGS count data and for the benchmarking of computational methods for 16S-seq.

  18. Cheating in Business Schools, the Millennial Generation, Gender and Racial Diversity: Has the Paradigm Shifted?

    Science.gov (United States)

    Mathison, David L.

    2010-01-01

    Cheating in college is not new. In 1960 over 50 percent of students admitted they cheated. In the second decade of the 21st century has anything changed? This research project looked at three possible new variables, the Millennial Generation, Gender, and Diversity. Results suggest the amount of reported cheating remains the same even with current…

  19. Constitution of Drop-Tube-Generated Coal Chars from Vitrinite- and Inertinite-Rich South African Coals

    Energy Technology Data Exchange (ETDEWEB)

    Louw, Enette B.; Mitchell, Gareth D.; Wang, Juan; Winans, Randall E.; Mathews, Jonathan P.

    2016-01-21

    The structural transformations of coal and the resultant char morphologies are strongly dependent on the initial structure and degree of thermoplasticity achieved during coal-to-char transition. These are a function of petrographic composition, rank, particle size, and heating rate and strongly affect combustion behavior. This study compares the devolatilization and subsequent combustion behavior of an inertinite-rich (87.7% dmmf) and a vitrinite-rich (91.8% dmmf) South African coal, wet-screened to a narrow particle size distribution of 200 x 400 mesh. Pyrolysis chars were generated under rapid-heating conditions (104-105 °C/s) in a drop-tube reactor to closely resemble chars generated in pulverized combustion conditions. The inertinite-rich coal took ~ 400 ms to devolatilize in the drop-tube, compared to only ~ 240 ms for the vitrinite-rich sample. The chemical and physical structure (the constitution) of the chars were investigated through a range of chemical, physical, and optical characteristics including the maceral differences, and high ash yields. To evaluate the combustion reactivity non-isothermal burn-out profiles were obtained through thermogravimetrical analyses (TGA) in air. The vitrinite-rich char had on average 20% higher reaction rates than the inertinite-rich char under the various combustion conditions. The char samples were de-ashed with HCl and HF acid which resulted in an increase in combustion reactivity. The maximum reaction rate of the high-ash (36% ash yield) inertinite-rich char increased with 80% after de-ashing. While the vitrinite-rich char with an ash yield of 15%, had a 20% increase in reactivity after de-ashing. The ash acted as a barrier, and the removal of ash most likely increased the access to reactive surface area. The chemical and physical structures of the chars were characterized through a range of different analytical techniques to quantify the factors contributing to reactivity differences. The morphologies of the chars

  20. Generation of topologically diverse acoustic vortex beams using a compact metamaterial aperture

    CERN Document Server

    Naify, Christina J; Martin, Theodore P; Nicholas, Michael; Guild, Matthew D; Orris, Gregory J

    2016-01-01

    Vortex waves, which carry orbital angular momentum, have found use in a range of fields from quantum communications to particle manipulation. Due to their widespread influence, significant attention has been paid to the methods by which vortex waves are generated. For example, active phased arrays generate diverse vortex modes at the cost of electronic complexity and power consumption. Conversely, analog apertures, such as spiral phase plates, metasurfaces, and gratings require separate apertures to generate each mode. Here we present a new class of metamaterial-based acoustic vortex generators, which are both geometrically and electronically simple, and topologically tunable. Our metamaterial approach generates vortex waves by wrapping an acoustic leaky wave antenna back upon itself. Exploiting the antennas frequency-varying refractive index, we demonstrate experimentally and analytically that this analog structure generates both integer, and non-integer vortex modes. The metamaterial design makes the apertu...

  1. In the time of significant generational diversity - surgical leadership must step up!

    Science.gov (United States)

    Money, Samuel R; O'Donnell, Mark E; Gray, Richard J

    2014-02-01

    The diverse attitudes and motivations of surgeons and surgical trainees within different age groups present an important challenge for surgical leaders and educators. These challenges to surgical leadership are not unique, and other industries have likewise needed to grapple with how best to manage these various age groups. The authors will herein explore management and leadership for surgeons in a time of age diversity, define generational variations within "Baby-Boomer", "Generation X" and "Generation Y" populations, and identify work ethos concepts amongst these three groups. The surgical community must understand and embrace these concepts in order to continue to attract a stellar pool of applicants from medical school. By not accepting the changing attitudes and motivations of young trainees and medical students, we may disenfranchise a high percentage of potential future surgeons. Surgical training programs will fill, but will they contain the highest quality trainees?

  2. RF SOI CMOS technology on 1st and 2nd generation trap-rich high resistivity SOI wafers

    Science.gov (United States)

    Kazemi Esfeh, B.; Makovejev, S.; Basso, Didier; Desbonnets, Eric; Kilchytska, V.; Flandre, D.; Raskin, J.-P.

    2017-02-01

    In this work three different types of UNIBOND™ Silicon-on-Insulator (SOI) wafers including one standard HR-SOI and two types of trap-rich high resistivity HR-SOI substrates named enhanced signal integrity high resistivity silicon-on-insulator (eSI HR-SOI) provided by SOITEC are studied and compared. The DC and RF performances of these wafers are compared by means of passive and active devices such as coplanar waveguide (CPW) lines, crosstalk- and noise injection-structures as well as partially-depleted (PD) SOI MOSFETs. It is demonstrated that by employing enhanced signal integrity high resistivity silicon-on-insulator (eSI HR-SOI) compared to HR-SOI wafer, a reduction of 24 dB is measured on both generations of trap-rich HR-SOI for 2nd harmonics. Furthermore, it is shown that in eSI HR-SOI, digital substrate noise is effectively reduced compared with HR-SOI. Purely capacitive behavior of eSI HR-SOI is demonstrated by crosstalk structure. Reduction of self-heating effect in the trap-rich HR-SOI with thinner BOX is finally studied.

  3. One-generation reproductive toxicity study of DHA-rich oil in rats

    NARCIS (Netherlands)

    Blum, R.; Kiy, T.; Waalkens-Berendsen, I.; Wong, A.W.; Roberts, A.

    2007-01-01

    Polyunsaturated fatty acids, including docosahexaenoic acid (DHA), are natural constituents of the human diet. DHA-algal oil is produced through the use of the marine protist, Ulkenia sp. The reproductive toxicity of DHA-algal oil was assessed in a one-generation study. Rats were provided diets

  4. One-generation reproductive toxicity study of DHA-rich oil in rats

    NARCIS (Netherlands)

    Blum, R.; Kiy, T.; Waalkens-Berendsen, I.; Wong, A.W.; Roberts, A.

    2007-01-01

    Polyunsaturated fatty acids, including docosahexaenoic acid (DHA), are natural constituents of the human diet. DHA-algal oil is produced through the use of the marine protist, Ulkenia sp. The reproductive toxicity of DHA-algal oil was assessed in a one-generation study. Rats were provided diets cont

  5. Synthesis of sp3-rich scaffolds for molecular libraries through complexity-generating cascade reactions

    DEFF Research Database (Denmark)

    Flagstad, Thomas; Min, Geanna; Bonnet, K.

    2016-01-01

    An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented. Key steps of the strategy include tandem Petasis and Diels–Alder reactions, and divergent complexity-generating cyclization cascades from a key dialdehyde intermediate. The methodology is ...

  6. Richness, biomass, and nutrient content of a wetland macrophyte community affect soil nitrogen cycling in a diversity-ecosystem functioning experiment

    Science.gov (United States)

    Korol, Alicia R.; Ahn, Changwoo; Noe, Gregory

    2016-01-01

    The development of soil nitrogen (N) cycling in created wetlands promotes the maturation of multiple biogeochemical cycles necessary for ecosystem functioning. This development proceeds from gradual changes in soil physicochemical properties and influential characteristics of the plant community, such as competitive behavior, phenology, productivity, and nutrient composition. In the context of a 2-year diversity experiment in freshwater mesocosms (0, 1, 2, 3, or 4 richness levels), we assessed the direct and indirect impacts of three plant community characteristics – species richness, total biomass, and tissue N concentration – on three processes in the soil N cycle – soil net ammonification, net nitrification, and denitrification potentials. Species richness had a positive effect on net ammonification potential (NAP) through higher redox potentials and likely faster microbial respiration. All NAP rates were negative, however, due to immobilization and high rates of ammonium removal. Net nitrification was inhibited at higher species richness without mediation from the measured soil properties. Higher species richness also inhibited denitrification potential through increased redox potential and decreased nitrification. Both lower biomass and/or higher tissue ratios of carbon to nitrogen, characteristics indicative of the two annual plants, were shown to have stimulatory effects on all three soil N processes. The two mediating physicochemical links between the young macrophyte community and microbial N processes were soil redox potential and temperature. Our results suggest that early-successional annual plant communities play an important role in the development of ecosystem N multifunctionality in newly created wetland soils.

  7. Processing of Snake Venom Metalloproteinases: Generation of Toxin Diversity and Enzyme Inactivation

    Directory of Open Access Journals (Sweden)

    Ana M. Moura-da-Silva

    2016-06-01

    Full Text Available Snake venom metalloproteinases (SVMPs are abundant in the venoms of vipers and rattlesnakes, playing important roles for the snake adaptation to different environments, and are related to most of the pathological effects of these venoms in human victims. The effectiveness of SVMPs is greatly due to their functional diversity, targeting important physiological proteins or receptors in different tissues and in the coagulation system. Functional diversity is often related to the genetic diversification of the snake venom. In this review, we discuss some published evidence that posit that processing and post-translational modifications are great contributors for the generation of functional diversity and for maintaining latency or inactivation of enzymes belonging to this relevant family of venom toxins.

  8. Geochemical diversity in first rocks examined by the Curiosity Rover in Gale Crater: Evidence for and significance of an alkali and volatile-rich igneous source

    Science.gov (United States)

    Schmidt, M. E.; Campbell, J. L.; Gellert, R.; Perrett, G. M.; Treiman, A. H.; Blaney, D. L.; Olilla, A.; Calef, F. J.; Edgar, L.; Elliott, B. E.; Grotzinger, J.; Hurowitz, J.; King, P. L.; Minitti, M. E.; Sautter, V.; Stack, K.; Berger, J. A.; Bridges, J. C.; Ehlmann, B. L.; Forni, O.; Leshin, L. A.; Lewis, K. W.; McLennan, S. M.; Ming, D. W.; Newsom, H.; Pradler, I.; Squyres, S. W.; Stolper, E. M.; Thompson, L.; VanBommel, S.; Wiens, R. C.

    2014-01-01

    first four rocks examined by the Mars Science Laboratory Alpha Particle X-ray Spectrometer indicate that Curiosity landed in a lithologically diverse region of Mars. These rocks, collectively dubbed the Bradbury assemblage, were studied along an eastward traverse (sols 46-102). Compositions range from Na- and Al-rich mugearite Jake_Matijevic to Fe-, Mg-, and Zn-rich alkali-rich basalt/hawaiite Bathurst_Inlet and span nearly the entire range in FeO* and MnO of the data sets from previous Martian missions and Martian meteorites. The Bradbury assemblage is also enriched in K and moderately volatile metals (Zn and Ge). These elements do not correlate with Cl or S, suggesting that they are associated with the rocks themselves and not with salt-rich coatings. Three out of the four Bradbury rocks plot along a line in elemental variation diagrams, suggesting mixing between Al-rich and Fe-rich components. ChemCam analyses give insight to their degree of chemical heterogeneity and grain size. Variations in trace elements detected by ChemCam suggest chemical weathering (Li) and concentration in mineral phases (e.g., Rb and Sr in feldspars). We interpret the Bradbury assemblage to be broadly volcanic and/or volcaniclastic, derived either from near the Gale crater rim and transported by the Peace Vallis fan network, or from a local volcanic source within Gale Crater. High Fe and Fe/Mn in Et_Then likely reflect secondary precipitation of Fe3+ oxides as a cement or rind. The K-rich signature of the Bradbury assemblage, if igneous in origin, may have formed by small degrees of partial melting of metasomatized mantle.

  9. Overcoming viral escape with vaccines that generate and display antigen diversity in vivo

    Directory of Open Access Journals (Sweden)

    García-Quintanilla Albert

    2007-11-01

    Full Text Available Abstract Background Viral diversity is a key problem for the design of effective and universal vaccines. Virtually, a vaccine candidate including most of the diversity for a given epitope would force the virus to create escape mutants above the viability threshold or with a high fitness cost. Presentation of the hypothesis Therefore, I hypothesize that priming the immune system with polyvalent vaccines where each single vehicle generates and displays multiple antigen variants in vivo, will elicit a broad and long-lasting immune response able to avoid viral escape. Testing the hypothesis To this purpose, I propose the use of yeasts that carry virus-like particles designed to pack the antigen-coding RNA inside and replicate it via RNA-dependent RNA polymerase. This would produce diversity in vivo limited to the target of interest and without killing the vaccine vehicle. Implications of the hypothesis This approach is in contrast with peptide cocktails synthesized in vitro and polyvalent strategies where every cell or vector displays a single or definite number of mutants; but similarly to all them, it should be able to overcome original antigenic sin, avoid major histocompatibility complex restriction, and elicit broad cross-reactive immune responses. Here I discuss additional advantages such as minimal global antagonism or those derived from using a yeast vehicle, and potential drawbacks like autoimmunity. Diversity generated by this method could be monitored both genotypically and phenotypically, and therefore selected or discarded before use if needed.

  10. The diversity and richness of tree species of Tambang Sawah forest Kerinci-Seblat National Park Sumatra Indonesia

    Directory of Open Access Journals (Sweden)

    Agus Susatya

    2010-12-01

    Full Text Available The conservation of tropical ecosystem is increasingly relevant as the recent global warming and climate change generate serious impacts on human life. Tropical forest becomes an important ecosystem to fight global warming due to its capability to sequester atmospheric carbon and to mitigate climate change. It is very unfortunate that such a vital ecosystem has been severely subjected to conversion to both plantations and illegal loggings. The tropical ecosystem has long been recognized to have high species diversity, but very few individual trees per species. The latter is almost ignored, even though can certainly bring serious difficulties on tree conservation. The objectives of the research were to know the tree community structure of Tambang Sawah Forest, Kerinci-Seblat National Park, and to determine the rareness of tree species. A plot of 1 ha was established at Tambang Sawah, Kerinci-Seblat National Park, Lebong Regency. All trees with BDH of > 5 cm were collected their herbarium specimens, and identifi ed. The results showed that Tambang Sawah forest consists of 42 families, 94 genera, and 185 tree species/ha. It has 19.51% (8 families, and 26.82% (10 families respectively categorized as very rare and rare. The pattern also occurs at genus level, where both categories contribute to 81.91% (78 genera of the total genera. In species level, both are respectively 90 and 28 species, and altogether contribute to 63.78% of the total species. These values appeared higher than that of the other forests in Bengkulu. Across taxon level, very rare and rare categories appeared to be an ecological attribute in Sumatran forests. This implies that the loss of single tree can cause the loss of entire family. The conservation works even turn into more difficult, because tropical trees are commonly diocious, even bisexual trees, they tend to be self-incompatible, and out-crossed, and required at least 200 mature trees to ensure sexual regeneration and to

  11. Immigrant Generation and Sexual Initiation Among a Diverse Racial/Ethnic Group of Urban Youth.

    Science.gov (United States)

    Coleman-Minahan, Kate; Chavez, Marisol; Bull, Sheana

    2016-04-21

    Foreign-born youth have a lower risk of sexual initiation than native born youth, yet most research has focused on Latinos. An ethnically diverse sample of 200, 14-21 year-old youth were surveyed in Denver in 2014. We used logistic regression models to predict the odds of intentions to have sex and sexual experience, adding covariates that could account for differences in outcomes by immigrant generation. First generation youth were less likely to intend to have sex and to have sexual experience than third generation youth after controlling for racial/ethnic group, suggesting that first generation immigrants of multiple racial/ethnic groups, not just Latinos alone, have a lower risk for sexual initiation. Having a supportive community reduced the odds of sexual intentions and sexual experience. Our findings support future research using a larger sample of black, white, and Asian immigrant youth to corroborate and to explore reasons behind these associations.

  12. Unveiling a Rich System of Faint Dwarf Galaxies in the Next Generation Fornax Survey

    CERN Document Server

    Munoz, Roberto P; Puzia, Thomas H; Taylor, Matthew A; Ordenes-Briceno, Yasna; Alamo-Martinez, Karla; Ribbeck, Karen X; Angel, Simon; Capaccioli, Massimo; Cote, Patrick; Ferrarese, Laura; Galaz, Gaspar; Hempel, Maren; Hilker, Michael; Jordan, Andres; Lancon, Ariane; Mieske, Steffen; Paolillo, Maurizio; Richtler, Tom; Sanchez-Janssen, Ruben; Zhang, Hongxin

    2015-01-01

    We report the discovery of 158 previously undetected dwarf galaxies in the Fornax cluster central regions using a deep coadded $u, g$ and $i$-band image obtained with the DECam wide-field camera mounted on the 4-meter Blanco telescope at the Cerro Tololo Interamerican Observatory as part of the {\\it Next Generation Fornax Survey} (NGFS). The new dwarf galaxies have quasi-exponential light profiles, effective radii $0.1\\!\\!75\\%$ at luminosities brighter than $M_i\\!\\simeq\\!-15.0$ mag to $0\\%$ at luminosities fainter than $M_i\\!\\simeq\\!-10.0$ mag. The two-point correlation function analysis of the NGFS dwarf sample shows an excess on length scales below $\\sim\\!100$ kpc, pointing to the clustering of dwarf galaxies in the Fornax cluster core.

  13. One-generation reproductive toxicity study of DHA-rich oil in rats.

    Science.gov (United States)

    Blum, René; Kiy, Thomas; Waalkens-Berendsen, Ine; Wong, Andrea W; Roberts, Ashley

    2007-12-01

    Polyunsaturated fatty acids, including docosahexaenoic acid (DHA), are natural constituents of the human diet. DHA-algal oil is produced through the use of the marine protist, Ulkenia sp. The reproductive toxicity of DHA-algal oil was assessed in a one-generation study. Rats were provided diets containing DHA-algal oil at concentrations of 1.5, 3.0, or 7.5%, and the control group received a diet containing 7.5% corn oil. Males and females were treated for 10 weeks prior to mating and during mating. Females continued to receive test diets during gestation and lactation. In parental animals, clinical observations, mortality, fertility, and reproductive performance were unaffected by treatment. Differences in food consumption, body weight, and liver weight in the treated groups were not considered to be due to an adverse effect of DHA-algal oil. Spleen weight increases in treated animals were associated with extramedullary hematopoiesis. Yellow discoloration of abdominal adipose tissue was observed in rats from the high-dose group, and histological examination revealed steatitis in all treated parental groups. Exposure to DHA-algal oil did not influence the physical development of F(1) animals. These results demonstrate that DHA-algal oil at dietary concentrations of up to 7.5% in rats does not affect reproductive capacity or pup development.

  14. No post-Cretaceous ecosystem depression in European forests? Rich insect-feeding damage on diverse middle Palaeocene plants, Menat, France.

    Science.gov (United States)

    Wappler, Torsten; Currano, Ellen D; Wilf, Peter; Rust, Jes; Labandeira, Conrad C

    2009-12-22

    Insect herbivores are considered vulnerable to extinctions of their plant hosts. Previous studies of insect-damaged fossil leaves in the US Western Interior showed major plant and insect herbivore extinction at the Cretaceous-Palaeogene (K-T) boundary. Further, the regional plant-insect system remained depressed or ecologically unbalanced throughout the Palaeocene. Whereas Cretaceous floras had high plant and insect-feeding diversity, all Palaeocene assemblages to date had low richness of plants, insect feeding or both. Here, we use leaf fossils from the middle Palaeocene Menat site, France, which has the oldest well-preserved leaf assemblage from the Palaeocene of Europe, to test the generality of the observed Palaeocene US pattern. Surprisingly, Menat combines high floral diversity with high insect activity, making it the first observation of a 'healthy' Palaeocene plant-insect system. Furthermore, rich and abundant leaf mines across plant species indicate well-developed host specialization. The diversity and complexity of plant-insect interactions at Menat suggest that the net effects of the K-T extinction were less at this greater distance from the Chicxulub, Mexico, impact site. Along with the available data from other regions, our results show that the end-Cretaceous event did not cause a uniform, long-lasting depression of global terrestrial ecosystems. Rather, it gave rise to varying regional patterns of ecological collapse and recovery that appear to have been strongly influenced by distance from the Chicxulub structure.

  15. Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products.

    Science.gov (United States)

    Banik, Jacob J; Craig, Jeffrey W; Calle, Paula Y; Brady, Sean F

    2010-11-10

    A detailed bioinformatics analysis of six glycopeptide biosynthetic gene clusters isolated from soil environmental DNA (eDNA) megalibraries indicates that a subset of these gene clusters contains collections of tailoring enzymes that are predicted to result in the production of new glycopeptide congeners. In particular, sulfotransferases appear in eDNA-derived gene clusters at a much higher frequency than would be predicted from the characterization of glycopeptides from cultured Actinomycetes . Enzymes found on tailoring-enzyme-rich eDNA clones associated with these six gene clusters were used to produce a series of new sulfated glycopeptide derivatives in both in vitro and in vivo derivatization studies. The derivatization of known natural products with eDNA-derived tailoring enzymes is likely to be a broadly applicable strategy for generating libraries of new natural product variants.

  16. The retinal projectome reveals brain-area-specific visual representations generated by ganglion cell diversity.

    Science.gov (United States)

    Robles, Estuardo; Laurell, Eva; Baier, Herwig

    2014-09-22

    Visual information is transmitted to the vertebrate brain exclusively via the axons of retinal ganglion cells (RGCs). The functional diversity of RGCs generates multiple representations of the visual environment that are transmitted to several brain areas. However, in no vertebrate species has a complete wiring diagram of RGC axonal projections been constructed. We employed sparse genetic labeling and in vivo imaging of the larval zebrafish to generate a cellular-resolution map of projections from the retina to the brain. Our data define 20 stereotyped axonal projection patterns, the majority of which innervate multiple brain areas. Morphometric analysis of pre- and postsynaptic RGC structure revealed more than 50 structural RGC types with unique combinations of dendritic and axonal morphologies, exceeding current estimates of RGC diversity in vertebrates. These single-cell projection mapping data indicate that specific projection patterns are nonuniformly specified in the retina to generate retinotopically biased visual maps throughout the brain. The retinal projectome also successfully predicted a functional subdivision of the pretectum. Our data indicate that RGC projection patterns are precisely coordinated to generate brain-area-specific visual representations originating from RGCs with distinct dendritic morphologies and topographic distributions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. ASSESSING THE EFFECTS OF LOGGING ACTIVITIES ON AVIAN RICHNESS AND DIVERSITY IN DIFFERENT AGED POST-HARVESTED HILL DIPTEROCARP TROPICAL RAINFOREST OF MALAYSIA

    Directory of Open Access Journals (Sweden)

    M. N. Rajpar

    2014-01-01

    Full Text Available Logging activities have encroached into the hill dipterocarp tropical rainforest area since the lowland dipterocarp forests have decreased in size. Hill dipterocarp tropical rainforest is rich in habitat diversity and provide a variety of resources for avian species such as food, habitat and shelter. Therefore it is important to examine the logging effects of hill dipterocarp rainforest on avian species. We compared the avian richness and diversity in different aged post-harvested hill dipterocarp tropical rainforest at the Berkelah Hill Dipterocarp Rainforest Reserve in Maran, Pahang, West Malaysia using mist-netting method. We captured a total of 1908 individuals representing 86 species and 29 families (i.e., 18.55% from two years post-harvested forest, 25.10% from ten years post-harvested, 23.90% from twenty years post-harvested and 32.44% from thirty five years post-harvested forests. Forty nine species were caught in two years and ten years, 55 species in twenty years and 59 species in thirty five years’ post-harvested forest. Seventeen species were common in all four types of forest. Pycnonotidae, Timaliidae and Nectariniidae were the most dominant families in all types of post-harvested hill dipterocarp tropical rainforest. Diversity analysis indicated that the bird species in twenty years post-harvested hill dipterocarp rainforest was most diverse (i.e., Fisher’s Alpha Diversity Index; 16.34 and evenly distributed (i.e., McIntosh Evenness index E; 0.933 as compared to two years, ten years and thirty five years post-harvested forest. However, thirty five years post-harvested forest was richest in avian species (i.e., Margalef’s Richness index R1; 9.02 as compared to other post-harvested forest. The findings of this study revealed that logging and recovery process may affects on avian distribution and diversity. However, these effects may vary from species to species.

  18. Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams

    DEFF Research Database (Denmark)

    Levi, Peter S.; Starnawski, Piotr; Poulsen, Britta

    2017-01-01

    Biofilms in streams play an integral role in ecosystem processes and function yet few studies have investigated the broad diversity of these complex prokaryotic and eukaryotic microbial communities. Physical habitat characteristics can affect the composition and abundance of microorganisms...

  19. 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...

  20. A comparative overview of immunoglobulin genes and the generation of their diversity in tetrapods.

    Science.gov (United States)

    Sun, Yi; Wei, Zhiguo; Li, Ning; Zhao, Yaofeng

    2013-01-01

    In the past several decades, immunoglobulin (Ig) genes have been extensively characterized in many tetrapod species. This review focuses on the expressed Ig isotypes and the diversity of Ig genes in mammals, birds, reptiles, and amphibians. With regard to heavy chains, five Ig isotypes - IgM, IgD, IgG, IgA, and IgE - have been reported in mammals. Among these isotypes, IgM, IgD, and IgA (or its analog, IgX) are also found in non-mammalian tetrapods. Birds, reptiles, and amphibians express IgY, which is considered the precursor of IgG and IgE. Some species have developed unique isotypes of Ig, such as IgO in the platypus, IgF in Xenopus, and IgY (ΔFc) in ducks and turtles. The κ and λ light chains are both utilized in tetrapods, but the usage frequencies of κ and λ chains differ greatly among species. The diversity of Ig genes depends on several factors, including the germline repertoire and recombinatorial and post-recombinatorial diversity, and different species have evolved distinct mechanisms to generate antibody diversity.

  1. Alkali metal salts of formazanate ligands : diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone

    NARCIS (Netherlands)

    Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

    2014-01-01

    Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available fo

  2. Local and regional variability in fish community structure, richness and diversity of 56 Danish lakes with contrasting depth and trophic state

    DEFF Research Database (Denmark)

    Menezes, Rosemberg; Borchsenius, Finn; Svenning, J.-C.

    /profundal zones. Nevertheless, information about how the within-lake variability in fish abundance, richness and diversity changes in the littoral and pelagic areas along contrasting depth and trophic state is scarce. It is expected that eutrophic lakes present lower within lake habit heterogeneity than...... oligotrophic lakes due to high turbidity leading to loss of submerged macrophytes and thus habitat variability. Also the influence of piscivorous birds on the fish distribution in the littoral zone may differ between lake types leading to a more homogeneous distribution along the littoral area in eutrophic...

  3. Diversification and coevolution in brood pollination mutualisms: Windows into the role of biotic interactions in generating biological diversity.

    Science.gov (United States)

    Hembry, David H; Althoff, David M

    2016-10-01

    Brood pollination mutualisms-interactions in which specialized insects are both the pollinators (as adults) and seed predators (as larvae) of their host plants-have been influential study systems for coevolutionary biology. These mutualisms include those between figs and fig wasps, yuccas and yucca moths, leafflowers and leafflower moths, globeflowers and globeflower flies, Silene plants and Hadena and Perizoma moths, saxifrages and Greya moths, and senita cacti and senita moths. The high reciprocal diversity and species-specificity of some of these mutualisms have been cited as evidence that coevolution between plants and pollinators drives their mutual diversification. However, the mechanisms by which these mutualisms diversify have received less attention. In this paper, we review key hypotheses about how these mutualisms diversify and what role coevolution between plants and pollinators may play in this process. We find that most species-rich brood pollination mutualisms show significant phylogenetic congruence at high taxonomic scales, but there is limited evidence for the processes of both cospeciation and duplication, and there are no unambiguous examples known of strict-sense contemporaneous cospeciation. Allopatric speciation appears important across multiple systems, particularly in the insects. Host-shifts appear to be common, and widespread host-shifts by pollinators may displace other pollinator lineages. There is relatively little evidence for a "coevolution through cospeciation" model or that coevolution promotes speciation in these systems. Although we have made great progress in understanding the mechanisms by which brood pollination mutualisms diversify, many opportunities remain to use these intriguing symbioses to understand the role of biotic interactions in generating biological diversity. © 2016 Botanical Society of America.

  4. Next-generation sequencing reveals significant bacterial diversity of botrytized wine.

    Directory of Open Access Journals (Sweden)

    Nicholas A Bokulich

    Full Text Available While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5. This study was designed to serve two goals: 1 to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP of LAB communities; and 2 to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the

  5. One-year survey of a single Micronesian reef reveals extraordinarily rich diversity of Symbiodinium types in soritid foraminifera

    Science.gov (United States)

    Pochon, X.; Garcia-Cuetos, L.; Baker, A. C.; Castella, E.; Pawlowski, J.

    2007-12-01

    Recent molecular studies of symbiotic dinoflagellates (genus Symbiodinium) from a wide array of invertebrate hosts have revealed exceptional fine-scale symbiont diversity whose distribution among hosts, regions and environments exhibits significant biogeographic, ecological and evolutionary patterns. Here, similar molecular approaches using the internal transcribed spacer-2 (ITS-2) region were applied to investigate cryptic diversity in Symbiodinium inhabiting soritid foraminifera. Approximately 1,000 soritid specimens were collected and examined during a 12-month period over a 40 m depth gradient from a single reef in Guam, Micronesia. Out of 61 ITS-2 types distinguished, 46 were novel. Most types found are specific for soritid hosts, except for three types (C1, C15 and C19) that are common in metazoan hosts. The distribution of these symbionts was compared with the phylotype of their foraminiferal hosts, based on soritid small subunit ribosomal DNA sequences, and three new phylotypes of soritid hosts were identified based on these sequences. Phylogenetic analyses of 645 host-symbiont pairings revealed that most Symbiodinium types associated specifically with a particular foraminiferal host genus or species, and that the genetic diversity of these symbiont types was positively correlated with the genetic diversity found within each of the three host genera. Compared to previous molecular studies of Symbiodinium from other locations worldwide, the diversity reported here is exceptional and suggests that Micronesian coral reefs are home to a remarkably large Symbiodinium assemblage.

  6. Yeast and bacterial diversity along a transect in an acidic, As-Fe rich environment revealed by cultural approaches.

    Science.gov (United States)

    Delavat, François; Lett, Marie-Claire; Lièvremont, Didier

    2013-10-01

    Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient.

  7. Exploring the potential of second-generation sequencing in diverse biological contexts

    DEFF Research Database (Denmark)

    Fordyce, Sarah Louise

    Second generation sequencing (SGS) has revolutionized the study of DNA, allowing massive parallel sequencing of nucleic acids with unprecedented depths of coverage. The research undertaken in this thesis occurred in parallel with the increased accessibility of SGS platforms for routine genetic...... H1N1 influenza A virus genomes. The results of these studies demonstrate the power of SGS for gaining insight into the genetic variation of diverse biological samples and highlight the importance of using optimized protocols for sequencing non-conventional samples....

  8. Diversity of total and functional microbiome of anammox reactors fed with complex and synthetic nitrogen-rich wastewaters

    DEFF Research Database (Denmark)

    Gülay, Arda; Pellicer i Nàcher, Carles; Mutlu, Ayten Gizem

    There are few comparitive studies of microbial structure, composition and phylogenetic diversity of the anammox reactors as a function of substrate complexity exist, representing a large gap in the scientific literature. In this study, we applied 16S rRNA gene (rDNA) tag-based 454 pyrosequencing ...

  9. Generation of topologically diverse acoustic vortex beams using a compact metamaterial aperture

    Energy Technology Data Exchange (ETDEWEB)

    Naify, Christina J., E-mail: christina.naify@nrl.navy.mil; Rohde, Charles A.; Martin, Theodore P.; Nicholas, Michael [U.S. Naval Research Laboratory, Code 7165, Washington, D.C. 20375 (United States); Guild, Matthew D. [National Research Council Research Associateship Program, U.S. Naval Research Laboratory, Washington, D.C. 20375 (United States); Orris, Gregory J. [U.S. Naval Research Laboratory, Code 7160, Washington, D.C. 20375 (United States)

    2016-05-30

    Here, we present a class of metamaterial-based acoustic vortex generators which are both geometrically simple and broadly tunable. The aperture overcomes the significant limitations of both active phasing systems and existing passive coded apertures. The metamaterial approach generates topologically diverse acoustic vortex waves motivated by recent advances in leaky wave antennas by wrapping the antenna back upon itself to produce an acoustic vortex wave antenna. We demonstrate both experimentally and analytically that this single analog structure is capable of creating multiple orthogonal orbital angular momentum modes using only a single transducer. The metamaterial design makes the aperture compact, with a diameter nearly equal to the excitation wavelength and can thus be easily integrated into high-density systems. Applications range from acoustic communications for high bit-rate multiplexing to biomedical devices such as microfluidic mixers.

  10. Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum.

    Science.gov (United States)

    Hahn, Andrea; Sanyal, Amit; Perez, Geovanny F; Colberg-Poley, Anamaris M; Campos, Joseph; Rose, Mary C; Pérez-Losada, Marcos

    2016-11-01

    Cystic fibrosis (CF) is an autosomal recessive disease characterized by recurrent lung infections. Studies of the lung microbiome have shown an association between decreasing diversity and progressive disease. 454 pyrosequencing has frequently been used to study the lung microbiome in CF, but will no longer be supported. We sought to identify the benefits and drawbacks of using two state-of-the-art next generation sequencing (NGS) platforms, MiSeq and PacBio RSII, to characterize the CF lung microbiome. Each has its advantages and limitations. Twelve samples of extracted bacterial DNA were sequenced on both MiSeq and PacBio NGS platforms. DNA was amplified for the V4 region of the 16S rRNA gene and libraries were sequenced on the MiSeq sequencing platform, while the full 16S rRNA gene was sequenced on the PacBio RSII sequencing platform. Raw FASTQ files generated by the MiSeq and PacBio platforms were processed in mothur v1.35.1. There was extreme discordance in alpha-diversity of the CF lung microbiome when using the two platforms. Because of its depth of coverage, sequencing of the 16S rRNA V4 gene region using MiSeq allowed for the observation of many more operational taxonomic units (OTUs) and higher Chao1 and Shannon indices than the PacBio RSII. Interestingly, several patients in our cohort had Escherichia, an unusual pathogen in CF. Also, likely because of its coverage of the complete 16S rRNA gene, only PacBio RSII was able to identify Burkholderia, an important CF pathogen. When comparing microbiome diversity in clinical samples from CF patients using 16S sequences, MiSeq and PacBio NGS platforms may generate different results in microbial community composition and structure. It may be necessary to use different platforms when trying to correctly identify dominant pathogens versus measuring alpha-diversity estimates, and it would be important to use the same platform for comparisons to minimize errors in interpretation. Copyright © 2016 Elsevier B.V. All

  11. Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola

    Directory of Open Access Journals (Sweden)

    Sutichot eNimkulrat

    2016-06-01

    Full Text Available Diversity-generating retroelements (DGRs are genetic cassettes that can produce massive protein sequence variation in prokaryotes. Presumably DGRs confer selective advantages to their hosts (bacteria or viruses by generating variants of target genes—typically resulting in target proteins with altered ligand-binding specificity—through a specialized error-prone reverse transcription process. The only extensively studied DGR system is from the Bordetella phage BPP-1, although DGRs are predicted to exist in other species. Using bioinformatics analysis, we discovered that the DGR system associated with the Treponema denticola species (a human oral-associated periopathogen is dynamic (with gains/losses of the system found in the isolates and diverse (with multiple types found in isolated genomes and the human microbiota. The T. denticola DGR is found in only nine of the 17 sequenced T. denticola strains. Analysis of the DGR-associated template regions and reverse transcriptase gene sequences revealed two types of DGR systems in T. denticola: the ATCC35405-type shared by seven isolates including ATCC35405; and the SP32-type shared by two isolates (SP32 and SP33, suggesting multiple DGR acquisitions. We detected additional variants of the T. denticola DGR systems in the human microbiomes, and found that the SP32-type DGR is more abundant than the ATCC35405-type in the healthy human oral microbiome, although the latter is found in more sequenced isolates. This is the first comprehensive study to characterize the DGRs associated with T. denticola in individual genomes as well as human microbiomes, demonstrating the importance of utilizing both individual genomes and metagenomes for characterizing the elements, and for analyzing their diversity and distribution in human populations.

  12. Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

    Science.gov (United States)

    Moore, Geromy G.; Elliott, Jacalyn L.; Singh, Rakhi; Horn, Bruce W.; Dorner, Joe W.; Stone, Eric A.; Chulze, Sofia N.; Barros, German G.; Naik, Manjunath K.; Wright, Graeme C.; Hell, Kerstin; Carbone, Ignazio

    2013-01-01

    Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more

  13. Sexuality generates diversity in the aflatoxin gene cluster: evidence on a global scale.

    Directory of Open Access Journals (Sweden)

    Geromy G Moore

    Full Text Available Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B₁ being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs. We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia, Africa (Benin, Argentina (Córdoba, Australia (Queensland and India (Karnataka. Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B₁-dominant and G₁-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of

  14. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Directory of Open Access Journals (Sweden)

    Antoine Claessens

    2014-12-01

    Full Text Available The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1 that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs were scattered across the genome, structural variants (deletions, duplications, translocations were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7-72.4% yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

  15. The influence of vegetation structure on spider species richness, diversity and community organization in the Apšuciems calcareous fen, Latvia

    Energy Technology Data Exchange (ETDEWEB)

    Štokmane, M.; Spuņģis, V.

    2016-07-01

    Calcareous fens are considered to be among the most threatened ecosystems of Europe. They are also one of the most diverse habitats as they support an incredibly rich and diverse range of plant and animal species. However, in spite of their diversity, calcareous fens are still poorly investigated, especially when referring to fen invertebrates, such as spiders. Because spiders are good bioindicators, knowledge of their ecology in rare and threatened habitats is of interest. The aim of this study was to document the composition and diversity of spider species, families and foraging guilds in the ground– and grass–layers of the Apšuciems calcareous fen, and to evaluate the influence of vegetation structure on spider community organization. In summer 2012, we collected ground–dwelling spiders using pitfall traps and grass–dwelling spiders using sweep–netting. A total of 2,937 spider individuals belonging to 19 families and 80 species was collected in the Apšuciems fen. Our results indicate that spider species and families tend to be stratified across the vertical structure of the habitat; the spider composition in the ground stratum differed from that in the grass stratum. On the contrary, however, the spider foraging guild structure between the ground–layer and the grass–layer was similar. Each of the two studied strata presented similar guilds in similar proportions. Our results also showed that spider composition differed considerably between fen parts and that much of this variability could be explained by the architectural properties of the habitat. More diverse vegetation generally supported a higher number of spider species. (Author)

  16. The influence of vegetation structure on spider species richness, diversity and community organization in the Apšuciems calcareous fen, Latvia

    Directory of Open Access Journals (Sweden)

    Štokmane, M.

    2016-07-01

    Full Text Available Calcareous fens are considered to be among the most threatened ecosystems of Europe. They are also one of the most diverse habitats as they support an incredibly rich and diverse range of plant and animal species. However, in spite of their diversity, calcareous fens are still poorly investigated, especially when referring to fen invertebrates, such as spiders. Because spiders are good bioindicators, knowledge of their ecology in rare and threatened habitats is of interest. The aim of this study was to document the composition and diversity of spider species, families and foraging guilds in the ground– and grass–layers of the Apšuciems calcareous fen, and to evaluate the influence of vegetation structure on spider community organization. In summer 2012, we collected ground–dwelling spiders using pitfall traps and grass–dwelling spiders using sweep–netting. A total of 2,937 spider individuals belonging to 19 families and 80 species was collected in the Apšuciems fen. Our results indicate that spider species and families tend to be stratified across the vertical structure of the habitat; the spider composition in the ground stratum differed from that in the grass stratum. On the contrary, however, the spider foraging guild structure between the ground–layer and the grass–layer was similar. Each of the two studied strata presented similar guilds in similar proportions. Our results also showed that spider composition differed considerably between fen parts and that much of this variability could be explained by the architectural properties of the habitat. More diverse vegetation generally supported a higher number of spider species.

  17. Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae

    Science.gov (United States)

    Marcelino, Vanessa Rossetto; Verbruggen, Heroen

    2016-01-01

    Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers (tufA, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic diversity of the green algae—the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful of endolithic species. We found more than 120 taxonomic units (near species level), including six family-level lineages mostly new to science. The results suggest that the existence of lineages with an endolithic lifestyle predates the existence of modern scleractinian corals by ca. 250my, and that this particular niche was independently invaded by over 20 lineages in green algae evolution. These results highlight the potential of the multi-marker approach to assist in species discovery and, when combined with a phylogenetic framework, clarify the evolutionary origins of host-microbiota associations. PMID:27545322

  18. Geography of Alaska Lake Districts: Identification, Description, and Analysis of Lake-Rich Regions of a Diverse and Dynamic State

    Science.gov (United States)

    Arp, Christopher D.; Jones, Benjamin M.

    2009-01-01

    Lakes are abundant landforms and important ecosystems in Alaska, but are unevenly distributed on the landscape with expansive lake-poor regions and several lake-rich regions. Such lake-rich areas are termed lake districts and have landscape characteristics that can be considered distinctive in similar respects to mountain ranges. In this report, we explore the nature of lake-rich areas by quantitatively identifying Alaska's lake districts, describing and comparing their physical characteristics, and analyzing how Alaska lake districts are naturally organized and correspond to climatic and geophysical characteristics, as well as studied and managed by people. We use a digital dataset (National Hydrography Dataset) of lakes greater than 1 hectare, which includes 409,040 individual lakes and represents 3.3 percent of the land-surface area of Alaska. The selection criteria we used to identify lake districts were (1) a lake area (termed limnetic ratio, in percent) greater than the mean for the State, and (2) a lake density (number of lakes per unit area) greater than the mean for the State using a pixel size scaled to the area of interest and number of lakes in the census. Pixels meeting these criteria were grouped and delineated and all groups greater than 1,000 square kilometers were identified as Alaska's lake districts. These lake districts were described according to lake size-frequency metrics, elevation distributions, geology, climate, and ecoregions to better understand their similarities and differences. We also looked at where lake research and relevant ecological monitoring has occurred in Alaska relative to lake districts and how lake district lands and waters are currently managed. We identified and delineated 20 lake districts in Alaska representing 16 percent of the State, but including 65 percent of lakes and 75 percent of lake area. The largest lake districts identified are the Yukon-Kuskokwim Delta, Arctic Coastal Plain, and Iliamna lake districts with

  19. Assessment of antibody library diversity through next generation sequencing and technical error compensation

    Science.gov (United States)

    Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

    2017-01-01

    Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error. PMID:28505201

  20. Determination of Microbial Diversity and Nitrogen Cycling from Kizildere Geothermal Field with Next Generation Sequencing

    Science.gov (United States)

    Gulecal, Y.; Dilek, Y.

    2012-12-01

    The deep terrestrial subsurface biosphere represents an emerging frontier for studies of biodiversity, the physiological limits to life, microbial mechanisms of adaptation, and potentially analogous environments for extraterrestrial life (1). Last decade, researches of deep boreholes in the United States, Finland, Sweden, Japan and South Africa, using molecular tools, have shown an an active biosphere composed of diverse groups of microorganisms. The microbial communities reported from different subsurface communities vary widely; such differences are due to different host rock types and varied water origins and chemistry, as well as geography. Furthermore, nitrogen cycling is studied intensely in hot springs for instance in situ nifH expression in Yellowstone National Park, is a new upper temperature limit for nitrogen fixation in alkaline, terrestrial hydrothermal environments (2). This study explores the genetic diversity of microbial communities and genes of nitrogen cycling in Kizildere Geothermal Field, Turkey. The Kizildere thermal waters are located in the northern part of the Büyük Menderes rift zone. The hydrothermal alteration includes phyllic, argillic, silicic,hematitized, and carbonatized alteration zones. The surface temperatures of Kizildere thermal waters in drill holes range from 95 to100°C and pH 9.0-9.5. Microbial communities were examined using culture independent methods, next generation sequencing. Nitrogen fixation, the diversity of nifH, ammonia oxidation (amoA), narG, nosZ genes are investigated in deeply-sourced fluids. We present field observations and interpret new data, establishing a geobiological baseline for previously undescribed sitres of subsurface ecosystems. (1)Fredrickson et al. 2006. Geomicrobial processes and biodiversity in the deep terrestrial subsurface. Geomicrobiology J. 23:345-356. (2) Loiacono et al. 2012. Evidence for high-temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin

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

    Science.gov (United States)

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

    2016-01-27

    Elucidating the mechanisms of high-altitude adaptation is an important research area in modern biology. To date, however, knowledge has been limited to the genetic mechanisms of adaptation to the lower oxygen and temperature levels prevalent at high altitudes, with adaptation to UV radiation largely neglected. Furthermore, few proteomic or peptidomic analyses of these factors have been performed. In this study, the molecular adaptation of high-altitude Odorrana andersonii and cavernicolous O. 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. This implied that O. andersonii evolved a much more complicated and powerful skin antioxidant peptide system to survive high-altitude UV levels. Our results provided valuable peptidomic clues for understanding the novel molecular basis for adaptation to high elevation habitats.

  2. Evaluating Re-Os systematics in organic-rich sedimentary rocks in response to petroleum generation using hydrous pyrolysis experiments

    Science.gov (United States)

    Rooney, A.D.; Selby, D.; Lewan, M.D.; Lillis, P.G.; Houzay, J.-P.

    2012-01-01

    Successful application of the 187Re–187Os geochronometer has enabled the determination of accurate and precise depositional ages for organic-rich sedimentary rocks (ORS) as well as establishing timing constraints of petroleum generation. However, we do not fully understand the systematics and transfer behaviour of Re and Os between ORS and petroleum products (e.g., bitumen and oil). To more fully understand the behaviour of Re–Os systematics in both source rocks and petroleum products we apply hydrous pyrolysis to two immature hydrocarbon source rocks: the Permian Phosphoria Formation (TOC = 17.4%; Type II-S kerogen) and the Jurassic Staffin Formation (TOC = 2.5%; Type III kerogen). The laboratory-based hydrous pyrolysis experiments were carried out for 72 h at 250, 300, 325 and 350 °C. These experiments provided us with whole rock, extracted rock and bitumen and in some cases expelled oil and asphaltene for evaluation of Re–Os isotopic and elemental abundance. The data from these experiments demonstrate that the majority (>95%) of Re and Os are housed within extracted rock and that thermal maturation does not result in significant transfer of Re or Os from the extracted rock into organic phases. Based on existing thermodynamic data our findings suggest that organic chelating sites have a greater affinity for the quadravalent states of Re and Os than sulphides. Across the temperature range of the hydrous pyrolysis experiments both whole rock and extracted rock 187Re/188Os ratios show small variations (3.3% and 4.7%, for Staffin, respectively and 6.3% and 4.9% for Phosphoria, respectively). Similarly, the 187Os/188Os ratios show only minor variations for the Staffin and Phosphoria whole rock and extracted rock samples (0.6% and 1.4% and 1.3% and 2.2%). These isotopic data strongly suggest that crude oil generation through hydrous pyrolysis experiments does not disturb the Re–Os systematics in ORS as supported by various studies on natural systems. The

  3. Evaluating Re-Os systematics in organic-rich sedimentary rocks in response to petroleum generation using hydrous pyrolysis experiments

    Science.gov (United States)

    Rooney, Alan D.; Selby, David; Lewan, Michael D.; Lillis, Paul G.; Houzay, Jean-Pierre

    2012-01-01

    Successful application of the 187Re-187Os geochronometer has enabled the determination of accurate and precise depositional ages for organic-rich sedimentary rocks (ORS) as well as establishing timing constraints of petroleum generation. However, we do not fully understand the systematics and transfer behaviour of Re and Os between ORS and petroleum products (e.g., bitumen and oil). To more fully understand the behaviour of Re-Os systematics in both source rocks and petroleum products we apply hydrous pyrolysis to two immature hydrocarbon source rocks: the Permian Phosphoria Formation (TOC = 17.4%; Type II-S kerogen) and the Jurassic Staffin Formation (TOC = 2.5%; Type III kerogen). The laboratory-based hydrous pyrolysis experiments were carried out for 72 h at 250, 300, 325 and 350 °C. These experiments provided us with whole rock, extracted rock and bitumen and in some cases expelled oil and asphaltene for evaluation of Re-Os isotopic and elemental abundance. The data from these experiments demonstrate that the majority (>95%) of Re and Os are housed within extracted rock and that thermal maturation does not result in significant transfer of Re or Os from the extracted rock into organic phases. Based on existing thermodynamic data our findings suggest that organic chelating sites have a greater affinity for the quadravalent states of Re and Os than sulphides. Across the temperature range of the hydrous pyrolysis experiments both whole rock and extracted rock 187Re/188Os ratios show small variations (3.3% and 4.7%, for Staffin, respectively and 6.3% and 4.9% for Phosphoria, respectively). Similarly, the 187Os/188Os ratios show only minor variations for the Staffin and Phosphoria whole rock and extracted rock samples (0.6% and 1.4% and 1.3% and 2.2%). These isotopic data strongly suggest that crude oil generation through hydrous pyrolysis experiments does not disturb the Re-Os systematics in ORS as supported by various studies on natural systems. The elemental

  4. Alternative polyadenylation in a family of paralogous EPB41 genes generates protein 4.1 diversity.

    Science.gov (United States)

    Rangel, Laura; Lospitao, Eva; Ruiz-Sáenz, Ana; Alonso, Miguel A; Correas, Isabel

    2017-02-01

    Alternative polyadenylation (APA) is a step in mRNA 3'-end processing that contributes to the complexity of the transcriptome by generating isoforms that differ in either their coding sequence or their 3'-untranslated regions (UTRs). The EPB41 genes, EPB41, EPB41L2, EPB41L3 and EPB41L1, encode an impressively complex array of structural adaptor proteins (designated 4.1R, 4.1G, 4.1B and 4.1N, respectively) by using alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing. The great variety of 4.1 proteins mainly results from 5'-end and internal processing of the EPB41 pre-mRNAs. Thus, 4.1 proteins can vary in their N-terminal extensions but all contain a highly homologous C-terminal domain (CTD). Here we study a new group of EPB41-related mRNAs that originate by APA and lack the exons encoding the CTD characteristic of prototypical 4.1 proteins, thereby encoding a new type of 4.1 protein. For the EPB41 gene, this type of processing was observed in all 11 human tissues analyzed. Comparative genomic analysis of EPB41 indicates that APA is conserved in various mammals. In addition, we show that APA also functions for the EPB41L2, EPB41L3 and EPB41L1 genes, but in a more restricted manner in the case of the latter 2 than it does for the EPB41 and EPB41L2 genes. Our study shows alternative polyadenylation to be an additional mechanism for the generation of 4.1 protein diversity in the already complex EPB41-related genes. Understanding the diversity of EPB41 RNA processing is essential for a full appreciation of the many 4.1 proteins expressed in normal and pathological tissues.

  5. Alkali metal salts of formazanate ligands: diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone.

    Science.gov (United States)

    Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

    2014-12-28

    Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available for bonding with the alkali metal. The potassium salt K[PhNNC(p-tol)NNPh]·2THF (1-K) is dimeric in the solid state and even in THF solution, as a result of the K atom bridging via interaction with a terminal N atom and the aromatic ring of a second unit. Conversely, for the compounds Na[MesNNC(CN)NNMes]·2THF (2-Na) and Na[PhNNC((t)Bu)NNPh] (3-Na) polymeric and hexameric structures are found in the solid state respectively. The preference for binding the alkali metal through internal N atoms (1-K and 2-Na) to give a 4-membered chelate, or via internal/external N atoms (5-membered chelate in 3-Na), contrasts with the 6-membered chelate mode observed in our recently reported formazanate zinc complexes.

  6. Generating information-rich high-throughput experimental materials genomes using functional clustering via multitree genetic programming and information theory.

    Science.gov (United States)

    Suram, Santosh K; Haber, Joel A; Jin, Jian; Gregoire, John M

    2015-04-13

    High-throughput experimental methodologies are capable of synthesizing, screening and characterizing vast arrays of combinatorial material libraries at a very rapid rate. These methodologies strategically employ tiered screening wherein the number of compositions screened decreases as the complexity, and very often the scientific information obtained from a screening experiment, increases. The algorithm used for down-selection of samples from higher throughput screening experiment to a lower throughput screening experiment is vital in achieving information-rich experimental materials genomes. The fundamental science of material discovery lies in the establishment of composition-structure-property relationships, motivating the development of advanced down-selection algorithms which consider the information value of the selected compositions, as opposed to simply selecting the best performing compositions from a high throughput experiment. Identification of property fields (composition regions with distinct composition-property relationships) in high throughput data enables down-selection algorithms to employ advanced selection strategies, such as the selection of representative compositions from each field or selection of compositions that span the composition space of the highest performing field. Such strategies would greatly enhance the generation of data-driven discoveries. We introduce an informatics-based clustering of composition-property functional relationships using a combination of information theory and multitree genetic programming concepts for identification of property fields in a composition library. We demonstrate our approach using a complex synthetic composition-property map for a 5 at. % step ternary library consisting of four distinct property fields and finally explore the application of this methodology for capturing relationships between composition and catalytic activity for the oxygen evolution reaction for 5429 catalyst compositions in a

  7. Second-generation Platelet Concentrate (Platelet-rich Fibrin) as a Scaffold in Regenerative Endodontics: A Case Series.

    Science.gov (United States)

    Bakhtiar, Hengameh; Esmaeili, Shahram; Fakhr Tabatabayi, Setareh; Ellini, Mohammad Reza; Nekoofar, Mohammad Hossein; Dummer, Paul M H

    2017-03-01

    The purpose of this case series was to report the clinical and radiographic results of a pulp regenerative procedure using platelet-rich fibrin (PRF), a second-generation platelet concentrate, in immature teeth with necrotic pulps. Root canal revascularization using PRF was performed on 4 immature teeth with necrotic pulps. After access cavity preparation, the root canals were irrigated with low concentration sodium hypochlorite solution (1.5% sodium hypochlorite [20 mL/canal, 5 minutes]) and then irrigated with saline (20 mL/canal, 5 minutes). Equal proportions (167 mg) of ciprofloxacin, metronidazole, and cefaclor were mixed and diluted to a final concentration of 1 g/mL. Finally, the canal was sealed with 3-4 mm of a temporary restorative material, and patients were dismissed for 2 to 3 weeks. At the second appointment, 9 mL of the patient's whole blood was obtained and centrifuged to prepare a PRF clot. Canals were irrigated with 17% EDTA, and a sharp spreader was inserted beyond the apex. Then, the PRF clot was placed inside the root canals, and Biodentine (Septodont, Saint-Maur, France) was placed directly over the PRF. The teeth were restored permanently with glass ionomer cement and composite resin. Clinical examinations revealed that all cases were asymptomatic at the recall appointments at 1, 3, 6, 12, and 18 months. Radiographs revealed resolution of the periapical lesions, further root development, and apical closure in all cases. On the basis of the short-term results up to 12 months, PRF clots acted as successful scaffolds for the regeneration of pulpal contents in immature teeth with necrotic pulps. Copyright © 2016 American Association of Endodontists. All rights reserved.

  8. Patterns of shrub species richness and abundance in relation to environmental factors on the Alxa Plateau:Prerequisites for conserving shrub diversity in extreme arid desert regions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Shrub species are considered the dominant plants in arid desert ecosystems,unlike in semiarid steppe zones or in grassland ecosystems.On the Alxa Plateau,northern China,sparse vegetation with cover ranging from 15% to 30% is characterized mainly by multifarious shrubs because herbaceous species are strongly restricted by the extreme drought climate,wind erosion,overgrazing and sand burial.Patterns in shrub species richness and species abundance in relation to environmental conditions were examined by DCA(detrended correspondence analysis) and interpreted by a biplot.The rela-tionships between species diversity and environmental factors were examined using regression analyses.Our results show that the distributions of the shrub species in response to environmental conditions can be grouped into four ecological types,corresponding with the biological traits of the shrubs and their responses to the gradients of soil texture and soil water content.Patterns in species richness and species abundance were mainly determined by the deeper soil water content,instead of the soil texture as hypothesized by numerous studies in semiarid grasslands.With exception of the deeper soil water content,soil organic matter and total N content were positively correlated with species abundance,while pH was negatively correlated with it.These findings imply that it is vital for cur-rent shrub diversity conservation to reduce agricultural water use in the middle reaches of the Heihe River,which supplies water for the lower reaches in the western parts of the plateau,and to reduce the amount of groundwater exploitation and urban and oasis water use,to increase the water supply from Helan Mountain to the eastern desert of the Alxa Plateau.

  9. Patterns of shrub species richness and abundance in relation to environmental factors on the Alxa Plateau: Prerequisites for conserving shrub diversity in extreme arid desert regions

    Institute of Scientific and Technical Information of China (English)

    LI XinRong; TAN HuiJuan; HE MingZhu; WANG XinPing; LI XiaoJun

    2009-01-01

    Shrub species are considered the dominant plants in arid desert ecosystems, unlike in semiarid steppe zones or in grassland ecosystems. On the Alxa Plateau, northern China, sparse vegetation with cover ranging from 15% to 30% is characterized mainly by multifarious shrubs because herbaceous species are strongly restricted by the extreme drought climate, wind erosion, overgrazing and sand burial. Patterns in shrub species richness and species abundance in relation to environmental conditions were examined by DCA (detrended correspondence analysis) and interpreted by a biplot. The rela-tionships between species diversity and environmental factors were examined using regression analyses. Our results show that the distributions of the shrub species in response to environmental conditions can be grouped into four ecological types, corresponding with the biological traits of the shrubs and their responses to the gradients of soil texture and soil water content. Patterns in species richness and species abundance were mainly determined by the deeper soil water content, instead of the soil texture as hypothesized by numerous studies in semiarid grasslands. With exception of the deeper soil water content, soil organic matter and total N content were positively correlated with spe-cies abundance, while pH was negatively correlated with it. These findings imply that it is vital for cur-rent shrub diversity conservation to reduce agricultural water use in the middle reaches of the Heihe River, which supplies water for the lower reaches in the western parts of the plateau, and to reduce the amount of groundwater exploitation and urban and oasis water use, to increase the water supply from Helan Mountain to the eastern desert of the Alxa Plateau.

  10. Visually representing the generation of older consumers as a diverse audience: towards a multidimensional market segmentation typology

    NARCIS (Netherlands)

    Loos, E.; Ekström, M.

    2014-01-01

    Television commercials and advertising often represent the generation of older consumers as eternally youthful, active and rich. Representations of senior citizens as fragile people needing services and products to help them to survive are also used, but less frequently. As individual differences be

  11. Visually representing the generation of older consumers as a diverse audience: Towards a multidimensional market segmentation typology

    NARCIS (Netherlands)

    Loos, Eugène; Ekström, M.

    2014-01-01

    Television commercials and advertising often represent the generation of older consumers as eternally youthful, active and rich. Representations of senior citizens as fragile people needing services and products to help them to survive are also used, but less frequently. As individual differences be

  12. Visually representing the generation of older consumers as a diverse audience: towards a multidimensional market segmentation typology

    NARCIS (Netherlands)

    Loos, E.; Ekström, M.

    2014-01-01

    Television commercials and advertising often represent the generation of older consumers as eternally youthful, active and rich. Representations of senior citizens as fragile people needing services and products to help them to survive are also used, but less frequently. As individual differences be

  13. Visually representing the generation of older consumers as a diverse audience: Towards a multidimensional market segmentation typology

    OpenAIRE

    Loos, Eugène; Ekström, M

    2014-01-01

    Television commercials and advertising often represent the generation of older consumers as eternally youthful, active and rich. Representations of senior citizens as fragile people needing services and products to help them to survive are also used, but less frequently. As individual differences between senior citizens increase as they grow older, it is important to avoid one-dimensional stereotyping images. In this essay we first discuss the notion of generations and literature related to t...

  14. Species Richness and Diversity of Resident and Migratory Landbirds in Remnant Forest Patches and Residential Areas in the Florida Keys, USA

    Directory of Open Access Journals (Sweden)

    Martin B. Main

    2011-01-01

    Full Text Available Conservation of migratory birds necessitates protecting suitable stopover habitat along migratory routes as well as destination habitats, especially near large geographic barriers such as the Gulf of Mexico. The Florida Keys (Keys are an important stopover and breeding destination for migratory landbirds. We documented 47 migratory and 21 resident landbird species via point counts during March–May 2004 and 2005. As a group, species richness, species diversity, and the effective number of species of migratory landbirds, including several species of conservation concern, was significantly and positively associated with percent cover of tropical hardwood hammock, a threatened upland forest type. The collective resident landbird community in the Keys was negatively associated with native hammock cover, although species diversity of the resident community was positively associated with the proximity of native hammock and several resident species, including species of conservation concern, were commonly or predominantly associated with native hammock. Consequently, conservation of native hammock habitat in the Keys is an important conservation priority for migratory birds and several resident species of conservation concern.

  15. Targeted recovery of novel phylogenetic diversity from next-generation sequence data.

    Science.gov (United States)

    Lynch, Michael D J; Bartram, Andrea K; Neufeld, Josh D

    2012-11-01

    Next-generation sequencing technologies have led to recognition of a so-called 'rare biosphere'. These microbial operational taxonomic units (OTUs) are defined by low relative abundance and may be specifically adapted to maintaining low population sizes. We hypothesized that mining of low-abundance next-generation 16S ribosomal RNA (rRNA) gene data would lead to the discovery of novel phylogenetic diversity, reflecting microorganisms not yet discovered by previous sampling efforts. Here, we test this hypothesis by combining molecular and bioinformatic approaches for targeted retrieval of phylogenetic novelty within rare biosphere OTUs. We combined BLASTN network analysis, phylogenetics and targeted primer design to amplify 16S rRNA gene sequences from unique potential bacterial lineages, comprising part of the rare biosphere from a multi-million sequence data set from an Arctic tundra soil sample. Demonstrating the feasibility of the protocol developed here, three of seven recovered phylogenetic lineages represented extremely divergent taxonomic entities. These divergent target sequences correspond to (a) a previously unknown lineage within the BRC1 candidate phylum, (b) a sister group to the early diverging and currently recognized monospecific Cyanobacteria Gloeobacter, a genus containing multiple plesiomorphic traits and (c) a highly divergent lineage phylogenetically resolved within mitochondria. A comparison to twelve next-generation data sets from additional soils suggested persistent low-abundance distributions of these novel 16S rRNA genes. The results demonstrate this sequence analysis and retrieval pipeline as applicable for exploring underrepresented phylogenetic novelty and recovering taxa that may represent significant steps in bacterial evolution.

  16. RET Aberrations in Diverse Cancers: Next-Generation Sequencing of 4,871 Patients.

    Science.gov (United States)

    Kato, Shumei; Subbiah, Vivek; Marchlik, Erica; Elkin, Sheryl K; Carter, Jennifer L; Kurzrock, Razelle

    2017-04-15

    Purpose: Aberrations in genetic sequences encoding the tyrosine kinase receptor RET lead to oncogenic signaling that is targetable with anti-RET multikinase inhibitors. Understanding the comprehensive genomic landscape of RET aberrations across multiple cancers may facilitate clinical trial development targeting RETExperimental Design: We interrogated the molecular portfolio of 4,871 patients with diverse malignancies for the presence of RET aberrations using Clinical Laboratory Improvement Amendments-certified targeted next-generation sequencing of 182 or 236 gene panels.Results: Among diverse cancers, RET aberrations were identified in 88 cases [1.8% (88/4, 871)], with mutations being the most common alteration [38.6% (34/88)], followed by fusions [30.7% (27/88), including a novel SQSTM1-RET] and amplifications [25% (22/88)]. Most patients had coexisting aberrations in addition to RET anomalies [81.8% (72/88)], with the most common being in TP53-associated genes [59.1% (52/88)], cell cycle-associated genes [39.8% (35/88)], the PI3K signaling pathway [30.7% (27/88)], MAPK effectors [22.7% (20/88)], or other tyrosine kinase families [21.6% (19/88)]. RET fusions were mutually exclusive with MAPK signaling pathway alterations. All 72 patients harboring coaberrations had distinct genomic portfolios, and most [98.6% (71/72)] had potentially targetable coaberrations with either an FDA-approved or an investigational agent. Two cases with lung (KIF5B-RET) and medullary thyroid carcinoma (RET M918T) that responded to a vandetanib (multikinase RET inhibitor)-containing regimen are shown.Conclusions:RET aberrations were seen in 1.8% of diverse cancers, with most cases harboring actionable, albeit distinct, coexisting alterations. The current report suggests that optimal targeting of patients with RET anomalies will require customized combination strategies. Clin Cancer Res; 23(8); 1988-97. ©2016 AACR. ©2016 American Association for Cancer Research.

  17. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing

    Science.gov (United States)

    Alana Alexander; Debbie Steel; Beth Slikas; Kendra Hoekzema; Colm Carraher; Matthew Parks; Richard Cronn; C. Scott Baker

    2012-01-01

    Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20...

  18. Reactions between komatiite and CO2-rich seawater at 250 and 350 °C, 500 bars: implications for hydrogen generation in the Hadean seafloor hydrothermal system

    Science.gov (United States)

    Ueda, Hisahiro; Shibuya, Takazo; Sawaki, Yusuke; Saitoh, Masafumi; Takai, Ken; Maruyama, Shigenori

    2016-12-01

    To understand the chemical nature of hydrothermal fluids in the komatiite-hosted seafloor hydrothermal system in the Hadean, we conducted two hydrothermal serpentinization experiments involving synthetic komatiite and a CO2-rich acidic NaCl fluid at 250 and 350 °C, 500 bars. During the experiments, the komatiites were strongly carbonated to yield iron-rich dolomite (3-9 wt.% FeO) at 250 °C and calcite (<0.8 wt.% FeO) at 350 °C, respectively. The carbonation of komatiites suppressed H2 generation in the fluids. The steady-state H2 concentrations in the fluid were approximately 0.024 and 2.9 mmol/kg at 250 and 350 °C, respectively. This correlation between the Fe content in carbonate mineral and the H2 concentration in the fluid suggests that the incorporation of ferrous iron into the carbonate mineral probably limited magnetite formation and consequent generation of hydrogen during the serpentinization of komatiites. The H2 concentration of the fluid at 350 °C corresponds to that of modern H2-rich seafloor hydrothermal systems, such as the Kairei hydrothermal field, where hydrogenotrophic methanogens dominate in the prosperous microbial ecosystem. Accordingly, the high-temperature serpentinization of komatiite would provide the H2-rich hydrothermal environments that were necessary for the emergence and early evolution of life in the Hadean ocean. In contrast, H2-rich fluids may not have been generated by serpentinization at temperatures below 250 °C because carbonate minerals become more stable with decreasing temperature in the komatiite-H2O-CO2 system.

  19. The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing

    Institute of Scientific and Technical Information of China (English)

    Alexander W Wyatt; Fan Mo; Yuzhuo Wang; Colin C Collins

    2013-01-01

    Prostate cancer is a leading cause of global cancer-related death but attempts to improve diagnoses and develop novel therapies have been confounded by significant patient heterogeneity.In recent years,the application of next-generation sequencing to hundreds of prostate tumours has defined novel molecular subtypes and characterized extensive genomic aberration underlying disease initiation and progression.It is now clear that the heterogeneity observed in the clinic is underpinned by a molecular landscape rife with complexity,where genomic rearrangements and rare mutations combine to amplify transcriptomic diversity.This review dissects our current understanding of prostate cancer ‘omics',including the sentinel role of copy number variation,the growing spectrum of oncogenic fusion genes,the potential influence of chromothripsis,and breakthroughs in defining mutation-associated subtypes.Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways,yet recurrent gene aberration appears rare.Therefore,it is critical that we continue to define individual tumour genomes,especially in the context of their expressed transcriptome.Only through improved characterisation of tumour to tumour variability can we advance to an age of precision therapy and personalized oncology.

  20. An Idea for Generating Diversity Conversations: Physics Jeopardy and the Future Faces of Physics Kit

    Science.gov (United States)

    Rand, Kendra; White, Gary

    2008-10-01

    Is there a way to engage typical physics undergraduates in a conversation about under-represented groups in physics that doesn't result in rolled-eyes or fingers-in-the-ears? The Society of Physics Students (SPS) has begun an experiment using a jeopardy-like game at physics meetings in an attempt to generate conversations about diversity. The physics jeopardy game is part of a "Future Faces of Physics" kit that includes a variety of materials that are of interest to those wanting to address under-represented audiences in physics, such as video clips exhibiting common physics words in sign language, tactile representations of the lunar surface for blind students, guidelines regarding lab procedures for the wheel-chair bound, and the book, Einstein on Race and Racism with a challenge letter directed at SPS chapters from the authors. While attempts to assess the impact of the game are modest, we report anecdotally some of the qualitative features seen in the discussions when the game is played. We also strive to indulge in a few physics jeopardy game moments to give a sense of how the game works. If you are hosting a meeting, large or small, and would like to receive this kit for use at your meeting, notify Kendra Rand, SPS Program Coordinator at krand@aip.org.

  1. Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

    Science.gov (United States)

    Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

    2005-01-01

    A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

  2. A Study of Two Generations of Culturally Diverse Community College Students Views on Leader Attributes in Self and Others

    Science.gov (United States)

    Hodkowski, Paula Jeanine

    2011-01-01

    One community college mission is preparing students for the expectations and opportunities of the workplace including roles as collaborators and leaders. Increasingly, representatives from "cultures" of generation, gender, and diverse ethnicities are gaining an education in community colleges. Research supports that cultural aspects and…

  3. Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

    Science.gov (United States)

    Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

    2005-01-01

    A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

  4. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

    Science.gov (United States)

    Dziewit, Lukasz; Pyzik, Adam; Szuplewska, Magdalena; Matlakowska, Renata; Mielnicki, Sebastian; Wibberg, Daniel; Schlüter, Andreas; Pühler, Alfred; Bartosik, Dariusz

    2015-01-01

    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 20 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. PMID:26074880

  5. 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.

  6. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals.

    Science.gov (United States)

    Dziewit, Lukasz; Pyzik, Adam; Szuplewska, Magdalena; Matlakowska, Renata; Mielnicki, Sebastian; Wibberg, Daniel; Schlüter, Andreas; Pühler, Alfred; Bartosik, Dariusz

    2015-01-01

    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 20 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.

  7. Utilization of fly ash to improve the quality of the acid mine drainage generated by oxidation of a sulphide-rich mining waste: Column experiments

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Lopez, R.; Nieto, J.M.; de Almodovar, G.R. [University of Huelva, Huelva (Spain). Dept. of Geology

    2007-04-15

    The production of Acid Mine Drainage (AMD) as a result of the oxidative dissolution of sulphides is one of the main pollution problems affecting natural watercourses in mining environments with sulphide-rich residues. In this work, the generation of AMD was prevented by means of the addition of fly ash to sulphide-rich residues in non-saturated column experiments. A column experiment filled with a pyrite-rich sludge with artificial irrigation leached acid drainages (pH approx. 2) containing high concentrations of sulphate, iron and other metals. However, non-saturated column experiments filled with pyritic-rich sludge and fly ash drained leachates characterized by alkaline pH (pH up to 10), low sulphate concentration, and lack of iron and other metals in solution. The pyrite oxidative dissolution at high pH, as a consequence of the leaching of fly ash, favours the metal precipitation inside the column (mainly iron), the coating of pyrite grains, and the attenuation of the oxidation process, resulting in a great improvement in the quality of the leachates.

  8. Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors

    Science.gov (United States)

    Dashper, Stuart G.; Mitchell, Helen L.; Seers, Christine A.; Gladman, Simon L.; Seemann, Torsten; Bulach, Dieter M.; Chandry, P. Scott; Cross, Keith J.; Cleal, Steven M.; Reynolds, Eric C.

    2017-01-01

    Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis. The virulence of P. gingivalis is reported to be strain related and there are currently a number of strain typing schemes based on variation in capsular polysaccharide, the major and minor fimbriae and adhesin domains of Lys-gingipain (Kgp), amongst other surface proteins. P. gingivalis can exchange chromosomal DNA between strains by natural competence and conjugation. The aim of this study was to determine the genetic variability of P. gingivalis strains sourced from international locations over a 25-year period and to determine if variability in surface virulence factors has a phylogenetic basis. Whole genome sequencing was performed on 13 strains and comparison made to 10 previously sequenced strains. A single nucleotide polymorphism-based phylogenetic analysis demonstrated a shallow tri-lobed phylogeny. There was a high level of reticulation in the phylogenetic network, demonstrating extensive horizontal gene transfer between the strains. Two highly conserved variants of the catalytic domain of the major virulence factor the Kgp proteinase (KgpcatI and KgpcatII) were found. There were three variants of the fourth Kgp C-terminal cleaved adhesin domain. Specific variants of the cell surface proteins FimA, FimCDE, MfaI, RagAB, Tpr, and PrtT were also identified. The occurrence of all these variants in the P. gingivalis strains formed a mosaic that was not related to the SNP-based phylogeny. In conclusion P. gingivalis uses domain rearrangements and genetic exchange to generate diversity in specific surface virulence factors. PMID:28184216

  9. Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development.

    Science.gov (United States)

    Dannemiller, K C; Mendell, M J; Macher, J M; Kumagai, K; Bradman, A; Holland, N; Harley, K; Eskenazi, B; Peccia, J

    2014-06-01

    Dampness and visible mold in homes are associated with asthma development, but causal mechanisms remain unclear. The goal of this research was to explore associations among measured dampness, fungal exposure, and childhood asthma development without the bias of culture-based microbial analysis. In the low-income, Latino CHAMACOS birth cohort, house dust was collected at age 12 months, and asthma status was determined at age 7 years.The current analysis included 13 asthma cases and 28 controls. Next-generation DNA sequencing methods quantified fungal taxa and diversity. Lower fungal diversity (number of fungal operational taxonomic units) was significantly associated with increased risk of asthma development: unadjusted odds ratio(OR) 4.80 (95% confidence interval (CI) 1.04–22.1). Control for potential confounders strengthened this relationship. Decreased diversity within the genus Cryptococcus was significantly associated with increased asthma risk (OR 21.0, 95% CI 2.16–204). No fungal taxon (species, genus, class) was significantly positively associated with asthma development, and one was significantly negatively associated. Elevated moisture was associated with increased fungal diversity, and moisture/mold indicators were associated with four fungal taxa. Next-generation DNA sequencing provided comprehensive estimates of fungal identity and diversity, demonstrating significant associations between low fungal diversity and childhood asthma development in this community. Early life exposure to low fungal diversity in house dust was associated with increased risk for later asthma developmen tin this low-income, immigrant community. No individual fungal taxon (species, genus, or class) was associated with asthma development, although exposure to low diversity within the genus Cryptococcus was associated with asthma development. Future asthma development studies should incorporate fungal diversity measurements, in addition to measuring individual fungal taxa

  10. Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells

    Directory of Open Access Journals (Sweden)

    Moser Ann B

    2013-02-01

    Full Text Available Abstract Background Humans and rodents with impaired phytanic acid (PA metabolism can accumulate toxic stores of PA that have deleterious effects on multiple organ systems. Ruminants and certain fish obtain PA from the microbial degradation of dietary chlorophyll and/or through chlorophyll-derived precursors. In contrast, humans cannot derive PA from chlorophyll and instead normally obtain it only from meat, dairy, and fish products. Results Captive apes and Old world monkeys had significantly higher red blood cell (RBC PA levels relative to humans when all subjects were fed PA-deficient diets. Given the adverse health effects resulting from PA over accumulation, we investigated the molecular evolution of thirteen PA metabolism genes in apes, Old world monkeys, and New world monkeys. All non-human primate (NHP orthologs are predicted to encode full-length proteins with the marmoset Phyh gene containing a rare, but functional, GA splice donor dinucleotide. Acox2, Scp2, and Pecr sequences had amino acid positions with accelerated substitution rates while Amacr had significant variation in evolutionary rates in apes relative to other primates. Conclusions Unlike humans, diverse captive NHPs with PA-deficient diets rich in plant products have substantial RBC PA levels. The favored hypothesis is that NHPs can derive significant amounts of PA from the degradation of ingested chlorophyll through gut fermentation. If correct, this raises the possibility that RBC PA levels could serve as a biomarker for evaluating the digestive health of captive NHPs. Furthermore, the evolutionary rates of the several genes relevant to PA metabolism provide candidate genetic adaptations to NHP diets.

  11. Analysis of fish diversion efficiency and survivorship in the fish return system at San Onofre Nuclear Generating Station

    OpenAIRE

    Love, Milton S.; Sandhu, Meenu; Stein, Jeffrey; Herbinson, Kevin T.; Moore, Robert H; Mullin, Michael; Stephens, John S.

    1989-01-01

    This study examined the efficiency of fish diversion and survivorship of diverted fishes in the San Onofre Nuclear Generating Station Fish Return System in 1984 and 1985. Generally, fishes were diverted back to the ocean with high frequency, particularly in 1984. Most species were diverted at rates of 80% or more. Over 90% of the most abundant species, Engraulis mordax, were diverted. The system worked particularly well for strong-swimming forms such as Paralobrax clothratus, Atherinopsis cal...

  12. Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

    Directory of Open Access Journals (Sweden)

    Min Ni

    2013-09-01

    Full Text Available Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution. We report here that sexual reproduction generates phenotypic and genotypic diversity in the human pathogenic yeast Cryptococcus neoformans, which is globally distributed and commonly infects individuals with compromised immunity, such as HIV/AIDS patients, causing life-threatening meningoencephalitis. C. neoformans has a defined a-α opposite sexual cycle; however, >99% of isolates are of the α mating type. Interestingly, α cells can undergo α-α unisexual reproduction, even involving genotypically identical cells. A central question is: Why would cells mate with themselves given that sex is costly and typically serves to admix preexisting genetic diversity from genetically divergent parents? In this study, we demonstrate that α-α unisexual reproduction frequently generates phenotypic diversity, and the majority of these variant progeny are aneuploid. Aneuploidy is responsible for the observed phenotypic changes, as chromosome loss restoring euploidy results in a wild-type phenotype. Other genetic changes, including diploidization, chromosome length polymorphisms, SNPs, and indels, were also generated. Phenotypic/genotypic changes were not observed following asexual mitotic reproduction. Aneuploidy was also detected in progeny from a-α opposite-sex congenic mating; thus, both homothallic and heterothallic sexual reproduction can generate phenotypic diversity de novo. Our study suggests that the ability to undergo unisexual reproduction may be an evolutionary strategy for eukaryotic microbial pathogens, enabling de novo genotypic and phenotypic plasticity and facilitating rapid adaptation to novel environments.

  13. Development of opto-mechanical tools and procedures for the new generation of RICH-detectors at CERN

    CERN Document Server

    Laub, M; Ullaland, O

    2001-01-01

    This thesis is focused on development of opto-mechanical tools and procedures, which would contribute to the achievement of the best possible performance of new Ring Imaging Cherenkov (RICH) detectors. On the base of requirements, given by the physics objective of the LHCb detector, and an analysis of the detector opto-mechanical system, specifications of individual opto-mechanical components were determined. Spherical mirrors, planar mirrors and mirror adjustable mounts were the components of interest. Next, their parameters to be characterised were defined. Possible measurement methods were studied and relevant set ups based on suitable methods were developed. Meanwhile, available modern metrology technologies, like laser operated instruments or digital image processing, were applied with an attempt to innovate them and to increase their achievable performance limits. When applicable, the set ups were automated in order to make the measurements fast and reliable. An optical laboratory, devoted to the charac...

  14. European Socio-cultural Change and Generational Diversity in the Post-Soviet Workforce.

    Directory of Open Access Journals (Sweden)

    Madara APSALONE

    2016-12-01

    Full Text Available In times of increased retirement age and senior employees staying in workforce longer, successfully managing generational differences in the workforce forms an increasingly important challenge for modern day management. In many ways, generations may vary in attitudes and approaches, reflecting deeper differences in their core values. This might be particularly true for the Post-Soviet countries, where earlier generations were educated and started their careers within a completely different socio-economic system. In this study we explore differences in approaches towards values and attitudes amongst four generations of retail sector employees – starting from those, who were still to great extent exposed to pre-Soviet values, continuing with employees, who started their careers during the Soviet times, and ending with those, who were educated and entered the workforce after the collapse of the Soviet Union. 208 Latvian service employees were surveyed to assess their personal values and likelihood of dishonest and unethical behavior from four generations currently active in the workforce - Post-War generation, Early Gen X, Transition generation and Millennials. We confirmed that despite dual morality and ambiguous ethics in the Soviet Union, older generations reported higher likelihood of honest behavior than younger generations. And Post-War and Early Generation X also rated honesty and responsibility higher as their personal values. We also found significant differences between Early Generation X and the Transition generation in a post-Soviet context.

  15. Generational Diversity in Associate Degree Nursing Students: Teaching Styles and Preferences in Pennsylvania

    Science.gov (United States)

    Kitko, Jennifer V.

    2011-01-01

    Nursing educators face the challenge of meeting the needs of a multi-generational classroom. The reality of having members from the Veteran and Baby Boomer generations in a classroom with Generation X and Y students provides an immediate need for faculty to examine students' teaching method preferences as well as their own use of teaching methods.…

  16. Can parasites be indicators of free-living diversity? Relationships between the species richness and abundance of larval trematodes with that of local fishes and benthos

    OpenAIRE

    Hechinger, Ryan F.; Lafferty, K D; Huspeni, T C; A. J. Brooks; Kuris, A M

    2007-01-01

    Measuring biodiversity is difficult. This has spawned efforts to seek taxa whose species richness correlates with the species richness of other taxa. Such indicator taxa could then reduce the time and cost of assessing the biodiversity of the more extensive community. However, the search for species richness correlations has yielded mixed results. This may primarily be due to the lack of functional relationships between the taxa studied. Trematode parasites are highly promising bioindica...

  17. The diversity-generating benefits of a prokaryotic adaptive immune system.

    Science.gov (United States)

    van Houte, Stineke; Ekroth, Alice K E; Broniewski, Jenny M; Chabas, Hélène; Ashby, Ben; Bondy-Denomy, Joseph; Gandon, Sylvain; Boots, Mike; Paterson, Steve; Buckling, Angus; Westra, Edze R

    2016-04-21

    Prokaryotic CRISPR-Cas adaptive immune systems insert spacers derived from viruses and other parasitic DNA elements into CRISPR loci to provide sequence-specific immunity. This frequently results in high within-population spacer diversity, but it is unclear if and why this is important. Here we show that, as a result of this spacer diversity, viruses can no longer evolve to overcome CRISPR-Cas by point mutation, which results in rapid virus extinction. This effect arises from synergy between spacer diversity and the high specificity of infection, which greatly increases overall population resistance. We propose that the resulting short-lived nature of CRISPR-dependent bacteria-virus coevolution has provided strong selection for the evolution of sophisticated virus-encoded anti-CRISPR mechanisms.

  18. New heterocyclic precursors for thermal generation of reactive, electron-rich 1,2-diaza-1,3-butadienes.

    Science.gov (United States)

    Boeckman, R K; Ge, P; Reed, J E

    2001-11-15

    [reaction--see text] [corrected] The preparation and thermolysis of new stable heterocyclic precursors of 1,2-diaza-1,3-butadienes is described. The resulting reactive diazadienes are trapped in situ with N-phenylmaleimide [corrected]. The effect of precursor structure on the temperature at which the diazadienes are generated is discussed.

  19. Diversity of fuel sources for electricity generation in an evolving U.S. power sector

    Science.gov (United States)

    DiLuccia, Janelle G.

    Policymakers increasingly have shown interest in options to boost the relative share of renewable or clean electricity generating sources in order to reduce negative environmental externalities from fossil fuels, guard against possible resource constraints, and capture economic advantages from developing new technologies and industries. Electric utilities and non-utility generators make decisions regarding their generation mix based on a number of different factors that may or may not align with societal goals. This paper examines the makeup of the electric power sector to determine how the type of generator and the presence (or lack) of competition in electricity markets at the state level may relate to the types of fuel sources used for generation. Using state-level electricity generation data from the U.S. Energy Information Administration from 1990 through 2010, this paper employs state and time fixed-effects regression modeling to attempt to isolate the impacts of state-level restructuring policies and the emergence of non-utility generators on states' generation from coal, from fossil fuel and from renewable sources. While the analysis has significant limitations, I do find that state-level electricity restructuring has a small but significant association with lowering electricity generation from coal specifically and fossil fuels more generally. Further research into the relationship between competition and fuel sources would aid policymakers considering legislative options to influence the generation mix.

  20. Biological effects of carbon nanotubes generated in forest wildfire ecosystems rich in resinous trees on native plants

    Directory of Open Access Journals (Sweden)

    Javier Lara-Romero

    2017-08-01

    Full Text Available Carbon nanotubes (CNTs have a broad range of applications and are generally considered human-engineered nanomaterials. However, carbon nanostructures have been found in ice cores and oil wells, suggesting that nature may provide appropriate conditions for CNT synthesis. During forest wildfires, materials such as turpentine and conifer tissues containing iron under high temperatures may create chemical conditions favorable for CNT generation, similar to those in synthetic methods. Here, we show evidence of naturally occurring multiwalled carbon nanotubes (MWCNTs produced from Pinus oocarpa and Pinus pseudostrobus, following a forest wildfire. The MWCNTs showed an average of 10 walls, with internal diameters of ∼2.5 nm and outer diameters of ∼14.5 nm. To verify whether MWCNT generation during forest wildfires has a biological effect on some characteristic plant species of these ecosystems, germination and development of seedlings were conducted. Results show that the utilization of comparable synthetic MWCNTs increased seed germination rates and the development of Lupinus elegans and Eysenhardtia polystachya, two plants species found in the burned forest ecosystem. The finding provides evidence that supports the generation and possible ecological functions of MWCNTs in nature.

  1. Plate-based diversity subset screening generation 2: an improved paradigm for high-throughput screening of large compound files.

    Science.gov (United States)

    Bell, Andrew S; Bradley, Joseph; Everett, Jeremy R; Loesel, Jens; McLoughlin, David; Mills, James; Peakman, Marie-Claire; Sharp, Robert E; Williams, Christine; Zhu, Hongyao

    2016-11-01

    High-throughput screening (HTS) is an effective method for lead and probe discovery that is widely used in industry and academia to identify novel chemical matter and to initiate the drug discovery process. However, HTS can be time consuming and costly and the use of subsets as an efficient alternative to screening entire compound collections has been investigated. Subsets may be selected on the basis of chemical diversity, molecular properties, biological activity diversity or biological target focus. Previously, we described a novel form of subset screening: plate-based diversity subset (PBDS) screening, in which the screening subset is constructed by plate selection (rather than individual compound cherry-picking), using algorithms that select for compound quality and chemical diversity on a plate basis. In this paper, we describe a second-generation approach to the construction of an updated subset: PBDS2, using both plate and individual compound selection, that has an improved coverage of the chemical space of the screening file, whilst only selecting the same number of plates for screening. We describe the validation of PBDS2 and its successful use in hit and lead discovery. PBDS2 screening became the default mode of singleton (one compound per well) HTS for lead discovery in Pfizer.

  2. Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

    DEFF Research Database (Denmark)

    Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse

    2016-01-01

    Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions, but is also a proven contaminant of human samples and surgical wounds. Its...... significance as a pathogen is consequently a matter of debate.In the present study we investigated the presence of P. acnes DNA in 250 next generation sequencing datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial...... reads were detected in most samples analysed, though the proportions in most shotgun-sequenced samples were low.Our results show that P. acnes can be detected in practically all sample types when employing molecular methods such as next generation sequencing. The possibility of contamination from...

  3. Convergent evolution as a generator of phenotypic diversity in threespine stickleback.

    Science.gov (United States)

    McGee, Matthew D; Wainwright, Peter C

    2013-04-01

    Convergent evolution, in which populations produce similar phenotypes in response to similar selection pressure, is strong evidence for the role of natural selection in shaping biological diversity. In some cases, closely related populations can produce functionally similar but phenotypically divergence forms in response to selection. Functional convergence with morphological divergence has been observed in laboratory selection experiments and computer simulations, but while potentially common, is rarely recognized in nature. Here, we present data from the North Pacific threespine stickleback radiation showing that ecologically and functionally similar, but morphologically divergent phenotypes rapidly evolved when an ancestral population colonized freshwater benthic habitats in parallel. In addition, we show that in this system, functional convergence substantially increases morphospace occupation relative to ancestral phenotypes, which suggests that convergent evolution may, paradoxically, be an important and previously underappreciated source of morphological diversity. © 2013 The Author(s). Evolution© 2013 The Society for the Study of Evolution.

  4. Generational diversity in associate degree nursing students: Teaching styles and preferences in Pennsylvania

    Science.gov (United States)

    Kitko, Jennifer V.

    2011-12-01

    Nursing educators face the challenge of meeting the needs of a multi-generational classroom. The reality of having members from the Veteran and Baby Boomer generations in a classroom with Generation X and Y students provides an immediate need for faculty to examine students' teaching method preferences as well as their own use of teaching methods. Most importantly, faculty must facilitate an effective multi-generational learning environment. Research has shown that the generation to which a person belongs is likely to affect the ways in which he/she learns (Hammill, 2005). Characterized by its own attitudes, behaviors, beliefs, and motivational needs, each generation also has distinct educational expectations. It is imperative, therefore, that nurse educators be aware of these differences and develop skills through which to communicate with the different generations, thereby reducing teaching/learning problems in the classroom. This is a quantitative, descriptive study that compared the teaching methods preferred by different generations of associate degree nursing students with the teaching methods that the instructors actually use. The research study included 289 participants; 244 nursing student participants and 45 nursing faculty participants from four nursing departments in colleges in Pennsylvania. Overall, the results of the study found many statistically significant findings. The results of the ANOVA test revealed eight statistically significant findings among Generation Y, Generation X and Baby boomers. The preferred teaching methods included: lecture, self-directed learning, web-based course with no class meetings, important for faculty to know my name, classroom structure, know why I am learning what I am learning, learning for the sake of learning and grade is all that matters. Lecture was found to be the most frequently used teaching method by faculty as well as the most preferred teaching methods by students. Overall, the support for a variety of

  5. Geochemical and stable isotopic constraints on the generation and passive treatment of acidic, Fe-SO4 rich waters.

    Science.gov (United States)

    Matthies, Romy; Aplin, Andrew C; Boyce, Adrian J; Jarvis, Adam P

    2012-03-15

    Reducing and Alkalinity Producing Systems (RAPS) remediate net-acidic metalliferous mine drainage by creating anoxic conditions in which bacterial sulfate reduction (BSR) raises alkalinity and drives the precipitation of iron and other chalcophilic elements as sulfides. We report chemical and stable isotopic data from a study monitoring the biogeochemical processes involved in the generation of mine waters and their remediation by two RAPS. Sulfur isotopes show that sulfate in all mine waters has a common source (pyrite oxidation), whilst oxygen isotopes show that oxidation of pyritic sulfur is mediated by Fe(III)(aq). The isotopic composition of dissolved sulfide, combined with the sulfur and oxygen isotopic composition of sulfate in RAPS effluents, proves BSR and details its dual isotope systematics. The occurrence and isotopic composition of solid phase iron sulfides indicate the removal of reduced sulfur within the RAPS, with significant amounts of elemental sulfur indicating reoxidation steps. However, only 0 to 9% of solid phase iron occurs as Fe sulfides, with approximately 70% of the removed iron occurs as Fe(III) (hydr)oxides. Some of the (hydr)oxide is supplied to the wetland as solids and is simply filtered by the wetland substrate, playing no role in alkalinity generation or proton removal. However, the majority of iron is supplied as dissolved Fe(II), indicating that acid generating oxidation and hydrolysis reactions dominate iron removal. The overall contribution of BSR to the sulfur geochemistry in the RAPS is limited and sulfate retention is dominated by sulfate precipitation, comparable to aerobic treatment systems, and show that the proton acidity resulting from iron oxidation and hydrolysis must be subsequently neutralised by calcite dissolution and/or BSR deeper in the RAPS sediments. BSR is not as important as previously thought for metal removal in RAPS. The results have practical consequences for the design, treatment performance and long

  6. Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

    Science.gov (United States)

    Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

    2013-04-15

    In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

  7. Geochemical and stable isotopic constraints on the generation and passive treatment of acidic, Fe-SO{sub 4} rich waters

    Energy Technology Data Exchange (ETDEWEB)

    Matthies, Romy, E-mail: rmatthies@uwaterloo.ca [School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU (United Kingdom); Aplin, Andrew C., E-mail: andrew.aplin@ncl.ac.uk [School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU (United Kingdom); Boyce, Adrian J., E-mail: a.boyce@suerc.gla.ac.uk [Scottish Universities Environment Research Centre, East Kilbride, G75 0QF (United Kingdom); Jarvis, Adam P., E-mail: a.p.jarvis@ncl.ac.uk [School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU (United Kingdom)

    2012-03-15

    Reducing and Alkalinity Producing Systems (RAPS) remediate net-acidic metalliferous mine drainage by creating anoxic conditions in which bacterial sulfate reduction (BSR) raises alkalinity and drives the precipitation of iron and other chalcophilic elements as sulfides. We report chemical and stable isotopic data from a study monitoring the biogeochemical processes involved in the generation of mine waters and their remediation by two RAPS. Sulfur isotopes show that sulfate in all mine waters has a common source (pyrite oxidation), whilst oxygen isotopes show that oxidation of pyritic sulfur is mediated by Fe(III){sub aq}. The isotopic composition of dissolved sulfide, combined with the sulfur and oxygen isotopic composition of sulfate in RAPS effluents, proves BSR and details its dual isotope systematics. The occurrence and isotopic composition of solid phase iron sulfides indicate the removal of reduced sulfur within the RAPS, with significant amounts of elemental sulfur indicating reoxidation steps. However, only 0 to 9% of solid phase iron occurs as Fe sulfides, with approximately 70% of the removed iron occurs as Fe(III) (hydr)oxides. Some of the (hydr)oxide is supplied to the wetland as solids and is simply filtered by the wetland substrate, playing no role in alkalinity generation or proton removal. However, the majority of iron is supplied as dissolved Fe(II), indicating that acid generating oxidation and hydrolysis reactions dominate iron removal. The overall contribution of BSR to the sulfur geochemistry in the RAPS is limited and sulfate retention is dominated by sulfate precipitation, comparable to aerobic treatment systems, and show that the proton acidity resulting from iron oxidation and hydrolysis must be subsequently neutralised by calcite dissolution and/or BSR deeper in the RAPS sediments. BSR is not as important as previously thought for metal removal in RAPS. The results have practical consequences for the design, treatment performance and long

  8. The association of Alu repeats with the generation of potential AU-rich elements (ARE at 3' untranslated regions.

    Directory of Open Access Journals (Sweden)

    Bhak Jonghwa

    2004-12-01

    Full Text Available Abstract Background A significant portion (about 8% in the human genome of mammalian mRNA sequences contains AU (Adenine and Uracil rich elements or AREs at their 3' untranslated regions (UTR. These mRNA sequences are usually stable. However, an increasing number of observations have been made of unstable species, possibly depending on certain elements such as Alu repeats. ARE motifs are repeats of the tetramer AUUU and a monomer A at the end of the repeats ((AUUUnA. The importance of AREs in biology is that they make certain mRNA unstable. Proto-oncogene, such as c-fos, c-myc, and c-jun in humans, are associated with AREs. Although it has been known that the increased number of ARE motifs caused the decrease of the half-life of mRNA containing ARE repeats, the exact mechanism is as of yet unknown. We analyzed the occurrences of AREs and Alu and propose a possible mechanism for how human mRNA could acquire and keep AREs at its 3' UTR originating from Alu repeats. Results Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A regions at its end, which lead to poly-thymine (poly-T regions at the end of its complementary Alu. It has been found that AREs are present at the poly-T regions. From the 3' UTR of the NCBI's reference mRNA sequence database, we found nearly 40% (38.5% of ARE (Class I were associated with Alu sequences (Table 1 within one mismatch allowance in ARE sequences. Other ARE classes had statistically significant associations as well. This is far from a random occurrence given their limited quantity. At each ARE class, random distribution was simulated 1,000 times, and it was shown that there is a special relationship between ARE patterns and the Alu repeats. Table 1 Defined ARE classes. (Symbol marks are used in this study instead of full sequences. Symbol ARE sequence Class I (AUUU5A AUUUAUUUAUUUAUUUAUUUA Class II (AUUU4A AUUUAUUUAUUUAUUUA Class III U(AUUU3AU

  9. Single-neuron diversity generated by Protocadherin-β cluster in mouse central and peripheral nervous systems

    Directory of Open Access Journals (Sweden)

    Keizo eHirano

    2012-08-01

    Full Text Available The generation of complex neural circuits depends on the correct wiring of neurons with diverse individual characteristics. To understand the complexity of the nervous system, the molecular mechanisms for specifying the identity and diversity of individual neurons must be elucidated. The clustered protocadherins (Pcdh in mammals consist of approximately 50 Pcdh genes (Pcdh-α, Pcdh-β, and Pcdh-γ that encode cadherin-family cell surface adhesion proteins. Individual neurons express a random combination of Pcdh-α and Pcdh-γ, whereas the expression patterns for the Pcdh-β genes, 22 one-exon genes in mouse, are not fully understood. Here we show that the Pcdh-β genes are expressed in a 3’-polyadenylated form in mouse brain. In situ hybridization using a pan-Pcdh-β probe against a conserved Pcdh-β sequence showed widespread labeling in the brain, with prominent signals in the olfactory bulb, hippocampus, and cerebellum. In situ hybridization with specific probes for individual Pcdh-β genes showed their expression to be scattered in Purkinje cells from P10 to P150. The scattered expression patterns were confirmed by performing a newly developed single-cell 3’-RACE analysis of Purkinje cells, which clearly demonstrated that the Pcdh-β genes are expressed monoallelically and combinatorially in individual Purkinje cells. Scattered expression patterns of individual Pcdh-β genes were also observed in pyramidal neurons in the hippocampus and cerebral cortex, neurons in the trigeminal and dorsal root ganglion, GABAergic interneurons, and cholinergic neurons. Our results extend previous observations of diversity at the single-neuron level generated by Pcdh expression and suggest that the Pcdh-β cluster genes contribute to specifying the identity and diversity of individual neurons.

  10. Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

    Science.gov (United States)

    Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

    2015-09-25

    In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

  11. Understanding and leading the quad matrix: four generations in the workplace: the Traditional Generation, Boomers, Gen-X, Nexters.

    Science.gov (United States)

    Gerke, M L

    2001-09-01

    Generational diversity is not new, but 4 generations working side by side has not occurred before. This climate of 4 generational workers offers challenges and opportunities for leaders. Leaders must show the opportunities of a diverse workforce and provide the encouragement and enthusiasm of working in a 4-generation environment. This article will define the 4 generations, the perspectives, values and motivations of each and the opportunity to tap into this rich tapestry.

  12. Diversity and Inclusion in Information Technology from an Age Perspective: Motivating and Managing Information Technology Professionals across Multiple Generations in the Workforce

    Science.gov (United States)

    Kenan-Smalls, Yottie Marie

    2011-01-01

    The purpose of this quantitative study was to investigate diversity and inclusion from an age perspective among information technology (IT) professionals that were categorized as 4 different generations in the workforce today: Traditionalists, Baby Boomers, Generation X, and Generation Y. At the same time, this study sought to examine motivational…

  13. Diversity and Inclusion in Information Technology from an Age Perspective: Motivating and Managing Information Technology Professionals across Multiple Generations in the Workforce

    Science.gov (United States)

    Kenan-Smalls, Yottie Marie

    2011-01-01

    The purpose of this quantitative study was to investigate diversity and inclusion from an age perspective among information technology (IT) professionals that were categorized as 4 different generations in the workforce today: Traditionalists, Baby Boomers, Generation X, and Generation Y. At the same time, this study sought to examine motivational…

  14. The role of climatic and geological events in generating diversity in Ethiopian grass frogs (genus Ptychadena).

    Science.gov (United States)

    Smith, Megan L; Noonan, Brice P; Colston, Timothy J

    2017-08-01

    Ethiopia is a world biodiversity hotspot and harbours levels of biotic endemism unmatched in the Horn of Africa, largely due to topographic-and thus habitat-complexity, which results from a very active geological and climatic history. Among Ethiopian vertebrate fauna, amphibians harbour the highest levels of endemism, making amphibians a compelling system for the exploration of the impacts of Ethiopia's complex abiotic history on biotic diversification. Grass frogs of the genus Ptychadena are notably diverse in Ethiopia, where they have undergone an evolutionary radiation. We used molecular data and expanded taxon sampling to test for cryptic diversity and to explore diversification patterns in both the highland radiation and two widespread lowland Ptychadena. Species delimitation results support the presence of nine highland species and four lowland species in our dataset, and divergence dating suggests that both geologic events and climatic fluctuations played a complex and confounded role in the diversification of Ptychadena in Ethiopia. We rectify the taxonomy of the endemic P. neumanni species complex, elevating one formally synonymized name and describing three novel taxa. Finally, we describe two novel lowland Ptychadena species that occur in Ethiopia and may be more broadly distributed.

  15. Neutron Generation from Laser-Accelerated Ion Beams: Use of Alternative Deuteron-Rich Targets for Improved Neutron Yield and Control of Neutron Spectra

    Science.gov (United States)

    Albright, B. J.; Yin, L.; Favalli, A.

    2016-10-01

    Laser-ion-beam generation in the break-out afterburner (BOA) acceleration regime has been modeled for several deuteron-rich solid-density targets using the VPIC particle-in-cell code. Monte Carlo modeling of the transport of these beams in a beryllium converter in a pitcher-catcher neutron source configuration shows significant increases in neutron yields may be achievable through judicious choices of laser target material. Additionally, species-separation dynamics in some target materials during the BOA ion acceleration phase can be exploited to control the shapes of the neutron spectra. Work performed under the auspices of the U.S. DOE by the LANS, LLC, Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. Funding provided by the Los Alamos National Laboratory Directed Research and Development Program.

  16. Platelet-rich fibrin (PRF): a second-generation platelet concentrate. Part III: leucocyte activation: a new feature for platelet concentrates?

    Science.gov (United States)

    Dohan, David M; Choukroun, Joseph; Diss, Antoine; Dohan, Steve L; Dohan, Anthony J J; Mouhyi, Jaafar; Gogly, Bruno

    2006-03-01

    Platelet-rich fibrin (PRF) belongs to a new generation of platelet concentrates, with simplified processing and without biochemical blood handling. In this third article, we investigate the immune features of this biomaterial. During PRF processing, leucocytes could also secrete cytokines in reaction to the hemostatic and inflammatory phenomena artificially induced in the centrifuged tube. We therefore undertook to quantify 5 significant cell mediators within platelet poor plasma supernatant and PRF clot exudate serum: 3 proinflammatory cytokines (IL-1beta, IL-6, and TNF-alpha), an antiinflammatory cytokine (IL-4), and a key growth promoter of angiogenesis (VEGF). Our data are correlated with that obtained in plasma (nonactivated blood) and in sera (activated blood). These initial analyses revealed that PRF could be an immune regulation node with inflammation retrocontrol abilities. This concept could explain the reduction of postoperative infections when PRF is used as surgical additive.

  17. The effect of single nucleotide polymorphisms in G-rich regions of high-risk human papillomaviruses on structural diversity of DNA.

    Science.gov (United States)

    Marušič, Maja; Hošnjak, Lea; Krafčikova, Petra; Poljak, Mario; Viglasky, Viktor; Plavec, Janez

    2017-05-01

    Infection with high-risk human papillomaviruses (HPVs) can lead to development of cancer of the head and neck and anogenital regions. G-rich sequences found in genomes of high-risk HPVs can fold into non-canonical secondary structures that could serve as 3D motifs distinct from double-stranded DNA and present recognition sites for ligands and opportunity for gene expression modulation. Combination of UV, CD and NMR spectroscopy and PAGE electrophoresis were used as they offer complementary insights into structural changes of G-rich oligonucleotides. G-rich region of HPV16 is shown to preferentially form hairpin structures, while regions of HPV18, HPV52 and HPV58 fold into four-stranded DNA structures called G-quadruplexes. Single nucleotide polymorphisms found in G-rich sequences have been found to promote formation of hairpin structures of HPV16 and have affected number of species formed in G-rich region of HPV52, whereas they have exhibited minimal effect on the formation of HPV18 and HPV58 G-quadruplex structures. These structural changes were reflected in differences in apparent thermal stabilities. Potential of G-rich sequences as drug targets was evaluated based on the results of the current study. HPV16 and HPV18 are considered less appropriate targets due to several single nucleotide polymorphisms and low stability, respectively. On the other hand, HPV52 and HPV58 could be used for small-molecule mediated stabilization. G-rich sequences occurring in high-risk HPVs can fold into hairpin and G-quadruplex structures that could be potentially utilized as drug targets. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

    DEFF Research Database (Denmark)

    Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse

    2016-01-01

    Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions, but is also a proven contaminant of human samples and surgical wounds. Its...... significance as a pathogen is consequently a matter of debate.In the present study we investigated the presence of P. acnes DNA in 250 next generation sequencing datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial...... enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun-sequenced.We detected high proportions of P. acnes in enriched samples, particularly skin derived and other tissue samples, with levels being higher in enriched compared to shotgun-sequenced samples. P. acnes...

  19. Testing the effect of the rock record on diversity: a multidisciplinary approach to elucidating the generic richness of sauropodomorph dinosaurs through time.

    Science.gov (United States)

    Mannion, Philip D; Upchurch, Paul; Carrano, Matthew T; Barrett, Paul M

    2011-02-01

    The accurate reconstruction of palaeobiodiversity patterns is central to a detailed understanding of the macroevolutionary history of a group of organisms. However, there is increasing evidence that diversity patterns observed directly from the fossil record are strongly influenced by fluctuations in the quality of our sampling of the rock record; thus, any patterns we see may reflect sampling biases, rather than genuine biological signals. Previous dinosaur diversity studies have suggested that fluctuations in sauropodomorph palaeobiodiversity reflect genuine biological signals, in comparison to theropods and ornithischians whose diversity seems to be largely controlled by the rock record. Most previous diversity analyses that have attempted to take into account the effects of sampling biases have used only a single method or proxy: here we use a number of techniques in order to elucidate diversity. A global database of all known sauropodomorph body fossil occurrences (2024) was constructed. A taxic diversity curve for all valid sauropodomorph genera was extracted from this database and compared statistically with several sampling proxies (rock outcrop area and dinosaur-bearing formations and collections), each of which captures a different aspect of fossil record sampling. Phylogenetic diversity estimates, residuals and sample-based rarefaction (including the first attempt to capture 'cryptic' diversity in dinosaurs) were implemented to investigate further the effects of sampling. After 'removal' of biases, sauropodomorph diversity appears to be genuinely high in the Norian, Pliensbachian-Toarcian, Bathonian-Callovian and Kimmeridgian-Tithonian (with a small peak in the Aptian), whereas low diversity levels are recorded for the Oxfordian and Berriasian-Barremian, with the Jurassic/Cretaceous boundary seemingly representing a real diversity trough. Observed diversity in the remaining Triassic-Jurassic stages appears to be largely driven by sampling effort. Late

  20. Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands

    Science.gov (United States)

    Jarvi, S.I.; Farias, M.E.; Lapointe, D.A.; Belcaid, M.; Atkinson, C.T.

    2013-01-01

    Next-generation 454 sequencing techniques were used to re-examine diversity of mitochondrial cytochrome b lineages of avian malaria (Plasmodium relictum) in Hawaii. We document a minimum of 23 variant lineages of the parasite based on single nucleotide transitional changes, in addition to the previously reported single lineage (GRW4). A new, publicly available portal (Integroomer) was developed for initial parsing of 454 datasets. Mean variant prevalence and frequency was higher in low elevation Hawaii Amakihi (Hemignathus virens) with Avipoxvirus-like lesions (P = 0·001), suggesting that the variants may be biologically distinct. By contrast, variant prevalence and frequency did not differ significantly among mid-elevation Apapane (Himatione sanguinea) with or without lesions (P = 0·691). The low frequency and the lack of detection of variants independent of GRW4 suggest that multiple independent introductions of P. relictum to Hawaii are unlikely. Multiple variants may have been introduced in heteroplasmy with GRW4 or exist within the tandem repeat structure of the mitochondrial genome. The discovery of multiple mitochondrial lineages of P. relictum in Hawaii provides a measure of genetic diversity within a geographically isolated population of this parasite and suggests the origins and evolution of parasite diversity may be more complicated than previously recognized.

  1. Second generation sequencing for elucidating the diversity of bacteria and plasmids in soil

    DEFF Research Database (Denmark)

    Holmsgaard, Peter Nikolai

    and amplicon pyrosequencing and briefly the related bioinformatics. This is followed by six papers of which one is published and five are manuscripts. In the first paper, amplicon pyrosequencing of the 16S rRNA gene was use to investigate the bias in cell extraction from soil imposed by Nycodenz density......, paper microcosms with material from a pre-adapted biopurification system (BPS) were spiked with the herbicide linuron and the effect on the bacterial and plasmid community was studied. The genus Variovorax previously shown to degrade linuron was found to be one of the main positive responders...... and plasmid diversity in different soil environments while papers I and VI use different molecular methods to study the bias imposed on bacterial community studies by different techniques....

  2. Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and mice

    Science.gov (United States)

    Serup, Palle; Gustavsen, Carsten; Klein, Tino; Potter, Leah A.; Lin, Robert; Mullapudi, Nandita; Wandzioch, Ewa; Hines, Angela; Davis, Ashley; Bruun, Christine; Engberg, Nina; Petersen, Dorthe R.; Peterslund, Janny M. L.; MacDonald, Raymond J.; Grapin-Botton, Anne; Magnuson, Mark A.; Zaret, Kenneth S.

    2012-01-01

    SUMMARY Extracellular signals in development, physiology, homeostasis and disease often act by regulating transcription. Herein we describe a general method and specific resources for determining where and when such signaling occurs in live animals and for systematically comparing the timing and extent of different signals in different cellular contexts. We used recombinase-mediated cassette exchange (RMCE) to test the effect of successively deleting conserved genomic regions of the ubiquitously active Rosa26 promoter and substituting the deleted regions for regulatory sequences that respond to diverse extracellular signals. We thereby created an allelic series of embryonic stem cells and mice, each containing a signal-responsive sentinel with different fluorescent reporters that respond with sensitivity and specificity to retinoic acids, bone morphogenic proteins, activin A, Wnts or Notch, and that can be adapted to any pathway that acts via DNA elements. PMID:22888097

  3. Habitat heterogeneity drives the host-diversity-begets-parasite-diversity relationship: evidence from experimental and field studies.

    Science.gov (United States)

    Johnson, Pieter T J; Wood, Chelsea L; Joseph, Maxwell B; Preston, Daniel L; Haas, Sarah E; Springer, Yuri P

    2016-07-01

    Despite a century of research into the factors that generate and maintain biodiversity, we know remarkably little about the drivers of parasite diversity. To identify the mechanisms governing parasite diversity, we combined surveys of 8100 amphibian hosts with an outdoor experiment that tested theory developed for free-living species. Our analyses revealed that parasite diversity increased consistently with host diversity due to habitat (i.e. host) heterogeneity, with secondary contributions from parasite colonisation and host abundance. Results of the experiment, in which host diversity was manipulated while parasite colonisation and host abundance were fixed, further reinforced this conclusion. Finally, the coefficient of host diversity on parasite diversity increased with spatial grain, which was driven by differences in their species-area curves: while host richness quickly saturated, parasite richness continued to increase with neighbourhood size. These results offer mechanistic insights into drivers of parasite diversity and provide a hierarchical framework for multi-scale disease research.

  4. Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water.

    Science.gov (United States)

    Aguilar, Maria; Richardson, Elisabeth; Tan, BoonFei; Walker, Giselle; Dunfield, Peter F; Bass, David; Nesbø, Camilla; Foght, Julia; Dacks, Joel B

    2016-11-01

    Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  5. GENETIC STRUCTURE AND ALLEL DIVERSITY OF THREE BALINESE GENERATIONS BASED ON FIVE AUTOSOMAL MICROSATELLITE DNA LOCI

    Directory of Open Access Journals (Sweden)

    Ayu Saka Laksmita

    2015-09-01

    Full Text Available This research was aimed to find out the genetic structures of three generations of Balinese population, in order to determine the best loci used for paternity testing among this population, and observed the mutation rate of these loci. The DNA samples were taken from the epithelium cell of 25 families which were collected from the children, father, mother, grandfather and grandmother of the children, from both mother and father sides (family with three generations. The DNA was extracted in Phenol-Chloroform method with modifications. DNA amplification was conducted in PCR method using pairs of primer 5, namely: FGA, D18S51, D2S1338, TPOX, and D16S539, and its products were electrophoresed and visualized in 10% of PAGE, stained in silver nitrate. The genetic structures of the three family generations showed 30 variants with different frequencies in each locus. The highest heterozygosity value was detected in FGA (8 alleles, then followed by D18S51 (7 alleles, TPOX (6 alleles, D16S539 (5 alleles, and the lowest was in D2S1338 (4 alleles. The highest value of heterozigosity and Power of Discrimination were found in FGA, followed by TPOX, D18S51, D2S1338, and the lowest was in D16S539. Therefore, it can be concluded that out of five loci tested, 4 of them can be recommended to be used for paternity testing of Balinese population, except D16S539

  6. Non-heme iron oxygenases generate natural structural diversity in carbapenem antibiotics.

    Science.gov (United States)

    Bodner, Micah J; Phelan, Ryan M; Freeman, Michael F; Li, Rongfeng; Townsend, Craig A

    2010-01-13

    Carbapenems are a clinically important antibiotic family. More than 50 naturally occurring carbapenam/ems are known and are distinguished primarily by their C-2/C-6 side chains where many are only differentiated by the oxidation states of these substituents. With a limited palette of variations the carbapenem family comprises a natural combinatorial library, and C-2/C-6 oxidation is associated with increased efficacy. We demonstrate that ThnG and ThnQ encoded by the thienamycin gene cluster in Streptomyces cattleya oxidize the C-2 and C-6 moieties of carbapenems, respectively. ThnQ stereospecifically hydroxylates PS-5 (5) giving N-acetyl thienamycin (2). ThnG catalyzes sequential desaturation and sulfoxidation of PS-5 (5), giving PS-7 (7) and its sulfoxide (9). The enzymes are relatively substrate selective but are proposed to give rise to the oxidative diversity of carbapenems produced by S. cattleya, and orthologues likely function similarly in allied streptomyces. Elucidating the roles of ThnG and ThnQ will focus further investigations of carbapenem antibiotic biosynthesis.

  7. Imprinting in plants as a mechanism to generate seed phenotypic diversity

    Directory of Open Access Journals (Sweden)

    A Mark eSettles

    2015-01-01

    Full Text Available Normal plant development requires epigenetic regulation to enforce changes in developmental fate. Genomic imprinting is a type of epigenetic regulation in which identical alleles of genes are expressed in a parent-of-origin dependent manner. Deep sequencing of transcriptomes has identified hundreds of imprinted genes with scarce evidence for the developmental importance of individual imprinted loci. Imprinting is regulated through global DNA demethylation in the central cell prior to fertilization and directed repression of individual loci with the Polycomb Repressive Complex 2 (PRC2. There is significant evidence for transposable elements and repeat sequences near genes acting as cis-elements to determine imprinting status of a gene, implying that imprinted gene expression patterns may evolve randomly and at high frequency. Detailed genetic analysis of a few imprinted loci suggests an imprinted pattern of gene expression is often dispensable for seed development. Few genes show conserved imprinted expression within or between plant species. These data are not fully explained by current models for the evolution of imprinting in plant seeds. We suggest that imprinting may have evolved to provide a mechanism for rapid neofunctionalization of genes during seed development to increase phenotypic diversity of seeds.

  8. Diverse landscapes have a higher abundance and species richness of spring wild bees by providing complementary floral resources over bees’ foraging periods

    Science.gov (United States)

    Landscape simplification and natural habitat loss can negatively affect wild bees. Alternatively, anthropogenic land-use change can potentially diversify landscapes to create complementary habitats that increase overall resource continuity and diversity. We examined the effects of landscape composit...

  9. Automatic generation control of multi-area power systems with diverse energy sources using Teaching Learning Based Optimization algorithm

    Directory of Open Access Journals (Sweden)

    Rabindra Kumar Sahu

    2016-03-01

    Full Text Available This paper presents the design and analysis of Proportional-Integral-Double Derivative (PIDD controller for Automatic Generation Control (AGC of multi-area power systems with diverse energy sources using Teaching Learning Based Optimization (TLBO algorithm. At first, a two-area reheat thermal power system with appropriate Generation Rate Constraint (GRC is considered. The design problem is formulated as an optimization problem and TLBO is employed to optimize the parameters of the PIDD controller. The superiority of the proposed TLBO based PIDD controller has been demonstrated by comparing the results with recently published optimization technique such as hybrid Firefly Algorithm and Pattern Search (hFA-PS, Firefly Algorithm (FA, Bacteria Foraging Optimization Algorithm (BFOA, Genetic Algorithm (GA and conventional Ziegler Nichols (ZN for the same interconnected power system. Also, the proposed approach has been extended to two-area power system with diverse sources of generation like thermal, hydro, wind and diesel units. The system model includes boiler dynamics, GRC and Governor Dead Band (GDB non-linearity. It is observed from simulation results that the performance of the proposed approach provides better dynamic responses by comparing the results with recently published in the literature. Further, the study is extended to a three unequal-area thermal power system with different controllers in each area and the results are compared with published FA optimized PID controller for the same system under study. Finally, sensitivity analysis is performed by varying the system parameters and operating load conditions in the range of ±25% from their nominal values to test the robustness.

  10. Simulating Flying Insects Using Dynamics and Data-Driven Noise Modeling to Generate Diverse Collective Behaviors.

    Science.gov (United States)

    Ren, Jiaping; Wang, Xinjie; Jin, Xiaogang; Manocha, Dinesh

    2016-01-01

    We present a biologically plausible dynamics model to simulate swarms of flying insects. Our formulation, which is based on biological conclusions and experimental observations, is designed to simulate large insect swarms of varying densities. We use a force-based model that captures different interactions between the insects and the environment and computes collision-free trajectories for each individual insect. Furthermore, we model the noise as a constructive force at the collective level and present a technique to generate noise-induced insect movements in a large swarm that are similar to those observed in real-world trajectories. We use a data-driven formulation that is based on pre-recorded insect trajectories. We also present a novel evaluation metric and a statistical validation approach that takes into account various characteristics of insect motions. In practice, the combination of Curl noise function with our dynamics model is used to generate realistic swarm simulations and emergent behaviors. We highlight its performance for simulating large flying swarms of midges, fruit fly, locusts and moths and demonstrate many collective behaviors, including aggregation, migration, phase transition, and escape responses.

  11. Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms.

    Science.gov (United States)

    Bagella, Simonetta; Filigheddu, Rossella; Caria, Maria Carmela; Girlanda, Mariangela; Roggero, Pier Paolo

    2014-12-01

    The aims of this paper were (i) to define how contrasting land uses affected plant biodiversity in Mediterranean agro-silvo-pastoral-systems across a gradient of disturbance regimes: cork oak forests, secondary grasslands, hay crops, grass covered vineyards, tilled vineyards; (ii) to determine whether these patterns mirrored those of below-ground microorganisms and whether the components of γ-diversity followed a similar model. The disturbance regimes affected plant assemblage composition. Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops. Plant assemblage composition patterns mirrored those of Basidiomycota and Ascomycota. Richness in Basidiomycota, denitrifying bacteria and microbial biomass showed the same trend as that observed for vascular plant richness. The Shannon index pattern of below-ground microorganisms was different from that of plants. The plant γ-diversity component model weakly mirrored those of Ascomycota. Patchy diversity patterns suggest that the maintenance of contrasting land uses associated with different productions typical of agro-silvo-pastoral-systems can guarantee the conservation of biodiversity.

  12. Student-generated reading questions: diagnosing student thinking with diverse formative assessments.

    Science.gov (United States)

    Offerdahl, Erika G; Montplaisir, Lisa

    2014-01-01

    Formative assessment has long been identified as a critical element to teaching for conceptual development in science. It is therefore important for university instructors to have an arsenal of formative assessment tools at their disposal which enable them to effectively uncover and diagnose all students' thinking, not just the most vocal or assertive. We illustrate the utility of one type of formative assessment prompt (reading question assignment) in producing high-quality evidence of student thinking (student-generated reading questions). Specifically, we characterized student assessment data using three distinct analytic frames to exemplify their effectiveness in diagnosing student learning in relationship to three sample learning outcomes. Our data will be useful for university faculty, particularly those engaged in teaching upper-level biochemistry courses and their prerequisites, as they provide an alternative mechanism for uncovering and diagnosing student understanding.

  13. Anaerobic coculture of microalgae with Thermosipho globiformans and Methanocaldococcus jannaschii at 68°C enhances generation of n-alkane-rich biofuels after pyrolysis.

    Science.gov (United States)

    Yamane, Kunio; Matsuyama, Shigeru; Igarashi, Kensuke; Utsumi, Motoo; Shiraiwa, Yoshihiro; Kuwabara, Tomohiko

    2013-02-01

    We tested different alga-bacterium-archaeon consortia to investigate the production of oil-like mixtures, expecting that n-alkane-rich biofuels might be synthesized after pyrolysis. Thermosipho globiformans and Methanocaldococcus jannaschii were cocultured at 68°C with microalgae for 9 days under two anaerobic conditions, followed by pyrolysis at 300°C for 4 days. Arthrospira platensis (Cyanobacteria), Dunaliella tertiolecta (Chlorophyta), Emiliania huxleyi (Haptophyta), and Euglena gracilis (Euglenophyta) served as microalgal raw materials. D. tertiolecta, E. huxleyi, and E. gracilis cocultured with the bacterium and archaeon inhibited their growth and CH(4) production. E. huxleyi had the strongest inhibitory effect. Biofuel generation was enhanced by reducing impurities containing alkanenitriles during pyrolysis. The composition and amounts of n-alkanes produced by pyrolysis were closely related to the lipid contents and composition of the microalgae. Pyrolysis of A. platensis and D. tertiolecta containing mainly phospholipids and glycolipids generated short-carbon-chain n-alkanes (n-tridecane to n-nonadecane) and considerable amounts of isoprenoids. E. gracilis also produced mainly short n-alkanes. In contrast, E. huxleyi containing long-chain (31 and 33 carbon atoms) alkenes and very long-chain (37 to 39 carbon atoms) alkenones, in addition to phospholipids and glycolipids, generated a high yield of n-alkanes of various lengths (n-tridecane to n-pentatriacontane). The gas chromatography-mass spectrometry (GC-MS) profiles of these n-alkanes were similar to those of native petroleum crude oils despite containing a considerable amount of n-hentriacontane. The ratio of phytane to n-octadecane was also similar to that of native crude oils.

  14. Anaerobic Coculture of Microalgae with Thermosipho globiformans and Methanocaldococcus jannaschii at 68°C Enhances Generation of n-Alkane-Rich Biofuels after Pyrolysis

    Science.gov (United States)

    Matsuyama, Shigeru; Igarashi, Kensuke; Utsumi, Motoo; Shiraiwa, Yoshihiro; Kuwabara, Tomohiko

    2013-01-01

    We tested different alga-bacterium-archaeon consortia to investigate the production of oil-like mixtures, expecting that n-alkane-rich biofuels might be synthesized after pyrolysis. Thermosipho globiformans and Methanocaldococcus jannaschii were cocultured at 68°C with microalgae for 9 days under two anaerobic conditions, followed by pyrolysis at 300°C for 4 days. Arthrospira platensis (Cyanobacteria), Dunaliella tertiolecta (Chlorophyta), Emiliania huxleyi (Haptophyta), and Euglena gracilis (Euglenophyta) served as microalgal raw materials. D. tertiolecta, E. huxleyi, and E. gracilis cocultured with the bacterium and archaeon inhibited their growth and CH4 production. E. huxleyi had the strongest inhibitory effect. Biofuel generation was enhanced by reducing impurities containing alkanenitriles during pyrolysis. The composition and amounts of n-alkanes produced by pyrolysis were closely related to the lipid contents and composition of the microalgae. Pyrolysis of A. platensis and D. tertiolecta containing mainly phospholipids and glycolipids generated short-carbon-chain n-alkanes (n-tridecane to n-nonadecane) and considerable amounts of isoprenoids. E. gracilis also produced mainly short n-alkanes. In contrast, E. huxleyi containing long-chain (31 and 33 carbon atoms) alkenes and very long-chain (37 to 39 carbon atoms) alkenones, in addition to phospholipids and glycolipids, generated a high yield of n-alkanes of various lengths (n-tridecane to n-pentatriacontane). The gas chromatography-mass spectrometry (GC-MS) profiles of these n-alkanes were similar to those of native petroleum crude oils despite containing a considerable amount of n-hentriacontane. The ratio of phytane to n-octadecane was also similar to that of native crude oils. PMID:23183975

  15. Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

    Science.gov (United States)

    Friis-Nielsen, Jens; Vinner, Lasse; Hansen, Thomas Arn; Richter, Stine Raith; Fridholm, Helena; Herrera, Jose Alejandro Romero; Lund, Ole; Brunak, Søren; Izarzugaza, Jose M. G.; Mourier, Tobias; Nielsen, Lars Peter

    2016-01-01

    Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition. PMID:26818667

  16. Generating phenotypic diversity in a fungal biocatalyst to investigate alcohol stress tolerance encountered during microbial cellulosic biofuel production.

    Directory of Open Access Journals (Sweden)

    Rosanna C Hennessy

    Full Text Available Consolidated bioprocessing (CBP of lignocellulosic biomass offers an alternative route to renewable energy. The crop pathogen Fusarium oxysporum is a promising fungal biocatalyst because of its broad host range and innate ability to co-saccharify and ferment lignocellulose to bioethanol. A major challenge for cellulolytic CBP-enabling microbes is alcohol inhibition. This research tested the hypothesis that Agrobacterium tumefaciens--mediated transformation (ATMT could be exploited as a tool to generate phenotypic diversity in F. oxysporum to investigate alcohol stress tolerance encountered during CBP. A random mutagenesis library of gene disruption transformants (n=1,563 was constructed and screened for alcohol tolerance in order to isolate alcohol sensitive or tolerant phenotypes. Following three rounds of screening, exposure of select transformants to 6% ethanol and 0.75% n-butanol resulted respectively in increased (≥ 11.74% and decreased (≤ 43.01% growth compared to the wild -type (WT. Principal component analysis (PCA quantified the level of phenotypic diversity across the population of genetically transformed individuals and isolated candidate strains for analysis. Characterisation of one strain, Tr. 259, ascertained a reduced growth phenotype under alcohol stress relative to WT and indicated the disruption of a coding region homologous to a putative sugar transporter (FOXG_09625. Quantitative PCR (RT-PCR showed FOXG_09625 was differentially expressed in Tr. 259 compared to WT during alcohol-induced stress (P<0.05. Phylogenetic analysis of putative sugar transporters suggests diverse functional roles in F. oxysporum and other filamentous fungi compared to yeast for which sugar transporters form part of a relatively conserved family. This study has confirmed the potential of ATMT coupled with a phenotypic screening program to select for genetic variation induced in response to alcohol stress. This research represents a first step in the

  17. Expanded therapeutic potential in activity space of next-generation 5-nitroimidazole antimicrobials with broad structural diversity.

    Science.gov (United States)

    Miyamoto, Yukiko; Kalisiak, Jaroslaw; Korthals, Keith; Lauwaet, Tineke; Cheung, Dae Young; Lozano, Ricardo; Cobo, Eduardo R; Upcroft, Peter; Upcroft, Jacqueline A; Berg, Douglas E; Gillin, Frances D; Fokin, Valery V; Sharpless, K Barry; Eckmann, Lars

    2013-10-22

    Metronidazole and other 5-nitroimidazoles (5-NI) are among the most effective antimicrobials available against many important anaerobic pathogens, but evolving resistance is threatening their long-term clinical utility. The common 5-NIs were developed decades ago, yet little 5-NI drug development has since taken place, leaving the true potential of this important drug class unexplored. Here we report on a unique approach to the modular synthesis of diversified 5-NIs for broad exploration of their antimicrobial potential. Many of the more than 650 synthesized compounds, carrying structurally diverse functional groups, have vastly improved activity against a range of microbes, including the pathogenic protozoa Giardia lamblia and Trichomonas vaginalis, and the bacterial pathogens Helicobacter pylori, Clostridium difficile, and Bacteroides fragilis. Furthermore, they can overcome different forms of drug resistance, and are active and nontoxic in animal infection models. These findings provide impetus to the development of structurally diverse, next-generation 5-NI drugs as agents in the antimicrobial armamentarium, thus ensuring their future viability as primary therapeutic agents against many clinically important infections.

  18. New records of rotifers (Rotifera: Eurotatoria from Deepor Beel - a Ramsar site of India with an update on its rich rotifer diversity.

    Directory of Open Access Journals (Sweden)

    B.K. Sharma

    2015-03-01

    Full Text Available Plankton samples collected from Deepor Beel (a Ramsar site, during July 2011 to June 2013, revealed 155 species of Rotifera, belonging to 35 genera and 20 families.  Of these, 16 species belonging to eight genera and seven families are new records to the rotifer fauna of this wetland of northeast India.  Our observations raise the total richness of the phylum known till date from this important floodplain lake (beel of the Brahmaputra river basin to 171 species and thus highlight its biodiversity value as one of the globally rich Rotifera habitats.  The updated list is interesting for following meta-analyses of rotifer occurrence in this only well sampled freshwater ecosystem of the Indian sub-region. 

  19. Riqueza y diversidad de especies de aves asociadas a manglar en tres sistemas lagunares en la región costera de Oaxaca, México Richness and diversity of bird species associated with mangrove in three lagoon systems in the coastal region of Oaxaca, Mexico

    Directory of Open Access Journals (Sweden)

    José Cruz Bojorges-Baños

    2011-03-01

    Full Text Available Se documentó la riqueza y diversidad avifaunística mediante capturas y conteos en las lagunas de Chacahua, Manialtepec y La Ventanilla. La diversidad de Shannon-Wiener se comparó mediante pruebas t de Hutcheson y la similitud de la riqueza avifaunística y se determinaron diferencias entre la abundancia de especies. Se generaron curvas de acumulación de especies y se estimó la riqueza con el indicador de cobertura basado en frecuencia. Se registraron 17 órdenes, 39 familias y 94 especies: 69 residentes y 25 migratorias. La abundancia no presentó diferencias (p>0.05. Hubo diferencias en la diversidad de especies entre las lagunas; La Ventanilla presentó la más elevada (3.51. La mayor similitud se obtuvo entre Chacahua y Manialtepec con 56% y la menor entre Manialtepec y La Ventanilla con 42%. La riqueza y proporción de especies residentes y migratorias fue similar en las 3 áreas; no obstante, por la baja similitud, se infiere que la diferencia en la composición de especies es significativa y que existe la posibilidad de registrar otras. Esta información complementa estudios previos, representa un inventario actualizado e indica que la avifauna asociada a manglar no se ha documentado totalmente.Avian richness and diversity was recorded in the lagoons of Chacahua, Manialtepec and La Ventanilla, using counts and captures. Shannon-Wiener diversity was compared using the Hutcheson's t-test, similarity of species richness was determined, as were differences in abundance. Species accumulation curves were generated and richness was estimated using the Incidence-based Estimator. 17 orders, 39 families and 94 species were registered, 65 of which were resident and 25 of which were migratory. While no difference in abundance was detected (p > 0.05, there was difference in diversity between the lagoons, with La Ventanilla presenting the highest index (3.51. The greatest similarity obtained was between Chacahua and Manialtepec, with 56%, and the

  20. Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Chun-Jun; Sun, Wei-Wen; Bruno, Kenneth S.; Oakley, Berl R.; Keller, Nancy P.; Wang, Clay C.

    2015-07-13

    In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes or non-ribosomal peptide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPS-like genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. More interestingly, further experiments revealed that the aspulvinone E produced by two different genes accumulates in different fungal compartments. And this spatial control of aspulvinone E production is likely to be regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is inserted in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. The study also identified one trans-prenyltransferase AbpB which is capable of prenylating two different substrates aspulvinones and butyrolactones. In total, our study shows the first example in which the locally distribution of the same natural product could lead to its incorporation into different SM pathways.

  1. Variation in fish community structure, richness, and diversity in 56 Danish lakes with contrasting depth, size, and trophic state: does the method matter?

    DEFF Research Database (Denmark)

    Menezes, Rosemberg; Borchsenius, Finn; Svenning, J.-C.

    2013-01-01

    The distribution of freshwater fish is influenced by food availability, habitat heterogeneity, competition, predation, trophic state, and presence/absence of macrophytes. This poses a challenge to monitoring, and researchers have been struggling to develop accurate sampling methods for obtaining...... community, as all methods miss some important species that other methods capture. However, electrofishing seems to be a fast alternative to gillnets for monitoring fish species richness and composition in littoral habitats of Danish lakes....

  2. Atypical beta(s) haplotypes are generated by diverse genetic mechanisms.

    Science.gov (United States)

    Zago, M A; Silva, W A; Dalle, B; Gualandro, S; Hutz, M H; Lapoumeroulie, C; Tavella, M H; Araujo, A G; Krieger, J E; Elion, J; Krishnamoorthy, R

    2000-02-01

    The majority of the chromosomes with the beta(S) gene have one of the five common haplotypes, designated as Benin, Bantu, Senegal, Cameroon, and Arab-Indian haplotypes. However, in every large series of sickle cell patients, 5-10% of the chromosomes have less common haplotypes, usually referred to as "atypical" haplotypes. In order to explore the genetic mechanisms that could generate these atypical haplotypes, we extended our analysis to other rarely studied polymorphic markers of the beta(S)-gene cluster, in a total of 40 chromosomes with uncommon haplotypes from Brazil and Cameroon. The following polymorphisms were examined: seven restriction site polymorphisms of the epsilongammadeltabeta-cluster, the pre-(G)gamma framework sequence including the 6-bp deletion/insertion pattern, HS-2 LCR (AT)xR(AT)y and pre-beta (AT)xTy repeat motifs, the GC/TT polymorphism at -1105-1106 of (G)gamma-globin gene, the C/T polymorphism at -551 of the beta-globin gene, and the intragenic beta-globin gene framework. Among the Brazilian subjects, the most common atypical structure (7/16) was a Bantu 3'-subhaplotype associated with different 5'-sequences, while in two chromosomes a Benin 3'-subhaplotype was associated with two different 5'-subhaplotypes. A hybrid Benin/Bantu configuration was also observed. In three chromosomes, the atypical haplotype differed from the typical one by the change of a single restriction site. In 2/134 chromosomes identified as having a typical Bantu RFLP-haplotype, a discrepant LCR repeat sequence was observed, probably owing to a crossover 5' to the epsilon-gene. Among 80 beta(S) chromosomes from Cameroon, 22 were associated with an atypical haplotype. The most common structure was represented by a Benin haplotype (from the LCR to the beta-gene) with a non-Benin segment 3' to the beta-globin gene. In two cases a Bantu LCR was associated with a Benin haplotype and a non-Benin segment 3' to the beta-globin gene. In three other cases, a more complex

  3. Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo

    Science.gov (United States)

    Wilkinson, Eduan; Vallari, Ana; McArthur, Carole; Sthreshley, Larry; Brennan, Catherine A.; Cloherty, Gavin; de Oliveira, Tulio

    2017-01-01

    ABSTRACT As the epidemiological epicenter of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43.02%), but 7 other subtypes (33.14%), 20 circulating recombinant forms (CRFs; 11.63%), and 20 unclassified (11.63%) sequences were also found. Of the rare and unclassified subtypes, 18 specimens were selected for next-generation sequencing (NGS) by a modified HIV-switching mechanism at the 5′ end of the RNA template (SMART) method to obtain full-genome sequences. NGS produced 14 new complete genomes, which included pure subtype C (n = 2), D (n = 1), F1 (n = 1), H (n = 3), and J (n = 1) genomes. The two subtype C genomes and one of the subtype H genomes branched basal to their respective subtype branches but had no evidence of recombination. The remaining 6 genomes were complex recombinants of 2 or more subtypes, including subtypes A1, F, G, H, J, and K and unclassified fragments, including one subtype CRF25 isolate, which branched basal to all CRF25 references. Notably, all recombinant subtype H fragments branched basal to the H clade. Spatial-geographical analysis indicated that the diverse sequences identified here did not expand globally. The full-genome and subgenomic sequences identified in our study population significantly increase the documented diversity of the strains involved in the continually evolving HIV-1 pandemic. IMPORTANCE Very little is known about the ancestral HIV-1 strains that founded the global pandemic, and very few complete genome sequences are available from patients in the Congo Basin, where HIV-1 expanded early in the global pandemic

  4. Platelet-rich fibrin (PRF): a second-generation platelet concentrate. Part V: histologic evaluations of PRF effects on bone allograft maturation in sinus lift.

    Science.gov (United States)

    Choukroun, Joseph; Diss, Antoine; Simonpieri, Alain; Girard, Marie-Odile; Schoeffler, Christian; Dohan, Steve L; Dohan, Anthony J J; Mouhyi, Jaafar; Dohan, David M

    2006-03-01

    Platelet-rich fibrin (PRF) belongs to a new generation of platelet concentrates, with simplified processing and without biochemical blood handling. The use of platelet gel to improve bone regeneration is a recent technique in implantology. However, the biologic properties and real effects of such products remain controversial. In this article, we therefore attempt to evaluate the potential of PRF in combination with freeze-dried bone allograft (FDBA) (Phoenix; TBF, France) to enhance bone regeneration in sinus floor elevation. Nine sinus floor augmentations were performed. In 6 sites, PRF was added to FDBA particles (test group), and in 3 sites FDBA without PRF was used (control group). Four months later for the test group and 8 months later for the control group, bone specimens were harvested from the augmented region during the implant insertion procedure. These specimens were treated for histologic analysis. Histologic evaluations reveal the presence of residual bone surrounded by newly formed bone and connective tissue. After 4 months of healing time, histologic maturation of the test group appears to be identical to that of the control group after a period of 8 months. Moreover, the quantities of newly formed bone were equivalent between the 2 protocols. Sinus floor augmentation with FDBA and PRF leads to a reduction of healing time prior to implant placement. From a histologic point of view, this healing time could be reduced to 4 months, but large-scale studies are still necessary to validate these first results.

  5. Acute, reproductive toxicity and two-generation teratology studies of a standardized quassinoid-rich extract of Eurycoma longifolia Jack in Sprague-Dawley rats.

    Science.gov (United States)

    Low, Bin-Seng; Das, Prashanta Kumar; Chan, Kit-Lam

    2014-07-01

    The roots of Eurycoma longifolia Jack are popularly sought as herbal medicinal supplements to improve libido and general health amongst the local ethnic population. The major quassinoids of E. longifolia improved spermatogenesis and fertility but toxicity studies have not been well documented. The reproductive toxicity, two generation of foetus teratology and the up-and-down acute toxicity were investigated in Sprague-Dawley rats orally treated with quassinoid-rich E. longifolia extract (TAF273). The results showed that the median lethal dose (LD50 ) of TAF273 for female and male rats was 1293 and >2000 mg/kg, respectively. Fertility index and litter size of the TAF273 treated were significantly increased when compared with those of the non-treated animals. The TAF273-treated dams decreased in percentage of pre-implantation loss, post-implantation loss and late resorption. No toxic symptoms were observed on the TAF273-treated pregnant female rats and their foetuses were normal. The no-observed adverse effect level (NOAEL) obtained from reproductive toxicity and teratology studies of TAF273 in rats was 100 mg/kg body weight/day, being more than 10-fold lower than the LD50 value. Thus, any human dose derived from converting the rat doses of 100 mg/kg and below may be considered as safe for further clinical studies.

  6. Diversity oriented synthesis: a challenge for synthetic chemists.

    Science.gov (United States)

    Bender, A; Fergus, S; Galloway, W R J D; Glansdorp, F G; Marsden, D M; Nicholson, R L; Spandl, R J; Thomas, G L; Wyatt, E E; Glen, R C; Spring, D R

    2006-01-01

    This article covers the diversity-oriented synthesis (DOS) of small molecules in order to generate a collection of pure compounds that are attractive for lead generation in a phenotypic, high-throughput screening approach useful for chemical genetics and drug discovery programmes. Nature synthesizes a rich structural diversity of small molecules, however, unfortunately, there are some disadvantages with using natural product sources for diverse small-molecule discovery. Nevertheless we have a lot to learn from nature. The efficient chemical synthesis of structural diversity (and complexity) is the aim of DOS. Highlights of this article include a discussion of nature's and synthetic chemists' strategies to obtain structural diversity and an analysis of molecular descriptors used to classify compounds. The assessment of how successful one diversity-oriented synthesis is vs another is subjective; therefore we use freely available software (www.cheminformatics.org/diversity) to assess structural diversity in any combinatorial synthesis.

  7. DNA barcoding, microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants.

    Science.gov (United States)

    Sarwat, Maryam; Yamdagni, Manu Mayank

    2016-01-01

    DNA barcoding, microarray technology and next generation sequencing have emerged as promising tools for the elucidation of plant genetic diversity and its conservation. They are proving to be immensely helpful in authenticating the useful medicinal plants for herbal drug preparations. These newer versions of molecular markers utilize short genetic markers in the genome to characterize the organism to a particular species. This has the potential not only to classify the known and yet unknown species but also has a promising future to link the medicinally important plants according to their properties. The newer trends being followed in DNA chips and barcoding pave the way for a future with many different possibilities. Several of these possibilities might be: characterization of unknown species in a considerably less time than usual, identification of newer medicinal properties possessed by the species and also updating the data of the already existing but unnoticed properties. This can assist us to cure many different diseases and will also generate novel opportunities in medicinal drug delivery and targeting.

  8. Diversity begets diversity: host expansions and the diversification of plant-feeding insects

    Directory of Open Access Journals (Sweden)

    Nylin Sören

    2006-01-01

    Full Text Available Abstract Background Plant-feeding insects make up a large part of earth's total biodiversity. While it has been shown that herbivory has repeatedly led to increased diversification rates in insects, there has been no compelling explanation for how plant-feeding has promoted speciation rates. There is a growing awareness that ecological factors can lead to rapid diversification and, as one of the most prominent features of most insect-plant interactions, specialization onto a diverse resource has often been assumed to be the main process behind this diversification. However, specialization is mainly a pruning process, and is not able to actually generate diversity by itself. Here we investigate the role of host colonizations in generating insect diversity, by testing if insect speciation rate is correlated with resource diversity. Results By applying a variant of independent contrast analysis, specially tailored for use on questions of species richness (MacroCAIC, we show that species richness is strongly correlated with diversity of host use in the butterfly family Nymphalidae. Furthermore, by comparing the results from reciprocal sister group selection, where sister groups were selected either on the basis of diversity of host use or species richness, we find that it is likely that diversity of host use is driving species richness, rather than vice versa. Conclusion We conclude that resource diversity is correlated with species richness in the Nymphalidae and suggest a scenario based on recurring oscillations between host expansions – the incorporation of new plants into the repertoire – and specialization, as an important driving force behind the diversification of plant-feeding insects.

  9. Robust algorithm to generate a diverse class of dense disordered and ordered sphere packings via linear programming.

    Science.gov (United States)

    Torquato, S; Jiao, Y

    2010-12-01

    We have formulated the problem of generating dense packings of nonoverlapping, nontiling nonspherical particles within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem called the adaptive-shrinking cell (ASC) formulation [S. Torquato and Y. Jiao, Phys. Rev. E 80, 041104 (2009)]. Because the objective function and impenetrability constraints can be exactly linearized for sphere packings with a size distribution in d-dimensional Euclidean space R(d), it is most suitable and natural to solve the corresponding ASC optimization problem using sequential-linear-programming (SLP) techniques. We implement an SLP solution to produce robustly a wide spectrum of jammed sphere packings in R(d) for d=2, 3, 4, 5, and 6 with a diversity of disorder and densities up to the respective maximal densities. A novel feature of this deterministic algorithm is that it can produce a broad range of inherent structures (locally maximally dense and mechanically stable packings), besides the usual disordered ones (such as the maximally random jammed state), with very small computational cost compared to that of the best known packing algorithms by tuning the radius of the influence sphere. For example, in three dimensions, we show that it can produce with high probability a variety of strictly jammed packings with a packing density anywhere in the wide range [0.6, 0.7408...], where π/√18 = 0.7408... corresponds to the density of the densest packing. We also apply the algorithm to generate various disordered packings as well as the maximally dense packings for d=2, 4, 5, and 6. Our jammed sphere packings are characterized and compared to the corresponding packings generated by the well-known Lubachevsky-Stillinger (LS) molecular-dynamics packing algorithm. Compared to the LS procedure, our SLP protocol is able to ensure that the final packings are truly jammed, produces disordered jammed packings with anomalously low densities, and is appreciably

  10. Direct interaction between Tks proteins and the N-terminal proline-rich region (PRR) of NoxA1 mediates Nox1-dependent ROS generation.

    Science.gov (United States)

    Gianni, Davide; DerMardirossian, Céline; Bokoch, Gary M

    2011-01-01

    NADPH oxidase (Nox) family enzymes are one of the main sources of cellular reactive oxygen species (ROS), which have been implicated in several physiological and pathophysiological processes. To date seven members of this family have been reported, including Nox1-5 and Duox1 and 2. With the exception of Nox2, the regulation of the Nox enzymes is still poorly understood. Nox1 is highly expressed in the colon, and requires two cytosolic regulators, the organizer subunit NoxO1 and the activator subunit NoxA1, as well as the binding of Rac1 GTPase, for its activity. Recently, we identified the c-Src substrate proteins Tks4 and Tks5 as functional members of a p47(phox)-related organizer superfamily. As a functional consequence of this interaction, Nox1 localizes to invadopodia, actin-rich membrane protrusions of cancer cells which facilitate pericellular proteolysis and invasive behavior. Here, we report that Tks4 and Tks5 directly bind to NoxA1. Moreover, the integrity of the N-terminal PRR of NoxA1 is essential for this direct interaction with the Tks proteins. When the PRR in NoxA1 is disrupted, Tks proteins cannot bind NoxA1 and lose their ability to support Nox1-dependent ROS generation. Consistent with this, Tks4 and Tks5 are unable to act as organizers for Nox2 because of their inability to interact with p67(phox), which lacks the N-terminal PRR, thus conferring a unique specificity to Tks4 and 5. Taken together, these results clarify the molecular basis for the interaction between NoxA1 and the Tks proteins and may provide new insights into the pharmacological design of a more effective anti-metastatic strategy.

  11. Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution.

    Science.gov (United States)

    Benedek, Tibor; Vajna, Balázs; Táncsics, András; Márialigeti, Károly; Lányi, Szabolcs; Máthé, István

    2013-11-01

    Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the long-term impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the α-, β-, γ-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the β-, γ-Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

  12. Understanding the effect of an in situ generated and integrated spinel phase on a layered Li-rich cathode material using a non-stoichiometric strategy.

    Science.gov (United States)

    Zhang, Jicheng; Gao, Rui; Sun, Limei; Li, Zhengyao; Zhang, Heng; Hu, Zhongbo; Liu, Xiangfeng

    2016-09-14

    Recently, spinel-layered integrated Li-rich cathode materials have attracted great interest due to the large enhancement of their electrochemical performances. However, the modification mechanism and the effect of the integrated spinel phase on Li-rich layered cathode materials are still not very clear. Herein, we have successfully synthesized the spinel-layered integrated Li-rich cathode material using a facile non-stoichiometric strategy (NS-LNCMO). The rate capability (84 mA h g(-1)vs. 28 mA h g(-1), 10 C), cycling stability (92.4% vs. 80.5%, 0.2 C), low temperature electrochemical capability (96.5 mA h g(-1)vs. 59 mA h g(-1), -20 °C), initial coulomb efficiency (92% vs. 79%) and voltage fading (2.77 V vs. 3.02 V, 200 cycles@1 C) of spinel-layered integrated Li-rich cathode materials have been significantly improved compared with a pure Li-rich phase cathode. Some new insights into the effect of the integrated spinel phase on a layered Li-rich cathode have been proposed through a comparison of the structure evolution of the integrated and Li-rich only materials before and after cycling. The Li-ion diffusion coefficient of NS-LNCMO has been enlarged by about 3 times and almost does not change even after 100 cycles indicating an enhanced structure stability. The integration of the spinel phase not only enhances the structure stability of the layered Li-rich phase during charging-discharging but also expands the interslab spacing of the Li-ion diffusion layer, and elongates TM-O covalent bond lengths, which lowers the activation barrier of Li(+)-transportation, and alleviates the structure strain during the cycling procedure.

  13. Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change

    Directory of Open Access Journals (Sweden)

    Juha M. Alatalo

    2014-05-01

    Full Text Available We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years responses are good predictors for medium-term (7 years changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-term responses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both, different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity–diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant–plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the

  14. Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

    KAUST Repository

    Arif, Chatchanit

    2014-09-01

    The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.

  15. Tree Species Diversity, Richness, and Similarity in Intact and Degraded Forest in the Tropical Rainforest of the Congo Basin: Case of the Forest of Likouala in the Republic of Congo

    Directory of Open Access Journals (Sweden)

    Suspense Averti Ifo

    2016-01-01

    Full Text Available Trees species diversity, richness, and similarity were studied in fifteen plots of the tropical rainforests in the northeast of the Republic of Congo, based on trees inventories conducted on fifteen 0.25 ha plots installed along different types of forests developed on terra firma, seasonally flooded, and on flooded terra. In all of the plots installed, all trees with diameter at breast height, DBH ≥ 5 cm, were measured. The Shannon diversity index, species richness, equitability, and species dominance were computed to see the variation in tree community among plots but also between primary forest and secondary forest. A total of 1611 trees representing 114 species and 35 families were recorded from a total area of 3.75 ha. Euphorbiaceae was the dominant family in the forest with 12 species, followed by Fabaceae-Mimosoideae (10 species and Phyllanthaceae (6 species and Guttiferae (6 species. The biodiversity did not vary greatly from plot to plot on the whole of the study area (3.75 ha. The low value of Shannon index was obtained in plot 11 (H′=0.75 whereas the highest value was obtained in plot 12 (H′=4.46. The values of this index vary from 0.23 to 0.95 in plots P11 and P15, respectively. Results obtained revealed high biodiversity of trees of the forest of Impfondo-Dongou. The information on tree species structure and function can provide baseline information for conservation of the biodiversity of the tropical forest in this area.

  16. Diversity: A Philosophical Perspective

    Directory of Open Access Journals (Sweden)

    Sahotra Sarkar

    2010-01-01

    Full Text Available In recent years, diversity, whether it be ecological, biological, cultural, or linguistic diversity, has emerged as a major cultural value. This paper analyzes whether a single concept of diversity can underwrite discussions of diversity in different disciplines. More importantly, it analyzes the normative justification for the endorsement of diversity as a goal in all contexts. It concludes that no more than a relatively trivial concept of diversity as richness is common to all contexts. Moreover, there is no universal justification for the endorsement of diversity. Arguments to justify the protection of diversity must be tailored to individual contexts.

  17. Environmental heterogeneity predicts species richness of freshwater mollusks in sub-Saharan Africa

    Science.gov (United States)

    Hauffe, T.; Schultheiß, R.; Van Bocxlaer, B.; Prömmel, K.; Albrecht, C.

    2016-09-01

    Species diversity and how it is structured on a continental scale is influenced by stochastic, ecological, and evolutionary driving forces, but hypotheses on determining factors have been mainly examined for terrestrial and marine organisms. The extant diversity of African freshwater mollusks is in general well assessed to facilitate conservation strategies and because of the medical importance of several taxa as intermediate hosts for tropical parasites. This historical accumulation of knowledge has, however, not resulted in substantial macroecological studies on the spatial distribution of freshwater mollusks. Here, we use continental distribution data and a recently developed method of random and cohesive allocation of species distribution ranges to test the relative importance of various factors in shaping species richness of Bivalvia and Gastropoda. We show that the mid-domain effect, that is, a hump-shaped richness gradient in a geographically bounded system despite the absence of environmental gradients, plays a minor role in determining species richness of freshwater mollusks in sub-Saharan Africa. The western branch of the East African Rift System was included as dispersal barrier in richness models, but these simulation results did not fit observed diversity patterns significantly better than models where this effect was not included, which suggests that the rift has played a more complex role in generating diversity patterns. Present-day precipitation and temperature explain richness patterns better than Eemian climatic condition. Therefore, the availability of water and energy for primary productivity during the past does not influence current species richness patterns much, and observed diversity patterns appear to be in equilibrium with contemporary climate. The availability of surface waters was the best predictor of bivalve and gastropod richness. Our data indicate that habitat diversity causes the observed species-area relationship, and hence, that

  18. Coral diversity and the severity of disease outbreaks: a cross-regional comparison of Acropora white syndrome in a species-rich region (American Samoa) with a species-poor region (Northwestern Hawaiian Islands).

    Science.gov (United States)

    Aeby, G.S.; Bourne, D.G.; Wilson, B.; Work, Thierry M.

    2011-01-01

    The dynamics of the coral disease, Acropora white syndrome (AWS), was directly compared on reefs in the species-poor region of the Northwestern Hawaiian Islands (NWHI) and the species-rich region of American Samoa (AS) with results suggesting that biodiversity, which can affect the abundance of susceptible hosts, is important in influencing the impacts of coral disease outbreaks. The diversity-disease hypothesis predicts that decreased host species diversity should result in increased disease severity of specialist pathogens. We found that AWS was more prevalent and had a higher incidence within the NWHI as compared to AS. Individual Acropora colonies affected by AWS showed high mortality in both regions, but case fatality rate and disease severity was higher in the NWHI. The site within the NWHI had a monospecific stand of A. cytherea; a species that is highly susceptible to AWS. Once AWS entered the site, it spread easily amongst the abundant susceptible hosts. The site within AS contained numerous Acropora species, which differed in their apparent susceptibility to infection and disease severity, which in turn reduced disease spread. Manipulative studies showed AWS was transmissible through direct contact in three Acropora species. These results will help managers predict and respond to disease outbreaks.

  19. Controlling noncovalent interactions between a lysine-rich α-helical peptide and self-assembled monolayers of alkanethiols on Au through functional group diversity

    Science.gov (United States)

    Raigoza, Annette F.; Onyirioha, Kristeen; Webb, Lauren J.

    2017-02-01

    Reliably attaching a structured biomolecule to an inorganic substrate would enable the preparation of surfaces that incorporate both biological and inorganic functions and structures. To this end, we have previously developed a procedure using the copper(I)-catalyzed click reaction to tether synthetic α-helical peptides carrying two alkyne groups to well-ordered alkanethiol self-assembled monolayers (SAM) on a Au(111) surface, in which the SAM is composed of a mixture of methyl and azide termination. Proteins, however, are composed of many diverse functional groups, and this composition directly effects protein structure, interactions, and reactivity. Here, we explore the utility of mixed SAMs with alternative terminating functional groups to tune and direct the reactivity of the surface through noncovalent peptide-surface interactions. We study both polar surfaces (OH-terminated) and charged surfaces (COOH- and NH3-terminated, which are negatively and positively charged, respectively, under our reaction conditions). Surfaces were functionalized with a bipolar peptide composed of Lys and Leu residues that could express different interactions through either hydrophilic and/or charge (Lys) or hydrophobic (Leu) influences. X-ray photoelectron spectroscopy (XPS) and surface infrared spectroscopy were used to characterize surfaces at all stages of the peptide functionalization procedure. This strategy resulted in a high density of surface-bound α-helices without aggregation. Mixed SAMs that included a positively charged alkanethiol along with the azide-terminated thiol resulted in a more efficient reaction and better alignment of the peptide with the azide on the surface. Negatively charged surfaces increased physisorption of the peptide, which was then removed during sample rinsing. This work demonstrates that varying easily controlled chemical inputs during the functionalization steps allows the reaction conditions to be balanced for the chemical needs of a

  20. Unity in Diversity.

    Science.gov (United States)

    Purves, Alan C.

    The cultural diversities of peoples and dialects in the United States have brought a richness to the English language that has made it one of the most supple of all the languages in the world. In addition to the diversity in the language are the diversities in literature, technology, nationality, politics, and styles of teaching. Teachers of…

  1. Unity in Diversity.

    Science.gov (United States)

    Purves, Alan C.

    The cultural diversities of peoples and dialects in the United States have brought a richness to the English language that has made it one of the most supple of all the languages in the world. In addition to the diversity in the language are the diversities in literature, technology, nationality, politics, and styles of teaching. Teachers of…

  2. Generations.

    Science.gov (United States)

    Chambers, David W

    2005-01-01

    Groups naturally promote their strengths and prefer values and rules that give them an identity and an advantage. This shows up as generational tensions across cohorts who share common experiences, including common elders. Dramatic cultural events in America since 1925 can help create an understanding of the differing value structures of the Silents, the Boomers, Gen Xers, and the Millennials. Differences in how these generations see motivation and values, fundamental reality, relations with others, and work are presented, as are some applications of these differences to the dental profession.

  3. Productivity is a poor predictor of plant species richness

    Science.gov (United States)

    Adler, Peter B.; Seabloom, Eric W.; Borer, Elizabeth T.; Hillebrand, Helmut; Hautier, Yann; Hector, Andy; Harpole, W. Stanley; O'Halloran, Lydia R.; Grace, James B.; Anderson, T. Michael; Bakker, Jonathan D.; Biederman, Lori A.; Brown, Cynthia S.; Buckley, Yvonne M.; Calabrese, Laura B.; Chu, Cheng-Jin; Cleland, Elsa E.; Collins, Scott L.; Cottingham, Kathryn L.; Crawley, Michael J.; Damschen, Ellen Ingman; Davies, Kendi F.; DeCrappeo, Nicole M.; Fay, Philip A.; Firn, Jennifer; Frater, Paul; Gasarch, Eve I.; Gruner, Daneil S.; Hagenah, Nicole; Lambers, Janneke Hille Ris; Humphries, Hope; Jin, Virginia L.; Kay, Adam D.; Kirkman, Kevin P.; Klein, Julia A.; Knops, Johannes M.H.; La Pierre, Kimberly J.; Lambrinos, John G.; Li, Wei; MacDougall, Andrew S.; McCulley, Rebecca L.; Melbourne, Brett A.; Mitchell, Charles E.; Moore, Joslin L.; Morgan, John W.; Mortensen, Brent; Orrock, John L.; Prober, Suzanne M.; Pyke, David A.; Risch, Anita C.; Schuetz, Martin; Smith, Melinda D.; Stevens, Carly J.; Sullivan, Lauren L.; Wang, Gang; Wragg, Peter D.; Wright, Justin P.; Yang, Louie H.

    2011-01-01

    For more than 30 years, the relationship between net primary productivity and species richness has generated intense debate in ecology about the processes regulating local diversity. The original view, which is still widely accepted, holds that the relationship is hump-shaped, with richness first rising and then declining with increasing productivity. Although recent meta-analyses questioned the generality of hump-shaped patterns, these syntheses have been criticized for failing to account for methodological differences among studies. We addressed such concerns by conducting standardized sampling in 48 herbaceous-dominated plant communities on five continents. We found no clear relationship between productivity and fine-scale (meters-2) richness within sites, within regions, or across the globe. Ecologists should focus on fresh, mechanistic approaches to understanding the multivariate links between productivity an

  4. Use of second-generation platelet concentrate (platelet-rich fibrin) and hydroxyapatite in the management of large periapical inflammatory lesion: a computed tomography scan analysis.

    Science.gov (United States)

    Hiremath, Hemalatha; Motiwala, Tejas; Jain, Pradeep; Kulkarni, Sadanand

    2014-01-01

    Periapical surgery is required when periradicular pathosis associated with endodontically treated teeth cannot be resolved by nonsurgical root canal therapy (retreatment), or when retreatment was unsuccessful, not feasible or contraindicated. Endodontic failures can occur when irritants remain within the confines of the root canal, or when an extraradicular infection cannot be eradicated by orthograde root canal treatment. Foreign-body responses toward filling materials, toward cholesterol crystals or radicular cysts, might prevent complete periapical healing. We present here a case report wherein, combination of platelet-rich fibrin (PRF) and the hydroxyapatite graft was used to achieve faster healing of the large periapical lesion. Healing was observed within 8 months, which were confirmed by computed tomography, following improved bone density. PRF has many advantages over platelet-rich plasma. It provides a physiologic architecture that is very favorable to the healing process, which is obtained due to the slow polymerization process.

  5. Use of second-generation platelet concentrate (platelet-rich fibrin and hydroxyapatite in the management of large periapical inflammatory lesion: A computed tomography scan analysis

    Directory of Open Access Journals (Sweden)

    Hemalatha Hiremath

    2014-01-01

    Full Text Available Periapical surgery is required when periradicular pathosis associated with endodontically treated teeth cannot be resolved by nonsurgical root canal therapy (retreatment, or when retreatment was unsuccessful, not feasible or contraindicated. Endodontic failures can occur when irritants remain within the confines of the root canal, or when an extraradicular infection cannot be eradicated by orthograde root canal treatment. Foreign-body responses toward filling materials, toward cholesterol crystals or radicular cysts, might prevent complete periapical healing. We present here a case report wherein, combination of platelet-rich fibrin (PRF and the hydroxyapatite graft was used to achieve faster healing of the large periapical lesion. Healing was observed within 8 months, which were confirmed by computed tomography, following improved bone density. PRF has many advantages over platelet-rich plasma. It provides a physiologic architecture that is very favorable to the healing process, which is obtained due to the slow polymerization process.

  6. Riqueza y diversidad de especies leñosas del bosque tropical caducifolio El Tarimo, Cuenca del Balsas, Guerrero Richness and diversity of woody species in the tropical dry forest of El Tarimo, Cuenca del Balsas, Guerrero

    Directory of Open Access Journals (Sweden)

    Fernando Pineda-García

    2007-06-01

    Full Text Available Se describe la composición florística, la riqueza y la diversidad de especies de un bosque tropical caducifolio en la provincia florística Cuenca del Balsas, México. Se seleccionaron 4 sitios de 1000 m² cada uno, censándose los árboles, arbustos y lianas con d.a.p. >1 cm. En total se registraron 1456 individuos, pertenecientes a 82 especies, 56 géneros y 24 familias. Independientemente del sitio y de la forma de crecimiento, Leguminosae fue la familia con mayor número de especies y de individuos. Los géneros más diversos fueron Bursera (Burseraceae y Cordia (Boraginaceae con 9 y 4 especies, respectivamente. La riqueza entre los sitios varió de 43 a 55 especies y su similitud fue más alta en el nivel de familia que en el de especie. Los árboles fueron la forma de crecimiento con mayor riqueza de especies. Respectoa otros bosques tropicales caducifolios de México y del mundo, los sitios que se estudiaron en este bosque ocupan una posición baja en cuanto a sus valores de riqueza y estructura.Floristic composition, species richness, and diversity of the seasonally dry tropical forest in the floristic province of the Balsas Depression, México, is described. We sampled four 1,000 m² sites and recorded species and dbh of trees, shrubs and lianas >1 cm dbh. Data from 1,456 individuals were recorded, representing 82 species, 56 genera, and 24 families. Independently of site or growth form, Leguminosae was the family with the highest number of species and individuals. Bursera (Burseraceae and Cordia (Boraginaceae were the most speciose genera, with nine and four species, respectively. Species richness among sites ranged from 43-55 species and their similarity was higher at the family level than the species level. Trees had higher numbers of species than shrubs and lianas. Our results indicate that these forests have low values of species richness and structure attributes in relation with other tropical dry forests of Mexico and the world.

  7. Beyond generational differences: a literature review of the impact of relational diversity on nurses' attitudes and work.

    Science.gov (United States)

    Wolff, Angela C; Ratner, Pamela A; Robinson, Sandra L; Oliffe, John L; Hall, Linda McGillis

    2010-11-01

    Based on a review of the empirical literature, we examine the influence of selected diversity attributes on nurses' work-related attitudes and behaviour. The nursing workforce has become increasingly heterogeneous in its age, educational attainment, and ethnicity/race distributions. There is considerable speculation, in the literature, that the work values of recent nursing graduates are discordant with more experienced nurses. A review of studies published between 1980 and 2009 in nursing, healthcare, psychology, and organizational behaviour led to the inclusion of 19 peer-reviewed research articles, from which our analyses are drawn. The findings indicate that age diversity leads to negative behaviour toward others in the workgroup (e.g. poor collegial relationships) whereas perceived work-values diversity is negatively associated with individuals' own attitudes and behaviour toward their work as well as toward other members of their workgroup. There is inconclusive evidence about the attributes that most significantly influence nurses' attitudes and work; however, preliminary evidence supports the salience of work values. Irrespective of the actual diversity within workgroups, how nurses see one another can have a significant impact on members of their workgroups and their functioning. Broader conceptualizations of diversity are necessary. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

  8. Aromatic C-H Bond Functionalization Induced by Electrochemically in Situ Generated Tris(p-bromophenyl)aminium Radical Cation: Cationic Chain Reactions of Electron-Rich Aromatics with Enamides.

    Science.gov (United States)

    Li, Long-Ji; Jiang, Yang-Ye; Lam, Chiu Marco; Zeng, Cheng-Chu; Hu, Li-Ming; Little, R Daniel

    2015-11-01

    An effective Friedel-Crafts alkylation reaction of electron-rich aromatics with N-vinylamides, induced by electrochemically in situ-generated TBPA radical cation, has been developed; the resulting adducts are produced in good to excellent yields. In the "ex-cell" type electrolysis, TBPA is transformed to its oxidized form in situ and subsequently employed as an electron transfer reagent to initiate a cationic chain reaction. An easily recoverable and reusable polymeric ionic liquid-carbon black (PIL-CB) composite was also utilized as a supporting electrolyte for the electrochemical generation of TBPA cation radical, without sacrificing efficiency or stability after four electrolyses. Cyclic voltammetry analysis and the results of control experiments demonstrate that the reaction of electron-rich aromatics and N-vinylamides occurs via a cationic chain reaction, which takes place though an oxidative activation of a C-H bond of electron-rich aromatics instead of oxidation of the N-vinylamide as previously assumed.

  9. Deepening Understanding of Prior Knowledge: What Diverse First-Generation College Students in the U.S. Can Teach Us

    Science.gov (United States)

    Castillo-Montoya, Milagros

    2017-01-01

    Educational research indicates that teachers revealing and utilizing students' prior knowledge supports students' academic learning. Yet, the variation in students' prior knowledge is not fully known. To better understand students' prior knowledge, I drew on sociocultural learning theories to examine racially and ethnically diverse college…

  10. Peridote-water interaction generating migration pathways of H2-rich fluids in subduction context: Common processes in the ophiolites of Oman, New-Caledonia, Philippines and Turkey

    Science.gov (United States)

    Deville, E. P.; Prinzhofer, A.; Pillot, D.; Vacquand, C.; Sissmann, O.

    2010-12-01

    The occurrence of H2 flows which were punctually known notably in the ophiolites of Oman, Zambales (Philippines) and Antalya (Turkey) appears to be a widespread phenomenon in these major peridotite massifs associated with ancient or active subduction processes. Similar H2-rich gas flows have been discovered also in the peridotite of New-Caledonia. H2 concentrations are locally high (commonly 60 to90% in Oman). H2 is frequently degassing in hyperalkaline springs but the highest flows were found directly expelled from fractures in the peridotites. Obviously, within the fracture systems, gas and associated hyperalkaline water separate at shallow depth close to the top of the upper aquifer level. Locally high flows of gas migrate vertically in the fractures, whereas water with degassing H2 tends to migrate laterally in the fracture network toward the creeks where most of the hyperalkaline springs are found. The genesis of natural H2 is interpreted as the result of the interaction, at depth, between ultrabasic mantle rocks in the upper plate and water expelled by the subducted sediments by oxidation of metals (Fe2+, Mn2+) and reduction of water during serpentinisation. CH4 is commonly associated to the H2-rich fluids and it is interpreted as the result of the reduction of available CO2 at depth. N2 is also commonly associated to the H2-rich fluids in the ophiolites, whereas N2 flows (within H2) were found in the subducted sediments (below the sole décollement of the peridotite) where it can be observed (Oman and New-Caledonia). Within the peridotites, the hyperalkaline water is rich in ions OH- and Ca2+ and characterized by high pH (between 11 and 12). Most alkaline springs are found in the vicinity of major faults and/or lithological discontinuities like the basal décollement of the ophiolites and the peridotite-gabbro contact (Moho). This hyperalkaline water migration induces a chain of diagenetic reactions starting at depth within the fracture systems by the

  11. Integrated, Marginal, and Resilient: Race, Class, and the Diverse Experiences of White First-Generation College Students

    Science.gov (United States)

    Stuber, Jenny Marie

    2011-01-01

    While first-generation college students are "at risk", the majority "do" persist. Using in-depth interviews with 28 white college students I ask: How do white, first-generation, working-class students understand their college experiences, especially in terms of their academic, social, and cultural adjustment? Moreover, what kinds of factors seem…

  12. Disentangling the roles of diversity resistance and priority effects in community assembly.

    Science.gov (United States)

    Viana, Duarte S; Cid, Bertha; Figuerola, Jordi; Santamaría, Luis

    2016-11-01

    The assembly of many biological communities is constrained by the resistance exerted by resident species to immigration (biotic resistance). Two important mechanisms contribute to the generation of biotic resistance: diversity resistance and priority effects. These mechanisms have been explored through theoretical models and laboratory experiments, but the importance of their interplay in the assembly of natural communities remains untested. We used a mesocosm experiment with communities of aquatic plants and zooplankton assembled from natural propagule banks to test whether and how diversity resistance, mediated by the diversity of the resident community, and priority effects, mediated by the timing of immigrants' arrival, affect the establishment of immigrant species and community diversity. In plant communities, immigration success decreased with increasing resident-species richness (diversity resistance) and arrival time (priority effects). Further, diversity resistance was stronger in communities colonized later in the season, indicating that these mechanisms interacted to reinforce biotic resistance. This interaction ultimately determined species richness and beta-diversity in plant communities. For zooplankton, in contrast, neither the diversity of resident communities nor the time of arrival affected the establishment of immigrant species. In these communities, beta-diversity was explained by species sorting, namely biotic effects mediated by plant assemblages. Our results show that the progressive buildup of communities generates an interaction between diversity resistance and priority effects that eventually determines community diversity, unless species sorting mediated by environmental filtering supersedes the effect of biotic resistance. Therefore, disentangling the mechanisms underlying biotic resistance contributes to understand how species diversity is ultimately determined.

  13. Rapid Mutation of Spirulina platensis by a New Mutagenesis System of Atmospheric and Room Temperature Plasmas (ARTP) and Generation of a Mutant Library with Diverse Phenotypes

    Science.gov (United States)

    Zhang, Chong; Tan, Yinyee; Jiang, Peixia; Ge, Nan; Heping Li; Xing, Xinhui

    2013-01-01

    In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9th subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae. PMID:24319517

  14. Rapid mutation of Spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP and generation of a mutant library with diverse phenotypes.

    Directory of Open Access Journals (Sweden)

    Mingyue Fang

    Full Text Available In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9(th subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae.

  15. 提高富硫溶剂再生装置效果的研究%Studies on Sulfur -rich Solvent Re -generation Effect Boosted by Apparatus

    Institute of Scientific and Technical Information of China (English)

    罗资琴; 王学平; 冯琛然

    2011-01-01

    In allusion to solvent re - generation equipment in the gas refining plant, this article concretely analyzes the factors that have impact on the effect of solvent re - generation, and combining with specific production data it puts forward an optimization scheme to make the total sulfur recovery rate come to be more than 99.8%%针对气体精制车间溶剂再生装置,具体分析了影响溶剂再生效果的因素,结合装置实际生产数据,提出优化方案,使装置总硫回收率达到99.8%以上。

  16. What about a Dimension of Engagement, Equity, and Diversity Practices? A Critique of the Next Generation Science Standards

    Science.gov (United States)

    Rodriguez, Alberto J.

    2015-01-01

    In this paper, I offer a critique of "A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas" (NRC, 2012) and of the "Next Generation Science Standards" (Achieve, 2013). While the new version of the science education standards and the arguments put forward to support them are an improvement…

  17. The generation of a diverse suite of Late Pleistocene and Holocene basalt through dacite lavas from the northern Cascade arc at Mount Baker, Washington

    Science.gov (United States)

    Baggerman, Troy David; Debari, S. M.

    2011-01-01

    Mt. Baker is a dominantly andesitic stratovolcano in the northern Cascade arc. In this study, we show that the andesites are not all derived from similar sources, and that open-system processes were dominant during their petrogenesis. To this end, we discuss petrographic observations, mineral chemistry, and whole rock major and trace element chemistry for three of Mt. Baker's late Pleistocene to Holocene lava flow units. These include the basalt and basaltic andesite of Sulphur Creek (SC) (51.4-55.8 wt% SiO2, Mg# 57-58), the Mg-rich andesite of Glacier Creek (GC) (58.3-58.7 wt% SiO2, Mg# 63-64), and the andesite and dacite of Boulder Glacier (BG) (60.2-64.2 wt% SiO2, Mg# 50-57). Phenocryst populations in all units display varying degrees of reaction and disequilibrium textures along with complicated zoning patterns indicative of open-system processes. All lavas are medium-K and calc-alkaline, but each unit displays distinctive trace element and REE characteristics that do not correlate with the average SiO2 content of the unit. The mafic lavas of SC have relatively elevated REE abundances with the lowest (La/Yb)N (~4.5). The intermediate GC andesites (Mg- and Ni-rich) have the lowest REE abundances and the highest (La/Yb)N (~6.7) with strongly depleted HREE. The more felsic BG lavas have intermediate REE abundances and (La/Yb)N (~6.4). The high-Mg character of the GC andesites can be explained by addition of 4% of a xenocrystic olivine component. However, their depleted REE patterns are similar to other high-Mg andesites reported from Mt. Baker and require a distinct mantle source. The two dominantly andesitic units (GC and BG) are different enough from each other that they could not have been derived from the same parent basalt. Nor could either of them have been derived from the SC basalt by crystal fractionation processes. Crystal fractionation also cannot explain the compositional diversity within each unit. Compositional diversity within the SC unit (basalt to

  18. Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

    Science.gov (United States)

    Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

    2014-11-01

    In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

  19. Get rich blogging

    CERN Document Server

    Griffin, Zoe

    2013-01-01

    The Sunday Mirror's former showbiz gossip columnist, Zoe Griffin, explains how she quit her job and started a blog in order to work less and earn more. In this book she explains how to Get Rich Blogging and how she has done just that with her Live Like A VIP blog ? which generates a six figure income. There is no need to be a technical wizard. All you need is this book, a laptop and internet access and you too could be blogging your way to wealth and happiness. Contributors include The Clothes Whisperer, The Fashion Editor at Large, Mumsnet, Tech Week, Music News and Mr Porter ? all finan

  20. Production of inulinase, fructosyltransferase and sucrase from fungi on low-value inulin-rich substrates and their use in generation of fructose and fructo-oligosaccharides.

    Science.gov (United States)

    Rawat, Hemant Kumar; Ganaie, Mohd Anis; Kango, Naveen

    2015-03-01

    Owing to applications in the food and nutraceutical industries, inulinases, fructosyltransferases and sucrases have gained considerable attention in recent times. Twenty-five fungal strains were screened for production of these enzymes on three different media formulated using inulin-rich plant extracts prepared from asparagus root, dahlia tuber and dandelion root extract. Culture filtrates of the fungi were examined for hydrolytic activities. Fungi belonging to genus Aspergillus, A. niger GNCC 2655 (11.3 U/ml), A. awamori MTCC 2879 (8.2 U/ml), A. niger ATCC 26011 (7.9 U/ml) secreted high titers of inulinase followed by Penicillium sp. NFCCI 2768 (2.6 U/ml) and Penicillium citrinum MTCC 1256 (1.1 U/ml). High sucrase activity was noticed in A. niger GNCC 2613 (113 U/ml) and A. awamori MTCC 2879 (107.8 U/ml). Analysis of end products of inulinase action by HPLC revealed that most of the enzymes were exo-inulinases liberating fructose exclusively from inulin. Five fungi, P. citrinum MTCC 1256, Penicillium rugulosum MTCC 3487, Penicillium sp. NFCCI 2768, A. fumigatus GNCC 1351 and A. niger ATCC 26011 however, produced a mixture of endo- and exo-inulinases liberating oligosaccharides (GF3 and GF2) along with fructose. High inulinase/sucrase yielding strains were evaluated for extracellular and intracellular hydrolytic and transfructosylating activities and intracellular enzyme profiles were found to be considerably different in terms of titers and end products.

  1. Pebble heater suppresses synthesis of dioxins and furans in off-gas generated by incineration of halogen-rich fuel from WEEE

    Energy Technology Data Exchange (ETDEWEB)

    Schlummer, M.; Gruber, L.; Maeurer, A.; Wolz, G. [Fraunhofer Institute for Process Engineering and Packaging IVV, Freising (Germany); Fischer, W.; Quicker, P. [ATZ-EVUS, Development Center for Process Engineering, Sulzbach-Rosenberg (Germany)

    2004-09-15

    Changes in German and European legislation have led to altered approaches for the disposal of polymer-rich shredding residues (SR). Whereas disposal in landfills was the strategy of choice in the last decades, thermal treatment is supported now. However, when waste electric and electronic equipment (WEEE) is the source of SR, thermal treatment is complicated by a bromine and chlorine load in the lower percent range the presence of polybrominated dioxins and furans (PBDD/F) in the ppb range and by brominated flame retardants including polybrominated biphenyl ethers, which serve as dioxin precursors. Here we present data of a pilot application of the pebble heater technology for the treatment of raw gas derived from the incineration of polymeric materials from WEEE. Since the pilot experiments were performed on an existing pebble heater test plant in the small-technical scale, waste throughput and experimental design had to be adjusted to the given circumstances. As the study focussed on exhaust treatment and not on the incineration process itself, a liquid fuel was applied as a model for SR from WEEE. The incineration of a liquid fuel was preferred, since it could be implemented in the given test plant by spray injection, thus minimising technical modifications of the test plant and optimising the combustion efficiency compared to incineration of solid polymer granulates. Fuel and exhaust gases, which passed the pebble heater bed, were sampled and analysed for PCDD/F and PBDD/F. The pilot incineration was tested for the compliance with the PCDD/F emission limits given by European directive 2000/76/EC, and overall mass balances were calculated for PCDD/F and PBDD/F.

  2. 祁连山天然气水合物赋存区钻孔细菌多样性%Bacterial diversity in bore holes of gas hydrate-rich deposit districts in Qilian Mountains of Northwest China

    Institute of Scientific and Technical Information of China (English)

    武淑娇; 韩路; 吕杰; 董建英; 祝有海

    2012-01-01

    samples could metabolize organic hydrocarbon. Our results indicated that in the gas hydrate-rich deposit districts in permafrost zone, environmental factors limited the diversity of microbes.

  3. Simultaneous bioelectricity generation and decolorization of methyl orange in a two-chambered microbial fuel cell and bacterial diversity.

    Science.gov (United States)

    Guo, Wei; Feng, Jinglan; Song, Hong; Sun, Jianhui

    2014-10-01

    The objectives of this study were to investigate the simultaneous bioelectricity generation and decolorization of methyl orange (MO) in the anode chamber of microbial fuel cells (MFCs) in a wide concentration range (from 50 to 800 mg L(-1)) and to reveal the microbial communities on the anode after the MFC was operated continuously for more than 6 months using MO-glucose mixtures as fuel. Interestingly, the added MO played an active role in the production of electricity. The maximum voltage outputs were 565, 658, 640, 629, 617, and 605 mV for the 1 g L(-1) glucose with 0, 50, 100, 200, 300, and 500 mg L(-1) of MO, respectively. The results of three groups of comparison experiments showed that accelerated decolorization of methyl orange (MO) was achieved in the MFC as compared to MFC in open circuit mode and MFC without extra carbon sources. The decolorization efficiency decreased with an increase of MO concentration in the studied concentration range for the dye load increased. A 454 high-throughput pyrosequencing revealed the microbial communities. Geobacter genus known to generate electricity was detected. Bacteroidia class, Desulfovibrio, and Trichococcus genus, which were most likely responsible for degrading methyl orange, were also detected.

  4. 东莞市“富二代”青少年问题行为调查%Survey of"second rich generation"adolescent problem behaviors of Dongguan city

    Institute of Scientific and Technical Information of China (English)

    曾家勇; 许志平

    2013-01-01

      The impact of adolescent problem behaviors receives the social concern in recent years. The purpose of this study is to explore the basic situation and influence factors of adolescent problem behavior in Dongguan city,, select the"noble"high school of junior and senior middle school students of 316 adolescents of 11-15 years old in Dongguan City (including"two rich generation"in 222 adolescents) as subjects, using the"adolescent behavior questionnaire","evaluation of Parents Parenting Style Scale"and self-designed questionnaire survey, results show that:(1) the difference of the total level of Dongguan city"second rich generation"adolescent problem behavior and ordinary adolescent problem behaviors is not significant. (2) difference of different gender, different grades of"second rich generation"youth in the overall level of problem behavior is significant. (3)"second rich generation"adolescent problem behaviors in the overall level of parenting style and strong correlation, stepwise regression analysis show that, father's emotional warmth and understanding, excessive interference and protection of mother, mother refusing to behavior problems have strong predictive power.%  “富二代”青少年问题行为带来的影响近年来备受社会关注。本研究旨在探究东莞市“富二代”青少年问题行为的基本情况及影响因素,选取了东莞市11-15岁“贵族中学”初高中生共316名青少年(其中“富二代”青少年222名)作被试,采用《青少年行为问卷》,《父母教养方式评价量表》及自制基本情况调查问卷施测,结果表明:(1)东莞市“富二代”青少年问题行为总体水平与普通青少年问题行为总体水平差异不显著。(2)不同性别、不同学业成绩的“富二代”青少年在问题行为总体水平上差异显著。(3)“富二代”青少年问题行为总体水平与父母亲教养方式有较强相关,采用逐步回归分析表明,父亲

  5. Intrinsic Origins of Crack Generation in Ni-rich LiNi0.8Co0.1Mn0.1O2 Layered Oxide Cathode Material

    Science.gov (United States)

    Lim, Jin-Myoung; Hwang, Taesoon; Kim, Duho; Park, Min-Sik; Cho, Kyeongjae; Cho, Maenghyo

    2017-01-01

    Ni-rich LiNi0.8Co0.1Mn0.1O2 layered oxide cathodes have been highlighted for large-scale energy applications due to their high energy density. Although its specific capacity is enhanced at higher voltages as Ni ratio increases, its structural degradation due to phase transformations and lattice distortions during cycling becomes severe. For these reasons, we focused on the origins of crack generation from phase transformations and structural distortions in Ni-rich LiNi0.8Co0.1Mn0.1O2 using multiscale approaches, from first-principles to meso-scale phase-field model. Atomic-scale structure analysis demonstrated that opposite changes in the lattice parameters are observed until the inverse Li content x = 0.75 then, structure collapses due to complete extraction of Li from between transition metal layers. Combined-phase investigations represent the highest phase barrier and steepest chemical potential after x = 0.75, leading to phase transformations to highly Li-deficient phases with an inactive character. Abrupt phase transformations with heterogeneous structural collapse after x = 0.81 (~220 mAh g‑1) were identified in the nanodomain. Further, meso-scale strain distributions show around 5% of anisotropic contraction with lower critical energy release rates, which cause not only micro-crack generations of secondary particles on the interfaces between the contracted primary particles, but also mechanical instability of primary particles from heterogeneous strain changes.

  6. Use of respondent driven sampling (RDS generates a very diverse sample of men who have sex with men (MSM in Buenos Aires, Argentina.

    Directory of Open Access Journals (Sweden)

    Alex Carballo-Diéguez

    Full Text Available BACKGROUND: Prior research focusing on men who have sex with men (MSM conducted in Buenos Aires, Argentina, used convenience samples that included mainly gay identified men. To increase MSM sample representativeness, we used Respondent Driven Sampling (RDS for the first time in Argentina. Using RDS, under certain specified conditions, the observed estimates for the percentage of the population with a specific trait are asymptotically unbiased. We describe, the diversity of the recruited sample, from the point of view of sexual orientation, and contrast the different subgroups in terms of their HIV sexual risk behavior. METHODOLOGY: 500 MSM were recruited using RDS. Behavioral data were collected through face-to-face interviews and Web-based CASI. CONCLUSION: In contrast with prior studies, RDS generated a very diverse sample of MSM from a sexual identity perspective. Only 24.5% of participants identified as gay; 36.2% identified as bisexual, 21.9% as heterosexual, and 17.4% were grouped as "other." Gay and non-gay identified MSM differed significantly in their sexual behavior, the former having higher numbers of partners, more frequent sexual contacts and less frequency of condom use. One third of the men (gay, 3%; bisexual, 34%, heterosexual, 51%; other, 49% reported having had sex with men, women and transvestites in the two months prior to the interview. This population requires further study and, potentially, HIV prevention strategies tailored to such diversity of partnerships. Our results highlight the potential effectiveness of using RDS to reach non-gay identified MSM. They also present lessons learned in the implementation of RDS to recruit MSM concerning both the importance and limitations of formative work, the need to tailor incentives to circumstances of the less affluent potential participants, the need to prevent masking, and the challenge of assessing network size.

  7. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

    Science.gov (United States)

    Medvedovic, Jasna; Ebert, Anja; Tagoh, Hiromi; Tamir, Ido M; Schwickert, Tanja A; Novatchkova, Maria; Sun, Qiong; Huis In 't Veld, Pim J; Guo, Chunguang; Yoon, Hye Suk; Denizot, Yves; Holwerda, Sjoerd J B; de Laat, Wouter; Cogné, Michel; Shi, Yang; Alt, Frederick W; Busslinger, Meinrad

    2013-08-22

    The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH-rearranged gene segment in the 3' proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro-B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator, or 3' regulatory region in the proximal Igh domain.

  8. Reactions between olivine and CO2-rich seawater at 300 °C: Implications for H2 generation and CO2 sequestration on the early Earth

    Directory of Open Access Journals (Sweden)

    Hisahiro Ueda

    2017-03-01

    Full Text Available To understand the influence of fluid CO2 on ultramafic rock-hosted seafloor hydrothermal systems on the early Earth, we monitored the reaction between San Carlos olivine and a CO2-rich NaCl fluid at 300 °C and 500 bars. During the experiments, the total carbonic acid concentration (ΣCO2 in the fluid decreased from approximately 65 to 9 mmol/kg. Carbonate minerals, magnesite, and subordinate amount of dolomite were formed via the water-rock interaction. The H2 concentration in the fluid reached approximately 39 mmol/kg within 2736 h, which is relatively lower than the concentration generated by the reaction between olivine and a CO2-free NaCl solution at the same temperature. As seen in previous hydrothermal experiments using komatiite, ferrous iron incorporation into Mg-bearing carbonate minerals likely limited iron oxidation in the fluids and the resulting H2 generation during the olivine alteration. Considering carbonate mineralogy over the temperature range of natural hydrothermal fields, H2 generation is likely suppressed at temperatures below approximately 300 °C due to the formation of the Mg-bearing carbonates. Nevertheless, H2 concentration in fluid at 300 °C could be still high due to the temperature dependency of magnetite stability in ultramafic systems. Moreover, the Mg-bearing carbonates may play a key role in the ocean-atmosphere system on the early Earth. Recent studies suggest that the subduction of carbonated ultramafic rocks may transport surface CO2 species into the deep mantle. This process may have reduced the huge initial amount of CO2 on the surface of the early Earth. Our approximate calculations demonstrate that the subduction of the Mg-bearing carbonates formed in komatiite likely played a crucial role as one of the CO2 carriers from the surface to the deep mantle, even in hot subduction zones.

  9. Bird functional diversity decreases with time since disturbance: Does patchy prescribed fire enhance ecosystem function?.

    Science.gov (United States)

    Sitters, Holly; Di Stefano, Julian; Christie, Fiona; Swan, Matthew; York, Alan

    2016-01-01

    Animal species diversity is often associated with time since disturbance, but the effects of disturbances such as fire on functional diversity are unknown. Functional diversity measures the range, abundance, and distribution of trait values in a community, and links changes in species composition with the consequences for ecosystem function. Improved understanding of the relationship between time since fire (TSF) and functional diversity is critical given that the frequency of both prescribed fire and wildfire is expected to increase. To address this knowledge gap, we examined responses of avian functional diversity to TSF and two direct measures of environmental heterogeneity, plant diversity, and structural heterogeneity. We surveyed birds across a 70-year chronosequence spanning four vegetation types in southeast Australia. Six bird functional traits were used to derive four functional diversity indices (richness, evenness, divergence, and dispersion) and the effects of TSF, plant diversity and structural heterogeneity on species richness and the functional diversity indices were examined using mixed models. We used a regression tree method to identify traits associated with species more common in young vegetation. Functional richness and dispersion were negatively associated with TSF in all vegetation types, suggesting that recent prescribed fire generates heterogeneous vegetation and provides greater opportunities for resource partitioning. Species richness was not significantly associated with TSF, and is probably an unreliable surrogate for functional diversity in fire-prone systems. A positive, relationship between functional evenness and structural heterogeneity was comnon to all vegetation types, suggesting that fine-scale (tens of meters) structural variation can enhance ecosystem function. Species more common in young vegetation were primarily linked by their specialist diets, indicating that ecosystem services such as seed dispersal and insect control

  10. Planejando estudos de diversidade e riqueza: uma abordagem para estudantes de graduação - DOI: 10.4025/actascibiolsci.v26i4.1511 Designing diversity and richness studies: an approach to undergraduate students - DOI: 10.4025/actascibiolsci.v26i4.1511

    Directory of Open Access Journals (Sweden)

    Sidclay Calaça Dias

    2004-04-01

    Full Text Available Neste trabalho são apresentados breves aspectos teóricos e práticos relativos ao estudo da diversidade e da riqueza de espécies destinadas aos estudantes de graduação. Questões relativas ao delineamento da pesquisa, à coleta e as análises dos dados são apresentadas e discutidas, brevemente, além de modelos de distribuição de abundância, índices de diversidade e estimadores de riqueza acompanhados de referências da literatura sobre o tema. Objetiva-se mostrar aos alunos, os reveses relativos ao uso inadequado de análises sobre os componentes da diversidade de espécies, aplicados a um conjunto de dadosAspects of theory and practice related to studies on species richness and diversity measurement are presented to Biology Sciences undergraduate students. Questions concerning the designing of the research, data collecting and analysis are presented. Models of relative abundance distribution, diversity indices and estimators of species richness are briefly discussed, followed by bibliographic references on the theme. Pitfalls related to the inadequate analysis of diversity of species components, applied to the data, are showed to the students

  11. Multiscale perspectives of species richness in East Africa

    NARCIS (Netherlands)

    Said, M.

    2003-01-01

    This dissertation describes and analyses animal species richness in East Africa from a multi-scale perspective. We studied diversity patterns at sub-continental, national and sub-national level. The study demonstrated that species diversity patterns were scale-dependent. Diversity patterns varied wi

  12. The effects of copper pollution on fouling assemblage diversity: a tropical-temperate comparison.

    Directory of Open Access Journals (Sweden)

    João Canning-Clode

    Full Text Available BACKGROUND: The invasion of habitats by non-indigenous species (NIS occurs at a global scale and can generate significant ecological, evolutionary, economic and social consequences. Estuarine and coastal ecosystems are particularly vulnerable to pollution from numerous sources due to years of human-induced degradation and shipping. Pollution is considered as a class of disturbance with anthropogenic roots and recent studies have concluded that high frequencies of disturbance may facilitate invasions by increasing the availability of resources. METHODOLOGY/PRINCIPAL FINDINGS: To examine the effects of heavy metal pollution as disturbance in shaping patterns of exotic versus native diversity in marine fouling communities we exposed fouling communities to different concentrations of copper in one temperate (Virginia and one tropical (Panama region. Diversity was categorized as total, native and non-indigenous and we also incorporated taxonomic and functional richness. Our findings indicate that total fouling diversity decreased with increasing copper pollution, whether taxonomic or functional diversity is considered. Both native and non-indigenous richness decreased with increasing copper concentrations at the tropical site whereas at the temperate site, non-indigenous richness was too low to detect any effect. CONCLUSIONS/SIGNIFICANCE: Non-indigenous richness decreased with increasing metal concentrations, contradicting previous investigations that evaluate the influence of heavy metal pollution on diversity and invasibility of fouling assemblages. These results provide first insights on how the invasive species pool in a certain region may play a key role in the disturbance vs. non-indigenous diversity relationship.

  13. The CAPRICE RICH detector

    Energy Technology Data Exchange (ETDEWEB)

    Basini, G. [INFN, Laboratori Nazionali di Frascati, Rome (Italy); Codino, A.; Grimani, C. [Perugia Univ. (Italy)]|[INFN, Perugia (Italy); De Pascale, M.P. [Rome Univ. `Tor Vergata` (Italy). Dip. di Fisica]|[INFN, Sezione Univ. `Tor Vergata` Rome (Italy); Cafagna, F. [Bari Univ. (Italy)]|[INFN, Bari (Italy); Golden, R.L. [New Mexico State Univ., Las Cruces, NM (United States). Particle Astrophysics Lab.; Brancaccio, F.; Bocciolini, M. [Florence Univ. (Italy)]|[INFN, Florence (Italy); Barbiellini, G.; Boezio, M. [Trieste Univ. (Italy)]|[INFN, Trieste (Italy)

    1995-09-01

    A compact RICH detector has been developed and used for particle identification in a balloon borne spectrometer to measure the flux of antimatter in the cosmic radiation. This is the first RICH detector ever used in space experiments that is capable of detecting unit charged particles, such as antiprotons. The RICH and all other detectors performed well during the 27 hours long flight.

  14. Evaluation of nickel-rich alloys for the electrolytic generation of hydrogen in an alkaline medium; Evaluacion de aleaciones ricas en niquel para la generacion electrolitica de hidrogeno en medio alcalino

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz Verdin, A.A.; Ortega Borges, R.; Trejo Cordova, G.; Meas Vong, Y. [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Pedro Escobedo, Queretaro (Mexico)]. E-mail: aortiz@cideteq.mx

    2009-09-15

    The simultaneous electrodeposition of Ni with metals such as Zn to form alloys enables obtaining surfaces with high electrocatalytic activity or particular characteristics that resist wear and abrasion. This work presents the results of the study of the electrochemical characterization of different types of nickel electrodeposition and compositions, used as cathodes, and measurements of the electrocatalytic activity in the release of hydrogen in an alkaline medium. Curves I through IV were generated, which were potentiostatically obtained in a nitrogen atmosphere in a NaOH alkaline solution. The morphology of the deposits was evaluated with sweep electron micrscopy(SEM). The results enabled evaluating its potential application as electrode materials for the generation of electrolytic hydrogen in alkaline medium, given the good electrocatalytic activity of nickel-rich materials. [Spanish] El electrodeposito simultaneo del Ni, con metales como el Zn para formar aleaciones, permite obtener superficies con elevada actividad electrocatalitica o con caracteristicas particulares de resistencia al desgaste y abrasion. En este trabajo se presentan los resultados del estudio de la caracterizacion electroquimica de los electrodepositos a base de niquel de diferente naturaleza y composicion utilizandolos como catodos midiendo la actividad electrocatalitica con respecto a la reaccion de desprendimiento de hidrogeno (RDH) en medio alcalino. Se realizaron curvas I vs V obtenidas potenciostaticamente bajo atmosfera de nitrogeno en una solucion alcalina de NaOH. La morfologia de los depositos se evaluo mediante SEM (microscopio electronico de barrido). Los resultados permiten evaluar su potencial aplicacion como materiales de electrodo para la generacion electrolitica de hidrogeno en medio alcalino, dada la buena actividad electrocatalitica de los materiales ricos en niquel.

  15. Urban thermal diversity

    Institute of Scientific and Technical Information of China (English)

    KoenSTEEMERS; MarylisRAMOS; MariaSINOU

    2003-01-01

    This paper introduces the interrelationships between urban form, microclimate and thermal comfort. It draws on recent research of monitoring, surveying and modelling urban thermal characteristics and proposes a method of mapping urban diversity. Because the urban context provides a rich and varied environment that influences the way we use urban spaces (movement, sequence, activity) and how we feel in them (stimulation, thermal comfort), the aim here is to highlight the notion of diversity. Thus thermal diversity is used as a measure of the urban environment, rather than more conventional spatially or temporally fixed average values.

  16. The SELEX Phototube RICH Detector

    CERN Document Server

    Engelfried, J; Kilmer, J; Kozhevnikov, A P; Kubarovskii, V P; Molchanov, V V; Nemitkin, A V; Ramberg, E; Rud, V I; Stutte, L

    1999-01-01

    In this article, construction, operation, and performance of the RICH detector of Fermilab experiment 781 (SELEX) are described. The detector utilizes a matrix of 2848 phototubes for the photocathode to detect Cherenkov photons generated in a 10m Neon radiator. For the central region an N0 of 104/cm, corresponding to 13.6 hits on a beta=1 ring, was obtained. The ring radius resolution measured is 1.6%.

  17. The SELEX phototube RICH detector

    Energy Technology Data Exchange (ETDEWEB)

    Engelfried, J.; Filimonov, I.; Kilmer, J.; Kozhevnikov, A.; Kubarovsky, V.; Molchanov, V.; Nemitkin, A.; Ramberg, E.; Rud, V.; Stutte, L

    1999-07-11

    In this article, construction, operation, and performance of the RICH detector of Fermilab experiment 781 (SELEX) are described. The detector utilizes a matrix of 2848 phototubes for the photocathode to detect Cherenkov photons generated in a 10 m neon radiator. For the central region an N{sub 0} of 104 cm{sup -1}, corresponding to 13.6 hits on a {beta}=1 ring, was obtained. The ring radius resolution measured is 1.6%. (author)

  18. The SELEX phototube RICH detector

    Science.gov (United States)

    Engelfried, J.; Filimonov, I.; Kilmer, J.; Kozhevnikov, A.; Kubarovsky, V.; Molchanov, V.; Nemitkin, A.; Ramberg, E.; Rud, V.; Stutte, L.

    1999-07-01

    In this article, construction, operation, and performance of the RICH detector of Fermilab experiment 781 (SELEX) are described. The detector utilizes a matrix of 2848 phototubes for the photocathode to detect Cherenkov photons generated in a 10 m neon radiator. For the central region an N0 of 104 cm-1, corresponding to 13.6 hits on a β=1 ring, was obtained. The ring radius resolution measured is 1.6%.

  19. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS).

    Science.gov (United States)

    Barbosa, Amanda D; Gofton, Alexander W; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%), T. gilletti (25%, 95% CI: 18.7-32.3%), T. copemani (27.4%, 95% CI: 20.8-34.8%) and T. vegrandis (10.1%, 95% CI: 6.0-15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21-35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the

  20. Development of lichen-rich communities

    NARCIS (Netherlands)

    Ketner-Oostra, R.; Sparrius, L.B.; Sýkora, K.V.; Fanta, J.; Siepel, H.

    2010-01-01

    The pioneer vegetation of inland dunes is known for its lichen diversity. The development of lichen-rich vegetation may take several decades after the first pioneer stage with Corynephorus canescens and Polytrichum piliferum. The neophytic moss Campylopus introflexus and atmospheric nitrogen deposit

  1. Evaluation of selected static methods used to estimate element mobility, acid-generating and acid-neutralizing potentials associated with geologically diverse mining wastes

    Science.gov (United States)

    Hageman, Philip L.; Seal, Robert R.; Diehl, Sharon F.; Piatak, Nadine M.; Lowers, Heather

    2015-01-01

    A comparison study of selected static leaching and acid–base accounting (ABA) methods using a mineralogically diverse set of 12 modern-style, metal mine waste samples was undertaken to understand the relative performance of the various tests. To complement this study, in-depth mineralogical studies were conducted in order to elucidate the relationships between sample mineralogy, weathering features, and leachate and ABA characteristics. In part one of the study, splits of the samples were leached using six commonly used leaching tests including paste pH, the U.S. Geological Survey (USGS) Field Leach Test (FLT) (both 5-min and 18-h agitation), the U.S. Environmental Protection Agency (USEPA) Method 1312 SPLP (both leachate pH 4.2 and leachate pH 5.0), and the USEPA Method 1311 TCLP (leachate pH 4.9). Leachate geochemical trends were compared in order to assess differences, if any, produced by the various leaching procedures. Results showed that the FLT (5-min agitation) was just as effective as the 18-h leaching tests in revealing the leachate geochemical characteristics of the samples. Leaching results also showed that the TCLP leaching test produces inconsistent results when compared to results produced from the other leaching tests. In part two of the study, the ABA was determined on splits of the samples using both well-established traditional static testing methods and a relatively quick, simplified net acid–base accounting (NABA) procedure. Results showed that the traditional methods, while time consuming, provide the most in-depth data on both the acid generating, and acid neutralizing tendencies of the samples. However, the simplified NABA method provided a relatively fast, effective estimation of the net acid–base account of the samples. Overall, this study showed that while most of the well-established methods are useful and effective, the use of a simplified leaching test and the NABA acid–base accounting method provide investigators fast

  2. The effects of forest destruction on the abundance, species richness ...

    African Journals Online (AJOL)

    SARAH

    2013-04-25

    Apr 25, 2013 ... species richness and diversity of butterflies in the. Bosomkese Forest Reserve ... reducing global warming (Myers, et al., 2000). According to Swanes et al. ..... negatively affected the butterfly species. Five butterfly families ...

  3. Changes in bird functional diversity across multiple land uses: interpretations of functional redundancy depend on functional group identity.

    Science.gov (United States)

    Luck, Gary W; Carter, Andrew; Smallbone, Lisa

    2013-01-01

    Examinations of the impact of land-use change on functional diversity link changes in ecological community structure driven by land modification with the consequences for ecosystem function. Yet, most studies have been small-scale, experimental analyses and primarily focussed on plants. There is a lack of research on fauna communities and at large-scales across multiple land uses. We assessed changes in the functional diversity of bird communities across 24 land uses aligned along an intensification gradient. We tested the hypothesis that functional diversity is higher in less intensively used landscapes, documented changes in diversity using four diversity metrics, and examined how functional diversity varied with species richness to identify levels of functional redundancy. Functional diversity, measured using a dendogram-based metric, increased from high to low intensity land uses, but observed values did not differ significantly from randomly-generated expected values. Values for functional evenness and functional divergence did not vary consistently with land-use intensification, although higher than expected values were mostly recorded in high intensity land uses. A total of 16 land uses had lower than expected values for functional dispersion and these were mostly low intensity native vegetation sites. Relations between functional diversity and bird species richness yielded strikingly different patterns for the entire bird community vs. particular functional groups. For all birds and insectivores, functional evenness, divergence and dispersion showed a linear decline with increasing species richness suggesting substantial functional redundancy across communities. However, for nectarivores, frugivores and carnivores, there was a significant hump-shaped or non-significant positive linear relationship between these functional measures and species richness indicating less redundancy. Hump-shaped relationships signify that the most functionally diverse

  4. Assessing nutritional diversity of cropping systems in African villages.

    Directory of Open Access Journals (Sweden)

    Roseline Remans

    Full Text Available BACKGROUND: In Sub-Saharan Africa, 40% of children under five years in age are chronically undernourished. As new investments and attention galvanize action on African agriculture to reduce hunger, there is an urgent need for metrics that monitor agricultural progress beyond calories produced per capita and address nutritional diversity essential for human health. In this study we demonstrate how an ecological tool, functional diversity (FD, has potential to address this need and provide new insights on nutritional diversity of cropping systems in rural Africa. METHODS AND FINDINGS: Data on edible plant species diversity, food security and diet diversity were collected for 170 farms in three rural settings in Sub-Saharan Africa. Nutritional FD metrics were calculated based on farm species composition and species nutritional composition. Iron and vitamin A deficiency were determined from blood samples of 90 adult women. Nutritional FD metrics summarized the diversity of nutrients provided by the farm and showed variability between farms and villages. Regression of nutritional FD against species richness and expected FD enabled identification of key species that add nutrient diversity to the system and assessed the degree of redundancy for nutrient traits. Nutritional FD analysis demonstrated that depending on the original composition of species on farm or village, adding or removing individual species can have radically different outcomes for nutritional diversity. While correlations between nutritional FD, food and nutrition indicators were not significant at household level, associations between these variables were observed at village level. CONCLUSION: This study provides novel metrics to address nutritional diversity in farming systems and examples of how these metrics can help guide agricultural interventions towards adequate nutrient diversity. New hypotheses on the link between agro-diversity, food security and human nutrition are

  5. Wüstite stability in the presence of a CO2-fluid and a carbonate-silicate melt: Implications for the graphite/diamond formation and generation of Fe-rich mantle metasomatic agents

    Science.gov (United States)

    Bataleva, Yuliya V.; Palyanov, Yuri N.; Sokol, Alexander G.; Borzdov, Yuri M.; Bayukov, Oleg A.

    2016-02-01

    Experimental simulation of the interaction of wüstite with a CO2-rich fluid and a carbonate-silicate melt was performed using a multianvil high-pressure split-sphere apparatus in the FeO-MgO-CaO-SiO2-Al2O3-CO2 system at a pressure of 6.3 GPa and temperatures in the range of 1150 °C-1650 °C and with run time of 20 h. At relatively low temperatures, decarbonation reactions occur in the system to form iron-rich garnet (Alm75Prp17Grs8), magnesiowüstite (Mg# ≤ 0.13), and CO2-rich fluid. Under these conditions, magnesiowüstite was found to be capable of partial reducing CO2 to C0 that leads to the formation of Fe3+-bearing magnesiowüstite, crystallization of magnetite and metastable graphite, and initial growth of diamond seeds. At T ≥ 1450 °C, an iron-rich carbonate-silicate melt (FeO ~ 56 wt.%, SiO2 ~ 12 wt.%) forms in the system. Interaction between (Fe,Mg)O, SiO2, fluid and melt leads to oxidation of magnesiowüstite and crystallization of fayalite-magnetite spinel solid solution (1450 °C) as well as to complete dissolution of magnesiowüstite in the carbonate-silicate melt (1550 °C-1650 °C). In the presence of both carbonate-silicate melt and CO2-rich fluid, dissolution (oxidation) of diamond and metastable graphite was found to occur. The study results demonstrate that under pressures of the lithospheric mantle in the presence of a CO2-rich fluid, wüstite/magnesiowüstite is stable only at relatively low temperatures when it is in the absolute excess relative to CO2-rich fluid. In this case, the redox reactions, which produce metastable graphite and diamond with concomitant partial oxidation of wüstite to magnetite, occur. Wüstite is unstable under high concentrations of a CO2-rich fluid as well as in the presence of a carbonate-silicate melt: it is either completely oxidized or dissolves in the melt or fluid phase, leading to the formation of Fe2 +- and Fe3 +-enriched carbonate-silicate melts, which are potential metasomatic agents in the

  6. Design Diversity

    DEFF Research Database (Denmark)

    Dankl, Kathrina

    2014-01-01

    The publication 'Design Diversity', an exhibition catalogue, focuses on aging and design – a product culture in transformation that aims to help change conventional notions of the later years of life. Age is positioned as a generational issue that has the same relevance for all age groups...... courageous projects for "best agers" and "golden agers" never get beyond the prototype stage, products that paint a more "beige" picture of everyday life can be found in large numbers. This fact raises some key questions: Does the existing product culture reflect today's views on old age? Do contemporary...... awareness of the fact that material culture shapes our view of aging, and therefore is also capable of changing it....

  7. Relative role of contemporary environment versus history in shaping diversity patterns of China's woody plants

    DEFF Research Database (Denmark)

    Wang, Zhiheng; Fang, Jingyun; Tang, Zhiyao

    2012-01-01

    What determines large-scale patterns of species diversity is a central and controversial topic in biogeography and ecology. In this study, we compared the effects of contemporary environment and historical contingencies on species richness patterns of woody plants in China, using fine-resolution ......-plant species richness across China, while historical contingencies generate regional deviations from this trend. Our findings imply that both species diversity and regional evolutionary and ecological histories should be taken into account for future nature conservation.......What determines large-scale patterns of species diversity is a central and controversial topic in biogeography and ecology. In this study, we compared the effects of contemporary environment and historical contingencies on species richness patterns of woody plants in China, using fine...... regions combined. This suggests different richness-environment relationships among regions. These results indicate important historical signals in the species richness patterns of woody plants across China. The signals are especially pronounced in the eastern Himalayas, the Mongolian Plateau...

  8. Áreas prioritarias para colectar germoplasma de Amaranthus en México con base en la diversidad y riqueza de especies Priority areas to collect Amaranthus germplasm in Mexico based on diversity and species richness

    Directory of Open Access Journals (Sweden)

    Eduardo Espitia Rangel

    Full Text Available Esta investigación tuvo como objetivo utilizar el Sistema de Información Geográfico, para crear mapas de índices de diversidad y riqueza de especies del género Amaranthus en México, para proyectar las mejores áreas de colecta de germoplasma. La máxima riqueza de especies se encontró en el centro occidente del Estado de México incluyendo el Distrito Federal y la costa del Pacífico, entre Jalisco y Colima, así como en Sinaloa. El índice de biodiversidad de Brillouin mostró alta diversidad en la costa del Pacífico, Sinaloa, entre los estados de Jalisco y Colima, además el centro occidente de Nuevo León, la región de la Huasteca del sureste de Tamaulipas y noreste de Veracruz, así como la zona noroeste de la Península de Yucatán. Las áreas prioritarias que se proponen son: la costa central de Sinaloa, sur de la región biogeográfica de Sonora, parte centro occidente del Estado de México incluyendo el Distrito Federal, región biogeográfica del Eje Volcánico Transmexicano y la costa del pacífico centro entre los estados de Jalisco y Colima, finalmente en la región biogeográfica de la costa pacífica mexicana.This investigation had as objective to use the Geographical Information System, to create maps of indexes of diversity and wealth of species of genus Amaranthus in Mexico, to plan the best areas of germplasm collection. The maximum wealth of species was in west center of State of Mexico including Distrito Federal and the Pacific coast, between Jalisco and Colima, as well as in Sinaloa. The Brillouin index of biodiversity showed high diversity in the Pacific coast, Sinaloa, between the states of Jalisco and Colima, also the west center of Nuevo León, the region of Huasteca of southeast of Tamaulipas and northeast of Veracruz, as well as the northwest area of Yucatán Peninsula. The priority areas proposed are: the central coast of Sinaloa, south of biogeographic region of Sonora, west center section of State of Mexico

  9. Microbial community diversity of organically rich cassava sago factory waste waters and their ability to use nitrate and N2O added as external N-sources for enhancing biomethanation and the purification efficiency.

    Science.gov (United States)

    Rajendran, Ranjiitkumar; Soora, Maya; Dananjeyan, Balachandar; Ratering, Stefan; Krishnamurthy, Kumar; Benckiser, Gero

    2012-12-15

    Water shortage necessitated South Indian sago factory owners, extracting starch out of cassava tubers, to install biogas plants where a starch utilizing microbial community multiplies and reduces the biological oxygen demand (BOD) of the waste waters by presently about 30%. The purification efficiency of sago factory waste waters, rich in solid particles and having wide C/N ratios, around 250, through unstirred biogas plants needs to be improved. Our approach was to apply instead of animal slurry nitrate (NO3(-)) and nitrous oxide (N2O) as external N-sources anticipating a better N-distribution in the unstirred biogas plants. Estimated cell numbers, bacterial community changes, on the basis of 16S rRNA gene clone libraries and changing CO2-, CH4-, N2O releases due to the presence of nitrate or N2O suggest that acid tolerant Lactobacillus spp. dominate the biogas plant inflows (pH 3.5). They were very less or not found in the outflows (pH 7.3). Assumingly, the phyla Bacteroidetes (Prevotella spp.), Proteobacteria (Rhizobium spp., Defluvibacter sp.), Firmicutes (Megasphaera spp., Dialister spp., Clostridium spp.) and Synergistetes (Thermanaerovibrio spp.), not-detectable in the biogas plant inflows, replaced them. Anaerobes, about 400cellsml(-1) in the inflows, increased to about 10(6)cellsml(-1) in the outflows. The methane formation, as confirmed by the incubation experiments, suggests that methanogens must have been present among the anaerobes. In the biogas plant in- and outflows also about 300cellsml(-1) denitrifying bacteria and up to 10(4)cfu fungi were found. Despite the low number of denitrifying bacteria nitrate added to the biogas plant in- and outflows was widely consumed and added N2O decreased considerably. Thus, wide C/N ratios substrates like sago factory waste waters keep the N2O emissions low by using N2O either as electron acceptor or by incorporating it into the growing biomass what needs to be confirmed. The biogas plant inflow samples have

  10. Lithium-Rich Giants in Globular Clusters

    CERN Document Server

    Kirby, Evan N; Zhang, Andrew J; Hong, Jerry; Guo, Michelle; Guo, Rachel; Cohen, Judith G; Cunha, Katia

    2016-01-01

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron-Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 +/- 0.1)% for the RGB, (1.6 +/- 1.1)% for the AGB, and (0.3 +/- 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propo...

  11. Strategies for designing and monitoring malaria vaccines targeting diverse antigens

    Directory of Open Access Journals (Sweden)

    Alyssa E Barry

    2014-07-01

    Full Text Available After more than 50 years of intensive research and development, only one malaria vaccine candidate, RTS,S, has progressed to Phase 3 clinical trials. Despite only partial efficacy, this candidate is now forecast to become the first licensed malaria vaccine. Hence, more efficacious second-generation malaria vaccines that can significantly reduce transmission are urgently needed. This review will focus on a major obstacle hindering development of effective malaria vaccines: parasite antigenic diversity. Despite extensive genetic diversity in leading candidate antigens, vaccines have been and continue to be formulated using recombinant antigens representing only one or two strains. These vaccine strains represent only a small fraction of the diversity circulating in natural parasite populations, leading to escape of non-vaccine strains and challenging investigators’ abilities to measure strain-specific efficacy in vaccine trials. Novel strategies are needed to overcome antigenic diversity in order for vaccine development to succeed. Many studies have now catalogued the global diversity of leading Plasmodium falciparum and Plasmodium vivax vaccine antigens. In this review, we describe how population genetic approaches can be applied to this rich data source to predict the alleles that best represent antigenic diversity, polymorphisms that contribute to it, and to identify key polymorphisms associated with antigenic escape. We also suggest an approach to summarise the known global diversity of a given antigen to predict antigenic diversity, how to select variants that best represent the strains circulating in natural parasite populations and how to investigate the strain-specific efficacy of vaccine trials. Use of these strategies in the design and monitoring of vaccine trials will not only shed light on the contribution of genetic diversity to the antigenic diversity of malaria, but will also maximise the potential of future malaria vaccine

  12. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index...... successfully colonized these archipelagos. Areas with unusually high phylogenetic diversity were located around biogeographic contact zones in Central America and southern China, and seem to have experienced high immigration or in situ diversification rates, combined with local persistence of old lineages...

  13. Unimodal latitudinal pattern of land-snail species richness across northern Eurasian lowlands.

    Science.gov (United States)

    Horsák, Michal; Chytrý, Milan

    2014-01-01

    Large-scale patterns of species richness and their causes are still poorly understood for most terrestrial invertebrates, although invertebrates can add important insights into the mechanisms that generate regional and global biodiversity patterns. Here we explore the general plausibility of the climate-based "water-energy dynamics" hypothesis using the latitudinal pattern of land-snail species richness across extensive topographically homogeneous lowlands of northern Eurasia. We established a 1480-km long latitudinal transect across the Western Siberian Plain (Russia) from the Russia-Kazakhstan border (54.5°N) to the Arctic Ocean (67.5°N), crossing eight latitudinal vegetation zones: steppe, forest-steppe, subtaiga, southern, middle and northern taiga, forest-tundra, and tundra. We sampled snails in forests and open habitats each half-degree of latitude and used generalized linear models to relate snail species richness to climatic variables and soil calcium content measured in situ. Contrary to the classical prediction of latitudinal biodiversity decrease, we found a striking unimodal pattern of snail species richness peaking in the subtaiga and southern-taiga zones between 57 and 59°N. The main south-to-north interchange of the two principal diversity constraints, i.e. drought stress vs. cold stress, explained most of the variance in the latitudinal diversity pattern. Water balance, calculated as annual precipitation minus potential evapotranspiration, was a single variable that could explain 81.7% of the variance in species richness. Our data suggest that the "water-energy dynamics" hypothesis can apply not only at the global scale but also at subcontinental scales of higher latitudes, as water availability was found to be the primary limiting factor also in this extratropical region with summer-warm and dry climate. A narrow zone with a sharp south-to-north switch in the two main diversity constraints seems to constitute the dominant and general pattern of

  14. Unimodal latitudinal pattern of land-snail species richness across northern Eurasian lowlands.

    Directory of Open Access Journals (Sweden)

    Michal Horsák

    Full Text Available Large-scale patterns of species richness and their causes are still poorly understood for most terrestrial invertebrates, although invertebrates can add important insights into the mechanisms that generate regional and global biodiversity patterns. Here we explore the general plausibility of the climate-based "water-energy dynamics" hypothesis using the latitudinal pattern of land-snail species richness across extensive topographically homogeneous lowlands of northern Eurasia. We established a 1480-km long latitudinal transect across the Western Siberian Plain (Russia from the Russia-Kazakhstan border (54.5°N to the Arctic Ocean (67.5°N, crossing eight latitudinal vegetation zones: steppe, forest-steppe, subtaiga, southern, middle and northern taiga, forest-tundra, and tundra. We sampled snails in forests and open habitats each half-degree of latitude and used generalized linear models to relate snail species richness to climatic variables and soil calcium content measured in situ. Contrary to the classical prediction of latitudinal biodiversity decrease, we found a striking unimodal pattern of snail species richness peaking in the subtaiga and southern-taiga zones between 57 and 59°N. The main south-to-north interchange of the two principal diversity constraints, i.e. drought stress vs. cold stress, explained most of the variance in the latitudinal diversity pattern. Water balance, calculated as annual precipitation minus potential evapotranspiration, was a single variable that could explain 81.7% of the variance in species richness. Our data suggest that the "water-energy dynamics" hypothesis can apply not only at the global scale but also at subcontinental scales of higher latitudes, as water availability was found to be the primary limiting factor also in this extratropical region with summer-warm and dry climate. A narrow zone with a sharp south-to-north switch in the two main diversity constraints seems to constitute the dominant and

  15. Counternarrating Racialized Expectations at School: The Diverse Enactments of "Non-Dominant" Identities among 1.5-Generation Japanese Immigrant Youth

    Science.gov (United States)

    Endo, R.

    2016-01-01

    This study adds to the research on the education of Asian immigrant adolescents by situating how generation, language, nationality, and race complexly impacted how a group of 1.5-generation Japanese youth have made sense of their multiple "non-dominant" identities as immigrant Americans and transnational students within an urban high…

  16. Counternarrating Racialized Expectations at School: The Diverse Enactments of "Non-Dominant" Identities among 1.5-Generation Japanese Immigrant Youth

    Science.gov (United States)

    Endo, R.

    2016-01-01

    This study adds to the research on the education of Asian immigrant adolescents by situating how generation, language, nationality, and race complexly impacted how a group of 1.5-generation Japanese youth have made sense of their multiple "non-dominant" identities as immigrant Americans and transnational students within an urban high…

  17. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Directory of Open Access Journals (Sweden)

    Leah C Blasiak

    Full Text Available Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  18. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Science.gov (United States)

    Blasiak, Leah C; Schmidt, Alex W; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P; Schmidt, Thomas M; Hill, Russell T

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  19. Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow.

    Science.gov (United States)

    Guirao-Rico, Sara; Sánchez-Gracia, Alejandro; Charlesworth, Deborah

    2017-03-01

    DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism. © 2016 John Wiley & Sons Ltd.

  20. Rich Internet Applications

    OpenAIRE

    Farré López, Xavier

    2005-01-01

    El propósito principal de este proyecto es estudiar el origen y funcionamiento de las Rich Internet Applicacions (RIA), que son un nuevo tipo de aplicaciones mucho más óptimas e impactantes que las tradicionales aplicaciones Web. Para llevarlo a cabo primero se ha definido el concepto de aplicación Web y se han expuesto las limitaciones que tienen. El siguiente paso ha sido definir el concepto de Rich Internet Applications y se han listado los objetivos por los que han sido ...

  1. The Omega RICH

    Energy Technology Data Exchange (ETDEWEB)

    Siebert, H.W. (Physikalisches Inst., Univ. Heidelberg (Germany)); Beusch, W. (CERN European Organization for Nuclear Research, Geneva (Switzerland)); Engelfried, J. (Physikalisches Inst., Univ. Heidelberg (Germany)); Faller, F. (Physikalisches Inst., Univ. Heidelberg (Germany)); Gerassimov, S.G. (Max-Planck-Inst. fuer Kernphysik, Heidelberg (Germany)); Lennert, P. (Physikalisches Inst., Univ. Heidelberg (Germany)); Martens, K. (Physikalisches Inst., Univ. Heidelberg (Germany)); Michaels, R. (Max-Planck-Inst. fuer Kernphysik, Heidelberg (Germany)); Mueller, U. (Inst. fuer Kernphysik, Univ. Mainz (Germany)); Rieseberg, H. (Physikalisches Inst., Univ. Heidelberg (Germany)); Waelder, G. (Physikalisches Inst., Univ. Heidelberg (Germany))

    1994-04-01

    A large-aperture RICH for identification of secondary particles is in operation at the Omega spectrometer since 1984. Photons are detected in drift chambers with quartz windows, using TMAE-loaded counting gases. The RICH was used by two experiments, WA69 and WA82, until 1988. It was then equipped with new drift chambers and mirrors and is in use since 1990 mainly for the hyperon beam experiment WA89. The present setup is described in more detail, and efficiencies, resolutions and particle separation achieved are discussed. (orig.)

  2. Effect of plant diversity on the diversity of soil organic compounds

    Science.gov (United States)

    El Moujahid, Lamiae; Michalet, Serge; Bellvert, Florian; Weigelt, Alexandra; Poly, Franck

    2017-01-01

    The effect of plant diversity on aboveground organisms and processes was largely studied but there is still a lack of knowledge regarding the link between plant diversity and soil characteristics. Here, we analyzed the effect of plant identity and diversity on the diversity of extractible soil organic compounds (ESOC) using 87 experimental grassland plots with different levels of plant diversity and based on a pool of over 50 plant species. Two pools of low molecular weight organic compounds, LMW1 and LMW2, were characterized by GC-MS and HPLC-DAD, respectively. These pools include specific organic acids, fatty acids and phenolics, with more organic acids in LMW1 and more phenolics in LMW2. Plant effect on the diversity of LMW1 and LMW2 compounds was strong and weak, respectively. LMW1 richness observed for bare soil was lower than that observed for all planted soils; and the richness of these soil compounds increased twofold when dominant plant species richness increased from 1 to 6. Comparing the richness of LMW1 compounds observed for a range of plant mixtures and for plant monocultures of species present in these mixtures, we showed that plant species richness increases the richness of these ESOC mainly through complementarity effects among plant species associated with contrasted spectra of soil compounds. This could explain previously reported effects of plant diversity on the diversity of soil heterotrophic microorganisms. PMID:28166250

  3. Effect of plant diversity on the diversity of soil organic compounds.

    Science.gov (United States)

    El Moujahid, Lamiae; Le Roux, Xavier; Michalet, Serge; Bellvert, Florian; Weigelt, Alexandra; Poly, Franck

    2017-01-01

    The effect of plant diversity on aboveground organisms and processes was largely studied but there is still a lack of knowledge regarding the link between plant diversity and soil characteristics. Here, we analyzed the effect of plant identity and diversity on the diversity of extractible soil organic compounds (ESOC) using 87 experimental grassland plots with different levels of plant diversity and based on a pool of over 50 plant species. Two pools of low molecular weight organic compounds, LMW1 and LMW2, were characterized by GC-MS and HPLC-DAD, respectively. These pools include specific organic acids, fatty acids and phenolics, with more organic acids in LMW1 and more phenolics in LMW2. Plant effect on the diversity of LMW1 and LMW2 compounds was strong and weak, respectively. LMW1 richness observed for bare soil was lower than that observed for all planted soils; and the richness of these soil compounds increased twofold when dominant plant species richness increased from 1 to 6. Comparing the richness of LMW1 compounds observed for a range of plant mixtures and for plant monocultures of species present in these mixtures, we showed that plant species richness increases the richness of these ESOC mainly through complementarity effects among plant species associated with contrasted spectra of soil compounds. This could explain previously reported effects of plant diversity on the diversity of soil heterotrophic microorganisms.

  4. Chamaedorea: diverse species in diverse habitats

    Directory of Open Access Journals (Sweden)

    1992-01-01

    Full Text Available DIVERSES ESPÈCES DANS DIVERS HABITATS. Des espèces extraordinairement diverses se trouvant dans des habitats également divers caractérisent Chamaedorea, un genre qui compte environ 90 espèces dioïques limitées aux sous-bois des forêts néo-tropicales constamment dans la pluie et les nuages du Mexique à la Bolivie et à l’Équateur. Une vaste gamme de formes biologiques, de tiges, de feuilles, d’inflorescences, de fleurs, et de fruits reflète la diversité des espèces. Bien que le genre soit plus riche en espèces dans les forêts denses et humides situées entre 800-1,500 mètres d’altitude, quelques espèces exceptionnelles se trouvent dans des forêts moins denses et/ou occasionnellement sèches, sur des substances dures ou dans d’autres habitats inhabituels. DIVERSAS ESPECIES EN DIVERSOS HÁBITATS. Especies notablemente diversas presentes en habitats igualmente diversos caracterizan a Chamaedorea, un genero de aproximadamente 90 especies dioicas limitadas al sotobosque de los bosques lluviosos y nubosos neotropicales desde Mexico hasta Bolivia y Ecuador. Una amplia gama de formas biológicas, tallos, hojas, inflorescencias, flores, y frutos refleja la diversidad de las especies. Aunque el género es más rico en especies en los bosques densos y húmedos de 800-1,500 metros de altura, unas pocas especies excepcionales ocurren en bosques abiertos o ocasionalmente secos, en substrato severo o en otros habitats extraordinarios. Remarkably diverse species occurring in equally diverse habitats characterize Chamaedorea, a genus of about 90, dioecious species restricted to the understory of neotropical rain and cloud forests from Mexico to Bolivia and Ecuador. A vast array of habits, stems, leaves, inflorescences, flowers, and fruits reflect the diversity of species. Although the genus is most species-rich in dense, moist or wet, diverse forests from 800-1,500 meters elevation, a few exceptional species occur in open and/or seasonally

  5. Arthropod diversity in a tropical forest

    DEFF Research Database (Denmark)

    Basset, Yves; Cizek, Lukas; Cuénoud, Philippe

    2012-01-01

    Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic...

  6. Adaptive Practice: Next Generation Evidence-Based Practice in Digital Environments.

    Science.gov (United States)

    Kennedy, Margaret Ann

    2016-01-01

    Evidence-based practice in nursing is considered foundational to safe, competent care. To date, rigid traditional perceptions of what constitutes 'evidence' have constrained the recognition and use of practice-based evidence and the exploitation of novel forms of evidence from data rich environments. Advancements such as the conceptualization of clinical intelligence, the prevalence of increasingly sophisticated digital health information systems, and the advancement of the Big Data phenomenon have converged to generate a new contemporary context. In today's dynamic data-rich environments, clinicians have new sources of valid evidence, and need a new paradigm supporting clinical practice that is adaptive to information generated by diverse electronic sources. This opinion paper presents adaptive practice as the next generation of evidence-based practice in contemporary evidence-rich environments and provides recommendations for the next phase of evolution.

  7. 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

  8. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    – The work can encourage policy makers, diversity and HR managers to question their own practices and assumptions leading to more theoretical informed diversity management practices. Originality/value – The theoretical connections between identity and diversity literature have so far not been reviewed...... systematically. The work foregrounds how important it is for diversity scholars to consider identity underpinnings of diversity research to help further develop the field within and beyond the three streams the authors discuss.......The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...

  9. Lithium-rich Giants in Globular Clusters

    Science.gov (United States)

    Kirby, Evan N.; Guhathakurta, Puragra; Zhang, Andrew J.; Hong, Jerry; Guo, Michelle; Guo, Rachel; Cohen, Judith G.; Cunha, Katia

    2016-03-01

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron-Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval. The data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

  10. LITHIUM-RICH GIANTS IN GLOBULAR CLUSTERS

    Energy Technology Data Exchange (ETDEWEB)

    Kirby, Evan N.; Cohen, Judith G. [California Institute of Technology, 1200 E. California Boulevard, MC 249-17, Pasadena, CA 91125 (United States); Guhathakurta, Puragra [UCO/Lick Observatory and Department of Astronomy and Astrophysics, University of California, 1156 High Street, Santa Cruz, CA 95064 (United States); Zhang, Andrew J. [The Harker School, 500 Saratoga Avenue, San Jose, CA 95129 (United States); Hong, Jerry [Palo Alto High School, 50 Embarcadero Road, Palo Alto, CA, 94301 (United States); Guo, Michelle [Stanford University, 450 Serra Mall, Stanford, CA 94305 (United States); Guo, Rachel [Irvington High School, 41800 Blacow Road, Fremont, CA 94538 (United States); Cunha, Katia [Observatório Nacional, São Cristóvão Rio de Janeiro (Brazil)

    2016-03-10

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron–Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval.

  11. The Role of Nuclear Power in Reducing Risk of the Fossil Fuel Prices and Diversity of Electricity Generation in Tunisia: A Portfolio Approach

    Science.gov (United States)

    Abdelhamid, Mohamed Ben; Aloui, Chaker; Chaton, Corinne; Souissi, Jomâa

    2010-04-01

    This paper applies real options and mean-variance portfolio theories to analyze the electricity generation planning into presence of nuclear power plant for the Tunisian case. First, we analyze the choice between fossil fuel and nuclear production. A dynamic model is presented to illustrate the impact of fossil fuel cost uncertainty on the optimal timing to switch from gas to nuclear. Next, we use the portfolio theory to manage risk of the electricity generation portfolio and to determine the optimal fuel mix with the nuclear alternative. Based on portfolio theory, the results show that there is other optimal mix than the mix fixed for the Tunisian mix for the horizon 2010-2020, with lower cost for the same risk degree. In the presence of nuclear technology, we found that the optimal generating portfolio must include 13% of nuclear power technology share.

  12. Diverse levels of an inwardly rectifying potassium conductance generate heterogeneous neuronal behavior in a population of dorsal cochlear nucleus pyramidal neurons.

    Science.gov (United States)

    Leao, Ricardo M; Li, Shuang; Doiron, Brent; Tzounopoulos, Thanos

    2012-06-01

    Homeostatic mechanisms maintain homogeneous neuronal behavior among neurons that exhibit substantial variability in the expression levels of their ionic conductances. In contrast, the mechanisms, which generate heterogeneous neuronal behavior across a neuronal population, remain poorly understood. We addressed this problem in the dorsal cochlear nucleus, where principal neurons exist in two qualitatively distinct states: spontaneously active or not spontaneously active. Our studies reveal that distinct activity states are generated by the differential levels of a Ba(2+)-sensitive, inwardly rectifying potassium conductance (K(ir)). Variability in K(ir) maximal conductance causes variations in the resting membrane potential (RMP). Low K(ir) conductance depolarizes RMP to voltages above the threshold for activating subthreshold-persistent sodium channels (Na(p)). Once Na(p) channels are activated, the RMP becomes unstable, and spontaneous firing is triggered. Our results provide a biophysical mechanism for generating neural heterogeneity, which may play a role in the encoding of sensory information.

  13. eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes.

    Science.gov (United States)

    Reddy, Boojala Vijay B; Milshteyn, Aleksandr; Charlop-Powers, Zachary; Brady, Sean F

    2014-08-14

    Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. Using PCR-generated sequence tags, the eSNaPD data-analysis pipeline profiles biosynthetic diversity hidden within (meta)genomes by comparing sequence tags to a reference data set of characterized gene clusters. Sample mapping, molecule discovery, library mapping, and new clade visualization modules facilitate the interrogation of large (meta)genomic sequence data sets for diverse downstream analyses, including, but not limited to, the identification of environments rich in untapped biosynthetic diversity, targeted molecule discovery efforts, and chemical ecology studies. eSNaPD is designed to generate a global atlas of biosynthetic diversity that can facilitate a systematic, sequence-based interrogation of nature's biosynthetic potential.

  14. The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity

    DEFF Research Database (Denmark)

    Hermann-Bank, Marie Louise; Skovgaard, Kerstin; Stockmarr, Anders

    2013-01-01

    ®) followed by next generation sequencing. Primers were designed if necessary and all primer sets were screened against DNA extracted from pure cultures of 15 representative bacterial species. Subsequently the setup was tested on DNA extracted from small and large intestinal content from piglets...

  15. Global diversity of sponges (Porifera.

    Directory of Open Access Journals (Sweden)

    Rob W M Van Soest

    Full Text Available With the completion of a single unified classification, the Systema Porifera (SP and subsequent development of an online species database, the World Porifera Database (WPD, we are now equipped to provide a first comprehensive picture of the global biodiversity of the Porifera. An introductory overview of the four classes of the Porifera is followed by a description of the structure of our main source of data for this paper, the WPD. From this we extracted numbers of all 'known' sponges to date: the number of valid Recent sponges is established at 8,553, with the vast majority, 83%, belonging to the class Demospongiae. We also mapped for the first time the species richness of a comprehensive set of marine ecoregions of the world, data also extracted from the WPD. Perhaps not surprisingly, these distributions appear to show a strong bias towards collection and taxonomy efforts. Only when species richness is accumulated into large marine realms does a pattern emerge that is also recognized in many other marine animal groups: high numbers in tropical regions, lesser numbers in the colder parts of the world oceans. Preliminary similarity analysis of a matrix of species and marine ecoregions extracted from the WPD failed to yield a consistent hierarchical pattern of ecoregions into marine provinces. Global sponge diversity information is mostly generated in regional projects and resources: results obtained demonstrate that regional approaches to analytical biogeography are at present more likely to achieve insights into the biogeographic history of sponges than a global perspective, which appears currently too ambitious. We also review information on invasive sponges that might well have some influence on distribution patterns of the future.

  16. Global diversity of sponges (Porifera).

    Science.gov (United States)

    Van Soest, Rob W M; Boury-Esnault, Nicole; Vacelet, Jean; Dohrmann, Martin; Erpenbeck, Dirk; De Voogd, Nicole J; Santodomingo, Nadiezhda; Vanhoorne, Bart; Kelly, Michelle; Hooper, John N A

    2012-01-01

    With the completion of a single unified classification, the Systema Porifera (SP) and subsequent development of an online species database, the World Porifera Database (WPD), we are now equipped to provide a first comprehensive picture of the global biodiversity of the Porifera. An introductory overview of the four classes of the Porifera is followed by a description of the structure of our main source of data for this paper, the WPD. From this we extracted numbers of all 'known' sponges to date: the number of valid Recent sponges is established at 8,553, with the vast majority, 83%, belonging to the class Demospongiae. We also mapped for the first time the species richness of a comprehensive set of marine ecoregions of the world, data also extracted from the WPD. Perhaps not surprisingly, these distributions appear to show a strong bias towards collection and taxonomy efforts. Only when species richness is accumulated into large marine realms does a pattern emerge that is also recognized in many other marine animal groups: high numbers in tropical regions, lesser numbers in the colder parts of the world oceans. Preliminary similarity analysis of a matrix of species and marine ecoregions extracted from the WPD failed to yield a consistent hierarchical pattern of ecoregions into marine provinces. Global sponge diversity information is mostly generated in regional projects and resources: results obtained demonstrate that regional approaches to analytical biogeography are at present more likely to achieve insights into the biogeographic history of sponges than a global perspective, which appears currently too ambitious. We also review information on invasive sponges that might well have some influence on distribution patterns of the future.

  17. Kings Today, Rich Tomorrow

    DEFF Research Database (Denmark)

    Fattoum, Asma

    2013-01-01

    This study investigates the King vs. Rich dilemma that founder-CEOs face at IPO. When undertaking IPO, founders face two options. They can either get rich, but then run the risk of losing the control over their firms; or they can remain kings by introducing defensive mechanisms, but this is likely...... to lead to lower IPO valuation. Using psychological ownership theory, we argue founder-CEOs to be more likely to choose the King option. This option forces them to leave money on the table at the IPO. However, their stewardship behavior allows them to recover that money on the long-run post IPO. We...... provide support for all hypotheses using a unique hand-collected dataset covering the full population of 467 IPOs undertaken in France between 1992 and 2011....

  18. Stoichiometric differences in DNA molecules containing the atpA gene suggest mechanisms for the generation of mitochondrial genome diversity in maize.

    Science.gov (United States)

    Small, I D; Isaac, P G; Leaver, C J

    1987-04-01

    Four genomic arrangements of the maize mitochondrial atpA gene (encoding the alpha subunit of the F(1) ATPase), have been characterized. Most N (fertile) and S (male-sterile) cytoplasms contain two atpA arrangements of equal abundance. Prolonged exposure of blots of maize mitochondrial DNA probed with atpA-specific sequences show that cytoplasms previously reported to lack one of the atpA arrangements do contain the second arrangement but at low levels. Similarly, restriction fragments containing the atpA gene previously thought unique to male-sterile S and T cytoplasms are present in low abundance in fertile cytoplasms. These observations suggest that fertile and male-sterile cytoplasms of maize may be more closely related than previously thought, and suggest possible mechanisms to explain the observed mitochondrial genome diversity.

  19. Metal-rich organometallics.

    Science.gov (United States)

    Krüger, Robin A; Baumgartner, Thomas

    2010-07-07

    The scope of organometallics has recently been expanded considerably, when researchers have started to employ these compounds in the context of materials chemistry. Traditionally, organometallic complexes have been and continue to be important tools for many (catalytic) chemical transformations. This perspective highlights how metal-rich organometallics, that is compounds with more than one type of metal, can play an important role in the advancement of new value-added functional materials.

  20. RecJ, ExoI and RecG are required for genome maintenance but not for generation of genetic diversity by repeat-mediated phase variation in Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Gaurav A.; Woodhall, Mark R.; Hood, Derek W.; Moxon, E. Richard [Molecular Infectious Diseases Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS (United Kingdom); Bayliss, Christopher D. [Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH (United Kingdom)], E-mail: cdb12@le.ac.uk

    2008-04-02

    High levels of genetic diversity are generated in Haemophilus influenzae populations through DNA repeat-mediated phase variation and recombination with DNA fragments acquired by uptake from the external milieu. Conversely, multiple pathways for maintenance of the genome sequence are encoded in H. influenzae genomes. In Escherichia coli, mutations in single-stranded-DNA exonucleases destabilise tandem DNA repeats whilst inactivation of recG can stabilise repeat tracts. These enzymes also have varying effects on recombination. Deletion mutations were constructed in H. influenzae genes encoding homologs of ExoI, RecJ and RecG whilst ExoVII was refractory to mutation. Inactivation of RecJ and RecG, but not ExoI, increased sensitivity to irradiation with ultraviolet light. An increase in spontaneous mutation rate was not observed in single mutants but only when both RecJ and ExoI were mutated. None of the single- or double-mutations increased or decreased the rates of slippage in tetranucleotide repeat tracts. Furthermore, the exonuclease mutants did not exhibit significant defects in horizontal gene transfer. We conclude that RecJ, ExoI and RecG are required for maintenance of the H. influenzae genome but none of these enzymes influence the generation of genetic diversity through mutations in the tetranucleotide repeat tracts of this species.

  1. Sulfate-rich Archean Oceans

    Science.gov (United States)

    Brainard, J. L.; Choney, A. P.; Ohmoto, H.

    2012-12-01

    - contents. Contrary to a widely held belief, pyrite- and organic C rich black Archean shales are quite common, such as the 2.7 Ga Jeerinah and the 2.5 Ga McRae Shales in WA. Our modeling suggests that the formation of such pyrite-rich shales requires seawater SO4 contents greater than ~1 mM. As for the main source of SO4 in the Archean oceans, the current paradigm, based on mass independent fractionation of sulfur isotopes (MIF-S) in some pyrite and barite samples from some pre-2.4 Ga sedimentary rocks, postulates that the seawater SO4 was produced by UV photolysis of volcanic SO2 gas in an O2-poor atmosphere. However, the recent findings of the absence of MIF-S in many Archean sedimentary rocks, as well as those of oxidized paleosols of Archean ages, suggest that the abundant SO4 in the Archean oceans were generated by the oxidative weathering of sulfides.

  2. Small leucine-rich proteoglycans in the aging skeleton

    DEFF Research Database (Denmark)

    Young, M F; Bi, Y; Ameye, L

    2006-01-01

    Small Leucine-Rich Proteoglyans (SLRPs) are major skeletal extracellular matrix (ECM) components that comprise a family of 13 members containing repeats of a leucine-rich motif. To examine SLRP function, we generated mice deficient in one or more member and analyzed them at the tissue, cell...

  3. Evolutionary and biogeographic origins of high tropical diversity in old world frogs (Ranidae).

    Science.gov (United States)

    Wiens, John J; Sukumaran, Jeet; Pyron, R Alexander; Brown, Rafe M

    2009-05-01

    Differences in species richness between regions are ultimately explained by patterns of speciation, extinction, and biogeographic dispersal. Yet, few studies have considered the role of all three processes in generating the high biodiversity of tropical regions. A recent study of a speciose group of predominately New World frogs (Hylidae) showed that their low diversity in temperate regions was associated with relatively recent colonization of these regions, rather than latitudinal differences in diversification rates (rates of speciation-extinction). Here, we perform parallel analyses on the most species-rich group of Old World frogs (Ranidae; approximately 1300 species) to determine if similar processes drive the latitudinal diversity gradient. We estimate a time-calibrated phylogeny for 390 ranid species and use this phylogeny to analyze patterns of biogeography and diversification rates. As in hylids, we find a strong relationship between the timing of colonization of each region and its current diversity, with recent colonization of temperate regions from tropical regions. Diversification rates are similar in tropical and temperate clades, suggesting that neither accelerated tropical speciation rates nor greater temperate extinction rates explain high tropical diversity in this group. Instead, these results show the importance of historical biogeography in explaining high species richness in both the New World and Old World tropics.

  4. Cultural diversity

    OpenAIRE

    Raghavan, Raghu

    2011-01-01

    The concept of cultural diversity has emerged as an influential one having impact on multiple policy and legal instruments especially following the adoption of the UNESCO Convention on the Protection and Promotion of the Diversity of Cultural Expressions in 2005. The discussions on its appropriate implementation are however profoundly fragmented and often laden with political considerations. The present brief paper offers some thoughts on the meaning of cultural diversity and its implementati...

  5. Functional diversity of human basic helix-loop-helix transcription factor TCF4 isoforms generated by alternative 5' exon usage and splicing.

    Directory of Open Access Journals (Sweden)

    Mari Sepp

    Full Text Available BACKGROUND: Transcription factor 4 (TCF4 alias ITF2, E2-2, ME2 or SEF2 is a ubiquitous class A basic helix-loop-helix protein that binds to E-box DNA sequences (CANNTG. While involved in the development and functioning of many different cell types, recent studies point to important roles for TCF4 in the nervous system. Specifically, human TCF4 gene is implicated in susceptibility to schizophrenia and TCF4 haploinsufficiency is the cause of the Pitt-Hopkins mental retardation syndrome. However, the structure, expression and coding potential of the human TCF4 gene have not been described in detail. PRINCIPAL FINDINGS: In the present study we used human tissue samples to characterize human TCF4 gene structure and TCF4 expression at mRNA and protein level. We report that although widely expressed, human TCF4 mRNA expression is particularly high in the brain. We demonstrate that usage of numerous 5' exons of the human TCF4 gene potentially yields in TCF4 protein isoforms with 18 different N-termini. In addition, the diversity of isoforms is increased by alternative splicing of several internal exons. For functional characterization of TCF4 isoforms, we overexpressed individual isoforms in cultured human cells. Our analysis revealed that subcellular distribution of TCF4 isoforms is differentially regulated: Some isoforms contain a bipartite nuclear localization signal and are exclusively nuclear, whereas distribution of other isoforms relies on heterodimerization partners. Furthermore, the ability of different TCF4 isoforms to regulate E-box controlled reporter gene transcription is varied depending on whether one or both of the two TCF4 transcription activation domains are present in the protein. Both TCF4 activation domains are able to activate transcription independently, but act synergistically in combination. CONCLUSIONS: Altogether, in this study we have described the inter-tissue variability of TCF4 expression in human and provided evidence

  6. Fungal biogeography. Global diversity and geography of soil fungi.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S; Wijesundera, Ravi; Villarreal Ruiz, Luis; Vasco-Palacios, Aída M; Thu, Pham Quang; Suija, Ave; Smith, Matthew E; Sharp, Cathy; Saluveer, Erki; Saitta, Alessandro; Rosas, Miguel; Riit, Taavi; Ratkowsky, David; Pritsch, Karin; Põldmaa, Kadri; Piepenbring, Meike; Phosri, Cherdchai; Peterson, Marko; Parts, Kaarin; Pärtel, Kadri; Otsing, Eveli; Nouhra, Eduardo; Njouonkou, André L; Nilsson, R Henrik; Morgado, Luis N; Mayor, Jordan; May, Tom W; Majuakim, Luiza; Lodge, D Jean; Lee, Su See; Larsson, Karl-Henrik; Kohout, Petr; Hosaka, Kentaro; Hiiesalu, Indrek; Henkel, Terry W; Harend, Helery; Guo, Liang-dong; Greslebin, Alina; Grelet, Gwen; Geml, Jozsef; Gates, Genevieve; Dunstan, William; Dunk, Chris; Drenkhan, Rein; Dearnaley, John; De Kesel, André; Dang, Tan; Chen, Xin; Buegger, Franz; Brearley, Francis Q; Bonito, Gregory; Anslan, Sten; Abell, Sandra; Abarenkov, Kessy

    2014-11-28

    Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

  7. Increasing diversity in the species-rich genus Guatteria (Annonaceae)

    NARCIS (Netherlands)

    Erkens, R.H.J.; Westra, L.Y.Th.; Maas, P.J.M.

    2008-01-01

    During a taxonomic treatment of Annonaceae for the Flora of the Guianas project, an unusual new species of Guatteria Ruiz & Pav., G. anteridifera from French Guiana and Amapá in Brazil (Northern South America) was found and described herein.

  8. Hotspots of species richness, threat and endemism for terrestrial vertebrates in SW Europe

    Science.gov (United States)

    Pascual, López-López; Luigi, Maiorano; Alessandra, Falcucci; Emilio, Barba; Luigi, Boitani

    2011-09-01

    The Mediterranean basin, and the Iberian Peninsula in particular, represent an outstanding "hotspot" of biological diversity with a long history of integration between natural ecosystems and human activities. Using deductive distribution models, and considering both Spain and Portugal, we downscaled traditional range maps for terrestrial vertebrates (amphibians, breeding birds, mammals and reptiles) to the finest possible resolution with the data at hand, and we identified hotspots based on three criteria: i) species richness; ii) vulnerability, and iii) endemism. We also provided a first evaluation of the conservation status of biodiversity hotspots based on these three criteria considering both existing and proposed protected areas (i.e., Natura 2000). For the identification of hotspots, we used a method based on the cumulative distribution functions of species richness values. We found no clear surrogacy among the different types of hotspots in the Iberian Peninsula. The most important hotspots (considering all criteria) are located in the western and southwestern portions of the study area, in the Mediterranean biogeographical region. Existing protected areas are not specifically concentrated in areas of high species richness, with only 5.2% of the hotspots of total richness being currently protected. The Natura 2000 network can potentially constitute an important baseline for protecting vertebrate diversity in the Iberian Peninsula although further improvements are needed. We suggest taking a step forward in conservation planning in the Mediterranean basin, explicitly considering the history of the region as well as its present environmental context. This would allow moving from traditional reserve networks (conservation focused on "patterns") to considerations about the "processes" that generated present biodiversity.

  9. Oil palm plantations fail to support mammal diversity.

    Science.gov (United States)

    Yue, Sam; Brodie, Jedediah F; Zipkin, Elise F; Bernard, Henry

    2015-12-01

    Agricultural expansion is the largest threat to global biodiversity. In particular, the rapid spread of tree plantations is a primary driver of deforestation in hyperdiverse tropical regions. Plantations tend to support considerably lower biodiversity than native forest, but it remains unclear whether plantation traits affect their ability to sustain native wildlife populations, particularly for threatened taxa. If animal diversity varies across plantations with different characteristics, these traits could be manipulated to make plantations more "wildlife friendly." The degree to which plantations create edge effects that degrade habitat quality in adjacent forest also remains unclear, limiting our ability to predict wildlife persistence in mixed-use landscapes. We used systematic camera trapping to investigate mammal occurrence and diversity in oil palm plantations and adjacent forest in Sabah, Malaysian Borneo. Mammals within plantations were largely constrained to locations near native forest; the occurrence of most species and overall species richness declined abruptly with decreasing forest proximity from an estimated 14 species at the forest ecotone to -1 species 2 km into the plantation. Neither tree height nor canopy cover within plantations strongly affected mammal diversity or occurrence, suggesting that manipulating tree spacing or planting cycles might not make plantations more wildlife friendly. Plantations did not appear to generate strong edge effects; mammal richness within forest remained high and consistent up to the plantation ecotone. Our results suggest that land-sparing strategies, as opposed to efforts to make plantations more wildlife-friendly, are required for regional wildlife conservation in biodiverse tropical ecosystems.

  10. Diversity Management

    DEFF Research Database (Denmark)

    Ravazzani, Silvia

    2016-01-01

    This entry provides an overview of diversity management which, in the context of organizations, consists in the strategic process of harnessing the potential of all employees to create an inclusive environment and, at the same time, contribute to meeting organizational goals. The entry first...... describes the complex construct of diversity that has been variously conceptualized in the literature, embracing multiple social and informational diversity dimensions such as gender, age, culture, values, and workstyle. This is followed by illustration of the historical development of diversity-management...... discourse and practice, and possible overarching approaches guiding organizations. It goes on to elucidate elements linked to the implementation of diversity management: positive and negative outcomes, most spread practices including communication, and contingency factors shaping the understanding...

  11. Everyday Diversity

    Directory of Open Access Journals (Sweden)

    Christina Ho

    2015-03-01

    Full Text Available The Cosmopolitan Civil Societies Journal has been an important forum for discussing issues around cultural diversity. Articles on cultural diversity have been present in virtually every issue of the journal. These have ranged from conceptual pieces on cosmopolitanism, identity, dialogue, prejudice, pluralism, cultural and social capital and social inclusion, to articles embedded in empirical research on ethnic precincts and segregation in cities, experiences of religious minorities, immigrant entrepreneurs, and more. Over its five year history, the journal has also had themed editions on cultural diversity issues, including one on embracing diversity in sport, and another on the Chinese in Australian politics. The scope of this work has been wide, and authors have brought a range of disciplinary and methodological approaches to the journal.   The purpose of this paper is to draw together some of the work that has been published around cultural diversity, particularly relating to everyday experiences of cosmopolitanism and racism. Focusing on everyday social relations has been an important part of recent scholarship on cultural diversity in Australia (e.g. Wise and Velayutham 2009. In contrast to research framed around multicultural policy or mediated representations of diversity, the scholarship of the ‘everyday’ aims to explore people’s lived experiences and daily interactions with others.

  12. Understanding Diversity in Millennial Students

    Science.gov (United States)

    Broido, Ellen M.

    2004-01-01

    The Millennial generation of college students has demographics and attitudes toward diversity issues different from their predecessors; this chapter explores those differences and their implications for student affairs work.

  13. Understanding Diversity in Millennial Students

    Science.gov (United States)

    Broido, Ellen M.

    2004-01-01

    The Millennial generation of college students has demographics and attitudes toward diversity issues different from their predecessors; this chapter explores those differences and their implications for student affairs work.

  14. Investigating the diversity of the 18S SSU rRNA hyper-variable region of Theileria in cattle and Cape buffalo (Syncerus caffer) from southern Africa using a next generation sequencing approach.

    Science.gov (United States)

    Mans, Ben J; Pienaar, Ronel; Ratabane, John; Pule, Boitumelo; Latif, Abdalla A

    2016-07-01

    Molecular classification and systematics of the Theileria is based on the analysis of the 18S rRNA gene. Reverse line blot or conventional sequencing approaches have disadvantages in the study of 18S rRNA diversity and a next-generation 454 sequencing approach was investigated. The 18S rRNA gene was amplified using RLB primers coupled to 96 unique sequence identifiers (MIDs). Theileria positive samples from African buffalo (672) and cattle (480) from southern Africa were combined in batches of 96 and sequenced using the GS Junior 454 sequencer to produce 825711 informative sequences. Sequences were extracted based on MIDs and analysed to identify Theileria genotypes. Genotypes observed in buffalo and cattle were confirmed in the current study, while no new genotypes were discovered. Genotypes showed specific geographic distributions, most probably linked with vector distributions. Host specificity of buffalo and cattle specific genotypes were confirmed and prevalence data as well as relative parasitemia trends indicate preference for different hosts. Mixed infections are common with African buffalo carrying more genotypes compared to cattle. Associative or exclusion co-infection profiles were observed between genotypes that may have implications for speciation and systematics: specifically that more Theileria species may exist in cattle and buffalo than currently recognized. Analysis of primers used for Theileria parva diagnostics indicate that no new genotypes will be amplified by the current primer sets confirming their specificity. T. parva SNP variants that occur in the 18S rRNA hypervariable region were confirmed. A next generation sequencing approach is useful in obtaining comprehensive knowledge regarding 18S rRNA diversity and prevalence for the Theileria, allowing for the assessment of systematics and diagnostic assays based on the 18S gene.

  15. Plant species richness regulates soil respiration through changes in productivity

    NARCIS (Netherlands)

    Dias, A.A.; Ruijven, van J.; Berendse, F.

    2010-01-01

    Soil respiration is an important pathway of the C cycle. However, it is still poorly understood how changes in plant community diversity can affect this ecosystem process. Here we used a long-term experiment consisting of a gradient of grassland plant species richness to test for effects of

  16. Effects of grazing and climate change on species diversity in sandy grassland, Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Toshiya; Okuro

    2009-01-01

    To understand the effects of animal grazing activities and climate change on sandy grassland vegetation in northern China, a field grazing and protected enclosure experiment was conducted from 1992 through 2006 in Horqin Sand Land, Inner Mongolia. The results showed that (1) the grazing was primary responsible for changes of the vegetation richness and diversity in the grazing grassland and that changing climate was the main reason for changes in the species richness and diversity in the grassland protected from grazing; (2) light and moderate grazing can promote restoration of the richness and the diversity in the degraded grassland, and heavy grazing could result in a decrease of the richness and diversity; (3) heavy grazing can result in significant decrease of the perennial diversity, and moderate and light grazing promotes increase of the perennial diversity; the grazing, whether heavy or moderate and light grazing, was beneficial to increase of the annual diversity; (4) heavy grazing was not beneficial to diversity of Graminean and Chenopodiaceae, and moderate and light grazing was favorable the diversity of Compositae and Chenopodiaceae; (5) the warm-humid climate was favorable to increase of the richness and the diversity, and the warm-drought climate could result in decease of the richness and the diversity; (6) increased precipitation was favorable to perennial diversity and the diversity of Graminean, Leguminosae, and Compositae, and decreased precipitation had few effects on the annual diversity and Chenopodiaceae diversity.

  17. Validation of Next-Generation Sequencing of Entire Mitochondrial Genomes and the Diversity of Mitochondrial DNA Mutations in Oral Squamous Cell Carcinoma.

    Directory of Open Access Journals (Sweden)

    Anita Kloss-Brandstätter

    Full Text Available Oral squamous cell carcinoma (OSCC is mainly caused by smoking and alcohol abuse and shows a five-year survival rate of ~50%. We aimed to explore the variation of somatic mitochondrial DNA (mtDNA mutations in primary oral tumors, recurrences and metastases.We performed an in-depth validation of mtDNA next-generation sequencing (NGS on an Illumina HiSeq 2500 platform for its application to cancer tissues, with the goal to detect low-level heteroplasmies and to avoid artifacts. Therefore we genotyped the mitochondrial genome (16.6 kb from 85 tissue samples (tumors, recurrences, resection edges, metastases and blood collected from 28 prospectively recruited OSCC patients applying both Sanger sequencing and high-coverage NGS (~35,000 reads per base.We observed a strong correlation between Sanger sequencing and NGS in estimating the mixture ratio of heteroplasmies (r = 0.99; p10% were predominant. Four out of six patients who developed a local tumor recurrence showed mutations in the recurrence that had also been observed in the primary tumor. Three out of five patients, who had tumor metastases in the lymph nodes of their necks, shared mtDNA mutations between primary tumors and lymph node metastases. The percentage of mutation heteroplasmy increased from the primary tumor to lymph node metastases.We conclude that Sanger sequencing is valid for heteroplasmy quantification for heteroplasmies ≥10% and that NGS is capable of reliably detecting and quantifying heteroplasmies down to the 1%-level. The finding of shared mutations between primary tumors, recurrences and metastasis indicates a clonal origin of malignant cells in oral cancer.

  18. Metabolic and growth characteristics of novel diverse microbes isolated from deep cores collected at the Next Generation Ecosystem Experiment (NGEE)-Arctic site in Barrow, Alaska

    Science.gov (United States)

    Chakraborty, R.; Pettenato, A.; Tas, N.; Hubbard, S. S.; Jansson, J.

    2013-12-01

    The Arctic is characterized by vast amounts of carbon stored in permafrost and is an important focal point for the study of climate change as increasing temperature may accelerate microbially mediated release of Carbon stored in permafrost into the atmosphere as CO2 and CH4. Yet surprisingly, very little is known about the vulnerability of permafrost and response of microorganisms in the permafrost to their changing environment. This deficiency is largely due to the difficulty in study of largely uncultivated and unknown permafrost microbes. As part of the U.S. Department of Energy (DOE) Next Generation Ecosystem Experiment (NGEE) in the Arctic, we collected permafrost cores in an effort to isolate resident microbes. The cores were from the Barrow Environmental Observatory (BEO), located at the northern most location on the Alaskan Arctic Coastal Plain near Barrow, AK, and up to 3m in depth. In this location, permafrost starts from 0.5m in depth and is characterized by variable water content and higher pH than surface soils. Enrichments for heterotrophic bacteria were initiated at 4°C and 1°C in the dark in several different media types, under both aerobic and anaerobic conditions. Positive enrichments were identified by an increase in optical density and cell counts after incubation period ranging from two to four weeks. After serial transfers into fresh media, individual colonies were obtained on agar surface. Several strains were isolated that include Firmicutes such as Bacillus, Clostridium, Sporosarcina, and Paenibacillus species and Iron-reducing Betaproteobacteria such as Rhodoferax species. In addition, methanogenic enrichments continue to grow and produce methane gas at 2°C. In this study, we present the characterization, carbon substrate utilization, pH, temperature and osmotic tolerance, as well as the effect of increasing climate change parameters on the growth rate and respiratory gas production from these permafrost isolates.

  19. Understanding Diversity

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan)

    2007-01-01

    textabstractDaan van Knippenberg is Professor of Organizational Behavior at RSM Erasmus University, Erasmus University Rotterdam, The Netherlands. His research interests include work group performance, especially work group diversity and group decision making, leadership, in particular the roles of

  20. Gender Diversities

    DEFF Research Database (Denmark)

    Agustin, Lise Rolandsen; Siim, Birte

    2014-01-01

    The article analyses the European Year for Combating Poverty and Social Exclusion (2010) (EY 2010) with the aim of identifying the nature of gender diversities in EU policies. We argue that the EU handles issues related to gender and diversity in particular ways; this approach is characterized...... by non-citizen/citizen and redistribution/recognition divisions. Employing intersectionality as the methodological approach to gender diversities, the article shows how gender and ethnicity are articulated in the policy-making process which led to the adoption of EY 201, the activities undertaken during...... the EY 2010, and the evaluation of EY 2010. The case study is suitable for developing a dynamic multi-level model for analysing gendered diversities at the transnationmal level: It illustrates how the EU policy frame interacts with particular national contexts in promoting or hundering the advancement...

  1. Understanding Diversity

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan)

    2007-01-01

    textabstractDaan van Knippenberg is Professor of Organizational Behavior at RSM Erasmus University, Erasmus University Rotterdam, The Netherlands. His research interests include work group performance, especially work group diversity and group decision making, leadership, in particular the roles of

  2. Impact of Forest Management on Species Richness: Global Meta-Analysis and Economic Trade-Offs

    Science.gov (United States)

    Chaudhary, Abhishek; Burivalova, Zuzana; Koh, Lian Pin; Hellweg, Stefanie

    2016-04-01

    Forests managed for timber have an important role to play in conserving global biodiversity. We evaluated the most common timber production systems worldwide in terms of their impact on local species richness by conducting a categorical meta-analysis. We reviewed 287 published studies containing 1008 comparisons of species richness in managed and unmanaged forests and derived management, taxon, and continent specific effect sizes. We show that in terms of local species richness loss, forest management types can be ranked, from best to worse, as follows: selection and retention systems, reduced impact logging, conventional selective logging, clear-cutting, agroforestry, timber plantations, fuelwood plantations. Next, we calculated the economic profitability in terms of the net present value of timber harvesting from 10 hypothetical wood-producing Forest Management Units (FMU) from around the globe. The ranking of management types is altered when the species loss per unit profit generated from the FMU is considered. This is due to differences in yield, timber species prices, rotation cycle length and production costs. We thus conclude that it would be erroneous to dismiss or prioritize timber production regimes, based solely on their ranking of alpha diversity impacts.

  3. Generative Contexts

    Science.gov (United States)

    Lyles, Dan Allen

    Educational research has identified how science, technology, engineering, and mathematics (STEM) practice and education have underperforming metrics in racial and gender diversity, despite decades of intervention. These disparities are part of the construction of a culture of science that is alienating to these populations. Recent studies in a social science framework described as "Generative Justice" have suggested that the context of social and scientific practice might be modified to bring about more just and equitable relations among the disenfranchised by circulating the value they and their non-human allies create back to them in unalienated forms. What is not known are the underlying principles of social and material space that makes a system more or less generative. I employ an autoethnographic method at four sites: a high school science class; a farm committed to "Black and Brown liberation"; a summer program geared towards youth environmental mapping; and a summer workshop for Harlem middle school students. My findings suggest that by identifying instances where material affinity, participatory voice, and creative solidarity are mutually reinforcing, it is possible to create educational contexts that generate unalienated value, and circulate it back to the producers themselves. This cycle of generation may help explain how to create systems of justice that strengthen and grow themselves through successive iterations. The problem of lack of diversity in STEM may be addressed not merely by recruiting the best and the brightest from underrepresented populations, but by changing the context of STEM education to provide tools for its own systematic restructuring.

  4. Effects of Sulfur-rich Amino Acids Transgenic Soybeans on Soil Organic Elements and Microbial Community Diversity%富含硫氨基酸转基因大豆对根际土壤有机元素含量和微生物群落多样性的影响

    Institute of Scientific and Technical Information of China (English)

    陈丰; 彭欣; 华小梅; 张培培; 桂恒; 戚金亮; 喻德跃; 杨永华

    2012-01-01

    In this study .the effects of sulfur-rich ammo acids transgenic soybeans on soil organic elements and functional diversity of microbial community were investigated to reveal the safety of transgenic soybeans on soil ecology environment. Microorganism community of transgenic soybeans (Group A: three transgenic soybean lines OE-8, OE-7, RNAi-3 and their recipient Nannong 88-1;Group B:three transgenic soybean lines Gagal l7-4,Gagal 21-8, Gagal 57 and their recipient N2899)in mature stage were analyzed by Biolog ECO/GN/GP/FF systems. The results showed that sulfur contents in rhizosphere soil were significantly decreased in the soil of all transgenic soybean lines (P<0.01). There were also differences in activities, community diversities and richness of soil microbial between transgenic soybeans and non-transgenic soybeans. Two groups of soybeans showed different patterns because of their different recipient genotypes. In Group A,average well color developments(AWCDs) and Mclntosh indexes of transgenic soybeans were lower than CK1,especially AWCDs of gram-negative bacteria,and AWCDs, Mclntosh indexes of gram-positive bacteria. In rhizosphere soil of three transgenic soybeans,AWCDs of gram-negative bacteria were significantly lower than Nannong88-1 ( P < 0.01), and Mclntosh index of gram-positive bacteria were significantly lower than Nannong88-1(P<0.05). Mclntosh index of fungi in rhizosphere soil of transgenic soybean OE-8 was significantly lower than Nannong88-1 (P <0.01). In Group B,AWCDs of gram-positive bacteria of Gagal 17-4 and Gaga! 21-8 were significantly higher than N2899,while AWCD of gram-positive bacteria of Gagal 57 was significantly lower than N2899(P<0.05). As for both groups,there were no significant differences in whole microorganisms when we compared AWCDs and indexes of community diversity in Biolog ECO plates. These results suggested that transgenie soybeans in our study could change activities of gram-negative and gram-positive bacteria

  5. Ensemble One-class Classifiers Based on Hybrid Diversity Generation and Pruning%基于混合多样性生成与修剪的集成单类分类算法

    Institute of Scientific and Technical Information of China (English)

    刘家辰; 苗启广; 曹莹; 宋建锋; 权义宁

    2015-01-01

    针对传统集成学习方法直接应用于单类分类器效果不理想的问题,该文首先证明了集成学习方法能够提升单类分类器的性能,同时证明了若基分类器集不经选择会导致集成后性能下降;接着指出了经典集成方法直接应用于单类分类器集成时存在基分类器多样性严重不足的问题,并提出了一种能够提高多样性的基单类分类器混合生成策略;最后从集成损失构成的角度拆分集成单类分类器的损失函数,针对性地构造了集成单类分类器修剪策略并提出一种基于混合多样性生成和修剪的单类分类器集成算法,简称为PHD-EOC。在UCI标准数据集和恶意程序行为检测数据集上的实验结果表明,PHD-EOC算法兼顾多样性与单类分类性能,在各种单类分类器评价指标上均较经典集成学习方法有更好的表现,并降低了决策阶段的时间复杂度。%Combining one-class classifiers using the classical ensemble methods is not satisfactory. To address this problem, this paper first proves that though one-class classification performance can be improved by a classifier ensemble, it can also degrade if the set of base classifiers are not selected carefully. On this basis, this study further analyzes that the lacking of diversity heavily accounts for performance degradation. Therefore, a hybrid method for generating diverse base classifiers is proposed. Secondly, in the combining phase, to find the most useful diversity, the one-class ensemble loss is split and analyzed theoretically to propose a diversity based pruning method. Finally, by combining these two steps, a novel ensemble one-class classifier named Pruned Hybrid Diverse Ensemble One-class Classifier (PHD-EOC) is proposed. The experimental results on the UCI datasets and a malicious software detection dataset show that the PHD-EOC strikes a better balance between the diverse base classifiers and classification

  6. Generativity and Flourishing

    Science.gov (United States)

    Snow, Nancy

    2015-01-01

    The psychological construct of "generativity" was introduced by Erik Erikson in "Childhood and Society" in 1950. This rich and complex notion encompasses the constellation of desires, concerns and commitments that motivate individuals and societies to pass on legacies to future generations. "Flourishing," which means,…

  7. Genome-Based Studies of Marine Microorganisms to Maximize the Diversity of Natural Products Discovery for Medical Treatments

    Directory of Open Access Journals (Sweden)

    Xin-Qing Zhao

    2011-01-01

    Full Text Available Marine microorganisms are rich source for natural products which play important roles in pharmaceutical industry. Over the past decade, genome-based studies of marine microorganisms have unveiled the tremendous diversity of the producers of natural products and also contributed to the efficiency of harness the strain diversity and chemical diversity, as well as the genetic diversity of marine microorganisms for the rapid discovery and generation of new natural products. In the meantime, genomic information retrieved from marine symbiotic microorganisms can also be employed for the discovery of new medical molecules from yet-unculturable microorganisms. In this paper, the recent progress in the genomic research of marine microorganisms is reviewed; new tools of genome mining as well as the advance in the activation of orphan pathways and metagenomic studies are summarized. Genome-based research of marine microorganisms will maximize the biodiscovery process and solve the problems of supply and sustainability of drug molecules for medical treatments.

  8. Consequences of harvesting for genetic diversity in American ginseng (Panax quinquefolius L.): A simulation study

    Science.gov (United States)

    Cruse-Sanders, J. M.; Hamrick, J.L.; Ahumada, J.A.

    2005-01-01

    American ginseng, Panax quinquefolius L., is one of the most heavily traded medicinal plants in North America. The effect of harvest on genetic diversity in ginseng was measured with a single generation culling simulation program. Culling scenarios included random harvest at varying levels, legal limit random harvest and legal limit mature plant harvest. The legal limit was determined by the proportion of legally harvestable plants per population (% mature plants per population). Random harvest at varying levels resulted in significant loss of genetic diversity, especially allelic richness. Relative to initial levels, average within-population genetic diversity (H e) was significantly lower when plants were culled randomly at the legal limit (Mann-Whitney U = 430, p ginseng populations. ?? Springer 2005.

  9. LHCB RICH gas system proposal

    CERN Document Server

    Bosteels, Michel; Haider, S

    2001-01-01

    Both LHCb RICH will be operated with fluorocarbon as gas radiator. RICH 1 will be filled with 4m^3 of C4F10 and RICH 2 with 100m^3 of CF4. The gas systems will run as a closed loop circulation and a gas recovery system within the closed loop is planned for RICH 1, where the recovery of the CF4 will only be realised during filling and emptying of the detector. Inline gas purification is foreseen for the gas systems in order to limit water and oxygen impurities.

  10. Developments on RICH detectors; Les developpements sur les detecteurs RICH

    Energy Technology Data Exchange (ETDEWEB)

    Besson, P.; Bourgeois, P. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. d`Astrophysique, de la Physique des Particules, de la Physique Nucleaire et de l`Instrumentation Associee

    1996-12-31

    The RICH (ring imaging Cherenkov) detector which is dedicated to Cherenkov radiation detection is described. An improvement made by replacing photo sensible vapor with solid photocathode is studied. A RICH detector prototype with a CsI photocathode has been built in Saclay and used with Saturne. The first results are presented. (A.C.) 13 refs.

  11. Predicting invasion in grassland ecosystems: is exotic dominance the real embarrassment of richness?

    Energy Technology Data Exchange (ETDEWEB)

    Seabloom, Eric W. [Department of Ecology, Evolution, and Behavior, University of MN, St. Paul MN 55108 USA; Borer, Elizabeth T. [Department of Ecology, Evolution, and Behavior, University of MN, St. Paul MN 55108 USA; Buckley, Yvonne [ARC Centre of Excellence for Environmental Decisions, School of Biological Sciences, The University of Queensland, Brisbane Queensland 4072 Australia; Cleland, Elsa E. [Ecology, Behavior & Evolution Section, University of California, San Diego La Jolla CA 92093 USA; Davies, Kendi [Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO 80309 USA; Firn, Jennifer [Queensland University of Technology, Biogeosciences, Brisbane Queensland 4000 Australia; Harpole, W. Stanley [Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA; Hautier, Yann [Department of Ecology, Evolution, and Behavior, University of MN, St. Paul MN 55108 USA; Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190 CH-8057 Zurich Switzerland; Lind, Eric [Department of Ecology, Evolution, and Behavior, University of MN, St. Paul MN 55108 USA; MacDougall, Andrew [Department of Integrative Biology, University of Guelph, Guelph Ontario N1G 2W1 Canada; Orrock, John L. [Department of Zoology, University of Wisconsin, Madison WI 53706 USA; Prober, Suzanne M. [CSIRO Ecosystem Sciences, Private Bag 5 Wembley WA 6913 Australia; Adler, Peter [Department of Wildland Resources and the Ecology Center, Utah State University, Logan UT 84322 USA; Alberti, Juan [Instituto de Investigaciones Marinas y Costeras (UNMdP-CONICET), Mar del Plata Argentina; Michael Anderson, T. [Department of Biology, Wake Forest University, Winston-Salem NC 27109 USA; Bakker, Jonathan D. [School of Environmental and Forest Sciences, University of Washington, Seattle WA 98195-4115 USA; Biederman, Lori A. [Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA; Blumenthal, Dana [Rangeland Resources Research Unit, USDA Agricultural Research Service, Fort Collins CO 80526 USA; Brown, Cynthia S. [Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins CO 80523 USA; Brudvig, Lars A. [Department of Plant Biology, Michigan State University, East Lansing MI 48824 USA; Caldeira, Maria [Centro de Estudos Florestais, Instituto Superior de Agronomia, Technical University of Lisbon, Lisbon Portugal; Chu, Chengjin [School of Life Sciences, Lanzhou University, Lanzhou 730000 China; Crawley, Michael J. [Department of Biology, Imperial College London, Silwood Park Ascot SL5 7PY UK; Daleo, Pedro [Instituto de Investigaciones Marinas y Costeras (UNMdP-CONICET), Mar del Plata Argentina; Damschen, Ellen I. [Department of Zoology, University of Wisconsin, Madison WI 53706 USA; D' Antonio, Carla M. [Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara CA 93106 USA; DeCrappeo, Nicole M. [U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, Corvallis OR 97331 USA; Dickman, Chris R. [Desert Ecology Research Group, School of Biological Sciences, University of Sydney, Sydney NSW 2006 Australia; Du, Guozhen [School of Life Sciences, Lanzhou University, Lanzhou 730000 China; Fay, Philip A. [USDA-ARS Grassland Soil and Water Research Lab, Temple TX 76502 USA; Frater, Paul [Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA; Gruner, Daniel S. [Department of Entomology, University of Maryland, College Park MD 20742 USA; Hagenah, Nicole [School of Life Sciences, University of KwaZulu-Natal, Scottsville Pietermaritzburg 3209 South Africa; Department of Ecology, Evolutionary Biology, Yale University, New Haven CT 06520 USA; Hector, Andrew [Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190 CH-8057 Zurich Switzerland; Helm, Aveliina [Institute of Ecology and Earth Sciences, University of Tartu, Tartu Estonia; Hillebrand, Helmut [Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University, Wilhelmshaven Germany; Hofmockel, Kirsten S. [Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA; Humphries, Hope C. [INSTAAR, University of Colorado, Boulder CO 80309-0450 USA; Iribarne, Oscar [Instituto de Investigaciones Marinas y Costeras (UNMdP-CONICET), Mar del Plata Argentina; Jin, Virginia L. [USDA-ARS Agroecosystem Management Research Unit, Lincoln NE 68583 USA; Kay, Adam [Biology Department, University of St. Thomas, Saint Paul MN 55105 USA; Kirkman, Kevin P. [School of Life Sciences, University of KwaZulu-Natal, Scottsville Pietermaritzburg 3209 South Africa; Klein, Julia A. [Department Forest, Rangeland & Watershed Stewardship, Colorado State University, Fort Collins CO 80523-1472 USA; Knops, Johannes M. H. [School of Biological Sciences, University of Nebraska, Lincoln NE 68588 USA; La Pierre, Kimberly J. [Department of Ecology, Evolutionary Biology, Yale University, New Haven CT 06520 USA; Ladwig, Laura M. [Department of Biology, University of New Mexico, Albuquerque NM 87103 USA; Lambrinos, John G. [Department of Horticulture, Oregon State University, Corvallis OR 97331 USA; Leakey, Andrew D. B. [Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana IL 61801 USA; Li, Qi [Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008 Qinghai China; Li, Wei [Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming 650224 China; McCulley, Rebecca [Department of Plant & Soil Sciences, University of Kentucky, Lexington KY 40546 USA; Melbourne, Brett [Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO 80309 USA; Mitchell, Charles E. [Department of Biology, University of North Carolina, Chapel Hill NC 27599 USA; Moore, Joslin L. [Australian Research Centre for Urban Ecology, Melbourne, c/o School of Botany, University of Melbourne, Melbourne Victoria 3010 Australia; Morgan, John [Department of Botany, La Trobe University, Bundoora 3086 Victoria Australia; Mortensen, Brent [Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA; O' Halloran, Lydia R. [Department of Zoology, Oregon State University, Corvallis OR 97331 USA; Pärtel, Meelis [Institute of Ecology and Earth Sciences, University of Tartu, Tartu Estonia; Pascual, Jesús [Instituto de Investigaciones Marinas y Costeras (UNMdP-CONICET), Mar del Plata Argentina; Pyke, David A. [U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, Corvallis OR 97331 USA; Risch, Anita C. [Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf Switzerland; Salguero-Gómez, Roberto [ARC Centre of Excellence for Environmental Decisions, School of Biological Sciences, The University of Queensland, Brisbane Queensland 4072 Australia; Sankaran, Mahesh [National Centre for Biological Sciences, GKVK Campus, Bellary Road Bangalore 560065 India; Schuetz, Martin [Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf Switzerland; Simonsen, Anna [Department of Ecology & Evolutionary Biology, University of Toronto, Toronto ON M5S 3B2 Canada; Smith, Melinda [Department of Biology, Colorado State University, Fort Collins CO 80523 USA; Stevens, Carly [Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ UK; Sullivan, Lauren [Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011 USA; Wardle, Glenda M. [Desert Ecology Research Group, School of Biological Sciences, University of Sydney, Sydney NSW 2006 Australia; Wolkovich, Elizabeth M. [Biodiversity Research Centre, University of British Columbia, Vancouver V6T 1Z4 Canada; Wragg, Peter D. [Department of Ecology, Evolution, and Behavior, University of MN, St. Paul MN 55108 USA; Wright, Justin [Department of Biology, Duke University, Durham NC 27708 USA; Yang, Louie [Department of Entomology, University of California, Davis CA 95616 USA

    2013-10-16

    Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, native community diversity, herbivore pressure, and nutrient limitation on exotic plant dominance. Despite its widespread use, exotic richness was a poor proxy for exotic dominance at low exotic richness, because sites that contained few exotic species ranged from relatively pristine (low exotic richness and cover) to almost completely exotic-dominated ones (low exotic richness but high exotic cover). Both exotic cover and richness were predicted by native plant diversity (native grass richness) and land use (distance to cultivation). Although climate was important for predicting both exotic cover and richness, climatic factors predicting cover (precipitation variability) differed from those predicting richness (maximum temperature and mean temperature in the wettest quarter). Herbivory and nutrient limitation did not predict exotic richness or cover. Exotic dominance was greatest in areas with low native grass richness at the site- or regional-scale. Although this could reflect native grass displacement, a lack of biotic resistance is a more likely explanation, given that grasses comprise the most aggressive invaders. These findings underscore the need to move beyond richness as a surrogate for the extent of invasion, because this metric confounds monodominance with invasion resistance. Monitoring

  12. Predicting invasion in grassland ecosystems: is exotic dominance the real embarrassment of richness?

    Science.gov (United States)

    Seabloom, Eric; Borer, Elizabeth; Buckley, Yvonne; Cleland, Elsa E.; Davies, Kendi; Firn, Jennifer; Harpole, W. Stanley; Hautier, Yann; Lind, Eric M.; MacDougall, Andrew; Orrock, John L.; Prober, Suzanne M.; Adler, Peter; Alberti, Juan; Anderson, T. Michael; Bakker, Jonathan D.; Biederman, Lori A.; Blumenthal, Dana; Brown, Cynthia S.; Brudvig, Lars A.; Caldeira, Maria; Chu, Cheng-Jin; Crawley, Michael J.; Daleo, Pedro; Damschen, Ellen Ingman; D'Antonio, Carla M.; DeCrappeo, Nicole M.; Dickman, Chris R.; Du, Guozhen; Fay, Philip A.; Frater, Paul; Gruner, Daniel S.; Hagenah, Nicole; Hector, Andrew; Helm, Aveliina; Hillebrand, Helmut; Hofmockel, Kirsten S.; Humphries, Hope C.; Iribarne, Oscar; Jin, Virginia L.; Kay, Adam; Kirkman, Kevin P.; Klein, Julia A.; Knops, Johannes M.H.; La Pierre, Kimberly J.; Ladwig, Laura M.; ,; John, G.; Leakey, Andrew D.B.; Li, Qi; Li, Wei; McCulley, Rebecca; Melbourne, Brett; ,; Charles, E.; Moore, Joslin L.; Morgan, John; Mortensen, Brent; O'Halloran, Lydia R.; Pärtel, Meelis; Pascual, Jesús; Pyke, David A.; Risch, Anita C.; Salguero-Gómez, Roberto; Sankaran, Mahesh; Schuetz, Martin; Simonsen, Anna; Smith, Melinda; Stevens, Carly; Sullivan, Lauren; Wardle, Glenda M.; Wolkovich, Elizabeth M.; Wragg, Peter D.; Wright, Justin; Yang, Louie

    2013-01-01

    Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, native community diversity, herbivore pressure, and nutrient limitation on exotic plant dominance. Despite its widespread use, exotic richness was a poor proxy for exotic dominance at low exotic richness, because sites that contained few exotic species ranged from relatively pristine (low exotic richness and cover) to almost completely exotic-dominated ones (low exotic richness but high exotic cover). Both exotic cover and richness were predicted by native plant diversity (native grass richness) and land use (distance to cultivation). Although climate was important for predicting both exotic cover and richness, climatic factors predicting cover (precipitation variability) differed from those predicting richness (maximum temperature and mean temperature in the wettest quarter). Herbivory and nutrient limitation did not predict exotic richness or cover. Exotic dominance was greatest in areas with low native grass richness at the site- or regional-scale. Although this could reflect native grass displacement, a lack of biotic resistance is a more likely explanation, given that grasses comprise the most aggressive invaders. These findings underscore the need to move beyond richness as a surrogate for the extent of invasion, because this metric confounds monodominance with invasion resistance. Monitoring

  13. Predicting invasion in grassland ecosystems: Is exotic dominance the real embarrassment of richness?

    Science.gov (United States)

    Seabloom, Eric; Borer, Elizabeth; Buckley, Yvonne; Cleland, Elsa E.; Davies, Kendi; Firn, Jennifer; Harpole, W. Stanley; Hautier, Yann; Lind, Eric M.; MacDougall, Andrew; Orrock, John L.; Prober, Suzanne M.; Adler, Peter; Alberti, Juan; Anderson, T. Michael; Bakker, Jonathan D.; Biederman, Lori A.; Blumenthal, Dana; Brown, Cynthia S.; Brudvig, Lars A.; Caldeira, Maria; Chu, Cheng-Jin; Crawley, Michael J.; Daleo, Pedro; Damschen, Ellen Ingman; D'Antonio, Carla M.; DeCrappeo, Nicole M.; Dickman, Chris R.; Du, Guozhen; Fay, Philip A.; Frater, Paul; Gruner, Daniel S.; Hagenah, Nicole; Hector, Andrew; Helm, Aveliina; Hillebrand, Helmut; Hofmockel, Kirsten S.; Humphries, Hope C.; Iribarne, Oscar; Jin, Virginia L.; Kay, Adam; Kirkman, Kevin P.; Klein, Julia A.; Knops, Johannes M.H.; La Pierre, Kimberly J.; Ladwig, Laura M.; ,; John, G.; Leakey, Andrew D.B.; Li, Qi; Li, Wei; McCulley, Rebecca; Melbourne, Brett; ,; Charles, E.; Moore, Joslin L.; Morgan, John; Mortensen, Brent; O'Halloran, Lydia R.; Pärtel, Meelis; Pascual, Jesús; Pyke, David A.; Risch, Anita C.; Salguero-Gómez, Roberto; Sankaran, Mahesh; Schuetz, Martin; Simonsen, Anna; Smith, Melinda; Stevens, Carly; Sullivan, Lauren; Wardle, Glenda M.; Wolkovich, Elizabeth M.; Wragg, Peter D.; Wright, Justin; Yang, Louie

    2013-01-01

    Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, native community diversity, herbivore pressure, and nutrient limitation on exotic plant dominance. Despite its widespread use, exotic richness was a poor proxy for exotic dominance at low exotic richness, because sites that contained few exotic species ranged from relatively pristine (low exotic richness and cover) to almost completely exotic-dominated ones (low exotic richness but high exotic cover). Both exotic cover and richness were predicted by native plant diversity (native grass richness) and land use (distance to cultivation). Although climate was important for predicting both exotic cover and richness, climatic factors predicting cover (precipitation variability) differed from those predicting richness (maximum temperature and mean temperature in the wettest quarter). Herbivory and nutrient limitation did not predict exotic richness or cover. Exotic dominance was greatest in areas with low native grass richness at the site- or regional-scale. Although this could reflect native grass displacement, a lack of biotic resistance is a more likely explanation, given that grasses comprise the most aggressive invaders. These findings underscore the need to move beyond richness as a surrogate for the extent of invasion, because this metric confounds monodominance with invasion resistance. Monitoring

  14. Absorptive Capacity and Diversity

    DEFF Research Database (Denmark)

    Kristinsson, Kári

    overlooked area of research. Although research based on Cohen and Levinthal‘s work has made considerable impact, there is scarcity of research on certain fundamental points argued by Cohen and Levinthal. Among these is the importance of employee diversity as well as the type and nature of interaction between...... that contribute to the neo-Schumpeterian economics literature and hopefully inspires further research into this area. The main findings of the dissertation can be divided into four distinct parts. First, diversity of individuals within firms is associated with firm innovative performance. This is in line...... with the arguments put forth by Cohen and Levinthal and subsequent researchers, but has not been verified empirically before. Second, the relationship between the diversity of individuals and innovative performance and idea generation is moderated by adherence to goals. This result might help to explain...

  15. An Algorithmic Diversity Diet?

    DEFF Research Database (Denmark)

    Sørensen, Jannick Kirk; Schmidt, Jan-Hinrik

    2016-01-01

    With the growing influence of personalized algorithmic recommender systems on the exposure of media content to users, the relevance of discussing the diversity of recommendations increases, particularly as far as public service media (PSM) is concerned. An imagined implementation of a diversity...... diet system however triggers not only the classic discussion of the reach – distinctiveness balance for PSM, but also shows that ‘diversity’ is understood very differently in algorithmic recommender system communities than it is editorially and politically in the context of PSM. The design...... of a diversity diet system generates questions not just about editorial power, personal freedom and techno-paternalism, but also about the embedded politics of recommender systems as well as the human skills affiliated with PSM editorial work and the nature of PSM content....

  16. Organic farming and heterogeneous landscapes positively affect different measures of plant diversity

    National Research Council Canada - National Science Library

    Rader, Romina; Birkhofer, Klaus; Schmucki, Reto; Smith, Henrik G; Stjernman, Martin; Lindborg, Regina; McKenzie, Ailsa

    2014-01-01

    ...) and farm management intensity (organic vs. conventional farming). Plant species richness and functional diversity metrics all responded positively to landscape heterogeneity, with the strongest effect occurring on conventional...

  17. The Fynbos and sUcculent Karoo biomes do not have exceptional local ant richness.

    Science.gov (United States)

    Braschler, Brigitte; Chown, Steven L; Gaston, Kevin J

    2012-01-01

    The Fynbos (FB) and Succulent Karoo biomes (SKB) have high regional plant diversity despite relatively low productivity. Local diversity in the region varies but is moderate. For insects, previous work suggests that strict phytophages, but not other taxa, may have high regional richness. However, what has yet to be investigated is whether the local insect species richness of FB and SKB is unusual for a region of this productivity level at this latitude, and whether regional richness is also high. Here we determine whether this is the case for ants. We use species richness data from pitfall traps in the FB and SKB in the Western Cape Province, South Africa and a global dataset of local ant richness extracted from the literature. We then relate the globally derived values of local richness to two energy-related predictors--productive energy (NDVI) and temperature, and to precipitation, and compare the data from the FB and SKB with these relationships. We further compare our local richness estimates with that of similar habitats worldwide, and regional ant richness with estimates derived from other regions. The local ant species richness of the FB and SKB falls within the general global pattern relating ant richness to energy, and is similar to that in comparable habitats elsewhere. At a regional scale, the richness of ants across all of our sites is not exceptional by comparison with other regional estimates from across the globe. Local richness of ants in the FB and SKB is not exceptional by global standards. Initial analyses suggest that regional diversity is also not exceptional for the group. It seems unlikely that the mechanisms which have contributed to the development of extraordinarily high regional plant diversity in these biomes have had a strong influence on the ants.

  18. Plant functional diversity enhances associations of soil fungal diversity with vegetation and soil in the restoration of semiarid sandy grassland.

    Science.gov (United States)

    Zuo, Xiaoan; Wang, Shaokun; Lv, Peng; Zhou, Xin; Zhao, Xueyong; Zhang, Tonghui; Zhang, Jing

    2016-01-01

    The trait-based approach shows that plant functional diversity strongly affects ecosystem properties. However, few empirical studies show the relationship between soil fungal diversity and plant functional diversity in natural ecosystems. We investigated soil fungal diversity along a restoration gradient of sandy grassland (mobile dune, semifixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China, using the denaturing gradient gel electrophoresis of 18S rRNA and gene sequencing. We also examined associations of soil fungal diversity with plant functional diversity reflected by the dominant species' traits in community (community-weighted mean, CWM) and the dispersion of functional trait values (FD is). We further used the structure equation model (SEM) to evaluate how plant richness, biomass, functional diversity, and soil properties affect soil fungal diversity in sandy grassland restoration. Soil fungal richness in mobile dune and semifixed dune was markedly lower than those of fixed dune and grassland (P functional diversity explained nearly 70% variances of soil fungal richness. Strong association of soil fungal richness with the dominant species in the community supported the mass ratio hypothesis. Our results clearly highlight the role of plant functional diversity in enhancing associations of soil fungal diversity with community structure and soil properties in sandy grassland ecosystems.

  19. Flood disturbance and predator-prey effects on regional gradients in species diversity.

    Science.gov (United States)

    Mori, Terutaka; Saitoh, Takashi

    2014-01-01

    The effects of both abiotic factors and biotic interactions among guilds (i.e., inter-guild effects) have been suggested to be important for understanding spatial variation in species diversity; however, compared to the abiotic effects, the processes by which the inter-guild effects are mediated have been little described. Hence, we investigated stream invertebrate assemblages on Hokkaido Island, Japan, and assessed how the processes of determining regional patterns in species diversity differed among guilds (collector-filterers, collector-gatherers/shredders, scrapers, and predators) by taking both inter-guild and abiotic effects into consideration using Bayesian networks. Collector-gatherers/shredders, collector-filterers, and predators exhibited significant regional gradients in taxonomic richness. Gradients in the former two guilds can be generated by variation in flood disturbance regardless of interactions with other guilds. The gradient in predator taxonomic richness was indirectly related to the disturbance and was directly generated by bottom-up effects through their prey (collector-gatherers/shredders and collector-filterers). We found that not only environmental factors, but also inter-guild effects may be essential for forming the regional gradient in predators, unlike those for collector-gatherers/shredders and collector-filterers. The processes underlying the regional variation in taxonomic richness of the three guilds are interpreted in terms of the "more individuals" hypothesis, facilitation, and predator-prey relationships.

  20. Impact of HIV-1 genetic diversity on plasma HIV-1 RNA Quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test.

    Science.gov (United States)

    Rouet, François; Chaix, Marie-Laure; Nerrienet, Eric; Ngo-Giang-Huong, Nicole; Plantier, Jean-Christophe; Burgard, Marianne; Peeters, Martine; Damond, Florence; Ekouevi, Didier Koumavi; Msellati, Philippe; Ferradini, Laurent; Rukobo, Sandra; Maréchal, Valérie; Schvachsa, Nilda; Wakrim, Lahcen; Rafalimanana, Christian; Rakotoambinina, Benjamin; Viard, Jean-Paul; Seigneurin, Jean-Marie; Rouzioux, Christine

    2007-08-01

    The high genetic diversity of HIV-1 has a major impact on the quantification of plasma HIV-1 RNA, representing an increasingly difficult challenge. A total of 898 plasma specimens positive for HIV-1 RNA by commercial assays (Amplicor v1.5; Roche Diagnostic Systems, Alameda, CA or Versant v3.0; Bayer Diagnostics, Emeryville, CA) were tested using the Agence Nationale de Recherches sur le SIDA second-generation (G2) real-time reverse transcriptase polymerase chain reaction (RT-PCR) test: 518 samples containing HIV-1 of known subtype, including 88 from 2 subtype panels and 430 harboring B (n = 266) and non-B (n = 164) group M HIV-1 subtypes from patients followed up in 2002 through 2005 at Necker Hospital (Paris, France), and 380 samples from 10 different countries (Argentina, Cambodia, Cameroon, Central African Republic, France, Ivory Coast, Madagascar, Morocco, Thailand, and Zimbabwe). HIV-1 RNA values obtained by G2 real-time PCR were highly correlated with those obtained by the Amplicor v1.5 for B and non-B subtypes (R = 0.892 and 0.892, respectively) and for samples from diverse countries (R = 0.867 and 0.893 for real-time PCR vs. Amplicor v1.5 and real-time PCR vs. Versant v3.0, respectively). Approximately 30% of specimens harboring non-B subtypes were underquantified by at least -0.51 log10 in Amplicor v1.5 versus 5% underquantified in G2 real-time PCR. Discrepant results were also obtained with subtype B samples (14% underquantified by Amplicor v1.5 vs. 7% by G2 real-time PCR). Similar percentages were observed when comparing results obtained with the G2 real-time PCR assay with those obtained using the Versant assay. Addressing HIV-1 diversity, continual monitoring of HIV-1 RNA assays, together with molecular epidemiology studies, is required to improve the accuracy of all HIV RNA assays.

  1. Mesoscale architecture shapes initiation and richness of spontaneous network activity.

    Science.gov (United States)

    Okujeni, Samora; Kandler, Steffen; Egert, Ulrich

    2017-03-14

    Spontaneous activity in the absence of external input, including propagating waves of activity, is a robust feature of neuronal networks in vivo and in vitro. The neurophysiological and anatomical requirements for initiation and persistence of such activity, however, are poorly understood, as is their role in the function of neuronal networks. Computational network studies indicate that clustered connectivity may foster the generation, maintenance and richness of spontaneous activity. Since this mesoscale architecture cannot be systematically modified in intact tissue, testing these predictions is impracticable in vivo. Here, we investigate how the mesoscale structure shapes spontaneous activity in generic networks of rat cortical neurons in vitro. In these networks, neurons spontaneously arrange into local clusters with high neurite density and form fasciculating long-range axons. We modified this structure by modulation of protein kinase C, an enzyme regulating neurite growth and cell migration. Inhibition of protein kinase C reduced neuronal aggregation and fasciculation of axons, i.e. promoted uniform architecture. Conversely, activation of protein kinase C promoted aggregation of neurons into clusters, local connectivity and bundling of long-range axons. Supporting predictions from theory, clustered networks were more spontaneously active and generated diverse activity patterns. Neurons within clusters received stronger synaptic inputs and displayed increased membrane potential fluctuations. Intensified clustering promoted the initiation of synchronous bursting events but entailed incomplete network recruitment. Moderately clustered networks appear optimal for initiation and propagation of diverse patterns of activity. Our findings support a crucial role of the mesoscale architectures in the regulation of spontaneous activity dynamics.SIGNIFICANCE STATEMENTComputational studies predict richer and persisting spatio-temporal patterns of spontaneous activity in

  2. Diversity's Calling

    Science.gov (United States)

    Cooper, Kenneth J.

    2011-01-01

    This article discusses how a Harvard-educated scholar of English and poetry, Dr. M. Lee Pelton puts a prominent face on changes that are underway at Boston's Emerson College. Faced with a public controversy over its limited faculty diversity, Emerson College has responded with a spate of hirings and promotions of minorities, capped by the…

  3. Exposing diversity

    DEFF Research Database (Denmark)

    Nørtoft, Kamilla; Nordentoft, Helle Merete

    in the homes of older people and in pedagogical institutions targeting older people. In the paper we look at the potentials and challenges in working with ethnographic video narratives as a pedagogical tool. Our findings indicate that the use of video narratives has the potential to expose the diversity...

  4. Kitobo Forest of Kenya, a unique hotspot of herpetofaunal diversity

    Directory of Open Access Journals (Sweden)

    Patrick K. Malonza

    2011-12-01

    Full Text Available Herpetologically, the remoteness of Kitobo forest in south-eastern Kenya has partly contributed to it remaining virtually un-explored until 2007. Three surveys were conducted in December 2007, December 2009 and April 2010 aimed at generating a comprehensive list of the forest amphibians and reptiles. Using largely timed-species count method, 13 species of amphibians representing eight families and 32 reptiles belonging to 11 families were recorded. Overall species diversity was highest during the 2007 sampling. The richness and abundance of amphibians was highest during the April 2010 sampling period when the amount of rainfall was also highest. The results of species accumulation curves of the three sampling periods did not plateau demonstrating that more species occur in this forest. Pressure on this forest fragment from the adjacent local people is high which in addition to the annual floods threatens its long-term survival. For example the distribution and abundance of some forest associated species such as the tree frogs Leptopelis flavomaculatus and Hyperolius puncticulatus appear to fluctuate with flood events and may decline in future. Considering the forest associated herpetofanua recorded, Kitobo forest is zoogeographically assignable to the East African coastal forest biodiversity hotspot. The documentation of high species richness and diversity in this small forest fragment strongly highlight its biodiversity importance and place it among the most important sites for the conservation of reptiles and amphibians in Kenya.

  5. BALB/c and C57BL/6 Mice Differ in Polyreactive IgA Abundance, which Impacts the Generation of Antigen-Specific IgA and Microbiota Diversity

    NARCIS (Netherlands)

    Fransen, Floris; Zagato, Elena; Mazzini, Elisa; Fosso, Bruno; Manzari, Caterina; El Aidy, Sahar; Chiavelli, Andrea; D'Erchia, Anna Maria; Sethi, Maya K; Pabst, Oliver; Marzano, Marinella; Moretti, Silvia; Romani, Luigina; Penna, Giuseppe; Pesole, Graziano; Rescigno, Maria

    2015-01-01

    The interrelationship between IgAs and microbiota diversity is still unclear. Here we show that BALB/c mice had higher abundance and diversity of IgAs than C57BL/6 mice and that this correlated with increased microbiota diversity. We show that polyreactive IgAs mediated the entrance of non-invasive

  6. Response diversity determines the resilience of ecosystems to environmental change.

    Science.gov (United States)

    Mori, Akira S; Furukawa, Takuya; Sasaki, Takehiro

    2013-05-01

    A growing body of evidence highlights the importance of biodiversity for ecosystem stability and the maintenance of optimal ecosystem functionality. Conservation measures are thus essential to safeguard the ecosystem services that biodiversity provides and human society needs. Current anthropogenic threats may lead to detrimental (and perhaps irreversible) ecosystem degradation, providing strong motivation to evaluate the response of ecological communities to various anthropogenic pressures. In particular, ecosystem functions that sustain key ecosystem services should be identified and prioritized for conservation action. Traditional diversity measures (e.g. 'species richness') may not adequately capture the aspects of biodiversity most relevant to ecosystem stability and functionality, but several new concepts may be more appropriate. These include 'response diversity', describing the variation of responses to environmental change among species of a particular community. Response diversity may also be a key determinant of ecosystem resilience in the face of anthropogenic pressures and environmental uncertainty. However, current understanding of response diversity is poor, and we see an urgent need to disentangle the conceptual strands that pervade studies of the relationship between biodiversity and ecosystem functioning. Our review clarifies the links between response diversity and the maintenance of ecosystem functionality by focusing on the insurance hypothesis of biodiversity and the concept of functional redundancy. We provide a conceptual model to describe how loss of response diversity may cause ecosystem degradation through decreased ecosystem resilience. We explicitly explain how response diversity contributes to functional compensation and to spatio-temporal complementarity among species, leading to long-term maintenance of ecosystem multifunctionality. Recent quantitative studies suggest that traditional diversity measures may often be uncoupled from

  7. Riqueza, abundância e diversidade de Euglossina (Hymenoptera, Apidae em três áreas da Reserva Biológica Guaribas, Paraíba, Brasil Richness, abundance, and diversity of Euglossina (Hymenoptera, Apidae at three areas of the Guaribas Biological Reserve, Paraíba, Brazil

    Directory of Open Access Journals (Sweden)

    Alysson K. P. de Souza

    2005-06-01

    737 males belonging to five species were sampled, and from the Transition area 727 males belonging to six species were sampled. The highest diversity (H' = 0.94 and richness were obtained from the Forest area. The Sørensen binary similarity coefficient showed that regarding species composition Savanna-like vegetation and Transition were the most similar areas (Ss = 0.92. The Morisita similarity coefficient showed that Forest and Transition areas were identical (Cmh = 1 regarding relative abundance of species. Transition area is more similar to an open area of Savanna-like vegetation, in terms of composition and diversity, and more similar to the Forest area, regarding relative abundance, suggesting that some Forest species also forage in the Transition area.

  8. Semantic Richness Effects in Syntactic Classification: The Role of Feedback

    Science.gov (United States)

    Yap, Melvin J.; Pexman, Penny M.

    2016-01-01

    Words with richer semantic representations are recognized faster across a range of lexical processing tasks. The most influential account of this finding is based on the idea that semantic richness effects are mediated by feedback from semantic-level to lower-level representations. In an earlier lexical decision study, Yap et al. (2015) tested this claim by examining the joint effects of stimulus quality and four semantic richness dimensions (imageability, number of features, semantic neighborhood density, semantic diversity). The results of that study showed that joint effects of stimulus quality and richness were generally additive, consistent with the idea that semantic feedback does not typically reach the earliest levels of representation in lexical decision. The present study extends this earlier work by investigating the joint effects of stimulus quality and the same four semantic richness dimensions on syntactic classification performance (is this a noun or verb?), which places relatively more emphasis on semantic processing. Additive effects of stimulus quality and richness were found for two of the four targeted dimensions (concreteness, number of features) while semantic neighborhood density and semantic diversity did not seem to influence syntactic classification response times. These findings provide further support against the view that semantic information reaches early letter-level processes. PMID:27695431

  9. Richness and distribution of tropical oyster parasites in two oceans.

    Science.gov (United States)

    Pagenkopp Lohan, Katrina M; Hill-Spanik, Kristina M; Torchin, Mark E; Aguirre-Macedo, Leopoldina; Fleischer, Robert C; Ruiz, Gregory M

    2016-08-01

    Parasites can exert strong effects on population to ecosystem level processes, but data on parasites are limited for many global regions, especially tropical marine systems. Characterizing parasite diversity and distributions are the first steps towards understanding the potential impacts of parasites. The Panama Canal serves as an interesting location to examine tropical parasite diversity and distribution, as it is a conduit between two oceans and a hub for international trade. We examined metazoan and protistan parasites associated with ten oyster species collected from both Panamanian coasts, including the Panama Canal and Bocas del Toro. We found multiple metazoan taxa (pea crabs, Stylochus spp., Urastoma cyrinae). Our molecular screening for protistan parasites detected four species of Perkinsus (Perkinsus marinus, Perkinsus chesapeaki, Perkinsus olseni, Perkinsus beihaiensis) and several haplosporidians, including two genera (Minchinia, Haplosporidium). Species richness was higher for the protistan parasites than for the metazoans, with haplosporidian richness being higher than Perkinsus richness. Perkinsus species were the most frequently detected and most geographically widespread among parasite groups. Parasite richness and overlap differed between regions, locations and oyster hosts. These results have important implications for tropical parasite richness and the dispersal of parasites due to shipping associated with the Panama Canal.

  10. Multiscale assessment of patterns of avian species richness

    DEFF Research Database (Denmark)

    Rahbek, C; Graves, G R

    2001-01-01

    The search for a common cause of species richness gradients has spawned more than 100 explanatory hypotheses in just the past two decades. Despite recent conceptual advances, further refinement of the most plausible models has been stifled by the difficulty of compiling high-resolution databases...... (quadrat area, approximately 12,300 to approximately 1,225,000 km(2)). Topography, precipitation, topography x latitude, ecosystem diversity, and cloud cover emerged as the most important predictors of regional variability of species richness in regression models incorporating 16 independent variables...

  11. Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects.

    Science.gov (United States)

    Rainford, James L; Hofreiter, Michael; Nicholson, David B; Mayhew, Peter J

    2014-01-01

    Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward.

  12. Troubling Diversity?

    DEFF Research Database (Denmark)

    Jæger, Kirsten; Jensen, Annie Aarup

    2009-01-01

    Focussing on the cultural encounter between nurses and ethnic minority patients in Danish hospitals, this paper presents the results of a comprehensive analysis of nursing discourses on cultural difference and intercultural contact. Articles from the Danish professional journal ‘The Nurse......', published in the period from 2000 to 2008, pertaining to cultural contact and intercultural understanding have been analyzed in order to uncover nurses' experience of ethnic and cultural diversity and the ways, in which these experiences challenge their cultural and professional expertise. Results...... are related to recent contributions to diversity management theory and intercultural communication theory, calling for a strengthened focus on the historical, political, and social dimensions of intercultural contact. In continuation of these trends, an alternative, theoretical framework...

  13. Functional trait space and the latitudinal diversity gradient

    DEFF Research Database (Denmark)

    Lamanna, Christine; Blonder, Benjamin; Violle, Cyrille

    2014-01-01

    The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (wi...

  14. A healthy gastrointestinal microbiome is dependent on dietary diversity

    Directory of Open Access Journals (Sweden)

    Mark L. Heiman

    2016-05-01

    Major conclusion: Additional research into expanding gut microbial richness by dietary diversity is likely to expand concepts in healthy nutrition, stimulate discovery of new diagnostics, and open up novel therapeutic possibilities.

  15. Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT

    Directory of Open Access Journals (Sweden)

    Edson P. Amorim

    2009-01-01

    Full Text Available The aim of this work was to evaluate the carotenoid content and genetic variability of banana accessions from the Musa germplasm collection held at Embrapa Cassava and Tropical Fruits, Brazil. Forty-two samples were analyzed, including 21 diploids, 19 triploids and two tetraploids. The carotenoid content was analyzed spectrophotometrically and genetic variability was estimated using 653 DArT markers. The average carotenoid content was 4.73 µg.g-1, and ranged from 1.06 µg.g-1 for the triploid Nanica (Cavendish group to 19.24 µg.g-1 for the triploid Saney. The diploids Modok Gier and NBA-14 and the triploid Saney had a carotenoid content that was, respectively, 7-fold, 6-fold and 9-fold greater than that of cultivars from the Cavendish group (2.19 µg.g-1. The mean similarity among the 42 accessions was 0.63 (range: 0.24 to 1.00. DArT analysis revealed extensive genetic variability in accessions from the Embrapa Musa germplasm bank.

  16. Doing Diversity

    DEFF Research Database (Denmark)

    Just, Sine Nørholm; Christiansen, Tanja Juul

    2012-01-01

    Questions of agency in text–audience relations are less studied than other aspects of rhetorical agency. We suggest conceptualizing and analyzing the relationship between texts and audiences from the perspective of performativity, as it has been developed by Judith Butler. Thus, we argue that tex...... demonstrate the explanatory potential of the performative framework. Subsequently, we discuss how the concept of personae may provide a basis for alternatives to the restrictive positioning that currently dominates diversity management rhetoric....

  17. Teaching Diversity

    OpenAIRE

    Kay Young McChesney

    2015-01-01

    This article is targeted to faculty teaching race and ethnicity, racism, diversity, and multicultural courses. Many students equate race with skin color. The premise of this article is that to teach students about the social construction of race, teachers must first know enough science to teach students that race is not biological. This article examines the biology of race by showing how advances in DNA sequencing led ...

  18. The evolution of African plant diversity

    OpenAIRE

    Hans Peter Linder

    2014-01-01

    Sub-Saharan Africa includes some 45,000 plant species. The spatial patterns of this diversity have been well explored. We can group the species into a set of biogeographical regions (largely co-incident with regions defined for terrestrial vertebrate groups). Furthermore, we know that the diversity is unevenly distributed, with southern Africa (especially the south-western tip) disproportionally species rich, while the West African interior is disproportionally species poor. However, the ...

  19. Plant species richness leaves a legacy of enhanced root litter-induced decomposition in soil

    NARCIS (Netherlands)

    Cong, Wen-Feng; van Ruijven, Jasper; van der Werf, Wopke; De Deyn, Gerlinde B.; Mommer, Liesje; Berendse, Frank; Hoffland, Ellis

    2015-01-01

    Increasing plant species richness generally enhances plant biomass production, which may enhance accumulation of carbon (C) in soil. However, the net change in soil C also depends on the effect of plant diversity on C loss through decomposition of organic matter. Plant diversity can affect organic m

  20. How does pedogenesis drive plant diversity?

    Science.gov (United States)

    Laliberté, Etienne; Grace, James B.; Huston, Michael A.; Lambers, Hans; Teste, François P.; Turner, Benjamin L.; Wardle, David A.

    2013-01-01

    Some of the most species-rich plant communities occur on ancient, strongly weathered soils, whereas those on recently developed soils tend to be less diverse. Mechanisms underlying this well-known pattern, however, remain unresolved. Here, we present a conceptual model describing alternative mechanisms by which pedogenesis (the process of soil formation) might drive plant diversity. We suggest that long-term soil chronosequences offer great, yet largely untapped, potential as 'natural experiments' to determine edaphic controls over plant diversity. Finally, we discuss how our conceptual model can be evaluated quantitatively using structural equation modeling to advance multivariate theories about the determinants of local plant diversity. This should help us to understand broader-scale diversity patterns, such as the latitudinal gradient of plant diversity.

  1. Functionally and phylogenetically diverse plant communities key to soil biota.

    Science.gov (United States)

    Milcu, Alexandru; Allan, Eric; Roscher, Christiane; Jenkins, Tania; Meyer, Sebastian T; Flynn, Dan; Bessler, Holger; Buscot, François; Engels, Christof; Gubsch, Marlén; König, Stephan; Lipowsky, Annett; Loranger, Jessy; Renker, Carsten; Scherber, Christoph; Schmid, Bernhard; Thébault, Elisa; Wubet, Tesfaye; Weisser, Wolfgang W; Scheu, Stefan; Eisenhauer, Nico

    2013-08-01

    Recent studies assessing the role of biological diversity for ecosystem functioning indicate that the diversity of functional traits and the evolutionary history of species in a community, not the number of taxonomic units, ultimately drives the biodiversity--ecosystem-function relationship. Here, we simultaneously assessed the importance of plant functional trait and phylogenetic diversity as predictors of major trophic groups of soil biota (abundance and diversity), six years from the onset of a grassland biodiversity experiment. Plant functional and phylogenetic diversity were generally better predictors of soil biota than the traditionally used species or functional group richness. Functional diversity was a reliable predictor for most biota, with the exception of soil microorganisms, which were better predicted by phylogenetic diversity. These results provide empirical support for the idea that the diversity of plant functional traits and the diversity of evolutionary lineages in a community are important for maintaining higher abundances and diversity of soil communities.

  2. Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists.

    Science.gov (United States)

    Bass, David; Silberman, Jeffrey D; Brown, Matthew W; Pearce, Rebecca A; Tice, Alexander K; Jousset, Alexandre; Geisen, Stefan; Hartikainen, Hanna

    2016-05-01

    A wide diversity of organisms utilize faecal habitats as a rich nutrient source or a mechanism to traverse through animal hosts. We sequenced the 18S rRNA genes of the coprophilic, fruiting body-forming amoeba Guttulinopsis vulgaris and its non-fruiting relatives Rosculus 'ithacus' CCAP 1571/3, R. terrestris n. sp. and R. elongata n. sp. and demonstrate that they are related to the coprophilic flagellate Helkesimastix in a strongly supported, but highly divergent 18S sister clade. PCR primers specific to both clades were used to generate 18S amplicons from a range of environmental and faecal DNA samples. Phylogenetic analysis of the cloned sequences demonstrated a high diversity of uncharacterised sequence types within this clade, likely representing previously described members of the genera Guttulinopsis, Rosculus and Helkesimastix, as well as so-far unobserved organisms. Further, an Illumina MiSeq sequenced set of 18S V4-region amplicons generated from faecal DNAs using universal eukaryote primers showed that core-cercozoan assemblages in faecal samples are as diverse as those found in more conventionally examined habitats. These results reveal many novel lineages, some of which appear to occur preferentially in faecal material, in particular cercomonads and glissomonads. More broadly, we show that faecal habitats are likely untapped reservoirs of microbial eukaryotic diversity.

  3. Optics and radiators for RICH

    CERN Document Server

    Ekelöf, T J C

    1999-01-01

    An overview is given of the basic optics-design principles for Ring Imaging Cherenkov (RICH) counters in High-Energy Physics -- of the earlier evolution of these principles and of the new ideas and techniques that are currently being developed. The characteristics of the different gasses, liquids and solids that are employed as Cherenkov radiators, which are of fundamental importance to the optics design of a RICH counter, are also reviewed.

  4. Global taxonomic diversity of living reptiles.

    Science.gov (United States)

    Pincheira-Donoso, Daniel; Bauer, Aaron M; Meiri, Shai; Uetz, Peter

    2013-01-01

    Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world's diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

  5. An Improved Cluster Richness Estimator

    Energy Technology Data Exchange (ETDEWEB)

    Rozo, Eduardo; /Ohio State U.; Rykoff, Eli S.; /UC, Santa Barbara; Koester, Benjamin P.; /Chicago U. /KICP, Chicago; McKay, Timothy; /Michigan U.; Hao, Jiangang; /Michigan U.; Evrard, August; /Michigan U.; Wechsler, Risa H.; /SLAC; Hansen, Sarah; /Chicago U. /KICP, Chicago; Sheldon, Erin; /New York U.; Johnston, David; /Houston U.; Becker, Matthew R.; /Chicago U. /KICP, Chicago; Annis, James T.; /Fermilab; Bleem, Lindsey; /Chicago U.; Scranton, Ryan; /Pittsburgh U.

    2009-08-03

    Minimizing the scatter between cluster mass and accessible observables is an important goal for cluster cosmology. In this work, we introduce a new matched filter richness estimator, and test its performance using the maxBCG cluster catalog. Our new estimator significantly reduces the variance in the L{sub X}-richness relation, from {sigma}{sub lnL{sub X}}{sup 2} = (0.86 {+-} 0.02){sup 2} to {sigma}{sub lnL{sub X}}{sup 2} = (0.69 {+-} 0.02){sup 2}. Relative to the maxBCG richness estimate, it also removes the strong redshift dependence of the richness scaling relations, and is significantly more robust to photometric and redshift errors. These improvements are largely due to our more sophisticated treatment of galaxy color data. We also demonstrate the scatter in the L{sub X}-richness relation depends on the aperture used to estimate cluster richness, and introduce a novel approach for optimizing said aperture which can be easily generalized to other mass tracers.

  6. An Improved Cluster Richness Estimator

    CERN Document Server

    Rozo, Eduardo; Koester, Benjamin P; McKay, Timothy; Hao, Jiangang; Evrard, August; Wechsler, Risa H; Hansen, Sarah; Sheldon, Erin; Johnston, David; Becker, Matthew; Annis, James; Bleem, Lindsey; Scranton, Ryan

    2008-01-01

    Minimizing the scatter between cluster mass and accessible observables is an important goal for cluster cosmology. In this work, we introduce a new matched filter richness estimator, and test its performance using the maxBCG cluster catalog. Our new estimator significantly reduces the variance in the L_X-richness relation, from \\sigma_{\\ln L_X}^2=(0.86\\pm0.02)^2 to \\sigma_{\\ln L_X}^2=(0.69\\pm0.02)^2. Relative to the maxBCG richness estimate, it also removes the strong redshift dependence of the richness scaling relations, and is significantly more robust to photometric and redshift errors. These improvements are largely due to our more sophisticated treatment of galaxy color data. We also demonstrate the scatter in the L_X-richness relation depends on the aperture used to estimate cluster richness, and introduce a novel approach for optimizing said aperture which can be easily generalized to other mass tracers.

  7. Impacts of Urban Areas and Their Characteristics on Avian Functional Diversity

    Directory of Open Access Journals (Sweden)

    Emily Oliveira Hagen

    2017-07-01

    Full Text Available Urban development is rapidly expanding across the globe and is a major driver of environmental change. Despite considerable improvements in our understanding of how species richness responds to urbanization, there is still insufficient knowledge of how other measures of assemblage composition and structure respond to urban development. Functional diversity metrics provide a useful approach for quantifying ecological function. We compare avian functional diversity in 25 urban areas, located across the globe, with paired non-urban assemblages using a database of 27 functional traits that capture variation in resource use (amount and type of resources and how they are acquired across the 529 species occurring across these assemblages. Using three standard functional diversity metrics (FD, MNTD, and convex hull we quantify observed functional diversity and, using standardized effect sizes, how this diverges from that expected under random community assembly null models. We use regression trees to investigate whether human population density, amount of vegetation and city size (spatial extent of urban land, bio-region and use of semi-natural or agricultural assemblages as a baseline modulate the effect of urbanization on functional diversity. Our analyses suggest that observed functional diversity of urban avian assemblages is not consistently different from that of non-urban assemblages. After accounting for species richness avian functional diversity is higher in cities than areas of semi-natural habitat. This creates a paradox as species responses to urban development are determined by their ecological traits, which should generate assemblages clustered within a narrow range of trait space. Greater habitat diversity within cities compared to semi-natural areas dominated by a single habitat may enhance functional diversity in cities and explain this paradox. Regression trees further suggest that smaller urban areas, lower human population densities

  8. Opposing Responses of Bird Functional Diversity to Vegetation Structural Diversity in Wet and Dry Forest.

    Science.gov (United States)

    Sitters, Holly; York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian

    2016-01-01

    Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion) were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion) were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated with vegetation

  9. Strength in diversity

    CERN Multimedia

    2012-01-01

    Diversity has always been science’s big secret, yet it’s a secret we’ve always been keen to share. CERN was founded on the basis of bringing a diverse mix of people together to pursue common aims, and it’s one of the things that’s driven this Organization’s success over the decades.   Now, we are launching a new diversity programme aimed at strengthening our tradition of inclusiveness. This programme is being launched with a range of key goals in mind for the 2012-2014 timeframe. We’ll be striving to achieve a fair gender balance across all professional categories, and to provide strong gender role models across the Organization. We’ll be improving our career development processes to allow people to progress through both technical and managerial pathways, and we’ll be re-launching workshops that bring people from diverse professions and generations together to share their experience on key aspects of lif...

  10. Paleohydrologic controls on methanogenesis in organic-rich saline aquifers

    Science.gov (United States)

    McIntosh, J.; Petsch, S.; Schlegel, M.; Osborn, S.

    2007-12-01

    Freshwater recharge into the margins of sedimentary basins, during periods of continental glaciation, stimulated microbial methane generation in organic-rich shales and coal beds, by significantly diluting the ambient formation water salinity. Subglacial recharge may have also transported microorganisms and nutrients into the subsurface environment. Methane is generated by a diverse consortium of both acetoclastic and CO2-reducing methanogenic Archaea, and adsorbed onto the organic matter. These shallow methane accumulations account for ~20% of the total U.S. natural gas production. Anaerobic microbial metabolism of shales and coals is in part controlled by the volume of pore waters and fluid composition, amount of extractable organic matter and intermediary substrates, reservoir temperature, and mass transport processes that provide essential rock-derived nutrients and organic acids. Methanogens are most active in low salinity environments (coal cleats, which can in turn modify the subsurface hydrology. Microbial methanogenesis also imparts a strong control on the cycling of carbon, H2, and other elements in the subsurface environment. This presentation will focus on the timing of recharge and establishment of microbial communities within the Upper Devonian black shales, Pennsylvanian coal beds, and overlying glacial drift in the Illinois Basin, and the importance of continued groundwater flow on active methane generation and accumulation. There is an approximately 65-70 per mil depletion in 13C of CH4, relative to the precursor CO2 in the Upper Devonian shales, Pennsylvanian coals, and glacial drift. In addition, there is a linear correlation between the dD values of co- produced formation waters and CH4. Isotope mass-balance modeling results confirm that these isotopic shifts can be produced by coupled acetate fermentation and CO2-reduction. The lowest d13C values for CO2 and CH4 are found in the shallow glacial drift (-14 to 8 per mil, -80 to -68 per mil

  11. Combining geodiversity with climate and topography to account for threatened species richness.

    Science.gov (United States)

    Tukiainen, Helena; Bailey, Joseph J; Field, Richard; Kangas, Katja; Hjort, Jan

    2017-04-01

    Understanding threatened species diversity is important for long-term conservation planning. Geodiversity-the diversity of Earth surface materials, forms, and processes-may be a useful biodiversity surrogate for conservation and have conservation value itself. Geodiversity and species richness relationships have been demonstrated; establishing whether geodiversity relates to threatened species' diversity and distribution pattern is a logical next step for conservation. We used 4 geodiversity variables (rock-type and soil-type richness, geomorphological diversity, and hydrological feature diversity) and 4 climatic and topographic variables to model threatened species diversity across 31 of Finland's national parks. We also analyzed rarity-weighted richness (a measure of site complementarity) of threatened vascular plants, fungi, bryophytes, and all species combined. Our 1-km(2) resolution data set included 271 threatened species from 16 major taxa. We modeled threatened species richness (raw and rarity weighted) with boosted regression trees. Climatic variables, especially the annual temperature sum above 5 °C, dominated our models, which is consistent with the critical role of temperature in this boreal environment. Geodiversity added significant explanatory power. High geodiversity values were consistently associated with high threatened species richness across taxa. The combined effect of geodiversity variables was even more pronounced in the rarity-weighted richness analyses (except for fungi) than in those for species richness. Geodiversity measures correlated most strongly with species richness (raw and rarity weighted) of threatened vascular plants and bryophytes and were weakest for molluscs, lichens, and mammals. Although simple measures of topography improve biodiversity modeling, our results suggest that geodiversity data relating to geology, landforms, and hydrology are also worth including. This reinforces recent arguments that conserving nature

  12. When Generations Collide

    Science.gov (United States)

    Fogg, Piper

    2008-01-01

    When four generations converge in the academic workplace, it can create serious culture clashes. It is happening across college campuses--in offices as diverse as admissions, student affairs, legal affairs, and technology. It is especially striking in the faculty ranks, where generational challenges have extra significance amid recruiting efforts,…

  13. Exposing diversity

    DEFF Research Database (Denmark)

    Nørtoft, Kamilla; Nordentoft, Helle Merete

    . A prominent research theme in health care studies is, therefore, to explicate the gap between theory and practice. The question this paper addresses is how a learning environment can be designed to bridge this theory-practice gap, expose the differences in situated interactions and qualify health...... in the homes of older people and in pedagogical institutions targeting older people. In the paper we look at the potentials and challenges in working with ethnographic video narratives as a pedagogical tool. Our findings indicate that the use of video narratives has the potential to expose the diversity...

  14. Intransitive competition is widespread in plant communities and maintains their species richness

    Science.gov (United States)

    Soliveres, Santiago; Maestre, Fernando T.; Ulrich, Werner; Manning, Peter; Boch, Steffen; Bowker, Matthew A.; Prati, Daniel; Delgado-Baquerizo, Manuel; Quero, José L.; Schöning, Ingo; Gallardo, Antonio; Weisser, Wolfgang; Müller, Jörg; Socher, Stephanie A.; García-Gómez, Miguel; Ochoa, Victoria; Schulze, Ernst-Detlef; Fischer, Markus; Allan, Eric

    2017-01-01

    Intransitive competition networks, those in which there is no single best competitor, may ensure species coexistence. However, their frequency and importance in maintaining diversity in real-world ecosystems remains unclear. We used two large datasets from drylands and agricultural grasslands to assess: 1) the generality of intransitive competition, 2) intransitivity-richness relationships, and 3) effects of two major drivers of biodiversity loss (aridity and land-use intensification) on intransitivity and species richness. Intransitive competition occurred in >65% of sites and was associated with higher species richness. Intransitivity increased with aridity, partly buffering its negative effects on diversity, but was decreased by intensive land use, enhancing its negative effects on diversity. These contrasting responses likely arise because intransitivity is promoted by temporal heterogeneity, which is enhanced by aridity but may decline with land-use intensity. We show that intransitivity is widespread in nature and increases diversity, but it can be lost with environmental homogenization. PMID:26032242

  15. Chemical composition and antioxidant-prooxidant potential of a polyphenolic extract and a proanthocyanidin-rich fraction of apple skin

    Directory of Open Access Journals (Sweden)

    Ana María Mendoza-Wilson

    2016-02-01

    Full Text Available The apple is a food rich in diverse classes of polyphenols (PP, among which the proanthocyanidins (PCs, which are primarily concentrated in the skin, are one of the most abundant. These compounds are of considerable interest for their possible positive health effects because of their antioxidant properties. However, depending on the classes of PP present (chemical composition and their relative concentrations in the apple skin, their antioxidant effects vary and some of their components can even generate prooxidant effects. This work determined the chemical composition and antioxidant-prooxidant potential of a polyphenolic extract (PPE and a proanthocyanidin-rich fraction (PRF of apple skin, along with the contribution of their most abundant individual compounds, based on their copper chelating ability, ease in reducing peroxidase-generated free radicals and TEAC (Trolox-Equivalent Antioxidant Capacity assay. For this purpose, chromatographic and colorimetric methods were used. The majority compounds identified in PPE were flavan-3-ols (44.58%, flavonols (42.89% and dihydrochalcones (11.60%. In PRF, we detected monomers and oligomers from dimers to heptamers, which were composed of 97% (−-epicatechin and 3% (+-catechin. The antioxidant potential was notably higher in PRF than in PPE. The (−-epicatechin monomer and the procyanidin B2 dimer showed more ease in reducing peroxidase-generated free radicals compared to other compounds of the apple skin, whereas phloridzin dihydrochalcone produced prooxidant effects.

  16. Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes

    Science.gov (United States)

    García-Morales, Rodrigo; Badano, Ernesto I.; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E.; Ávila-Gómez, Eva S.

    2016-01-01

    Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others. PMID:27926923

  17. Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes.

    Science.gov (United States)

    García-Morales, Rodrigo; Moreno, Claudia E; Badano, Ernesto I; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E; Ávila-Gómez, Eva S

    2016-01-01

    Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others.

  18. Global variation in woodpecker species richness shaped by tree availability

    DEFF Research Database (Denmark)

    Ilsoe, Sigrid Kistrup; Kissling, W. Daniel; Fjeldsa, Jon

    2017-01-01

    a negative indirect effect on woodpecker species richness. Main conclusions: Global species richness of woodpeckers is primarily shaped by current tree cover and precipitation, reflecting a strong biotic association between woodpeckers and trees. Human influence can have a negative effect on woodpecker...... also showed a strong indirect effect on woodpecker richness via the effects on tree availability. Deep-time tree availability, Quaternary climate change, human influence and other abiotic factors showed weaker direct effects. Human influence had a negative effect on tree availability, and hence....... As an example, woodpeckers (Picidae) are closely associated with trees and woody habitats because of multiple morphological and ecological specializations. In this study, we test whether this strong biotic association causes woodpecker diversity to be closely linked to tree availability at a global scale...

  19. Implication of evolution and diversity in arbuscular and ectomycorrhizal symbioses.

    Science.gov (United States)

    Buscot, François

    2015-01-01

    Being highly sensitive to ecological variations, symbiotic associations should inherently have a limited occurrence in nature. To circumvent this sensitivity and reach their universal distribution, symbioses used three strategies during their evolution, which all generated high biodiversity levels: (i) specialization to a specific environment, (ii) protection of one partner via its internalization into the other, (iii) frequent partner exchange. Mycorrhizal associations follow the 3rd strategy, but also present traits of internalization. As most ancient type, arbuscular mycorrhiza (AM) formed by a monophyletic fungal group with reduced species richness did constantly support the mineral nutrition of terrestrial plants and enabled their ecological radiation and actual biodiversity level. In contrast ectomycorrhiza (EM) evolved later and independently within different taxa of fungi able to degrade complex organic plant residues, and the diversity levels of EM fungal and tree partners are balanced. Despite their different origins and diversity levels, AM and EM fungi display similar patterns of diversity dynamics in ecosystems. At each time or succession interval, a few dominant and many rare fungi are recruited by plants roots from a wide reservoir of propagules. However, the dominant fungal partners are frequently replaced in relation to changes in the vegetation or ecological conditions. While the initial establishment of AM and EM fungal communities corresponds to a neutral recruitment, their further succession is rather driven by niche differentiation dynamics.

  20. Uncovering unseen fungal diversity from plant DNA banks

    Directory of Open Access Journals (Sweden)

    Erin M. Datlof

    2017-08-01

    Full Text Available Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms’ associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae. Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.

  1. Reducing the loss of genetic diversity associated with assisted colonization-like introductions of animals

    Institute of Scientific and Technical Information of China (English)

    Jaana KEKKONEN; Jon E BROMMER

    2015-01-01

    Translocations, especially assisted colonizations, of animals are increasingly used as a conservation management tool. In many cases, however, limited funding and other logistic challenges limit the number of individuals available for translocation. In conservation genetics, small populations are predicted to rapidly lose genetic diversity which can deteriorate population sur-vival. Thus, how worried should we be about the loss of genetic diversity when introducing small, isolated populations? Histori-cal species introductions provide a means to assess these issues. Here we review 13 studies of “assisted colonization-like” intro-ductions of animals, where only a small known number of founders established an isolated population without secondary contact to the source population. We test which factors could be important in retaining genetic diversity in these cases. In many cases, loss in heterozygosity (-12.1%) was detected, and more seriously the loss in allelic richness (-27.8 %). Number of founders seemed to have an effect but it also indicated that high population growth rate could help to retain genetic diversity, i.e. future management actions could be effective even with a limited number of founders if population growth would be enhanced. On the contrary, translocated organisms with longer generation times did not seem to retain more genetic diversity. We advocate that, where possible, future studies on translocated animals should report the loss of genetic diversity (both heterozygosity and allelic richness), which is essential for meta-analyses like this one for deepening our understanding of the genetic consequences of as-sisted colonization, and justifying management decisions [Current Zoology 61 (5): 827–834, 2015].

  2. Vascular plant and vertebrate species richness in national parks of the eastern United States

    Science.gov (United States)

    Hatfield, Jeffrey S.; Myrick, Kaci E.; Huston, Michael A.; Weckerly, Floyd W.; Green, M. Clay

    2013-01-01

    Given the estimates that species diversity is diminishing at 50-100 times the normal rate, it is critical that we be able to evaluate changes in species richness in order to make informed decisions for conserving species diversity. In this study, we examined the potential of vascular plant species richness to be used as a surrogate for vertebrate species richness in the classes of amphibians, reptiles, birds, and mammals. Vascular plants, as primary producers, represent the biotic starting point for ecological community structure and are the logical place to start for understanding vertebrate species associations. We used data collected by the United States (US) National Park Service (NPS) on species presence within parks in the eastern US to estimate simple linear regressions between plant species richness and vertebrate richness. Because environmental factors may also influence species diversity, we performed simple linear regressions of species richness versus natural logarithm of park area, park latitude, mean annual precipitation, mean annual temperature, and human population density surrounding the parks. We then combined plant species richness and environmental variables in multiple regressions to determine the variables that remained as significant predictors of vertebrate species richness. As expected, we detected significant relationships between plant species richness and amphibian, bird, and mammal species richness. In some cases, plant species richness was predicted by park area alone. Species richness of mammals was only related to plant species richness. Reptile species richness, on the other hand, was related to plant species richness, park latitude and annual precipitation, while amphibian species richness was related to park latitude, park area, and plant species richness. Thus, plant species richness predicted species richness of different vertebrate groups to varying degrees and should not be used exclusively as a surrogate for vertebrate

  3. Adaptive Reactive Rich Internet Applications

    Science.gov (United States)

    Schmidt, Kay-Uwe; Stühmer, Roland; Dörflinger, Jörg; Rahmani, Tirdad; Thomas, Susan; Stojanovic, Ljiljana

    Rich Internet Applications significantly raise the user experience compared with legacy page-based Web applications because of their highly responsive user interfaces. Although this is a tremendous advance, it does not solve the problem of the one-size-fits-all approach1 of current Web applications. So although Rich Internet Applications put the user in a position to interact seamlessly with the Web application, they do not adapt to the context in which the user is currently working. In this paper we address the on-the-fly personalization of Rich Internet Applications. We introduce the concept of ARRIAs: Adaptive Reactive Rich Internet Applications and elaborate on how they are able to adapt to the current working context the user is engaged in. An architecture for the ad hoc adaptation of Rich Internet Applications is presented as well as a holistic framework and tools for the realization of our on-the-fly personalization approach. We divided both the architecture and the framework into two levels: offline/design-time and online/run-time. For design-time we explain how to use ontologies in order to annotate Rich Internet Applications and how to use these annotations for conceptual Web usage mining. Furthermore, we describe how to create client-side executable rules from the semantic data mining results. We present our declarative lightweight rule language tailored to the needs of being executed directly on the client. Because of the event-driven nature of the user interfaces of Rich Internet Applications, we designed a lightweight rule language based on the event-condition-action paradigm.2 At run-time the interactions of a user are tracked directly on the client and in real-time a user model is built up. The user model then acts as input to and is evaluated by our client-side complex event processing and rule engine.

  4. Archaeal viruses-novel, diverse and enigmatic

    DEFF Research Database (Denmark)

    Peng, Xu; Garrett, Roger Antony; She, Qunxin

    2012-01-01

    Recent research has revealed a remarkable diversity of viruses in archaeal-rich environments where spindles, spheres, filaments and rods are common, together with other exceptional morphotypes never recorded previously. Moreover, their double-stranded DNA genomes carry very few genes exhibiting...

  5. Equilibrium Bird Species Diversity in Atlantic Islands

    NARCIS (Netherlands)

    Valente, Luis; Illera, Juan Carlos; Havenstein, Katja; Pallien, Tamara; Etienne, Rampal S.; Tiedemann, Ralph

    2017-01-01

    Half a century ago, MacArthur and Wilson proposed that the number of species on islands tends toward a dynamic equilibrium diversity around which species richness fluctuates [1]. The current prevailing view in island biogeography accepts the fundamentals of MacArthur and Wilson's theory [2] but

  6. Richness-based masses of rich and famous galaxy clusters

    Science.gov (United States)

    Andreon, S.

    2016-03-01

    We present a catalog of galaxy cluster masses derived by exploiting the tight correlation between mass and richness, i.e., a properly computed number of bright cluster galaxies. The richness definition adopted in this work is properly calibrated, shows a small scatter with mass, and has a known evolution, which means that we can estimate accurate (0.16 dex) masses more precisely than by adopting any other richness estimates or X-ray or SZ-based proxies based on survey data. We measured a few hundred galaxy clusters at 0.05 web front-end is available at the URL http://www.brera.mi.astro.it/~andreon/famous.html

  7. Conus Peptides A Rich Pharmaceutical Treasure

    Institute of Scientific and Technical Information of China (English)

    Cheng-Zhong WANG; Cheng-Wu CHI

    2004-01-01

    Marine predatory cone snails (genus Conus) with over 500 species represent what is arguably the largest single genus of marine animals alive today. All Conus are venomous and utilize a complex mixture of Conus peptides to capture their preys and for other biological purposes. Each component of Conus peptides selectively targets a specific subtype of ion channels, neurotransmitter receptors or transporters.Owing to their diversity, more than 50,000 distinct active peptides are theoretically estimated in Conus venoms. These diversified toxins are generally categorized into several superfamilies and/or families based on their characteristic arrangements of cysteine residues and pharmacological actions. Some mechanisms underlying the remarkable diversity of Conus peptides have been postulated: the distinctive gene structure, gene duplication and/or allelic selection, genus speciation, and sophisticated expression pattern and posttranslational modification of these peptides. Due to their highly pharmacological potency and target selectivity, Conus peptides have attracted extensive attention with their potentials to be developed as new research tools in neuroscience field and as novel medications in clinic for pain, epilepsy and other neuropathic disorders. Several instructive lessons for our drug development could be also learnt from these neuropharmacological "expertises". Conus peptides comprise a rich resource for neuropharmacologists, and most of them await to be explored.

  8. Immigration Ethnic Diversity and Political Outcomes

    DEFF Research Database (Denmark)

    Harmon, Nikolaj Arpe

    2017-01-01

    I study the impact of immigration and increasing ethnic diversity on political outcomes in immigrant-receiving countries, focusing on immigration and election outcomes in Danish municipalities 1981-2001. A rich set of control variables isolates ethnic diversity effects from those of other immigrant...... characteristics and a novel IV strategy based on historical housing stock data addresses issues of endogenous location choices of immigrants. Increases in local ethnic diversity lead to right-ward shifts in election outcomes by shifting electoral support away from traditional "big government" left-wing parties...... and towards anti-immigrant nationalist parties in particular. These effects appear in both local and national elections....

  9. Oxygen-rich droplets and the enrichment of the ISM

    CERN Document Server

    Stasinska, G; Rodríguez, M; Henney, W J

    2007-01-01

    We argue that the discrepancies observed in HII regions between abundances derived from optical recombination lines (ORLs) and collisionally excited lines (CELs) might well be the signature of a scenario of the enrichment of the interstellar medium (ISM) proposed by Tenorio-Tagle (1996). In this scenario, the fresh oxygen released during massive supernova explosions is confined within the hot superbubbles as long as supernovae continue to explode. Only after the last massive supernova explosion, the metal-rich gas starts cooling down and falls on the galaxy within metal-rich droplets. Full mixing of these metal-rich droplets and the ISM occurs during photoionization by the next generations of massive stars. During this process, the metal-rich droplets give rise to strong recombination lines of the metals, leading to the observed ORL-CEL discrepancy. (The full version of this work is submitted to Astronomy and Astrophysics.)

  10. Towards global patterns in the diversity and community structure of ectomycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Toots, Märt; Diédhiou, Abdala G; Henkel, Terry W; Kjøller, Rasmus; Morris, Melissa H; Nara, Kazuhide; Nouhra, Eduardo; Peay, Kabir G; Põlme, Sergei; Ryberg, Martin; Smith, Matthew E; Kõljalg, Urmas

    2012-09-01

    Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.

  11. Genetic diversity of neotropical Myotis (chiroptera: vespertilionidae with an emphasis on South American species.

    Directory of Open Access Journals (Sweden)

    Roxanne J Larsen

    Full Text Available BACKGROUND: Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America. METHODOLOGY AND PRINCIPAL FINDINGS: Cytochrome-b sequences were generated and phylogenetically analyzed from 215 specimens, providing DNA sequence data for the most species of New World Myotis to date. Based on genetic data in our sample, and on comparisons with available DNA sequence data from GenBank, we estimate the number of species-level genetic lineages in South America alone to be at least 18, rather than the 15 species currently recognized. CONCLUSIONS: Our findings provide evidence that the perception of lower species richness in South American Myotis is largely due to a combination of cryptic morphological variation and insufficient sampling coverage in genetic-based systematic studies. A more accurate assessment of the level of diversity and species richness in New World Myotis is not only helpful for delimiting species boundaries, but also for understanding evolutionary processes within this globally distributed bat genus.

  12. Diversity Measures

    Directory of Open Access Journals (Sweden)

    MSc. Mentor Ademaj

    2012-06-01

    Full Text Available Diversity measures are a type of non-criminal measures foreseen in the Chapter IV of the Code of Juvenile Justice, which may be imposed on juvenile perpetrators of criminal acts. These measures can be applied in cases of minor offenses, for which is foreseen the criminal sanction with a fine or imprisonment up to three years or for criminal offenses committed by negligence for which is foreseen the sentence up to five years of imprisonment, except those cases that result in death. With the imposition of these measures is intended to prevent criminal proceedings against juveniles whenever is possible, rehabilitation and reintegration of juvenile in his/her community and the prevention of recidivist behaviour. Competent authority to impose them is the public prosecutor, the juvenile judge and juvenile court. And they are executed by the Kosovo Correctional Service.

  13. Estimating and comparing the diversity of marine actinobacteria.

    Science.gov (United States)

    Stach, James E M; Bull, Alan T

    2005-01-01

    This paper reviews the application of species richness estimators to microbial diversity data and describes phylogenetic approaches to comparing microbial communities. The techniques are demonstrated using a community of marine actinobacteria. Results demonstrate that marine environments harbour massive actinobacterial diversity. Furthermore, these predictions are likely to be severe underestimates due to the use of arbitrary OTU definitions.

  14. Species diversity and area-relationships in Danish beech forests

    NARCIS (Netherlands)

    Lawesson, J.E.; Blust, de G.; Grashof, C.; Firbanks, L.; Honnay, O.; Hermy, M.; Hobitz, P.; Jensen, L.M.

    1998-01-01

    The vascular flora of 62 Danish beech forests of eastern Jutland ranging in size from 1-445 ha, was investigated for species-area relations. Species richness reflecting total diversity, forest diversity, and of different habitat groups, were corrected for non-linearity by means of a log-log power fu

  15. Geographical patterns in the beta diversity of China's woody plants

    DEFF Research Database (Denmark)

    Wang, Zhiheng; Fang, Jingyun; Tang, Zhiyao

    2012-01-01

    Beta diversity (i.e. species turnover rate across space) is fundamental for understanding mechanisms controlling large-scale species richness patterns. However, the influences on beta diversity are still a matter of debate. In particular, the relative role of environmental and spatial processes (...

  16. Floral abundance, richness, and spatial distribution drive urban garden bee communities.

    Science.gov (United States)

    Plascencia, M; Philpott, S M

    2017-03-01

    In urban landscapes, gardens provide refuges for bee diversity, but conservation potential may depend on local and landscape features. Foraging and population persistence of bee species, as well as overall pollinator community structure, may be supported by the abundance, richness, and spatial distribution of floral resources. Floral resources strongly differ in urban gardens. Using hand netting and pan traps to survey bees, we examined whether abundance, richness, and spatial distribution of floral resources, as well as ground cover and garden landscape surroundings influence bee abundance, species richness, and diversity on the central coast of California. Differences in floral abundance and spatial distribution, as well as urban cover in the landscape, predicted different bee community variables. Abundance of all bees and of honeybees (Apis mellifera) was lower in sites with more urban land cover surrounding the gardens. Honeybee abundance was higher in sites with patchy floral resources, whereas bee species richness and bee diversity was higher in sites with more clustered floral resources. Surprisingly, bee species richness and bee diversity was lower in sites with very high floral abundance, possibly due to interactions with honeybees. Other studies have documented the importance of floral abundance and landscape surroundings for bees in urban gardens, but this study is the first to document that the spatial arrangement of flowers strongly predicts bee abundance and richness. Based on these findings, it is likely that garden managers may promote bee conservation by managing for floral connectivity and abundance within these ubiquitous urban habitats.

  17. Assessing and Broadening Genetic Diversity of Elymus sibiricus Germplasm for the Improvement of Seed Shattering

    Directory of Open Access Journals (Sweden)

    Zongyu Zhang

    2016-07-01

    Full Text Available Siberian wild rye (Elymus sibiricus L. is an important native grass in the Qinghai-Tibet Plateau of China. It is difficult to grow for commercial seed production, since seed shattering causes yield losses during harvest. Assessing the genetic diversity and relationships among germplasm from its primary distribution area contributes to evaluating the potential for its utilization as a gene pool to improve the desired agronomic traits. In the study, 40 EST-SSR primers were used to assess the genetic diversity and population structure of 36 E. sibiricus accessions with variation of seed shattering. A total of 380 bands were generated, with an average of 9.5 bands per primer. The polymorphic information content (PIC ranged from 0.23 to 0.50. The percentage of polymorphic bands (P for the species was 87.11%, suggesting a high degree of genetic diversity. Based on population structure analysis, four groups were formed, similar to results of principal coordinate analysis (PCoA. The molecular variance analysis (AMOVA revealed the majority of genetic variation occurred within geographical regions (83.40%. Two genotypes from Y1005 and ZhN06 were used to generate seven F1 hybrids. The molecular and morphological diversity analysis of F1 population revealed rich genetic variation and high level of seed shattering variation in F1 population, resulting in significant improvement of the genetic base and desired agronomic traits.

  18. Geographical, temporal and environmental determinants of bryophyte species richness in the Macaronesian islands.

    Science.gov (United States)

    Aranda, Silvia C; Gabriel, Rosalina; Borges, Paulo A V; Santos, Ana M C; de Azevedo, Eduardo Brito; Patiño, Jairo; Hortal, Joaquín; Lobo, Jorge M

    2014-01-01

    Species richness on oceanic islands has been related to a series of ecological factors including island size and isolation (i.e. the Equilibrium Model of Island Biogeography, EMIB), habitat diversity, climate (i.e., temperature and precipitation) and more recently island ontogeny (i.e. the General Dynamic Model of oceanic island biogeography, GDM). Here we evaluate the relationship of these factors with the diversity of bryophytes in the Macaronesian region (Azores, Madeira, Canary Islands and Cape Verde). The predictive power of EMIB, habitat diversity, climate and the GDM on total bryophyte richness, as well as moss and liverwort richness (the two dominant bryophyte groups), was evaluated through ordinary least squares regressions. After choosing the best subset of variables using inference statistics, we used partial regression analyses to identify the independent and shared effects of each model. The variables included within each model were similar for mosses and liverworts, with orographic mist layer being one of the most important predictors of richness. Models combining climate with either the GDM or habitat diversity explained most of richness variation (up to 91%). There was a high portion of shared variance between all pairwise combinations of factors in mosses, while in liverworts around half of the variability in species richness was accounted for exclusively by climate. Our results suggest that the effects of climate and habitat are strong and prevalent in this region, while geographical factors have limited influence on Macaronesian bryophyte diversity. Although climate is of great importance for liverwort richness, in mosses its effect is similar to or, at least, indiscernible from the effect of habitat diversity and, strikingly, the effect of island ontogeny. These results indicate that for highly vagile taxa on oceanic islands, the dispersal process may be less important for successful colonization than the availability of suitable ecological

  19. Geographical, temporal and environmental determinants of bryophyte species richness in the Macaronesian islands.

    Directory of Open Access Journals (Sweden)

    Silvia C Aranda

    Full Text Available Species richness on oceanic islands has been related to a series of ecological factors including island size and isolation (i.e. the Equilibrium Model of Island Biogeography, EMIB, habitat diversity, climate (i.e., temperature and precipitation and more recently island ontogeny (i.e. the General Dynamic Model of oceanic island biogeography, GDM. Here we evaluate the relationship of these factors with the diversity of bryophytes in the Macaronesian region (Azores, Madeira, Canary Islands and Cape Verde. The predictive power of EMIB, habitat diversity, climate and the GDM on total bryophyte richness, as well as moss and liverwort richness (the two dominant bryophyte groups, was evaluated through ordinary least squares regressions. After choosing the best subset of variables using inference statistics, we used partial regression analyses to identify the independent and shared effects of each model. The variables included within each model were similar for mosses and liverworts, with orographic mist layer being one of the most important predictors of richness. Models combining climate with either the GDM or habitat diversity explained most of richness variation (up to 91%. There was a high portion of shared variance between all pairwise combinations of factors in mosses, while in liverworts around half of the variability in species richness was accounted for exclusively by climate. Our results suggest that the effects of climate and habitat are strong and prevalent in this region, while geographical factors have limited influence on Macaronesian bryophyte diversity. Although climate is of great importance for liverwort richness, in mosses its effect is similar to or, at least, indiscernible from the effect of habitat diversity and, strikingly, the effect of island ontogeny. These results indicate that for highly vagile taxa on oceanic islands, the dispersal process may be less important for successful colonization than the availability of suitable

  20. Drivers of species richness in European Tenebrionidae (Coleoptera)

    Science.gov (United States)

    Fattorini, Simone; Ulrich, Werner

    2012-08-01

    The species-area relationship (SAR) and the latitudinal gradient in species richness are the most widespread and best-documented patterns in ecology, yet few studies have explored how the two patterns are interrelated. We used tenebrionid beetles as a species rich invertebrate group to investigate how area, habitat heterogeneity, climate, and ecological history act together in shaping species richness across Europe. We tested the effects of various climatic gradients on tenebrionid richness, with separate analyses for endemics and non-endemics. To take into account differences in area size among geographical units, we included species-area relationships using simultaneous autoregressive models. Although area had a significant effect on richness, the signal associated with temperature is so strong that it is still evident as a major driver. Also, the effect of area was only apparent when the effect of spatial coordinates had been accounted for, which has important implications for the use of SARs to locate diversity hotspots. The influence of latitude was mainly explained by a temperature gradient. Our findings support a postglacial European colonisation mainly from glacial southern refuges. Large Mediterranean islands were also important refugial areas.

  1. Tropical forests are not flat: how mountains affect herbivore diversity.

    Science.gov (United States)

    Rodríguez-Castañeda, Genoveva; Dyer, Lee A; Brehm, Gunnar; Connahs, Heidi; Forkner, Rebecca E; Walla, Thomas R

    2010-11-01

    Ecologists debate whether tropical insect diversity is better explained by higher plant diversity or by host plant species specialization. However, plant-herbivore studies are primarily based in lowland rainforests (RF) thus excluding topographical effects on biodiversity. We examined turnover in Eois (Geometridae) communities across elevation by studying elevational transects in Costa Rica and Ecuador. We found four distinct Eois communities existing across the elevational gradients. Herbivore diversity was highest in montane forests (MF), whereas host plant diversity was highest in lowland RF. This was correlated with higher specialization and species richness of Eois/host plant species we found in MF. Based on these relationships, Neotropical Eois richness was estimated to range from 313 (only lowland RF considered) to 2034 (considering variation with elevation). We conclude that tropical herbivore diversity and diet breadth covary significantly with elevation and urge the inclusion of montane ecosystems in host specialization and arthropod diversity estimates. © 2010 Blackwell Publishing Ltd/CNRS.

  2. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated t