Science.gov

Sample records for host community identifying

  1. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN HUMAN FECAL MICROBIAL COMMUNITIES

    EPA Science Inventory

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for mo...

  2. Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

    PubMed Central

    Faith, Jeremiah J.; Ahern, Philip P.; Ridaura, Vanessa K.; Cheng, Jiye; Gordon, Jeffrey I.

    2014-01-01

    Identifying a scalable, unbiased method for discovering which members of the human gut microbiota influence specific physiologic, metabolic and immunologic phenotypes remains a challenge. Here we describe a method in which a clonally-arrayed collection of cultured, sequenced bacteria was generated from one of several human fecal microbiota samples found to transmit a particular phenotype to recipient germ-free mice. Ninety-four bacterial consortia, of diverse size, randomly drawn from the culture collection, were introduced into germ-free animals. We identified an unanticipated range of bacterial strains that promoted accumulation of colonic regulatory T cells (Tregs) and expansion of Nrp1lo/− peripheral Tregs, as well as strains that modulated mouse adiposity and cecal metabolite concentrations using feature selection algorithms and follow-up mono-colonization. This combinatorial approach enabled a systems-level understanding of some of the microbial contributions to human biology. PMID:24452263

  3. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice.

    PubMed

    Faith, Jeremiah J; Ahern, Philip P; Ridaura, Vanessa K; Cheng, Jiye; Gordon, Jeffrey I

    2014-01-22

    Identifying a scalable, unbiased method for discovering which members of the human gut microbiota influence specific physiologic, metabolic, and immunologic phenotypes remains a challenge. We describe a method in which a clonally arrayed collection of cultured, sequenced bacteria was generated from one of several human fecal microbiota samples found to transmit a particular phenotype to recipient germ-free mice. Ninety-four bacterial consortia of diverse size, randomly drawn from the culture collection, were introduced into germ-free animals. We identified an unanticipated range of bacterial strains that promoted accumulation of colonic regulatory T cells (T(regs)) and expansion of Nrp1(lo/-) peripheral T(regs), as well as strains that modulated mouse adiposity and cecal metabolite concentrations, using feature selection algorithms and follow-up monocolonizations. This combinatorial approach enables a systems-level understanding of microbial contributions to human biology.

  4. Use of lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Price, R.D.; Osenton, P.C.

    2000-01-01

    The host specificity of avian lice (Phthiraptera) may be utilized by biologists to investigate the brood parasitism patterns of Brown-headed Cowbirds (Molothrus ater). As nestlings, brood parasites have a unique opportunity to encounter lice that are typically host specific. Lice are permanent hemimetabolic ectoparasites, a group found strictly on the body of the host, and they are transferred almost exclusively by bodily contact between hosts during care of young and at copulation. We investigated whether cowbird nestlings become infested with avian lice from their host parents and carry these lice away when they fledge, in effect bearing ectoparasite indicators of the species that raised them. The technique of examining the lice on cowbird fledglings to identify their foster parents would be much less costly than hiring a team of experts to determine parasitism patterns in the conventional way by finding hundreds of songbird nests. We examined 244 cowbird fledglings and found that they carried a rich fauna of lice representing 11 species and six genera, almost the entire spectrum of louse genera known to occur on passerines. We also examined 320 songbirds from 30 species, all known hosts of the Brown-headed Cowbird. As a group the host birds bore a diversity of louse species comparable to that on the fledgling cowbirds: 13 species of lice from seven genera. In contrast, most individual passerine host species yielded only 1 or 2 louse species, significantly fewer than the cowbird fledglings (p < 0.0001). Of 44 fledgling cowbirds carrying lice, 11 were linked to their probable avian foster parents via louse indicators, and these are the Wood Thrush and Red-winged Blackbird. Eighteen additional fledglings were linked to one of two possible foster parents. We concluded that cowbird fledglings do carry away host lice and this survey technique provides a partial assessment of local community parasitism patterns. The incomplete state of passerine louse taxonomy requires

  5. Examination of the relationship between host worm community structure on transmission of the parasite, Myxobolus cerebralis by developing taxon-specific probes for multiplex qPCR to identify worm taxa in stream communities

    NASA Astrophysics Data System (ADS)

    Fytilis, N.; Lamb, R.; Kerans, B.; Stevens, L.; Rizzo, D. M.

    2011-12-01

    Fish diseases are often caused by waterborne parasites, making them ideal systems for modeling the non-linear relationships between disease dynamics, stream dwelling oligochaete communities and geochemical features. Myxobolus cerebralis, the causative agent of whirling disease in salmonid fishes, has been a major contributor to the loss of wild rainbow trout populations in numerous streams within the Intermountain West. The parasite alternates between an invertebrate and vertebrate host, being transmitted between the sediment feeding worm Tubifex tubifex (T.tubifex) and salmonid fishes. Worm community biodiversity and abundance are influenced by biogeochemical features and have been linked to disease severity in fish. The worm (T.tubifex) lives in communities with 3-4 other types of worms in stream sediments. Unfortunately, taxonomic identification of oligochaetes is largely dependent on morphological characteristics of sexually mature adults. We have collected and identified ~700 worms from eight sites using molecular genetic probes and a taxonomic key. Additionally, ~1700 worms were identified using only molecular genetic probes. To facilitate distinguishing among tubificids, we developed two multiplex molecular genetic probe-based quantitative polymerase reaction (qPCR) assays to assess tubificid communities in the study area. Similar qPCR techniques specific for M.cerebralis used to determine if individual worms were infected with the parasite. We show how simple Bayesian analysis of the qPCR data can predict the worm community structure and reveal relationships between biodiversity of host communities and host-parasite dynamics. To our knowledge, this is the first study that combines molecular data of both the host and the parasite to examine the effects of host community structure on the transmission of a parasite. Our work can be extended to examine the links between worm community structure and biogeochemical features using molecular genetics and Bayesian

  6. Using lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Osenton, P.C.; Price, R.W.

    1995-01-01

    Avian lice may link fledgling Brown-headed Cowbirds to the host species that raised them. Lice, if host-specific and transferred to nestling cowbirds, could serve to identify the principal host species raising cowbirds in a local area. This approach of trapping cowbird fledglings in a feeding flock, then collecting and identifying the lice they carry is economical. The alternative requires a team of people to locate large numbers of parasitized host nests. We trapped 250 cowbird fledglings during June-August 1994 on Patuxent Research Center, and from them we collected 426 lice identified as representing 6 genera and 12 species. We. also collected and identified 347 lice from 30 known host species that were mist-netted on our Center. The lice found on cowbird fledglings in this population can be linked to Wood Thrush, Red-eyed Vireo, Common Yellowthroat, Rufous-sided Towhee, Red-winged Blackbird, Common Grackle, Song Sparrow, Field Sparrow, and Tree sparrow, based on this study and also on published reports.

  7. Signaling in host-associated microbial communities

    PubMed Central

    Fischbach, Michael A.; Segre, Julia A.

    2016-01-01

    Human-associated microbiota form and stabilize communities based on interspecies interactions. We review how these microbe-microbe and microbe-host interactions are communicated to shape communities over a human’s lifespan, including periods of health and disease. Modeling and dissecting signaling in host-associated communities is crucial to understand their function, and will open the door to therapies that prevent or correct microbial community dysfunction to promote health and treat disease. PMID:26967294

  8. Host partitioning by parasites in an intertidal crustacean community.

    PubMed

    Koehler, Anson V; Poulin, Robert

    2010-10-01

    Patterns of host use by parasites throughout a guild community of intermediate hosts can depend on several biological and ecological factors, including physiology, morphology, immunology, and behavior. We looked at parasite transmission in the intertidal crustacean community of Lower Portobello Bay, Dunedin, New Zealand, with the intent of: (1) mapping the flow of parasites throughout the major crustacean species, (2) identifying hosts that play the most important transmission role for each parasite, and (3) assessing the impact of parasitism on host populations. The most prevalent parasites found in 14 species of crustaceans (635 specimens) examined were the trematodes Maritrema novaezealandensis and Microphallus sp., the acanthocephalans Profilicollis spp., the nematode Ascarophis sp., and an acuariid nematode. Decapods were compatible hosts for M. novaezealandensis, while other crustaceans demonstrated lower host suitability as shown by high levels of melanized and immature parasite stages. Carapace thickness, gill morphology, and breathing style may contribute to the differential infection success of M. novaezealandensis and Microphallus sp. in the decapod species. Parasite-induced host mortality appears likely with M. novaezealandensis in the crabs Austrohelice crassa, Halicarcinus varius, Hemigrapsus sexdentatus, and Macrophthalmus hirtipes, and also with Microphallus sp. in A. crassa. Overall, the different parasite species make different use of available crustacean intermediate hosts and possibly contribute to intertidal community structure.

  9. Predictability of helminth parasite host range using information on geography, host traits and parasite community structure.

    PubMed

    Dallas, Tad; Park, Andrew W; Drake, John M

    2017-02-01

    Host-parasite associations are complex interactions dependent on aspects of hosts (e.g. traits, phylogeny or coevolutionary history), parasites (e.g. traits and parasite interactions) and geography (e.g. latitude). Predicting the permissive host set or the subset of the host community that a parasite can infect is a central goal of parasite ecology. Here we develop models that accurately predict the permissive host set of 562 helminth parasites in five different parasite taxonomic groups. We developed predictive models using host traits, host taxonomy, geographic covariates, and parasite community composition, finding that models trained on parasite community variables were more accurate than any other covariate group, even though parasite community covariates only captured a quarter of the variance in parasite community composition. This suggests that it is possible to predict the permissive host set for a given parasite, and that parasite community structure is an important predictor, potentially because parasite communities are interacting non-random assemblages.

  10. Dissecting host-associated communities with DNA barcodes

    PubMed Central

    Pierce, Naomi E.

    2016-01-01

    DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes. Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481780

  11. Identifying the host galaxy of gravitational wave signals

    SciTech Connect

    Nuttall, Laura K.; Sutton, Patrick J.

    2010-11-15

    One of the goals of the current LIGO-GEO-Virgo science run is to identify transient gravitational wave (GW) signals in near real time to allow follow-up electromagnetic (EM) observations. An EM counterpart could increase the confidence of the GW detection and provide insight into the nature of the source. Current GW-EM campaigns target potential host galaxies based on overlap with the GW sky error box. We propose a new statistic to identify the most likely host galaxy, ranking galaxies based on their position, distance, and luminosity. We test our statistic with Monte Carlo simulations of GWs produced by coalescing binaries of neutron stars and black holes, one of the most promising sources for ground-based GW detectors. Considering signals accessible to current detectors, we find that when imaging a single galaxy, our statistic correctly identifies the true host {approx}20% to {approx}50% of the time, depending on the masses of the binary components. With five narrow-field images the probability of imaging the true host increases from {approx}50% to {approx}80%. When collectively imaging groups of galaxies using large field-of-view telescopes, the probability improves from {approx}30% to {approx}60% for a single image and from {approx}70% to {approx}90% for five images. For the advanced generation of detectors (circa 2015+), and considering binaries within 100 Mpc (the reach of the galaxy catalogue used), the probability is {approx}40% for one narrow-field image, {approx}75% for five narrow-field images, {approx}65% for one wide-field image, and {approx}95% for five wide-field images, irrespective of binary type.

  12. Host Niches and Defensive Extended Phenotypes Structure Parasitoid Wasp Communities

    PubMed Central

    Bailey, Richard; Schönrogge, Karsten; Cook, James M.; Melika, George; Csóka, György; Thuróczy, Csaba; Stone, Graham N.

    2009-01-01

    Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies. Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the “Enemy Hypothesis,” which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness), supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed). The combined explanatory power of structural and spatiotemporal

  13. Identifying Francisella tularensis genes required for growth in host cells.

    PubMed

    Brunton, J; Steele, S; Miller, C; Lovullo, E; Taft-Benz, S; Kawula, T

    2015-08-01

    Francisella tularensis is a highly virulent Gram-negative intracellular pathogen capable of infecting a vast diversity of hosts, ranging from amoebae to humans. A hallmark of F. tularensis virulence is its ability to quickly grow to high densities within a diverse set of host cells, including, but not limited to, macrophages and epithelial cells. We developed a luminescence reporter system to facilitate a large-scale transposon mutagenesis screen to identify genes required for growth in macrophage and epithelial cell lines. We screened 7,454 individual mutants, 269 of which exhibited reduced intracellular growth. Transposon insertions in the 269 growth-defective strains mapped to 68 different genes. FTT_0924, a gene of unknown function but highly conserved among Francisella species, was identified in this screen to be defective for intracellular growth within both macrophage and epithelial cell lines. FTT_0924 was required for full Schu S4 virulence in a murine pulmonary infection model. The ΔFTT_0924 mutant bacterial membrane is permeable when replicating in hypotonic solution and within macrophages, resulting in strongly reduced viability. The permeability and reduced viability were rescued when the mutant was grown in a hypertonic solution, indicating that FTT_0924 is required for resisting osmotic stress. The ΔFTT_0924 mutant was also significantly more sensitive to β-lactam antibiotics than Schu S4. Taken together, the data strongly suggest that FTT_0924 is required for maintaining peptidoglycan integrity and virulence.

  14. Identifying Francisella tularensis Genes Required for Growth in Host Cells

    PubMed Central

    Brunton, J.; Steele, S.; Miller, C.; Lovullo, E.; Taft-Benz, S.

    2015-01-01

    Francisella tularensis is a highly virulent Gram-negative intracellular pathogen capable of infecting a vast diversity of hosts, ranging from amoebae to humans. A hallmark of F. tularensis virulence is its ability to quickly grow to high densities within a diverse set of host cells, including, but not limited to, macrophages and epithelial cells. We developed a luminescence reporter system to facilitate a large-scale transposon mutagenesis screen to identify genes required for growth in macrophage and epithelial cell lines. We screened 7,454 individual mutants, 269 of which exhibited reduced intracellular growth. Transposon insertions in the 269 growth-defective strains mapped to 68 different genes. FTT_0924, a gene of unknown function but highly conserved among Francisella species, was identified in this screen to be defective for intracellular growth within both macrophage and epithelial cell lines. FTT_0924 was required for full Schu S4 virulence in a murine pulmonary infection model. The ΔFTT_0924 mutant bacterial membrane is permeable when replicating in hypotonic solution and within macrophages, resulting in strongly reduced viability. The permeability and reduced viability were rescued when the mutant was grown in a hypertonic solution, indicating that FTT_0924 is required for resisting osmotic stress. The ΔFTT_0924 mutant was also significantly more sensitive to β-lactam antibiotics than Schu S4. Taken together, the data strongly suggest that FTT_0924 is required for maintaining peptidoglycan integrity and virulence. PMID:25987704

  15. Identifying hidden sexual bridging communities in Chicago.

    PubMed

    Youm, Yoosik; Mackesy-Amiti, Mary Ellen; Williams, Chyvette T; Ouellet, Lawrence J

    2009-07-01

    Bridge populations can play a central role in the spread of human immunodeficiency virus (HIV) by providing transmission links between higher and lower prevalence populations. While social network methods are well suited to the study of bridge populations, analyses tend to focus on dyads (i.e., risk between drug and/or sex partners) and ignore bridges between distinct subpopulations. This study takes initial steps toward moving the analysis of sexual network linkages beyond individual and risk group levels to a community level in which Chicago's 77 community areas are examined as subpopulations for the purpose of identifying potential bridging communities. Of particular interest are "hidden" bridging communities; that is, areas with above-average levels of sexual ties with other areas but whose below-average AIDS prevalence may hide their potential importance for HIV prevention. Data for this analysis came from the first wave of recruiting at the Chicago Sexual Acquisition and Transmission of HIV Cooperative Agreement Program site. Between August 2005 through October 2006, respondent-driven sampling was used to recruit users of heroin, cocaine, or methamphetamine, men who have sex with men regardless of drug use, the sex partners of these two groups, and sex partners of the sex partners. In this cross-sectional study of the sexual transmission of HIV, participants completed a network-focused computer-assisted self-administered interview, which included questions about the geographic locations of sexual contacts with up to six recent partners. Bridging scores for each area were determined using a matrix representing Chicago's 77 community areas and were assessed using two measures: non-redundant ties and flow betweenness. Bridging measures and acquired immunodeficiency syndrome (AIDS) case prevalence rates were plotted for each community area on charts representing four conditions: below-average bridging and AIDS prevalence, below-average bridging and above

  16. Identifying natural flow regimes using fish communities

    NASA Astrophysics Data System (ADS)

    Chang, Fi-John; Tsai, Wen-Ping; Wu, Tzu-Ching; Chen, Hung-kwai; Herricks, Edwin E.

    2011-10-01

    SummaryModern water resources management has adopted natural flow regimes as reasonable targets for river restoration and conservation. The characterization of a natural flow regime begins with the development of hydrologic statistics from flow records. However, little guidance exists for defining the period of record needed for regime determination. In Taiwan, the Taiwan Eco-hydrological Indicator System (TEIS), a group of hydrologic statistics selected for fisheries relevance, is being used to evaluate ecological flows. The TEIS consists of a group of hydrologic statistics selected to characterize the relationships between flow and the life history of indigenous species. Using the TEIS and biosurvey data for Taiwan, this paper identifies the length of hydrologic record sufficient for natural flow regime characterization. To define the ecological hydrology of fish communities, this study connected hydrologic statistics to fish communities by using methods to define antecedent conditions that influence existing community composition. A moving average method was applied to TEIS statistics to reflect the effects of antecedent flow condition and a point-biserial correlation method was used to relate fisheries collections with TEIS statistics. The resulting fish species-TEIS (FISH-TEIS) hydrologic statistics matrix takes full advantage of historical flows and fisheries data. The analysis indicates that, in the watersheds analyzed, averaging TEIS statistics for the present year and 3 years prior to the sampling date, termed MA(4), is sufficient to develop a natural flow regime. This result suggests that flow regimes based on hydrologic statistics for the period of record can be replaced by regimes developed for sampled fish communities.

  17. Biodiversity decreases disease through predictable changes in host community competence.

    PubMed

    Johnson, Pieter T J; Preston, Daniel L; Hoverman, Jason T; Richgels, Katherine L D

    2013-02-14

    Accelerating rates of species extinctions and disease emergence underscore the importance of understanding how changes in biodiversity affect disease outcomes. Over the past decade, a growing number of studies have reported negative correlations between host biodiversity and disease risk, prompting suggestions that biodiversity conservation could promote human and wildlife health. Yet the generality of the diversity-disease linkage remains conjectural, in part because empirical evidence of a relationship between host competence (the ability to maintain and transmit infections) and the order in which communities assemble has proven elusive. Here we integrate high-resolution field data with multi-scale experiments to show that host diversity inhibits transmission of the virulent pathogen Ribeiroia ondatrae and reduces amphibian disease as a result of consistent linkages among species richness, host composition and community competence. Surveys of 345 wetlands indicated that community composition changed nonrandomly with species richness, such that highly competent hosts dominated in species-poor assemblages whereas more resistant species became progressively more common in diverse assemblages. As a result, amphibian species richness strongly moderated pathogen transmission and disease pathology among 24,215 examined hosts, with a 78.4% decline in realized transmission in richer assemblages. Laboratory and mesocosm manipulations revealed an approximately 50% decrease in pathogen transmission and host pathology across a realistic diversity gradient while controlling for host density, helping to establish mechanisms underlying the diversity-disease relationship and their consequences for host fitness. By revealing a consistent link between species richness and community competence, these findings highlight the influence of biodiversity on infection risk and emphasize the benefit of a community-based approach to understanding infectious diseases.

  18. Host densities as determinants of abundance in parasite communities

    PubMed Central

    Arneberg, P.; Skorping, A.; Grenfell, B.; Read, A. F.

    1998-01-01

    Several epidemiological models predict a positive relationship between host population density and abundance of directly transmitted macroparasites. Here, we generalize these, and test the prediction by a comparative study. We used data on communities of gastrointestinal strongylid nematodes from 19 mammalian species, representing examination of 6670 individual hosts. We studied both the average abundance of all strongylid nematodes within a host species, and the two components of abundance, prevalence and intensity. The effects of host body weight, diet, fecundity and age at maturity and parasite body size were controlled for directly, and the phylogenetically independent contrast method was used to control for confounding factors more generally. Host population density and average parasite abundance were strongly positively correlated within mammalian taxa, and across all species when the effects of host body weight were controlled for. Controlling for other variables did not change this. Even when looking at single parasite species occurring in several host species, abundance was highest in the host species with the highest population density. Prevalence and intensity showed similar patterns. These patterns provide the first macroecological evidence consistent with the prediction that transmission rates depend on host population density in natural parasite communities.

  19. Mock communities highlight the diversity of host-associated eukaryotes.

    PubMed

    Wegener Parfrey, Laura

    2015-09-01

    Host-associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High-throughput sequencing (HTS) tools have illuminated the vast diversity of host-associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall-Ngai et al. ). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al. ) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host-associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host-associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. ; Simon et al. ; de Vargas et al. ). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al. )]. In this issue of Molecular Ecology, Geisen et al. () use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free-living. By isolating the host-associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high-throughput sequencing (HTS) and reinforce the ubiquity of these host-associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free-living, but instead need to design studies that specifically enumerate the diversity and function of host-associated eukaryotes. Doing so will allow the field to

  20. Identifying Francisella tularensis genes required for growth in host cells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Technical Abstract: Francisella tularensis is a highly virulent Gram negative intracellular pathogen capable of infecting a vast diversity of hosts, ranging from amoebae to humans. A hallmark of F. tularensis virulence is its ability to quickly grow to high densities within a diverse set of host cel...

  1. Identifying the host galaxy of the short GRB 100628A

    NASA Astrophysics Data System (ADS)

    Nicuesa Guelbenzu, A.; Klose, S.; Palazzi, E.; Greiner, J.; Michałowski, M. J.; Kann, D. A.; Hunt, L. K.; Malesani, D.; Rossi, A.; Savaglio, S.; Schulze, S.; Xu, D.; Afonso, P. M. J.; Elliott, J.; Ferrero, P.; Filgas, R.; Hartmann, D. H.; Krühler, T.; Knust, F.; Masetti, N.; Olivares E., F.; Rau, A.; Schady, P.; Schmidl, S.; Tanga, M.; Updike, A. C.; Varela, K.

    2015-11-01

    We report on the results of a comprehensive observing campaign to reveal the host galaxy of the short GRB 100628A. This burst was followed by a faint X-ray afterglow but no optical counterpart was discovered. However, inside the X-ray error circle a potential host galaxy at a redshift of z = 0.102 was soon reported in the literature. If this system is the host, then GRB 100628A was the cosmologically most nearby unambiguous short burst with a measured redshift so far. We used the multi-colour imager GROND at the ESO/La Silla MPG 2.2 m telescope, ESO/VLT spectroscopy, and deep Australia Telescope Compact Array (ATCA) radio-continuum observations together with publicly available Gemini imaging data to study the putative host and the galaxies in the field of GRB 100628A. We confirm that inside the X-ray error circle the most probable host-galaxy candidate is the morphologically disturbed, interacting galaxy system at z = 0.102. The interacting galaxies are connected by a several kpc long tidal stream, which our VLT/FORS2 spectroscopy reveals strong emission lines of [O ii], [O iii], Hα and Hβ, characteristic for the class of extreme emission-line galaxies and indicative of ongoing star formation. The latter leaves open the possibility that the GRB progenitor was a member of a young stellar population. However, we indentify a second host-galaxy candidate slightly outside the X-ray error circle. It is a radio-bright, luminous elliptical galaxy at a redshift z = 0.311. With a K-band luminosity of 2 × 1011L⊙ this galaxy resembles the probable giant elliptical host of the first well-localized short burst, GRB 050509B. If this is the host, then the progenitor of GRB 100628A was a member of an old stellar population. Based on observations collected at the Very Large Telescope of the European Southern Observatory, Paranal, Chile (ESO programme 087.D-0503 and 290.D-5194; PI: A. Nicuesa Guelbenzu; 090.A-0825; PI: D. Malesani), GROND (PI: J. Greiner), and ATCA (Program C

  2. The consequences of reservoir host eradication on disease epidemiology in animal communities

    PubMed Central

    Al-Shorbaji, Farah; Roche, Benjamin; Gozlan, Rodolphe; Britton, Robert; Andreou, Demetra

    2016-01-01

    Non-native species have often been linked with introduction of novel pathogens that spill over into native communities, and the amplification of the prevalence of native parasites. In the case of introduced generalist pathogens, their disease epidemiology in the extant communities remains poorly understood. Here, Sphaerothecum destruens, a generalist fungal-like fish pathogen with bi-modal transmission (direct and environmental) was used to characterise the biological drivers responsible for disease emergence in temperate fish communities. A range of biotic factors relating to both the pathogen and the surrounding host communities were used in a novel susceptible-exposed-infectious-recovered (SEIR) model to test how these factors affected disease epidemiology. These included: (i) pathogen prevalence in an introduced reservoir host (Pseudorasbora parva); (ii) the impact of reservoir host eradication and its timing and (iii) the density of potential hosts in surrounding communities and their connectedness. These were modelled across 23 combinations and indicated that the spill-over of pathogen propagules via environmental transmission resulted in rapid establishment in adjacent fish communities (<1 year). Although disease dynamics were initially driven by environmental transmission in these communities, once sufficient numbers of native hosts were infected, the disease dynamics were driven by intra-species transmission. Subsequent eradication of the introduced host, irrespective of its timing (after one, two or three years), had limited impact on the long-term disease dynamics among local fish communities. These outputs reinforced the importance of rapid detection and eradication of non-native species, in particular when such species are identified as healthy reservoirs of a generalist pathogen. PMID:27165562

  3. Co-extinction in a host-parasite network: identifying key hosts for network stability.

    PubMed

    Dallas, Tad; Cornelius, Emily

    2015-08-17

    Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.

  4. Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development.

    PubMed

    Martínez-García, Laura B; Richardson, Sarah J; Tylianakis, Jason M; Peltzer, Duane A; Dickie, Ian A

    2015-03-01

    Little is known about the response of arbuscular mycorrhizal fungal communities to ecosystem development. We use a long-term soil chronosequence that includes ecosystem progression and retrogression to quantify the importance of host plant identity as a factor driving fungal community composition during ecosystem development. We identified arbuscular mycorrhizal fungi and plant species from 50 individual roots from each of 10 sites spanning 5-120 000 yr of ecosystem age using terminal restriction fragment length polymorphism (T-RFLP), Sanger sequencing and pyrosequencing. Arbuscular mycorrhizal fungal communities were highly structured by ecosystem age. There was strong niche differentiation, with different groups of operational taxonomic units (OTUs) being characteristic of early succession, ecosystem progression and ecosystem retrogression. Fungal alpha diversity decreased with ecosystem age, whereas beta diversity was high at early stages and lower in subsequent stages. A total of 39% of the variance in fungal communities was explained by host plant and site age, 29% of which was attributed to host and the interaction between host and site (24% and 5%, respectively). The strong response of arbuscular mycorrhizal fungi to ecosystem development appears to be largely driven by plant host identity, supporting the concept that plant and fungal communities are tightly coupled rather than independently responding to habitat.

  5. Identifying community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Shao, Chenxi; Duan, Yubing

    2015-07-01

    A wide variety of applications could be formulated to resolve the problem of finding all communities from a given network, ranging from social and biological network analysis to web mining and searching. In this study, we propose the concept of virtual attractive strength between each pair of node in networks, and then give the definition of community structure based on the proposed attractive strength. Furthermore, we present a community detection method by moving vertices to the clusters that produce the largest attractive strengths to them until the division of network reaches unchanged. Experimental results on synthetic and real networks indicate that the proposed approach has favorite effectiveness and fast convergence speed, which provides an efficient method for exploring and analyzing complex systems.

  6. Panamanian frog species host unique skin bacterial communities

    PubMed Central

    Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N.

    2015-01-01

    Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont

  7. Effectively identifying user profiles in network and host metrics

    NASA Astrophysics Data System (ADS)

    Murphy, John P.; Berk, Vincent H.; Gregorio-de Souza, Ian

    2010-04-01

    This work presents a collection of methods that is used to effectively identify users of computers systems based on their particular usage of the software and the network. Not only are we able to identify individual computer users by their behavioral patterns, we are also able to detect significant deviations in their typical computer usage over time, or compared to a group of their peers. For instance, most people have a small, and relatively unique selection of regularly visited websites, certain email services, daily work hours, and typical preferred applications for mandated tasks. We argue that these habitual patterns are sufficiently specific to identify fully anonymized network users. We demonstrate that with only a modest data collection capability, profiles of individual computer users can be constructed so as to uniquely identify a profiled user from among their peers. As time progresses and habits or circumstances change, the methods presented update each profile so that changes in user behavior can be reliably detected over both abrupt and gradual time frames, without losing the ability to identify the profiled user. The primary benefit of our methodology allows one to efficiently detect deviant behaviors, such as subverted user accounts, or organizational policy violations. Thanks to the relative robustness, these techniques can be used in scenarios with very diverse data collection capabilities, and data privacy requirements. In addition to behavioral change detection, the generated profiles can also be compared against pre-defined examples of known adversarial patterns.

  8. Evolving a NASA Digital Object Identifiers System with Community Engagement

    NASA Technical Reports Server (NTRS)

    Wanchoo, Lalit; James, Nathan

    2016-01-01

    To demonstrate how the ESDIS (Earth Science Data and Information System) DOI (Digital Object Identifier) system and its processes have evolved over these years based on the recommendations provided by the user community (whether the community members create and manage DOI information or use DOIs in the data citations). The user community is comprised of people with common interests and needs for data identifiers who are actively involved in the creation and usage process. Engagement describes the interactive context wherein the community provides information, evaluates the proposed processes, and provides guidance in the area of identifiers.

  9. Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

    PubMed

    Marzinelli, Ezequiel M; Campbell, Alexandra H; Zozaya Valdes, Enrique; Vergés, Adriana; Nielsen, Shaun; Wernberg, Thomas; de Bettignies, Thibaut; Bennett, Scott; Caporaso, J Gregory; Thomas, Torsten; Steinberg, Peter D

    2015-10-01

    Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.

  10. Phylogenetic composition of host plant communities drives plant-herbivore food web structure.

    PubMed

    Volf, Martin; Pyszko, Petr; Abe, Tomokazu; Libra, Martin; Kotásková, Nela; Šigut, Martin; Kumar, Rajesh; Kaman, Ondřej; Butterill, Philip T; Šipoš, Jan; Abe, Haruka; Fukushima, Hiroaki; Drozd, Pavel; Kamata, Naoto; Murakami, Masashi; Novotny, Vojtech

    2017-02-01

    Insects tend to feed on related hosts. The phylogenetic composition of host plant communities thus plays a prominent role in determining insect specialization, food web structure, and diversity. Previous studies showed a high preference of insect herbivores for congeneric and confamilial hosts suggesting that some levels of host plant relationships may play more prominent role that others. We aim to quantify the effects of host phylogeny on the structure of quantitative plant-herbivore food webs. Further, we identify specific patterns in three insect guilds with different life histories and discuss the role of host plant phylogeny in maintaining their diversity. We studied herbivore assemblages in three temperate forests in Japan and the Czech Republic. Sampling from a canopy crane, a cherry picker and felled trees allowed a complete census of plant-herbivore interactions within three 0·1 ha plots for leaf chewing larvae, miners, and gallers. We analyzed the effects of host phylogeny by comparing the observed food webs with randomized models of host selection. Larval leaf chewers exhibited high generality at all three sites, whereas gallers and miners were almost exclusively monophagous. Leaf chewer generality dropped rapidly when older host lineages (5-80 myr) were collated into a single lineage but only decreased slightly when the most closely related congeneric hosts were collated. This shows that leaf chewer generality has been maintained by feeding on confamilial hosts while only a few herbivores were shared between more distant plant lineages and, surprisingly, between some congeneric hosts. In contrast, miner and galler generality was maintained mainly by the terminal nodes of the host phylogeny and dropped immediately after collating congeneric hosts into single lineages. We show that not all levels of host plant phylogeny are equal in their effect on structuring plant-herbivore food webs. In the case of generalist guilds, it is the phylogeny of deeper

  11. Host tissues as microhabitats for Wolbachia and quantitative insights into the bacterial community in terrestrial isopods.

    PubMed

    Dittmer, J; Beltran-Bech, S; Lesobre, J; Raimond, M; Johnson, M; Bouchon, D

    2014-05-01

    Animal-bacterial symbioses are highly dynamic in terms of multipartite interactions, both between the host and its symbionts as well as between the different bacteria constituting the symbiotic community. These interactions will be reflected by the titres of the individual bacterial taxa, for example via host regulation of bacterial loads or competition for resources between symbionts. Moreover, different host tissues represent heterogeneous microhabitats for bacteria, meaning that host-associated bacteria might establish tissue-specific bacterial communities. Wolbachia are widespread endosymbiotic bacteria, infecting a large number of arthropods and filarial nematodes. However, relatively little is known regarding direct interactions between Wolbachia and other bacteria. This study represents the first quantitative investigation of tissue-specific Wolbachia-microbiota interactions in the terrestrial isopod Armadillidium vulgare. To this end, we obtained a more complete picture of the Wolbachia distribution patterns across all major host tissues, integrating all three feminizing Wolbachia strains (wVulM, wVulC, wVulP) identified to date in this host. Interestingly, the different Wolbachia strains exhibited strain-specific tissue distribution patterns, with wVulM reaching lower titres in most tissues. These patterns were consistent across different host genetic backgrounds and might reflect different co-evolutionary histories between the Wolbachia strains and A. vulgare. Moreover, Wolbachia-infected females carried higher total bacterial loads in several, but not all, tissues, irrespective of the Wolbachia strain. Taken together, this quantitative approach indicates that Wolbachia is part of a potentially more diverse bacterial community, as exemplified by the presence of highly abundant bacterial taxa in the midgut caeca of several A. vulgare populations.

  12. Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters.

    PubMed

    Cleary, Daniel F R; Becking, Leontine E; de Voogd, Nicole J; Pires, Ana C C; Polónia, Ana R M; Egas, Conceição; Gomes, Newton C M

    2013-09-01

    Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific.

  13. A combined parasitological molecular approach for noninvasive characterization of parasitic nematode communities in wild hosts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most hosts are concurrently or sequentially infected with multiple parasites, thus fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, non-invasive methods for obtaining quantita...

  14. Quantifying and identifying the overlapping community structure in networks

    NASA Astrophysics Data System (ADS)

    Shen, Hua-Wei; Cheng, Xue-Qi; Guo, Jia-Feng

    2009-07-01

    It has been shown that the communities of complex networks often overlap with each other. However, there is no effective method to quantify the overlapping community structure. In this paper, we propose a metric to address this problem. Instead of assuming that one node can only belong to one community, our metric assumes that a maximal clique only belongs to one community. In this way, the overlaps between communities are allowed. To identify the overlapping community structure, we construct a maximal clique network from the original network, and prove that the optimization of our metric on the original network is equivalent to the optimization of Newman's modularity on the maximal clique network. Thus the overlapping community structure can be identified through partitioning the maximal clique network using any modularity optimization method. The effectiveness of our metric is demonstrated by extensive tests on both artificial networks and real world networks with a known community structure. The application to the word association network also reproduces excellent results.

  15. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

    PubMed Central

    Klümper, Uli; Riber, Leise; Dechesne, Arnaud; Sannazzarro, Analia; Hansen, Lars H; Sørensen, Søren J; Smets, Barth F

    2015-01-01

    Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids. PMID:25333461

  16. Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host

    PubMed Central

    Staudacher, Heike; Kaltenpoth, Martin; Breeuwer, Johannes A. J.; Menken, Steph B. J.; Heckel, David G.; Groot, Astrid T.

    2016-01-01

    Microbes associated with insects can confer a wide range of ecologically relevant benefits to their hosts. Since insect-associated bacteria often increase the nutritive value of their hosts' diets, the study of bacterial communities is especially interesting in species that are important agricultural pests. We investigated the composition of bacterial communities in the noctuid moth Heliothis virescens and its variability in relation to developmental stage, diet and population (field and laboratory), using bacterial tag-encoded FLX pyrosequencing of 16S rRNA amplicons. In larvae, bacterial communities differed depending on the food plant on which they had been reared, although the within-group variation between biological replicates was high as well. Moreover, larvae originating from a field or laboratory population did not share any OTUs. Interestingly, Enterococcus sp. was found to be the dominant taxon in laboratory-reared larvae, but was completely absent from field larvae, indicating dramatic shifts in microbial community profiles upon cultivation of the moths in the laboratory. Furthermore, microbiota composition varied strongly across developmental stages in individuals of the field population, and we found no evidence for vertical transmission of bacteria from mothers to offspring. Since sample sizes in our study were small due to pooling of samples for sequencing, we cautiously conclude that the high variability in bacterial communities suggests a loose and temporary association of the identified bacteria with H. virescens. PMID:27139886

  17. Dynamics in microbial communities: Unraveling mechanisms to identify principles

    SciTech Connect

    Konopka, Allan; Lindemann, Stephen R.; Fredrickson, Jim K.

    2015-07-01

    Diversity begets higher order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions, and it is this “system” that is the basis for higher order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

  18. Dynamics in microbial communities: unraveling mechanisms to identify principles

    PubMed Central

    Konopka, Allan; Lindemann, Stephen; Fredrickson, Jim

    2015-01-01

    Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this ‘system' that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions. PMID:25526370

  19. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

    PubMed Central

    Burns, Adam R; Stephens, W Zac; Stagaman, Keaton; Wong, Sandi; Rawls, John F; Guillemin, Karen; Bohannan, Brendan JM

    2016-01-01

    Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions. PMID:26296066

  20. Ectomycorrhizal fungal communities coinvading with Pinaceae host plants in Argentina: Gringos bajo el bosque.

    PubMed

    Hayward, Jeremy; Horton, Thomas R; Nuñez, Martin A

    2015-10-01

    Coinvasive ectomycorrhizal (ECM) fungi allow Pinaceae species to invade regions otherwise lacking compatible symbionts, but ECM fungal communities permitting Pinaceae invasions are poorly understood. In the context of Pinaceae invasions on Isla Victoria, Nahuel Huapi National Park, Argentina, we asked: what ECM fungi are coinvading with Pinaceae hosts on Isla Victoria; are some ECM fungal species or genera more prone to invade than others; and are all ECM fungal species that associate with Northern Hemisphere hosts also nonnative, or are some native fungi compatible with nonnative plants? We sampled ECMs from 226 Pinaceae host plant individuals, both planted individuals and recruits, growing inside and invading from plantations. We used molecular techniques to examine ECM fungal communities associating with these trees. A distinctive subset of the ECM fungal community predominated far from plantations, indicating differences between highly invasive and less invasive ECM fungi. Some fungal invaders reported here have been detected in other locations around the world, suggesting strong invasion potential. Fungi that were frequently detected far from plantations are often found in early-successional sites in the native range, while fungi identified as late-successional species in the native range are rarely found far from plantations, suggesting a means for predicting potential fungal coinvaders.

  1. Effects of host plant environment and Ustilago maydis infection on the fungal endophyte community of maize (Zea mays).

    PubMed

    Pan, Jean J; Baumgarten, Andrew M; May, Georgiana

    2008-01-01

    The focus of many fungal endophyte studies has been how plants benefit from endophyte infection. Few studies have investigated the role of the host plant as an environment in shaping endophyte community diversity and composition. The effects that different attributes of the host plant, that is, host genetic variation, host variation in resistance to the fungal pathogen Ustilago maydis and U. maydis infection, have on the fungal endophyte communities in maize (Zea mays) was examined. The internal transcribed spacer (ITS) region of the rDNA was sequenced to identify fungi and the endophyte communities were compared in six maize lines that varied in their resistance to U. maydis. It was found that host genetic variation, as determined by maize line, had significant effects on species richness, while the interactions between line and U. maydis infection and line and field plot had significant effects on endophyte community composition. However, the effects of maize line were not dependent on whether lines were resistant or susceptible to U. maydis. Almost 3000 clones obtained from 58 plants were sequenced to characterize the maize endophyte community. These results suggest that the endophyte community is shaped by complex interactions and factors, such as inoculum pool and microclimate, may be important.

  2. Host-Parasite Associations in Small Mammal Communities in Semiarid Savanna Ecosystems of East Africa.

    PubMed

    Guerra, Ana Sofia; Eckerlin, Ralph P; Dowling, Ashley P G; Durden, Lance A; Robbins, Richard G; Dittmar, Katharina; Helgen, Kristofer M; Agwanda, Bernard; Allan, Brian F; Hedlund, Tyler; Young, Hillary S

    2016-07-01

    Despite the established importance of rodents as reservoirs of vector-borne zoonoses in East Africa, there is relatively limited information regarding the infestation parameters and host associations of ectoparasites that vector many such pathogens among small mammals in this region. Between 2009 and 2013, small mammals were live-trapped in the semiarid savanna of Kenya. A subset of these individual hosts, including 20 distinct host taxa, was examined for ectoparasites, which were identified to species. Species of fleas, ticks, mites, and sucking lice were recorded. Based on these data, we calculated host-specific infestation parameters, documented host preferences among ectoparasites, conducted a rarefaction analysis and extrapolation to determine if ectoparasites were adequately sampled, and assessed nestedness for fleas to understand how pathogens might spread in this system. We found that the flea community structure was significantly nested. Understanding the ectoparasite network structure may have significant human relevance, as at least seven of the ectoparasite species collected are known vectors of pathogens of medical importance in the region, including Yersinia pestis, Rickettsia spp., and Theileria parva, the causative agents of plague, spotted fevers and other rickettsial illnesses in humans, and theileriosis, respectively.

  3. Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees.

    PubMed

    McFrederick, Quinn S; Wcislo, William T; Hout, Michael C; Mueller, Ulrich G

    2014-05-01

    Social transmission and host developmental stage are thought to profoundly affect the structure of bacterial communities associated with honey bees and bumble bees, but these ideas have not been explored in other bee species. The halictid bees Megalopta centralis and M. genalis exhibit intrapopulation social polymorphism, which we exploit to test whether bacterial communities differ by host social structure, developmental stage, or host species. We collected social and solitary Megalopta nests and sampled bees and nest contents from all stages of host development. To survey these bacterial communities, we used 16S rRNA gene 454 pyrosequencing. We found no effect of social structure, but found differences by host species and developmental stage. Wolbachia prevalence differed between the two host species. Bacterial communities associated with different developmental stages appeared to be driven by environmentally acquired bacteria. A Lactobacillus kunkeei clade bacterium that is consistently associated with other bee species was dominant in pollen provisions and larval samples, but less abundant in mature larvae and pupae. Foraging adults appeared to often reacquire L. kunkeei clade bacteria, likely while foraging at flowers. Environmental transmission appears to be more important than social transmission for Megalopta bees at the cusp between social and solitary behavior.

  4. Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses

    PubMed Central

    Eng, Christine L. P.; Tong, Joo Chuan; Tan, Tin Wee

    2016-01-01

    Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak. PMID:26915079

  5. Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses.

    PubMed

    Eng, Christine L P; Tong, Joo Chuan; Tan, Tin Wee

    2016-01-01

    Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak.

  6. Culture-independent methods for identifying microbial communities in cheese.

    PubMed

    Jany, Jean-Luc; Barbier, Georges

    2008-10-01

    This review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets.

  7. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

    EPA Science Inventory

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  8. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN CATTLE FECAL SAMPLES - ABSTRACT

    EPA Science Inventory

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  9. A Human Proteome Array Approach to Identifying Key Host Proteins Targeted by Toxoplasma Kinase ROP18.

    PubMed

    Yang, Zhaoshou; Hou, Yongheng; Hao, Taofang; Rho, Hee-Sool; Wan, Jun; Luan, Yizhao; Gao, Xin; Yao, Jianping; Pan, Aihua; Xie, Zhi; Qian, Jiang; Liao, Wanqin; Zhu, Heng; Zhou, Xingwang

    2017-03-01

    Toxoplasma kinase ROP18 is a key molecule responsible for the virulence of Toxoplasma gondii; however, the mechanisms by which ROP18 exerts parasite virulence via interaction with host proteins remain limited to a small number of identified substrates. To identify a broader array of ROP18 substrates, we successfully purified bioactive mature ROP18 and used it to probe a human proteome array. Sixty eight new putative host targets were identified. Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase activity and phosphorylation, cell growth, apoptosis and cell death, and immunity, indicating a pleiotropic role of ROP18 kinase. Among these proteins, four candidates, p53, p38, UBE2N, and Smad1, were further validated. We demonstrated that ROP18 targets p53, p38, UBE2N, and Smad1 for degradation. Importantly, we demonstrated that ROP18 phosphorylates Smad1 Ser-187 to trigger its proteasome-dependent degradation. Further functional characterization of the substrates of ROP18 may enhance understanding of the pathogenesis of Toxoplasma infection and provide new therapeutic targets. Similar strategies could be used to identify novel host targets for other microbial kinases functioning at the pathogen-host interface.

  10. Identifying the Local Impacts of National ATE Centers on Their Host Institutions: An Exploratory Study

    ERIC Educational Resources Information Center

    Henderson, Charles; Fynewever, Herb; Petcovic, Heather; Bierema, Andrea

    2012-01-01

    The purpose of this study is to identify the local impacts of national advanced technological education (ATE) centers on their host institutions. A sample of three mature, national ATE centers are chosen, with each center serving as a case for a mixed-methods, collective case study research design. Results, drawn from interviews and surveys,…

  11. Identifying Community Needs and Resources in a Native Community: A Research Partnership in the Pacific Northwest

    PubMed Central

    Donovan, Dennis M.; Sigo, Robin L. W.

    2012-01-01

    Indigenous communities have engaged in needs and resources assessments for thousands of years. By blending CBPR/TPR approaches with community-driven assets and needs assessments, academic and community based researchers can work together to better understand and identify community strengths as well as issues of concern in Native communities. This best practice approach can set research agendas that are relevant to Native communities and result in interventions and health promotion programs that are respectful of Tribal sovereignty and that incorporate unique traditions and strengths of Native communities. A successful research partnership to develop and implement a needs and resources assessment using CBPR/TPR approaches is presented using a case study that can be used as a model for other research partnerships. PMID:23123765

  12. Phylogenetic dispersion of host use in a tropical insect herbivore community.

    PubMed

    Weiblen, George D; Webb, Campbell O; Novotny, Vojtech; Basset, Yves; Miller, Scott E

    2006-07-01

    Theory has long predicted that insect community structure should be related to host plant phylogeny. We examined the distribution of insect herbivore associations with respect to host plant phylogeny for caterpillars (Lepidoptera), beetles (Coleoptera), and grasshoppers and relatives (orthopteroids) in a New Guinea rain forest. We collected herbivores from three lineages of closely related woody plants and from more distantly related plant lineages in the same locality to examine the phylogenetic scale at which host specificity can be detected in a community sample. By grafting molecular phylogenies inferred from three different genes into a supertree, we developed a phylogenetic hypothesis for the host community. Feeding experiments were performed on more than 100 000 live insects collected from the 62 host species. We examined patterns of host use with respect to the host plant phylogeny. As predicted, we found a negative relationship between faunal similarity, defined as the proportion of all herbivores feeding on two hosts that are shared between the hosts, and the phylogenetic distance between hosts based on DNA sequence divergence. Host phylogenetic distance explained a significant fraction of the variance (25%) in herbivore community similarity, in spite of the many ecological factors that probably influence feeding patterns. Herbivore community similarity among congeneric hosts was high (50% on average) compared to overlap among host families (20-30% on average). We confirmed this pattern using the nearest taxon index (NTI) and net relatedness index (NRI) to quantify the extent of phylogenetic clustering in particular herbivore associations and to test whether patterns are significantly different from chance expectations. We found that 40% of caterpillar species showed significant phylogenetic clustering with respect to host plant associations, somewhat more so than for beetles or orthopteroids. We interpret this as evidence that a substantial fraction of

  13. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors.

    PubMed

    Park, Ryan J; Wang, Tim; Koundakjian, Dylan; Hultquist, Judd F; Lamothe-Molina, Pedro; Monel, Blandine; Schumann, Kathrin; Yu, Haiyan; Krupzcak, Kevin M; Garcia-Beltran, Wilfredo; Piechocka-Trocha, Alicja; Krogan, Nevan J; Marson, Alexander; Sabatini, David M; Lander, Eric S; Hacohen, Nir; Walker, Bruce D

    2017-02-01

    Host proteins are essential for HIV entry and replication and can be important nonviral therapeutic targets. Large-scale RNA interference (RNAi)-based screens have identified nearly a thousand candidate host factors, but there is little agreement among studies and few factors have been validated. Here we demonstrate that a genome-wide CRISPR-based screen identifies host factors in a physiologically relevant cell system. We identify five factors, including the HIV co-receptors CD4 and CCR5, that are required for HIV infection yet are dispensable for cellular proliferation and viability. Tyrosylprotein sulfotransferase 2 (TPST2) and solute carrier family 35 member B2 (SLC35B2) function in a common pathway to sulfate CCR5 on extracellular tyrosine residues, facilitating CCR5 recognition by the HIV envelope. Activated leukocyte cell adhesion molecule (ALCAM) mediates cell aggregation, which is required for cell-to-cell HIV transmission. We validated these pathways in primary human CD4(+) T cells through Cas9-mediated knockout and antibody blockade. Our findings indicate that HIV infection and replication rely on a limited set of host-dispensable genes and suggest that these pathways can be studied for therapeutic intervention.

  14. Feature selection methods for identifying genetic determinants of host species in RNA viruses.

    PubMed

    Aguas, Ricardo; Ferguson, Neil M

    2013-01-01

    Despite environmental, social and ecological dependencies, emergence of zoonotic viruses in human populations is clearly also affected by genetic factors which determine cross-species transmission potential. RNA viruses pose an interesting case study given their mutation rates are orders of magnitude higher than any other pathogen--as reflected by the recent emergence of SARS and Influenza for example. Here, we show how feature selection techniques can be used to reliably classify viral sequences by host species, and to identify the crucial minority of host-specific sites in pathogen genomic data. The variability in alleles at those sites can be translated into prediction probabilities that a particular pathogen isolate is adapted to a given host. We illustrate the power of these methods by: 1) identifying the sites explaining SARS coronavirus differences between human, bat and palm civet samples; 2) showing how cross species jumps of rabies virus among bat populations can be readily identified; and 3) de novo identification of likely functional influenza host discriminant markers.

  15. Symbiodinium (Dinophyceae) community patterns in invertebrate hosts from inshore marginal reefs of the southern Great Barrier Reef, Australia.

    PubMed

    Tonk, Linda; Sampayo, Eugenia M; Chai, Aaron; Schrameyer, Verena; Hoegh-Guldberg, Ove

    2017-02-14

    The broad range in physiological variation displayed by Symbiodinium spp. has proven imperative during periods of environmental change and contribute to the survival of their coral host. Characterizing how host and Symbiodinium community assemblages differ across environmentally distinct habitats provides useful information to predict how corals will respond to major environmental change. Despite the extensive characterizations of Symbiodinium diversity found amongst reef cnidarians on the Great Barrier Reef (GBR) substantial biogeographic gaps exist, especially across inshore habitats. Here, we investigate Symbiodinium community patterns in invertebrates from inshore and mid-shelf reefs on the southern GBR, Australia. Dominant Symbiodinium types were characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Twenty one genetically distinct Symbiodinium types including four novel types were identified from 321 reef-invertebrate samples comprising three sub-generic clades (A, C, and D). A range of host genera harbored C22a, which is normally rare or absent from inshore or low latitude reefs in the GBR. Multivariate analysis showed that host identity and sea surface temperature best explained the variation in symbiont communities across sites. Patterns of changes in Symbiodinium community assemblage over small geographic distances (100s of kilometers or less) indicate the likelihood that shifts in Symbiodinium distributions and associated host populations, may occur in response to future climate change impacting the GBR.

  16. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses.

    PubMed

    Chung, Seung Ho; Scully, Erin D; Peiffer, Michelle; Geib, Scott M; Rosa, Cristina; Hoover, Kelli; Felton, Gary W

    2017-01-03

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore's ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants.

  17. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

    PubMed Central

    Chung, Seung Ho; Scully, Erin D.; Peiffer, Michelle; Geib, Scott M.; Rosa, Cristina; Hoover, Kelli; Felton, Gary W.

    2017-01-01

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore’s ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants. PMID:28045052

  18. Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis.

    PubMed

    López, Vladimir; Villar, Margarita; Queirós, João; Vicente, Joaquín; Mateos-Hernández, Lourdes; Díez-Delgado, Iratxe; Contreras, Marinela; Alves, Paulo C; Alberdi, Pilar; Gortázar, Christian; de la Fuente, José

    2016-03-01

    Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly impact human and animal health worldwide. The mycobacterial life cycle is complex, and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Eurasian wild boar (Sus scrofa) are natural reservoir hosts for MTBC and a model for mycobacterial infection and tuberculosis (TB). In the wild boar TB model, mycobacterial infection affects the expression of innate and adaptive immune response genes in mandibular lymph nodes and oropharyngeal tonsils, and biomarkers have been proposed as correlates with resistance to natural infection. However, the mechanisms used by mycobacteria to manipulate host immune response are not fully characterized. Our hypothesis is that the immune system proteins under-represented in infected animals, when compared to uninfected controls, are used by mycobacteria to guarantee pathogen infection and transmission. To address this hypothesis, a comparative proteomics approach was used to compare host response between uninfected (TB-) and M. bovis-infected young (TB+) and adult animals with different infection status [TB lesions localized in the head (TB+) or affecting multiple organs (TB++)]. The results identified host immune system proteins that play an important role in host response to mycobacteria. Calcium binding protein A9, Heme peroxidase, Lactotransferrin, Cathelicidin and Peptidoglycan-recognition protein were under-represented in TB+ animals when compared to uninfected TB- controls, but protein levels were higher as infection progressed in TB++ animals when compared to TB- and/or TB+ adult wild boar. MHCI was the only protein over-represented in TB+ adult wild boar when compared to uninfected TB- controls. The results reported here suggest that M. bovis manipulates host immune response by reducing the production of immune system proteins. However, as infection progresses, wild boar immune response recovers to limit pathogen

  19. Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis

    PubMed Central

    López, Vladimir; Villar, Margarita; Queirós, João; Vicente, Joaquín; Mateos-Hernández, Lourdes; Díez-Delgado, Iratxe; Contreras, Marinela; Alves, Paulo C.; Alberdi, Pilar; Gortázar, Christian; de la Fuente, José

    2016-01-01

    Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly impact human and animal health worldwide. The mycobacterial life cycle is complex, and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Eurasian wild boar (Sus scrofa) are natural reservoir hosts for MTBC and a model for mycobacterial infection and tuberculosis (TB). In the wild boar TB model, mycobacterial infection affects the expression of innate and adaptive immune response genes in mandibular lymph nodes and oropharyngeal tonsils, and biomarkers have been proposed as correlates with resistance to natural infection. However, the mechanisms used by mycobacteria to manipulate host immune response are not fully characterized. Our hypothesis is that the immune system proteins under-represented in infected animals, when compared to uninfected controls, are used by mycobacteria to guarantee pathogen infection and transmission. To address this hypothesis, a comparative proteomics approach was used to compare host response between uninfected (TB-) and M. bovis-infected young (TB+) and adult animals with different infection status [TB lesions localized in the head (TB+) or affecting multiple organs (TB++)]. The results identified host immune system proteins that play an important role in host response to mycobacteria. Calcium binding protein A9, Heme peroxidase, Lactotransferrin, Cathelicidin and Peptidoglycan-recognition protein were under-represented in TB+ animals when compared to uninfected TB- controls, but protein levels were higher as infection progressed in TB++ animals when compared to TB- and/or TB+ adult wild boar. MHCI was the only protein over-represented in TB+ adult wild boar when compared to uninfected TB- controls. The results reported here suggest that M. bovis manipulates host immune response by reducing the production of immune system proteins. However, as infection progresses, wild boar immune response recovers to limit pathogen

  20. Quantifying Community Assembly Processes and Identifying Features that Impose Them

    SciTech Connect

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Chen, Xingyuan; Kennedy, David W.; Murray, Christopher J.; Rockhold, Mark L.; Konopka, Allan

    2013-06-06

    Across a set of ecological communities connected to each other through organismal dispersal (a ‘meta-community’), turnover in composition is governed by (ecological) Drift, Selection, and Dispersal Limitation. Quantitative estimates of these processes remain elusive, but would represent a common currency needed to unify community ecology. Using a novel analytical framework we quantitatively estimate the relative influences of Drift, Selection, and Dispersal Limitation on subsurface, sediment-associated microbial meta-communities. The communities we study are distributed across two geologic formations encompassing ~12,500m3 of uranium-contaminated sediments within the Hanford Site in eastern Washington State. We find that Drift consistently governs ~25% of spatial turnover in community composition; Selection dominates (governing ~60% of turnover) across spatially-structured habitats associated with fine-grained, low permeability sediments; and Dispersal Limitation is most influential (governing ~40% of turnover) across spatially-unstructured habitats associated with coarse-grained, highly-permeable sediments. Quantitative influences of Selection and Dispersal Limitation may therefore be predictable from knowledge of environmental structure. To develop a system-level conceptual model we extend our analytical framework to compare process estimates across formations, characterize measured and unmeasured environmental variables that impose Selection, and identify abiotic features that limit dispersal. Insights gained here suggest that community ecology can benefit from a shift in perspective; the quantitative approach developed here goes beyond the ‘niche vs. neutral’ dichotomy by moving towards a style of natural history in which estimates of Selection, Dispersal Limitation and Drift can be described, mapped and compared across ecological systems.

  1. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    PubMed

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors.

  2. Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

    PubMed Central

    Eisen, Jonathan A.; Kopp, Artyom

    2012-01-01

    The combination of ecological diversity with genetic and experimental tractability makes Drosophila a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in Drosophila physiology, behavior, and fitness, most recent work has focused on Drosophila-bacterial interactions. In order to get a more complete understanding of the Drosophila microbiome, we characterized the yeast communities associated with different Drosophila species collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of the Drosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed in Drosophila bacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach. PMID:22885750

  3. Community Engagement for Identifying Cancer Education Needs in Puerto Rico.

    PubMed

    Jiménez, Julio; Ramos, Axel; Ramos-Rivera, Francisco E; Gwede, Clement; Quinn, Gwendolyn P; Vadaparampil, Susan; Brandon, Thomas; Simmons, Vani; Castro, Eida

    2016-10-10

    Cancer is the leading cause of death in Puerto Rico, suggesting a need for improved strategies, programs, and resources devoted to cancer prevention. Enhanced prevention needs in Puerto Rico were initially identified in pilot studies conducted by the Ponce School of Medicine (PSM) in collaboration with the H. Lee Moffitt Cancer Center (MCC). In the current study, we used community engagement to identify specific needs in cancer prevention and education and strategies to create culturally attuned, effective cancer prevention education programs. A total of 37 participants attended a community forum and were assigned to one of three discussion groups: patients/survivors (n = 14); family/caregivers (n = 11); or healthcare providers (n = 12). Most participants were women (73 %), over 35 years of age, and a majority were married (58 %) and had a university education (81 %). The sessions were recorded and transcribed and analyzed for key themes. Participants wanted improved awareness of cancer prevention in Puerto Rico and believed cancer prevention education should start early, ideally in elementary school. Participants also stressed the importance of creating partnerships with private and government agencies to coordinate educational efforts. Suggested strategies included outreach to communities with limited resources, incorporating the testimony of cancer survivors, and utilizing social media to disseminate cancer prevention information.

  4. [Dependence of the structure of component parasite communities on host age].

    PubMed

    Dorovskikh, G N; Stepanov, V G

    2008-01-01

    Dependence of the structure of component parasite communities on host age is studied by the example of parasite communities in minnow and grayling from the North Dvina and Pechora rivers basins. Parasite communities from immature host groups are revealed to be different from those in mature fishes by lesser number of parasite individuals and biomass, number of groups discriminated by the ratio of biomasses, and frequently by lesser number of species. Indices of diversity describing parasite communities from hosts of different ages are nearly always the same in the area examined. This observation needs in verification because values of the indices characterizing parasite communities from fishes of different ages are not equal in the parasite communities from grayling of different age from the Pinega river and minnow from the Chovju river (Dorovskikh, 2002).

  5. Identifying Key Hospital Service Quality Factors in Online Health Communities

    PubMed Central

    Jung, Yuchul; Hur, Cinyoung; Jung, Dain

    2015-01-01

    Background The volume of health-related user-created content, especially hospital-related questions and answers in online health communities, has rapidly increased. Patients and caregivers participate in online community activities to share their experiences, exchange information, and ask about recommended or discredited hospitals. However, there is little research on how to identify hospital service quality automatically from the online communities. In the past, in-depth analysis of hospitals has used random sampling surveys. However, such surveys are becoming impractical owing to the rapidly increasing volume of online data and the diverse analysis requirements of related stakeholders. Objective As a solution for utilizing large-scale health-related information, we propose a novel approach to identify hospital service quality factors and overtime trends automatically from online health communities, especially hospital-related questions and answers. Methods We defined social media–based key quality factors for hospitals. In addition, we developed text mining techniques to detect such factors that frequently occur in online health communities. After detecting these factors that represent qualitative aspects of hospitals, we applied a sentiment analysis to recognize the types of recommendations in messages posted within online health communities. Korea’s two biggest online portals were used to test the effectiveness of detection of social media–based key quality factors for hospitals. Results To evaluate the proposed text mining techniques, we performed manual evaluations on the extraction and classification results, such as hospital name, service quality factors, and recommendation types using a random sample of messages (ie, 5.44% (9450/173,748) of the total messages). Service quality factor detection and hospital name extraction achieved average F1 scores of 91% and 78%, respectively. In terms of recommendation classification, performance (ie, precision) is

  6. Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

    PubMed Central

    Brooks, Andrew W.; Kohl, Kevin D.; Brucker, Robert M.; van Opstal, Edward J.; Bordenstein, Seth R.

    2016-01-01

    Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids. We demonstrate three key findings. First, intraspecific microbiota variation is consistently less than interspecific microbiota variation, and microbiota-based models predict host species origin with high accuracy across the dataset. Interestingly, the age of host clade divergence positively associates with the degree of microbial community distinguishability between species within the host clades, spanning recent host speciation events (~1 million y ago) to more distantly related host genera (~108 million y ago). Second, topological congruence analyses of each group's complete phylogeny and microbiota dendrogram reveal significant degrees of phylosymbiosis, irrespective of host clade age or taxonomy. Third, consistent with selection on host–microbiota interactions driving phylosymbiosis, there are survival and performance reductions when interspecific microbiota transplants are conducted between closely related and divergent host species pairs. Overall, these findings indicate that the composition and functional effects of an animal's microbial community can be closely allied with host evolution, even across wide-ranging timescales and diverse animal systems reared under controlled conditions. PMID:27861590

  7. Host identity impacts rhizosphere fungal communities associated with three alpine plant species.

    PubMed

    Becklin, Katie M; Hertweck, Kate L; Jumpponen, Ari

    2012-04-01

    Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect

  8. Host and parasite diversity jointly control disease risk in complex communities

    PubMed Central

    Johnson, Pieter T. J.; Preston, Daniel L.; Hoverman, Jason T.; LaFonte, Bryan E.

    2013-01-01

    Host–parasite interactions are embedded within complex communities composed of multiple host species and a cryptic assemblage of other parasites. To date, however, surprisingly few studies have explored the joint effects of host and parasite richness on disease risk, despite growing interest in the diversity–disease relationship. Here, we combined field surveys and mechanistic experiments to test how transmission of the virulent trematode Ribeiroia ondatrae was affected by the diversity of both amphibian hosts and coinfecting parasites. Within natural wetlands, host and parasite species richness correlated positively, consistent with theoretical predictions. Among sites that supported Ribeiroia, however, host and parasite richness interacted to negatively affect Ribeiroia transmission between its snail and amphibian hosts, particularly in species-poor assemblages. In laboratory and outdoor experiments designed to decouple the relative contributions of host and parasite diversity, increases in host richness decreased Ribeiroia infection by 11–65%. Host richness also tended to decrease total infections by other parasite species (four of six instances), such that more diverse host assemblages exhibited ∼40% fewer infections overall. Importantly, parasite richness further reduced both per capita and total Ribeiroia infection by 15–20%, possibly owing to intrahost competition among coinfecting species. These findings provide evidence that parasitic and free-living diversity jointly regulate disease risk, help to resolve apparent contradictions in the diversity–disease relationship, and emphasize the challenges of integrating research on coinfection and host heterogeneity to develop a community ecology-based approach to infectious diseases. PMID:24082092

  9. Host Protein Biomarkers Identify Active Tuberculosis in HIV Uninfected and Co-infected Individuals

    PubMed Central

    Achkar, Jacqueline M.; Cortes, Laetitia; Croteau, Pascal; Yanofsky, Corey; Mentinova, Marija; Rajotte, Isabelle; Schirm, Michael; Zhou, Yiyong; Junqueira-Kipnis, Ana Paula; Kasprowicz, Victoria O.; Larsen, Michelle; Allard, René; Hunter, Joanna; Paramithiotis, Eustache

    2015-01-01

    Biomarkers for active tuberculosis (TB) are urgently needed to improve rapid TB diagnosis. The objective of this study was to identify serum protein expression changes associated with TB but not latent Mycobacterium tuberculosis infection (LTBI), uninfected states, or respiratory diseases other than TB (ORD). Serum samples from 209 HIV uninfected (HIV−) and co-infected (HIV+) individuals were studied. In the discovery phase samples were analyzed via liquid chromatography and mass spectrometry, and in the verification phase biologically independent samples were analyzed via a multiplex multiple reaction monitoring mass spectrometry (MRM-MS) assay. Compared to LTBI and ORD, host proteins were significantly differentially expressed in TB, and involved in the immune response, tissue repair, and lipid metabolism. Biomarker panels whose composition differed according to HIV status, and consisted of 8 host proteins in HIV− individuals (CD14, SEPP1, SELL, TNXB, LUM, PEPD, QSOX1, COMP, APOC1), or 10 host proteins in HIV+ individuals (CD14, SEPP1, PGLYRP2, PFN1, VASN, CPN2, TAGLN2, IGFBP6), respectively, distinguished TB from ORD with excellent accuracy (AUC = 0.96 for HIV− TB, 0.95 for HIV+ TB). These results warrant validation in larger studies but provide promise that host protein biomarkers could be the basis for a rapid, blood-based test for TB. PMID:26501113

  10. Global assessment of molecularly identified Anisakis Dujardin, 1845 (Nematoda: Anisakidae) in their teleost intermediate hosts.

    PubMed

    Kuhn, Thomas; Hailer, Frank; Palm, Harry W; Klimpel, Sven

    2013-05-01

    Here, we present the ITS ribosomal DNA (rDNA) sequence data on 330 larvae of nematodes of the genus Anisakis Dujardin, 1845 collected from 26 different bony fish species from 21 sampling locations and different climatic zones. New host records are provided for Anisakis simplex (Rudolphi, 1809) sensu stricto (s.s.) and A. pegreffli Campana-Rouget et Biocca, 1955 from Anoplopoma fimbria (Pallas) (Santa Barbara, East Pacific), A. typica (Diesing, 1860) from Caesio cuning (Bloch), Lepturacanthus savala (Cuvier) and Katsuwonus pelamis (Linnaeus) (Indonesia, West Pacific), A. simplex s.s. from Cololabis saira (Brevoort) (Hawaii, Central Pacific), A. simplex C of Nascetti et al. (1986) from Sebastolobus alascanus Bean (Santa Barbara, East Pacific) and A. physeteris Baylis, 1923 from Synaphobranchus kaupii Johnson (Namibia, East Atlantic). Comparison with host records from 60 previous molecular studies of Anisakis species reveals the teleost host range so far recorded for the genus. Perciform (57 species) and gadiform (21) fishes were the most frequently infected orders, followed by pleuronectiforms (15) and scorpaeniforms (15). Most commonly infected fish families were Scombridae (12), Gadidae (10), Carangidae (8) and Clupeidae (7), with Merluccius merluccius (Linnaeus) alone harbouring eight Anisakis species. Different intermediate host compositions implicate differing life cycles for the so far molecularly identified Anisakis sibling species.

  11. Visual Genome-Wide RNAi Screening to Identify Human Host Factors Required for Trypanosoma cruzi Infection

    PubMed Central

    de Macedo Dossin, Fernando; Choi, Seo Yeon; Kim, Nam Youl; Kim, Hi Chul; Jung, Sung Yong; Schenkman, Sergio; Almeida, Igor C.; Emans, Neil; Freitas-Junior, Lucio H.

    2011-01-01

    The protozoan parasite Trypanosoma cruzi is the etiologic agent of Chagas disease, a neglected tropical infection that affects millions of people in the Americas. Current chemotherapy relies on only two drugs that have limited efficacy and considerable side effects. Therefore, the development of new and more effective drugs is of paramount importance. Although some host cellular factors that play a role in T. cruzi infection have been uncovered, the molecular requirements for intracellular parasite growth and persistence are still not well understood. To further study these host-parasite interactions and identify human host factors required for T. cruzi infection, we performed a genome-wide RNAi screen using cellular microarrays of a printed siRNA library that spanned the whole human genome. The screening was reproduced 6 times and a customized algorithm was used to select as hits those genes whose silencing visually impaired parasite infection. The 162 strongest hits were subjected to a secondary screening and subsequently validated in two different cell lines. Among the fourteen hits confirmed, we recognized some cellular membrane proteins that might function as cell receptors for parasite entry and others that may be related to calcium release triggered by parasites during cell invasion. In addition, two of the hits are related to the TGF-beta signaling pathway, whose inhibition is already known to diminish levels of T. cruzi infection. This study represents a significant step toward unveiling the key molecular requirements for host cell invasion and revealing new potential targets for antiparasitic therapy. PMID:21625474

  12. Short-term volunteer health trips: aligning host community preferences and organizer practices

    PubMed Central

    Rozier, Michael D.; Lasker, Judith N.; Compton, Bruce

    2017-01-01

    ABSTRACT Background: Short-term medical missions (STMMs) are quite common and largely understood to be a response to health needs in low-income countries. Yet most information about STMM practices is anecdotal. Even less is known about the preferences of in-country host communities regarding STMMs. Objective: We aimed to gather enough quantitative and qualitative information from both STMM organizers and host community staff to compare dominant practices of organizers as well as preferences of host community staff. We use these data to discover differences between practices and preferences and suggest ways in which STMMs can be more responsive to the communities they serve. Methods: Researchers gathered online survey responses from 334 STMM organizers and conducted interviews to determine existing practices. Similar methods were used to collect 49 online survey responses from, and conduct 75 interviews with, host community staff. Results: Organizer practices and host community staff preferences are different in several areas. Organizers admit to minimal screening and preparation of volunteers whereas host staff have clear ideas of topics that should be covered in preparation, including culture and basic language skills. Organizers prioritize provision of clinical care during trips whereas host staff prioritize capacity building. Practices and preferences also differ in relation to the length of STMMs, the nature of the partnership itself, and the type of assessment and evaluation that is needed. Conclusions: The large amount of data gathered for this study allows us to confidently say that organizer practices are often not aligned with host community staff preferences. Several concrete changes can be made to STMMs to bring practices more in line with the desires of the communities they serve. PMID:28218547

  13. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We prev...

  14. Relationships between community structure of freshwater mussels and host fishes in a central Ohio watershed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The diversity of freshwater mussel communities has declined over the past several decades within watersheds in the Midwestern United States. Host fishes play an important role in the life cycle of freshwater mussels because they serve as hosts for parasitic mussel larvae to ensure successful mussel ...

  15. Creating a Community Capacity Assessment to Identify Agency Outcomes Related to Occupational Therapy Student Community Partnerships.

    PubMed

    Kramlinger, Anne; Strecker Neufeld, Peggy; Berg, Christine

    2016-07-01

    Service-learning experiences immerse students in authentic situations and build partnerships with community agencies to support the health of those we serve in practice. Most occupational therapy curriculum evaluations do not systematically capture community agency benefits. Through the use of qualitative interviews and Q Methodology, the Community Agency Capacity Questionnaire (CACQ) was developed to capture the agency experience in these partnerships. This paper describes the iterative analytic process that resulted in the CACQ with 29 statements covering 6 domains: programming, evaluation, partnership, staff, funding, and marketing. The CACQ offers a means to identify outcomes from the service-learning partners' perspective.

  16. Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae).

    PubMed

    Zhou, Mei-Jiao; Xiao, Jin-Hua; Bian, Sheng-Nan; Li, Yan-Wei; Niu, Li-Ming; Hu, Hao-Yuan; Wu, Wen-Shan; Murphy, Robert W; Huang, Da-Wei

    2012-07-01

    Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in-depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps' enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co-occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching.

  17. Motivation for Knowledge Sharing by Expert Participants in Company-Hosted Online User Communities

    ERIC Educational Resources Information Center

    Cheng, Jingli

    2014-01-01

    Company-hosted online user communities are increasingly popular as firms continue to search for ways to provide their customers with high quality and reliable support in a low cost and scalable way. Yet, empirical understanding of motivations for knowledge sharing in this type of online communities is lacking, especially with regard to an…

  18. Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities

    PubMed Central

    Messika, Irit; Cohen, Carmit; Toh, Evelyn; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith; Hawlena, Hadas

    2014-01-01

    Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts. PMID:25343259

  19. Association of host and microbial species diversity across spatial scales in desert rodent communities.

    PubMed

    Gavish, Yoni; Kedem, Hadar; Messika, Irit; Cohen, Carmit; Toh, Evelyn; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith; Hawlena, Hadas

    2014-01-01

    Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.

  20. Identifying contextual influences of community reintegration among injured servicemembers.

    PubMed

    Hawkins, Brent L; McGuire, Francis A; Britt, Thomas W; Linder, Sandra M

    2015-01-01

    Research suggests that community reintegration (CR) after injury and rehabilitation is difficult for many injured servicemembers. However, little is known about the influence of the contextual factors, both personal and environmental, that influence CR. Framed within the International Classification of Functioning, Disability and Health and Social Cognitive Theory, the quantitative portion of a larger mixed-methods study of 51 injured, community-dwelling servicemembers compared the relative contribution of contextual factors between groups of servicemembers with different levels of CR. Cluster analysis indicated three groups of servicemembers showing low, moderate, and high levels of CR. Statistical analyses identified contextual factors (e.g., personal and environmental factors) that significantly discriminated between CR clusters. Multivariate analysis of variance and discriminant analysis indicated significant contributions of general self-efficacy, services and assistance barriers, physical and structural barriers, attitudes and support barriers, perceived level of disability and/or handicap, work and school barriers, and policy barriers on CR scores. Overall, analyses indicated that injured servicemembers with lower CR scores had lower general self-efficacy scores, reported more difficulty with environmental barriers, and reported their injuries as more disabling.

  1. Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

    PubMed Central

    Milshteyn, Aleksandr; Schneider, Jessica S.; Brady, Sean F.

    2014-01-01

    Summary Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of re-invigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities. PMID:25237864

  2. Genome-Wide RNAi Screen Identifies Novel Host Proteins Required for Alphavirus Entry

    PubMed Central

    Taylor, Gwen M.; Kielian, Margaret

    2013-01-01

    The enveloped alphaviruses include important and emerging human pathogens such as Chikungunya virus and Eastern equine encephalitis virus. Alphaviruses enter cells by clathrin-mediated endocytosis, and exit by budding from the plasma membrane. While there has been considerable progress in defining the structure and function of the viral proteins, relatively little is known about the host factors involved in alphavirus infection. We used a genome-wide siRNA screen to identify host factors that promote or inhibit alphavirus infection in human cells. Fuzzy homologue (FUZ), a protein with reported roles in planar cell polarity and cilia biogenesis, was required for the clathrin-dependent internalization of both alphaviruses and the classical endocytic ligand transferrin. The tetraspanin membrane protein TSPAN9 was critical for the efficient fusion of low pH-triggered virus with the endosome membrane. FUZ and TSPAN9 were broadly required for infection by the alphaviruses Sindbis virus, Semliki Forest virus, and Chikungunya virus, but were not required by the structurally-related flavivirus Dengue virus. Our results highlight the unanticipated functions of FUZ and TSPAN9 in distinct steps of alphavirus entry and suggest novel host proteins that may serve as targets for antiviral therapy. PMID:24367265

  3. Relationships between host phylogeny, host type and bacterial community diversity in cold-water coral reef sponges.

    PubMed

    Schöttner, Sandra; Hoffmann, Friederike; Cárdenas, Paco; Rapp, Hans Tore; Boetius, Antje; Ramette, Alban

    2013-01-01

    Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level), as well as sponge type (high versus low microbial abundance), and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that as many as 345 (79%) of the 437 different bacterial operational taxonomic units (OTUs) detected in the dataset were shared between sponges and sediments, while only 70 (16%) appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation), sponge family (52%) or sponge type (30%), whereas mesoscale geographic distances and water depth showed comparatively small effects (<5% each). In addition, a highly significant, positive relationship between bacterial community dissimilarity and sponge phylogenetic distance was observed within the ancient family of the Geodiidae. Overall, the high diversity of sponges in cold-water coral reefs, combined with the observed sponge-related variation in bacterial community structure, support the idea that sponges represent heterogeneous, yet structured microbial habitats that contribute significantly to enhancing bacterial diversity in deep-sea ecosystems.

  4. Gypsum-hosted endolithic communities of the Lake St. Martin impact structure, Manitoba, Canada: spectroscopic detectability and implications for Mars

    NASA Astrophysics Data System (ADS)

    Rhind, T.; Ronholm, J.; Berg, B.; Mann, P.; Applin, D.; Stromberg, J.; Sharma, R.; Whyte, L. G.; Cloutis, E. A.

    2014-09-01

    There is increasing evidence that Mars may have once been a habitable environment. Gypsum is targeted in the search for Martian biosignatures because it can host extensive cryptoendolithic communities in extreme terrestrial environments and is widespread on Mars. In this study the viability of using different spectroscopy-based techniques to identify the presence of gypsum endolithic communities was investigated by analysing various cryptoendoliths collected from the Lake St. Martin impact crater (LSM), a Mars analogue site found in Manitoba, Canada. Concurrently, the cryptoendolithic microbial community structure present was also analysed to aid in assigning spectroscopic features to microbial community members. Two main morphologies of endolithic communities were collected from gypsum deposits at LSM: true cryptoendolithic communities and annular deposits on partially buried boulders and cobbles <1 cm below the soil surface. Endolithic communities were found to be visibly present only in gypsum with a high degree of translucency and could occur as deep as 3 cm below the exterior surface. The bacterial community was dominated by a phylum (Chloroflexi) that has not been previously observed in gypsum endoliths. The exterior surfaces of gypsum boulders and cobbles are devoid of spectroscopic features attributable to organic molecules and detectable by reflectance, Raman, or ultraviolet-induced fluorescence spectroscopies. However, exposed interior surfaces show unique endolithic signatures detectable by each spectroscopic technique. This indicates that cryptoendolithic communities can be detected via spectroscopy-based techniques, provided they are either partially or fully exposed and enough photon-target interactions occur to enable detection.

  5. Influences of Host Community Characteristics on Borrelia burgdorferi Infection Prevalence in Blacklegged Ticks

    PubMed Central

    Chiu, Grace S.; Smouse, Peter E.; Fonseca, Dina M.; Brisson, Dustin; Morin, Peter J.; Ostfeld, Richard S.

    2017-01-01

    Lyme disease is a major vector-borne bacterial disease in the USA. The disease is caused by Borrelia burgdorferi, and transmitted among hosts and humans, primarily by blacklegged ticks (Ixodes scapularis). The ~25 B. burgdorferi genotypes, based on genotypic variation of their outer surface protein C (ospC), can be phenotypically separated as strains that primarily cause human diseases—human invasive strains (HIS)—or those that rarely do. Additionally, the genotypes are non-randomly associated with host species. The goal of this study was to examine the extent to which phenotypic outcomes of B. burgdorferi could be explained by the host communities fed upon by blacklegged ticks. In 2006 and 2009, we determined the host community composition based on abundance estimates of the vertebrate hosts, and collected host-seeking nymphal ticks in 2007 and 2010 to determine the ospC genotypes within infected ticks. We regressed instances of B. burgdorferi phenotypes on site-specific characteristics of host communities by constructing Bayesian hierarchical models that properly handled missing data. The models provided quantitative support for the relevance of host composition on Lyme disease risk pertaining to B. burgdorferi prevalence (i.e. overall nymphal infection prevalence, or NIPAll) and HIS prevalence among the infected ticks (NIPHIS). In each year, NIPAll and NIPHIS was found to be associated with host relative abundances and diversity. For mice and chipmunks, the association with NIPAll was positive, but tended to be negative with NIPHIS in both years. However, the direction of association between shrew relative abundance with NIPAll or NIPHIS differed across the two years. And, diversity (H') had a negative association with NIPAll, but positive association with NIPHIS in both years. Our analyses highlight that the relationships between the relative abundances of three primary hosts and the community diversity with NIPAll, and NIPHIS, are variable in time and

  6. Genome-wide in vivo screen identifies novel host regulators of metastatic colonization.

    PubMed

    van der Weyden, Louise; Arends, Mark J; Campbell, Andrew D; Bald, Tobias; Wardle-Jones, Hannah; Griggs, Nicola; Velasco-Herrera, Martin Del Castillo; Tüting, Thomas; Sansom, Owen J; Karp, Natasha A; Clare, Simon; Gleeson, Diane; Ryder, Edward; Galli, Antonella; Tuck, Elizabeth; Cambridge, Emma L; Voet, Thierry; Macaulay, Iain C; Wong, Kim; Spiegel, Sarah; Speak, Anneliese O; Adams, David J

    2017-01-12

    Metastasis is the leading cause of death for cancer patients. This multi-stage process requires tumour cells to survive in the circulation, extravasate at distant sites, then proliferate; it involves contributions from both the tumour cell and tumour microenvironment ('host', which includes stromal cells and the immune system). Studies suggest the early steps of the metastatic process are relatively efficient, with the post-extravasation regulation of tumour growth ('colonization') being critical in determining metastatic outcome. Here we show the results of screening 810 mutant mouse lines using an in vivo assay to identify microenvironmental regulators of metastatic colonization. We identify 23 genes that, when disrupted in mouse, modify the ability of tumour cells to establish metastatic foci, with 19 of these genes not previously demonstrated to play a role in host control of metastasis. The largest reduction in pulmonary metastasis was observed in sphingosine-1-phosphate (S1P) transporter spinster homologue 2 (Spns2)-deficient mice. We demonstrate a novel outcome of S1P-mediated regulation of lymphocyte trafficking, whereby deletion of Spns2, either globally or in a lymphatic endothelial-specific manner, creates a circulating lymphopenia and a higher percentage of effector T cells and natural killer (NK) cells present in the lung. This allows for potent tumour cell killing, and an overall decreased metastatic burden.

  7. Bartonella Species Identified in Rodent and Feline Hosts from Island and Mainland Western Australia.

    PubMed

    Dybing, Narelle A; Jacobson, Caroline; Irwin, Peter; Algar, Dave; Adams, Peter J

    2016-04-01

    Bacteria of the genus Bartonella have been described in multiple mammalian hosts with many species capable of causing disease in humans. Cats and various species of rats have been reported to play a role as vertebrate hosts to a number of Bartonella spp. This study aimed to identify Bartonella spp. in Western Australia, Dirk Hartog Island (DHI), and Christmas Island (CI) and to investigate the presence of potential arthropod vectors. Feral cats were collected from CI (n = 35), DHI (n = 23) and southwest Western Australia (swWA; n = 58), and black rats were collected from CI (n = 48). Individuals were necropsied, ectoparasites were collected by external examination of carcasses, and splenic tissue was collected for polymerase chain reaction analysis to detect Bartonella DNA. Bartonella henselae DNA was detected from two cats and Bartonella koehlerae DNA from one cat in southwest WA, but Bartonella DNA was not identified in cats on DHI or CI. Bartonella phoceensis (28/48 = 58.3%) and a novel Bartonella genotype (8/48 = 16.7%) based on the internal transcribed space region were detected in the spleens of black rats on CI. Detection of Bartonella spp. in each location corresponded to the presence of ectoparasites. Cats from southwest WA harbored four species of fleas, including Ctenocephalides felis, and black rats on CI were infested with multiple species of ectoparasites, including mites, fleas, and lice. Conversely, cats on Dirk Hartog and CI were free of ectoparasites. This study has identified the DNA of Bartonella species from island and mainland swWA with some (B. henselae and B. koehlerae) of known zoonotic importance. This study further extends the geographical range for the pathogenic B. koehlerae. The association of Bartonella with ectoparasites is unsurprising, but little is known about the specific vector competence of the ectoparasites identified in this study.

  8. Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees.

    PubMed

    Vincent, J B; Weiblen, G D; May, G

    2016-02-01

    Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.

  9. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.

    PubMed

    Staubach, Fabian; Baines, John F; Künzel, Sven; Bik, Elisabeth M; Petrov, Dmitri A

    2013-01-01

    The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

  10. Community interactions govern host-switching with implications for host–parasite coevolutionary history

    PubMed Central

    Harbison, Christopher W.; Clayton, Dale H.

    2011-01-01

    Reciprocal selective effects between coevolving species are often influenced by interactions with the broader ecological community. Community-level interactions may also influence macroevolutionary patterns of coevolution, such as cospeciation, but this hypothesis has received little attention. We studied two groups of ecologically similar feather lice (Phthiraptera: Ischnocera) that differ in their patterns of association with a single group of hosts. The two groups, “body lice” and “wing lice,” are both parasites of pigeons and doves (Columbiformes). Body lice are more host-specific and show greater population genetic structure than wing lice. The macroevolutionary history of body lice also parallels that of their columbiform hosts more closely than does the evolutionary history of wing lice. The closer association of body lice with hosts, compared with wing lice, can be explained if body lice are less capable of switching hosts than wing lice. Wing lice sometimes disperse phoretically on parasitic flies (Diptera: Hippoboscidae), but body lice seldom engage in this behavior. We tested the hypothesis that wing lice switch host species more often than body lice, and that the difference is governed by phoresis. Our results show that, where flies are present, wing lice switch to novel host species in sufficient numbers to establish viable populations on the new host. Body lice do not switch hosts, even where flies are present. Thus, differences in the coevolutionary history of wing and body lice can be explained by differences in host-switching, mediated by a member of the broader parasite community. PMID:21606369

  11. Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti

    PubMed Central

    Lembo, T; Haydon, D.T; Velasco-Villa, A; Rupprecht, C.E; Packer, C; Brandão, P.E; Kuzmin, I.V; Fooks, A.R; Barrat, J; Cleaveland, S

    2007-01-01

    Understanding the transmission dynamics of generalist pathogens that infect multiple host species is essential for their effective control. Only by identifying those host populations that are critical to the permanent maintenance of the pathogen, as opposed to populations in which outbreaks are the result of ‘spillover’ infections, can control measures be appropriately directed. Rabies virus is capable of infecting a wide range of host species, but in many ecosystems, particular variants circulate among only a limited range of potential host populations. The Serengeti ecosystem (in northwestern Tanzania) supports a complex community of wild carnivores that are threatened by generalist pathogens that also circulate in domestic dog populations surrounding the park boundaries. While the combined assemblage of host species appears capable of permanently maintaining rabies in the ecosystem, little is known about the patterns of circulation within and between these host populations. Here we use molecular phylogenetics to test whether distinct virus–host associations occur in this species-rich carnivore community. Our analysis identifies a single major variant belonging to the group of southern Africa canid-associated viruses (Africa 1b) to be circulating within this ecosystem, and no evidence for species-specific grouping. A statistical parsimony analysis of nucleoprotein and glycoprotein gene sequence data is consistent with both within- and between-species transmission events. While likely differential sampling effort between host species precludes a definitive inference, the results are most consistent with dogs comprising the reservoir of rabies and emphasize the importance of applying control efforts in dog populations. PMID:17609187

  12. Carbon fixation by basalt-hosted microbial communities.

    PubMed

    Orcutt, Beth N; Sylvan, Jason B; Rogers, Daniel R; Delaney, Jennifer; Lee, Raymond W; Girguis, Peter R

    2015-01-01

    Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with (13)C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of (13)C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of (13)C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1-10 nmol C g(-1) rock d(-1) could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 10(9)-10(12) g C year(-1), which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment.

  13. Carbon fixation by basalt-hosted microbial communities

    PubMed Central

    Orcutt, Beth N.; Sylvan, Jason B.; Rogers, Daniel R.; Delaney, Jennifer; Lee, Raymond W.; Girguis, Peter R.

    2015-01-01

    Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with 13C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of 13C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of 13C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1–10 nmol C g-1rock d-1 could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 109–1012 g C year-1, which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment. PMID:26441854

  14. The structure of parasite communities in fish hosts: ecology meets geography and climate.

    PubMed

    Poulin, R

    2007-09-01

    Parasite communities in fish hosts are not uniform in space: their diversity, composition and abundance vary across the geographical range of a host species. Increasingly urgently, we need to understand the geographic component of parasite communities to better predict how they will respond to global climate change. Patterns of geographical variation in the abundance of parasite populations, and in the diversity and composition of parasite communities, are explored here, and the ways in which they may be affected by climate change are discussed. The time has come to transform fish parasite ecology from a mostly descriptive discipline into a predictive science, capable of integrating complex ecological data to generate forecasts about the future state of host-parasite systems.

  15. Chromosomes Emission of Planet Candidate Host Stars: A Way to Identify False Positives

    NASA Astrophysics Data System (ADS)

    Karoff, Christoffer; Albrecht, Simon; Bonanno, Alfio; Faurschou Knudsen, Mads

    2016-10-01

    It has been hypothesized that the presence of closely orbiting giant planets is associated with enhanced chromospheric emission of their host stars. The main cause for such a relation would likely be enhanced dynamo action induced by the planet. We present measurements of chromospheric emission in 234 planet candidate systems from the Kepler mission. This ensemble includes 37 systems with giant-planet candidates, which show a clear emission enhancement. The enhancement, however, disappears when systems that are also identified as eclipsing binary candidates are removed from the ensemble. This suggests that a large fraction of the giant-planet candidate systems with chromospheric emission stronger than the Sun are not giant-planet systems, but false positives. Such false-positive systems could be tidally interacting binaries with strong chromospheric emission. This hypothesis is supported by an analysis of 188 eclipsing binary candidates that show increasing chromospheric emission as function of decreasing orbital period.

  16. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    PubMed

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  17. Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA

    PubMed Central

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  18. Odontonema cuspidatum and Psychotria punctata, two new cucumber mosaic virus hosts identified in Florida

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The wide host range of Cucumber mosaic virus (CMV) has been expanded by the identification of Odontonema cuspidatum (firespike) and Psychotria punctata (dotted wild coffee) as CMV hosts in Florida....

  19. Identifying Elements Critical for Functional and Sustainable Professional Learning Communities

    ERIC Educational Resources Information Center

    Richmond, Gail; Manokore, Viola

    2011-01-01

    In this paper, we examined data collected as part of a 5-year project designed to foster reform-based urban science teaching through teachers' communities of inquiry. Drawing upon a distributed leadership framework, we analyzed teacher "talk" during professional learning community (PLC) meetings. This analysis yielded five elements:…

  20. Hazardous Drinking and Military Community Functioning: Identifying Mediating Risk Factors

    ERIC Educational Resources Information Center

    Foran, Heather M.; Heyman, Richard E.; Slep, Amy M. Smith

    2011-01-01

    Objective: Hazardous drinking is a serious societal concern in military populations. Efforts to reduce hazardous drinking among military personnel have been limited in effectiveness. There is a need for a deeper understanding of how community-based prevention models apply to hazardous drinking in the military. Community-wide prevention efforts may…

  1. Molecular approaches to identify cryptic species and polymorphic species within a complex community of fig wasps.

    PubMed

    Xiao, Jin-Hua; Wang, Ning-Xin; Li, Yan-Wei; Murphy, Robert W; Wan, Dong-Guang; Niu, Li-Ming; Hu, Hao-Yuan; Fu, Yue-Guan; Huang, Da-Wei

    2010-11-29

    Cryptic and polymorphic species can complicate traditional taxonomic research and both of these concerns are common in fig wasp communities. Species identification is very difficult, despite great effort and the ecological importance of fig wasps. Herein, we try to identify all chalcidoid wasp species hosted by one species of fig, using both morphological and molecular methods. We compare the efficiency of four different DNA regions and find that ITS2 is highly effective for species identification, while mitochondrial COI and Cytb regions appear less reliable, possibly due to the interference signals from either nuclear copies of mtDNA, i.e. NUMTs, or the effects of Wolbachia infections. The analyses suggest that combining multiple markers is the best choice for inferring species identifications as any one marker may be unsuitable in a given case.

  2. Plants of the fynbos biome harbour host species-specific bacterial communities.

    PubMed

    Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

    2016-08-01

    The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth.

  3. Host genetics is associated with the gut microbial community membership rather than the structure.

    PubMed

    Zhao, Peihua; Irwin, David M; Dong, Dong

    2016-04-26

    The issue of what factors shape the gut microbiota has been studied for years. However, questions on the contribution of host genetics to the colonizing process of the gut microbiota and to the extent that host genetics affect the gut microbiota have not yet been clearly answered. Most recently published reports have concluded that host genetics make a smaller contribution than other factors, such as diet, in determining the gut microbiota. Here we have exploited the increasing amount of fecal 16S rRNA gene sequencing data that are becoming available to conduct an analysis to assess the influence of host genetics on the diversity of the gut microbiota. By re-analyzing data obtained from over 5000 stool samples, representing individuals living on five continents and ranging in age from 3 days to 87 years, we found that the strength of the various factors affecting the membership or structure of the gut microbiota are quite different, which leads us to a hypothesis that the presence or absence of taxa is largely controlled by host genetics, whereas non-genetic factors regulate the abundance of each taxon. This hypothesis is supported by the finding that the genome similarity positively correlates with the similarity of community membership. Finally, we showed that only severe perturbations are able to alter the gut microbial community membership. In summary, our work provides new insights into understanding the complexities of the gut microbial community and how it responds to changes imposed on it.

  4. Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification.

    PubMed

    Lenarcic, Erik M; Landry, Dori M; Greco, Todd M; Cristea, Ileana M; Thompson, Sunnie R

    2013-08-01

    Eukaryotic RNA viruses are known to utilize host factors; however, the identity of these factors and their role in the virus life cycle remain largely undefined. Here, we report a method to identify proteins bound to the viral RNA during amplification in cell culture: thiouracil cross-linking mass spectrometry (TUX-MS). TUX-MS relies on incorporation of a zero-distance cross-linker into the viral RNA during infection. Proteins bound to viral RNA are cross-linked prior to cell lysis, purified, and identified using mass spectrometry. Using the TUX-MS method, an unbiased screen for poliovirus (PV) host factors was conducted. All host and viral proteins that are known to interact with the poliovirus RNA were identified. In addition, TUX-MS identified an additional 66 host proteins that have not been previously described in poliovirus amplification. From these candidates, eight were selected and validated. Furthermore, we demonstrate that small interfering RNA (siRNA)-mediated knockdown of two of these uncharacterized host factors results in either a decrease in copy number of positive-stranded RNA or a decrease in PV translation. These data demonstrate that TUX-MS is a robust, unbiased method to identify previously unknown host cell factors that influence virus growth. This method is broadly applicable to a range of RNA viruses, such as flaviviruses, alphaviruses, picornaviruses, bunyaviruses, and coronaviruses.

  5. The relative importance of host-plant genetic diversity in structuring the associated herbivore community.

    PubMed

    Tack, Ayco J M; Roslin, Tomas

    2011-08-01

    Recent studies suggest that intraspecific genetic diversity in one species may leave a substantial imprint on the surrounding community and ecosystem. Here, we test the hypothesis that genetic diversity within host-plant patches translates into consistent and ecologically important changes in the associated herbivore community. More specifically, we use potted, grafted oak saplings to construct 41 patches of four saplings each, with one, two, or four tree genotypes represented among the host plants. These patches were divided among two common gardens. Focusing first at the level of individual trees, we assess how tree-specific genotypic identity, patch-level genetic diversity, garden-level environmental variation, and their interactions affect the structure of the herbivore community. At the level of host-plant patches, we analyze whether the joint responses of herbivore species to environmental variation and genetic diversity result in differences in species diversity among tree quartets. Strikingly, both species-specific abundances and species diversity varied substantially among host-tree genotypes, among common gardens, and among specific locations within individual gardens. In contrast, the genetic diversity of the patch left a detectable imprint on local abundances of only two herbivore taxa. In both cases, the effect of genetic diversity was inconsistent among gardens and among host-plant genotypes. While the insect community differed significantly among individual host-plant genotypes, there were no interactive effects of the number of different genotypes within the patch. Overall, additive effects of intraspecific genetic diversity of the host plant explained a similar or lower proportion (7-10%) of variation in herbivore species diversity than did variation among common gardens. Combined with the few previous studies published to date, our study suggests that the impact of host-plant genetic diversity on the herbivore community can range from none to

  6. Helminth communities of loggerhead turtles (Caretta caretta) from Central and Western Mediterranean Sea: the importance of host's ontogeny.

    PubMed

    Santoro, Mario; Badillo, Francisco J; Mattiucci, Simonetta; Nascetti, Giuseppe; Bentivegna, Flegra; Insacco, Gianni; Travaglini, Andrea; Paoletti, Michela; Kinsella, John M; Tomás, Jesús; Raga, Juan A; Aznar, Francisco J

    2010-09-01

    We investigated the factors providing structure to the helminth communities of 182 loggerhead sea turtles, Caretta caretta, collected in 6 localities from Central and Western Mediterranean. Fifteen helminth taxa (10 digeneans, 4 nematodes and 1 acanthocephalan) were identified, of which 12 were specialist to marine turtles; very low numbers of immature individuals of 3 species typical from fish or cetaceans were also found. These observations confirm the hypothesis that phylogenetic factors restrict community composition to helminth species specific to marine turtles. There were significant community dissimilarities between turtles from different localities, the overall pattern being compatible with the hypothesis that parasite communities reflect the ontogenetic shift that juvenile loggerheads undergo from oceanic to neritic habitats. The smallest turtles at the putative oceanic, pelagic-feeding stage harboured only the 2 digenean species that were regionally the most frequent, i.e. Enodiotrema megachondrus and Calycodes anthos; the largest turtles at the putative neritic, bottom-feeding stage harboured 11 helminth taxa, including 3 nematode species that were rare or absent in turtles that fed partially on pelagic prey. Mean species richness per host was low (range: 1.60-1.89) and did not differ between localities. Variance ratio tests indicated independent colonization of each helminth species. Both features are expected in ectothermic and vagrant hosts living in the marine environment.

  7. Use of host factors to identify people at high risk for cutaneous malignant melanoma .

    PubMed Central

    Marrett, L D; King, W D; Walter, S D; From, L

    1992-01-01

    OBJECTIVE: To determine which host characteristics are risk factors for cutaneous malignant melanoma in order to aim prevention and early detection programs at people at high risk. DESIGN: Case-control study. SETTING: Southern Ontario. SUBJECTS: The 583 case subjects were aged 20 to 69 years and had had malignant melanoma newly diagnosed between Oct. 1, 1984, and Sept. 30, 1986. The 608 control subjects were randomly selected from a list of residents in the study area and were stratum matched for age, sex and municipality. INTERVENTION: Through in-person interviews the interviewer ascertained exposure to putative external risk factors and assessed skin colour and number of nevi on the arm, and the subject reported his or her natural hair colour at age 20 years, eye colour, skin reaction to repeated sun exposure, and freckle and whole-body nevus densities. RESULTS: Although all the host factors mentioned were significantly associated with melanoma risk when considered separately, only hair colour, skin reaction to repeated sun exposure, and self-reported freckle and nevus densities remained significant after backward logistic regression analysis. The odds ratio for melanoma was estimated to be 10.7 in people who had many nevi compared with those who had none (95% confidence interval [CI] 6.6 to 17.4), 4.0 in people who had red hair compared with those who had black hair (95% CI 1.9 to 8.2), 1.9 in people who had many freckles compared with those who had none or few (95% CI 1.3 to 2.8) and 1.4 respectively in people who burned and had a subsequent increase in tan and those who burned and had no increase in tan after repeated sun exposure compared with those who did not burn [corrected]. CONCLUSIONS: Four risk factors for malignant melanoma have been identified. Prospective evaluation of their predictive value should be done. In the meantime, however, these factors should be used to identify people apparently at high risk for malignant melanoma, who can then be

  8. Identifying Etiological Agents Causing Diarrhea in Low Income Ecuadorian Communities

    PubMed Central

    Vasco, Gabriela; Trueba, Gabriel; Atherton, Richard; Calvopiña, Manuel; Cevallos, William; Andrade, Thamara; Eguiguren, Martha; Eisenberg, Joseph N. S.

    2014-01-01

    Continued success in decreasing diarrheal disease burden requires targeted interventions. To develop such interventions, it is crucial to understand which pathogens cause diarrhea. Using a case-control design we tested stool samples, collected in both rural and urban Ecuador, for 15 pathogenic microorganisms. Pathogens were present in 51% of case and 27% of control samples from the urban community, and 62% of case and 18% of control samples collected from the rural community. Rotavirus and Shigellae were associated with diarrhea in the urban community; co-infections were more pathogenic than single infection; Campylobacter and Entamoeba histolytica were found in large numbers in cases and controls; and non-typhi Salmonella and enteropathogenic Escherichia coli were not found in any samples. Consistent with the Global Enteric Multicenter Study, focused in south Asia and sub-Saharan Africa, we found that in Ecuador a small group of pathogens accounted for a significant amount of the diarrheal disease burden. PMID:25048373

  9. Host ontogeny and the temporal decay of similarity in parasite communities of marine fish.

    PubMed

    Timi, Juan T; Luque, José L; Poulin, Robert

    2010-07-01

    Geographical distances between host populations are key determinants of how many parasite species they share. In principle, decay in similarity should also occur with increasing distance along any other dimension that characterizes some form of separation between communities. Here, we apply the biogeographical concept of distance decay in similarity to ontogenetic changes in the metazoan parasite communities of three species of marine fish from the Atlantic coast of South America. Using differences in body length between all possible pairs of size classes as measures of ontogenetic distances, we find that, using an index of similarity (Bray-Curtis) that takes into account the abundance of each parasite species, the similarity in parasite communities showed a very clear decay pattern; using an index (Jaccard) based on presence/absence of species only, we obtained slightly weaker but nevertheless similar patterns. As we predicted, the slope of the decay relationship was significantly steeper in the fish Cynoscion guatucupa, which goes through clear ontogenetic changes in diet and therefore in exposure to parasites, than in the other species, Engraulis anchoita and Micropogonias furnieri, which maintain a roughly similar diet throughout their lives. In addition, we found that for any given ontogenetic distance, i.e. for a given length difference between two size classes, the similarity in parasite communities was almost always higher if they were adult size classes, and almost always lower if they were juvenile size classes. This, combined with comparisons among individual fish within size classes, shows that parasite communities in juvenile fish are variable and subject to stochastic effects. We propose the distance decay approach as a rigorous and quantitative method to measure rates of community change as a function of host age, and for comparisons across host species to elucidate the role of host ecology in the development of parasite assemblages.

  10. Identifying influential user communities on the social network

    NASA Astrophysics Data System (ADS)

    Hu, Weishu; Gong, Zhiguo; Hou U, Leong; Guo, Jingzhi

    2015-10-01

    Nowadays social network services have been popularly used in electronic commerce systems. Users on the social network can develop different relationships based on their common interests and activities. In order to promote the business, it is interesting to explore hidden relationships among users developed on the social network. Such knowledge can be used to locate target users for different advertisements and to provide effective product recommendations. In this paper, we define and study a novel community detection problem that is to discover the hidden community structure in large social networks based on their common interests. We observe that the users typically pay more attention to those users who share similar interests, which enable a way to partition the users into different communities according to their common interests. We propose two algorithms to detect influential communities using common interests in large social networks efficiently and effectively. We conduct our experimental evaluation using a data set from Epinions, which demonstrates that our method achieves 4-11.8% accuracy improvement over the state-of-the-art method.

  11. Multiple Horizontal Transfers of Bacteriophage WO and Host Wolbachia in Fig Wasps in a Closed Community

    PubMed Central

    Wang, Ningxin; Jia, Sisi; Xu, Heng; Liu, Yong; Huang, Dawei

    2016-01-01

    Wolbachia-bacteriophage WO is a good model system for studying interactions between bacteria and viruses. Previous surveys of insect hosts have been conducted via sampling from open or semi-open communities; however, no studies have reported the infection patterns of phage WO of insects living in a closed community. Figs and fig wasps form a peculiar closed community in which the Ficus tree provides a compact syconium habitat for a variety of fig wasp. Therefore, in this study, we performed a thorough survey of Wolbachia and bacteriophage WO infection patterns in a total of 1406 individuals from 23 fig wasps species living on three different fig tree species. The infection rates of Wolbachia and phage WO were 82.6% (19/23) and 39.1% (9/23), respectively. Additionally, phage WO from fig wasps showed strong insect host specificity based on orf7 sequences from fig wasps and 21 other insect species. Probably due to the physical barrier of fig syconium, most phage WO from fig wasps form a specific clade. Phylogenetic analysis showed the absence of congruence between WO and host Wolbachia, WO and insect host, as well as Wolbachia and fig wasps, suggesting that both Wolbachia and phage WO exchanged frequently and independently within the closed syconium. Thus, the infection pattern of bacteriophage WO from fig wasps appeared quite different from that in other insects living outside, although the effect and the transfer routes of phage WO are unclear, which need to be investigated in the future. PMID:26913026

  12. Multiple Horizontal Transfers of Bacteriophage WO and Host Wolbachia in Fig Wasps in a Closed Community.

    PubMed

    Wang, Ningxin; Jia, Sisi; Xu, Heng; Liu, Yong; Huang, Dawei

    2016-01-01

    Wolbachia-bacteriophage WO is a good model system for studying interactions between bacteria and viruses. Previous surveys of insect hosts have been conducted via sampling from open or semi-open communities; however, no studies have reported the infection patterns of phage WO of insects living in a closed community. Figs and fig wasps form a peculiar closed community in which the Ficus tree provides a compact syconium habitat for a variety of fig wasp. Therefore, in this study, we performed a thorough survey of Wolbachia and bacteriophage WO infection patterns in a total of 1406 individuals from 23 fig wasps species living on three different fig tree species. The infection rates of Wolbachia and phage WO were 82.6% (19/23) and 39.1% (9/23), respectively. Additionally, phage WO from fig wasps showed strong insect host specificity based on orf7 sequences from fig wasps and 21 other insect species. Probably due to the physical barrier of fig syconium, most phage WO from fig wasps form a specific clade. Phylogenetic analysis showed the absence of congruence between WO and host Wolbachia, WO and insect host, as well as Wolbachia and fig wasps, suggesting that both Wolbachia and phage WO exchanged frequently and independently within the closed syconium. Thus, the infection pattern of bacteriophage WO from fig wasps appeared quite different from that in other insects living outside, although the effect and the transfer routes of phage WO are unclear, which need to be investigated in the future.

  13. Development of a high-throughput microsphere-based molecular assay to identify fifteen common bloodmeal hosts of Culex mosquitoes

    PubMed Central

    Thiemann, TC; Brault, AC; Ernest, HB; Reisen, WK

    2011-01-01

    For vectorborne infections, host selection by bloodfeeding arthropods dictates the interaction between host and pathogen. Because Culex mosquitoes that transmit West Nile virus (WNV) feed both on mammalian and avian hosts with varying competence, understanding the bloodfeeding patterns of these mosquitoes is important for understanding the transmission dynamics of WNV. Herein, we describe a new microsphere-based assay using Luminex xMAP® technology to rapidly identify 15 common hosts of Culex mosquitoes at our California study sites. The assay was verified with over 100 known vertebrate species samples and was used in conjunction with DNA sequencing to identify over 125 avian and mammalian host species from unknown Culex bloodmeals, more quickly and with less expense than sequencing alone. In addition, with multiplexed labeled probes, this microsphere array identified mixed bloodmeals that were difficult to discern with traditional sequencing. The microsphere set was easily expanded or reduced according to host range in a specific area, and this assay has made it possible to rapidly screen thousands of Culex spp. bloodmeals to extend our understanding of WNV transmission patterns. PMID:22136215

  14. Changes in epiphytic bacterial communities of intertidal seaweeds modulated by host, temporality, and copper enrichment.

    PubMed

    Hengst, Martha B; Andrade, Santiago; González, Bernardo; Correa, Juan A

    2010-08-01

    This study reports on the factors involved in regulating the composition and structure of bacterial communities epiphytic on intertidal macroalgae, exploring their temporal variability and the role of copper pollution. Culture-independent, molecular approaches were chosen for this purpose and three host species were used as models: the ephemeral Ulva spp. (Chlorophyceae) and Scytosiphon lomentaria (Phaeophyceae) and the long-living Lessonia nigrescens (Phaeophyceae). The algae were collected from two coastal areas in Northern Chile, where the main contrast was the concentration of copper in the seawater column resulting from copper-mine waste disposals. We found a clear and strong effect in the structure of the bacterial communities associated with the algal species serving as host. The structure of the bacterial communities also varied through time. The effect of copper on the structure of the epiphytic bacterial communities was significant in Ulva spp., but not on L. nigrescens. The use of 16S rRNA gene library analysis to compare bacterial communities in Ulva revealed that they were composed of five phyla and six classes, with approximately 35 bacterial species, dominated by members of Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) and α-Proteobacteria, in both non-polluted and polluted sites. Less common groups, such as the Verrucomicrobiae, were exclusively found in polluted sites. This work shows that the structure of bacterial communities epiphytic on macroalgae is hierarchically determined by algal species > temporal changes > copper levels.

  15. Mapping radioactivity in groundwater to identify elevated exposure in remote and rural communities.

    PubMed

    Kleinschmidt, Ross; Black, Jeffrey; Akber, Riaz

    2011-03-01

    A survey of radioactivity in groundwater (110 sites) was conducted as a precursor to providing a baseline of radiation exposure in rural and remote communities in Queensland, Australia, that may be impacted upon by exposure pathways associated with the supply, treatment, use and wastewater treatment of the resource. Radionuclides in groundwater, including ²³⁸U, ²²⁶Ra, ²²²Rn, ²²⁸Ra, ²²⁴Ra and ⁴⁰K were measured and found to contain activity concentration levels of up to 0.71 BqL⁻¹, 0.96 BqL⁻¹, 108 BqL⁻¹, 2.8 BqL⁻¹, 0.11 BqL⁻¹ and 0.19 BqL⁻¹ respectively. Activity concentration results were classified by aquifer lithology, showing correlation between increased radium isotope concentration and basic volcanic host rock. The groundwater survey and mapping results were further assessed using an investigation assessment tool to identify seven remote or rural communities that may require additional radiation dose assessment beyond that attributed to ingestion of potable water.

  16. Microcavia australis (Caviidae, Rodentia), a new highly competent host of Trypanosoma cruzi I in rural communities of northwestern Argentina.

    PubMed

    Cecere, M Carla; Cardinal, Marta V; Arrabal, Juan P; Moreno, Claudio; Gürtler, Ricardo E

    2015-02-01

    Rodents are well-known hosts of Trypanosoma cruzi but little is known on the role of some caviomorph rodents. We assessed the occurrence and prevalence of T. cruzi infection in Microcavia australis ("southern mountain, desert or small cavy") and its infectiousness to the vector Triatoma infestans in four rural communities of Tafí del Valle department, northwestern Argentina. Parasite detection was performed by xenodiagnosis and polymerase chain reaction amplification of the hyper-variable region of kinetoplast DNA minicircles of T. cruzi (kDNA-PCR) from blood samples. A total of 51 cavies was captured in traps set up along cavy paths in peridomestic dry-shrub fences located between 25 and 85 m from the nearest domicile. We document the first record of M. australis naturally infected by T. cruzi. Cavies presented a very high prevalence of infection (46.3%; 95% confidence interval, CI=33.0-59.6%). Only one (4%) of 23 cavies negative by xenodiagnosis was found infected by kDNA-PCR. TcI was the only discrete typing unit identified in 12 cavies with a positive xenodiagnosis. The infectiousness to T. infestans of cavies positive by xenodiagnosis or kDNA-PCR was very high (mean, 55.8%; CI=48.4-63.1%) and exceeded 80% in 44% of the hosts. Cavies are highly-competent hosts of T. cruzi in peridomestic habitats near human dwellings in rural communities of Tucumán province in northwestern Argentina.

  17. Identifying common practices in community-based rape prevention programs.

    PubMed

    Townsend, Stephanie M; Campbell, Rebecca

    2008-01-01

    Community-based rape prevention programs have received little attention in the research literature. In this study qualitative methods were used to describe such programs and to assess the degree of homogeneity in their practices. In-depth interviews were conducted with representatives of 10 community-based prevention programs in a single state. Findings suggest that two typologies exist: short programs and extended programs. Homogeneity across programs was common as most programs emphasized secondary and tertiary prevention and relied on short curricula that are implemented with mixed-gender groups of students. A comparison to practices found in the research literature indicate that they are mostly using the same practices and these practices have not been demonstrated to have sustained behavioral effects that would reduce the incidence of sexual violence. Implications for future practice are discussed.

  18. Monogenean community structure of Oreochromis niloticus in relation to heavy metal pollution and host reproductive cycle.

    PubMed

    Soliman, Maha F M; Ibrahim, Mohamed M

    2012-04-01

    The community structure of monogenean parasites of Oreochromis niloticus and its relation to the variations of heavy metal concentrations in water and the host reproductive cycle (gonadosomatic index, GSI) was studied. Fish were collected from Fishermen Lake, Ismailia. Monogenea community consisted of seven species, Cichlidogyrus halli typicus (57.8%), C. thurstonae (35.3%), C. ergensi (13.8 %), C. tiberianus (16.4%), C. arthracanthus (13.8%), Scutogyrus longicornis (22.4%) and Gyrodadtylus cicchlidarum (18.9 %). The overall mean species richness per host was 4.45 +/- 0.34. Responses of monogenea regarding their prevalence, abundance and intensity to the host sex and seasonal variations varied according to the species. Monogenean community showed different responses to the heavy metal concentrations and GSI. Positive correlations were found between species richness and both gonadosomatic index (rs = 0.2, P = 0.03) and Cd concentrations (rs = 0.89, P=0.04). Prevalence of C. halli typicus and C. thurstonae showed significant negative and positive correlations, respectively with the levels of Cu and Pb. G. cicchlidarus showed significant positive correlation with Cd level. The abundance and intensity of those species showed also correlations with the metal concentrations. Other monogenean species did not show any response to the metal levels such as C. tiberianus. Zn did not show any effect on the infection parameters of any species of monogenean community. The possibility of using some monogenean species to act as indicators for environmental pollution was discussed.

  19. Ectomycorrhizal fungus diversity and community structure with natural and cultivated truffle hosts: applying lessons learned to future truffle culture.

    PubMed

    De Miguel, Ana María; Águeda, Beatriz; Sánchez, Sergio; Parladé, Javier

    2014-04-01

    Since the first truffle plantations were established in France, Italy and other parts in the world, many studies have been carried out to improve their productivity and sustainability. Success of plantations is clearly related to the mycorrhizal status of the host trees over the years, from inoculated seedlings to truffle-producing trees. The experience gained in monitoring the ectomycorrhizal fungus status in cultivated truffle grounds has allowed us to develop an extensive catalogue of the ectomycorrhizal fungi present in truffle plantations. Herein, we summarize fungal community data from 85 references that represent different truffle studies in natural habitats and plantations. Approximately 25% of the ectomycorrhizae reported in the 85 references are common to most of the studies. In general, more fungal species are detected in productive plantations than in the non-productive ones. Truffle plantations display a diverse ectomycorrhizal fungal community, in which species of the genus Tuber are well represented. Tuber rufum and some members of Boletales are typically restricted to productive truffle plots. On the other hand, Hebeloma, Laccaria and Russula species are mostly associated with unproductive plots. Ectomycorrhizae belonging to Thelephoraceae are frequently found in mature truffle orchards but do not seem to affect sporocarp production. Several biotic and abiotic factors affect the ectomycorrhizal fungus communities associated with truffle orchards. Among them are plantation age, host species and its growth, the surrounding environment (particularly the presence of other ectomycorrhizal hosts), and plantation management. Understanding the ectomycorrhizal fungal communities inhabiting different plantations may give us clues about the dynamics of the targeted truffles and the possibility of identifying mycorrhizal fungal species that are good indicators of successful truffle plantations.

  20. Phylogenetic relationships among host plants explain differences in fungal species richness and community composition in ectomycorrhizal symbiosis.

    PubMed

    Tedersoo, Leho; Mett, Marit; Ishida, Takahide A; Bahram, Mohammad

    2013-08-01

    Geographic and taxonomic host ranges determine the distribution of biotrophic organisms. Host phylogenetic distance strongly affects the community composition of pathogens and parasites, but little is known about the host phylogeny effect on communities of mutualists, such as plant-pollinator and plant-mycorrhizal fungi systems. By incorporating phylogenetic eigenvectors into univariate and multivariate models, we aimed to determine the relative contribution of host phylogeny and environmental variables to mycorrhizal traits and community composition of ectomycorrhizal (EcM) fungi in Salicaceae at the local scale. Host phylogeny explained 75% of the variation in fungal species richness and 20% of the variation in community composition. We also re-analyzed a system involving eight hosts from Japan, in which host phylogeny explained 26% and 9% of the variation in fungal richness and community composition, respectively. [Correction added after online publication 21 May 2013: in the preceding sentence the values 9% and 26% have been transposed.] Phylogenetic eigenvectors that differentially account for clades and terminal taxa across the phylogeny revealed stronger host effects than did the treatment of host species as categorical or dummy variables in multiregression models, and in comparison with methods such as Mantel test and its analogs. Our results indicate the usefulness of the eigenvector method for the quantification of the host phylogeny effect, which represents an integrated complex function of taxonomic sampling effect and phylogenetic distance per se.

  1. Resource dependence in a new ecosystem: A host plant and its colonizing community

    NASA Astrophysics Data System (ADS)

    Lakatos, K. Tímea; László, Zoltán; Tóthmérész, Béla

    2016-05-01

    The introduced black locust (Robinia pseudoacacia) has become an invasive plant species in Europe. The introduction of alien plants such as the black locust may modify ecosystem composition and functioning. In response to the presence of a potential host plant, herbivores can adapt and shift to the consumption of the new host plant. In Eastern-Central Europe, the seed predator Bruchophagus robiniae (Hymenoptera: Eurytomidae) is an important consumer of black locust seeds which presumably shifted from its formerly host species to black locust. We tested the influence of host plant abundance on a seed predator - parasitoid community. We found that the seed predator B. robiniae was present in higher numbers in woodlots than in small patches of black locust. The density of the specialist parasitoid Mesopolobus sp. was lower in woodlots than in small patches, while the generalist parasitoid Eupelmus urozonos was evenly distributed between woodlots and small patches of black locust. We found that parasitoid species are influenced by the patch size of host plants, thus characteristics of introduced host plants can also manifest in higher trophic levels.

  2. Making Bunyaviruses Talk: Interrogation Tactics to Identify Host Factors Required for Infection

    PubMed Central

    Riblett, Amber M.; Doms, Robert W.

    2016-01-01

    The identification of host cellular genes that act as either proviral or antiviral factors has been aided by the development of an increasingly large number of high-throughput screening approaches. Here, we review recent advances in which these new technologies have been used to interrogate host genes for the ability to impact bunyavirus infection, both in terms of technical advances as well as a summary of biological insights gained from these studies. PMID:27187446

  3. [Host age and structure of the component communities of parasites in river minnow Phoxinus phoxinus (L.)].

    PubMed

    Dorovskikh, G N; Stepanov, V G

    2007-01-01

    Species composition and structure of the communities of fish parasites in river minnow Phoxinus phoxinus (L.) from the Pechora river were investigated in two of the Pechora-Ilychsky Biosphere Nature Reserve, Komi Republic. The component communities of the parasites in river minnow are shown to have a one-year cycle including the states of development, completion, and destruction. Communities in the state of development are characterized by a low variety of species, low values of Shannon index, often high values of domination index, presence of only two groups of parasites in the structure described by variational curved of the conditional biomasses of species, deviation of the conditional biomasses of species from the linear regression, and sum of errors of the regression equations lower a threshold value. The communities consist of young individual parasites and their larval stages. Completed community is characterized by the following properties. There are three groups of parasites, differing in allometric index, in the structure, discerned by the ratio of conditional biomasses of the species included. Conditional biomasses of species in ecologically safe reservoirs lie on the segments of straight lines. Species variety reaches its maximum. Species are presented mainly by mature specimens and larval stages of the parasites using fish as intermediate host. Community in the state of destruction shows low values of domination index and relatively small variety pf species. Such community is consist of one or two groups of species, which are represented by mature, oviparous, and dying individuals. There are larval stages of parasites using fish as intermediate hosts. Dominant species or species groups, as well as values of indexes describing the component communities of parasites, can be different in mature river minnow from different geographical regions. However, the number of groups of parasites, formed by the ratio of conditional biomasses, remains constant, and

  4. Subalpine conifers in different geographical locations host highly similar foliar bacterial endophyte communities.

    PubMed

    Carrell, Alyssa A; Carper, Dana L; Frank, A Carolin

    2016-08-01

    Pines in the subalpine environment at Niwot Ridge, CO, have been found to host communities of acetic acid bacteria (AAB) within their needles. The significance and ubiquity of this pattern is not known, but recent evidence of nitrogen (N)-fixing activity in Pinus flexilis (limber pine) foliage calls for a better understanding of the processes that regulate endophytic communities in forest tree canopies. Here, to test if AAB dominate the foliar bacterial microbiota in other subalpine locations, we compared the 16S rRNA community in needles from P. flexilis and P. contorta (lodgepole pine) growing in the Eastern Sierra Nevada, CA, and Niwot Ridge, CO. AAB made up the majority of the bacterial community in both species at both sites. Multiple distinct AAB taxa, resolved at the single nucleotide level, were shared across host species and sites, with dominant OTUs identical or highly similar to database sequences from cold environments, including high altitude air sampled in Colorado, and the endosphere of Arctic plants. Our results suggest strong selection for community composition, potentially amplified by the long lifespan of individual Pinus needles, along with low dispersal constraints on canopy bacteria.

  5. Effect of host tree species on cellulase activity and bacterial community composition in the gut of larval Asian longhorned beetle.

    PubMed

    Geib, Scott M; Jimenez-Gasco, Maria Del Mar; Carlson, John E; Tien, Ming; Hoover, Kelli

    2009-06-01

    Anoplophora glabripennis, the Asian longhorned beetle, is a wood-boring insect that can develop in a wide range of healthy deciduous hosts and requires gut microbes to aid in wood degradation and digestion. Here we show that larval A. glabripennis harbor a diverse gut bacterial community, and this community can be extremely variable when reared in different host trees. A. glabripennis reared in a preferred host (Acer saccharum) had the highest gut bacterial diversity compared with larvae reared either in a secondary host (Quercus palustris), a resistant host (Pyrus calleryana), or on artificial diet. The gut microbial community of larval A. glabripennis collected from field populations on Brooklyn, NY, showed the highest degree of complexity among all samples in this study. Overall, when larvae fed on a preferred host, they harbored a broad diversity of gut bacteria spanning the alpha-, beta-, gamma-Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Cellulase activities (beta-1,4-endoglucanase, beta-1,4-exoglucanase, and beta-1,4-glucosidase) in the guts of larvae fed in a preferred host (A. saccharum) or a secondary host (Q. palustris) were significantly higher than that of artificial diet fed larvae. Larvae that fed on wood from a resistant host (P. calleryana) showed suppressed total gut cellulase activity. Results show that the host tree can impact both gut microbial community complexity and cellulase activity in A. glabripennis.

  6. Host tree phenology affects vascular epiphytes at the physiological, demographic and community level

    PubMed Central

    Einzmann, Helena J. R.; Beyschlag, Joachim; Hofhansl, Florian; Wanek, Wolfgang; Zotz, Gerhard

    2015-01-01

    The processes that govern diverse tropical plant communities have rarely been studied in life forms other than trees. Structurally dependent vascular epiphytes, a major part of tropical biodiversity, grow in a three-dimensional matrix defined by their hosts, but trees differ in their architecture, bark structure/chemistry and leaf phenology. We hypothesized that the resulting seasonal differences in microclimatic conditions in evergreen vs. deciduous trees would affect epiphytes at different levels, from organ physiology to community structure. We studied the influence of tree leaf phenology on vascular epiphytes on the Island of Barro Colorado, Panama. Five tree species were selected, which were deciduous, semi-deciduous or evergreen. The crowns of drought-deciduous trees, characterized by sunnier and drier microclimates, hosted fewer individuals and less diverse epiphyte assemblages. Differences were also observed at a functional level, e.g. epiphyte assemblages in deciduous trees had larger proportions of Crassulacean acid metabolism species and individuals. At the population level a drier microclimate was associated with lower individual growth and survival in a xerophytic fern. Some species also showed, as expected, lower specific leaf area and higher δ13C values when growing in deciduous trees compared with evergreen trees. As hypothesized, host tree leaf phenology influences vascular epiphytes at different levels. Our results suggest a cascading effect of tree composition and associated differences in tree phenology on the diversity and functioning of epiphyte communities in tropical lowland forests. PMID:25392188

  7. Host tree phenology affects vascular epiphytes at the physiological, demographic and community level.

    PubMed

    Einzmann, Helena J R; Beyschlag, Joachim; Hofhansl, Florian; Wanek, Wolfgang; Zotz, Gerhard

    2014-11-11

    The processes that govern diverse tropical plant communities have rarely been studied in life forms other than trees. Structurally dependent vascular epiphytes, a major part of tropical biodiversity, grow in a three-dimensional matrix defined by their hosts, but trees differ in their architecture, bark structure/chemistry and leaf phenology. We hypothesized that the resulting seasonal differences in microclimatic conditions in evergreen vs. deciduous trees would affect epiphytes at different levels, from organ physiology to community structure. We studied the influence of tree leaf phenology on vascular epiphytes on the Island of Barro Colorado, Panama. Five tree species were selected, which were deciduous, semi-deciduous or evergreen. The crowns of drought-deciduous trees, characterized by sunnier and drier microclimates, hosted fewer individuals and less diverse epiphyte assemblages. Differences were also observed at a functional level, e.g. epiphyte assemblages in deciduous trees had larger proportions of Crassulacean acid metabolism species and individuals. At the population level a drier microclimate was associated with lower individual growth and survival in a xerophytic fern. Some species also showed, as expected, lower specific leaf area and higher δ(13)C values when growing in deciduous trees compared with evergreen trees. As hypothesized, host tree leaf phenology influences vascular epiphytes at different levels. Our results suggest a cascading effect of tree composition and associated differences in tree phenology on the diversity and functioning of epiphyte communities in tropical lowland forests.

  8. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

    PubMed Central

    Aires, Tânia; Serrão, Ester A.; Engelen, Aschwin H.

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  9. From Structure to Function: the Ecology of Host-Associated Microbial Communities

    PubMed Central

    Robinson, Courtney J.; Bohannan, Brendan J. M.; Young, Vincent B.

    2010-01-01

    Summary: In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota. PMID:20805407

  10. Nuclear crisis relocation: Issues for a host community-the case of Greenfield, Massachusetts, USA

    NASA Astrophysics Data System (ADS)

    Platt, Rutherford H.

    1986-03-01

    US civil defense planning for nuclear attack since 1974 has emphasized the doctrine of “crisis relocation.” Under this doctrine, some 150 million people would evacuate from urban areas and other probable targets to rural “host communities.” The population of the latter would “stay put” to assist the relocatees. Local communities would be responsible for the welfare of up to ten times their normal population for an indefinite period of time. This study examined certain implications of crisis relocation for the town of Greenfield, Massachusetts, USA, a typical host community. Various assumptions were articulated regarding the timing of events, the season of year, weather, and social behavior. Assumptions were favorable to the success of crisis relocation. Nevertheless, Greenfield would face impossible burdens in attempting to provide fallout protection, water, food, medical care, and civil order. Additional pressures would arise from adjoining communities which are functionally dependent upon Greenfield for normal goods and services, but which would receive their own allotment of relocatees. Crisis relocation is not taken seriously in Greenfield and virtually no preparations have been made to implement it.

  11. Structural and Practical Identifiability Issues of Immuno-Epidemiological Vector-Host Models with Application to Rift Valley Fever.

    PubMed

    Tuncer, Necibe; Gulbudak, Hayriye; Cannataro, Vincent L; Martcheva, Maia

    2016-09-01

    In this article, we discuss the structural and practical identifiability of a nested immuno-epidemiological model of arbovirus diseases, where host-vector transmission rate, host recovery, and disease-induced death rates are governed by the within-host immune system. We incorporate the newest ideas and the most up-to-date features of numerical methods to fit multi-scale models to multi-scale data. For an immunological model, we use Rift Valley Fever Virus (RVFV) time-series data obtained from livestock under laboratory experiments, and for an epidemiological model we incorporate a human compartment to the nested model and use the number of human RVFV cases reported by the CDC during the 2006-2007 Kenya outbreak. We show that the immunological model is not structurally identifiable for the measurements of time-series viremia concentrations in the host. Thus, we study the non-dimensionalized and scaled versions of the immunological model and prove that both are structurally globally identifiable. After fixing estimated parameter values for the immunological model derived from the scaled model, we develop a numerical method to fit observable RVFV epidemiological data to the nested model for the remaining parameter values of the multi-scale system. For the given (CDC) data set, Monte Carlo simulations indicate that only three parameters of the epidemiological model are practically identifiable when the immune model parameters are fixed. Alternatively, we fit the multi-scale data to the multi-scale model simultaneously. Monte Carlo simulations for the simultaneous fitting suggest that the parameters of the immunological model and the parameters of the immuno-epidemiological model are practically identifiable. We suggest that analytic approaches for studying the structural identifiability of nested models are a necessity, so that identifiable parameter combinations can be derived to reparameterize the nested model to obtain an identifiable one. This is a crucial step in

  12. Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts*

    PubMed Central

    Anderson, Jonathan P.; Hane, James K.; Stoll, Thomas; Pain, Nicholas; Hastie, Marcus L.; Kaur, Parwinder; Hoogland, Christine; Gorman, Jeffrey J.; Singh, Karam B.

    2016-01-01

    Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806. PMID:26811357

  13. Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts.

    PubMed

    Anderson, Jonathan P; Hane, James K; Stoll, Thomas; Pain, Nicholas; Hastie, Marcus L; Kaur, Parwinder; Hoogland, Christine; Gorman, Jeffrey J; Singh, Karam B

    2016-04-01

    Rhizoctonia solaniis an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about howR. solanicauses disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility toR. solaniwhen expressed inNicotiana benthamiana In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806.

  14. Bacterial Communities Differ among Drosophila melanogaster Populations and Affect Host Resistance against Parasitoids

    PubMed Central

    Dini-Andreote, Francisco; Falcao Salles, Joana

    2016-01-01

    In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population background effects, we characterized the bacterial communities in larvae of six genetically differentiated and geographically distant D. melanogaster lines collected from natural populations across Europe. The diet for these six lines had been identical for ca. 50 generations, thus any differences in the composition of the microbiome originates from the host populations. We also investigated whether induced shifts in the microbiome—in this case by controlled antibiotic administration—alters the hosts’ resistance to parasitism. Our data revealed a clear signature of population background on the diversity and composition of D. melanogaster microbiome that differed across lines, even after hosts had been maintained at the same diet and laboratory conditions for over 4 years. In particular, the number of bacterial OTUs per line ranged from 8 to 39 OTUs. Each line harboured 2 to 28 unique OTUs, and OTUs that were highly abundant in some lines were entirely missing in others. Moreover, we found that the response to antibiotic treatment differed among the lines and significantly altered the host resistance to the parasitoid Asobara tabida in one of the six lines. Wolbachia, a widespread intracellular endosymbiont associated with parasitoid resistance, was lacking in this line, suggesting that other components of the Drosophila microbiome caused a change in host resistance. Collectively, our results revealed that lines that originate from different population backgrounds show significant differences in the established Drosophila microbiome, outpacing the long-term effect of diet. Perturbations on these naturally assembled microbiomes to some degree influenced the hosts

  15. Identifying and Characterizing Key Nodes among Communities Based on Electrical-Circuit Networks

    PubMed Central

    Zhu, Fenghui; Wang, Wenxu; Di, Zengru; Fan, Ying

    2014-01-01

    Complex networks with community structures are ubiquitous in the real world. Despite many approaches developed for detecting communities, we continue to lack tools for identifying overlapping and bridging nodes that play crucial roles in the interactions and communications among communities in complex networks. Here we develop an algorithm based on the local flow conservation to effectively and efficiently identify and distinguish the two types of nodes. Our method is applicable in both undirected and directed networks without a priori knowledge of the community structure. Our method bypasses the extremely challenging problem of partitioning communities in the presence of overlapping nodes that may belong to multiple communities. Due to the fact that overlapping and bridging nodes are of paramount importance in maintaining the function of many social and biological networks, our tools open new avenues towards understanding and controlling real complex networks with communities accompanied with the key nodes. PMID:24897125

  16. Identifying and characterizing key nodes among communities based on electrical-circuit networks.

    PubMed

    Zhu, Fenghui; Wang, Wenxu; Di, Zengru; Fan, Ying

    2014-01-01

    Complex networks with community structures are ubiquitous in the real world. Despite many approaches developed for detecting communities, we continue to lack tools for identifying overlapping and bridging nodes that play crucial roles in the interactions and communications among communities in complex networks. Here we develop an algorithm based on the local flow conservation to effectively and efficiently identify and distinguish the two types of nodes. Our method is applicable in both undirected and directed networks without a priori knowledge of the community structure. Our method bypasses the extremely challenging problem of partitioning communities in the presence of overlapping nodes that may belong to multiple communities. Due to the fact that overlapping and bridging nodes are of paramount importance in maintaining the function of many social and biological networks, our tools open new avenues towards understanding and controlling real complex networks with communities accompanied with the key nodes.

  17. A host-based RT-PCR gene expression signature to identify acute respiratory viral infection.

    PubMed

    Zaas, Aimee K; Burke, Thomas; Chen, Minhua; McClain, Micah; Nicholson, Bradly; Veldman, Timothy; Tsalik, Ephraim L; Fowler, Vance; Rivers, Emanuel P; Otero, Ronny; Kingsmore, Stephen F; Voora, Deepak; Lucas, Joseph; Hero, Alfred O; Carin, Lawrence; Woods, Christopher W; Ginsburg, Geoffrey S

    2013-09-18

    Improved ways to diagnose acute respiratory viral infections could decrease inappropriate antibacterial use and serve as a vital triage mechanism in the event of a potential viral pandemic. Measurement of the host response to infection is an alternative to pathogen-based diagnostic testing and may improve diagnostic accuracy. We have developed a host-based assay with a reverse transcription polymerase chain reaction (RT-PCR) TaqMan low-density array (TLDA) platform for classifying respiratory viral infection. We developed the assay using two cohorts experimentally infected with influenza A H3N2/Wisconsin or influenza A H1N1/Brisbane, and validated the assay in a sample of adults presenting to the emergency department with fever (n = 102) and in healthy volunteers (n = 41). Peripheral blood RNA samples were obtained from individuals who underwent experimental viral challenge or who presented to the emergency department and had microbiologically proven viral respiratory infection or systemic bacterial infection. The selected gene set on the RT-PCR TLDA assay classified participants with experimentally induced influenza H3N2 and H1N1 infection with 100 and 87% accuracy, respectively. We validated this host gene expression signature in a cohort of 102 individuals arriving at the emergency department. The sensitivity of the RT-PCR test was 89% [95% confidence interval (CI), 72 to 98%], and the specificity was 94% (95% CI, 86 to 99%). These results show that RT-PCR-based detection of a host gene expression signature can classify individuals with respiratory viral infection and sets the stage for prospective evaluation of this diagnostic approach in a clinical setting.

  18. Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae)

    PubMed Central

    Britayev, Temir A.; Mekhova, Elena; Deart, Yury

    2017-01-01

    To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. (n = 11) and Chaetopterus cf. appendiculatus (n = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae, the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes, all of which, except O. fowleri, seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus, suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in community

  19. Community risk perception: a case study in a rural community hosting a waste site used by a large municipality.

    PubMed

    Ostry, A S; Hertzman, C; Teschke, K

    1993-01-01

    Using a model of risk perception which divides the community into attitudinal and behavioural subgroups based on awareness, concern and action in relation to a waste management facility, we conducted a survey in a community with an operating landfill and a ten-year history of controversy over the unsuccessful siting of a hazardous waste facility (HWF). The purpose of the survey was to study community attitudes to waste management in general, attitudes specific to landfills and HWFs, and to identify factors which shape community attitudes in both cases. Levels of concern and activism were lower for the landfill; activism and concern were more likely among younger subjects and those with children. In the case of the HWF, greater concern and activism were more likely among married people and those without a university education. Gender differences in relation to environmental "concern" were not found for either the landfill or the HWF siting attempts.

  20. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird

    PubMed Central

    Rodríguez-Ruano, Sonia M.; Martín-Vivaldi, Manuel; Martín-Platero, Antonio M.; López-López, J. Pablo; Peralta-Sánchez, Juan M.; Ruiz-Rodríguez, Magdalena; Soler, Juan J.; Valdivia, Eva; Martínez-Bueno, Manuel

    2015-01-01

    Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host. PMID:26445111

  1. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird.

    PubMed

    Rodríguez-Ruano, Sonia M; Martín-Vivaldi, Manuel; Martín-Platero, Antonio M; López-López, J Pablo; Peralta-Sánchez, Juan M; Ruiz-Rodríguez, Magdalena; Soler, Juan J; Valdivia, Eva; Martínez-Bueno, Manuel

    2015-01-01

    Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.

  2. Community structure of fleas within and among populations of three closely related rodent hosts: nestedness and beta-diversity.

    PubMed

    VAN DER Mescht, Luther; Krasnov, Boris R; Matthee, Conrad A; Matthee, Sonja

    2016-09-01

    We studied nestedness and its relationships with beta-diversity in flea communities harboured by three closely related rodent species (Rhabdomys pumilio, Rhabdomys intermedius, Rhabdomys dilectus) at two spatial scales (within and among host populations) in South Africa and asked (a) whether variation in species composition of flea communities within and among host populations follows a non-random pattern; if yes, (b) what are the contributions of nestedness and species turnover to dissimilarity (= beta-diversity) among flea communities at the two scales; and (c) do the degree of nestedness and its contribution to beta-diversity differ among host species (social vs solitary) and between scales. We found that nestedness in flea assemblages was more pronounced (a) in social than solitary host species and (b) at lower (among host individuals within populations) than at higher scale (among host populations). We also found that higher degree of nestedness was associated with its higher contribution to beta-diversity. Our findings support earlier ideas that parasite community structure results from the processes of parasite accumulation by hosts rather than from the processes acting within parasite communities.

  3. Two coexisting tank bromeliads host distinct algal communities on a tropical inselberg.

    PubMed

    Carrias, J-F; Céréghino, R; Brouard, O; Pélozuelo, L; Dejean, A; Couté, A; Corbara, B; Leroy, C

    2014-09-01

    The tank bromeliads Aechmea aquilega (Salisb.) and Catopsis berteroniana (Schultes f.) coexist on a sun-exposed Neotropical inselberg in French Guiana, where they permit conspicuous freshwater pools to form that differ in size, complexity and detritus content. We sampled the algal communities (both eukaryotic and cyanobacterial taxa, including colourless forms) inhabiting either A. aquilega (n = 31) or C. berteroniana (n = 30) and examined differences in community composition and biomass patterns in relation to several biotic and abiotic variables. Chlorella sp. and Bumilleriopsis sp. were the most common taxa and dominated the algal biomass in A. aquilega and C. berteroniana, respectively. Using a redundancy analysis, we found that water volume, habitat complexity and the density of phagotrophic protozoa and collector-gatherer invertebrates were the main factors explaining the distribution of the algal taxa among the samples. Hierarchical clustering procedures based on abundance and presence/absence data clearly segregated the samples according to bromeliad species, revealing that the algal communities in the smaller bromeliad species were not a subset of the communities found in the larger bromeliad species. We conclude that, even though two coexisting tank bromeliad populations create adjacent aquatic habitats, each population hosts a distinct algal community. Hence, bromeliad diversity is thought to promote the local diversity of freshwater algae in the Neotropics.

  4. Dynamics of Vector-Host Interactions in Avian Communities in Four Eastern Equine Encephalitis Virus Foci in the Northeastern U.S.

    PubMed Central

    Molaei, Goudarz; Thomas, Michael C.; Muller, Tim; Medlock, Jan; Shepard, John J.; Armstrong, Philip M.; Andreadis, Theodore G.

    2016-01-01

    Background Eastern equine encephalitis (EEE) virus (Togaviridae, Alphavirus) is a highly pathogenic mosquito-borne zoonosis that is responsible for occasional outbreaks of severe disease in humans and equines, resulting in high mortality and neurological impairment in most survivors. In the past, human disease outbreaks in the northeastern U.S. have occurred intermittently with no apparent pattern; however, during the last decade we have witnessed recurring annual emergence where EEE virus activity had been historically rare, and expansion into northern New England where the virus had been previously unknown. In the northeastern U.S., EEE virus is maintained in an enzootic cycle involving the ornithophagic mosquito, Culiseta melanura, and wild passerine (perching) birds in freshwater hardwood swamps. However, the identity of key avian species that serve as principal virus reservoir and amplification hosts has not been established. The efficiency with which pathogen transmission occurs within an avian community is largely determined by the relative reservoir competence of each species and by ecological factors that influence contact rates between these avian hosts and mosquito vectors. Methodology and principle findings Contacts between vector mosquitoes and potential avian hosts may be directly quantified by analyzing the blood meal contents of field-collected specimens. We used PCR-based molecular methods and direct sequencing of the mitochondrial cytochrome b gene for profiling of blood meals in Cs. melanura, in an effort to quantify its feeding behavior on specific vertebrate hosts, and to infer epidemiologic implications in four historic EEE virus foci in the northeastern U.S. Avian point count surveys were conducted to determine spatiotemporal host community composition. Of 1,127 blood meals successfully identified to species level, >99% of blood meals were from 65 avian hosts in 27 families and 11 orders, and only seven were from mammalian hosts representing

  5. A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules

    PubMed Central

    2012-01-01

    Background We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like) protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon) identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria. Conclusions Based on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process. PMID:22587634

  6. Using bimodal MRI/fluorescence imaging to identify host angiogenic response to implants

    PubMed Central

    Berdichevski, Alexandra; Simaan Yameen, Haneen; Dafni, Hagit; Neeman, Michal; Seliktar, Dror

    2015-01-01

    Therapies that promote angiogenesis have been successfully applied using various combinations of proangiogenic factors together with a biodegradable delivery vehicle. In this study we used bimodal noninvasive monitoring to show that the host response to a proangiogenic biomaterial can be drastically affected by the mode of implantation and the surface area-to-volume ratio of the implant material. Fluorescence/MRI probes were covalently conjugated to VEGF-bearing biodegradable PEG-fibrinogen hydrogel implants and used to document the in vivo degradation and liberation of bioactive constituents in an s.c. rat implantation model. The hydrogel biodegradation and angiogenic host response with three types of VEGF-bearing implant configurations were compared: preformed cylindrical plugs, preformed injectable microbeads, and hydrogel precursor, injected and polymerized in situ. Although all three were made with identical amounts of precursor constituents, the MRI data revealed that in situ polymerized hydrogels were fully degraded within 2 wk; microbead degradation was more moderate, and plugs degraded significantly more slowly than the other configurations. The presence of hydrogel degradation products containing the fluorescent label in the surrounding tissues revealed a distinct biphasic release profile for each type of implant configuration. The purported in vivo VEGF release profile from the microbeads resulted in highly vascularized s.c. tissue containing up to 16-fold more capillaries in comparison with controls. These findings demonstrate that the configuration of an implant can play an important role not only in the degradation and resorption properties of the materials, but also in consequent host angiogenic response. PMID:25825771

  7. The Bacteriome of Bat Flies (Nycteribiidae) from the Malagasy Region: a Community Shaped by Host Ecology, Bacterial Transmission Mode, and Host-Vector Specificity

    PubMed Central

    Duron, Olivier; Cordonin, Colette; Gomard, Yann; Ramasindrazana, Beza; Mavingui, Patrick; Goodman, Steven M.; Tortosa, Pablo

    2016-01-01

    The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) flies that parasitize bats. Depending on species, these wingless flies exhibit either high specialism or generalism toward their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bat populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission through egg cytoplasm to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development, but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles that were obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes Rickettsia, Wolbachia, and several Arsenophonus-like organisms, as well as other members of the Enterobacteriales and a widespread association of Bartonella bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are important drivers of bacterial community structure. PMID:26746715

  8. Identifying environmental health priorities in underserved populations: a study of rural versus urban communities

    PubMed Central

    Bernhard, M.C.; Evans, M.B.; Kent, S.T.; Johnson, E.; Threadgill, S.L.; Tyson, S.; Becker, S.M.; Gohlke, J.M.

    2013-01-01

    Objectives Understanding and effectively addressing persistent health disparities in minority communities requires a clear picture of members’ concerns and priorities. This study was intended to engage residents in urban and rural communities in order to identify environmental health priorities. Specific emphasis was placed on how the communities defined the term environment, their perceptions of environmental exposures as affecting their health, specific priorities in their communities, and differences in urban versus rural populations. Study design A community-engaged approach was used to develop and implement focus groups and compare environmental health priorities in urban versus rural communities. Methods A total of eight focus groups were conducted: four in rural and four in urban communities. Topics included defining the term environment, how the environment may affect health, and environmental priorities within their communities, using both open discussion and a predefined list. Data were analysed both qualitatively and quantitatively to identify patterns and trends. Results There were important areas of overlap in priorities between urban and rural communities; both emphasized the importance of the social environment and shared a concern over air pollution from industrial sources. In contrast, for urban focus groups, abandoned houses and their social and physical sequelae were a high priority while concerns about adequate sewer and water services and road maintenance were high priorities in rural communities. Conclusions This study was able to identify environmental health priorities in urban versus rural minority communities. In contrast to some previous risk perception research, the results of this study suggest prioritization of tangible, known risks in everyday life instead of rare, disaster-related events, even in communities that have recently experienced devastating damage from tornadoes. The findings can help inform future efforts to study

  9. Transcriptional analysis of murine macrophages infected with different Toxoplasma strains identifies novel regulation of host signaling pathways.

    PubMed

    Melo, Mariane B; Nguyen, Quynh P; Cordeiro, Cynthia; Hassan, Musa A; Yang, Ninghan; McKell, Renée; Rosowski, Emily E; Julien, Lindsay; Butty, Vincent; Dardé, Marie-Laure; Ajzenberg, Daniel; Fitzgerald, Katherine; Young, Lucy H; Saeij, Jeroen P J

    2013-01-01

    Most isolates of Toxoplasma from Europe and North America fall into one of three genetically distinct clonal lineages, the type I, II and III lineages. However, in South America these strains are rarely isolated and instead a great variety of other strains are found. T. gondii strains differ widely in a number of phenotypes in mice, such as virulence, persistence, oral infectivity, migratory capacity, induction of cytokine expression and modulation of host gene expression. The outcome of toxoplasmosis in patients is also variable and we hypothesize that, besides host and environmental factors, the genotype of the parasite strain plays a major role. The molecular basis for these differences in pathogenesis, especially in strains other than the clonal lineages, remains largely unexplored. Macrophages play an essential role in the early immune response against T. gondii and are also the cell type preferentially infected in vivo. To determine if non-canonical Toxoplasma strains have unique interactions with the host cell, we infected murine macrophages with 29 different Toxoplasma strains, representing global diversity, and used RNA-sequencing to determine host and parasite transcriptomes. We identified large differences between strains in the expression level of known parasite effectors and large chromosomal structural variation in some strains. We also identified novel strain-specifically regulated host pathways, including the regulation of the type I interferon response by some atypical strains. IFNβ production by infected cells was associated with parasite killing, independent of interferon gamma activation, and dependent on endosomal Toll-like receptors in macrophages and the cytoplasmic receptor retinoic acid-inducible gene 1 (RIG-I) in fibroblasts.

  10. Transcriptional Analysis of Murine Macrophages Infected with Different Toxoplasma Strains Identifies Novel Regulation of Host Signaling Pathways

    PubMed Central

    Melo, Mariane B.; Nguyen, Quynh P.; Cordeiro, Cynthia; Hassan, Musa A.; Yang, Ninghan; McKell, Renée; Rosowski, Emily E.; Julien, Lindsay; Butty, Vincent; Dardé, Marie-Laure; Ajzenberg, Daniel; Fitzgerald, Katherine; Young, Lucy H.; Saeij, Jeroen P. J.

    2013-01-01

    Most isolates of Toxoplasma from Europe and North America fall into one of three genetically distinct clonal lineages, the type I, II and III lineages. However, in South America these strains are rarely isolated and instead a great variety of other strains are found. T. gondii strains differ widely in a number of phenotypes in mice, such as virulence, persistence, oral infectivity, migratory capacity, induction of cytokine expression and modulation of host gene expression. The outcome of toxoplasmosis in patients is also variable and we hypothesize that, besides host and environmental factors, the genotype of the parasite strain plays a major role. The molecular basis for these differences in pathogenesis, especially in strains other than the clonal lineages, remains largely unexplored. Macrophages play an essential role in the early immune response against T. gondii and are also the cell type preferentially infected in vivo. To determine if non-canonical Toxoplasma strains have unique interactions with the host cell, we infected murine macrophages with 29 different Toxoplasma strains, representing global diversity, and used RNA-sequencing to determine host and parasite transcriptomes. We identified large differences between strains in the expression level of known parasite effectors and large chromosomal structural variation in some strains. We also identified novel strain-specifically regulated host pathways, including the regulation of the type I interferon response by some atypical strains. IFNβ production by infected cells was associated with parasite killing, independent of interferon gamma activation, and dependent on endosomal Toll-like receptors in macrophages and the cytoplasmic receptor retinoic acid-inducible gene 1 (RIG-I) in fibroblasts. PMID:24367253

  11. A competitive index assay identifies several Ralstonia solanacearum type III effector mutant strains with reduced fitness in host plants.

    PubMed

    Macho, Alberto P; Guidot, Alice; Barberis, Patrick; Beuzón, Carmen R; Genin, Stéphane

    2010-09-01

    Ralstonia solanacearum, the causal agent of bacterial wilt, is a soil bacterium which can naturally infect a wide range of host plants through the root system. Pathogenicity relies on a type III secretion system which delivers a large set of approximately 75 type III effectors (T3E) into plant cells. On several plants, pathogenicity assays based on quantification of wilting symptoms failed to detect a significant contribution of R. solanacearum T3E in this process, thus revealing the collective effect of T3E in pathogenesis. We developed a mixed infection-based method with R. solanacearum to monitor bacterial fitness in plant leaf tissues as a virulence assay. This accurate and sensitive assay provides evidence that growth defects can be detected for T3E mutants: we identified 12 genes contributing to bacterial fitness in eggplant leaves and 3 of them were also implicated in bacterial fitness on two other hosts, tomato and bean. Contribution to fitness of several T3E appears to be host specific, and we show that some known avirulence determinants such as popP2 or avrA do provide competitive advantages on some susceptible host plants. In addition, this assay revealed that the efe gene, which directs the production of ethylene by bacteria in plant tissues, and hdfB, involved in the biosynthesis of the secondary metabolite 3-hydroxy-oxindole, are also required for optimal growth in plant leaf tissues.

  12. Microbial Community Diversity in Fault-Associated and Ophiolite-Hosted Springs

    NASA Astrophysics Data System (ADS)

    Meyer-Dombard, D. R.; Cardace, D.; Uzunlar, N.; Gulecal, Y.; Yargicoglu, E. N.; Carbone, J. N.

    2010-12-01

    Deep biosphere habitats and hydrothermal systems are ideal candidates for analog ecosystems to life on Early Earth and Astrobiological targets. They also likely harbor vast repositories of novel biological and genetic diversity. This study compares the biological and genetic diversity of microbial communities in terrestrial hydrothermal and cool fluid seeps and springs, occuring in both ophiolite-hosted and non-ophiolite sequences. Fluids and solids (biofilms and sediment) with variable fractions of ultramafic-sourced and serpentinizing reaction fluids and mineral fragments were collected from surface seeps and deeply-sourced springs associated with the Northern Anatolian Fault Zone (NAFZ, Turkey) and the Anita Shear Zone (ASZ, New Zealand). Comparisons are drawn between three regimes: 1) cool fluid systems in ophiolite-hosted sequences in NAFZ vs. ASZ, 2) cool fluid vs. hydrothermal fluid systems in the NAFZ, and 3) hydrothermal systems in NAFZ ophiolite-hosted vs. non-ophiolite sequences. These comparisons help differentiate microbial community structure and metabolic strategies between hydrothermal and serpentinizing input to these ecosystems. The integration of geobiological data from these sites clarifies how microbial systems respond to even subtle shifts in geochemistry of the water-rock system, and our consideration of mafic/ultramafic rocks as habitable formations brings new astrobiological relevance to this work. Microbial communities were examined using a suite of culture-dependant and independent methods, co-registered with a network of geochemical contextual samples. Geochemical datasets allow prediction of available sources of energy in these nutrient-limited ecosystems. Sample locations varied in temperature 30-90C and pH 6.5-9.0 Potential sources of energy and carbon include dissolved organic carbon, CO2, sulfide, sulfate, and ferrous iron, depending on the sample location. Enrichments were obtained using a variety of carbon and energy sources, in

  13. IDENTIFYING THE LOCATION IN THE HOST GALAXY OF THE SHORT GRB 111117A WITH THE CHANDRA SUBARCSECOND POSITION

    SciTech Connect

    Sakamoto, T.; Troja, E.; Aoki, K.; Guiriec, S.; Barthelmy, S. D.; Im, M.; Jeon, Y.; Leloudas, G.; Malesani, D.; De Ugarte Postigo, A.; Andersen, M. I.; Melandri, A.; D'Avanzo, P.; Urata, Y.; Xu, D.; Gorosabel, J.; Sanchez-Ramirez, R.; Briggs, M. S.; Foley, S.; and others

    2013-03-20

    We present our successful Chandra program designed to identify, with subarcsecond accuracy, the X-ray afterglow of the short GRB 111117A, which was discovered by Swift and Fermi. Thanks to our rapid target of opportunity request, Chandra clearly detected the X-ray afterglow, though no optical afterglow was found in deep optical observations. The host galaxy was clearly detected in the optical and near-infrared band, with the best photometric redshift of z=1.31{sub -0.23}{sup +0.46} (90% confidence), making it one of the highest known short gamma-ray burst (GRB) redshifts. Furthermore, we see an offset of 1.0 {+-} 0.2 arcsec, which corresponds to 8.4 {+-} 1.7 kpc, between the host and the afterglow position. We discuss the importance of using Chandra for obtaining subarcsecond X-ray localizations of short GRB afterglows to study GRB environments.

  14. Land-use intensity and host plant simultaneously shape the composition of arbuscular mycorrhizal fungal communities in a Mediterranean drained peatland.

    PubMed

    Ciccolini, Valentina; Ercoli, Laura; Davison, John; Vasar, Martti; Öpik, Maarja; Pellegrino, Elisa

    2016-12-01

    Land-use change is known to be a major threat to biodiversity and ecosystem services in Mediterranean areas. However, the potential for different host plants to modulate the effect of land-use intensification on community composition of arbuscular mycorrhizal fungi (AMF) is still poorly understood. To test the hypothesis that low land-use intensity promotes AMF diversity at different taxonomic scales and to determine whether any response is dependent upon host plant species identity, we characterised AMF communities in the roots of 10 plant species across four land use types of differing intensity in a Mediterranean peatland system. AMF were identified using 454 pyrosequencing. This revealed an overall low level of AMF richness in the peaty soils; lowest AMF richness in the intense cropping system at both virtual taxa and family level; strong modulation by the host plant of the impact of land-use intensification on AMF communities at the virtual taxa level; and a significant effect of land-use intensification on AMF communities at the family level. These findings have implications for understanding ecosystem stability and productivity and should be considered when developing soil-improvement strategies in fragile ecosystems, such as Mediterranean peatlands.

  15. Viral Predation and Host Immunity Structure Microbial Communities in a Terrestrial Deep Subsurface, Hydraulically Fractured Shale System

    NASA Astrophysics Data System (ADS)

    Daly, R. A.; Mouser, P. J.; Trexler, R.; Wrighton, K. C.

    2014-12-01

    Despite a growing appreciation for the ecological role of viruses in marine and gut systems, little is known about their role in the terrestrial deep (> 2000 m) subsurface. We used assembly-based metagenomics to examine the viral component in fluids from hydraulically fractured Marcellus shale gas wells. Here we reconstructed microbial and viral genomes from samples collected 7, 82, and 328 days post fracturing. Viruses accounted for 4.14%, 0.92% and 0.59% of the sample reads that mapped to the assembly. We identified 6 complete, circularized viral genomes and an additional 92 viral contigs > 5 kb with a maximum contig size of 73.6 kb. A BLAST comparison to NCBI viral genomes revealed that 85% of viral contigs had significant hits to the viral order Caudovirales, with 43% of sequences belonging to the family Siphoviridae, 38% to Myoviridae, and 12% to Podoviridae. Enrichment of Caudovirales viruses was supported by a large number of predicted proteins characteristic of tailed viruses including terminases (TerL), tape measure, tail formation, and baseplate related proteins. The viral contigs included evidence of lytic and temperate lifestyles, with the 7 day sample having the greatest number of detected lytic viruses. Notably in this sample, the most abundant virus was lytic and its inferred host, a member of the Vibrionaceae, was not detected at later time points. Analyses of CRISPR sequences (a viral and foreign DNA immune system in bacteria and archaea), linked 18 viral contigs to hosts. CRISPR linkages increased through time and all bacterial and archaeal genomes recovered in the final time point had genes for CRISPR-mediated viral defense. The majority of CRISPR sequences linked phage genomes to several Halanaerobium strains, which are the dominant and persisting members of the community inferred to be responsible for carbon and sulfur cycling in these shales. Network analysis revealed that several viruses were present in the 82 and 328 day samples; this viral

  16. Genome-wide RNAi screening identifies host restriction factors critical for in vivo AAV transduction.

    PubMed

    Mano, Miguel; Ippodrino, Rudy; Zentilin, Lorena; Zacchigna, Serena; Giacca, Mauro

    2015-09-08

    Viral vectors based on the adeno-associated virus (AAV) hold great promise for in vivo gene transfer; several unknowns, however, still limit the vectors' broader and more efficient application. Here, we report the results of a high-throughput, whole-genome siRNA screening aimed at identifying cellular factors regulating AAV transduction. We identified 1,483 genes affecting vector efficiency more than 4-fold and up to 50-fold, either negatively or positively. Most of these factors have not previously been associated to AAV infection. The most effective siRNAs were independent from the virus serotype or analyzed cell type and were equally evident for single-stranded and self-complementary AAV vectors. A common characteristic of the most effective siRNAs was the induction of cellular DNA damage and activation of a cell cycle checkpoint. This information can be exploited for the development of more efficient AAV-based gene delivery procedures. Administration of the most effective siRNAs identified by the screening to the liver significantly improved in vivo AAV transduction efficiency.

  17. Host-specific microbial communities in three sympatric North Sea sponges.

    PubMed

    Naim, Mohd Azrul; Morillo, Jose A; Sørensen, Søren J; Waleed, Abu Al-Soud; Smidt, Hauke; Sipkema, Detmer

    2014-11-01

    The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An α-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86-92% similar to known sequences.

  18. Parasite communities of icefish (Chionodraco hamatus) in the Ross Sea (Antarctica): influence of the host sex on the helminth infracommunity structure.

    PubMed

    Santoro, Mario; Mattiucci, Simonetta; Cipriani, Paolo; Bellisario, Bruno; Romanelli, Francesco; Cimmaruta, Roberta; Nascetti, Giuseppe

    2014-01-01

    Parasite communities of Chionodraco hamatus were investigated from Terra Nova Bay (Ross Sea, Antarctica) during host spawning time. Special attention was given to helminth infracommunities and effect of host sex on its structure. A total of 21 taxa including 5 ecto-parasites and 16 endo-parasites were identified. The number of ecto and endo-parasite species per individual host ranged from 1 to 3 and 3 to 10, respectively, while the mean numbers of parasite specimens per individual host were 4.7 and 1309.7, respectively. The rich abundance of infection suggests a rich concentration of helminth intermediate/paratenic hosts in the coastal waters of Terra Nova Bay. Chionodraco hamatus serves as a definitive host for 10 helminth taxa, while it acts as an intermediate/paratenic host for 6 helminth taxa. Larvae of 6 helminth taxa for which C. hamatus serves as intermediate/paratenic host represented 98.7% of all specimens found. Of these, the tetraphyllidean and diphyllobothridean cestodes and the nematode Contracaecum osculatum s.l. were the most prevalent and abundant. 'Larval' infracommunities had significantly higher species richness, total abundance and diversity than 'adult' infracommunities, suggesting the important role of C. hamatus in supporting the life cycles of those parasites in the study area as a paratenic/intermediate host. Significant differences in the pattern of helminth infracommunities of larval forms between male and female fish were found. These differences could be caused by physiological, and most probably by behavioral differences between sexes suggesting that sex is an important factor influencing parasite burden in C. hamatus during reproductive season.

  19. Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants.

    PubMed

    Vályi, Kriszta; Rillig, Matthias C; Hempel, Stefan

    2015-03-01

    We studied the effect of host plant identity and land-use intensity (LUI) on arbuscular mycorrhizal fungi (AMF, Glomeromycota) communities in roots of grassland plants. These are relevant factors for intraradical AMF communities in temperate grasslands, which are habitats where AMF are present in high abundance and diversity. In order to focus on fungi that directly interact with the plant at the time, we investigated root-colonizing communities. Our study sites represent an LUI gradient with different combinations of grazing, mowing, and fertilization. We used massively parallel multitag pyrosequencing to investigate AMF communities in a large number of root samples, while being able to track the identity of the host. We showed that host plants significantly differed in AMF community composition, while land use modified this effect in a plant species-specific manner. Communities in medium and low land-use sites were subsets of high land-use communities, suggesting a differential effect of land use on the dispersal of AMF species with different abundances and competitive abilities. We demonstrate that in these grasslands, there is a small group of highly abundant, generalist fungi which represent the dominating species in the AMF community.

  20. Eimeria falciformis infection of the mouse caecum identifies opposing roles of IFNγ-regulated host pathways for the parasite development.

    PubMed

    Schmid, Manuela; Heitlinger, Emanuel; Spork, Simone; Mollenkopf, Hans-Joachim; Lucius, Richard; Gupta, Nishith

    2014-07-01

    Intracellular parasites reprogram host functions for their survival and reproduction. The extent and relevance of parasite-mediated host responses in vivo remains poorly studied, however. We utilized Eimeria falciformis, a parasite infecting the mouse intestinal epithelium, to identify and validate host determinants of parasite infection. Most prominent mouse genes induced during the onset of asexual and sexual growth of parasite comprise interferon γ (IFNγ)-regulated factors, e.g., immunity-related GTPases (IRGA6/B6/D/M2/M3), guanylate-binding proteins (GBP2/3/5/6/8), chemokines (CxCL9-11), and several enzymes of the kynurenine pathway including indoleamine 2,3-dioxygenase 1 (IDO1). These results indicated a multifarious innate defense (tryptophan catabolism, IRG, GBP, and chemokine signaling), and a consequential adaptive immune response (chemokine-cytokine signaling and lymphocyte recruitment). The inflammation- and immunity-associated transcripts were increased during the course of infection, following influx of B cells, T cells, and macrophages to the parasitized caecum tissue. Consistently, parasite growth was enhanced in animals inhibited for CxCr3, a major receptor for CxCL9-11 present on immune cells. Interestingly, despite a prominent induction, mouse IRGB6 failed to bind and disrupt the parasitophorous vacuole, implying an immune evasion by E. falciformis. Furthermore, oocyst output was impaired in IFNγ-R(-/-) and IDO1(-/-) mice, both of which suggest a subversion of IFNγ signaling by the parasite to promote its growth.

  1. Identifying the Location in the Host Galaxy of Short GRB 1111l7A with the Chandra Sub- Arcsecond Position

    NASA Technical Reports Server (NTRS)

    Sakamoto, Takanori; Troja, E.; Aoki, K.; Guiriec, S.; Im, M.; Leloudas, G.; Malesani, D.; Melandri, A.; deUgartePostigo, A.; Urata, Y.; Xu, D.; DAvanzo, P.; Gorosabel, J.; Anderson, M. I.; Fynbo, J. P. U.; Aoki, K.; Sanchez-Ramirez, R.

    2012-01-01

    We present our successful program using Chandra for identifying the X-ray afterglow with sub-arcsecond accuracy for the short GRB 111117A d iscovered by Swift and Fermi. Thanks to our rapid target of opportuni ty request, Chandra clearly detected the X-ray afterglow, whereas no optical afterglow was found in deep optical observations. Instead, we clearly detect the host galaxy in optica; and also in near-infrared b ands. We found that the best photometric redshift fitofthe host is z = 1.31:(+0.46/-0.23) (90% confidence), making it one of the highest redshift short GRBs. Furthermore, we see an offset of 1.0+/-O.2 arcseco nds, which corresponds to 8.4+/-1.7 kpc aSBuming z= 1.31, between the host and the afterglow position. We discuss the importance of using Chandra for obtaining sub-arcsecond localization of the afterglow in X -rays for short GRBs to study GRB environments in great detail.

  2. Identifying Young Kepler Planet Host Stars from Keck-HIRES Spectra of Lithium

    NASA Astrophysics Data System (ADS)

    Berger, Travis Allen; Howard, Andrew; Boesgaard, Ann M.

    2017-01-01

    The lithium doublet at 6708 A provides an age diagnostic for FGK stars. We measured the abundance of lithium in 1149 stars with detected transiting planets from the Kepler Mission using high resolution spectroscopy. Our catalog of lithium measurements from this sample have a range of abundance from A(Li) = 3.13 +/- 0.05 to a lower limit of -0.79. For a magnitude-limited sample that comprises 930 of the 1149 stars, our Keck-HIRES spectra have a median S/N = 45 per pixel at spectral resolution R = 55,000. We identify 79 young stars that have A(Li) values greater than the Hyades at their respective effective temperatures; these stars are younger than ~650 Myr old, the approximate age of the Hyades. We then compare the distribution of A(Li) with planet size, disposition, multiplicity, orbital period, and insolation flux.

  3. Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis.

    PubMed

    Scholey, R A; Evans, N J; Blowey, R W; Massey, J P; Murray, R D; Smith, R F; Ollier, W E; Carter, S D

    2013-09-01

    Digital dermatitis is a painful foot disease compromising welfare in dairy cattle. The disease has a complex multibacterial aetiology, but little is known about its pathogenesis. In this study, gene expression in skin biopsies from five bovine digital dermatitis lesions and five healthy bovine feet was compared using RNA-Seq technology. Differential gene expression was determined after mapping transcripts to the Btau 4.0 genome. Pathway analysis identified gene networks involving differentially expressed transcripts. Bovine digital dermatitis lesions had increased expression of mRNA for α2-macroglobulin-like 1, a protein potentially involved in bacterial immune evasion and bacterial survival. There was increased expression of keratin 6A and interleukin 1β mRNA in bovine digital dermatitis lesions, but reduced expression of most other keratin and keratin-associated genes. There was little evidence of local immune reactions to the bacterial infection present in lesions.

  4. A Generalized Entropy Measure of Within-Host Viral Diversity for Identifying Recent HIV-1 Infections

    PubMed Central

    Wu, Julia Wei; Patterson-Lomba, Oscar; Novitsky, Vladimir; Pagano, Marcello

    2015-01-01

    Abstract There is a need for incidence assays that accurately estimate HIV incidence based on cross-sectional specimens. Viral diversity-based assays have shown promises but are not particularly accurate. We hypothesize that certain viral genetic regions are more predictive of recent infection than others and aim to improve assay accuracy by using classification algorithms that focus on highly informative regions (HIRs). We analyzed HIV gag sequences from a cohort in Botswana. Forty-two subjects newly infected by HIV-1 Subtype C were followed through 500 days post-seroconversion. Using sliding window analysis, we screened for genetic regions within gag that best differentiate recent versus chronic infections. We used both nonparametric and parametric approaches to evaluate the discriminatory abilities of sequence regions. Segmented Shannon Entropy measures of HIRs were aggregated to develop generalized entropy measures to improve prediction of recency. Using logistic regression as the basis for our classification algorithm, we evaluated the predictive power of these novel biomarkers and compared them with recently reported viral diversity measures using area under the curve (AUC) analysis. Change of diversity over time varied across different sequence regions within gag. We identified the top 50% of the most informative regions by both nonparametric and parametric approaches. In both cases, HIRs were in more variable regions of gag and less likely in the p24 coding region. Entropy measures based on HIRs outperformed previously reported viral-diversity-based biomarkers. These methods are better suited for population-level estimation of HIV recency. The patterns of diversification of certain regions within the gag gene are more predictive of recency of infection than others. We expect this result to apply in other HIV genetic regions as well. Focusing on these informative regions, our generalized entropy measure of viral diversity demonstrates the potential for

  5. A Generalized Entropy Measure of Within-Host Viral Diversity for Identifying Recent HIV-1 Infections.

    PubMed

    Wu, Julia Wei; Patterson-Lomba, Oscar; Novitsky, Vladimir; Pagano, Marcello

    2015-10-01

    There is a need for incidence assays that accurately estimate HIV incidence based on cross-sectional specimens. Viral diversity-based assays have shown promises but are not particularly accurate. We hypothesize that certain viral genetic regions are more predictive of recent infection than others and aim to improve assay accuracy by using classification algorithms that focus on highly informative regions (HIRs).We analyzed HIV gag sequences from a cohort in Botswana. Forty-two subjects newly infected by HIV-1 Subtype C were followed through 500 days post-seroconversion. Using sliding window analysis, we screened for genetic regions within gag that best differentiate recent versus chronic infections. We used both nonparametric and parametric approaches to evaluate the discriminatory abilities of sequence regions. Segmented Shannon Entropy measures of HIRs were aggregated to develop generalized entropy measures to improve prediction of recency. Using logistic regression as the basis for our classification algorithm, we evaluated the predictive power of these novel biomarkers and compared them with recently reported viral diversity measures using area under the curve (AUC) analysis.Change of diversity over time varied across different sequence regions within gag. We identified the top 50% of the most informative regions by both nonparametric and parametric approaches. In both cases, HIRs were in more variable regions of gag and less likely in the p24 coding region. Entropy measures based on HIRs outperformed previously reported viral-diversity-based biomarkers. These methods are better suited for population-level estimation of HIV recency.The patterns of diversification of certain regions within the gag gene are more predictive of recency of infection than others. We expect this result to apply in other HIV genetic regions as well. Focusing on these informative regions, our generalized entropy measure of viral diversity demonstrates the potential for improving

  6. Climate forcing of an emerging pathogenic fungus across a montane multi-host community

    PubMed Central

    Clare, Frances C.; Halder, Julia B.; Daniel, Olivia; Bielby, Jon; Semenov, Mikhail A.; Jombart, Thibaut; Loyau, Adeline; Schmeller, Dirk S.; Cunningham, Andrew A.; Rowcliffe, Marcus; Bosch, Jaime

    2016-01-01

    Changes in the timings of seasonality as a result of anthropogenic climate change are predicted to occur over the coming decades. While this is expected to have widespread impacts on the dynamics of infectious disease through environmental forcing, empirical data are lacking. Here, we investigated whether seasonality, specifically the timing of spring ice-thaw, affected susceptibility to infection by the emerging pathogenic fungus Batrachochytrium dendrobatidis (Bd) across a montane community of amphibians that are suffering declines and extirpations as a consequence of this infection. We found a robust temporal association between the timing of the spring thaw and Bd infection in two host species, where we show that an early onset of spring forced high prevalences of infection. A third highly susceptible species (the midwife toad, Alytes obstetricans) maintained a high prevalence of infection independent of time of spring thaw. Our data show that perennially overwintering midwife toad larvae may act as a year-round reservoir of infection with variation in time of spring thaw determining the extent to which infection spills over into sympatric species. We used future temperature projections based on global climate models to demonstrate that the timing of spring thaw in this region will advance markedly by the 2050s, indicating that climate change will further force the severity of infection. Our findings on the effect of annual variability on multi-host infection dynamics show that the community-level impact of fungal infectious disease on biodiversity will need to be re-evaluated in the face of climate change. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’. PMID:28080980

  7. siRNA Screen Identifies Trafficking Host Factors that Modulate Alphavirus Infection

    PubMed Central

    Radoshitzky, Sheli R.; Pegoraro, Gianluca; Chī, Xiǎolì; Dǒng, Lián; Chiang, Chih-Yuan; Jozwick, Lucas; Clester, Jeremiah C.; Cooper, Christopher L.; Courier, Duane; Langan, David P.; Underwood, Knashka; Kuehl, Kathleen A.; Sun, Mei G.; Caì, Yíngyún; Yú, Shuǐqìng; Burk, Robin; Zamani, Rouzbeh; Kota, Krishna; Kuhn, Jens H.; Bavari, Sina

    2016-01-01

    Little is known about the repertoire of cellular factors involved in the replication of pathogenic alphaviruses. To uncover molecular regulators of alphavirus infection, and to identify candidate drug targets, we performed a high-content imaging-based siRNA screen. We revealed an actin-remodeling pathway involving Rac1, PIP5K1- α, and Arp3, as essential for infection by pathogenic alphaviruses. Infection causes cellular actin rearrangements into large bundles of actin filaments termed actin foci. Actin foci are generated late in infection concomitantly with alphavirus envelope (E2) expression and are dependent on the activities of Rac1 and Arp3. E2 associates with actin in alphavirus-infected cells and co-localizes with Rac1–PIP5K1-α along actin filaments in the context of actin foci. Finally, Rac1, Arp3, and actin polymerization inhibitors interfere with E2 trafficking from the trans-Golgi network to the cell surface, suggesting a plausible model in which transport of E2 to the cell surface is mediated via Rac1- and Arp3-dependent actin remodeling. PMID:27031835

  8. siRNA Screen Identifies Trafficking Host Factors that Modulate Alphavirus Infection.

    PubMed

    Radoshitzky, Sheli R; Pegoraro, Gianluca; Chī, Xi Olì; D Ng, Lián; Chiang, Chih-Yuan; Jozwick, Lucas; Clester, Jeremiah C; Cooper, Christopher L; Courier, Duane; Langan, David P; Underwood, Knashka; Kuehl, Kathleen A; Sun, Mei G; Caì, Yíngyún; Yú, Shu Qìng; Burk, Robin; Zamani, Rouzbeh; Kota, Krishna; Kuhn, Jens H; Bavari, Sina

    2016-03-01

    Little is known about the repertoire of cellular factors involved in the replication of pathogenic alphaviruses. To uncover molecular regulators of alphavirus infection, and to identify candidate drug targets, we performed a high-content imaging-based siRNA screen. We revealed an actin-remodeling pathway involving Rac1, PIP5K1- α, and Arp3, as essential for infection by pathogenic alphaviruses. Infection causes cellular actin rearrangements into large bundles of actin filaments termed actin foci. Actin foci are generated late in infection concomitantly with alphavirus envelope (E2) expression and are dependent on the activities of Rac1 and Arp3. E2 associates with actin in alphavirus-infected cells and co-localizes with Rac1-PIP5K1-α along actin filaments in the context of actin foci. Finally, Rac1, Arp3, and actin polymerization inhibitors interfere with E2 trafficking from the trans-Golgi network to the cell surface, suggesting a plausible model in which transport of E2 to the cell surface is mediated via Rac1- and Arp3-dependent actin remodeling.

  9. Identifying Perceived Neighborhood Stressors Across Diverse Communities in New York City.

    PubMed

    Shmool, Jessie L C; Yonas, Michael A; Newman, Ogonnaya Dotson; Kubzansky, Laura D; Joseph, Evelyn; Parks, Ana; Callaway, Charles; Chubb, Lauren G; Shepard, Peggy; Clougherty, Jane E

    2015-09-01

    There is growing interest in the role of psychosocial stress in health disparities. Identifying which social stressors are most important to community residents is critical for accurately incorporating stressor exposures into health research. Using a community-academic partnered approach, we designed a multi-community study across the five boroughs of New York City to characterize resident perceptions of key neighborhood stressors. We conducted 14 community focus groups; two to three in each borough, with one adolescent group and one Spanish-speaking group per borough. We then used systematic content analysis and participant ranking data to describe prominent neighborhood stressors and identify dominant themes. Three inter-related themes regarding the social and structural sources of stressful experiences were most commonly identified across neighborhoods: (1) physical disorder and perceived neglect, (2) harassment by police and perceived safety and (3) gentrification and racial discrimination. Our findings suggest that multiple sources of distress, including social, political, physical and economic factors, should be considered when investigating health effects of community stressor exposures and psychological distress. Community expertise is essential for comprehensively characterizing the range of neighborhood stressors that may be implicated in psychosocial exposure pathways.

  10. Mapping of Chikungunya Virus Interactions with Host Proteins Identified nsP2 as a Highly Connected Viral Component

    PubMed Central

    Bouraï, Mehdi; Lucas-Hourani, Marianne; Gad, Hans Henrik; Drosten, Christian; Jacob, Yves; Tafforeau, Lionel; Cassonnet, Patricia; Jones, Louis M.; Judith, Delphine; Couderc, Thérèse; Lecuit, Marc; André, Patrice; Kümmerer, Beate Mareike; Lotteau, Vincent; Desprès, Philippe; Vidalain, Pierre-Olivier

    2012-01-01

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has been responsible for an epidemic outbreak of unprecedented magnitude in recent years. Since then, significant efforts have been made to better understand the biology of this virus, but we still have poor knowledge of CHIKV interactions with host cell components at the molecular level. Here we describe the extensive use of high-throughput yeast two-hybrid (HT-Y2H) assays to characterize interactions between CHIKV and human proteins. A total of 22 high-confidence interactions, which essentially involved the viral nonstructural protein nsP2, were identified and further validated in protein complementation assay (PCA). These results were integrated to a larger network obtained by extensive mining of the literature for reports on alphavirus-host interactions. To investigate the role of cellular proteins interacting with nsP2, gene silencing experiments were performed in cells infected by a recombinant CHIKV expressing Renilla luciferase as a reporter. Collected data showed that heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and ubiquilin 4 (UBQLN4) participate in CHIKV replication in vitro. In addition, we showed that CHIKV nsP2 induces a cellular shutoff, as previously reported for other Old World alphaviruses, and determined that among binding partners identified by yeast two-hybrid methods, the tetratricopeptide repeat protein 7B (TTC7B) plays a significant role in this activity. Altogether, this report provides the first interaction map between CHIKV and human proteins and describes new host cell proteins involved in the replication cycle of this virus. PMID:22258240

  11. Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component.

    PubMed

    Bouraï, Mehdi; Lucas-Hourani, Marianne; Gad, Hans Henrik; Drosten, Christian; Jacob, Yves; Tafforeau, Lionel; Cassonnet, Patricia; Jones, Louis M; Judith, Delphine; Couderc, Thérèse; Lecuit, Marc; André, Patrice; Kümmerer, Beate Mareike; Lotteau, Vincent; Desprès, Philippe; Tangy, Frédéric; Vidalain, Pierre-Olivier

    2012-03-01

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has been responsible for an epidemic outbreak of unprecedented magnitude in recent years. Since then, significant efforts have been made to better understand the biology of this virus, but we still have poor knowledge of CHIKV interactions with host cell components at the molecular level. Here we describe the extensive use of high-throughput yeast two-hybrid (HT-Y2H) assays to characterize interactions between CHIKV and human proteins. A total of 22 high-confidence interactions, which essentially involved the viral nonstructural protein nsP2, were identified and further validated in protein complementation assay (PCA). These results were integrated to a larger network obtained by extensive mining of the literature for reports on alphavirus-host interactions. To investigate the role of cellular proteins interacting with nsP2, gene silencing experiments were performed in cells infected by a recombinant CHIKV expressing Renilla luciferase as a reporter. Collected data showed that heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and ubiquilin 4 (UBQLN4) participate in CHIKV replication in vitro. In addition, we showed that CHIKV nsP2 induces a cellular shutoff, as previously reported for other Old World alphaviruses, and determined that among binding partners identified by yeast two-hybrid methods, the tetratricopeptide repeat protein 7B (TTC7B) plays a significant role in this activity. Altogether, this report provides the first interaction map between CHIKV and human proteins and describes new host cell proteins involved in the replication cycle of this virus.

  12. Novel MicroRNA Involved in Host Response to Avian Pathogenic Escherichia coli Identified by Deep Sequencing and Integration Analysis

    PubMed Central

    Jia, Xinzheng; Zhang, Xiquan; Nolan, Lisa K.

    2016-01-01

    ABSTRACT Avian pathogenic Escherichia coli (APEC) causes one of the most common bacterial diseases of poultry worldwide. Effective control methods are therefore desirable and will be facilitated by a better understanding of the host response to the pathogen. Currently, microRNAs (miRNAs) involved in host resistance to APEC are unknown. Here, we applied RNA sequencing to explore the changed miRNAs and deregulated genes in the spleen of three groups of broilers: nonchallenged (NC), APEC-challenged with mild pathology (CM), and APEC-challenged with severe pathology (CS). Twenty-seven differentially expressed miRNAs (fold change >1.5; P value <0.01) were identified, including 13 miRNAs between the NC and CM, 17 between the NC and CS, and 14 between the CM and CS groups. Through functional analysis of these miRNA targets, 12 immune-related biological processes were found to be significantly enriched. Based on combined analyses of differentially expressed miRNAs and mRNAs within each of the three groups, 43 miRNA-mRNA pairs displayed significantly negative correlations (r < −0.8). Notably, gga-miR-429 was greatly increased in the CS group compared to levels in both the CM and NC groups. In vitro, gga-miR-429 directly repressed luciferase reporter gene activity via binding to 3′ untranslated regions of TMEFF2, NTRK2, and SHISA2. Overexpression of gga-miR-429 in the HD11 macrophage cell line significantly inhibited TMEFF2 and SHISA2 expression, which are involved in the lipopolysaccharide-induced platelet-derived growth factor (PDGF) and Wnt signaling pathways. In summary, we provide the first report characterizing the miRNA changes during APEC infection, which may help to shed light on the roles of these recently identified genetic elements in the mechanisms of host resistance and susceptibility to APEC. PMID:27795362

  13. Host specificity and the structure of helminth parasite communities of fishes in a Neotropical river in Mexico

    PubMed Central

    Salgado-Maldonado, Guillermo; Novelo-Turcotte, María Teresa; Caspeta-Mandujano, Juan Manuel; Vazquez-Hurtado, Gabriela; Quiroz-Martínez, Benjamin; Mercado-Silva, Norman; Favila, Mario

    2016-01-01

    In a tropical locality of Río La Antigua, Veracruz, Mexico, 11 fish species, represented by 244 individual fish from six freshwater fish families living sympatrically and synchronically, were examined for helminth parasites. A total of 36 taxa of helminths were recorded, 24 autogenic and 12 allogenic forms, including 6 monogeneans, 14 trematodes, 1 cestode, and 15 nematodes. Most helminth taxa were recovered for 10/11 of the component communities we analyzed. The results contribute empirical evidence that host specificity is an important force in the development of helminth communities of freshwater fishes. Each fish family has their own set of parasites, host species belonging to the same taxon share parasite species. High component community similarity among related host species was recorded, demonstrated by high prevalence and abundance, as well as dominance, of autogenic specialist species in each component community. Most autogenic helminth species are numerically and reproductively successful in relatively few host species. Autogenic helminths common in one host species are not common in others. Our findings give empirical support to the idea that low levels of sharing of parasites favor animal coexistence and high species richness, because large phylogenetic differences allow potentially competing animals to consume the same resources without being sensitive of another’s parasites. PMID:28004635

  14. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

    DOE PAGES

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; ...

    2015-10-21

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

  15. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

    SciTech Connect

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; Shaw, George M.; Hahn, Beatrice H.; Montefiori, David C.; Alam, S. Munir; Bonsignori, Mattia; Moody, M. Anthony; Liao, Hua-Xin; Gao, Feng; Haynes, Barton

    2015-10-21

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.

  16. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

    PubMed Central

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena E.; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; Shaw, George M.; Hahn, Beatrice H.; Montefiori, David C.; Alam, S. Munir; Bonsignori, Mattia; Moody, M. Anthony; Liao, Hua-Xin; Gao, Feng; Haynes, Barton F.

    2015-01-01

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. With well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines. PMID:26506369

  17. A reverse-phase protein microarray-based screen identifies host signaling dynamics upon Burkholderia spp. infection

    PubMed Central

    Chiang, Chih-Yuan; Uzoma, Ijeoma; Lane, Douglas J.; Memišević, Vesna; Alem, Farhang; Yao, Kuan; Kota, Krishna P.; Bavari, Sina; Wallqvist, Anders; Hakami, Ramin M.; Panchal, Rekha G.

    2015-01-01

    Burkholderia is a diverse genus of gram-negative bacteria that causes high mortality rate in humans, equines and cattle. The lack of effective therapeutic treatments poses serious public health threats. Developing insights toward host-Burkholderia spp. interaction is critical for understanding the pathogenesis of infection as well as identifying therapeutic targets for drug development. Reverse-phase protein microarray technology was previously proven to identify and characterize novel biomarkers and molecular signatures associated with infectious disease and cancer. In the present study, this technology was utilized to interrogate changes in host protein expression and phosphorylation events in macrophages infected with a collection of geographically diverse strains of Burkholderia spp. The expression or phosphorylation state of 25 proteins was altered during Burkholderia spp. infections of which eight proteins were selected for further characterization by immunoblotting. Increased phosphorylation of AMPK-α1, Src, and GSK3β suggested the importance of their roles in regulating Burkholderia spp. mediated innate immune response. Modulating the inflammatory response by perturbing their activities may provide therapeutic routes for future treatments. PMID:26284031

  18. Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model.

    PubMed

    Green, Richard; Wilkins, Courtney; Thomas, Sunil; Sekine, Aimee; Ireton, Renee C; Ferris, Martin T; Hendrick, Duncan M; Voss, Kathleen; de Villena, Fernando Pardo-Manuel; Baric, Ralph; Heise, Mark; Gale, Michael

    2016-12-01

    Flaviviruses are hematophagous arthropod-viruses that pose global challenges to human health. Like Zika virus, West Nile Virus (WNV) is a flavivirus for which no approved vaccine exists [1]. The role host genetics play in early detection and response to WNV still remains largely unexplained. In order to capture the impact of genetic variation on innate immune responses, we studied gene expression following WNV infection using the collaborative cross (CC). The CC is a mouse genetics resource composed of hundreds of independently bred, octo-parental recombinant inbred mouse lines [2]. To accurately capture the host immune gene expression signatures of West Nile infection, we used the nanostring platform to evaluate expression in spleen tissue isolated from CC mice infected with WNV over a time course of 4, 7, and 12 days' post-infection [3]. Nanostring is a non-amplification based digital method to quantitate gene expression that uses color-coded molecular barcodes to detect hundreds of transcripts in a sample. Using this approach, we identified unique gene signatures in spleen tissue at days 4, 7, and 12 following WNV infection, which delineated distinct differences between asymptomatic and symptomatic CC lines. We also identified novel immune genes. Data was deposited into the Gene Expression Omnibus under accession GSE86000.

  19. Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.

    PubMed

    David, Aaron S; Seabloom, Eric W; May, Georgiana

    2016-05-01

    Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

  20. Community next steps for making globally unique identifiers work for biocollections data.

    PubMed

    Guralnick, Robert P; Cellinese, Nico; Deck, John; Pyle, Richard L; Kunze, John; Penev, Lyubomir; Walls, Ramona; Hagedorn, Gregor; Agosti, Donat; Wieczorek, John; Catapano, Terry; Page, Roderic D M

    2015-01-01

    Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

  1. Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data

    PubMed Central

    Guralnick, Robert P.; Cellinese, Nico; Deck, John; Pyle, Richard L.; Kunze, John; Penev, Lyubomir; Walls, Ramona; Hagedorn, Gregor; Agosti, Donat; Wieczorek, John; Catapano, Terry; Page, Roderic D. M.

    2015-01-01

    Abstract Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided. PMID:25901117

  2. Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality.

    PubMed

    Zhang, Fan; Pita, Lucía; Erwin, Patrick M; Abaid, Summara; López-Legentil, Susanna; Hill, Russell T

    2014-12-01

    Archaea associated with marine sponges are active and influence the nitrogen metabolism of sponges. However, we know little about their occurrence, specificity, and persistence. We aimed to elucidate the relative importance of host specificity and biogeographic background in shaping the symbiotic archaeal communities. We investigated these communities in sympatric sponges from the Mediterranean (Ircinia fasciculata and Ircinia oros, sampled in summer and winter) and from the Caribbean (Ircinia strobilina and Mycale laxissima). PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. We found that the communities were dominated by ammonia-oxidizing archaea closely related to Nitrosopumilus. The community in M. laxissima differed from that in Ircinia spp., including the sympatric sponge I. strobilina; yet, geographical clusters within Ircinia spp. were observed. Whereas archaeal phylotypes in Ircinia spp. were persistent and belong to 'sponge-enriched' clusters, archaea in M. laxissima were closely related with those from diverse habitats (i.e. seawater and sediments). For all four sponge species, the expression of the archaeal amoA gene was confirmed. Our results indicate that host-specific processes, such as host ecological strategy and evolutionary history, control the sponge-archaeal communities.

  3. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    SciTech Connect

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  4. Spatial variation in helminth community structure in the red-legged partridge (Alectoris rufa L.): effects of definitive host density.

    PubMed

    Calvete, C; Blanco-Aguiar, J A; Virgós, E; Cabezas-Díaz, S; Villafuerte, R

    2004-07-01

    Parasite community ecology has recently focused on understanding the forces structuring these communities. There are few surveys, however, designed to study the spatial repeatability and predictability of parasite communities at the local scale in one host. The purpose of our study was to address the relationship between infracommunity and component community richness, and to describe spatial variations on the local scale, of helminth parasite communities in an avian host, the red-legged partridge (Alectoris rufta). We sampled 235 wild partridges from 8 separate localities, with different partridge population densities, in the Ciudad Real and Toledo provinces of central Spain, and we determined their overall and intestinal helminth species. We found that habitat variables (mean temperature and land use) were not significantly associated with any component community. The partridge population abundance index was directly correlated with the prevalence and mean intensity of infection but not with component community species richness. There was a curvilinear relationship between infracommunity and component community species richness, as well as negative interspecific associations, for the helminth species assemblage parasitizing the intestine. A nestedness/anti-nestedness pattern, considered as part of a continuum, was associated with prevalence, mean intensity and partridge population abundance index, but not with component community richness. Increases in the partridge population abundance index and the prevalence and mean intensity of infection were associated with increases in helminth community nestedness. Although negative interactions between helminth species could not be ruled out as forces structuring helminth communities, our results suggest that parasite community structure in the red-legged partridge was primarily determined by the extrinsic influence of parasite habitat heterogeneity and its amplification of the differing probabilities of colonization of

  5. Engaging Communities in Identifying Local Strategies for Expanding Integrated Employment during and after High School

    ERIC Educational Resources Information Center

    Carter, Erik W.; Blustein, Carly L.; Bumble, Jennifer L.; Harvey, Sarah; Henderson, Lynnette M.; McMillan, Elise D.

    2016-01-01

    Amidst decades of attention directed toward improving employment outcomes for people with intellectual and developmental disabilities (IDD), few efforts have been made to engage communities in identifying local solutions for expanding integrated employment opportunities. We examined the implementation and outcomes of "community…

  6. Identifying Effective Methods of Instruction for Adult Emergent Readers through Community-Based Research

    ERIC Educational Resources Information Center

    Blackmer, Rachel; Hayes-Harb, Rachel

    2016-01-01

    We present a community-based research project aimed at identifying effective methods and materials for teaching English literacy skills to adult English as a second language emergent readers. We conducted a quasi-experimental study whereby we evaluated the efficacy of two approaches, one based on current practices at the English Skills Learning…

  7. Identifying the Factors That Predict Degree Completion for Entirely Online Community College Students

    ERIC Educational Resources Information Center

    Brock, Kishia R.

    2014-01-01

    The purpose of this research study was to identify demographic characteristics, academic factors, and student behaviors that contributed to successful degree and certificate completion for entirely online, nontraditional undergraduate students at a large community college. A discrete-time event history analysis was used to model the retention of…

  8. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

    PubMed Central

    Frade, Pedro R.; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J.

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity. PMID:26788724

  9. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs.

    PubMed

    Frade, Pedro R; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.

  10. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture.

    PubMed Central

    González, J M; Whitman, W B; Hodson, R E; Moran, M A

    1996-01-01

    Culturable bacteria that were numerically important members of a marine enrichment community were identified and characterized phylogenetically. Selective and nonselective isolation methods were used to obtain 133 culturable bacterial isolates from model marine communities enriched with the high-molecular-weight (lignin-rich) fraction of pulp mill effluent. The culture collection was screened against community DNA from the lignin enrichments by whole-genome hybridization methods, and three marine bacterial isolates were identified as being numerically important in the communities. One isolate was in the alpha-subclass of Proteobacteria, and the other two were in the gamma-subclass of Proteobacteria. Isolate-specific 16S rRNA oligonucleotide probes designed to precisely quantify the isolates in the lignin enrichment communities indicated contributions ranging from 2 to 32% of enrichment DNA, values nearly identical to those originally obtained by the simpler whole-genome hybridization method. Two 16S rRNA sequences closely related to that of one of the isolates, although not identical, were amplified via PCR from the seawater sample originally used to inoculate the enrichment medium. Partial sequences of 14 other isolates revealed significant phylogenetic diversity and unusual sequences among the culturable lignin enrichment bacteria, with the Proteobacteria, Cytophaga-Flavobacterium, and gram-positive groups represented. PMID:8953714

  11. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range.

    PubMed

    Henderson, Gemma; Cox, Faith; Ganesh, Siva; Jonker, Arjan; Young, Wayne; Janssen, Peter H

    2015-10-09

    Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

  12. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

    PubMed Central

    Henderson, Gemma; Cox, Faith; Ganesh, Siva; Jonker, Arjan; Young, Wayne; Abecia, Leticia; Angarita, Erika; Aravena, Paula; Nora Arenas, Graciela; Ariza, Claudia; Attwood, Graeme T.; Mauricio Avila, Jose; Avila-Stagno, Jorge; Bannink, André; Barahona, Rolando; Batistotti, Mariano; Bertelsen, Mads F.; Brown-Kav, Aya; Carvajal, Andres M.; Cersosimo, Laura; Vieira Chaves, Alexandre; Church, John; Clipson, Nicholas; Cobos-Peralta, Mario A.; Cookson, Adrian L.; Cravero, Silvio; Cristobal Carballo, Omar; Crosley, Katie; Cruz, Gustavo; Cerón Cucchi, María; de la Barra, Rodrigo; De Menezes, Alexandre B.; Detmann, Edenio; Dieho, Kasper; Dijkstra, Jan; dos Reis, William L. S.; Dugan, Mike E. R.; Hadi Ebrahimi, Seyed; Eythórsdóttir, Emma; Nde Fon, Fabian; Fraga, Martín; Franco, Francisco; Friedeman, Chris; Fukuma, Naoki; Gagić, Dragana; Gangnat, Isabelle; Javier Grilli, Diego; Guan, Le Luo; Heidarian Miri, Vahideh; Hernandez-Sanabria, Emma; Gomez, Alma Ximena Ibarra; Isah, Olubukola A.; Ishaq, Suzanne; Jami, Elie; Jelincic, Juan; Kantanen, Juha; Kelly, William J.; Kim, Seon-Ho; Klieve, Athol; Kobayashi, Yasuo; Koike, Satoshi; Kopecny, Jan; Nygaard Kristensen, Torsten; Julie Krizsan, Sophie; LaChance, Hannah; Lachman, Medora; Lamberson, William R.; Lambie, Suzanne; Lassen, Jan; Leahy, Sinead C.; Lee, Sang-Suk; Leiber, Florian; Lewis, Eva; Lin, Bo; Lira, Raúl; Lund, Peter; Macipe, Edgar; Mamuad, Lovelia L.; Cuquetto Mantovani, Hilário; Marcoppido, Gisela Ariana; Márquez, Cristian; Martin, Cécile; Martinez, Gonzalo; Eugenia Martinez, Maria; Lucía Mayorga, Olga; McAllister, Tim A.; McSweeney, Chris; Mestre, Lorena; Minnee, Elena; Mitsumori, Makoto; Mizrahi, Itzhak; Molina, Isabel; Muenger, Andreas; Munoz, Camila; Murovec, Bostjan; Newbold, John; Nsereko, Victor; O’Donovan, Michael; Okunade, Sunday; O’Neill, Brendan; Ospina, Sonia; Ouwerkerk, Diane; Parra, Diana; Pereira, Luiz Gustavo Ribeiro; Pinares-Patino, Cesar; Pope, Phil B.; Poulsen, Morten; Rodehutscord, Markus; Rodriguez, Tatiana; Saito, Kunihiko; Sales, Francisco; Sauer, Catherine; Shingfield, Kevin; Shoji, Noriaki; Simunek, Jiri; Stojanović-Radić, Zorica; Stres, Blaz; Sun, Xuezhao; Swartz, Jeffery; Liang Tan, Zhi; Tapio, Ilma; Taxis, Tasia M.; Tomkins, Nigel; Ungerfeld, Emilio; Valizadeh, Reza; van Adrichem, Peter; Van Hamme, Jonathan; Van Hoven, Woulter; Waghorn, Garry; John Wallace, R.; Wang, Min; Waters, Sinéad M.; Keogh, Kate; Witzig, Maren; Wright, Andre-Denis G.; Yamano, Hidehisa; Yan, Tianhai; Yanez-Ruiz, David R.; Yeoman, Carl J.; Zambrano, Ricardo; Zeitz, Johanna; Zhou, Mi; Wei Zhou, Hua; Xia Zou, Cai; Zunino, Pablo; Janssen, Peter H.

    2015-01-01

    Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. PMID:26449758

  13. Lipid and Phylogenetic Analysis of a Gypsum-hosted Endoevaporitic Microbial Community

    NASA Astrophysics Data System (ADS)

    Turk, K. A.; Jahnke, L. L.; Green, S. J.; Kubo, M. D.; Vogel, M. B.; Des Marais, D. J.

    2007-12-01

    Gypsum evaporites host diverse, productive and volumetrically significant microbial communities and are relevant modern-day analogs to both Precambrian sabkha deposits and, potentially, Martian evaporites. Extensive evaporites form in subaqueous environments of high salinity ponds (>150 permil) maintained by the Exportadora de Sal, S. A. (ESSA) in Guerrero Negro, B.C.S., Mexico. A gypsarenite (reworked clastic gypsum) crust found along the southeast margin of ESSA's Pond 9 was collected in February 2004 and each vibrantly colored layer in the top centimeter was sampled. Extant microbial communities from each layer were characterized using complementary culture-independent molecular techniques, lipid biomarker analysis, and compound specific isotopic analysis. Coupling molecular analysis with lipid biomarker analysis revealed that oxygenic photosynthetic organisms dominate the surface layers (top 3 mm). Polar lipids from the surface layers consisted predominantly of glycolipids, which are characteristic of algae, cyanobacteria and green anoxygenic photosynthetic bacteria. Consistent with prior analyses of gypsum evaporites, 16S rRNA gene clone libraries indicate that cyanobacterial populations belong primarily to the genus Cyanothece. The bacterial community below the surface layers is more diverse and dominated by anaerobic organisms. Phototrophic purple sulfur bacteria, sulfate-reducing bacteria (SRB), and Bacteroidetes were particularly abundant. The relative abundances of SRB increased with depth; Desulfobacteraceae clones were distributed throughout the crust, but not at the surface, while Desulfovibrionaceae clones were found predominantly in the deepest layers. These molecular results are consistent with fatty acid biomarker analysis. δ13C values of major lipid classes in the crust and sediment range from 14 to 36‰, which is considerably lower than corresponding values for benthic Microcoleus-dominated cyanobacterial mats found at lower salinities at ESSA

  14. Host responses to historical climate change shape parasite communities in North America’s intermountain west

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Host-parasite co-speciation, in which parasite divergence occurs in response to host divergence, is commonly proposed as a driver of parasite diversification, yet few empirical examples of strict co-speciation exist. Host-parasite co-evolutionary histories commonly reflect complex mosaics of co-spe...

  15. Effects of nutrient supplementation on host-pathogen dynamics of the amphibian chytrid fungus: a community approach

    PubMed Central

    BUCK, JULIA C.; ROHR, JASON R.; BLAUSTEIN, ANDREW R.

    2016-01-01

    SUMMARY Anthropogenic stressors may influence hosts and their pathogens directly or may alter host–pathogen dynamics indirectly through interactions with other species. For example, in aquatic ecosystems, eutrophication may be associated with increased or decreased disease risk. Conversely, pathogens can influence community structure and function and are increasingly recognised as important members of the ecological communities in which they exist.In outdoor mesocosms, we experimentally manipulated nutrients (nitrogen and phosphorus) and the presence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), and examined the effects on Bd abundance on larval amphibian hosts (Pseudacris regilla: Hylidae), amphibian traits and community dynamics. We predicted that resource supplementation would mitigate negative effects of Bd on tadpole growth and development and that indirect effects of treatments would propagate through the community.Nutrient additions caused changes in algal growth, which benefitted tadpoles through increased mass, development and survival. Bd-exposed tadpoles metamorphosed sooner than unexposed individuals, but their mass at metamorphosis was not affected by Bd exposure. We detected additive rather than interactive effects of nutrient supplementation and Bd in this experiment.Nutrient supplementation was not a significant predictor of infection load of larval amphibians. However, a structural equation model revealed that resource supplementation and exposure of amphibians to Bd altered the structure of the aquatic community. This is the first demonstration that sublethal effects of Bd on amphibians can alter aquatic community dynamics. PMID:25432573

  16. Parasite communities of two three-spined stickleback populations in subarctic Norway--effects of a small spatial-scale host introduction.

    PubMed

    Kuhn, Jesper A; Kristoffersen, Roar; Knudsen, Rune; Jakobsen, Jonas; Marcogliese, David J; Locke, Sean A; Primicerio, Raul; Amundsen, Per-Arne

    2015-04-01

    Co-introduction and colonization of parasites with the introduction of new host species into aquatic habitats may depend on the host specificity and dispersal capabilities of the parasites. We compared the metazoan parasite community of an introduced three-spined stickleback (Gasterosteus aculeatus) population with that of the nearby source population in subarctic Norway. As expected from a small spatial scale (5 km), the parasite component communities in the two lakes were highly similar. All identifiable allogenic parasite taxa (Diphyllobothrium dendriticum, Diphyllobothrium ditremum, Diphyllobothrium spp., Schistocephalus solidus, Apatemon sp. and Diplostomum spp.) were also observed in both lakes while inter-lake differences were driven by autogenic parasite taxa (Eubothrium spp., Crepidostomum spp., Nematoda spp., Proteocephalus sp. and Gyrodactylus arcuatus). Contrary to expectation, the total number of parasite taxa was higher in the introduced stickleback population (12) compared to that found in the source population (9) with three parasite taxa (Eubothrium spp., Crepidostomum spp., Nematoda spp.) only occurring in the introduced population. These parasites were uncommon however and normally restricted to salmonids. Sticklebacks from both populations were heavily infected, particularly with eye-infecting metacercariae. Sequences from the DNA barcode region of cytochrome oxidase 1 indicated that these include Diplostomum lineage 6, a member of the Diplostomum baeri complex and a member of the Strigeinae. Despite high similarity between the two component communities, quantitative inter-lake differences were found at the infracommunity level. At this scale, parasite intensity was significantly higher in the source population for the two autogenic stickleback specialists: G. arcuatus and Proteocephalus sp., assumed to be the autogenic stickleback specialist Proteocephalus filicollis. Parasite infracommunities within each lake also resembled each other

  17. Identifying the dominant metabolic strategies used by microorganisms within basalt-hosted, anoxic deep subsurface basement fluids via environmental genomics

    NASA Astrophysics Data System (ADS)

    Rappe, M. S.; Jungbluth, S.; Carr, S. A.; Lin, H. T.; Hsieh, C. C.; Nigro, O. D.; Steward, G. F.; Orcutt, B.

    2014-12-01

    A microbial ecosystem distinct from both overlying sediments and bottom seawater lies within the basaltic crust of the Juan de Fuca Ridge flank. The metabolic potential and genomic characteristics of microbes residing in fluids of this remote, anoxic region of the subsurface ocean were investigated using environmental DNA extracted from large-volume fluid samples obtained from advanced borehole observatories installed at two recently drilled IODP Boreholes, U1362A and U1362B. Fluids were collected from the deep (204 meters sub-basement) horizon of Borehole U1362A and shallow (40 meters sub-basement) horizon of Borehole U1362B and used to generate 503 and 705 million base-pairs of genomic DNA sequence data, respectively. Phylogenetically informative genes revealed that the community structure recovered via metagenomics was generally consistent with that obtained previously by 16S rRNA gene sequencing and was dominated by uncultivated bacterial lineages of Proteobacteria, Nitrospirae, Candidate Division OP8 (Aminicenantes), Thermotoga and archaeal groups THSCG, MCG (Bathyarchaeota), MBGE, and Archaeoglobus. Genes involved in phage integration, chemotaxis, nitrate reduction, methanogenesis, and amino acid degradation were all detected, revealing potentially dynamic microbial communities. Putative sulfate reduction genes were discovered within previously identified Firmicutes lineage Candidatus Desulforudis, along with other groups (e.g. Archaeoglobus). Significant metagenome assembly resulted in 72 and 105 contigs of >100 Kbp from U1362B and U1362A, respectively, including 1137, 977 and 356 Kbp-long contigs from Candidate Division OP8 residing in U1362B. These assemblies have revealed novel metabolic potential within abundant members of the deep subsurface microbial community, which can be directly related to their survival in the deep oceanic crust.

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

    PubMed Central

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

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

    PubMed

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

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

  20. Ionotropic Receptors Identified within the Tentacle of the Freshwater Snail Biomphalaria glabrata, an Intermediate Host of Schistosoma mansoni

    PubMed Central

    Liang, Di; Wang, Tianfang; Rotgans, Bronwyn A.; McManus, Donald P.; Cummins, Scott F.

    2016-01-01

    Biomphalaria glabrata (B. glabrata) is an air-breathing aquatic mollusc found in freshwater habitats across the Western Hemisphere. It is most well-known for its recognized capacity to act as a major intermediate host for Schistosoma mansoni, the human blood fluke parasite. Ionotropic receptors (IRs), a variant family of the ionotropic glutamate receptors (iGluR), have an evolutionary ancient function in detecting odors to initiate chemosensory signaling. In this study, we applied an array of methods towards the goal of identifying IR-like family members in B. glabrata, ultimately revealing two types, the iGluR and IR. Sequence alignment showed that three ligand-binding residues are conserved in most Biomphalaria iGluR sequences, while the IRs did exhibit a variable pattern, lacking some or all known glutamate-interactingresidues, supporting their distinct classification from the iGluRs. We show that B. glabrata contains 7 putative IRs, some of which are expressed within its chemosensory organs. To further investigate a role for the more ancient IR25a type in chemoreception, we tested its spatial distribution pattern within the snail cephalic tentacle by in situ hybridization. The presence of IR25a within presumptive sensory neurons supports a role for this receptor in olfactory processing, contributing to our understanding of the molecular pathways that are involved in Biomphalaria olfactory processing. PMID:27253696

  1. A Global Genomic Characterization of Nairoviruses Identifies Nine Discrete Genogroups with Distinctive Structural Characteristics and Host-Vector Associations

    PubMed Central

    Walker, Peter J.; Widen, Steven G.; Wood, Thomas G.; Guzman, Hilda; Tesh, Robert B.; Vasilakis, Nikolaos

    2016-01-01

    Nairoviruses are primarily tick-borne bunyaviruses, some of which are known to cause mild-to-severe febrile illness in humans or livestock. We describe the genome sequences of 11 poorly characterized nairoviruses that have ecological associations with either birds (Farallon, Punta Salinas, Sapphire II, Zirqa, Avalon, Clo Mor, Taggert, and Abu Hammad viruses), rodents (Qalyub and Bandia viruses), or camels (Dera Ghazi Khan virus). Global phylogenetic analyses of proteins encoded in the L, M, and S RNA segments of these and 20 other available nairovirus genomes identified nine well-supported genogroups (Nairobi sheep disease, Thiafora, Sakhalin, Keterah, Qalyub, Kasokero, Dera Ghazi Khan, Hughes, and Tamdy). Genogroup-specific structural variations were evident, particularly in the M segment encoding a polyprotein from which virion envelope glycoproteins (Gn and Gc) are generated by proteolytic processing. Structural variations include the extension, abbreviation, or absence sequences encoding an O-glycosylated mucin-like protein in the N-terminal domain, distinctive patterns of conserved cysteine residues in the GP38-like domain, insertion of sequences encoding a double-membrane-spanning protein (NSm) between the Gn and Gc domains, and the presence of an alternative long open reading frame encoding a viroporin-like transmembrane protein (Gx). We also observed strong genogroup-specific associations with categories of hosts and tick vectors. PMID:26903607

  2. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

    PubMed Central

    Steinert, Georg; Taylor, Michael W.; Deines, Peter; Simister, Rachel L.; de Voogd, Nicole J.; Hoggard, Michael

    2016-01-01

    Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges. PMID:27114882

  3. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity.

    PubMed

    Steinert, Georg; Taylor, Michael W; Deines, Peter; Simister, Rachel L; de Voogd, Nicole J; Hoggard, Michael; Schupp, Peter J

    2016-01-01

    Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.

  4. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

  5. Building persistent identifier systems for geoscience research - Technical solutions and community governance

    NASA Astrophysics Data System (ADS)

    Klump, J. F.; Lehnert, K. A.; Huber, R.

    2015-12-01

    The emergence of the Internet gave rise to the expectation that the internet would lead to greater accessibility, transparency and reproducibility of research results. New communication technologies enabled far easier and faster collaboration in larger, geographically more distributed networks. However, the distributed and disorganised nature of the internet not only allowed new technologies to emerge, it also made it difficult to maintain a persistent record of science. Persistent identifiers were invented to allow unambiguous identification of resources on the net. At first, these resources referred to scholarly literature and related resources. The concept of using persistent identifiers has since been expanded to other, non-textual resources, like datasets and geological specimens, and more recently to authors and contributors of scholarly works, and to software and instruments.Setting up identifier systems is technically trivial. The real challenge lies in creating a governance system for the respective identifiers. While Digital Object Identifiers (DOI) were originally invented by the publishing industry, they quickly became an established way for the identification of research resources. Other identifier systems, some of them using DOI as an example, were developed as grass-roots efforts by the scientific community.Together with semantic technologies and linked data, unambiguous identification allows us to harness information at large scales beyond human comprehension. The technical possibilities offered by technology challenge some of the norms of scholarly cooperation, such as using and sharing resources beyond the emulation of paper-based publications.This presentation will discuss the development of persistent identification of research resources as a community effort, using the technical and governance patterns developed for DOI and for IGSN for data as an example.

  6. Host-associated differentiation in a pecan and water hickory Aphidomorpha community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Host-Associated Differentiation (HAD) is the formation of genetically distinct, host-associated populations created and maintained by ecologically-mediated reproductive isolation. HAD potentially accounts for a high level of species diversity in parasites, including herbivorous insects. While case s...

  7. Towards a community effort to identify ethical principles for research in hydrology

    NASA Astrophysics Data System (ADS)

    Montanari, Alberto

    2010-05-01

    The hydrological community in Europe is growing rapidly in both size and, more importantly, scientific relevance and integrity. The Hydrological Sciences (HS) Division of EGU actively is promoting the above development by identifying research targets, stimulating the involvement of young scientists and managing a scientific open access journal based on a public peer review process. The management of the Division itself and the organisation of the General Assembly are carried out transparently, with the aim to seek an improved involvement of top and young scientists, with a bottom up approach. I believe the HS community is animated by a strong enthusiasm which, however, is not adequately supported by economical funding. In my opinion this is a major problem which HS should consider and discuss. The relevance of the societal and environmental problems dealt with by hydrologists, in a professional way and with exceptional scientific skills, is without doubt and therefore the limited amount of funding is not justified in practice. In my opinion, in order to refine the structure of the HS community, and promote its visibility, we should formally identify HS ethical principles for research in environmental science. The principles should highlight the role of hydrology as well as the ethical and scientific solidity of the HS community. Establishing ethical principles is even more important in view of the transparent approach HS is adopting for reviewing and publishing contributions and in view of the increasing need to transparently prove how public funding for research is administered. Establishing ethical principles for hydrology is not a trivial task. Hydrology is characterised by a relevant uncertainty in data, models and parameters. Hydrology is also relying on a large variety of approaches, ranging from statistical to physically based. The purpose of this poster is to present a collection of ethical principles for scientific research presented by the literature and

  8. A Study of Community Leaders in a Nuclear Host Community: Local Issues, Expectations and Support and Opposition.

    ERIC Educational Resources Information Center

    Bronfman, B. H.

    As part of a continuing effort to assess the social impacts on communities of energy facility planning, construction, operation, and decommissioning, a May 1977 survey of 37 community leaders in Hartsville, Tennessee (site of a nuclear power plant) establishes major local issues (past, present, and future) which leaders feel are important to…

  9. Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections

    PubMed Central

    2013-01-01

    Lawsonia intracellularis is an obligate intracellular bacterium and the causative agent of proliferative enteropathy (PE). The disease is endemic in pigs, emerging in horses and has also been reported in a variety of other animal species, including nonhuman primates. Comparing the whole genome sequences of a homologous porcine L. intracellularis isolate cultivated for 10 and 60 passages in vitro, we identified a 18-kb prophage-associated genomic island in the passage 10 (pathogenic variant) that was lost in the passage 60 (non-pathogenic variant). This chromosomal island comprises 15 genes downstream from the prophage DLP12 integrase gene. The prevalence of this genetic element was evaluated in 12 other L. intracellularis isolates and in 53 infected animals and was found to be conserved in all porcine isolates cultivated for up to 20 passages and was lost in isolates cultivated for more than 40 passages. Furthermore, the prophage region was also present in 26 fecal samples derived from pigs clinically affected with both acute and chronic forms of the disease. Nevertheless, equine L. intracellularis isolates evaluated did not harbor this genomic island regardless of the passage in vitro. Additionally, fecal samples from 21 clinically affected horses and four wild rabbits trapped in horse farms experiencing PE outbreaks did not show this prophage-associated island. Although the presence of this prophage-associated island was not essential for a virulent L. intracellularis phenotype, this genetic element was porcine isolate-specific and potentially contributed to the ecological specialization of this organism for the swine host. PMID:23826661

  10. Bacteriophages with potential for inactivation of fish pathogenic bacteria: survival, host specificity and effect on bacterial community structure.

    PubMed

    Pereira, Carla; Silva, Yolanda J; Santos, Ana L; Cunha, Angela; Gomes, Newton C M; Almeida, Adelaide

    2011-01-01

    Phage therapy may represent a viable alternative to antibiotics to inactivate fish pathogenic bacteria. Its use, however, requires the awareness of novel kinetics phenomena not applied to conventional drug treatments. The main objective of this work was to isolate bacteriophages with potential to inactivate fish pathogenic bacteria, without major effects on the structure of natural bacterial communities of aquaculture waters. The survival was determined in marine water, through quantification by the soft agar overlay technique. The host specificity was evaluated by cross infection. The ecological impact of phage addition on the structure of the bacterial community was evaluated by DGGE of PCR amplified 16S rRNA gene fragments. The survival period varied between 12 and 91 days, with a higher viability for Aeromonas salmonicida phages. The phages of Vibrio parahaemolyticus and of A. salmonicida infected bacteria of different families with a high efficacy of plating. The specific phages of pathogenic bacteria had no detectable impact on the structure of the bacterial community. In conclusion, V. parahaemolyticus and A. salmonicida phages show good survival time in marine water, have only a moderated impact on the overall bacterial community structure and the desired specificity for host pathogenic bacteria, being potential candidates for therapy of fish infectious diseases in marine aquaculture systems.

  11. Estimating coextinction risks from epidemic tree death: affiliate lichen communities among diseased host tree populations of Fraxinus excelsior.

    PubMed

    Jönsson, Mari T; Thor, Göran

    2012-01-01

    At least 10% of the world's tree species are threatened with extinction and pathogens are increasingly implicated in tree threats. Coextinction and threats to affiliates as a consequence of the loss or decline of their host trees is a poorly understood phenomenon. Ash dieback is an emerging infectious disease causing severe dieback of common ash Fraxinus excelsior throughout Europe. We utilized available empirical data on affiliate epiphytic lichen diversity (174 species and 17,800 observations) among 20 ash dieback infected host tree populations of F. excelsior on the island Gotland in the Baltic Sea, Sweden. From this, we used structured scenario projections scaled with empirical data of ash dieback disease to generate probabilistic models for estimating local and regional lichen coextinction risks. Average coextinction probabilities (Ā) were 0.38 (95% CI ± 0.09) for lichens occurring on F. excelsior and 0.14 (95% CI ± 0.03) when considering lichen persistence on all tree species. Ā was strongly linked to local disease incidence levels and generally increasing with lichen host specificity to F. excelsior and decreasing population size. Coextinctions reduced affiliate community viability, with significant local reductions in species richness and shifts in lichen species composition. Affiliates were projected to become locally extirpated before their hosts, illuminating the need to also consider host tree declines. Traditionally managed open wooded meadows had the highest incidence of ash dieback disease and significantly higher proportions of affiliate species projected to go extinct, compared with unmanaged closed forests and semi-open grazed sites. Most cothreatened species were not previously red-listed, which suggest that tree epidemics cause many unforeseen threats to species. Our analysis shows that epidemic tree deaths represent an insidious, mostly overlooked, threat to sessile affiliate communities in forested environments. Current conservation and

  12. Know Your Monkey: Identifying Primate Conservation Challenges in an Indigenous Kichwa Community Using an Ethnoprimatological Approach.

    PubMed

    Stafford, Ciara A; Alarcon-Valenzuela, Javiera; Patiño, Javier; Preziosi, Richard F; Sellers, William I

    2016-01-01

    Increasing pressure on tropical forests is continually highlighting the need to find new solutions that mitigate the impact of human populations on biodiversity. However, developing solutions that can tackle the drivers of anthropogenic pressure, or at least take them into account, hinges upon building a good understanding of the culture and perceptions of local people. This study aims to provide an overview of the ethnoprimatology of an indigenous Kichwa community in the Ecuadorian Amazon that maintains a traditional lifestyle but also has good access to markets. We examine whether primates are seen as a distinctive group and their relative importance as sources of bushmeat and as household pets. Pile-sorting exercises revealed that although locals generally group members of the order Primates together, tree-dwelling non-primates including sloths, coatis, kinkajous and tamanduas are also frequently classified as 'monkeys'. The perceived importance of primates to the forest and the community lay more in their potential as bushmeat, and only 1 respondent identified an ecological role for the group in terms of seed dispersal. Gaining a better understanding of local perceptions will allow for better-informed conservation decisions that are more aware of potential impacts and are more likely to gain community support.

  13. What determines Alnus-associated ectomycorrhizal community diversity and specificity? A comparison of host and habitat effects at a regional scale.

    PubMed

    Roy, Mélanie; Rochet, Juliette; Manzi, Sophie; Jargeat, Patricia; Gryta, Hervé; Moreau, Pierre-Arthur; Gardes, Monique

    2013-06-01

    · Global-scale analyses of ectomycorrhizal (ECM) fungi communities emphasize host plant families as the main drivers of diversity. This study aims to test, on Alnus-ECM communities, which fungi are said to be 'host-specific', to what extent host species, habitat and distance explain their alpha and beta diversity variations, and their specificity. · In France, ECM communities associated with two subgenera and five species of Alnus, were sampled on 165 trees from 39 lowland to subalpine sites. In all, 1178 internal transcribed spacer (ITS) sequences of ECM fungi clustered in 86 molecular operational taxonomic units (MOTUs). · The species richness was low but still variable, and the evenness of communities was lower on organic soils and in Corsica. Similarity between communities was influenced both by host, soil parameters, altitude and longitude, but not by climate and distance. A large majority of 'specific' fungi were shared between host species within a subgenus, and showed habitat preferences within the subgenus distribution range. · Our study confirms that Alnus ECM communities are low in diversity, highly conserved at a regional scale, and partly shared between congeneric host species. A large part of alpha and beta diversity variations remained unexplained, and other processes may shape these communities.

  14. Avian host community structure and prevalence of West Nile virus in Chicago, Illinois.

    PubMed

    Loss, Scott R; Hamer, Gabriel L; Walker, Edward D; Ruiz, Marilyn O; Goldberg, Tony L; Kitron, Uriel D; Brawn, Jeffrey D

    2009-03-01

    Vertebrate host diversity has been postulated to mediate prevalence of zoonotic, vector-borne diseases, such that as diversity increases, transmission dampens. This "dilution effect" is thought to be caused by distribution of infective bites to incompetent reservoir hosts. We quantified avian species richness, avian seroprevalence for antibodies to West Nile virus (WNV), and infection of WNV in Culex mosquitoes, in the Chicago metropolitan area, Illinois, USA, a region of historically high WNV activity. Results indicated high overall avian seroprevalence and variation in seroprevalence across host species; however, there was no negative correlation between avian richness and Culex infection rate or between richness and infection status in individual birds. Bird species with high seroprevalence, especially northern cardinals and mourning doves, may be important sentinels for WNV in Chicago, since they were common and widespread among all study sites. Overall, our results suggest no net effect of increasing species richness to West Nile virus transmission in Chicago. Other intrinsic and extrinsic factors, such as variation in mosquito host preference, reservoir host competence, temperature, and precipitation, may be more important than host diversity for driving interannual variation in WNV transmission. These results from a fine-scale study call into question the generality of a dilution effect for WNV at coarser spatial scales.

  15. Identifying the mathematics middle year students use as they address a community issue

    NASA Astrophysics Data System (ADS)

    Marshman, Margaret

    2017-03-01

    Middle year students often do not see the mathematics in the real world whereas the Australian Curriculum: Mathematics aims for students to be "confident and creative users and communicators of mathematics" (Australian Curriculum Assessment and Reporting Authority [ACARA] 2012). Using authentic and real mathematics tasks can address this situation. This paper is an account of how, working within a Knowledge Producing Schools' framework, a group of middle year students addressed a real community issue, the problem of the lack of a teenage safe space using mathematics and technology. Data were collected for this case study via journal observations and reflections, semi-structured interviews, samples of the students' work and videos of students working. The data were analysed by identifying the mathematics the students used determining the function and location of the space and focused on problem negotiation, formulation and solving through the statistical investigation cycle. The paper will identify the mathematics and statistics these students used as they addressed a real problem in their local community.

  16. Tricholoma matsutake in a natural Pinus densiflora forest: correspondence between above- and below-ground genets, association with multiple host trees and alteration of existing ectomycorrhizal communities.

    PubMed

    Lian, Chunlan; Narimatsu, Maki; Nara, Kazuhide; Hogetsu, Taizo

    2006-01-01

    Tricholoma matsutake (matsutake) is an ectomycorrhizal (ECM) fungus that produces economically important mushrooms in Japan. Here, we use microsatellite markers to identify genets of matsutake sporocarps and below-ground ECM tips, as well as associated host genotypes of Pinus densiflora. We also studied ECM fungal community structure inside, beneath and outside the matsutake fairy rings, using morphological and internal transcribed spacer (ITS) polymorphism analysis. Based on sporocarp samples, one to four genets were found within each fairy ring, and no genetic differentiation among six sites was detected. Matsutake ECM tips were only found beneath fairy rings and corresponded with the genotypes of the above-ground sporocarps. We detected nine below-ground matsutake genets, all of which colonized multiple pine trees (three to seven trees per genet). The ECM fungal community beneath fairy rings was species-poor and significantly differed from those inside and outside the fairy rings. We conclude that matsutake genets occasionally establish from basidiospores and expand on the root systems of multiple host trees. Although matsutake mycelia suppress other ECM fungi during expansion, most of them may recover after the passage of the fairy rings.

  17. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

    PubMed Central

    Messier, Christian; Kembel, Steven W.

    2016-01-01

    Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual

  18. Nestedness in Riverine Freshwater Mussel Communities: Patterns Across Sites and Fish Hosts

    EPA Science Inventory

    The pattern of nestedness, where species present in depauperate locations are subsets of species present in locations with higher species diversity, is often found in ecological communities. The pattern may indicate the mechanism by which the communities are structured and can be...

  19. Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus.

    PubMed

    dos Reis, Mario; Hay, Alan J; Goldstein, Richard A

    2009-10-01

    Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens evolving in different hosts. It has been noticed that influenza viruses show marked differences in nucleotide composition in human and avian hosts. We take advantage of this fact to identify the host shift event that led to the 1918 'Spanish' influenza. This disease killed over 50 million people worldwide, ranking it as the deadliest pandemic in recorded history. Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882-1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913-1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.

  20. Geographic Mapping as a Tool for Identifying Communities at High Risk for Fires.

    PubMed

    Fahey, Erin; Lehna, Carlee; Hanchette, Carol; Coty, Mary-Beth

    2016-01-01

    The purpose of this study was to evaluate whether the sample of older adults in a home fire safety (HFS) study captured participants living in the areas at highest risk for fire occurrence. The secondary aim was to identify high risk areas to focus future HFS interventions. Geographic information systems software was used to identify census tracts where study participants resided. Census data for these tracts were compared with participant data based on seven risk factors (ie, age greater than 65 years, nonwhite race, below high school education, low socioeconomic status, rented housing, year home built, home value) previously identified in a fire risk model. The distribution of participants and census tracts among risk categories determined how well higher risk census tracts were sampled. Of the 46 census tracts where the HFS intervention was implemented, 78% (n = 36) were identified as high or severe risk according to the fire risk model. Study participants' means for median annual family income (P < .0001) and median home value (P < .0001) were significantly lower than the census tract means (n = 46), indicating participants were at higher risk of fire occurrence. Of the 92 census tracts identified as high or severe risk in the entire county, the study intervention was implemented in 39% (n = 36), indicating 56 census tracts as potential areas for future HFS interventions. The Geographic information system-based fire risk model is an underutilized but important tool for practice that allows community agencies to develop, plan, and evaluate their outreach efforts and ensure the most effective use of scarce resources.

  1. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    SciTech Connect

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

  2. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    PubMed Central

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-01-01

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact. PMID:25954263

  3. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests.

    PubMed

    Hesse, Cedar N; Mueller, Rebecca C; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D; Zak, Donald R; Kuske, Cheryl R

    2015-01-01

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

  4. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    DOE PAGES

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; ...

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes)more » in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.« less

  5. Assessment of a Novel Approach to Identify Trichiasis Cases Using Community Treatment Assistants in Tanzania

    PubMed Central

    Greene, Gregory S.; West, Sheila K.; Mkocha, Harran; Munoz, Beatriz; Merbs, Shannath L.

    2015-01-01

    Background Simple surgical intervention advocated by the World Health Organization can alleviate trachomatous trichiasis (TT) and prevent subsequent blindness. A large backlog of TT cases remain unidentified and untreated. To increase identification and referral of TT cases, a novel approach using standard screening questions, a card, and simple training for Community Treatment Assistants (CTAs) to use during Mass Drug Administration (MDA) was developed and evaluated in Kongwa District, a trachoma-endemic area of central Tanzania. Methodology/Principal Findings A community randomized trial was conducted in 36 communities during MDA. CTAs in intervention villages received an additional half-day of training and a TT screening card in addition to the training received by CTAs in villages assigned to usual care. All MDA participants 15 years and older were screened for TT, and senior TT graders confirmed case status by evaluating all screened-positive cases. A random sample of those screened negative for TT and those who did not present at MDA were also evaluated by the master graders. Intervention CTAs identified 5.6 times as many cases (n = 50) as those assigned to usual care (n = 9, p < 0.05). While specificity was above 90% for both groups, the sensitivity for the novel screening tool was 31.2% compared to 5.6% for the usual care group (p < 0.05). Conclusions/Significance CTAs appear to be viable resources for the identification of TT cases. Additional training and use of a TT screening card significantly increased the ability of CTAs to recognize and refer TT cases during MDA; however, further efforts are needed to improve case detection and reduce the number of false positive cases. PMID:26658938

  6. Quality of Dementia Care in the Community: Identifying Key Quality Assurance Components

    PubMed Central

    Heckman, George A.; Boscart, Veronique M.; Franco, Bryan B.; Hillier, Loretta; Crutchlow, Lauren; Lee, Linda; Molnar, Frank; Seitz, Dallas; Stolee, Paul

    2016-01-01

    Background Primary care-based memory clinics (PCMCs) have been established in several jurisdictions to improve the care for persons with Alzheimer’s disease and related dementias. We sought to identify key quality indicators (QIs), quality improvement mechanisms, and potential barriers and facilitators to the establishment of a quality assurance framework for PCMCs. Methods We employed a Delphi approach to obtain consensus from PCMC clinicians and specialist physicians on QIs and quality improvement mechanisms. Thirty-eight candidate QIs and 19 potential quality improvement mechanisms were presented to participants in two rounds of electronic Delphi surveys. Written comments were collected and descriptively analyzed. Results The response rate for the first and second rounds were 21.3% (n = 179) and 12.8% (n = 88), respectively. The majority of respondents were physicians. Fourteen QIs remained after the consensus process. Ten quality improvement mechanisms were selected with those characterized by specialist integration, such as case discussions and mentorships, being ranked highly. Written comments revealed three major themes related to potential barriers and facilitators to quality assurance: 1) perceived importance, 2) collaboration and role clarity, and 3) implementation process. Conclusion We successfully utilized a consultative process among primary and specialty providers to identify core QIs and quality improvement mechanisms for PCMCs. Identified quality improvement mechanisms highlight desire for multi-modal education. System integration and closer integration between PCMCs and specialists were emphasized as essential for the provision of high-quality dementia care in community settings. PMID:28050221

  7. Community-Engaged Research to Identify House Parent Perspectives on Support and Risk within the House and Ball Scene

    PubMed Central

    Kubicek, Katrina; Beyer, William H.; McNeeley, Miles; Weiss, George; Omni, Legendary Father Taz Ultra; Kipke, Michele D.

    2012-01-01

    This paper describes a community-engaged study with the Los Angeles House and Ball scene, in which the perspectives of the leaders of these communities are captured to better understand how the House and Ball communities may protect and/or increase its members’ risks for HIV infection. Data were collected through in-depth interviews with House parents (N=26). This study identified key features of both support (e.g., family and support; acceptance; validation and recognition) and risk (e.g., members’ struggle to maintain status in the Ballroom scene; sex work; substance use; danger of becoming too involved in the Ball community; perception and stigma of Ballroom scene within the larger gay community) within these communities. Findings are discussed in relation to framing how to leverage the supportive aspects of the House and Ball communities to design relevant HIV prevention interventions. PMID:22206442

  8. Community-engaged research to identify house parent perspectives on support and risk within the House and Ball scene.

    PubMed

    Kubicek, Katrina; Beyer, William H; McNeeley, Miles; Weiss, George; Omni, Legendary Father Taz Ultra; Kipke, Michele D

    2013-01-01

    This article describes a community-engaged study with the Los Angeles House and Ball scene in which the perspectives of the leaders of these communities are captured to better understand how the House and Ball communities may protect or increase its members' risks for HIV infection. Data were collected through in-depth interviews with House parents (N = 26). This study identified key features of both support (e.g., family and support, acceptance, and validation and recognition) and risk (e.g., members' struggles to maintain status in the Ballroom scene, sex work, substance use, danger of becoming too involved in the Ball community, and perception and stigma of the Ballroom scene within the larger gay community) within these communities. Findings are discussed in relation to framing how to leverage the supportive aspects of the House and Ball communities to design relevant HIV-prevention interventions.

  9. How to Identify Community Leaders, Problems, Resources: A Model Guidebook. Resource Materials and Training Aids. Second Revision.

    ERIC Educational Resources Information Center

    Lippincott, Kenneth; Radig, John

    This package has been developed as a resource guide and training aid to assist school administrators who want to improve school-community relations, to involve people meaningfully in decision-making, and to create learning experiences of quality in the community's lifelong educational process. The guidebook lists steps for identifying formal and…

  10. Finding Needles in a Haystack: A Methodology for Identifying and Sampling Community-Based Youth Smoking Cessation Programs

    ERIC Educational Resources Information Center

    Emery, Sherry; Lee, Jungwha; Curry, Susan J.; Johnson, Tim; Sporer, Amy K.; Mermelstein, Robin; Flay, Brian; Warnecke, Richard

    2010-01-01

    Background: Surveys of community-based programs are difficult to conduct when there is virtually no information about the number or locations of the programs of interest. This article describes the methodology used by the Helping Young Smokers Quit (HYSQ) initiative to identify and profile community-based youth smoking cessation programs in the…

  11. Sporadic cases of community acquired legionnaires' disease: an ecological study to identify new sources of contamination

    PubMed Central

    Che, D; Decludt, B; Campese, C; Desenclos, J

    2003-01-01

    Study objective: To explore the relation between incidence of sporadic and community acquired legionnaires' disease and exposure to potentially contaminated industrial aerosols. Design: Geographical ecological approach using the postcode as the statistical unit. A multivariate Poisson regression model was used to model the relation between exposure to industrial aerosols and legionnaires' disease. Setting: Metropolitan France. Main results: More than 1000 sources of industrial exposure (aerosol and plume of smoke) were identified in 42 French departments. After adjusting for confounding factors, there was a statistically increased incidence of legionnaires' disease in postcodes with plume of smoke in comparison with postcodes without (RR=1.45, 95% CI=1.12 to 1.87), and in postcodes with more than one aerosol in comparison with postcodes without (RR=1.37, 95% CI=1.04 to 1.79). Conclusion: These findings highlight that any industrial systems generating water aerosols should be regarded as potential sources of contamination for legionnaires' disease. PMID:12775798

  12. Identifying and defining the dimensions of community capacity to provide a basis for measurement.

    PubMed

    Goodman, R M; Speers, M A; McLeroy, K; Fawcett, S; Kegler, M; Parker, E; Smith, S R; Sterling, T D; Wallerstein, N

    1998-06-01

    Although community capacity is a central concern of community development experts, the concept requires clarification. Because of the potential importance of community capacity to health promotion, the Division of Chronic Disease Control and Community Intervention, Centers for Disease Control and Prevention (CDC), convened a symposium in December 1995 with the hope that a consensus might emerge regarding the dimensions that are integral to community capacity. This article describes the dimensions that the symposium participants suggested as central to the construct, including participation and leadership, skills, resources, social and interorganizational networks, sense of community, understanding of community history, community power, community values, and critical reflection. The dimensions are not exhaustive but may serve as a point of departure to extend and refine the construct and to operationalize ways to assess capacity in communities.

  13. Circles of Influence and Chains of Command: The Social Processes Whereby Ethnic Communities Influence Host Societies

    ERIC Educational Resources Information Center

    Orum, Anthony M.

    2005-01-01

    Research into immigration has for many years focused most of its attention on the issue of how immigrants adapt to host societies. This tendency is especially true in the work of sociologists. Yet if we acknowledge the growing ethnic diversity today in the United States and elsewhere, the most interesting questions arise as to how immigrants…

  14. Shifting fungal endophyte communities colonize Bouteloua gracilis: effect of host tissue and geographical distribution.

    PubMed

    Herrera, José; Khidir, Hana H; Eudy, Douglas M; Porras-Alfaro, Andrea; Natvig, Donald O; Sinsabaugh, Robert L

    2010-01-01

    Communities of root-associated fungi (RAF) commonly have been studied under the auspices of arbuscular mycorrhizal fungi (AMF) or ectomycorrhizal fungi. However many studies now indicate that other groups of endophytic RAF, including dark septate endophytes (DSE) are more abundant in some plants and environments. The common forage grass, Bouteloua gracilis, was used as a model to examine whether RAF also colonize different organs within the same plant and to compare RAF communities from sites across North America, spanning the latitudinal range of B. gracilis (from Canada to Mexico). We compared the RAF communities of organs within individual plants at one site and within plant roots among six sites. With the possible exception of one group related to genus Paraphaeosphaeria there was little evidence that RAF colonized vertically beyond the crowns. Furthermore, although there was some variation in the constitution of rare members of the RAF communities, several taxonomically related groups dominated the RAF community at all sites. These dominant taxa included members in the Pleosporales (related to the DSE, Paraphaeosphaeria spp.), Agaricales (related to Moniliophthora spp., or Campanella spp.) and Hypocreales (related to Fusarium spp.). AMF were notable by their near absence. Similar phylotypes from the dominant groups clustered around adjacent sites so that similarity of the RAF communities was negatively correlated to site inter-distance and the RAF communities appeared to group by country. These results increase the possibility that at least some of these common and widely distributed core members of the RAF community form important, intimate and long lasting relationships with grasses.

  15. Environmental Enteric Dysfunction Is Associated With Poor Linear Growth and Can Be Identified by Host Fecal mRNAs

    PubMed Central

    Ordiz, Maria Isabel; Shaikh, Nurmohammad; Trehan, Indi; Maleta, Ken; Stauber, Jennifer; Shulman, Robert; Devaraj, Sridevi; Tarr, Phillip I.; Manary, Mark J.

    2016-01-01

    ABSTRACT Objective: Environmental enteric dysfunction (EED) can be assessed by the lactulose:mannitol (L:M) test. Our objective was to determine if selected host fecal transcripts were correlated with EED, and whether transcripts and clinical characteristics could be used to predict EED in rural African children. Methods: Demographic and sanitation characteristics, along with L:M testing and host fecal transcript analyses from 798 asymptomatic Malawian children aged 12 to 61 months were compared with linear growth over the subsequent 3 months. Fecal host mRNA analysis included quantification of expression of 18 transcripts associated with L:M. Permeability was categorized as normal (L:M ≤ 0.15), moderate (0.15host fecal transcripts can be used in a random forest model as a noninvasive biomarker for categories of EED in rural African children. PMID:27347722

  16. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

    PubMed Central

    Schwartz, Allison R.; Potnis, Neha; Timilsina, Sujan; Wilson, Mark; Patané, José; Martins, Joaquim; Minsavage, Gerald V.; Dahlbeck, Douglas; Akhunova, Alina; Almeida, Nalvo; Vallad, Gary E.; Barak, Jeri D.; White, Frank F.; Miller, Sally A.; Ritchie, David; Goss, Erica; Bart, Rebecca S.; Setubal, João C.; Jones, Jeffrey B.; Staskawicz, Brian J.

    2015-01-01

    Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors. PMID:26089818

  17. Diversity, host, and habitat specificity of oomycete communities in declining reed stands (Phragmites australis) of a large freshwater lake.

    PubMed

    Nechwatal, Jan; Wielgoss, Anna; Mendgen, Kurt

    2008-06-01

    We studied the diversity of oomycetes in a declining reed belt (Phragmites australis) of Lake Constance, Germany, using conventional baiting with specific reed and standard oak baits, accompanied by molecular techniques. Apart from an Aphanomyces sp. and a Phytophthora sp., baiting from reed rhizosphere samples from flooded, as well as drier, littoral sites revealed only Pythium spp. A total of 67 oomycete isolates was classified according to PCR-RFLP banding patterns and ITS sequencing, and 18 different sequence types could be separated. The majority of these seemed previously unknown species, as indicated by the degree of similarity to those deposited in nucleotide databases. Species communities in both flooded and drier habitats or both reed and oak baits clearly differed from one another, and only few species occurred in both dry and flooded sites, or in both oak and reed baits. A frequently occurring group of related Pythium species appeared to be specifically associated with reed, and these were the only species that proved pathogenic towards this host in vitro. Our study proved that unexplored natural ecosystems harbour diverse communities of oomycete species with specific habitat and host preferences within close-by, but ecologically contrasting, sites. Among the species isolated, those associated with the predominating plant might accumulate and thus may be reed pathogens of considerable importance.

  18. The case of a city where 1 in 6 residents is a refugee: ecological factors and host community adaptation in successful resettlement.

    PubMed

    Smith, R Scott

    2008-12-01

    The notable success of an upstate New York community in resettling refugees raises the question of whether multiple waves of resettlement over a 15-year period have resulted in greater accommodation to refugees. Structured interviews based on transactional models of acculturation were used along with archival data to explore ecological factors supporting a host community's behavioral flexibility and perseverance in response to the influx of refugees. Evidence suggests that socioeconomic climate, historical background/social norms, and the organizational structure of agencies involved in resettlement moderate successful inclusion of refugees into a host community in a bidirectional process.

  19. Extremely alkaline (pH > 12) ground water hosts diverse microbial community.

    PubMed

    Roadcap, George S; Sanford, Robert A; Jin, Qusheng; Pardinas, José R; Bethke, Craig M

    2006-01-01

    Chemically unusual ground water can provide an environment for novel communities of bacteria to develop. Here, we describe a diverse microbial community that inhabits extremely alkaline (pH > 12) ground water from the Lake Calumet area of Chicago, Illinois, where historic dumping of steel slag has filled in a wetland. Using microbial 16S ribosomal ribonucleic acid gene sequencing and microcosm experiments, we confirmed the presence and growth of a variety of alkaliphilic beta-Proteobacteria, Bacillus, and Clostridium species at pH up to 13.2. Many of the bacterial sequences most closely matched those of other alkaliphiles found in more moderately alkaline water around the world. Oxidation of dihydrogen produced by reaction of water with steel slag is likely a primary energy source to the community. The widespread occurrence of iron-oxidizing bacteria suggests that reduced iron serves as an additional energy source. These results extend upward the known range of pH tolerance for a microbial community by as much as 2 pH units. The community may provide a source of novel microbes and enzymes that can be exploited under alkaline conditions.

  20. Insect responses to host plant provision beyond natural boundaries: latitudinal and altitudinal variation in a Chinese fig wasp community

    PubMed Central

    Wang, Rong; Compton, Stephen G; Quinnell, Rupert J; Peng, Yan-Qiong; Barwell, Louise; Chen, Yan

    2015-01-01

    Many plants are grown outside their natural ranges. Plantings adjacent to native ranges provide an opportunity to monitor community assembly among associated insects and their parasitoids in novel environments, to determine whether gradients in species richness emerge and to examine their consequences for host plant reproductive success. We recorded the fig wasps (Chalcidoidea) associated with a single plant resource (ovules of Ficus microcarpa) along a 1200 km transect in southwest China that extended for 1000 km beyond the tree's natural northern range margin. The fig wasps included the tree's agaonid pollinator and other species that feed on the ovules or are their parasitoids. Phytophagous fig wasps (12 species) were more numerous than parasitoids (nine species). The proportion of figs occupied by fig wasps declined with increasing latitude, as did the proportion of utilized ovules in occupied figs. Species richness, diversity, and abundance of fig wasps also significantly changed along both latitudinal and altitudinal gradients. Parasitoids declined more steeply with latitude than phytophages. Seed production declined beyond the natural northern range margin, and at high elevation, because pollinator fig wasps became rare or absent. This suggests that pollinator climatic tolerances helped limit the tree's natural distribution, although competition with another species may have excluded pollinators at the highest altitude site. Isolation by distance may prevent colonization of northern sites by some fig wasps and act in combination with direct and host-mediated climatic effects to generate gradients in community composition, with parasitoids inherently more sensitive because of declines in the abundance of potential hosts. PMID:26380693

  1. Insect responses to host plant provision beyond natural boundaries: latitudinal and altitudinal variation in a Chinese fig wasp community.

    PubMed

    Wang, Rong; Compton, Stephen G; Quinnell, Rupert J; Peng, Yan-Qiong; Barwell, Louise; Chen, Yan

    2015-09-01

    Many plants are grown outside their natural ranges. Plantings adjacent to native ranges provide an opportunity to monitor community assembly among associated insects and their parasitoids in novel environments, to determine whether gradients in species richness emerge and to examine their consequences for host plant reproductive success. We recorded the fig wasps (Chalcidoidea) associated with a single plant resource (ovules of Ficus microcarpa) along a 1200 km transect in southwest China that extended for 1000 km beyond the tree's natural northern range margin. The fig wasps included the tree's agaonid pollinator and other species that feed on the ovules or are their parasitoids. Phytophagous fig wasps (12 species) were more numerous than parasitoids (nine species). The proportion of figs occupied by fig wasps declined with increasing latitude, as did the proportion of utilized ovules in occupied figs. Species richness, diversity, and abundance of fig wasps also significantly changed along both latitudinal and altitudinal gradients. Parasitoids declined more steeply with latitude than phytophages. Seed production declined beyond the natural northern range margin, and at high elevation, because pollinator fig wasps became rare or absent. This suggests that pollinator climatic tolerances helped limit the tree's natural distribution, although competition with another species may have excluded pollinators at the highest altitude site. Isolation by distance may prevent colonization of northern sites by some fig wasps and act in combination with direct and host-mediated climatic effects to generate gradients in community composition, with parasitoids inherently more sensitive because of declines in the abundance of potential hosts.

  2. Who is Next? Identifying Communities with the Potential for Increased Implementation of Sustainability Policies and Programs

    EPA Science Inventory

    Understanding the system of connections between societal contexts and policy outcomes in municipal governments provides important insights into how community sustainability happens, and why it happens differently in various communities. A growing body of research in recent years ...

  3. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    PubMed

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  4. Identifying Overlapping Language Communities: The Case of Chiriquí and Panamanian Signed Languages

    ERIC Educational Resources Information Center

    Parks, Elizabeth S.

    2016-01-01

    In this paper, I use a holographic metaphor to explain the identification of overlapping sign language communities in Panama. By visualizing Panama's complex signing communities as emitting community "hotspots" through social drama on multiple stages, I employ ethnographic methods to explore overlapping contours of Panama's sign language…

  5. In the Wake of Hurricane Katrina: Delivering Crisis Mental Health Services to Host Communities

    ERIC Educational Resources Information Center

    Marbley, Aretha Faye

    2007-01-01

    Throughout the country and especially in Texas, local communities opened their arms to hurricane Katrina evacuees. Like the federal government, emergency health and mental health entities were unprepared for the massive numbers of people needing assistance. Mental health professionals, though armed with a wealth of crisis intervention information,…

  6. Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence.

    PubMed

    Schimann, Heidy; Bach, Cyrille; Lengelle, Juliette; Louisanna, Eliane; Barantal, Sandra; Murat, Claude; Buée, Marc

    2017-02-01

    The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.

  7. Think Tank: Identifying and Creating the Next Generation of Community-Based Cancer Prevention Studies | Division of Cancer Prevention

    Cancer.gov

    In late 2015, the NCI Division of Cancer Prevention convened cancer prevention research experts and stakeholders to discuss the current state of cancer prevention research, identify key prevention research priorities for the NCI, and identify studies that could be conducted within the NCI Community Oncology Research Program. Read the Cancer Prevention Research journal article (PDF, 532KB). |

  8. An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses

    PubMed Central

    Schreiber, Claire A.; Sakuma, Toshie; Izumiya, Yoshihiro; Holditch, Sara J.; Hickey, Raymond D.; Bressin, Robert K.; Basu, Upamanyu; Koide, Kazunori; Asokan, Aravind; Ikeda, Yasuhiro

    2015-01-01

    Adeno-associated viruses (AAV) have evolved to exploit the dynamic reorganization of host cell machinery during co-infection by adenoviruses and other helper viruses. In the absence of helper viruses, host factors such as the proteasome and DNA damage response machinery have been shown to effectively inhibit AAV transduction by restricting processes ranging from nuclear entry to second-strand DNA synthesis. To identify host factors that might affect other key steps in AAV infection, we screened an siRNA library that revealed several candidate genes including the PHD finger-like domain protein 5A (PHF5A), a U2 snRNP-associated protein. Disruption of PHF5A expression selectively enhanced transgene expression from AAV by increasing transcript levels and appears to influence a step after second-strand synthesis in a serotype and cell type-independent manner. Genetic disruption of U2 snRNP and associated proteins, such as SF3B1 and U2AF1, also increased expression from AAV vector, suggesting the critical role of U2 snRNP spliceosome complex in this host-mediated restriction. Notably, adenoviral co-infection and U2 snRNP inhibition appeared to target a common pathway in increasing expression from AAV vectors. Moreover, pharmacological inhibition of U2 snRNP by meayamycin B, a potent SF3B1 inhibitor, substantially enhanced AAV vector transduction of clinically relevant cell types. Further analysis suggested that U2 snRNP proteins suppress AAV vector transgene expression through direct recognition of intact AAV capsids. In summary, we identify U2 snRNP and associated splicing factors, which are known to be affected during adenoviral infection, as novel host restriction factors that effectively limit AAV transgene expression. Concurrently, we postulate that pharmacological/genetic manipulation of components of the spliceosomal machinery might enable more effective gene transfer modalities with recombinant AAV vectors. PMID:26244496

  9. Perceptions of the Role of Short-Term Volunteerism in International Development: Views from Volunteers, Local Hosts, and Community Members

    PubMed Central

    Loiseau, Bethina; Sibbald, Rebekah; Raman, Salem A.; Darren, Benedict; Loh, Lawrence C.

    2016-01-01

    Background. Short-term international volunteer trips traditionally involve volunteers from high-income countries travelling to low- and middle-income countries to assist in service-related development activities. Their duration typically ranges from 7 to 90 days. The city of La Romana, Dominican Republic, receives hundreds of short-term international volunteers annually. They participate in activities aimed at improving conditions faced by a marginalized ethnic-Haitian community living in bateyes. Methods. This qualitative analysis examined perceptions of short-term international volunteerism, held by three key stakeholder groups in La Romana: local hosts, international volunteers, and community members. Responses from semistructured interviews were recorded and analysed by thematic analysis. Results. Themes from the 3 groups were broadly categorized into general perceptions of short-term volunteerism and proposed best practices. These were further subdivided into perceptions of value, harms, and motivations associated with volunteer teams for the former and best practices around volunteer composition and selection, partnership, and skill sets and predeparture training for the latter. Conclusion. Notable challenges were associated with short-term volunteering, including an overemphasis on the material benefits from volunteer groups expressed by community member respondents; misalignment of the desired and actual skill sets of volunteers; duplicate and uncoordinated volunteer efforts; and the perpetuation of stereotypes suggesting that international volunteers possess superior knowledge or skills. Addressing these challenges is critical to optimizing the conduct of short-term volunteerism. PMID:27382372

  10. MIIB: A Metric to Identify Top Influential Bloggers in a Community

    PubMed Central

    Khan, Hikmat Ullah; Daud, Ali; Malik, Tahir Afzal

    2015-01-01

    Social networking has revolutionized the use of conventional web and has converted World Wide Web into the social web as users can generate their own content. This change has been possible due to social web platforms like forums, wikis, and blogs. Blogs are more commonly being used as a form of virtual communication to express an opinion about an event, product or experience and can reach a large audience. Users can influence others to buy a product, have certain political or social views, etc. Therefore, identifying the most influential bloggers has become very significant as this can help us in the fields of commerce, advertisement and product knowledge searching. Existing approaches consider some basic features, but lack to consider some other features like the importance of the blog on which the post has been created. This paper presents a new metric, MIIB (Metric for Identification of Influential Bloggers), based on various features of bloggers’ productivity and popularity. Productivity refers to bloggers’ blogging activity and popularity measures bloggers’ influence in the blogging community. The novel module of BlogRank depicts the importance of blog sites where bloggers create their posts. The MIIB has been evaluated against the standard model and existing metrics for finding the influential bloggers using dataset from the real-world blogosphere. The obtained results confirm that the MIIB is able to find the most influential bloggers in a more effective manner. PMID:26414063

  11. MIIB: A Metric to Identify Top Influential Bloggers in a Community.

    PubMed

    Khan, Hikmat Ullah; Daud, Ali; Malik, Tahir Afzal

    2015-01-01

    Social networking has revolutionized the use of conventional web and has converted World Wide Web into the social web as users can generate their own content. This change has been possible due to social web platforms like forums, wikis, and blogs. Blogs are more commonly being used as a form of virtual communication to express an opinion about an event, product or experience and can reach a large audience. Users can influence others to buy a product, have certain political or social views, etc. Therefore, identifying the most influential bloggers has become very significant as this can help us in the fields of commerce, advertisement and product knowledge searching. Existing approaches consider some basic features, but lack to consider some other features like the importance of the blog on which the post has been created. This paper presents a new metric, MIIB (Metric for Identification of Influential Bloggers), based on various features of bloggers' productivity and popularity. Productivity refers to bloggers' blogging activity and popularity measures bloggers' influence in the blogging community. The novel module of BlogRank depicts the importance of blog sites where bloggers create their posts. The MIIB has been evaluated against the standard model and existing metrics for finding the influential bloggers using dataset from the real-world blogosphere. The obtained results confirm that the MIIB is able to find the most influential bloggers in a more effective manner.

  12. Identifying transboundary aquifers in need of international resource management in the Southern African Development Community region

    NASA Astrophysics Data System (ADS)

    Davies, Jeff; Robins, Nick S.; Farr, John; Sorensen, James; Beetlestone, Philip; Cobbing, Jude E.

    2013-03-01

    Transboundary aquifer (TBA) management, in part, seeks to mitigate degradation of groundwater resources caused either by an imbalance of abstraction between countries or by cross-border pollution. Fourteen potential TBAs were identified within a hydrogeological mapping programme based on simple hydrogeological selection criteria for the Southern African Development Community (SADC) region. These have been reassessed against a set of data associated with five categories: (1) groundwater flow and vulnerability (which is perceived as the over-arching influence on the activity level of each TBA), (2) knowledge and understanding, (3) governance capability, (4) socio-economic/water-demand factors, and (5) environmental issues. These assessments enable the TBAs to be classified according to their need for cross-border co-operation and management. The study shows that only two of the 14 TBAs have potential to be the cause of tension between neighbouring states, while nine are potentially troublesome and three are unlikely to become problematic even in the future. The classification highlights the need to focus on data gathering to enable improved understanding of the TBAs that could potentially become troublesome in the future due to, for example, change in demographics and climate.

  13. Mountain Pine Beetles Colonizing Historical and Naïve Host Trees Are Associated with a Bacterial Community Highly Enriched in Genes Contributing to Terpene Metabolism

    PubMed Central

    Adams, Aaron S.; Aylward, Frank O.; Adams, Sandye M.; Erbilgin, Nadir; Aukema, Brian H.; Currie, Cameron R.

    2013-01-01

    The mountain pine beetle, Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta, and their more recent host, hybrid P. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas, Rahnella, Serratia, and Burkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment. PMID:23542624

  14. Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism.

    PubMed

    Adams, Aaron S; Aylward, Frank O; Adams, Sandye M; Erbilgin, Nadir; Aukema, Brian H; Currie, Cameron R; Suen, Garret; Raffa, Kenneth F

    2013-06-01

    The mountain pine beetle, Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta, and their more recent host, hybrid P. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas, Rahnella, Serratia, and Burkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.

  15. Characterization of host-dependent mutations of apple fruit crinkle viroid replicating in newly identified experimental hosts suggests maintenance of stem-loop structures in the left-hand half of the molecule is important for replication.

    PubMed

    Suzuki, Takahiro; Fujibayashi, Misato; Hataya, Tatsuji; Taneda, Akito; He, Ying-Hong; Tsushima, Taro; Duraisamy, Ganesh Selvaraj; Siglová, Kristyna; Matoušek, Jaroslav; Sano, Teruo

    2017-03-01

    Apple fruit crinkle viroid (AFCVd) is a tentative member of the genus Apscaviroid, family Pospiviroidae. AFCVd has a narrow host range and is known to infect apple, hop and persimmon as natural hosts. In this study, tomato, cucumber and wild hop have been identified as new experimental herbaceous hosts. Foliar symptoms were very mild or virtually undetectable, but fruits of infected tomato were small, cracked and distorted. These symptoms resemble those observed on some AFCVd-sensitive apple cultivars. After transfer to tomato, cucumber and wild hop, sequence changes were detected in a natural AFCVd isolate from hop, and major variants in tomato, cucumber and wild hop differed in 10, 8 or 2 nucleotides, respectively, from the predominant one in the inoculum. The major variants in tomato and cucumber were almost identical, and the one in wild hop was very similar to the one in cultivated hop. Detailed analyses of the host-dependent sequence changes that appear in a naturally occurring AFCVd isolate from hop after transfer to tomato using small RNA deep sequence data and infectivity studies with dimeric RNA transcripts followed by progeny analysis indicate that the major AFCVd variant in tomato emerged by selection of a minor variant present in the inoculum (i.e. hop) followed by one to two host-dependent de novo mutations. Comparison of the secondary structures of major variants in hop, tomato and persimmon after transfer to tomato suggested that maintenance of stem-loop structures in the left-hand half of the molecule is critical for infection.

  16. Cholesterol gallstones and bile host diverse bacterial communities with potential to promote the formation of gallstones.

    PubMed

    Peng, Yuhong; Yang, Yang; Liu, Yongkang; Nie, Yuanyang; Xu, Peilun; Xia, Baixue; Tian, Fuzhou; Sun, Qun

    2015-01-01

    The prevalence of cholesterol gallstones has increased in recent years. Bacterial infection correlates with the formation of gallstones. We studied the composition and function of bacterial communities in cholesterol gallstones and bile from 22 cholesterol gallstone patients using culture-dependent and culture-independent methods. Altogether fourteen and eight bacterial genera were detected in cholesterol gallstones and bile, respectively. Pseudomonas spp. were the dominant bacteria in both cholesterol gallstones and bile. As judged by diversity indices, hierarchical clustering and principal component analysis, the bacterial communities in gallstones were different from those in bile. The gallstone microbiome was considered more stable than that of bile. The different microbial communities may be partially explained by differences in their habitats. We found that 30% of the culturable strains from cholesterol gallstones secreted β-glucuronidase and phospholipase A2. Pseudomonas aeruginosa strains showed the highest β-glucuronidase activity and produced the highest concentration of phospholipase A2, indicating that Ps. aeruginosa may be a major agent in the formation of cholesterol gallstones.

  17. Novel high throughput pooled shRNA screening identifies NQO1 as a potential drug target for host directed therapy for tuberculosis

    PubMed Central

    Li, Qing; Karim, Ahmad F.; Ding, Xuedong; Das, Biswajit; Dobrowolski, Curtis; Gibson, Richard M.; Quiñones-Mateu, Miguel E.; Karn, Jonathan; Rojas, Roxana E.

    2016-01-01

    Chemical regulation of macrophage function is one key strategy for developing host-directed adjuvant therapies for tuberculosis (TB). A critical step to develop these therapies is the identification and characterization of specific macrophage molecules and pathways with a high potential to serve as drug targets. Using a barcoded lentivirus-based pooled short-hairpin RNA (shRNA) library combined with next generation sequencing, we identified 205 silenced host genes highly enriched in mycobacteria-resistant macrophages. Twenty-one of these “hits” belonged to the oxidoreductase functional category. NAD(P)H:quinone oxidoreductase 1 (NQO1) was the top oxidoreductase “hit”. NQO1 expression was increased after mycobacterial infection, and NQO1 knockdown increased macrophage differentiation, NF-κB activation, and the secretion of pro-inflammatory cytokines TNF-α and IL-1β in response to infection. This suggests that mycobacteria hijacks NQO1 to down-regulate pro-inflammatory and anti-bacterial functions. The competitive inhibitor of NQO1 dicoumarol synergized with rifampin to promote intracellular killing of mycobacteria. Thus, NQO1 is a new host target in mycobacterial infection that could potentially be exploited to increase antibiotic efficacy in vivo. Our findings also suggest that pooled shRNA libraries could be valuable tools for genome-wide screening in the search for novel druggable host targets for adjunctive TB therapies. PMID:27297123

  18. Symbiotic bacterial communities in ants are modified by invasion pathway bottlenecks and alter host behavior.

    PubMed

    Lester, Philip J; Sébastien, Alexandra; Suarez, Andrew V; Barbieri, Rafael F; Gruber, Monica A M

    2017-03-01

    Biological invasions are a threat to global biodiversity and provide unique opportunities to study ecological processes. Population bottlenecks are a common feature of biological invasions and the severity of these bottlenecks is likely to be compounded as an invasive species spreads from initial invasion sites to additional locations. Despite extensive work on the genetic consequences of bottlenecks, we know little about how they influence microbial communities of the invaders themselves. Due to serial bottlenecks, invasive species may lose microbial symbionts including pathogenic taxa (the enemy release hypothesis) and/or may accumulate natural enemies with increasing time after invasion (the pathogen accumulation and invasive decline hypothesis). We tested these alternate hypotheses by surveying bacterial communities of Argentine ants (Linepithema humile). We found evidence for serial symbiont bottlenecks: the bacterial community richness declined over the invasion pathway from Argentina to New Zealand. The abundance of some genera, such as Lactobacillus, also significantly declined over the invasion pathway. Argentine ants from populations in the United States shared the most genera with ants from their native range in Argentina, while New Zealand shared the least (120 vs. 57, respectively). Nine genera were present in all sites around the globe possibly indicating a core group of obligate microbes. In accordance with the pathogen accumulation and invasive decline hypothesis, Argentine ants acquired genera unique to each specific invaded country. The United States had the most unique genera, though even within New Zealand these ants acquired symbionts. In addition to our biogeographic sampling, we administered antibiotics to Argentine ants to determine if changes in the micro-symbiont community could influence behavior and survival in interspecific interactions. Treatment with the antibiotics spectinomycin and kanamycin only slightly increased Argentine ant

  19. Identifying What Matters to Students: Improving Satisfaction and Defining Priorities at Santa Fe Community College

    ERIC Educational Resources Information Center

    Kress, Anne M.

    2006-01-01

    This chapter describes Santa Fe Community College's use of the Noel-Levitz Student Satisfaction Inventory to guide iterative development of institutional improvements associated with student satisfaction.

  20. Fish population studies using parasites from the Southeastern Pacific Ocean: considering host population changes and species body size as sources of variability of parasite communities.

    PubMed

    George-Nascimento, Mario; Oliva, Marcelo

    2015-01-01

    Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

  1. Richmond Latino needs assessment: a community-university partnership to identify health concerns and service needs for Latino youth.

    PubMed

    Corona, Rosalie; Gonzalez, Tanya; Cohen, Robert; Edwards, Charlene; Edmonds, Torey

    2009-06-01

    The presence of Latinos in Virginia is a new phenomenon and as a result, less is known about the health needs of these newest community members. We formed a community-university partnership to identify health concerns and service needs as they relate to Latino youth living in Richmond, Virginia and the surrounding area. Using a mixed-method approach, survey data was obtained from 212 Latino adults, qualitative interviews were conducted with 15 community leaders and focus groups with 23 Latino parents (16 mothers, 7 fathers) and 6 Latino boys. Participants expressed concern about sexually transmitted infections/pregnancy among youth (76%), youth behavior problems at home/school (75%), and mental health problems (75%). Participants also expressed worry that youth would lose their connection to their Latin culture (83%). Qualitative data provided more information regarding these concerns by linking them with inter-ethnic tensions, and immigration and acculturation-related stressors. Survey participants also indicated a need for bilingual mental health services (88%) and after-school programs for youth (94%). This study provided the local community with information on the health concerns and service needs of a new group of community youth-Latino youth. Findings were presented to local community and City organizations that used the information to respond to the identified needs and/or concerns. The process in which the data was obtained may prove useful to other individuals interested in obtaining local level health information in emerging communities.

  2. Changes in deep-sea carbonate-hosted microbial communities associated with high and low methane flux

    NASA Astrophysics Data System (ADS)

    Case, D. H.; Steele, J. A.; Chadwick, G.; Mendoza, G. F.; Levin, L. A.; Orphan, V. J.

    2012-12-01

    Methane seeps on continental shelves are rich in authigenic carbonates built of methane-derived carbon. These authigenic carbonates are home to micro- and macroscopic communities whose compositions are thus far poorly constrained but are known to broadly depend on local methane flux. The formation of authigenic carbonates is itself a result of microbial metabolic activity, as associations of anaerobic methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB) in the sediment subsurface increase both dissolved inorganic carbon (DIC) and alkalinity in pore waters. This 1:1 increase in DIC and alkalinity promotes the precipitation of authigenic carbonates. In this study, we performed in situ manipulations to test the response of micro- and macrofaunal communities to a change in methane flux. Methane-derived authigenic carbonates from two locations at Hydrate Ridge, OR, USA (depth range 595-604 mbsl), were transplanted from "active" cold seep sites (high methane flux) to "inactive" background sites (low methane flux), and vise versa, for one year. Community diversity surveys using T-RFLP and 16S rRNA clone libraries revealed how both bacterial and archaeal assemblages respond to this change in local environment, specifically demonstrating reproducible shifts in different ANME groups (ANME-1 vs. ANME-2). Animal assemblage composition also shifted during transplantation; gastropod representation increased (relative to control rocks) when substrates were moved from inactive to active sites and polychaete, crustacean and echinoderm representation increased when substrates were moved from active to inactive sites. Combined with organic and inorganic carbon δ13C measurements and mineralogy, this unique in situ experiment demonstrates that authigenic carbonates are viable habitats, hosting microbial and macrofaunal communities capable of responding to changes in external environment over relatively short time periods.

  3. Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy).

    PubMed

    Quéméneur, Marianne; Palvadeau, Alexandra; Postec, Anne; Monnin, Christophe; Chavagnac, Valérie; Ollivier, Bernard; Erauso, Gaël

    2015-09-01

    The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2% of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/'Serpentinomonas', respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems.

  4. Whole genome sequencing to identify host genetic risk factors for severe outcomes of hepatitis a virus infection.

    PubMed

    Long, Dustin; Fix, Oren K; Deng, Xutao; Seielstad, Mark; Lauring, Adam S

    2014-10-01

    Acute liver failure is a severe, but rare, outcome of hepatitis A virus infection. Unusual presentations of prevalent infections have often been attributed to pathogen-specific immune deficits that exhibit Mendelian inheritance. Genome-wide resequencing of unrelated cases has proven to be a powerful approach for identifying highly penetrant risk alleles that underlie such syndromes. Rare mutations likely to affect protein expression or function can be identified from sequence data, and their association with a similarly rare phenotype rests on their existence in multiple affected individuals. A rare or novel sequence variant that is enriched to a significant degree in a genetically diverse cohort suggests a candidate susceptibility allele. Whole genome sequencing of ten individuals from ethnically diverse backgrounds with HAV-associated acute liver failure was performed. A set of rational filtering criteria was used to identify genetic variants that are rare in the population, but enriched in this cohort. Single nucleotide polymorphisms, insertions, and deletions were considered and autosomal dominant, autosomal recessive, and polygenic models were applied. Analysis of the protein-coding exome identified no single gene with putatively deleterious mutations shared by multiple individuals, arguing against a simple Mendelian model of inheritance. A number of rare variants were significantly enriched in this cohort, consistent with a complex and genetically heterogeneous trait. Several of the variants identified in this genome-wide study lie within genes important to hepatic pathophysiology and are candidate susceptibility alleles for hepatitis A virus infection.

  5. Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

    PubMed Central

    Silva, Joana C.; Cornillot, Emmanuel; McCracken, Carrie; Usmani-Brown, Sahar; Dwivedi, Ankit; Ifeonu, Olukemi O.; Crabtree, Jonathan; Gotia, Hanzel T.; Virji, Azan Z.; Reynes, Christelle; Colinge, Jacques; Kumar, Vidya; Lawres, Lauren; Pazzi, Joseph E.; Pablo, Jozelyn V.; Hung, Chris; Brancato, Jana; Kumari, Priti; Orvis, Joshua; Tretina, Kyle; Chibucos, Marcus; Ott, Sandy; Sadzewicz, Lisa; Sengamalay, Naomi; Shetty, Amol C.; Su, Qi; Tallon, Luke; Fraser, Claire M.; Frutos, Roger; Molina, Douglas M.; Krause, Peter J.; Ben Mamoun, Choukri

    2016-01-01

    Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution. PMID:27752055

  6. Using Institutional Data to Identify Students at Risk for Leaving Community College: An Event History Approach

    ERIC Educational Resources Information Center

    Bachler, Paul T.

    2013-01-01

    Community colleges have been criticized for having lower graduation rates than four year colleges, but few studies have looked at non-graduation transfer, in which a student leaves the community college for a four-year college without taking an associate degree. The current study utilizes institutional data and a discrete-time event history model…

  7. Identifying Factors That Encourage and Hinder Knowledge Sharing in a Longstanding Online Community of Practice

    ERIC Educational Resources Information Center

    Hew, Khe Foon; Hara, Noriko

    2006-01-01

    Despite the strong interests among practitioners, there is a knowledge gap with regard to online communities of practice. This study examines knowledge sharing among critical-care and advanced-practice nurses, who are engaged in a longstanding online community of practice. Data were collected about members' online knowledge contribution as well as…

  8. Molecular evidence indicates that subarctic willow communities in Scotland support a diversity of host-associated Melampsora rust taxa.

    PubMed

    Milne, Jeremy M; Helfer, Stephan; Kirk, Calum; Hollingsworth, Peter M; Ennos, Richard A

    2012-05-01

    Rare and threatened subarctic willow scrub communities in the UK are the subject of ongoing conservation programmes, yet little is known about the diversity of fungal taxa that they support. Isolates of the rust genus Melampsora were sampled from 112 leaves of eight subarctic willow (Salix) taxa and their hybrids from twelve sites in the UK. In order to determine the number of Melampsora taxa present in the samples, isolates were sequenced for the Internal Transcribed Spacer (ITS) region of rDNA and data were subject to phylogenetic analysis. Maximum likelihood and Bayesian analysis indicated that the isolates fell into three strongly supported host-associated clades. Clade I contained only isolates from Salix herbacea and was distinguished morphologically by dense urediniospore echinulation and thin cell walls. Clade II contained isolates from Salix arbuscula and Salix reticulata only. These could not be distinguished morphologically from isolates in Clade III which were found on Salix lapponum, Salix myrsinites, Salix myrsinifolia, Salix aurita, Salix lanata, and their hybrids. Clade II was most distinct in ITS sequence, differing by 50 bases from Clades I and III, while the latter clades differed in sequence by only 24 bases on average. Clades I and III are likely to represent the previously recognised taxa Melampsora alpina Juel 1894 and Melampsora epitea Thüm. 1879 respectively, but Clade II has not apparently been described before. Significant differences in the intensity of infection by isolates of Clade III were found among different Salix species at a single site, suggesting either differences in resistance among Salix taxa, or the presence of further cryptic taxa within Clade III. The study illustrates the power of molecular phylogenetic analysis to reveal cryptic biodiversity within Melampsora, and suggests that conserving Salix host diversity within subarctic willow communities will ensure that a diversity of associated Melampsora taxa is maintained.

  9. Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

    PubMed Central

    Brazelton, William J.; Nelson, Bridget; Schrenk, Matthew O.

    2012-01-01

    Ultramafic rocks in the Earth’s mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). In order to assess the potential for microbial H2 utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H2-oxidizers. Both sites also yielded metagenomic evidence for microbial H2 production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood–Ljungdahl pathway. In general, our results point to H2-oxidizing Betaproteobacteria thriving in shallow, oxic–anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H2-powered primary production in serpentinite-hosted subsurface habitats. PMID:22232619

  10. Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar.

    PubMed

    Tedersoo, Leho; Bahram, Mohammad; Jairus, Teele; Bechem, Eneke; Chinoya, Stephen; Mpumba, Rebecca; Leal, Miguel; Randrianjohany, Emile; Razafimandimbison, Sylvain; Sadam, Ave; Naadel, Triin; Kõljalg, Urmas

    2011-07-01

    Mycorrhizal fungi play a key role in mineral nutrition of terrestrial plants, but the factors affecting natural distribution, diversity and community composition of particularly tropical fungi remain poorly understood. This study addresses shifts in community structure and species frequency of ectomycorrhizal (EcM) fungi in relation to host taxa, soil depth and spatial structure in four contrasting African ecosystems. We used the rDNA and plastid trnL intron sequence analysis for identification of fungi and host plants, respectively. By partitioning out spatial autocorrelation in plant and fungal distribution, we suggest that African EcM fungal communities are little structured by soil horizon and host at the plant species and family levels. These findings contrast with patterns of vegetation in these forests and EcM fungal communities in other tropical and temperate ecosystems. The low level of host preference indirectly supports an earlier hypothesis that pioneer Phyllanthaceae may facilitate the establishment of late successional Fabaceae and potentially other EcM host trees by providing compatible fungal inoculum in deforested and naturally disturbed ecosystems of tropical Africa.

  11. Can Community Members Identify Tropical Tree Species for REDD+ Carbon and Biodiversity Measurements?

    PubMed Central

    Zhao, Mingxu; Brofeldt, Søren; Li, Qiaohong; Xu, Jianchu; Danielsen, Finn; Læssøe, Simon Bjarke Lægaard; Poulsen, Michael Køie; Gottlieb, Anna

    2016-01-01

    Biodiversity conservation is a required co-benefit of REDD+. Biodiversity monitoring is therefore needed, yet in most areas it will be constrained by limitations in the available human professional and financial resources. REDD+ programs that use forest plots for biomass monitoring may be able to take advantage of the same data for detecting changes in the tree diversity, using the richness and abundance of canopy trees as a proxy for biodiversity. If local community members are already assessing the above-ground biomass in a representative network of forest vegetation plots, it may require minimal further effort to collect data on the diversity of trees. We compare community members and trained scientists’ data on tree diversity in permanent vegetation plots in montane forest in Yunnan, China. We show that local community members here can collect tree diversity data of comparable quality to trained botanists, at one third the cost. Without access to herbaria, identification guides or the Internet, community members could provide the ethno-taxonomical names for 95% of 1071 trees in 60 vegetation plots. Moreover, we show that the community-led survey spent 89% of the expenses at village level as opposed to 23% of funds in the monitoring by botanists. In participatory REDD+ programs in areas where community members demonstrate great knowledge of forest trees, community-based collection of tree diversity data can be a cost-effective approach for obtaining tree diversity information. PMID:27814370

  12. Can Community Members Identify Tropical Tree Species for REDD+ Carbon and Biodiversity Measurements?

    PubMed

    Zhao, Mingxu; Brofeldt, Søren; Li, Qiaohong; Xu, Jianchu; Danielsen, Finn; Læssøe, Simon Bjarke Lægaard; Poulsen, Michael Køie; Gottlieb, Anna; Maxwell, James Franklin; Theilade, Ida

    2016-01-01

    Biodiversity conservation is a required co-benefit of REDD+. Biodiversity monitoring is therefore needed, yet in most areas it will be constrained by limitations in the available human professional and financial resources. REDD+ programs that use forest plots for biomass monitoring may be able to take advantage of the same data for detecting changes in the tree diversity, using the richness and abundance of canopy trees as a proxy for biodiversity. If local community members are already assessing the above-ground biomass in a representative network of forest vegetation plots, it may require minimal further effort to collect data on the diversity of trees. We compare community members and trained scientists' data on tree diversity in permanent vegetation plots in montane forest in Yunnan, China. We show that local community members here can collect tree diversity data of comparable quality to trained botanists, at one third the cost. Without access to herbaria, identification guides or the Internet, community members could provide the ethno-taxonomical names for 95% of 1071 trees in 60 vegetation plots. Moreover, we show that the community-led survey spent 89% of the expenses at village level as opposed to 23% of funds in the monitoring by botanists. In participatory REDD+ programs in areas where community members demonstrate great knowledge of forest trees, community-based collection of tree diversity data can be a cost-effective approach for obtaining tree diversity information.

  13. Apparent competition drives community-wide parasitism rates and changes in host abundance across ecosystem boundaries

    PubMed Central

    Frost, Carol M.; Peralta, Guadalupe; Rand, Tatyana A.; Didham, Raphael K.; Varsani, Arvind; Tylianakis, Jason M.

    2016-01-01

    Species have strong indirect effects on others, and predicting these effects is a central challenge in ecology. Prey species sharing an enemy (predator or parasitoid) can be linked by apparent competition, but it is unknown whether this process is strong enough to be a community-wide structuring mechanism that could be used to predict future states of diverse food webs. Whether species abundances are spatially coupled by enemy movement across different habitats is also untested. Here, using a field experiment, we show that predicted apparent competitive effects between species, mediated via shared parasitoids, can significantly explain future parasitism rates and herbivore abundances. These predictions are successful even across edges between natural and managed forests, following experimental reduction of herbivore densities by aerial spraying of insecticide over 20 hectares. This result shows that trophic indirect effects propagate across networks and habitats in important, predictable ways, with implications for landscape planning, invasion biology and biological control. PMID:27577948

  14. NERSC 'Visualization Greenbook' Future visualization needs of the DOE computational science community hosted at NERSC

    SciTech Connect

    Hamann, Bernd; Bethel, E. Wes; Simon, Horst; Meza, Juan

    2002-11-04

    This report presents the findings and recommendations that emerged from a one-day workshop held at Lawrence Berkeley National Laboratory (LBNL) on June 5, 2002, in conjunction with the NERSC User Group (NUG) Meeting. The motivation for this workshop was to solicit direct input from the application science community on the subject of visualization. The workshop speakers and participants included computational scientists from a cross-section of disciplines that use the NERSC facility, as well as visualization researchers from across the country. We asked the workshop contributors how they currently visualize their results, and how they would like to do visualization in the future. We were especially interested in each individual's view of how visualization tools and services could be improved in order to better meet the needs of future computational science projects. The outcome of this workshop is a set of findings and recommendations that are presented in more detail later in this report, and briefly summarized here.

  15. Using Community-Based Participatory Research to Prevent HIV Disparities: Assumptions and Opportunities Identified by The Latino Partnership

    PubMed Central

    Rhodes, Scott D.; Duck, Stacy; Alonzo, Jorge; Daniel-Ulloa, Jason; Aronson, Robert E.

    2013-01-01

    Background HIV disproportionately affects vulnerable populations in the United States (US), including recently arrived immigrant Latinos. However, the current arsenal of effective approaches to increase adherence to risk-reduction strategies and treatment within Latino populations remains insufficient. Methods Our community-based participatory research (CBPR) partnership blends multiple perspectives of community members, organizational representatives, local business leaders, and academic researchers to explore and intervene on HIV risk within Latino populations. We used CBPR to develop, implement, and evaluate two interventions that were found to be efficacious. Results We identified seven assumptions of CBPR as an approach to research, including more authentic study designs, stronger measurement, and improved quality of knowledge gained; increased community capacity to tackle other health disparities; the need to focus on community priorities; increased participation and retention rates; more successful interventions; reduced generalizability; and increased sustainability. Conclusions Despite the advancement of CBPR as an approach to research, key assumptions remain. Further research is needed to compare CBPR to other more traditional approaches to research. Such research would move us from assuming the value of CBPR to identifying its actual value in health disparity reduction. After all, communities carrying disproportionate burden of HIV, including immigrant Latino communities, deserve the best science possible. PMID:23673883

  16. Clinical impact of the use of 16S rRNA sequencing method for the identification of "difficult-to-identify" bacteria in immunocompromised hosts.

    PubMed

    Bharadwaj, R; Swaminathan, S; Salimnia, H; Fairfax, M; Frey, A; Chandrasekar, P H

    2012-04-01

    Molecular method of 16S rRNA sequencing is reported to be helpful in the accurate identification of organisms with ambiguous phenotypic profiles. We analyzed the use of 16S rRNA sequencing method to identify clinically significant, "difficult-to-identify" bacteria recovered from clinical specimens, and evaluated its role in patient management and consequent clinical outcome. Among the 172 "difficult-to-identify" bacteria recovered over a 4-year period, 140 were gram-positive cocci or gram-negative bacilli; identification by 16S rRNA did not play a role in the management of patients infected with these bacteria. From 32 patients, 33 "difficult-to-identify" gram-positive bacilli were identified; the organisms were mycobacteria, Nocardia, Tsukamurella, Rhodococcus, and Gordonia. In 24 patients for whom clinical data were available, results from the 16S rRNA sequencing method led to treatment change in 14 immunocompromised patients (including 7 hematopoietic stem cell recipients and 1 liver transplant recipient). Therapy was modified in 9 patients, initiated in 3 patients, and discontinued in 2 patients. Most patients' therapy was switched to oral antibiotics with discontinuation of intravascular catheters, facilitating early hospital discharge. All 14 patients were alive 30 days after infection onset. The present study demonstrates the clinical application of 16S rRNA sequencing method to identify "difficult-to-identify" mycobacteria and other gram-positive bacilli in clinical specimens, particularly in immunocompromised hosts.

  17. Identifying and Caring for Rare Books in the Community or Junior College with No Special Collections Department.

    ERIC Educational Resources Information Center

    Visser, Michelle

    2003-01-01

    Discusses issues of identifying, storing, handling, and providing access to rare books and materials in institutions without special collections departments. Suggests that although many community colleges do not collect rare materials, they may nonetheless be in possession of books that are rare and that should receive special care. (ontains four…

  18. Lessons Learned from the Niger Delta Conflict: A Policy Recommendation for a New Framework for Relations Between Extractive Companies and Host Communities

    NASA Astrophysics Data System (ADS)

    Gilman, Alison

    The tumultuous experience of the Shell Petroleum Development Company of Nigeria Ltd (SPDC) in the Niger Delta region of Nigeria has contributed to the debates surrounding the role of transnational companies in their host communities and the impact that resource extraction has on the economic development of emerging countries. The case study demonstrates that methods used by extraction companies for interacting with their host communities are ineffective and superficial. Using the lessons learned from the Niger Delta conflict, this thesis proposes a new strategy, entitled community- corporate diplomacy, and a protocol for companies to implement before opening production sites in Africa. The proposed strategy and an accompanying protocol offer a break from the status quo in that they are built upon an understanding of the specificities of the African continent, that host communities need to be respected as key stakeholders, and that extraction activities have a higher risk of negatively impacting neighboring communities. The recommendation could be applied to other countries and industries, but the increasing importance of African natural resources, the particularities of African political and social structures and the effects of extraction activities make this proposal especially important for extractive companies beginning production in Africa. Keywords: Nigeria, Niger Delta, Shell, corporate social responsibility, transnational advocacy networks, multi-stakeholder initiatives, community relations, corporate diplomacy, Africa, extractive industries.

  19. Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities.

    PubMed

    Taschen, Elisa; Sauve, Mathieu; Taudiere, Adrien; Parlade, Javier; Selosse, Marc-André; Richard, Franck

    2015-08-01

    In the Mediterranean region, patches of vegetation recovering from disturbance and transiently dominated by shrubs produce one of the world's most prized fungi, the black truffle (Tuber melanosporum). In these successional plant communities, we have fragmentary knowledge of the distribution of T. melanosporum in space among ectomycorrhizal (ECM) host species and in time. Molecular identification of hosts (Restriction Fragment Length Polymorphism) and fungi (Internal Transcribed Spacer sequencing) and quantification of T. melanosporum mycelium (quantitative Polymerase Chain Reaction) were employed to evaluate the presence of T. melanosporum on four dominant ECM host species (Quercus ilex, Quercus  coccifera, Arbutus unedo, Cistus albidus) and the extent to which their respective ECM communities shared fungal diversity, over the course of development of truffle grounds, from recent unproductive brûlés to senescent ones where production has stopped. We found that truffle grounds host rich communities in which multi-host fungal species dominate in frequency. When considering both ECM tips and soil mycelia, we documented a dynamic and spatially heterogeneous pattern of T. melanosporum distribution in soils and a presence of ECM tips restricted to Q. ilex roots. This study advances our knowledge of the ecology of T. melanosporum, and provides insight into the extent of ECM fungal sharing among plant species that dominate Mediterranean landscapes.

  20. A study to identify winning strategies for the business community during the next pandemic.

    PubMed

    Spriggs, Martin

    2013-01-01

    This study examines the relationship between the healthcare system and the corporate sector to answer the following research question: how does the healthcare system best prepare small to medium-sized businesses for the next pandemic influenza? Data were collected and collated through a literature review, electronic survey and semi-structured follow-up telephone interviews. The participants were businesses with membership in the Alberta Chambers of Commerce, a provincial lobby group in Alberta, Canada. The findings indicate strategies that were effective in minimising impact to the business community during the H1N1 pandemic and suggest areas for the business community to improve in preparation for the next pandemic influenza. Recommendations focus on establishing new links for communication between the business community and the healthcare sector and improving strategies to increase the resilience of small to medium-sized businesses for the next pandemic influenza.

  1. Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments

    PubMed Central

    Lladó, Salvador; Baldrian, Petr

    2017-01-01

    Community-level physiological profiling (CLPP) analyses from very diverse environments are frequently used with the aim of characterizing the metabolic versatility of whole environmental bacterial communities. While the limitations of the methodology for the characterization of whole communities are well known, we propose that CLPP combined with high-throughput sequencing and qPCR can be utilized to identify the copiotrophic, fast-growing fraction of the bacterial community of soil environments, where oligotrophic taxa are usually dominant. In the present work we have used this approach to analyze samples of litter and soil from a coniferous forest in the Czech Republic using BIOLOG GN2 plates. Monosaccharides and amino acids were utilized significantly faster than other C substrates, such as organic acids, in both litter and soil samples. Bacterial biodiversity in CLPP wells was significantly lower than in the original community, independently of the carbon source. Bacterial communities became highly enriched in taxa that typically showed low abundance in the original soil, belonging mostly to the Gammaproteobacteria and the genus Pseudomonas, indicating that the copiotrophic strains, favoured by the high nutrient content, are rare in forest litter and soil. In contrast, taxa abundant in the original samples were rarely found to grow at sufficient rates under the CLPP conditions. Our results show that CLPP is useful to detect copiotrophic bacteria from the soil environments and that bacterial growth is substrate specific. PMID:28170446

  2. Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

    SciTech Connect

    Schryver, Jack C.; Brandt, Craig C.; Pfiffner, Susan M.; Palumbo, A V.; Peacock, Aaron D.; White, David C.; McKinley, James P.; Long, Philip E.

    2006-02-01

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

  3. The Counselor as a Social Force: Identifying Counselor Role and Functions in the Community College.

    ERIC Educational Resources Information Center

    Whitehead, Everett

    School counselors face identity crises since they must respond to the conflicting demands of students, faculty members, administrators, commercial and industrial interests, parents, and the local community. In order to defend themselves against public criticism, counselors must find a way of illustrating their effectiveness. Data obtained from an…

  4. Developing and Sustaining a Healthy School Community: Essential Elements Identified by School Health Champions

    ERIC Educational Resources Information Center

    Stolp, Sean; Wilkins, Emma; Raine, Kim D.

    2015-01-01

    Background: Comprehensive School Health (CSH) approaches to developing a healthy school community can be effective in supporting chronic disease prevention while positively impacting on student behaviour and academic performance. Although a CSH framework provides principles for action, there is a lack of evidence regarding the processes that best…

  5. Connecting Classrooms & Communities: Identifying Student Needs & Assets Inside & Outside of School

    ERIC Educational Resources Information Center

    Favela, Alejandra; Torres, Danielle

    2014-01-01

    This article provides suggestions to tap cultural assets and establish links between school personnel and community resources in order to support low income and minority students. The authors are faculty members from different graduate programs who co-teach in order to model collaborative practice for pre-service teachers and school counselors.…

  6. Student Engagement and Institutional Graduation Rates: Identifying High-Impact Educational Practices for Community Colleges

    ERIC Educational Resources Information Center

    Price, Derek V.; Tovar, Esau

    2014-01-01

    Philanthropists, researchers, policymakers, and practitioners are increasingly focused on a college completion crisis in the United States. Collectively and independently, they have called for increasing the number of adults with postsecondary certificates and degrees as a national imperative. Using the 2007 administration of the Community College…

  7. Application of nonlinear analysis methods for identifying relationships between microbial community structure and groundwater geochemistry.

    PubMed

    Schryver, Jack C; Brandt, Craig C; Pfiffner, Susan M; Palumbo, Anthony V; Peacock, Aaron D; White, David C; McKinley, James P; Long, Philip E

    2006-02-01

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

  8. How Communities and American Indian Parents Can Identify and Remove Culturally Biased Books from Schools.

    ERIC Educational Resources Information Center

    Robbins, Rebecca

    Removal from the schools of educational material objectionable to American Indians is a matter of concern to teachers, parents, Indian communities and organizations, and educational decision makers. To appeal to a wider market, publishers often produce materials favoring the interests of the predominant society. Thus, textbooks and other…

  9. Identifying Churches for Community-Based Mammography Promotion: Lessons from the LAMP Study

    ERIC Educational Resources Information Center

    Duan, Naihua; Fox, Sarah; Derose, Kathryn Pitkin; Carson, Sally; Stockdale, Susan

    2005-01-01

    There is great potential in public health and faith communities partnering to promote health education and research. This article describes lessons learned from the design and implementation of such a partnership, the Los Angeles Mammography Promotion in Churches Program (LAMP). It is feasible, although challenging, to enumerate and survey…

  10. The Perfect Burrow, but for What? Identifying Local Habitat Conditions Promoting the Presence of the Host and Vector Species in the Kazakh Plague System

    PubMed Central

    Wilschut, Liesbeth; Addink, Elisabeth; Ageyev, Vladimir; Yeszhanov, Aidyn; Sapozhnikov, Valerij; Belayev, Alexander; Davydova, Tania; Eagle, Sally; Begon, Mike

    2015-01-01

    Introduction The wildlife plague system in the Pre-Balkhash desert of Kazakhstan has been a subject of study for many years. Much progress has been made in generating a method of predicting outbreaks of the disease (infection by the gram negative bacterium Yersinia pestis) but existing methods are not yet accurate enough to inform public health planning. The present study aimed to identify characteristics of individual mammalian host (Rhombomys opimus) burrows related to and potentially predictive of the presence of R.opimus and the dominant flea vectors (Xenopsylla spp.). Methods Over four seasons, burrow characteristics, their current occupancy status, and flea and tick burden of the occupants were recorded in the field. A second data set was generated of long term occupancy trends by recording the occupancy status of specific burrows over multiple occasions. Generalised linear mixed models were constructed to identify potential burrow properties predictive of either occupancy or flea burden. Results At the burrow level, it was identified that a burrow being occupied by Rhombomys, and remaining occupied, were both related to the characteristics of the sediment in which the burrow was constructed. The flea burden of Rhombomys in a burrow was found to be related to the tick burden. Further larger scale properties were also identified as being related to both Rhombomys and flea presence, including latitudinal position and the season. Conclusions Therefore, in advancing our current predictions of plague in Kazakhstan, we must consider the landscape at this local level to increase our accuracy in predicting the dynamics of gerbil and flea populations. Furthermore this demonstrates that in other zoonotic systems, it may be useful to consider the distribution and location of suitable habitat for both host and vector species at this fine scale to accurately predict future epizootics. PMID:26325073

  11. Identifying the core microbial community in the gut of fungus-growing termites.

    PubMed

    Otani, Saria; Mikaelyan, Aram; Nobre, Tânia; Hansen, Lars H; Koné, N'Golo A; Sørensen, Søren J; Aanen, Duur K; Boomsma, Jacobus J; Brune, Andreas; Poulsen, Michael

    2014-09-01

    Gut microbes play a crucial role in decomposing lignocellulose to fuel termite societies, with protists in the lower termites and prokaryotes in the higher termites providing these services. However, a single basal subfamily of the higher termites, the Macrotermitinae, also domesticated a plant biomass-degrading fungus (Termitomyces), and how this symbiont acquisition has affected the fungus-growing termite gut microbiota has remained unclear. The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus-growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. Using 454-pyrosequencing of the 16S rRNA gene, we show that gut communities have representatives of 26 bacterial phyla and are dominated by Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria and Synergistetes. A set of 42 genus-level taxa was present in all termite species and accounted for 56-68% of the species-specific reads. Gut communities of termites from the same genus were more similar than distantly related species, suggesting that phylogenetic ancestry matters, possibly in connection with specific termite genus-level ecological niches. Finally, we show that gut communities of fungus-growing termites are similar to cockroaches, both at the bacterial phylum level and in a comparison of the core Macrotermitinae taxa abundances with representative cockroach, lower termite and higher nonfungus-growing termites. These results suggest that the obligate association with Termitomyces has forced the bacterial gut communities of the fungus-growing termites towards a relatively uniform composition with higher similarity to their omnivorous relatives than to more closely related termites.

  12. Identifying Catchment-Scale Predictors of Coal Mining Impacts on New Zealand Stream Communities.

    PubMed

    Clapcott, Joanne E; Goodwin, Eric O; Harding, Jon S

    2016-03-01

    Coal mining activities can have severe and long-term impacts on freshwater ecosystems. At the individual stream scale, these impacts have been well studied; however, few attempts have been made to determine the predictors of mine impacts at a regional scale. We investigated whether catchment-scale measures of mining impacts could be used to predict biological responses. We collated data from multiple studies and analyzed algae, benthic invertebrate, and fish community data from 186 stream sites, including un-mined streams, and those associated with 620 mines on the West Coast of the South Island, New Zealand. Algal, invertebrate, and fish richness responded to mine impacts and were significantly higher in un-mined compared to mine-impacted streams. Changes in community composition toward more acid- and metal-tolerant species were evident for algae and invertebrates, whereas changes in fish communities were significant and driven by a loss of nonmigratory native species. Consistent catchment-scale predictors of mining activities affecting biota included the time post mining (years), mining density (the number of mines upstream per catchment area), and mining intensity (tons of coal production per catchment area). Mining was associated with a decline in stream biodiversity irrespective of catchment size, and recovery was not evident until at least 30 years after mining activities have ceased. These catchment-scale predictors can provide managers and regulators with practical metrics to focus on management and remediation decisions.

  13. Identifying Catchment-Scale Predictors of Coal Mining Impacts on New Zealand Stream Communities

    NASA Astrophysics Data System (ADS)

    Clapcott, Joanne E.; Goodwin, Eric O.; Harding, Jon S.

    2016-03-01

    Coal mining activities can have severe and long-term impacts on freshwater ecosystems. At the individual stream scale, these impacts have been well studied; however, few attempts have been made to determine the predictors of mine impacts at a regional scale. We investigated whether catchment-scale measures of mining impacts could be used to predict biological responses. We collated data from multiple studies and analyzed algae, benthic invertebrate, and fish community data from 186 stream sites, including un-mined streams, and those associated with 620 mines on the West Coast of the South Island, New Zealand. Algal, invertebrate, and fish richness responded to mine impacts and were significantly higher in un-mined compared to mine-impacted streams. Changes in community composition toward more acid- and metal-tolerant species were evident for algae and invertebrates, whereas changes in fish communities were significant and driven by a loss of nonmigratory native species. Consistent catchment-scale predictors of mining activities affecting biota included the time post mining (years), mining density (the number of mines upstream per catchment area), and mining intensity (tons of coal production per catchment area). Mining was associated with a decline in stream biodiversity irrespective of catchment size, and recovery was not evident until at least 30 years after mining activities have ceased. These catchment-scale predictors can provide managers and regulators with practical metrics to focus on management and remediation decisions.

  14. Multistep greedy algorithm identifies community structure in real-world and computer-generated networks

    NASA Astrophysics Data System (ADS)

    Schuetz, Philipp; Caflisch, Amedeo

    2008-08-01

    We have recently introduced a multistep extension of the greedy algorithm for modularity optimization. The extension is based on the idea that merging l pairs of communities (l>1) at each iteration prevents premature condensation into few large communities. Here, an empirical formula is presented for the choice of the step width l that generates partitions with (close to) optimal modularity for 17 real-world and 1100 computer-generated networks. Furthermore, an in-depth analysis of the communities of two real-world networks (the metabolic network of the bacterium E. coli and the graph of coappearing words in the titles of papers coauthored by Martin Karplus) provides evidence that the partition obtained by the multistep greedy algorithm is superior to the one generated by the original greedy algorithm not only with respect to modularity, but also according to objective criteria. In other words, the multistep extension of the greedy algorithm reduces the danger of getting trapped in local optima of modularity and generates more reasonable partitions.

  15. Use of a high-throughput screen to identify Leptospira mutants unable to colonize the carrier host or cause disease in the acute model of infection.

    PubMed

    Marcsisin, Renee A; Bartpho, Thanatchaporn; Bulach, Dieter M; Srikram, Amporn; Sermswan, Rasana W; Adler, Ben; Murray, Gerald L

    2013-10-01

    The molecular basis for leptospirosis infection and colonization remains poorly understood, with no efficient methods available for screening libraries of mutants for attenuation. We analysed the attenuation of leptospiral transposon mutants in vivo using a high-throughput method by infecting animals with pooled sets of transposon mutants. A total of 95 mutants was analysed by this method in the hamster model of acute infection, and one mutant was identified as attenuated (M1233, lb058 mutant). All virulence factors identified in Leptospira to date have been characterized in the acute model of infection, neglecting the carrier host. To address this, a BALB/c mouse colonization model was established. The lb058 mutant and two mutants defective in LPS synthesis were colonization deficient in the mouse model. By applying the high-throughput screening method, a further five colonization-deficient mutants were identified for the mouse model; these included two mutants in genes encoding proteins with a predicted role in iron uptake (LB191/HbpA and LB194). Two attenuated mutants had transposon insertions in either la0589 or la2786 (encoding proteins of unknown function). The final attenuated mutant had an unexpected deletion of genes la0969-la0975 at the point of transposon insertion. This is the first description of defined, colonization-deficient mutants in a carrier host for Leptospira. These mutants were either not attenuated or only weakly attenuated in the hamster model of acute leptospirosis, thus illustrating that different factors that may be required in the carrier and acute models of leptospiral infection. High-throughput screening can reduce the number of animals used in virulence studies and increase the capacity to screen mutants for attenuation, thereby enhancing the likelihood of detecting unique virulence factors. A comparison of virulence factors required in the carrier and acute models of infection will help to unravel colonization and dissemination

  16. Endophytic bacterial communities in three arctic plants from low arctic fell tundra are cold-adapted and host-plant specific.

    PubMed

    Nissinen, Riitta M; Männistö, Minna K; van Elsas, Jan Dirk

    2012-11-01

    Endophytic bacteria inhabit internal plant tissues, and have been isolated from a large diversity of plants, where they form nonpathogenic relationships with their hosts. This study combines molecular and culture-dependent approaches to characterize endophytic bacterial communities of three arcto-alpine plant species (Oxyria digyna, Diapensia lapponica and Juncus trifidus) sampled in the low Arctic (69°03'N). Analyses of a 325 bacterial endophyte isolates, as well as seven clone libraries, revealed a high diversity. In particular, members of the Actinobacteria, Bacteroidetes, Firmicutes, Acidobacteria, and Proteobacteria were found. The compositions of the endophytic bacterial communities were dependent on host-plant species as well as on snow cover at sampling sites. Several bacterial genera were found to be associated tightly with specific host-plant species. In particular, Sphingomonas spp. were characteristic for D. lapponica and O. digyna, and their phylogenetic grouping corresponded to the host plant. Most of the endophyte isolates grew well and retained activity at +4 °C, and isolate as well as clone library sequences were often highly similar to sequences from bacteria from cold environments. Taken together, this study shows that arctic plants harbour a diverse community of bacterial endophytes, a portion of which seems to be tightly associated with specific plant species.

  17. One fig to bind them all: host conservatism in a fig wasp community unraveled by cospeciation analyses among pollinating and nonpollinating fig wasps.

    PubMed

    Jousselin, Emmanuelle; van Noort, Simon; Berry, Vincent; Rasplus, Jean-Yves; Rønsted, Nina; Erasmus, J Christoff; Greeff, Jaco M

    2008-07-01

    The study of chalcid wasps that live within syconia of fig trees (Moraceae, Ficus), provides a unique opportunity to investigate the evolution of specialized communities of insects. By conducting cospeciation analyses between figs of section Galoglychia and some of their associated fig wasps, we show that, although host switches and duplication have evidently played a role in the construction of the current associations, the global picture is one of significant cospeciation throughout the evolution of these communities. Contrary to common belief, nonpollinating wasps are at least as constrained as pollinators by their host association in their diversification in this section. By adapting a randomization test in a supertree context, we further confirm that wasp phylogenies are significantly congruent with each other, and build a "wasp community" supertree that retrieves Galoglychia taxonomic subdivisions. Altogether, these results probably reflect wasp host specialization but also, to some extent, they might indicate that niche saturation within the fig prevents recurrent intrahost speciation and host switching. Finally, a comparison of ITS2 sequence divergence of cospeciating pairs of wasps suggests that the diversification of some pollinating and nonpollinating wasps of Galoglychia figs has been synchronous but that pollinating wasps exhibit a higher rate of molecular evolution.

  18. Response of a gall wasp community to genetic variation in the host plant Quercus crispula: a test using half-sib families

    NASA Astrophysics Data System (ADS)

    Ito, Masato; Ozaki, Kenichi

    2005-02-01

    The structure of a herbivore community may change consistently along the genetic cline of a host plant, change at particular points along the cline, or respond independently of the cline. To reveal such relationships between a gall wasp community and genetic variation in the host plant Quercus crispula, we examined patterns in the species richness and abundance of gall wasps along a genetic cline of the host plant, using 12 half-sib families from six different regions. The genetic relationships among the half-sib families of Q. crispula were quantified on the basis of leaf morphology, which represented a morphological cline from leaves typical of Q. crispula to leaves resembling another oak species, Q. dentata. The morphological cline could be regarded as a genetic cline caused by a history of hybridization with Q. dentata. The mean numbers of gall types varied among the half-sib families, but did not show a consistent increase or decrease along the genetic cline. This pattern could be explained by the fact that responses to host plant variation differed among the gall wasp species. The half-sib families were classified into three groups based on an ordination analysis of the species composition of the gall wasp community that to some extent also reflected the genetic cline of Q. crispula. This suggests that the species composition of gall wasps changed intermittently along the genetic cline, rather than gradually and consistently along the cline.

  19. Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

    PubMed Central

    von Beeren, Christoph; Maruyama, Munetoshi; Kronauer, Daniel J. C.

    2016-01-01

    Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks. PMID:27829037

  20. Urbanization breaks up host-parasite interactions: a case study on parasite community ecology of rufous-bellied thrushes (Turdus rufiventris) along a rural-urban gradient.

    PubMed

    Calegaro-Marques, Cláudia; Amato, Suzana B

    2014-01-01

    Urbanization drastically alters natural ecosystems and the structure of their plant and animal communities. Whereas some species cope successfully with these environmental changes, others may go extinct. In the case of parasite communities, the expansion of urban areas has a critical effect by changing the availability of suitable substrates for the eggs or free-larval stages of those species with direct life cycles or for the range of hosts of those species with complex cycles. In this study we investigated the influence of the degree of urbanization and environmental heterogeneity on helminth richness, abundance and community structure of rufous-bellied thrushes (Turdus rufiventris) along a rural-urban gradient in the metropolitan region of Porto Alegre, State of Rio Grande do Sul, Brazil. This common native bird species of southern Brazil hosts 15 endoparasite species at the study region. A total of 144 thrushes were collected with mist nets at 11 sites. The degree of urbanization and environmental heterogeneity were estimated by quantifying five landscape elements: buildings, woodlands, fields, bare lands, and water. Landscape analyses were performed at two spatial scales (10 and 100 ha) taking into account home range size and the potential dispersal distance of thrushes and their prey (intermediate hosts). Mean parasite richness showed an inverse relationship with the degree of urbanization, but a positive relationship with environmental heterogeneity. Changes in the structure of component communities along the rural-urban gradient resulted from responses to the availability of particular landscape elements that are compatible with the parasites' life cycles. We found that the replacement of natural environments with buildings breaks up host-parasite interactions, whereas a higher environmental (substrate) diversity allows the survival of a wider range of intermediate hosts and vectors and their associated parasites.

  1. Urbanization Breaks Up Host-Parasite Interactions: A Case Study on Parasite Community Ecology of Rufous-Bellied Thrushes (Turdus rufiventris) along a Rural-Urban Gradient

    PubMed Central

    Calegaro-Marques, Cláudia; Amato, Suzana B.

    2014-01-01

    Urbanization drastically alters natural ecosystems and the structure of their plant and animal communities. Whereas some species cope successfully with these environmental changes, others may go extinct. In the case of parasite communities, the expansion of urban areas has a critical effect by changing the availability of suitable substrates for the eggs or free-larval stages of those species with direct life cycles or for the range of hosts of those species with complex cycles. In this study we investigated the influence of the degree of urbanization and environmental heterogeneity on helminth richness, abundance and community structure of rufous-bellied thrushes (Turdus rufiventris) along a rural-urban gradient in the metropolitan region of Porto Alegre, State of Rio Grande do Sul, Brazil. This common native bird species of southern Brazil hosts 15 endoparasite species at the study region. A total of 144 thrushes were collected with mist nets at 11 sites. The degree of urbanization and environmental heterogeneity were estimated by quantifying five landscape elements: buildings, woodlands, fields, bare lands, and water. Landscape analyses were performed at two spatial scales (10 and 100 ha) taking into account home range size and the potential dispersal distance of thrushes and their prey (intermediate hosts). Mean parasite richness showed an inverse relationship with the degree of urbanization, but a positive relationship with environmental heterogeneity. Changes in the structure of component communities along the rural-urban gradient resulted from responses to the availability of particular landscape elements that are compatible with the parasites' life cycles. We found that the replacement of natural environments with buildings breaks up host-parasite interactions, whereas a higher environmental (substrate) diversity allows the survival of a wider range of intermediate hosts and vectors and their associated parasites. PMID:25068271

  2. Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants

    PubMed Central

    Gehring, Catherine A.; Mueller, Rebecca C.; Haskins, Kristin E.; Rubow, Tine K.; Whitham, Thomas G.

    2014-01-01

    Plants and mycorrhizal fungi influence each other’s abundance, diversity, and distribution. How other biotic interactions affect the mycorrhizal symbiosis is less well understood. Likewise, we know little about the effects of climate change on the fungal component of the symbiosis or its function. We synthesized our long-term studies on the influence of plant parasites, insect herbivores, competing trees, and drought on the ectomycorrhizal fungal communities associated with a foundation tree species of the southwestern United States, pinyon pine (Pinus edulis), and described how these changes feed back to affect host plant performance. We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa. Ectomycorrhizal fungi responded similarly to each of these stressors resulting in a predictable trajectory of community disassembly, consistent with ecological theory. Although we predicted that the fungal communities associated with trees stressed by drought, herbivory, competition, and parasitism would be poor mutualists, we found the opposite pattern in field studies. Our results suggest that climate change and the increased importance of herbivores, competitors, and parasites that can be associated with it, may ultimately lead to reductions in ectomycorrhizal fungal diversity, but that the remaining fungal community may be beneficial to host trees under the current climate and the warmer, drier climate predicted for the future. PMID:25009537

  3. Multi-element fingerprinting and high throughput sequencing identify multiple elements that affect fungal communities in Quercus macrocarpa foliage.

    PubMed

    Jumpponen, Ari; Keating, Karen; Gadbury, Gary; Jones, Kenneth L; Mattox, J David

    2010-09-01

    Diverse fungal mutualists, pathogens and saprobes colonize plant leaves. These fungi face a complex environment, in which stochastic dispersal interplays with abiotic and biotic filters. However, identification of the specific factors that drive the community assembly seems unattainable. We mined two broad data sets and identified chemical elements, to which dominant molecular operational taxonomic units (OTUs) in the foliage of a native tree respond most extremely. While many associations could be identified, potential complicating issues emerged. Those were related to unevenly distributed OTU frequency data, a large number of potentially explanatory variables, and the disproportionate effects of outlier observations.

  4. Parasitism rate, parasitoid community composition and host specificity on exposed and semi-concealed caterpillars from a tropical rainforest.

    PubMed

    Hrcek, Jan; Miller, Scott E; Whitfield, James B; Shima, Hiroshi; Novotny, Vojtech

    2013-10-01

    The processes maintaining the enormous diversity of herbivore-parasitoid food webs depend on parasitism rate and parasitoid host specificity. The two parameters have to be evaluated in concert to make conclusions about the importance of parasitoids as natural enemies and guide biological control. We document parasitism rate and host specificity in a highly diverse caterpillar-parasitoid food web encompassing 266 species of lepidopteran hosts and 172 species of hymenopteran or dipteran parasitoids from a lowland tropical forest in Papua New Guinea. We found that semi-concealed hosts (leaf rollers and leaf tiers) represented 84% of all caterpillars, suffered a higher parasitism rate than exposed caterpillars (12 vs. 5%) and their parasitoids were also more host specific. Semi-concealed hosts may therefore be generally more amenable to biological control by parasitoids than exposed ones. Parasitoid host specificity was highest in Braconidae, lower in Diptera: Tachinidae, and, unexpectedly, the lowest in Ichneumonidae. This result challenges the long-standing view of low host specificity in caterpillar-attacking Tachinidae and suggests higher suitability of Braconidae and lower suitability of Ichneumonidae for biological control of caterpillars. Semi-concealed hosts and their parasitoids are the largest, yet understudied component of caterpillar-parasitoid food webs. However, they still remain much closer in parasitism patterns to exposed hosts than to what literature reports on fully concealed leaf miners. Specifically, semi-concealed hosts keep an equally low share of idiobionts (2%) as exposed caterpillars.

  5. Identifying unprotected and potentially at risk plant communities in the western USA

    USGS Publications Warehouse

    Wright, R.G.; Scott, J.M.; Mann, S.; Murray, M.

    2001-01-01

    We analyzed the conservation status of 73 vegetation cover types distributed across a 1.76 million km2 region in 10 states of the western USA. We found that 25 vegetation cover types had at least 10% of their area in nature reserves. These were generally plant communities located at higher elevations and thus more commonly associated with national parks and wilderness areas. All but three of the remaining 48 cover types occurred with sufficient area on publically owned lands in the region to imply that transforming land management intent on these lands could also increase their protection. We also analyzed the level of protection afforded each cover type across its entire geographic distribution in the region. Most cover types that were at least minimally protected in total across the region were also at least minimally protected in most areas of their occurrence. Our results show that there is a realistic opportunity to design a system of biodiversity reserves in this region that represent the full range of environmental conditions in which the various plant communities occur. Conducting this type of broad-scale analysis is a necessary first step in that process and provides a database for others to work from. Published by Elsevier Science Ltd.

  6. Generation of a Novel Bacteriophage Library Displaying scFv Antibody Fragments from the Natural Buffalo Host to Identify Antigens from Adult Schistosoma japonicum for Diagnostic Development

    PubMed Central

    Hosking, Christopher G.; McWilliam, Hamish E. G.; Driguez, Patrick; Piedrafita, David; Li, Yuesheng; McManus, Donald P.; Ilag, Leodevico L.; Meeusen, Els N. T.; de Veer, Michael J.

    2015-01-01

    The development of effective diagnostic tools will be essential in the continuing fight to reduce schistosome infection; however, the diagnostic tests available to date are generally laborious and difficult to implement in current parasite control strategies. We generated a series of single-chain antibody Fv domain (scFv) phage display libraries from the portal lymph node of field exposed water buffaloes, Bubalus bubalis, 11–12 days post challenge with Schistosoma japonicum cercariae. The selected scFv-phages showed clear enrichment towards adult schistosomes and excretory-secretory (ES) proteins by immunofluorescence, ELISA and western blot analysis. The enriched libraries were used to probe a schistosome specific protein microarray resulting in the recognition of a number of proteins, five of which were specific to schistosomes, with RNA expression predominantly in the adult life-stage based on interrogation of schistosome expressed sequence tags (EST). As the libraries were enriched by panning against ES products, these antigens may be excreted or secreted into the host vasculature and hence may make good targets for a diagnostic assay. Further selection of the scFv library against infected mouse sera identified five soluble scFv clones that could selectively recognise soluble whole adult preparations (SWAP) relative to an irrelevant protein control (ovalbumin). Furthermore, two of the identified scFv clones also selectively recognised SWAP proteins when spiked into naïve mouse sera. These host B-cell derived scFvs that specifically bind to schistosome protein preparations will be valuable reagents for further development of a cost effective point-of-care diagnostic test. PMID:26684756

  7. Two known and one new species of Proctoeces from Australian teleosts: Variable host-specificity for closely related species identified through multi-locus molecular data.

    PubMed

    Wee, Nicholas Q-X; Cribb, Thomas H; Bray, Rodney A; Cutmore, Scott C

    2017-04-01

    Species of Proctoeces Odhner, 1911 (Trematoda: Fellodistomidae) have been reported from a wide range of marine animals globally. Members of the genus tend to lack strongly distinguishing morphological features for diagnosis, making identification difficult and the true number of species in the genus contentious. Combined morphological and molecular analyses were used to characterise three species of Proctoeces from Moreton Bay and the southern Great Barrier Reef. Data for two ribosomal regions and one mitochondrial region were generated for specimens collected from Australia. Three unique 18S-genotypes were identified which corresponded to subtle, but reliable, morphological differences. Two species of Proctoeces were identified from fishes of Moreton Bay, Proctoeces insolitus (Nicoll, 1915) Yamaguti, 1953 and P. major Yamaguti, 1934, and a third, P. choerodoni n. sp. from off Heron Island on the southern Great Barrier Reef. Phylogenetic analyses of partial 18S and partial 28S rDNA indicated that these three species differ from the four species reported outside of Australia for which sequence data are available. Phylogenetically, Proctoeces proved to be a reliable concept, with all species of Proctoeces that have been characterised genetically forming a well-supported clade in all analyses. Dramatically different patterns of host-specificity were identified for each of the three Australian species; P. insolitus apparently infects a single species of fish, P. choerodoni n. sp. infects multiple species of a single genus of fish, and P. major infects multiple species of two teleost orders.

  8. Identifying pious and heretical citizens in a permanent supported housing community.

    PubMed

    Wright, Anthony

    2015-01-01

    This article offers an analysis of the impact of recovery-oriented treatment discourses and practices on tenant-staff relationships in the context of the Pinewood Apartments, a Texas-based permanent supported housing community. Drawing on 6 months of ethnographic research and personal experience of working as a caregiver at Pinewood, I demonstrate how tenant-staff relationships were compromised by service providers' negative evaluations of certain tenants in the context of emotionally charged service interactions. These negative evaluations, I argue, stem from deeply held ideas about valuable citizenship that are embedded in the philosophy and practices of recovery, which emphasizes client choice, self-sufficiency, and autonomy. It should be noted, though, that negative evaluations were not necessarily definitive; both tenants and service providers at times exhibited sympathy and forgiveness for each other.

  9. Identifying the microbial communities and operational conditions for optimized wastewater treatment in microbial fuel cells.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Wu, Angela; Yamanaka, Yuko; Nealson, Kenneth H; Bretschger, Orianna

    2013-12-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as "biocatalysts" to recover energy from organic matter in the form of electricity. MFCs have been explored as possible energy neutral wastewater treatment systems; however, fundamental knowledge is still required about how MFC-associated microbial communities are affected by different operational conditions and can be optimized for accelerated wastewater treatment rates. In this study, we explored how electricity-generating microbial biofilms were established at MFC anodes and responded to three different operational conditions during wastewater treatment: 1) MFC operation using a 750 Ω external resistor (0.3 mA current production); 2) set-potential (SP) operation with the anode electrode potentiostatically controlled to +100 mV vs SHE (4.0 mA current production); and 3) open circuit (OC) operation (zero current generation). For all reactors, primary clarifier effluent collected from a municipal wastewater plant was used as the sole carbon and microbial source. Batch operation demonstrated nearly complete organic matter consumption after a residence time of 8-12 days for the MFC condition, 4-6 days for the SP condition, and 15-20 days for the OC condition. These results indicate that higher current generation accelerates organic matter degradation during MFC wastewater treatment. The microbial community analysis was conducted for the three reactors using 16S rRNA gene sequencing. Although the inoculated wastewater was dominated by members of Epsilonproteobacteria, Gammaproteobacteria, and Bacteroidetes species, the electricity-generating biofilms in MFC and SP reactors were dominated by Deltaproteobacteria and Bacteroidetes. Within Deltaproteobacteria, phylotypes classified to family Desulfobulbaceae and Geobacteraceae increased significantly under the SP condition with higher current generation; however those phylotypes were not found in the OC reactor. These analyses suggest that species

  10. Using cluster analysis of cytokines to identify patterns of inflammation in hospitalized patients with community-acquired pneumonia: a pilot study

    PubMed Central

    Wiemken, Timothy L; Kelley, Robert R; Fernandez-Botran, Rafael; Mattingly, William A.; Arnold, Forest W.; Furmanek, Stephen P; Restrepo, Marcos I; Chalmers, James D; Peyrani, Paula; Cavallazzi, Rodrigo; Bordon, Jose; Aliberti, Stefano; Ramirez, Julio A.

    2017-01-01

    Introduction Patients with severe community-acquired pneumonia (CAP) are believed to have an exaggerated inflammatory response to bacterial infection. Therapies aiming to modulate the inflammatory response have been largely unsuccessful, perhaps reflecting that CAP is a heterogeneous disorder that cannot be modulated by a single anti-inflammatory approach. We hypothesize that the host inflammatory response to pneumonia may be characterized by distinct cytokine patterns, which can be harnessed for personalized therapies. Methods Here, we use hierarchical cluster analysis of cytokines to examine if patterns of inflammatory response in 13 hospitalized patients with CAP can be defined. This was a secondary data analysis of the Community-Acquired Pneumonia Inflammatory Study Group (CAPISG) database. The following cytokines were measured in plasma and sputum on the day of admission: interleukin (IL)-1β, IL-1 receptor antagonist (IL-1ra), IL-6, CXCL8 (IL-8), IL-10, IL-12p40, IL-17, interferon (IFN)γ, tumor necrosis factor (TNF)α, and CXCL10 (IP-10). Hierarchical agglomerative clustering algorithms were used to evaluate clusters of patients within plasma and sputum cytokine determinations. Results A total of thirteen patients were included in this pilot study. Cluster analysis identified distinct inflammatory response patterns of cytokines in the plasma, sputum, and the ratio of plasma to sputum. Conclusions Inflammatory response patterns in plasma and sputum can be identified in hospitalized patients with CAP. Characterization of the local and systemic inflammatory response may help to better discriminate patients for enrollment into clinical trials of immunomodulatory therapies. PMID:28393141

  11. Illicit Drug Use in a Community-Based Sample of Heterosexually Identified Emerging Adults

    ERIC Educational Resources Information Center

    Halkitis, Perry N.; Manasse, Ashley N.; McCready, Karen C.

    2010-01-01

    In this study we assess lifetime and recent drug use patterns among 261 heterosexually identified 18- to 25-year-olds through brief street intercept surveys conducted in New York City. Marijuana, hallucinogens, powder cocaine, and ecstasy were the most frequently reported drugs for both lifetime and recent use. Findings further suggest significant…

  12. Identifying Persuasive Public Health Messages to Change Community Knowledge and Attitudes About Bulimia Nervosa.

    PubMed

    McLean, Siân A; Paxton, Susan J; Massey, Robin; Hay, Phillipa J; Mond, Jonathan M; Rodgers, Bryan

    2016-01-01

    Addressing stigma through social marketing campaigns has the potential to enhance currently low rates of treatment seeking and improve the well-being of individuals with the eating disorder bulimia nervosa. This study aimed to evaluate the persuasiveness of health messages designed to reduce stigma and improve mental health literacy about this disorder. A community sample of 1,936 adults (48.2% male, 51.8% female) from Victoria, Australia, provided (a) self-report information on knowledge and stigma about bulimia nervosa and (b) ratings of the persuasiveness of 9 brief health messages on dimensions of convincingness and likelihood of changing attitudes. Messages were rated moderately to very convincing and a little to moderately likely to change attitudes toward bulimia nervosa. The most persuasive messages were those that emphasized that bulimia nervosa is a serious mental illness and is not attributable to personal failings. Higher ratings of convincingness were associated with being female, with having more knowledge about bulimia nervosa, and with lower levels of stigma about bulimia nervosa. Higher ratings for likelihood of changing attitudes were associated with being female and with ratings of the convincingness of the corresponding message. This study provides direction for persuasive content to be included in social marketing campaigns to reduce stigma toward bulimia nervosa.

  13. Identifying zooplankton community changes between shallow and upper-mesophotic reefs on the Mesoamerican Barrier Reef, Caribbean

    PubMed Central

    Head, Catherine E. I.; Exton, Dan A.; Hunt, Christina L.; Hendrix, Alicia; Gress, Erika; Rogers, Alex D.

    2017-01-01

    Mesophotic coral ecosystems (MCEs, reefs 30–150 m) are understudied, yet the limited research conducted has been biased towards large sessile taxa, such as scleractinian corals and sponges, or mobile taxa such as fishes. Here we investigate zooplankton communities on shallow reefs and MCEs around Utila on the southern Mesoamerican Barrier Reef using planktonic light traps. Zooplankton samples were sorted into broad taxonomic groups. Our results indicate similar taxonomic zooplankton richness and overall biomass between shallow reefs and MCEs. However, the abundance of larger bodied (>2 mm) zooplanktonic groups, including decapod crab zoea, mysid shrimps and peracarid crustaceans, was higher on MCEs than shallow reefs. Our findings highlight the importance of considering zooplankton when identifying broader reef community shifts across the shallow reef to MCE depth gradient. PMID:28168098

  14. Identifying zooplankton community changes between shallow and upper-mesophotic reefs on the Mesoamerican Barrier Reef, Caribbean.

    PubMed

    Andradi-Brown, Dominic A; Head, Catherine E I; Exton, Dan A; Hunt, Christina L; Hendrix, Alicia; Gress, Erika; Rogers, Alex D

    2017-01-01

    Mesophotic coral ecosystems (MCEs, reefs 30-150 m) are understudied, yet the limited research conducted has been biased towards large sessile taxa, such as scleractinian corals and sponges, or mobile taxa such as fishes. Here we investigate zooplankton communities on shallow reefs and MCEs around Utila on the southern Mesoamerican Barrier Reef using planktonic light traps. Zooplankton samples were sorted into broad taxonomic groups. Our results indicate similar taxonomic zooplankton richness and overall biomass between shallow reefs and MCEs. However, the abundance of larger bodied (>2 mm) zooplanktonic groups, including decapod crab zoea, mysid shrimps and peracarid crustaceans, was higher on MCEs than shallow reefs. Our findings highlight the importance of considering zooplankton when identifying broader reef community shifts across the shallow reef to MCE depth gradient.

  15. Identifying host sources, human health risk and indicators of Cryptosporidium and Giardia in a Canadian watershed influenced by urban and rural activities.

    PubMed

    Van Dyke, Michele I; Ong, Corinne S L; Prystajecky, Natalie A; Isaac-Renton, Judith L; Huck, Peter M

    2012-06-01

    Cryptosporidium and Giardia were characterized in a watershed in southern Ontario, Canada, over a 2½ year period. River samples were collected every two weeks, primarily near a municipal drinking water treatment plant intake. Cryptosporidium and Giardia were frequently detected with an overall occurrence rate of 88 and 97%, respectively. Giardia concentrations were higher than Cryptosporidium, with median values of 80 cysts 100 L(-1) and 12 oocysts 100 L(-1), respectively. Although pathogens rarely show a significant relationship with fecal or water quality indicators, this study determined that Cryptosporidium, but not Giardia, was significantly correlated with Escherichia coli, turbidity and river flow. There was no correlation between the two types of protozoa, and only Giardia showed a seasonal trend with higher concentrations at cold water temperatures. Cryptosporidium genotyping of all samples found that farm animals and wildlife were an important contributor of oocysts in the watershed, and that Cryptosporidium strains/genotypes of medium to high risk for human infection (C. hominis, C. parvum and C. ubiquitum) were detected in 16% of samples. This study was able to identify Cryptosporidium host sources and human health risk, and to identify differences between Cryptosporidium and Giardia occurrence in the watershed.

  16. Ethics in Community-University-Artist Partnered Research: Tensions, Contradictions and Gaps Identified in an 'Arts for Social Change' Project.

    PubMed

    Yassi, Annalee; Spiegel, Jennifer Beth; Lockhart, Karen; Fels, Lynn; Boydell, Katherine; Marcuse, Judith

    Academics from diverse disciplines are recognizing not only the procedural ethical issues involved in research, but also the complexity of everyday "micro" ethical issues that arise. While ethical guidelines are being developed for research in aboriginal populations and low-and-middle-income countries, multi-partnered research initiatives examining arts-based interventions to promote social change pose a unique set of ethical dilemmas not yet fully explored. Our research team, comprising health, education, and social scientists, critical theorists, artists and community-activists launched a five-year research partnership on arts-for-social change. Funded by the Social Science and Humanities Research Council in Canada and based in six universities, including over 40 community-based collaborators, and informed by five main field projects (circus with street youth, theatre by people with disabilities, dance for people with Parkinson's disease, participatory theatre with refugees and artsinfused dialogue), we set out to synthesize existing knowledge and lessons we learned. We summarized these learnings into 12 key points for reflection, grouped into three categories: community-university partnership concerns (n = 3), dilemmas related to the arts (n = 5), and team issues (n = 4). In addition to addressing previous concerns outlined in the literature (e.g., related to consent, anonymity, dangerous emotional terrain, etc.), we identified power dynamics (visible and hidden) hindering meaningful participation of community partners and university-based teams that need to be addressed within a reflective critical framework of ethical practice. We present how our team has been addressing these issues, as examples of how such concerns could be approached in community-university partnerships in arts for social change.

  17. Key seabird areas in southern New England identified using a community occupancy model

    USGS Publications Warehouse

    O'Connell, Allan F.; Flanders, Nicholas P.; Gardner, Beth; Winiarski, Kristopher J.; Paton, Peter W. C.; Allison, Taber

    2015-01-01

    Seabirds are of conservation concern, and as new potential risks to seabirds are arising, the need to provide unbiased estimates of species’ distributions is growing. We applied community occupancy models to detection/non-detection data collected from repeated aerial strip-transect surveys conducted in 2 large study plots off southern New England, USA; one off the coast of Rhode Island and the other in Nantucket Sound. A total of 17 seabird species were observed at least once in each study plot. We found that detection varied by survey date and effort for most species and the average detection probability across species was less than 0.4. We estimated the influence of water depth, sea surface temperature, and sea surface chl a concentration on species-specific occupancy. Diving species showed large differences between the 2 study plots in their predicted winter distributions, which were largely explained by water depth acting as a stronger predictor of occupancy in Rhode Island than in Nantucket Sound. Conversely, similarities between the 2 study plots in predicted winter distributions of surface-feeding species were explained by sea surface temperature or chlorophyll a concentration acting as predictors of these species’ occupancy in both study plots. We predicted the number of species at each site using the observed data in order to detect ‘hot-spots’ of seabird diversity and use in the 2 study plots. These results provide new information on detection of species, areas of use, and relationships with environmental variables that will be valuable for biologists and planners interested in seabird conservation in the region.

  18. Identifying Risk Factors Associated with Inappropriate Use of Acid Suppressive Therapy at a Community Hospital

    PubMed Central

    Bodukam, Vijay; Saigal, Kirit; Bahl, Jaya; Wang, Yvette; Hanlon, Alexandra; Lu, Yinghui; Davis, Michael

    2016-01-01

    Purpose. By examining the prescribing patterns and inappropriate use of acid suppressive therapy (AST) during hospitalization and at discharge we sought to identify the risk factors associated with such practices. Methods. In this retrospective observational study, inpatient records were reviewed from January 2011 to December 2013. Treatment with AST was considered appropriate if the patient had a known specific indication or met criteria for stress ulcer prophylaxis. Results. In 2011, out of 58 patients who were on AST on admission, 32 were newly started on it and 23 (72%) were inappropriate cases. In 2012, out of 97 patients on AST, 61 were newly started on it and 51 (84%) were inappropriate cases. In 2013, 99 patients were on AST, of which 48 were newly started on it and 36 (75%) were inappropriate cases. 19% of the patients inappropriately started on AST were discharged on it in three years. Younger age, female sex, and 1 or more handoffs between services were significantly associated with increased risk of inappropriate AST. Conclusion. Our findings reflect inappropriate prescription of AST which leads to increase in costs of care and unnecessarily puts the patient at risk for potential adverse events. The results of this study emphasize the importance of examining the patient's need for AST at each level of care especially when the identified risk factors are present. PMID:27818680

  19. Identifying solutions to increase participation in physical activity interventions within a socio-economically disadvantaged community: a qualitative study

    PubMed Central

    2014-01-01

    Background There is an urgent need to increase population levels of physical activity, particularly amongst those who are socio-economically disadvantaged. Multiple factors influence physical activity behaviour but the generalisability of current evidence to such ‘hard-to-reach’ population subgroups is limited by difficulties in recruiting them into studies. Also, rigorous qualitative studies of lay perceptions and perceptions of community leaders about public health efforts to increase physical activity are sparse. We sought to explore, within a socio-economically disadvantaged community, residents’ and community leaders’ perceptions of physical activity (PA) interventions and issues regarding their implementation, in order to improve understanding of needs, expectations, and social/environmental factors relevant to future interventions. Methods Within an ongoing regeneration project (Connswater Community Greenway), in a socio-economically disadvantaged community in Belfast, we collaborated with a Community Development Agency to purposively sample leaders from public- and voluntary-sector community groups and residents. Individual semi-structured interviews were conducted with 12 leaders. Residents (n = 113), of both genders and a range of ages (14 to 86 years) participated in focus groups (n = 14) in local facilities. Interviews and focus groups were recorded, transcribed verbatim and analysed using a thematic framework. Results Three main themes were identified: awareness of PA interventions; factors contributing to intervention effectiveness; and barriers to participation in PA interventions. Participants reported awareness only of interventions in which they were involved directly, highlighting a need for better communications, both inter- and intra-sectoral, and with residents. Meaningful engagement of residents in planning/organisation, tailoring to local context, supporting volunteers, providing relevant resources and an ‘exit strategy

  20. Isolated and Community Contexts Produce Distinct Responses by Host Plants to the Presence of Ant-Aphid Interaction: Plant Productivity and Seed Viability.

    PubMed

    Canedo-Júnior, Ernesto Oliveira; Santiago, Graziele Silva; Zurlo, Luana Fonseca; Ribas, Carla Rodrigues; Carvalho, Rafaela Pereira; Alves, Guilherme Pereira; Carvalho, Mariana Comanucci Silva; Souza, Brígida

    2017-01-01

    Ant-aphid interactions may affect host plants in several ways, however, most studies measure only the amount of fruit and seed produced, and do not test seed viability. Therefore, the aim of this study was to assess the effects of the presence of ant-aphid interactions upon host plant productivity and seed viability in two different contexts: isolated and within an arthropod community. For this purpose we tested the hypothesis that in both isolated and community contexts, the presence of an ant-aphid interaction will have a positive effect on fruit and seed production, seed biomass and rate of seed germination, and a negative effect on abnormal seedling rates, in comparison to plants without ants. We performed a field mesocosm experiment containing five treatments: Ant-aphid, Aphid, Community, Ant-free community and Control. We counted fruits and seeds produced by each treatment, and conducted experiments for seed biomass and germinability. We found that in the community context the presence of an ant-aphid interaction negatively affected fruit and seed production. We think this may be because aphid attendance by tending-ants promotes aphid damage to the host plant, but without an affect on seed weight and viability. On the other hand, when isolated, the presence of an ant-aphid interaction positively affected fruit and seed production. These positive effects are related to the cleaning services offered to aphids by tending-ants, which prevent the development of saprophytic fungi on the surface of leaves, which would cause a decrease in photosynthetic rates. Our study is important because we evaluated some parameters of plant fitness that have not been addressed very well by other studies involving the effects of ant-aphid interactions mainly on plants with short life cycles. Lastly, our context dependent approach sheds new light on how ecological interactions can vary among different methods of crop management.

  1. Isolated and Community Contexts Produce Distinct Responses by Host Plants to the Presence of Ant-Aphid Interaction: Plant Productivity and Seed Viability

    PubMed Central

    Santiago, Graziele Silva; Zurlo, Luana Fonseca; Ribas, Carla Rodrigues; Carvalho, Rafaela Pereira; Alves, Guilherme Pereira; Carvalho, Mariana Comanucci Silva; Souza, Brígida

    2017-01-01

    Ant-aphid interactions may affect host plants in several ways, however, most studies measure only the amount of fruit and seed produced, and do not test seed viability. Therefore, the aim of this study was to assess the effects of the presence of ant-aphid interactions upon host plant productivity and seed viability in two different contexts: isolated and within an arthropod community. For this purpose we tested the hypothesis that in both isolated and community contexts, the presence of an ant-aphid interaction will have a positive effect on fruit and seed production, seed biomass and rate of seed germination, and a negative effect on abnormal seedling rates, in comparison to plants without ants. We performed a field mesocosm experiment containing five treatments: Ant-aphid, Aphid, Community, Ant-free community and Control. We counted fruits and seeds produced by each treatment, and conducted experiments for seed biomass and germinability. We found that in the community context the presence of an ant-aphid interaction negatively affected fruit and seed production. We think this may be because aphid attendance by tending-ants promotes aphid damage to the host plant, but without an affect on seed weight and viability. On the other hand, when isolated, the presence of an ant-aphid interaction positively affected fruit and seed production. These positive effects are related to the cleaning services offered to aphids by tending-ants, which prevent the development of saprophytic fungi on the surface of leaves, which would cause a decrease in photosynthetic rates. Our study is important because we evaluated some parameters of plant fitness that have not been addressed very well by other studies involving the effects of ant-aphid interactions mainly on plants with short life cycles. Lastly, our context dependent approach sheds new light on how ecological interactions can vary among different methods of crop management. PMID:28141849

  2. Using a service sector segmented approach to identify community stakeholders who can improve access to suicide prevention services for veterans.

    PubMed

    Matthieu, Monica M; Gardiner, Giovanina; Ziegemeier, Ellen; Buxton, Miranda

    2014-04-01

    Veterans in need of social services may access many different community agencies within the public and private sectors. Each of these settings has the potential to be a pipeline for attaining needed health, mental health, and benefits services; however, many service providers lack information on how to conceptualize where Veterans go for services within their local community. This article describes a conceptual framework for outreach that uses a service sector segmented approach. This framework was developed to aid recruitment of a provider-based sample of stakeholders (N = 70) for a study on improving access to the Department of Veterans Affairs and community-based suicide prevention services. Results indicate that although there are statistically significant differences in the percent of Veterans served by the different service sectors (F(9, 55) = 2.71, p = 0.04), exposure to suicidal Veterans and providers' referral behavior is consistent across the sectors. Challenges to using this framework include isolating the appropriate sectors for targeted outreach efforts. The service sector segmented approach holds promise for identifying and referring at-risk Veterans in need of services.

  3. Conceptual and Operational Considerations in Identifying Socioenvironmental Factors Associated with Disability among Community-Dwelling Adults

    PubMed Central

    Philibert, Mathieu; Pampalon, Robert; Daniel, Mark

    2015-01-01

    Disability is conceived as a person–context interaction. Physical and social environments are identified as intervention targets for improving social participation and independence. In comparison to the body of research on place and health, relatively few reports have been published on residential environments and disability in the health sciences literature. We reviewed studies evaluating the socioenvironmental correlates of disability. Searches were conducted in Medline, Embase and CINAHL databases for peer-reviewed articles published between 1997 and 2014. We found many environmental factors to be associated with disability, particularly area-level socioeconomic status and rurality. However, diversity in conceptual and methodological approaches to such research yields a limited basis for comparing studies. Conceptual inconsistencies in operational measures of disability and conceptual disagreement between studies potentially affect understanding of socioenvironmental influences. Similarly, greater precision in socioenvironmental measures and in study designs are likely to improve inference. Consistent and generalisable support for socioenvironmental influences on disability in the general adult population is scarce. PMID:25854297

  4. Host range and community structure of avian nest parasites in the genus Philornis (Diptera: Muscidae) on the island of Trinidad

    PubMed Central

    Bulgarella, Mariana; Heimpel, George E

    2015-01-01

    Parasite host range can be influenced by physiological, behavioral, and ecological factors. Combining data sets on host–parasite associations with phylogenetic information of the hosts and the parasites involved can generate evolutionary hypotheses about the selective forces shaping host range. Here, we analyzed associations between the nest-parasitic flies in the genus Philornis and their host birds on Trinidad. Four of ten Philornis species were only reared from one species of bird. Of the parasite species with more than one host bird species, P. falsificus was the least specific and P. deceptivus the most specific attacking only Passeriformes. Philornis flies in Trinidad thus include both specialists and generalists, with varying degrees of specificity within the generalists. We used three quantities to more formally compare the host range of Philornis flies: the number of bird species attacked by each species of Philornis, a phylogenetically informed host specificity index (Poulin and Mouillot's STD), and a branch length-based STD. We then assessed the phylogenetic signal of these measures of host range for 29 bird species. None of these measures showed significant phylogenetic signal, suggesting that clades of Philornis did not differ significantly in their ability to exploit hosts. We also calculated two quantities of parasite species load for the birds – the parasite species richness, and a variant of the STD index based on nodes rather than on taxonomic levels – and assessed the signal of these measures on the bird phylogeny. We did not find significant phylogenetic signal for the parasite species load or the node-based STD index. Finally, we calculated the parasite associations for all bird pairs using the Jaccard index and regressed these similarity values against the number of nodes in the phylogeny separating bird pairs. This analysis showed that Philornis on Trinidad tend to feed on closely related bird species more often than expected by

  5. Structural Elements in a Persistent Identifier Infrastructure and Resulting Benefits for the Earth Science Community

    NASA Astrophysics Data System (ADS)

    Weigel, T.; Toussaiant, F.; Stockhause, M.; Höck, H.; Kindermann, S.; Lautenschlager, M.; Ludwig, T.

    2012-12-01

    We propose a wide adoption of structural elements (typed links, collections, trees) in the Handle System to improve identification and access of scientific data, metadata and software as well as traceability of data provenance. Typed links target the issue of data provenance as a means to assess the quality of scientific data. Data provenance is seen here as a directed acyclic graph with nodes representing data and vertices representing derivative operations (Moreau 2010). Landing pages can allow a human user to explore the provenance graph back to the primary unprocessed data, thereby also giving credit to the original data producer. As in Earth System Modeling no single infrastructure with complete data lifecycle coverage exists, we propose to split the problem domain in two parts. Project-specific infrastructures such as the German project C3-Grid or the Earth System Grid Federation (ESGF) for CMIP5 data are aware of data and data operations (Toussaint et al. 2012) and can thus detect and accumulate single nodes and vertices in the provenance graph, assigning Handles to data, metadata and software. With a common schema for typed links, the provenance graph is established as downstream infrastructures refer incoming Handles. Data in this context is for example hierarchically structured Earth System model output data, which receives DataCite DOIs only for the most coarse-granular elements. Using Handle tree structures, the lower levels of the hierarchy can also receive Handles, allowing authors to more precisely identify the data they used (Lawrence et al. 2011). We can e.g. define a DOI for just the 2m-temperature variable of CMIP5 data across many CMIP5 experiments or a DOI for model and observational data coming from different sources. The structural elements should be implemented through Handle values at the Handle infrastructure level for two reasons. Handle values are more durable than downstream websites or databases, and thus the provenance chain does not

  6. An ultra scale-down approach identifies host cell protein differences across a panel of mAb producing CHO cell line variants.

    PubMed

    Hogwood, Catherine E M; Ahmad, Shahina S; Tarrant, Richard D; Bracewell, Daniel G; Smales, C Mark

    2016-03-01

    During the manufacture of biopharmaceutical products, the final product must lie within strict pre-set specifications, for example the host cell protein (HCP) content. A number of specific HCPs have been identified in particular products and the interactions between product/HCPs have also been recently investigated; however, a comparison of the HCP dynamics between related cell lines and their response to early downstream processing to aid process development and cell line selection has not been published. We have utilised a proteomic approach coupled with an ultra scale-down study to determine the HCP profile dynamics, at harvest and during early downstream processing, across a panel of recombinant GS-CHOK1SV antibody producing cell lines. The results reveal that cell culture viability upon harvest has the greatest impact upon shear sensitivity and HCP concentration. Whilst the general HCP population/profile was broadly similar across the cell lines, the actual amounts of some specific HCPs in the supernatant differed and a number of cell line specific differences in the response to early downstream processing were observed. We anticipate that such knowledge can now be applied to cell line selection and downstream processing development to target reduction/removal of general and specific problematic HCPs before and during downstream processing.

  7. An integrated approach to identify distribution of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in a mountainous region in China.

    PubMed

    Yang, Kun; Wang, Xian-Hong; Yang, Guo-Jing; Wu, Xiao-Hua; Qi, Yun-Liang; Li, Hong-Jun; Zhou, Xiao-Nong

    2008-07-01

    The aim of this study is to better understand ecological variability related to the distribution of Oncomelania hupensis, the snail intermediate host of Schistosoma japonicum, and predict the spatial distribution of O. hupensis at the local scale in order to develop a more effective control strategy for schistosomiasis in the hilly and mountainous regions of China. A two-pronged approach was applied in this study consisting of a landscape pattern analysis complemented with Bayesian spatial modelling. The parasitological data were collected by cross-sectional surveys carried out in 11 villages in 2006 and mapped based on global positioning system (GPS) coordinates. Environmental surrogates and landscape metrics were derived from remotely-sensed images and land-cover/land-use classification data. Bayesian non-spatial and spatial models were applied to investigate the variation of snail density in relation to environmental surrogates and landscape metrics at the local scale. A Bayesian spatial model, validated by the deviance information criterion (DIC), was found to be the best-fitting model. The mean shape index (MSI) and Shannon's evenness indexes (SEI) were significantly associated with snail density. These findings suggest that decreasing the heterogeneity of the landscape can reduce snail density. A prediction maps were generated by the Bayesian model together with environmental surrogates and landscape metrics. In conclusion, the risk areas of snail distribution at the local scale can be identified using an integrated approach with landscape pattern analysis supported by remote sensing and GIS technologies, as well as Bayesian modelling.

  8. Identifying Barriers to Healthcare to Reduce Health Disparity in Zuni Indians Using Focus Group Conducted by Community Health Workers

    PubMed Central

    Shah, Vallabh O.; Ghahate, Donica M; Bobelu, Jeanette; Sandy, Phillip; Newman, Sara; Helitzer, Deborah L.; Faber, Thomas; Zager, Philip

    2013-01-01

    The Zuni Pueblo is home to an economically disadvantaged population, which faces a public health challenge from the interrelated epidemics of obesity, diabetes and kidney disease. Efforts to decrease the impact of these epidemics have been complicated by historical, economic and cultural barriers, which may limit health-care utilization. The NIH supported Zuni Health Initiative (ZHI) conducted a study to identify barriers to heath care in the Zuni Pueblo. Community health representatives (CHRs) led 14 one-hour focus group sessions at which a total of 112 people participated posed unique questions that took into account the Zuni culture to elicit information on perceived barriers to health care. Audiotapes were translated and transcribed by bilingual ZHI staff. We reduced the text to thematic categories, constructed a coding dictionary and inserted the text into NVivo 9 program. We identified nine themes emerged regarding the barriers experienced in receiving health care and adhering to medical advice. These included distance; transportation; embarrassment; relating to healthcare professionals; navigating the medical system; awareness of available resources; waiting times; adhering to medication; and incentives in health promotion. In conclusion the implementation of culturally appropriate community based health promotion programs and preventive screening techniques will improve access to health care and diminish health disparities. PMID:24528897

  9. Pedigree structure and kinship measurements of a mid-Michigan community: a new North American population isolate identified.

    PubMed

    Bonner, Joseph D; Fisher, Rachel; Klein, James; Lu, Qing; Wilch, Ellen; Friderici, Karen H; Elfenbein, Jill L; Schutte, Debra L; Schutte, Brian C

    2014-01-01

    Previous studies identified a cluster of individuals with an autosomal recessive form of deafness that reside in a small region of mid-Michigan. We hypothesized that affected members from this community descend from a defined founder population. Using public records and personal interviews, we constructed a genealogical database that includes the affected individuals and their extended families as descendants of 461 settlers who emigrated from the Eifel region of Germany between 1836 and 1875. The genealogical database represents a 13-generation pedigree that includes 27,747 descendants of these settlers. Among these descendants, 13,784 are presumed living. Many of the extant descendants reside in a 90-square-mile area, and 52% were born to parents who share at least one common ancestor. Among those born to related parents, the median kinship coefficient is 3.7 × 10(-3). While the pedigree contains 2,510 founders, 344 of the 461 settlers accounted for 67% of the genome in the extant population. These data suggest that we identified a new population isolate in North America and that, as demonstrated for congenital hearing loss, this rural mid-Michigan community is a new resource to discover heritable factors that contribute to common health-related conditions.

  10. Combining a Climatic Niche Model of an Invasive Fungus with Its Host Species Distributions to Identify Risks to Natural Assets: Puccinia psidii Sensu Lato in Australia

    PubMed Central

    Kriticos, Darren J.; Morin, Louise; Leriche, Agathe; Anderson, Robert C.; Caley, Peter

    2013-01-01

    Puccinia psidii sensu lato (s.l.) is an invasive rust fungus threatening a wide range of plant species in the family Myrtaceae. Originating from Central and South America, it has invaded mainland USA and Hawai'i, parts of Asia and Australia. We used CLIMEX to develop a semi-mechanistic global climatic niche model based on new data on the distribution and biology of P. psidii s.l. The model was validated using independent distribution data from recently invaded areas in Australia, China and Japan. We combined this model with distribution data of its potential Myrtaceae host plant species present in Australia to identify areas and ecosystems most at risk. Myrtaceaeous species richness, threatened Myrtaceae and eucalypt plantations within the climatically suitable envelope for P. psidii s.l in Australia were mapped. Globally the model identifies climatically suitable areas for P. psidii s.l. throughout the wet tropics and sub-tropics where moist conditions with moderate temperatures prevail, and also into some cool regions with a mild Mediterranean climate. In Australia, the map of species richness of Myrtaceae within the P. psidii s.l. climatic envelope shows areas where epidemics are hypothetically more likely to be frequent and severe. These hotspots for epidemics are along the eastern coast of New South Wales, including the Sydney Basin, in the Brisbane and Cairns areas in Queensland, and in the coastal region from the south of Bunbury to Esperance in Western Australia. This new climatic niche model for P. psidii s.l. indicates a higher degree of cold tolerance; and hence a potential range that extends into higher altitudes and latitudes than has been indicated previously. The methods demonstrated here provide some insight into the impacts an invasive species might have within its climatically suited range, and can help inform biosecurity policies regarding the management of its spread and protection of valued threatened assets. PMID:23704988

  11. Is forced migration a barrier to treatment success? Similar HIV treatment outcomes among refugees and a surrounding host community in Kuala Lumpur, Malaysia.

    PubMed

    Mendelsohn, Joshua B; Schilperoord, Marian; Spiegel, Paul; Balasundaram, Susheela; Radhakrishnan, Anuradha; Lee, Christopher K C; Larke, Natasha; Grant, Alison D; Sondorp, Egbert; Ross, David A

    2014-02-01

    In response to an absence of studies among refugees and host communities accessing highly active antiretroviral therapy (HAART) in urban settings, our objective was to compare adherence and virological outcomes among clients attending a public clinic in Kuala Lumpur, Malaysia. A cross-sectional survey was conducted among adult clients (≥18 years). Data sources included a structured questionnaire that measured self-reported adherence, a pharmacy-based measure of HAART prescription refills over the previous 24 months, and HIV viral loads. The primary outcome was unsuppressed viral load (≥40 copies/mL). Among a sample of 153 refugees and 148 host community clients, refugees were younger (median age 35 [interquartile range, IQR 31, 39] vs 40 years [IQR 35, 48], p < 0.001), more likely to be female (36 vs 21 %, p = 0.004), and to have been on HAART for less time (61 [IQR 35, 108] vs 153 weeks [IQR 63, 298]; p < 0.001). Among all clients, similar proportions of refugee and host clients were <95 % adherent to pharmacy refills (26 vs 34 %, p = 0.15). When restricting to clients on treatment for ≥25 weeks, similar proportions from each group were not virologically suppressed (19 % of refugees vs 16 % of host clients, p = 0.54). Refugee status was not independently associated with the outcome (adjusted odds ratio, aOR = 1.28, 95 % CI 0.52, 3.14). Overall, the proportions of refugee and host community clients with unsuppressed viral loads and sub-optimal adherence were similar, supporting the idea that refugees in protracted asylum situations are able to sustain good treatment outcomes and should explicitly be included in the HIV strategic plans of host countries with a view to expanding access in accordance with national guidelines for HAART.

  12. Suicidal ideation: Are refugees more at risk compared to host population? Findings from a preliminary assessment in a refugee community in Nigeria.

    PubMed

    Akinyemi, O O; Atilola, O; Soyannwo, T

    2015-12-01

    Among the serious mental health problems that may be associated with being a refugee is suicidal behavior. This study aimed to assess the prevalence and correlates of suicidal ideation among African refugees in Oru-Ijebu Nigeria. Suicidal ideation was assessed using appropriate section in the Mini-International Neuropsychiatric Interview while the brief version of the WHO Quality of Life was used to assess quality of life as a clinical variable. Study involved 444 refugees and 527 non-refugee member of host community. Result showed that the prevalence of suicidal ideation was significantly higher among the refugees than the non-refugee comparison group (27.3% vs. 17.3%; p<0.001). Social status and quality of life was significantly poorer among the refugees compared with their non-refugee members of same community. Quality of life was the only factor independently associated with suicidal ideations among refugees. In conclusion, the study shows that the prevalence of suicidal ideation is significantly higher among the refugees than the non-refugee members of the host community and calls for innovative ways of extending mental health services to refugees at the study site.

  13. West nile virus prevalence across landscapes is mediated by local effects of agriculture on vector and host communities.

    PubMed

    Crowder, David W; Dykstra, Elizabeth A; Brauner, Jo Marie; Duffy, Anne; Reed, Caitlin; Martin, Emily; Peterson, Wade; Carrière, Yves; Dutilleul, Pierre; Owen, Jeb P

    2013-01-01

    Arthropod-borne viruses (arboviruses) threaten the health of humans, livestock, and wildlife. West Nile virus (WNV), the world's most widespread arbovirus, invaded the United States in 1999 and rapidly spread across the county. Although the ecology of vectors and hosts are key determinants of WNV prevalence across landscapes, the factors shaping local vector and host populations remain unclear. Here, we used spatially-explicit models to evaluate how three land-use types (orchards, vegetable/forage crops, natural) and two climatic variables (temperature, precipitation) influence the prevalence of WNV infections and vector/host distributions at landscape and local spatial scales. Across landscapes, we show that orchard habitats were associated with greater prevalence of WNV infections in reservoirs (birds) and incidental hosts (horses), while increased precipitation was associated with fewer infections. At local scales, orchard habitats increased the prevalence of WNV infections in vectors (mosquitoes) and the abundance of mosquitoes and two key reservoir species, the American robin and the house sparrow. Thus, orchard habitats benefitted WNV vectors and reservoir hosts locally, creating focal points for the transmission of WNV at landscape scales in the presence of suitable climatic conditions.

  14. Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria.

    PubMed

    Shen, Hongzhang; Ye, Fuqiang; Xie, Lu; Yang, Jianfeng; Li, Zhen; Xu, Peisong; Meng, Fei; Li, Lei; Chen, Ying; Bo, Xiaochen; Ni, Ming; Zhang, Xiaofeng

    2015-12-02

    Despite the high worldwide prevalence of gallstone disease, the role of the biliary microbiota in gallstone pathogenesis remains obscure. Next-generation sequencing offers advantages for systematically understanding the human microbiota; however, there have been few such investigations of the biliary microbiome. Here, we performed whole-metagenome shotgun (WMS) sequencing and 16S rRNA sequencing on bile samples from 15 Chinese patients with gallstone disease. Microbial communities of most individuals were clustered into two types, according to the relative enrichment of different intestinal bacterial species. In the bile samples, oral cavity/respiratory tract inhabitants were more prevalent than intestinal inhabitants and existed in both community types. Unexpectedly, the two types were not associated with fever status or surgical history, and many bacteria were patient-specific. We identified 13 novel biliary bacteria based on WMS sequencing, as well as genes encoding putative proteins related to gallstone formation and bile resistance (e.g., β-glucuronidase and multidrug efflux pumps). Bile samples from gallstone patients had reduced microbial diversity compared to healthy faecal samples. Patient samples were enriched in pathways related to oxidative stress and flagellar assembly, whereas carbohydrate metabolic pathways showed varying behaviours. As the first biliary WMS survey, our study reveals the complexity and specificity of biliary microecology.

  15. Unraveling the complexity of the zoo community: identifying the variables related to conservation performance in zoological parks.

    PubMed

    Fàbregas, María C; Guillén-Salazar, Federico; Garcés-Narro, Carlos

    2012-01-01

    Zoological parks make up a highly heterogeneous community. Ranging from small collections at shopping malls to highly developed bioparks, their contribution to conservation is expected to vary enormously. Although several studies have focused on assessing such contribution, the parameters used frequently do not apply when considering more modest zoos. The goals of this study are to determine, within the wide range of zoos, which type tend to fulfill the conservation mission of modern zoos and to identify the variables associated to their conservation performance. We used the requirements demanded by the European Community Zoos Directive 1999/22/EC, relating to the keeping of wild animals in zoological parks, to assess conservation performance in 72% of officially registered Spanish zoos. Sampled zoos were classified into groups according to their common characteristics, and then the variables related to how they met each of the Directive's requirements in the groups were assessed. We found that private zoological parks with large zoological collections, located within metropolitan areas, and members of a zoo association tended to fulfill the requirements. Being a member of a zoo association was the variable that better explained fulfillment of the requirements among the evaluated zoos. Data revealed that zoos not meeting any requirement were few, although those meeting all of them were not frequent. The requirement related to adequate record keeping showed the lowest level of fulfillment. We discuss the implications of our results and propose measures of change in order to promote the contribution of zoos to biodiversity conservation.

  16. Identifying the Correlation between Professional Learning Communities and Collective Teacher Efficacy for Math Data Teams in Kaua'i Complex Area Secondary Schools

    ERIC Educational Resources Information Center

    Ellwood, Cheryl Kathryn

    2013-01-01

    Professional learning communities and teacher efficacy are at the core of many of the current educational reform models. The intention of this dissertation was to identify the correlation between professional learning communities and collective teacher efficacy for math data teams in the six Kaua'i Complex Area secondary schools, as measured by…

  17. The Rural Wings Project: Bridging the Digital Divide with Satellite-Provided Internet. Phase I--Identifying and Analysing the Learning Needs of 31 Communities in 10 Countries

    ERIC Educational Resources Information Center

    Hansson, Henrik; Mihailidis, Paul; Larsson, Ken; Sotiriou, Menelaos; Sotiriou, Sofoklis; Uzunoglu, Nikolaos; Gargalakos, Michail

    2007-01-01

    The digitally marginalised communities are in focus in the EU-funded Rural Wings project 2006-2008. The aim is to identify and analyse the user learning needs in non-connected communities and to meet these needs by providing satellite Internet broadband connections, education and tools. This article reports the findings of the user needs…

  18. Geographic mapping as a tool for identifying communities at high risk of fire and burn injuries in children.

    PubMed

    Poulos, Roslyn G; Hayen, Andrew; Chong, Shanley S S; Finch, Caroline F

    2009-05-01

    Burns are a significant cause of morbidity and mortality in children. Although industrialized countries have achieved significant declines in deaths and hospitalizations for these injuries in recent decades, the benefits have not been shared equally by children across all socioeconomic groups. We used Bayesian methods to map posterior expected relative risks, as an estimate of smoothed hospital separation ratios for fire and burns in children, across local government areas in New South Wales, Australia. The geographic pattern of relative risk varied by age group; higher than average risks were observed for children residing in rural and remote areas, as well as in scattered local government areas closer to the coast and in some metropolitan regions. Mapping the occurrence of injury gives injury practitioners the opportunity to identify high risk communities for further investigation of risk factors and implementation of targeted interventions within a defined area.

  19. Classification algorithms to improve the accuracy of identifying patients hospitalized with community-acquired pneumonia using administrative data.

    PubMed

    Yu, O; Nelson, J C; Bounds, L; Jackson, L A

    2011-09-01

    In epidemiological studies of community-acquired pneumonia (CAP) that utilize administrative data, cases are typically defined by the presence of a pneumonia hospital discharge diagnosis code. However, not all such hospitalizations represent true CAP cases. We identified 3991 hospitalizations during 1997-2005 in a managed care organization, and validated them as CAP or not by reviewing medical records. To improve the accuracy of CAP identification, classification algorithms that incorporated additional administrative information associated with the hospitalization were developed using the classification and regression tree analysis. We found that a pneumonia code designated as the primary discharge diagnosis and duration of hospital stay improved the classification of CAP hospitalizations. Compared to the commonly used method that is based on the presence of a primary discharge diagnosis code of pneumonia alone, these algorithms had higher sensitivity (81-98%) and positive predictive values (82-84%) with only modest decreases in specificity (48-82%) and negative predictive values (75-90%).

  20. A retrospective observational analysis to identify patient and treatment-related predictors of outcomes in a community mental health programme

    PubMed Central

    Green, Stuart A; Honeybourne, Emmi; Chalkley, Sylvia R; Price, Geraint; Bell, Derek; Green, John

    2015-01-01

    Objectives This study aims to identify patient and treatment factors that affect clinical outcomes of community psychological therapy through the development of a predictive model using historic data from 2 services in London. In addition, the study aims to assess the completeness of data collection, explore how treatment outcomes are discriminated using current criteria for classifying recovery, and assess the feasibility and need for undertaking a future larger population analysis. Design Observational, retrospective discriminant analysis. Setting 2 London community mental health services that provide psychological therapies for common mental disorders including anxiety and depression. Participants A total of 7388 patients attended the services between February 2009 and May 2012, of which 4393 (59%) completed therapy, or there was an agreement to end therapy, and were included in the study. Primary and secondary outcome measures Different combinations of the clinical outcome scores for anxiety Generalised Anxiety Disorder-7 and depression Patient Health Questionnaire-9 were used to construct different treatment outcomes. Results The predictive models were able to assign a positive or negative clinical outcome to each patient based on 5 independent pre-treatment variables, with an accuracy of 69.4% and 79.3%, respectively: initial severity of anxiety and depression, ethnicity, deprivation and gender. The number of sessions attended/missed were also important factors identified in recovery. Conclusions Predicting whether patients are likely to have a positive outcome following treatment at entry might allow suitable modification of scheduled treatment, possibly resulting in improvements in outcomes. The model also highlights factors not only associated with poorer outcomes but inextricably linked to prevalence of common mental disorders, emphasising the importance of social determinants not only in poor health but also poor recovery. PMID:25995234

  1. EPA Hosts Environmental Justice Interagency Working Group Meeting in Atlanta to address Concerns in North Birmingham Communities

    EPA Pesticide Factsheets

    (ATLANTA - February 17, 2016) The U.S. Environmental Protection Agency (EPA) will host a Federal Interagency Working Group on Environmental Justice Meeting (EJ IWG) on Thursday, February 18, 2016 in the Sam Nunn Federal Building in Atlanta, GA. The EJ IWG

  2. A 10-year wildlife survey of 15 species of Canadian carnivores identifies new hosts or geographic locations for Trichinella genotypes T2, T4, T5, and T6.

    PubMed

    Gajadhar, Alvin A; Forbes, Lorry B

    2010-02-26

    A survey of wild carnivores in Canada was conducted over a 10-year period to determine the prevalence and genotypes of Trichinella. Muscle samples collected from 1409 animals representing 15 hosts species were enzymatically digested to recover Trichinella larvae. Larvae were recovered from a total of 287 (20.4%) animals and PCR identified four genotypes of Trichinella. Trichinella nativa was found in 5 host species and was the most commonly found genotype. Trichinella T6 was present in 7 species of carnivores, and coyote and badger are new host records for this genotype. The recovery of T. pseudospiralis and T. murrelli from cougars is the first documentation of these species in Canada and in cougars. The cougar was also the only host species in which all four genotypes of Trichinella were identified. Black bears and walruses had the highest tissue levels of larvae in this study and are also the species most frequently associated with human trichinellosis in Canada. This work identifies additional host species and expanded geographic ranges for 4 genotypes of Trichinella in North America. Failure to demonstrate T. spiralis in wildlife and continued negative results from ongoing surveillance activities in swine provide additional evidence that T. spiralis is not present in Canada.

  3. GIS-Mapping and Statistical Analyses to Identify Climate-Vulnerable Communities and Populations Exposed to Superfund Sites

    EPA Science Inventory

    Climate change-related cumulative health risks are expected to be disproportionately greater for overburdened communities, due to differential proximity and exposures to chemical sources and flood zones. Communities and populations vulnerable to climate change-associated impacts ...

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

    PubMed

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

    2016-10-01

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

  5. Sharing the tracks to good tucker: identifying the benefits and challenges of implementing community food programs for Aboriginal communities in Victoria.

    PubMed

    Murray, Margaret; Bonnell, Emily; Thorpe, Sharon; Browne, Jennifer; Barbour, Liza; MacDonald, Catherine; Palermo, Claire

    2014-01-01

    Food insecurity is a significant issue in the Victorian Aboriginal population, contributing to the health disparity and reduced life expectancy. Community food programs are a strategy used to minimise individual level food insecurity, with little evidence regarding their effectiveness for Aboriginal populations. The aim of this study was to explore the role of community food programs operating for Aboriginal people in Victoria and their perceived influence on food access and nutrition. Semistructured interviews were conducted with staff (n=23) from a purposive sample of 18 community food programs across Victoria. Interviews explored the programs' operation, key benefits to the community, challenges and recommendations for setting up a successful community food program. Results were analysed using a qualitative thematic approach and revealed three main themes regarding key factors for the success of community food programs: (1) community food programs for Aboriginal people should support access to safe, affordable, nutritious food in a socially and culturally acceptable environment; (2) a community development approach is essential for program sustainability; and (3) there is a need to build the capacity of community food programs as part of a strategy to ensure sustainability. Community food programs may be an effective initiative for reducing food insecurity in the Victorian Aboriginal population.

  6. Theoretical Soundness, Proven Effectiveness, and Implementation Fidelity of the HOSTS Language Arts Program among Children Identified as At-Risk in Urban Elementary Schools

    ERIC Educational Resources Information Center

    Senesac, Barbara V.; Burns, Matthew K.

    2008-01-01

    In order to fully evaluate the quality of evidence for any educational innovation, research is needed regarding consistency with theory, demonstrated effectiveness, and consistent implementation. The Help One Student to Succeed (HOSTS) Language Arts program was specifically mentioned in the "No Child Left Behind" act as a program that…

  7. Karrikins Identified in Biochars Indicate Post-Fire Chemical Cues Can Influence Community Diversity and Plant Development

    PubMed Central

    Kochanek, Jitka; Flematti, Gavin R.

    2016-01-01

    Background Karrikins are smoke-derived compounds that provide strong chemical cues to stimulate seed germination and seedling growth. The recent discovery in Arabidopsis that the karrikin perception system may be present throughout angiosperms implies a fundamental plant function. Here, we identify the most potent karrikin, karrikinolide (KAR1), in biochars and determine its role in species unique plant responses. Methods Biochars were prepared by three distinct commercial-scale pyrolysis technologies using systematically selected source material and their chemical properties, including karrikinolide, were quantified. Dose-response assays determined the effects of biochar on seed germination for two model species that require karrikinolide to break dormancy (Solanum orbiculatum, Brassica tourneforttii) and on seedling growth using two species that display plasticity to karrikins, biochar and phytotoxins (Lactuca sativa, Lycopersicon esculentum). Multivariate analysis examined relationships between biochar properties and the plant phenotype. Findings and Conclusions Results showed that karrikin abundant biochars stimulated dormant seed germination and seedling growth via mechanisms analogous to post-fire chemical cues. The individual species response was associated with its sensitivity to karrikinolide and inhibitory compounds within the biochars. These findings are critical for understanding why biochar influences community composition and plant physiology uniquely for different species and reaffirms that future pyrolysis technologies promise by-products that concomitantly sequester carbon and enhance plant growth for ecological and broader plant related applications. PMID:27536995

  8. Identifying the Organizational Changes Taking Place in Somali Community-Based Organization (CBO) in Response to New Patterns of Immigration: Implications for Adult Community Education

    ERIC Educational Resources Information Center

    Osman, Sirad Warfa

    2009-01-01

    This dissertation focuses on changes in the organizational development of community-based organizations (CBOs) within the context of new patterns of immigration, in the United States. Organizational development is considered within the context of dialects of growth, change and transformation of communities in transition. The primary goal of this…

  9. Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa.

    PubMed

    Arfi, Yonathan; Buée, Marc; Marchand, Cyril; Levasseur, Anthony; Record, Eric

    2012-02-01

    Fungi are important actors in ecological processes and trophic webs in mangroves. Although saprophytic fungi occurring in the intertidal part of mangrove have been well studied, little is known about the diversity and structure of the fungal communities in this ecosystem or about the importance of functional groups like pathogens and mutualists. Using tag-encoded 454 pyrosequencing of the ITS1, ITS2, nu-ssu-V5 and nu-ssu-V7 regions, we studied and compared the fungal communities found on the marine and aerial parts of Avicennia marina and Rhizophora stylosa trees in a mangrove in New Caledonia. A total of 209,544 reads were analysed, corresponding to several thousand molecular operational taxonomic units (OTU). There is a marked zonation in the species distribution, with most of the OTU being found specifically in one of the microhabitat studied. Ascomycetes are the dominant phylum (82%), Basidiomycetes are very rare (3%), and 15% of the sequences correspond to unknown taxa. Our results indicate that host specificity is a key factor in the distribution of the highly diverse fungal communities, in both the aerial and intertidal parts of the trees. This study also validates the usefulness of multiple markers in tag-encoded pyrosequencing to consolidate and refine the assessment of the taxonomic diversity.

  10. Fleas associated with non-flying small mammal communities from northern and central Chile: with new host and locality records.

    PubMed

    Bazán-León, E A; Lareschi, M; Sanchez, J; Soto-Nilo, G; Lazzoni, I; Venegas, C I; Poblete, Y; Vásquez, R A

    2013-12-01

    Fleas associated with small mammals from seven localities from northern and central Chile were assessed. We captured 352 small mammals belonging to 12 species from which we obtained 675 fleas belonging to 15 different species. The most frequently captured flea species were Neotyphloceras crassispina crassispina (n = 198) and N. chilensis (n = 175). High values of flea species richness and diversity were found in Fray Jorge National Park (NP), a north-central Chilean site, whereas the highest values of mean abundance (MA) and prevalence were found in three diverse sites that include Los Molles River, a high altitude site located in north-central Chile, Fray Jorge NP and Dichato, in south-central Chile. On the other hand, high values of flea richness and diversity were found on two rodent species, Abrothrix olivacea and A. longipilis, whereas the highest values of MA and prevalence were found on Oligoryzomys longicaudatus, A. longipilis and Phyllotis xanthopygus. A total of three new host recordings, nine new localities and nine new host species and locality recordings are reported. Also, this study represents the first known record of Tetrapsyllus (Tetrapsyllus) comis in Chile and the first ecological analysis of Neotyphloceras chilensis.

  11. Establishment and Validation of Whole-Cell Based Fluorescence Assays to Identify Anti-Mycobacterial Compounds Using the Acanthamoeba castellanii - Mycobacterium marinum Host-Pathogen System

    PubMed Central

    Kicka, Sébastien; Trofimov, Valentin; Harrison, Christopher; Ouertatani-Sakouhi, Hajer; McKinney, John; Scapozza, Leonardo; Hilbi, Hubert; Cosson, Pierre; Soldati, Thierry

    2014-01-01

    Tuberculosis is considered to be one of the world’s deadliest disease with 2 million deaths each year. The need for new antitubercular drugs is further exacerbated by the emergence of drug-resistance strains. Despite multiple recent efforts, the majority of the hits discovered by traditional target-based screening showed low efficiency in vivo. Therefore, there is heightened demand for whole-cell based approaches directly using host-pathogen systems. The phenotypic host-pathogen assay described here is based on the monitoring of GFP-expressing Mycobacterium marinum during infection of the amoeba Acanthamoeba castellanii. The assay showed straight-forward medium-throughput scalability, robustness and ease of manipulation, demonstrating its qualities as an efficient compound screening system. Validation with a series of known antitubercular compounds highlighted the advantages of the assay in comparison to previously published macrophage-Mycobacterium tuberculosis-based screening systems. Combination with secondary growth assays based on either GFP-expressing D. discoideum or M. marinum allowed us to further fine-tune compound characterization by distinguishing and quantifying growth inhibition, cytotoxic properties and antibiotic activities of the compounds. The simple and relatively low cost system described here is most suitable to detect anti-infective compounds, whether they present antibiotic activities or not, in which case they might exert anti-virulence or host defense boosting activities, both of which are largely overlooked by classical screening approaches. PMID:24498207

  12. An Exploration of Strategic Planning Perspectives and Processes within Community Colleges Identified as Being Distinctive in Their Strategic Planning Practices

    ERIC Educational Resources Information Center

    Augustyniak, Lisa J.

    2015-01-01

    Community college leaders face unprecedented change, and some have begun reexamining their institutional strategic planning processes. Yet, studies in higher education strategic planning spend little time examining how community colleges formulate their strategic plans. This mixed-method qualitative study used an expert sampling method to identify…

  13. Community College Administrative Roles in Identifying Faculty for Future Management Positions: A Phenomenological Study of Retired Administrators

    ERIC Educational Resources Information Center

    Knirk, Brian Doyle

    2013-01-01

    The community college system is beginning to see waves of retirements at all levels of the administrative structure. These retirements, in conjunction with expected growth in administrative positions, will result in system-wide administrative vacancies. Community colleges not already seeking new leaders are likely to find themselves in the midst…

  14. Leading Edge Technologies in a Community College Library Setting: Identifying Disconnects of Academic Libraries and Their Users

    ERIC Educational Resources Information Center

    Stanley, Theresa C.

    2010-01-01

    The intent of this research was to discover what, if any, disconnect exists between community college students' library perceptions and technology use. The researcher studied how students at a very-large southwestern community college are using the physical and virtual college library, and their overall technology and library technology use. The…

  15. Taking a Step to Identify How to Create Professional Learning Communities--Report of a Case Study of a Korean Public High School on How to Create and Sustain a School-Based Teacher Professional Learning Community

    ERIC Educational Resources Information Center

    Ahn, Joonkil

    2017-01-01

    This study intends to identify some key factors in creating and sustaining school-based teacher professional learning communities (PLCs) through a case study of a South Korean public high school. To achieve this, the study identified some essential infrastructure, preparation, and necessary social organization for creating PLCs. The ideal unit and…

  16. Combining the Power of Statistical Analyses and Community Interviews to Identify Adoption Barriers for Stormwater Best-Management Practices

    NASA Astrophysics Data System (ADS)

    Hoover, F. A.; Bowling, L. C.; Prokopy, L. S.

    2015-12-01

    Urban stormwater is an on-going management concern in municipalities of all sizes. In both combined or separated sewer systems, pollutants from stormwater runoff enter the natural waterway system during heavy rain events. Urban flooding during frequent and more intense storms are also a growing concern. Therefore, stormwater best-management practices (BMPs) are being implemented in efforts to reduce and manage stormwater pollution and overflow. The majority of BMP water quality studies focus on the small-scale, individual effects of the BMP, and the change in water quality directly from the runoff of these infrastructures. At the watershed scale, it is difficult to establish statistically whether or not these BMPs are making a difference in water quality, given that watershed scale monitoring is often costly and time consuming, relying on significant sources of funds, which a city may not have. Hence, there is a need to quantify the level of sampling needed to detect the water quality impact of BMPs at the watershed scale. In this study, a power analysis was performed on data from an urban watershed in Lafayette, Indiana, to determine the frequency of sampling required to detect a significant change in water quality measurements. Using the R platform, results indicate that detecting a significant change in watershed level water quality would require hundreds of weekly measurements, even when improvement is present. The second part of this study investigates whether the difficulty in demonstrating water quality change represents a barrier to adoption of stormwater BMPs. Semi-structured interviews of community residents and organizations in Chicago, IL are being used to investigate residents understanding of water quality and best management practices and identify their attitudes and perceptions towards stormwater BMPs. Second round interviews will examine how information on uncertainty in water quality improvements influences their BMP attitudes and perceptions.

  17. Identifying sources of strength: resilience from the perspective of older people receiving long-term community care.

    PubMed

    Janssen, Bienke M; Van Regenmortel, Tine; Abma, Tineke A

    2011-09-01

    This study seeks to explore the sources of strength giving rise to resilience among older people. Twenty-nine in-depth interviews were conducted with older people who receive long-term community care. The interviews were subjected to a thematic content analysis. The findings suggest that the main sources of strength identified among older people were constituted on three domains of analysis; the individual-, interactional and contextual domain. The individual domain refers to the qualities within older people and comprises of three sub-domains, namely beliefs about one's competence, efforts to exert control and the capacity to analyse and understand ones situation. Within these subdomains a variety of sources of strength were found like pride about ones personality, acceptance and openness about ones vulnerability, the anticipation on future losses, mastery by practising skills, the acceptance of help and support, having a balanced vision on life, not adapting the role of a victim and carpe-diem. The interactional domain is defined as the way older people cooperate and interact with others to achieve their personal goals. Sources of strength on this domain were empowering (in)formal relationships and the power of giving. Lastly, the contextual domain refers to a broader political-societal level and includes sources of strength like the accessibility of care, the availability of material resources and social policy. The three domains were found to be inherently linked to each other. The results can be used for the development of positive, proactive interventions aimed at helping older people build on the positive aspects of their lives.

  18. Phytophagous Insects on Native and Non-Native Host Plants: Combining the Community Approach and the Biogeographical Approach

    PubMed Central

    Meijer, Kim; Zemel, Hidde; Chiba, Satoshi; Smit, Christian; Beukeboom, Leo W.; Schilthuizen, Menno

    2015-01-01

    During the past centuries, humans have introduced many plant species in areas where they do not naturally occur. Some of these species establish populations and in some cases become invasive, causing economic and ecological damage. Which factors determine the success of non-native plants is still incompletely understood, but the absence of natural enemies in the invaded area (Enemy Release Hypothesis; ERH) is one of the most popular explanations. One of the predictions of the ERH, a reduced herbivore load on non-native plants compared with native ones, has been repeatedly tested. However, many studies have either used a community approach (sampling from native and non-native species in the same community) or a biogeographical approach (sampling from the same plant species in areas where it is native and where it is non-native). Either method can sometimes lead to inconclusive results. To resolve this, we here add to the small number of studies that combine both approaches. We do so in a single study of insect herbivory on 47 woody plant species (trees, shrubs, and vines) in the Netherlands and Japan. We find higher herbivore diversity, higher herbivore load and more herbivory on native plants than on non-native plants, generating support for the enemy release hypothesis. PMID:25955254

  19. Phytophagous insects on native and non-native host plants: combining the community approach and the biogeographical approach.

    PubMed

    Meijer, Kim; Zemel, Hidde; Chiba, Satoshi; Smit, Christian; Beukeboom, Leo W; Schilthuizen, Menno

    2015-01-01

    During the past centuries, humans have introduced many plant species in areas where they do not naturally occur. Some of these species establish populations and in some cases become invasive, causing economic and ecological damage. Which factors determine the success of non-native plants is still incompletely understood, but the absence of natural enemies in the invaded area (Enemy Release Hypothesis; ERH) is one of the most popular explanations. One of the predictions of the ERH, a reduced herbivore load on non-native plants compared with native ones, has been repeatedly tested. However, many studies have either used a community approach (sampling from native and non-native species in the same community) or a biogeographical approach (sampling from the same plant species in areas where it is native and where it is non-native). Either method can sometimes lead to inconclusive results. To resolve this, we here add to the small number of studies that combine both approaches. We do so in a single study of insect herbivory on 47 woody plant species (trees, shrubs, and vines) in the Netherlands and Japan. We find higher herbivore diversity, higher herbivore load and more herbivory on native plants than on non-native plants, generating support for the enemy release hypothesis.

  20. Effects of host species and life stage on the helminth communities of sympatric northern leopard frogs (Lithobates pipiens) and wood frogs (Lithobates sylvaticus) in the Sheyenne National Grasslands, North Dakota.

    PubMed

    Gustafson, Kyle D; Newman, Robert A; Tkach, Vasyl V

    2013-08-01

    We studied helminth communities in sympatric populations of leopard frogs (Lithobates pipiens) and wood frogs (Lithobates sylvaticus) and assessed the effects of host species and life stage on helminth community composition and helminth species richness. We examined 328 amphibians including 218 northern leopard frogs and 110 wood frogs collected between April and August of 2009 and 2010 in the Sheyenne National Grasslands of southeastern North Dakota. Echinostomatid metacercariae were the most common helminths found, with the highest prevalence in metamorphic wood frogs. Host species significantly influenced helminth community composition, and host life stage significantly influenced the component community composition of leopard frogs. In these sympatric populations, leopard frogs were common hosts for adult trematodes whereas wood frogs exhibited a higher prevalence of nematodes with direct life cycles. Metamorphic frogs were commonly infected with echinostomatid metacercariae and other larval trematodes whereas juvenile and adult frogs were most-frequently infected with directly transmitted nematodes and trophically transmitted trematodes. Accordingly, helminth species richness increased with the developmental life stage of the host.

  1. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities

    PubMed Central

    Henschel, Andreas; Anwar, Muhammad Zohaib; Manohar, Vimitha

    2015-01-01

    Comprehensive mapping of environmental microbiomes in terms of their compositional features remains a great challenge in understanding the microbial biosphere of the Earth. It bears promise to identify the driving forces behind the observed community patterns and whether community assembly happens deterministically. Advances in Next Generation Sequencing allow large community profiling studies, exceeding sequencing data output of conventional methods in scale by orders of magnitude. However, appropriate collection systems are still in a nascent state. We here present a database of 20,427 diverse environmental 16S rRNA profiles from 2,426 independent studies, which forms the foundation of our meta-analysis. We conducted a sample size adaptive all-against-all beta diversity comparison while also respecting phylogenetic relationships of Operational Taxonomic Units(OTUs). After conventional hierarchical clustering we systematically test for enrichment of Environmental Ontology terms and their abstractions in all possible clusters. This post-hoc algorithm provides a novel formalism that quantifies to what extend compositional and semantic similarity of microbial community samples coincide. We automatically visualize significantly enriched subclusters on a comprehensive dendrogram of microbial communities. As a result we obtain the hitherto most differentiated and comprehensive view on global patterns of microbial community diversity. We observe strong clusterability of microbial communities in ecosystems such as human/mammal-associated, geothermal, fresh water, plant-associated, soils and rhizosphere microbiomes, whereas hypersaline and anthropogenic samples are less homogeneous. Moreover, saline samples appear less cohesive in terms of compositional properties than previously reported. PMID:26458130

  2. Global sensitivity analysis of a mathematical model of acute inflammation identifies nonlinear dependence of cumulative tissue damage on host interleukin-6 responses.

    PubMed

    Mathew, Shibin; Bartels, John; Banerjee, Ipsita; Vodovotz, Yoram

    2014-10-07

    The precise inflammatory role of the cytokine interleukin (IL)-6 and its utility as a biomarker or therapeutic target have been the source of much debate, presumably due to the complex pro- and anti-inflammatory effects of this cytokine. We previously developed a nonlinear ordinary differential equation (ODE) model to explain the dynamics of endotoxin (lipopolysaccharide; LPS)-induced acute inflammation and associated whole-animal damage/dysfunction (a proxy for the health of the organism), along with the inflammatory mediators tumor necrosis factor (TNF)-α, IL-6, IL-10, and nitric oxide (NO). The model was partially calibrated using data from endotoxemic C57Bl/6 mice. Herein, we investigated the sensitivity of the area under the damage curve (AUCD) to the 51 rate parameters of the ODE model for different levels of simulated LPS challenges using a global sensitivity approach called Random Sampling High Dimensional Model Representation (RS-HDMR). We explored sufficient parametric Monte Carlo samples to generate the variance-based Sobol' global sensitivity indices, and found that inflammatory damage was highly sensitive to the parameters affecting the activity of IL-6 during the different stages of acute inflammation. The AUCIL6 showed a bimodal distribution, with the lower peak representing healthy response and the higher peak representing sustained inflammation. Damage was minimal at low AUCIL6, giving rise to a healthy response. In contrast, intermediate levels of AUCIL6 resulted in high damage, and this was due to the insufficiency of damage recovery driven by anti-inflammatory responses from IL-10 and the activation of positive feedback sustained by IL-6. At high AUCIL6, damage recovery was interestingly restored in some population of simulated animals due to the NO-mediated anti-inflammatory responses. These observations suggest that the host's health status during acute inflammation depends in a nonlinear fashion on the magnitude of the inflammatory stimulus

  3. Both host plant and ecosystem engineer identity influence leaf-tie impacts on the arthropod community of Quercus.

    PubMed

    Wang, H George; Marquis, Robert J; Baer, Christina S

    2012-10-01

    Many insect herbivores build shelters on plants, which are then colonized by other arthropod species. To understand the impacts of such ecosystem engineering on associated species, the contributions of ecosystem engineer and host-plant identities must be understood. We investigated these contingencies at the patch scale using two species of leaf-tying caterpillars, which vary in size and tie construction mode, on eight species of oak (Quercus) trees, which vary in leaf size and leaf chemistry. We created three types of artificial leaf ties by clipping together pairs of adjacent leaves using metal hair clips. We left the first type of leaf tie empty while adding individuals of the leaf-tying caterpillars of either Pseudotelphusa quercinigracella or Psilocorsis cryptolechiella to the other two. We also created a control treatment of untied leaves by affixing clips to single leaves. Leaf ties increased occupancy in the early season and arthropod alpha diversity throughout the experiment, on average fourfold. Furthermore, the presence of leaf ties increased arthropod species density on average three times and abundance 10-35 times, depending on the plant species. The mean phenolic content of the leaves of each oak species was positively correlated with the leaf-tie effect on abundance and negatively correlated with the leaf-tie effect on species diversity. Species diversity, but not abundance, was affected by the identity of the tie-maker. Arthropod species composition differed between untied leaves and artificial leaf ties, and between ties made by the two leaf-tier species. Our results demonstrate that the presence of leaf ties adds to habitat diversity within the oak-herbivore system, not only by creating a new kind of microhabitat (the leaf tie) within trees, but also by exacerbating differences among the eight oak species in apparent habitat quality. The identity of the leaf-tying caterpillar adds to this heterogeneity by creating leaf ties of different size, thus

  4. Using community-based participatory research to identify potential interventions to overcome barriers to adolescents’ healthy eating and physical activity

    PubMed Central

    Goh, Ying-Ying; Sipple-Asher, Bessie Ko; Uyeda, Kimberly; Hawes-Dawson, Jennifer; Olarita-Dhungana, Josephina; Ryan, Gery W.; Schuster, Mark A.

    2010-01-01

    Using a community-based participatory research approach, we explored adolescent, parent, and community stakeholder perspectives on barriers to healthy eating and physical activity, and intervention ideas to address adolescent obesity. We conducted 14 adolescent focus groups (n = 119), 8 parent focus groups (n = 63), and 28 interviews with community members (i.e., local experts knowledgeable about youth nutrition and physical activity). Participants described ecological and psychosocial barriers in neighborhoods (e.g., lack of accessible nutritious food), in schools (e.g., poor quality of physical education), at home (e.g., sedentary lifestyle), and at the individual level (e.g., lack of nutrition knowledge). Participants proposed interventions such as nutrition classes for families, addition of healthy school food options that appeal to students, and non-competitive physical education activities. Participants supported health education delivered by students. Findings demonstrate that community-based participatory research is useful for revealing potentially feasible interventions that are acceptable to community members. PMID:19544091

  5. Pathogen and host differences in bacterial adherence to human buccal epithelial cells in a northeast Brazilian community.

    PubMed Central

    Walser, B L; Newman, R D; Lima, A A; Guerrant, R L

    1992-01-01

    The adherence of several strains of Escherichia coli to human buccal epithelial cells was studied, using cells obtained from five groups: healthy adults, healthy children, children with acute diarrhea, children with persistent diarrhea associated with cryptosporidial parasites, and children with noncryptosporidial persistent diarrhea. All groups lived or worked in an urban slum in northeastern Brazil. Samples of buccal epithelial cells from subjects in each of these groups were incubated with wild-type E. coli K-12 (strain C600), the enteroaggregative E. coli strains 17-2 and PDAS 30-5, CFA/II-positive E. coli 1392+ and its plasmid-cured derivative 1392-, and hydrophobic E. coli 132-3. Samples were evaluated microscopically to determine background contamination and the percentage of cells with more than 15% of their surface area obscured by adherent bacteria after incubation and washing. The assay was tested under field conditions and was shown to produce reliable and consistent results. Both enteroaggregative strains of E. coli were shown to adhere to a significantly higher percentage of all groups of human buccal epithelial cells than any of the other tested strains. In addition, buccal epithelial cells from children with nonparasitic persistent diarrhea showed substantially more bacterial adherence in both the native state and with all tested strains of E. coli than did cells from children with persistent cryptosporidial diarrhea or acute diarrhea or from healthy controls. This study provides evidence that enteroaggregative strains of E. coli demonstrate increased adherence to human buccal epithelial cells (as well as to cultured HEp-2 cells) and that buccal epithelial cells from children with noncryptosporidial persistent diarrhea appear to be more susceptible to bacterial adherence and colonization than buccal epithelial cells from control groups. These findings suggest that host differences as well as pathogen differences are important in the pathogenesis of

  6. Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system

    PubMed Central

    Inagaki, Fumio; Kuypers, Marcel M. M.; Tsunogai, Urumu; Ishibashi, Jun-ichiro; Nakamura, Ko-ichi; Treude, Tina; Ohkubo, Satoru; Nakaseama, Miwako; Gena, Kaul; Chiba, Hitoshi; Hirayama, Hisako; Nunoura, Takuro; Takai, Ken; Jørgensen, Bo B.; Horikoshi, Koki; Boetius, Antje

    2006-01-01

    Increasing levels of CO2 in the atmosphere are expected to cause climatic change with negative effects on the earth's ecosystems and human society. Consequently, a variety of CO2 disposal options are discussed, including injection into the deep ocean. Because the dissolution of CO2 in seawater will decrease ambient pH considerably, negative consequences for deep-water ecosystems have been predicted. Hence, ecosystems associated with natural CO2 reservoirs in the deep sea, and the dynamics of gaseous, liquid, and solid CO2 in such environments, are of great interest to science and society. We report here a biogeochemical and microbiological characterization of a microbial community inhabiting deep-sea sediments overlying a natural CO2 lake at the Yonaguni Knoll IV hydrothermal field, southern Okinawa Trough. We found high abundances (>109 cm−3) of microbial cells in sediment pavements above the CO2 lake, decreasing to strikingly low cell numbers (107 cm−3) at the liquid CO2/CO2-hydrate interface. The key groups in these sediments were as follows: (i) the anaerobic methanotrophic archaea ANME-2c and the Eel-2 group of Deltaproteobacteria and (ii) sulfur-metabolizing chemolithotrophs within the Gamma- and Epsilonproteobacteria. The detection of functional genes related to one-carbon assimilation and the presence of highly 13C-depleted archaeal and bacterial lipid biomarkers suggest that microorganisms assimilating CO2 and/or CH4 dominate the liquid CO2 and CO2-hydrate-bearing sediments. Clearly, the Yonaguni Knoll is an exceptional natural laboratory for the study of consequences of CO2 disposal as well as of natural CO2 reservoirs as potential microbial habitats on early Earth and other celestial bodies. PMID:16959888

  7. Host-Parasite Interactions in Chagas Disease: Genetically Unidentical Isolates of a Single Trypanosoma cruzi Strain Identified In Vitro via LSSP-PCR

    PubMed Central

    Nogueira-Paiva, Nívia Carolina; Vieira, Paula Melo de Abreu; Oliveri, Larissa Maris Rezende; Fonseca, Kátia da Silva; Pound-Lana, Gwenaelle; de Oliveira, Maykon Tavares; de Lana, Marta; Veloso, Vanja Maria; Reis, Alexandre Barbosa; Carneiro, Cláudia Martins

    2015-01-01

    The present study aims at establishing whether the diversity in pathogenesis within a genetically diverse host population infected with a single polyclonal strain of Trypanosoma cruzi is due to selection of specific subpopulations within the strain. For this purpose we infected Swiss mice, a genetically diverse population, with the polyclonal strain of Trypanosoma cruzi Berenice-78 and characterized via LSSP-PCR the kinetoplast DNA of subpopulations isolated from blood samples collected from the animals at various times after inoculation (3, 6 and 12 months after inoculation). We examined the biological behavior of the isolates in acellular medium and in vitro profiles of infectivity in Vero cell medium. We compared the characteristics of the isolates with the inoculating strain and with another strain, Berenice 62, isolated from the same patient 16 years earlier. We found that one of the isolates had intermediate behavior in comparison with Berenice-78 and Berenice-62 and a significantly different genetic profile by LSSP-PCR in comparison with the inoculating strain. We hereby demonstrate that genetically distinct Trypanosoma cruzi isolates may be obtained upon experimental murine infection with a single polyclonal Trypanosoma cruzi strain. PMID:26359864

  8. Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem.

    PubMed

    Brown, Shawn P; Callaham, Mac A; Oliver, Alena K; Jumpponen, Ari

    2013-12-01

    Prescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000 + reads per sample after subsampling) indicate that frequent fires (3-year fire interval) shift soil fungus communities, whereas infrequent fires (6-year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals, whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that (1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; (2) frequent prescribed fires elicit a shift in soil fungal communities; and (3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives.

  9. Identifying and Compiling Information about Community Based Organizations' Efforts to Serve In-School Youth. Volume I: Final Notes.

    ERIC Educational Resources Information Center

    InterAmerica Research Associates, Rosslyn, VA.

    These final notes are the record of the activities which took place in a series of nineteen conferences held for state coordinators of career education and representatives of national community-based organizations. In the sessions, representatives of the national organizations and educators discussed how the organizations could cooperate with the…

  10. Host, vehicular and environmental factors responsible for road traffic crashes in a nigerian city: identifiable issues for road traffic injury control

    PubMed Central

    Adeoye, Peter Oladapo; Kadri, Dotun Musiliu; Bello, Jibril Oyekunle; Ofoegbu, Chima Kingsley Pascal; Abdur-Rahman, Lukman Olajide; Adekanye, Adedeji Olugbenga; Solagberu, Babatunde Akeeb

    2014-01-01

    Introduction Road traffic injury (RTI) has assumed major public health importance world-wide and the burden is heavier on the health-care infrastructure of countries in Sub-Saharan Africa. In Nigeria, RTI is the leading cause of trauma related morbidity and mortality. While there are some published epidemiological reports on RTI in the region, studies on the mechanism of causation of road traffic crashes (RTC) are not available. Methods Over a 9-month period, we prospectively captured the 571 victims of RTC presenting to a single tertiary health care center in Nigeria. Data collected include demographic data, Mechanism of causation of RTC, Injuries sustained and outcomes. Results Over three-quarters of the victims are young people and half were either traders (27.5%) or students (20%). Pedestrians, motorcycle riders and open truck occupants (people sitting at the rear loading compartment of trucks) often had fatal injuries. Analysis of collision patterns showed that lone crashes were the most frequent though car-to-motorcycle crashes caused a quarter of the deaths. Host factors (over-speeding driver, driver misjudgment, sleeping driver etc.) were responsible for four-fifths of the crashes while vehicular and environmental factors accounted for the remaining. On binary regression analysis, head injured victims had higher odds of dying than the non-head injured (Odds ratio = 6.5). Conclusion This paper elucidates the mechanisms of causation of and types of injuries sustained following RTC in Nigeria and thus provide opportunities for prevention and control of this unacceptable situation. PMID:25780490

  11. Community.

    ERIC Educational Resources Information Center

    Grauer, Kit, Ed.

    1995-01-01

    Art in context of community is the theme of this newsletter. The theme is introduced in an editorial "Community-Enlarging the Definition" (Kit Grauer). Related articles include: (1) "The Children's Bridge is not Destroyed: Heart in the Middle of the World" (Emil Robert Tanay); (2) "Making Bridges: The Sock Doll…

  12. Using Observational Assessment to Help Identify Factors Associated with Parent Participation Engagement in Community-Based Child Mental Health Services

    PubMed Central

    Stadnick, Nicole A.; Haine-Schlagel, Rachel; Martinez, Jonathan I.

    2016-01-01

    Background Parent engagement in child mental health (MH) services has received growing attention due to its significance in intervention outcomes and evidence-based care. In particular, parent participation engagement (PPE) reflects active and responsive contributions in and between sessions. Yet, limited research has examined factors associated with PPE, particularly within community-based MH services where PPE is low and highly diverse families are often served. Objective This study examined child, parent, and therapist factors associated with PPE in a sample of racially/ethnically diverse parent–child dyads receiving publicly-funded, community-based MH services. Methods This prospective study included 18 parent–child dyads receiving community-based MH services from 17 therapists in five outpatient clinics for child disruptive behaviors. PPE was measured using in-session observational assessment of therapy recordings. Child factors that were examined included age, first time child MH service use, and intensity of child behavior problems. Parent factors included ethnicity, education, depression symptoms, and parent motivation to participate in therapy. Therapist factors included therapist training in parent-mediation interventions, attitudes towards organizational functioning, and attitudes towards parent participation strategies. Results Results from linear regression analyses indicated that first time child MH service use, intensity of child behavior problems, parent ethnicity and motivation to participate in therapy, as well as therapists’ training and attitudes about their practice were each significantly associated with PPE. Conclusions Results highlight specific child, parent, and therapist characteristics that may impact observed PPE in child MH therapy. These findings underscore the importance of considering the influence of family and provider factors on PPE in community-based child MH services. PMID:27587943

  13. A unique midgut-associated bacterial community hosted by the cave beetle Cansiliella servadeii (Coleoptera: Leptodirini) reveals parallel phylogenetic divergences from universal gut-specific ancestors

    PubMed Central

    2013-01-01

    Background Cansiliella servadeii (Coleoptera) is an endemic troglobite living in deep carbonate caves in North-Eastern Italy. The beetle constantly moves and browses in its preferred habitat (consisting in flowing water and moonmilk, a soft speleothem colonized by microorganisms) self-preens to convey material from elytra, legs, and antennae towards the mouth. We investigated its inner and outer microbiota using microscopy and DNA-based approaches. Results Abundant microbial cell masses were observed on the external appendages. Cansiliella’s midgut is fully colonized by live microbes and culture-independent analyses yielded nearly 30 different 16S phylotypes that have no overlap with the community composition of the moonmilk. Many of the lineages, dominated by Gram positive groups, share very low similarity to database sequences. However for most cases, notwithstanding their very limited relatedness with existing records, phylotypes could be assigned to bacterial clades that had been retrieved from insect or other animals’ digestive traits. Conclusions Results suggest a history of remote separation from a common ancestor that harboured a set of gut-specific bacteria whose functions are supposedly critical for host physiology. The phylogenetic and coevolutionary implications of the parallel occurrences of these prokaryotic guilds appear to apply throughout a broad spectrum of animal diversity. Their persistence and conservation underlies a possibly critical role of precise bacterial assemblages in animal-bacteria interactions. PMID:23758657

  14. Contributions by Host Trees and Insect Activity to Bacterial Communities in Dendroctonus valens (Coleoptera: Curculionidae) Galleries, and Their High Overlap With Other Microbial Assemblages of Bark Beetles.

    PubMed

    Mason, Charles J; Hanshew, Alissa S; Raffa, Kenneth F

    2016-04-01

    Bark beetles are associated with a diversity of symbiotic microbiota that can mediate interactions with their host plants. Dendroctonus valens LeConte is a widely distributed bark beetle in North and Central America, and initiates solitary attacks on several species of Pinus in the Great Lakes region. In this study, we aimed to further characterize the bacterial community associated with D. valens feeding galleries using next-generation sequencing, and the possible contributions of both tree-resident and insect-associated bacteria to these consortia. We found that D. valens galleries harbor a diversity of microbial associates. Many of these associates were classified into a few taxonomic groups, of which Gammaproteobacteria were the most abundant class. Of the Gammaproteobacteria detected, many formed clades with 16S-rRNA sequences of bacteria previously associated with D. valens Many of the bacteria sequences detected in the galleries were similar to bacteria that function in detoxification, kairomone metabolism, and nitrogen fixation and cycling. The abundance of bacteria in galleries were 7× and 44× higher than in the surrounding uninfested tissues, and that were not attacked by D. valens, respectively. This suggests that the bacteria present in beetle galleries are largely introduced by D. valens and proliferate in this environment.

  15. Engaging the Public to Identify Opportunities to Improve Critical Care: A Qualitative Analysis of an Open Community Forum

    PubMed Central

    Potestio, Melissa L.; Boyd, Jamie M.; Bagshaw, Sean M.; Heyland, Daren; Oxland, Peter; Doig, Christopher J.; Zygun, Dave; Stelfox, Henry T.

    2015-01-01

    Objective To engage the public to understand how to improve the care of critically ill patients. Design A qualitative content analysis of an open community forum (Café Scientifique). Setting Public venue in Calgary, Alberta, Canada. Participants Members of the general public including patients, families of patients, health care providers, and members of the community at large. Methods A panel of researchers, decision-makers, and a family member led a Café Scientifique, an informal dialogue between the populace and experts, over three-hours to engage the public to understand how to improve the care of critically ill patients. Conventional qualitative content analysis was used to analyze the data. The inductive analysis occurred in three phases: coding, categorizing, and developing themes. Results Thirty-eight members of the public (former ICU patients, family members of patients, providers, community members) attended. Participants focused the discussion and provided concrete suggestions for improvement around communication (family as surrogate voice, timing of conversations, decision tools) and provider well-being and engagement, as opposed to medical interventions in critical care. Conclusions Café participants believe patient and family centered care is important to ensure high-quality care in the ICU. A Café Scientifique is a valuable forum to engage the public to contribute to priority setting areas for research in critical care, as well as a platform to share lived experience. Research stakeholders including health care organizations, governments, and funding organizations should provide more opportunities for the public to engage in meaningful conversations about how to best improve healthcare. PMID:26580406

  16. Natal Host Plants Can Alter Herbivore Competition

    PubMed Central

    Pan, Huipeng; Preisser, Evan L.; Su, Qi; Jiao, Xiaoguo; Xie, Wen; Wang, Shaoli; Wu, Qingjun

    2016-01-01

    Interspecific competition between herbivores is widely recognized as an important determinant of community structure. Although researchers have identified a number of factors capable of altering competitive interactions, few studies have addressed the influence of neighboring plant species. If adaptation to/ epigenetic effects of an herbivore’s natal host plant alter its performance on other host plants, then interspecific herbivore interactions may play out differently in heterogeneous and homogenous plant communities. We tested wether the natal host plant of a whitefly population affected interactions between the Middle-east Asia Minor 1 (MEAM1) and Mediterranean (MED) cryptic species of the whitefly Bemisia tabaci by rearing the offspring of a cabbage-derived MEAM1 population and a poinsettia-derived MED population together on three different host plants: cotton, poinsettia, and cabbage. We found that MED dominated on poinsettia and that MEAM1 dominated on cabbage, results consistent with previous research. MED also dominated when reared with MEAM1 on cotton, however, a result at odds with multiple otherwise-similar studies that reared both species on the same natal plant. Our work provides evidence that natal plants affect competitive interactions on another plant species, and highlights the potential importance of neighboring plant species on herbivore community composition in agricultral systems. PMID:28030636

  17. Host Genetic and Environmental Effects on Mouse Cecum Microbiota

    SciTech Connect

    Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana A; Campbell, Alisha G; Yang, Zamin Koo; Wymore, Ann; Palumbo, Anthony Vito; Podar, Mircea

    2012-01-01

    The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.

  18. Commercially Hosted Government Payloads: Lessons from Recent Programs

    NASA Technical Reports Server (NTRS)

    Andraschko, Mark A.; Antol, Jeffrey; Horan, Stephen; Neil, Doreen

    2011-01-01

    In a commercially hosted operational mode, a scientific instrument or operational device is attached to a spacecraft but operates independently from the spacecraft s primary mission. Despite the expected benefits of this arrangement, there are few examples of hosted payload programs actually being executed by government organizations. The lack of hosted payload programs is largely driven by programmatic challenges, both real and perceived, rather than by technical challenges. Partly for these reasons, NASA has not sponsored a hosted payload program, in spite of the benefits and visible community interest in doing so. In the interest of increasing the use of hosted payloads across the space community, this paper seeks to alleviate concerns about hosted payloads by identifying these programmatic challenges and presenting ways in which they can be avoided or mitigated. Despite the challenges, several recent hosted payload programs have been successfully completed or are currently in progress. This paper presents an assessment of these programs, with a focus on acquisition, costs, schedules, risks, and other programmatic aspects. The hosted payloads included in this study are the Federal Aviation Administration's Wide Area Augmentation System (WAAS) payloads, United States Coast Guard's Automatic Identification System (AIS) demonstration payload, Department of Defense's IP Router In Space (IRIS) demonstration payload, the United States Air Force's Commercially Hosted Infrared Payload (CHIRP), and the Australian Defence Force's Ultra High Frequency (UHF) payload. General descriptions of each of these programs are presented along with issues that have been encountered and lessons learned from those experiences. A set of recommended approaches for future hosted payload programs is presented, with a focus on addressing risks or potential problem areas through smart and flexible contracting up front. This set of lessons and recommendations is broadly applicable to future

  19. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities.

    PubMed

    Hettich, Robert L; Sharma, Ritin; Chourey, Karuna; Giannone, Richard J

    2012-06-01

    The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics-the characterization of the complement of proteins expressed by a microbial community in an environmental sample.

  20. Microbial metaproteomics: Identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

    SciTech Connect

    Hettich, Robert {Bob} L; Sharma, Ritin; Chourey, Karuna; Giannone, Richard J

    2012-01-01

    The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics - the characterization of the complement of proteins expressed by a microbial community in an environmental sample

  1. Developmental Profiles of Infants and Toddlers with Autism Spectrum Disorders Identified Prospectively in a Community-Based Setting

    ERIC Educational Resources Information Center

    Barbaro, Josephine; Dissanayake, Cheryl

    2012-01-01

    This prospective, longitudinal, study charted the developmental profiles of young children with Autism Spectrum Disorders (ASD) identified through routine developmental surveillance. 109 children with Autistic Disorder (AD), "broader" ASD, and developmental and/or language delays (DD/LD) were assessed using the Mullen Scales of Early Learning…

  2. Integrating human health and environmental health into the DPSIR framework: a tool to identify research opportunities for sustainable and healthy communities.

    PubMed

    Yee, Susan H; Bradley, Patricia; Fisher, William S; Perreault, Sally D; Quackenboss, James; Johnson, Eric D; Bousquin, Justin; Murphy, Patricia A

    2012-12-01

    The U.S. Environmental Protection Agency has recently realigned its research enterprise around the concept of sustainability. Scientists from across multiple disciplines have a role to play in contributing the information, methods, and tools needed to more fully understand the long-term impacts of decisions on the social and economic sustainability of communities. Success will depend on a shift in thinking to integrate, organize, and prioritize research within a systems context. We used the Driving forces-Pressures-State-Impact-Response (DPSIR) framework as a basis for integrating social, cultural, and economic aspects of environmental and human health into a single framework. To make the framework broadly applicable to sustainability research planning, we provide a hierarchical system of DPSIR keywords and guidelines for use as a communication tool. The applicability of the integrated framework was first tested on a public health issue (asthma disparities) for purposes of discussion. We then applied the framework at a science planning meeting to identify opportunities for sustainable and healthy communities research. We conclude that an integrated systems framework has many potential roles in science planning, including identifying key issues, visualizing interactions within the system, identifying research gaps, organizing information, developing computational models, and identifying indicators.

  3. Identifying perceived barriers and benefits to reducing energy consumption in an affordable housing complex using the Community-Based Social Marketing model

    NASA Astrophysics Data System (ADS)

    Reaves, Daniel

    Energy production and consumption has a negative impact on both environmental and human health. Energy consumption can be directly impacted by human behavior, especially in the residential sector. As a result, this sector has been studied significantly; however, energy reducing behavior change research focusing on the affordable housing sector has not been studied thoroughly to date. This study seeks to implement the first two phases of the Community Based Social Marketing (CBSM) framework in an affordable housing setting. The goals were to identify the optimal behaviors for energy reduction based on phase one survey results and to identify the perceived benefits and barriers associated with those behaviors. Additionally, this study identified nuances in the CBSM process that researchers should take into consideration when implementing CBSM in an affordable housing environment.

  4. Host specificity and co-speciation in avian haemosporidia in the Western Cape, South Africa.

    PubMed

    Okanga, Sharon; Cumming, Graeme S; Hockey, Philip A R; Nupen, Lisa; Peters, Jeffrey L

    2014-01-01

    Host and pathogen ecology are often closely linked, with evolutionary processes often leading to the development of host specificity traits in some pathogens. Host specificity may range from 'generalist', where pathogens infect any available competent host; to 'specialist', where pathogens repeatedly infect specific host species or families. Avian malaria ecology in the region remains largely unexplored, despite the presence of vulnerable endemic avian species. We analysed the expression of host specificity in avian haemosporidia, by applying a previously developed host specificity index to lineages isolated from wetland passerines in the Western Cape, South Africa. Parasite lineages were isolated using PCR and identified when possible using matching lineages deposited in GenBank and in MalAvi. Parasitic clades were constructed from phylogenetic trees consisting of Plasmodium and Haemoproteus lineages. Isolated lineages matched some strains of Plasmodium relictum, P. elongatum, Haemoproteus sylvae and H. lanii. Plasmodium lineages infected a wide range of hosts from several avian families in a generalist pattern of infection. Plasmodium spp. also exhibited an infection trend according to host abundance rather than host species. By contrast, Haemoproteus lineages were typically restricted to one or two host species or families, and displayed higher host fidelity than Plasmodium spp. The findings confirm that a range of host specificity traits are exhibited by avian haemosporidia in the region. The traits show the potential to not only impact infection prevalence within specific host species, but also to affect patterns of infection at the community level.

  5. Host Specificity And Co-Speciation In Avian Haemosporidia In The Western Cape, South Africa

    PubMed Central

    Okanga, Sharon; Cumming, Graeme S.; Hockey, Philip A. R.; Nupen, Lisa; Peters, Jeffrey L.

    2014-01-01

    Host and pathogen ecology are often closely linked, with evolutionary processes often leading to the development of host specificity traits in some pathogens. Host specificity may range from ‘generalist’, where pathogens infect any available competent host; to ‘specialist’, where pathogens repeatedly infect specific host species or families. Avian malaria ecology in the region remains largely unexplored, despite the presence of vulnerable endemic avian species. We analysed the expression of host specificity in avian haemosporidia, by applying a previously developed host specificity index to lineages isolated from wetland passerines in the Western Cape, South Africa. Parasite lineages were isolated using PCR and identified when possible using matching lineages deposited in GenBank and in MalAvi. Parasitic clades were constructed from phylogenetic trees consisting of Plasmodium and Haemoproteus lineages. Isolated lineages matched some strains of Plasmodium relictum, P. elongatum, Haemoproteus sylvae and H. lanii. Plasmodium lineages infected a wide range of hosts from several avian families in a generalist pattern of infection. Plasmodium spp. also exhibited an infection trend according to host abundance rather than host species. By contrast, Haemoproteus lineages were typically restricted to one or two host species or families, and displayed higher host fidelity than Plasmodium spp. The findings confirm that a range of host specificity traits are exhibited by avian haemosporidia in the region. The traits show the potential to not only impact infection prevalence within specific host species, but also to affect patterns of infection at the community level. PMID:24498273

  6. Uncertainty Analysis of Runoff Simulations and Parameter Identifiability in the Community Land Model – Evidence from MOPEX Basins

    SciTech Connect

    Huang, Maoyi; Hou, Zhangshuan; Leung, Lai-Yung R.; Ke, Yinghai; Liu, Ying; Fang, Zhufeng; Sun, Yu

    2013-12-01

    With the emergence of earth system models as important tools for understanding and predicting climate change and implications to mitigation and adaptation, it has become increasingly important to assess the fidelity of the land component within earth system models to capture realistic hydrological processes and their response to the changing climate and quantify the associated uncertainties. This study investigates the sensitivity of runoff simulations to major hydrologic parameters in version 4 of the Community Land Model (CLM4) by integrating CLM4 with a stochastic exploratory sensitivity analysis framework at 20 selected watersheds from the Model Parameter Estimation Experiment (MOPEX) spanning a wide range of climate and site conditions. We found that for runoff simulations, the most significant parameters are those related to the subsurface runoff parameterizations. Soil texture related parameters and surface runoff parameters are of secondary significance. Moreover, climate and soil conditions play important roles in the parameter sensitivity. In general, site conditions within water-limited hydrologic regimes and with finer soil texture result in stronger sensitivity of output variables, such as runoff and its surface and subsurface components, to the input parameters in CLM4. This study demonstrated the feasibility of parameter inversion for CLM4 using streamflow observations to improve runoff simulations. By ranking the significance of the input parameters, we showed that the parameter set dimensionality could be reduced for CLM4 parameter calibration under different hydrologic and climatic regimes so that the inverse problem is less ill posed.

  7. Novel Phenol-soluble Modulin Derivatives in Community-associated Methicillin-resistant Staphylococcus aureus Identified through Imaging Mass Spectrometry*

    PubMed Central

    Gonzalez, David J.; Okumura, Cheryl Y.; Hollands, Andrew; Kersten, Roland; Akong-Moore, Kathryn; Pence, Morgan A.; Malone, Cheryl L.; Derieux, Jaclyn; Moore, Bradley S.; Horswill, Alexander R.; Dixon, Jack E.; Dorrestein, Pieter C.; Nizet, Victor

    2012-01-01

    Staphylococcus aureus causes a wide range of human disease ranging from localized skin and soft tissue infections to potentially lethal systemic infections. S. aureus has the biosynthetic ability to generate numerous virulence factors that assist in circumventing the innate immune system during disease pathogenesis. Recent studies have uncovered a set of extracellular peptides produced by community-associated methicillin-resistant S. aureus (CA-MRSA) with homology to the phenol-soluble modulins (PSMs) from Staphylococcus epidermidis. CA-MRSA PSMs contribute to skin infection and recruit and lyse neutrophils, and truncated versions of these peptides possess antimicrobial activity. In this study, novel CA-MRSA PSM derivatives were discovered by the use of microbial imaging mass spectrometry. The novel PSM derivatives are compared with their parent full-length peptides for changes in hemolytic, cytolytic, and neutrophil-stimulating activity. A potential contribution of the major S. aureus secreted protease aureolysin in processing PSMs is demonstrated. Finally, we show that PSM processing occurs in multiple CA-MRSA strains by structural confirmation of additional novel derivatives. This work demonstrates that IMS can serve as a useful tool to go beyond genome predictions and expand our understanding of the important family of small peptide virulence factors. PMID:22371493

  8. Identifying motivators and barriers to older community-dwelling people participating in resistance training: A cross-sectional study.

    PubMed

    Burton, Elissa; Lewin, Gill; Pettigrew, Simone; Hill, Anne-Marie; Bainbridge, Liz; Farrier, Kaela; Langdon, Trish; Airey, Phil; Hill, Keith D

    2016-08-25

    Participation rates of older people in resistance training (RT) are low despite increasing research showing many health benefits. To increase the number of older people participating in RT it is important to know what would motivate people to become involved, what motivates those who participate to continue, and the factors preventing many older people from commencing participation. To investigate these issues, a questionnaire was mailed to three groups of older people: (1) those receiving home care services, (2) members of a peak non-government seniors' organisation and (3) those participating in a specific gym-based RT programme. In total, 1327 questionnaires were returned (response rate = 42.5%). To feel good physically and mentally were the main reasons motivating participation among all three groups, and falls prevention was identified as an important motivator for the home care respondents. Pain, injury and illness were the main barriers to participating, or continuing to participate. However, medical advice was a factor influencing participation commencement. The results suggest organisations providing RT programmes for older people should tailor the promotion and delivery of programmes to address key motivators and barriers specific to each group to increase the proportion of older people initiating and continuing to engage in RT.

  9. Predicting the spatial distribution of a seabird community to identify priority conservation areas in the Timor Sea.

    PubMed

    Lavers, Jennifer L; Miller, Mark G R; Carter, Michael J; Swann, George; Clarke, Rohan H

    2014-12-01

    Understanding spatial and temporal variability in the distribution of species is fundamental to the conservation of marine and terrestrial ecosystems. To support strategic decision making aimed at sustainable management of the oceans, such as the establishment of protected areas for marine wildlife, we identified areas predicted to support multispecies seabird aggregations in the Timor Sea. We developed species distribution models for 21 seabird species based on at-sea survey observations from 2000-2013 and oceanographic variables (e.g., bathymetry). We applied 4 statistical modeling techniques and combined the results into an ensemble model with robust performance. The ensemble model predicted the probability of seabird occurrence in areas where few or no surveys had been conducted and demonstrated 3 areas of high seabird richness that varied little between seasons. These were located within 150 km of Adele Island, Ashmore Reef, and the Lacepede Islands, 3 of the largest aggregations of breeding seabirds in Australia. Although these breeding islands were foci for high species richness, model performance was greatest for 3 nonbreeding migratory species that would have been overlooked had regional monitoring been restricted to islands. Our results indicate many seabird hotspots in the Timor Sea occur outside existing reserves (e.g., Ashmore Reef Marine Reserve), where shipping, fisheries, and offshore development likely pose a threat to resident and migratory populations. Our results highlight the need to expand marine spatial planning efforts to ensure biodiversity assets are appropriately represented in marine reserves. Correspondingly, our results support the designation of at least 4 new important bird areas, for example, surrounding Adele Island and Ashmore Reef.

  10. Identifying nutrient reference sites in nutrient-enriched regions-Using algal, invertebrate, and fish-community measures to identify stressor-breakpoint thresholds in Indiana rivers and streams, 2005-9

    USGS Publications Warehouse

    Caskey, Brian J.; Bunch, Aubrey R.; Shoda, Megan E.; Frey, Jeffrey W.; Selvaratnam, Shivi; Miltner, Robert J.

    2013-01-01

    Excess nutrients in aquatic ecosystems can lead to shifts in species composition, reduced dissolved oxygen concentrations, fish kills, and toxic algal blooms. In this study, nutrients, periphyton chlorophyll a (CHLa), and invertebrate- and fishcommunity data collected during 2005-9 were analyzed from 318 sites on Indiana rivers and streams. The objective of this study was to determine which invertebrate and fish-taxa attributes best reflect the conditions of streams in Indiana along a gradient of nutrient concentrations by (1) determining statistically and ecologically significant relations among the stressor (total nitrogen, total phosphorus, and periphyton CHLa) and response (invertebrate and fish community) variables; and (2) determining the levels at which invertebrate- and fish-community measures change in response to nutrients or periphyton CHLa. For water samples at the headwater sites, total nitrogen (TN) concentrations ranged from 0.343 to 21.6 milligrams per liter (mg/L) (median 2.12 mg/L), total phosphorus (TP) concentrations ranged from 0.050 to 1.44 mg/L (median 0.093 mg/L), and periphyton CHLa ranged from 0.947 to 629 mg/L (median 69.7 mg/L). At the wadable sites, TN concentrations ranged from 0.340 to 10.0 mg/L (median 2.31 mg/L), TP concentrations ranged from 0.050 to 1.24 mg/L (median 0.110 mg/L), and periphyton CHLa ranged from 0.383 to 719 mg/L (median 44.7 mg/L). Recursive partitioning identified statistically significant low and high breakpoint thresholds on invertebrate and fish measures, which demonstrated the ecological response in enriched conditions. The combined community (invertebrate and fish) mean low and high TN breakpoint thresholds were 1.03 and 2.61 mg/L, respectively. The mean low and high breakpoint thresholds for TP were 0.083 and 0.144 mg/L, respectively. The mean low and high breakpoint thresholds for periphyton CHLa were 20.9 and 98.6 milligrams per square meter (mg/m2), respectively. Additive quantile regression analysis

  11. Identifying and Creating the Next Generation of Community-Based Cancer Prevention Studies: Summary of a National Cancer Institute Think Tank.

    PubMed

    McCaskill-Stevens, Worta; Pearson, Deborah C; Kramer, Barnett S; Ford, Leslie G; Lippman, Scott M

    2017-02-01

    In late 2015, the NCI Division of Cancer Prevention convened cancer prevention research experts and stakeholders to discuss the current state of cancer prevention research, identify key prevention research priorities for the NCI, and identify studies that could be conducted within the NCI Community Oncology Research Program. Goals included identifying cancer prevention research opportunities offering the highest return on investment, exploring the concept of precision prevention and what is needed to advance this area of research, and identifying possible targets for prevention. Four study populations were considered for cancer prevention research: healthy people, those at increased risk for a specific cancer, people with preneoplastic lesions, and children, adolescents, and young adults. Priorities that emerged include screening (e.g., surveillance intervals, tomosynthesis vs. digital mammography), a pre-cancer genome atlas (PreTCGA), HPV vaccines, immunoprevention of noninfectious origins, and overdiagnosis. Challenges exist, as the priority list is ambitious and potentially expensive. Clinical trials need to be carefully designed to include and maximize prospective tissue collection. Exploring existing cofunding mechanisms will likely be necessary. Finally, relationships with a new generation of physician specialists will need to be cultivated to reach the target populations. Cancer Prev Res; 10(2); 99-107. ©2016 AACR.

  12. Broad host range plasmids.

    PubMed

    Jain, Aayushi; Srivastava, Preeti

    2013-11-01

    Plasmids are and will remain important cloning vehicles for biotechnology. They have also been associated with the spread of a number of diseases and therefore are a subject of environmental concern. With the advent of sequencing technologies, the database of plasmids is increasing. It will be of immense importance to identify the various bacterial hosts in which the plasmid can replicate. The present review article describes the features that confer broad host range to the plasmids, the molecular basis of plasmid host range evolution, and applications in recombinant DNA technology and environment.

  13. ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.

    PubMed

    Wei, Guifang; Pan, Li; Du, Huimin; Chen, Junyi; Zhao, Liping

    2004-10-01

    Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.

  14. The One Health approach to identify knowledge, attitudes and practices that affect community involvement in the control of Rift Valley fever outbreaks

    PubMed Central

    Hassan, Osama Ahmed; Affognon, Hippolyte; Rocklöv, Joacim; Mburu, Peter; Sang, Rosemary; Ahlm, Clas; Evander, Magnus

    2017-01-01

    Rift Valley fever (RVF) is a viral mosquito-borne disease with the potential for global expansion, causes hemorrhagic fever, and has a high case fatality rate in young animals and in humans. Using a cross-sectional community-based study design, we investigated the knowledge, attitudes and practices of people living in small village in Sudan with respect to RVF outbreaks. A special One Health questionnaire was developed to compile data from 235 heads of household concerning their knowledge, attitudes, and practices with regard to controlling RVF. Although the 2007 RVF outbreak in Sudan had negatively affected the participants’ food availability and livestock income, the participants did not fully understand how to identify RVF symptoms and risk factors for both humans and livestock. For example, the participants mistakenly believed that avoiding livestock that had suffered spontaneous abortions was the least important risk factor for RVF. Although the majority noticed an increase in mosquito population during the 2007 RVF outbreak, few used impregnated bed nets as preventive measures. The community was reluctant to notify the authorities about RVF suspicion in livestock, a sentinel for human RVF infection. Almost all the respondents stressed that they would not receive any compensation for their dead livestock if they notified the authorities. In addition, the participants believed that controlling RVF outbreaks was mainly the responsibility of human health authorities rather than veterinary authorities. The majority of the participants were aware that RVF could spread from one region to another within the country. Participants received most their information about RVF from social networks and the mass media, rather than the health system or veterinarians. Because the perceived role of the community in controlling RVF was fragmented, the probability of RVF spread increased. PMID:28207905

  15. Key Principles of Community-Based Natural Resource Management: A Synthesis and Interpretation of Identified Effective Approaches for Managing the Commons

    NASA Astrophysics Data System (ADS)

    Gruber, James S.

    2010-01-01

    This article examines recent research on approaches to community-based environmental and natural resource management and reviews the commonalities and differences between these interdisciplinary and multistakeholder initiatives. To identify the most effective characteristics of Community-based natural resource management (CBNRM), I collected a multiplicity of perspectives from research teams and then grouped findings into a matrix of organizational principles and key characteristics. The matrix was initially vetted (or “field tested”) by applying numerous case studies that were previously submitted to the World Bank International Workshop on CBNRM. These practitioner case studies were then compared and contrasted with the findings of the research teams. It is hoped that the developed matrix may be useful to researchers in further focusing research, understanding core characteristics of effective and sustainable CBNRM, providing practitioners with a framework for developing new CBNRM initiatives for managing the commons, and providing a potential resource for academic institutions during their evaluation of their practitioner-focused environmental management and leadership curriculum.

  16. Host specificity of insect herbivores in tropical forests.

    PubMed

    Novotny, Vojtech; Basset, Yves

    2005-06-07

    Studies of host specificity in tropical insect herbivores are evolving from a focus on insect distribution data obtained by canopy fogging and other mass collecting methods, to a focus on obtaining data on insect rearing and experimentally verified feeding patterns. We review this transition and identify persisting methodological problems. Replicated quantitative surveys of plant-herbivore food webs, based on sampling efforts of an order of magnitude greater than is customary at present, may be cost-effectively achieved by small research teams supported by local assistants. Survey designs that separate historical and ecological determinants of host specificity by studying herbivores feeding on the same plant species exposed to different environmental or experimental conditions are rare. Further, we advocate the use of host-specificity measures based on plant phylogeny. Existing data suggest that a minority of species in herbivore communities feed on a single plant species when alternative congeneric hosts are available. Thus, host plant range limits tend to coincide with those of plant genera, rather than species or suprageneric taxa. Host specificity among tropical herbivore guilds decreases in the sequence: granivores > leaf-miners > fructivore > leaf-chewers = sap-suckers > xylophages > root-feeders, thus paralleling patterns observed in temperate forests. Differences in host specificity between temperate and tropical forests are difficult to assess since data on tropical herbivores originate from recent field studies, whereas their temperate counterparts derive from regional host species lists, assembled over many years. No major increase in host specificity from temperate to tropical communities is evident. This conclusion, together with the recent downward revisions of extremely high estimates of tropical species richness, suggest that tropical ecosystems may not be as biodiverse as previously thought.

  17. RNAi of the translation inhibition gene 4E-BP identified from the hard tick, Haemaphysalis longicornis, affects lipid storage during the off-host starvation period of ticks.

    PubMed

    Kume, Aiko; Boldbaatar, Damdinsuren; Takazawa, Yuko; Umemiya-Shirafuji, Rika; Tanaka, Tetsuya; Fujisaki, Kozo

    2012-08-01

    4E-BP, an eIF4E-binding protein, is well known as a cap-dependent translation inhibitor. Here, the 4E-BP homolog, Hl4E-BP, was isolated and identified from the hard tick Haemaphysalis longicornis. Hl4E-BP transcripts were ubiquitously expressed in the active stages, including the larvae, nymphs, and female adults, and the transcription levels were found to be higher in unfed than engorged ticks. In contrast, the expression levels of non-phosphorylated Hl4E-BP, which is a 13.4-kDa protein detected by the anti-recombinant Hl4E-BP antibody, were the highest in engorged ticks and significantly decreased progressively during the unfed starvation period of ticks. The functional role of Hl4E-BP as a metabolic brake was verified by histochemical observations on the lipid storage in midguts and fat bodies during the starvation period using ticks injected with dsHl4E-BP. The results indicate that Hl4E-BP is highly relevant to the lipid storage of ticks during the non-feeding starvation period. Our results suggest, for the first time, that Hl4E-BP may have a crucial role in the starvation resistance of ticks in an off-host condition via lipid metabolism control, although it was unclear whether Hl4E-BP might be involved in lipid synthesis regulation and/or lipid consumption inhibition.

  18. Host-Specific Functional Significance of Caenorhabditis Gut Commensals

    PubMed Central

    Berg, Maureen; Zhou, Xiao Ying; Shapira, Michael

    2016-01-01

    The gut microbiota is an important contributor to host health and fitness. Given its importance, microbiota composition should not be left to chance. However, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. To gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of Caenorhabditis species spanning 200–300 million years of evolution, and raised on different composted soil environments. Comparisons were based on 16S rDNA deep sequencing data, as well as on functional evaluation of gut isolates. Worm microbiotas were distinct from those in their respective soil environment, and included bacteria previously identified as part of the C. elegans core microbiota. Microbiotas differed between experiments initiated with different soil communities, but within each experiment, worm microbiotas clustered according to host identity, demonstrating a dominant contribution of environmental diversity, but also a significant contribution of host genetics. The dominance of environmental contributions hindered identification of host-associated microbial taxa from 16S data. Characterization of gut isolates from C. elegans and C. briggsae, focusing on the core family Enterobacteriaceae, were also unable to expose phylogenetic distinctions between microbiotas of the two species. However, functional evaluation of the isolates revealed host-specific contributions, wherein gut commensals protected their own host from infection, but not a non-host. Identification of commensal host-specificity at the functional level, otherwise overlooked in standard sequence-based analyses, suggests that the contribution of host genetics to shaping of gut microbiotas may be greater than previously realized. PMID:27799924

  19. A Game of Russian Roulette for a Generalist Dinoflagellate Parasitoid: Host Susceptibility Is the Key to Success

    PubMed Central

    Alacid, Elisabet; Park, Myung G.; Turon, Marta; Petrou, Katherina; Garcés, Esther

    2016-01-01

    Marine microbial interactions involving eukaryotes and their parasites play an important role in shaping the structure of phytoplankton communities. These interactions may alter population densities of the main host, which in turn may have consequences for the other concurrent species. The effect generalist parasitoids exert on a community is strongly dependent on the degree of host specificity. Parvilucifera sinerae is a generalist parasitoid able to infect a wide range of dinoflagellates, including toxic-bloom-forming species. A density-dependent chemical cue has been identified as the trigger for the activation of the infective stage. Together these traits make Parvilucifera-dinoflagellate hosts a good model to investigate the degree of specificity of a generalist parasitoid, and the potential effects that it could have at the community level. Here, we present for the first time, the strategy by which a generalist dinoflagellate parasitoid seeks out its host and determine whether it exhibits host preferences, highlighting key factors in determining infection. Our results demonstrate that in its infective stage, P. sinerae is able to sense potential hosts, but does not actively select among them. Instead, the parasitoids contact the host at random, governed by the encounter probability rate and once encountered, the chance to penetrate inside the host cell and develop the infection strongly depends on the degree of host susceptibility. As such, their strategy for persistence is more of a game of Russian roulette, where the chance of survival is dependent on the susceptibility of the host. Our study identifies P. sinerae as a potential key player in community ecology, where in mixed dinoflagellate communities consisting of hosts that are highly susceptible to infection, parasitoid preferences may mediate coexistence between host species, reducing the dominance of the superior competitor. Alternatively, it may increase competition, leading to species exclusion. If

  20. Quantifying Heterogeneity in Host-Vector Contact: Tsetse (Glossina swynnertoni and G. pallidipes) Host Choice in Serengeti National Park, Tanzania

    PubMed Central

    Auty, Harriet; Cleaveland, Sarah; Malele, Imna; Masoy, Joseph; Lembo, Tiziana; Bessell, Paul; Torr, Stephen; Picozzi, Kim; Welburn, Susan C.

    2016-01-01

    Background Identifying hosts of blood-feeding insect vectors is crucial in understanding their role in disease transmission. Rhodesian human African trypanosomiasis (rHAT), also known as acute sleeping sickness is caused by Trypanosoma brucei rhodesiense and transmitted by tsetse flies. The disease is commonly associated with wilderness areas of east and southern Africa. Such areas hold a diverse range of species which form communities of hosts for disease maintenance. The relative importance of different wildlife hosts remains unclear. This study quantified tsetse feeding preferences in a wilderness area of great host species richness, Serengeti National Park, Tanzania, assessing tsetse feeding and host density contemporaneously. Methods Glossina swynnertoni and G. pallidipes were collected from six study sites. Bloodmeal sources were identified through matching Cytochrome B sequences amplified from bloodmeals from recently fed flies to published sequences. Densities of large mammal species in each site were quantified, and feeding indices calculated to assess the relative selection or avoidance of each host species by tsetse. Results The host species most commonly identified in G. swynnertoni bloodmeals, warthog (94/220), buffalo (48/220) and giraffe (46/220), were found at relatively low densities (3-11/km2) and fed on up to 15 times more frequently than expected by their relative density. Wildebeest, zebra, impala and Thomson’s gazelle, found at the highest densities, were never identified in bloodmeals. Commonly identified hosts for G. pallidipes were buffalo (26/46), giraffe (9/46) and elephant (5/46). Conclusions This study is the first to quantify tsetse host range by molecular analysis of tsetse diet with simultaneous assessment of host density in a wilderness area. Although G. swynnertoni and G. pallidipes can feed on a range of species, they are highly selective. Many host species are rarely fed on, despite being present in areas where tsetse are

  1. Mycobacterium bovis: characteristics of wildlife reservoir hosts.

    PubMed

    Palmer, M V

    2013-11-01

    Mycobacterium bovis is the cause of tuberculosis in animals and sometimes humans. Many developed nations have long-standing programmes to eradicate tuberculosis in livestock, principally cattle. As disease prevalence in cattle decreases these efforts are sometimes impeded by passage of M. bovis from wildlife to cattle. In epidemiological terms, disease can persist in some wildlife species, creating disease reservoirs, if the basic reproduction rate (R0) and critical community size (CCS) thresholds are achieved. Recognized wildlife reservoir hosts of M. bovis include the brushtail possum (Trichosurus vulpecula) in New Zealand, European badger (Meles meles) in Great Britain and Ireland, African buffalo (Syncerus caffer) in South Africa, wild boar (Sus scrofa) in the Iberian Peninsula and white-tailed deer (Odocoileus virginianus) in Michigan, USA. The epidemiological concepts of R0 and CCS are related to more tangible disease/pathogen characteristics such as prevalence, pathogen-induced pathology, host behaviour and ecology. An understanding of both epidemiological and disease/pathogen characteristics is necessary to identify wildlife reservoirs of M. bovis. In some cases, there is a single wildlife reservoir host involved in transmission of M. bovis to cattle. Complexity increases, however, in multihost systems where multiple potential reservoir hosts exist. Bovine tuberculosis eradication efforts require elimination of M. bovis transmission between wildlife reservoirs and cattle. For successful eradication identification of true wildlife reservoirs is critical, as disease control efforts are most effective when directed towards true reservoirs.

  2. A community engagement process identifies environmental priorities to prevent early childhood obesity: the Children's Healthy Living (CHL) program for remote underserved populations in the US Affiliated Pacific Islands, Hawaii and Alaska.

    PubMed

    Fialkowski, Marie Kainoa; DeBaryshe, Barbara; Bersamin, Andrea; Nigg, Claudio; Leon Guerrero, Rachael; Rojas, Gena; Areta, Aufa'i Apulu Ropeti; Vargo, Agnes; Belyeu-Camacho, Tayna; Castro, Rose; Luick, Bret; Novotny, Rachel

    2014-12-01

    Underserved minority populations in the US Affiliated Pacific Islands (USAPI), Hawaii, and Alaska display disproportionate rates of childhood obesity. The region's unique circumstance should be taken into account when designing obesity prevention interventions. The purpose of this paper is to (a), describe the community engagement process (CEP) used by the Children's Healthy Living (CHL) Program for remote underserved minority populations in the USAPI, Hawaii, and Alaska (b) report community-identified priorities for an environmental intervention addressing early childhood (ages 2-8 years) obesity, and (c) share lessons learned in the CEP. Four communities in each of five CHL jurisdictions (Alaska, American Samoa, Commonwealth of the Northern Mariana Islands, Guam, Hawai'i) were selected to participate in the community-randomized matched-pair trial. Over 900 community members including parents, teachers, and community leaders participated in the CEP over a 14 month period. The CEP was used to identify environmental intervention priorities to address six behavioral outcomes: increasing fruit/vegetable consumption, water intake, physical activity and sleep; and decreasing screen time and intake of sugar sweetened beverages. Community members were engaged through Local Advisory Committees, key informant interviews and participatory community meetings. Community-identified priorities centered on policy development; role modeling; enhancing access to healthy food, clean water, and physical activity venues; and healthy living education. Through the CEP, CHL identified culturally appropriate priorities for intervention that were also consistent with the literature on effective obesity prevention practices. Results of the CEP will guide the CHL intervention design and implementation. The CHL CEP may serve as a model for other underserved minority island populations.

  3. Infra-population and -community dynamics of the parasites Nosema apis and Nosema ceranae, and consequences for honey bee (Apis mellifera) hosts.

    PubMed

    Williams, Geoffrey R; Shutler, Dave; Burgher-MacLellan, Karen L; Rogers, Richard E L

    2014-01-01

    Nosema spp. fungal gut parasites are among myriad possible explanations for contemporary increased mortality of western honey bees (Apis mellifera, hereafter honey bee) in many regions of the world. Invasive Nosema ceranae is particularly worrisome because some evidence suggests it has greater virulence than its congener N. apis. N. ceranae appears to have recently switched hosts from Asian honey bees (Apis cerana) and now has a nearly global distribution in honey bees, apparently displacing N. apis. We examined parasite reproduction and effects of N. apis, N. ceranae, and mixed Nosema infections on honey bee hosts in laboratory experiments. Both infection intensity and honey bee mortality were significantly greater for N. ceranae than for N. apis or mixed infections; mixed infection resulted in mortality similar to N. apis parasitism and reduced spore intensity, possibly due to inter-specific competition. This is the first long-term laboratory study to demonstrate lethal consequences of N. apis and N. ceranae and mixed Nosema parasitism in honey bees, and suggests that differences in reproduction and intra-host competition may explain apparent heterogeneous exclusion of the historic parasite by the invasive species.

  4. The influence of geographical location, host maturity and sex on intestinal helminth communities of the double-crested cormorant Phalacrocorax auritus from the eastern United States.

    PubMed

    Sheehan, K L; Hanson-Dorr, K C; Dorr, B S; Yarrow, G K; Johnson, R J

    2016-09-28

    Here the intestinal helminth infracommunities of 218 double-crested cormorants (Phalacrocorax auritus) from 11 locations in Alabama, Minnesota, Mississippi and Vermont are documented. Trematode infections were present in 98% of hosts; 65% of cormorants carried cestode infections, 4% were infected with acanthocephalans and 66% had nematode intestinal parasites. Parasite infracommunities of hosts collected on wintering grounds had higher richness and diversity than did birds collected on breeding grounds. Differences in parasite richness and diversity between male and female P. auritus were also detected, but not between immature and mature bird hosts. Parasite intensity did not differ by sex, maturity, or between breeding and wintering season. The most common parasite was Drepanocephalus auritus (spathans), which is recognized as a disease agent that negatively impacts the catfish aquaculture industry in the US. Echinochasmus sp. in double-crested cormorants is documented for the first time in the United States. We suggest that the differences observed among parasite infracommunities could be associated with the foraging distances travelled by P. auritus during breeding and wintering seasons, which is limited by allocation of parental care during the breeding season.

  5. Infra-Population and -Community Dynamics of the Parasites Nosema apis and Nosema ceranae, and Consequences for Honey Bee (Apis mellifera) Hosts

    PubMed Central

    Williams, Geoffrey R.; Shutler, Dave; Burgher-MacLellan, Karen L.; Rogers, Richard E. L.

    2014-01-01

    Nosema spp. fungal gut parasites are among myriad possible explanations for contemporary increased mortality of western honey bees (Apis mellifera, hereafter honey bee) in many regions of the world. Invasive Nosema ceranae is particularly worrisome because some evidence suggests it has greater virulence than its congener N. apis. N. ceranae appears to have recently switched hosts from Asian honey bees (Apis cerana) and now has a nearly global distribution in honey bees, apparently displacing N. apis. We examined parasite reproduction and effects of N. apis, N. ceranae, and mixed Nosema infections on honey bee hosts in laboratory experiments. Both infection intensity and honey bee mortality were significantly greater for N. ceranae than for N. apis or mixed infections; mixed infection resulted in mortality similar to N. apis parasitism and reduced spore intensity, possibly due to inter-specific competition. This is the first long-term laboratory study to demonstrate lethal consequences of N. apis and N. ceranae and mixed Nosema parasitism in honey bees, and suggests that differences in reproduction and intra-host competition may explain apparent heterogeneous exclusion of the historic parasite by the invasive species. PMID:24987989

  6. Aspergillus parasiticus communities associated with sugarcane in the Rio Grande Valley of Texas: implications of global transport and host association within Aspergillus section Flavi.

    PubMed

    Garber, N P; Cotty, P J

    2014-05-01

    In the Rio Grande Valley of Texas (RGV), values of maize and cottonseed crops are significantly reduced by aflatoxin contamination. Aflatoxin contamination of susceptible crops is the product of communities of aflatoxin producers and the average aflatoxin-producing potentials of these communities influence aflatoxin contamination risk. Cropping pattern influences community composition and, thereby, the epidemiology of aflatoxin contamination. In 2004, Aspergillus parasiticus was isolated from two fields previously cropped to sugarcane but not from 23 fields without recent history of sugarcane cultivation. In 2004 and 2005, A. parasiticus composed 18 to 36% of Aspergillus section Flavi resident in agricultural soils within sugarcane-producing counties. A. parasiticus was not detected in counties that do not produce sugarcane. Aspergillus section Flavi soil communities within sugarcane-producing counties differed significantly dependent on sugarcane cropping history. Fields cropped to sugarcane within the previous 5 years had greater quantities of A. parasiticus (mean = 16 CFU/g) than fields not cropped to sugarcane (mean = 0.1 CFU/g). The percentage of Aspergillus section Flavi composed of A. parasiticus increased to 65% under continuous sugarcane cultivation and remained high the first season of rotation out of sugarcane. Section Flavi communities in fields rotated to non-sugarcane crops for 3 to 5 years were composed of <5% A. parasiticus, and fields with no sugarcane history averaged only 0.2% A. parasiticus. The section Flavi community infecting RGV sugarcane stems ranged from 95% A. parasiticus in billets prepared for commercial planting to 52% A. parasiticus in hand-collected sugarcane stems. Vegetative compatibility assays and multilocus phylogenies verified that aflatoxin contamination of raw sugar was previously attributed to similar A. parasiticus in Japan. Association of closely related A. parasiticus genotypes with sugarcane produced in Japan and RGV

  7. Secondary bacterial symbiont community in aphids responds to plant diversity.

    PubMed

    Zytynska, Sharon E; Meyer, Sebastian T; Sturm, Sarah; Ullmann, Wiebke; Mehrparvar, Mohsen; Weisser, Wolfgang W

    2016-03-01

    Biodiversity is important for ecosystem functioning and biotic interactions. In experimental grasslands, increasing plant species richness is known to increase the diversity of associated herbivores and their predators. If these interactions can also involve endosymbionts that reside within a plant or animal host is currently unknown. In plant-feeding aphids, secondary bacterial symbionts can have strong fitness effects on the host, e.g. resistance to natural enemies or fungal pathogens. We examined the secondary symbiont community in three species of aphid, each feeding on a unique host plant across experimental plots that varied in plant species richness. Aphids were collected in May and June, and the symbiont community identified using species-specific PCR assays. Aphis fabae aphids were found to host six different symbiont species with individual aphids co-hosting up to four symbionts. Uroleucon jaceae and Macrosiphum rosae hosted two and three symbiont species, respectively. We found that, at the aphid population level, increasing plant species richness increased the diversity of the aphid symbiont community, whereas at the individual aphid level, the opposite was found. These effects are potentially driven by varying selective pressures across different plant communities of varying diversities, mediated by defensive protection responses and a changing cost-benefit trade-off to the aphid for hosting multiple secondary symbionts. Our work extends documented effects of plant diversity beyond visible biotic interactions to changes in endosymbiont communities, with potentially far-reaching consequences to related ecosystem processes.

  8. PCR-TTGE Analysis of 16S rRNA from Rainbow Trout (Oncorhynchus mykiss) Gut Microbiota Reveals Host-Specific Communities of Active Bacteria

    PubMed Central

    Navarrete, Paola; Magne, Fabien; Araneda, Cristian; Fuentes, Pamela; Barros, Luis; Opazo, Rafael; Espejo, Romilio; Romero, Jaime

    2012-01-01

    This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota of rainbow trout. Full sibling fish from four unrelated families, each consisting of individuals derived from the mating of one male and one female belonging to a breeding program, were fed diets containing either vegetable proteins or vegetable oils for two months in comparison to a control diet consisting of only fish protein and fish oil. Two parallel approaches were applied on the same samples: transcriptionally active bacterial populations were examined based on RNA analysis and were compared with bacterial populations obtained from DNA analysis. Comparison of temporal temperature gradient gel electrophoresis (TTGE) profiles from DNA and RNA showed important differences, indicating that active bacterial populations were better described by RNA analysis. Results showed that some bacterial groups were significantly (P<0.05) associated with specific families, indicating that microbiota composition may be influenced by the host. In addition, the effect of diet on microbiota composition was dependent on the trout family. PMID:22393360

  9. Urban-Rural Differences in Motivation to Control Prejudice toward People with HIV/AIDS: The Impact of Perceived Identifiability in the Community

    ERIC Educational Resources Information Center

    Bunn, Janice Yanushka; Solomon, Sondra E.; Varni, Susan E.; Miller, Carol T.; Forehand, Rex L.; Ashikaga, Takamaru

    2008-01-01

    Context: HIV/AIDS is occurring with increasing frequency in rural areas of the United States, and people living with HIV/AIDS in rural communities report higher levels of perceived stigma than their more urban counterparts. The extent to which stigmatized individuals perceive stigma could be influenced, in part, by prevailing community attitudes.…

  10. Identifying Key Elements of Community-Based ESD: ESD-J's Projects to Collect ESD in Practice in Japan and Asia

    ERIC Educational Resources Information Center

    Noguchi, Fumiko

    2010-01-01

    Since its establishment in 2003, the Japan Council on the UN Decade of Education for Sustainable Development (ESD-J) has paid close attention to informal learning processes in community-based efforts to promote local sustainable development. ESD-J carried out two projects to collect information on and visualise community-based ESD practice: the…

  11. Diagnostic stability of autism spectrum disorder in toddlers prospectively identified in a community-based setting: Behavioural characteristics and predictors of change over time.

    PubMed

    Barbaro, Josephine; Dissanayake, Cheryl

    2016-07-28

    Autism spectrum disorder diagnoses in toddlers have been established as accurate and stable across time in high-risk siblings and clinic-referred samples. Few studies have investigated diagnostic stability in children prospective identified in community-based settings. Furthermore, there is a dearth of evidence on the individual behaviours that predict diagnostic change over time. The stability and change of autism spectrum disorder diagnoses were investigated from 24 to 48 months in 77 children drawn from the Social Attention and Communication Study. Diagnostic stability was high, with 88.3% overall stability and 85.5% autism spectrum disorder stability. The behavioural markers at 24 months that contributed to diagnostic shift off the autism spectrum by 48 months included better eye contact, more directed vocalisations, the integration of gaze and directed vocalisations/gestures and higher non-verbal developmental quotient. These four variables correctly predicted 88.7% of children into the autism spectrum disorder-stable and autism spectrum disorder-crossover groups overall, with excellent prediction for the stable group (96.2%) and modest prediction for the crossover group (44.4%). Furthermore, non-verbal developmental quotient at 24 months accounted for the significant improvement across time in 'Social Affect' scores on the Autism Diagnostic Observation Schedule for both groups and was the only unique predictor of diagnostic crossover. These findings contribute to the body of evidence on the feasibility of diagnoses at earlier ages to facilitate children's access to interventions to promote positive developmental outcomes.

  12. [The occurrence of tumors in the minnow Phoxinus phoxinus (L.), their influence upon the parasite fauna, component community of parasites, and organism of the host].

    PubMed

    Dorovskikh, G N; Sedriseva, V A; Stepanov, V G; Boznak, E I

    2006-01-01

    The occurrence of tumors, their influence upon the organism of Phoxinus phoxinus (L.), its parasite fauna, and parasite component community were investigated in the upstream of the Pechora River. According to the data obtained, tumors could occur in the fishes of every age group, but one-year (0+) or two-year (1+) old minnow is affected by tumors more frequently. The tumors lesion extensiveness ranges from 0.02 to 3 %. From 1 to 3 tumors were recorded on one fish specimen. The investigated tumors were in progressive stage (Georgiev, 2000), since the vascular ingrowth and dissemination (in few cases) of the tumors were observed. Tumors are colored in intensive-black and taupe. The taupe tumors usually have a compact capsule at its peripheries, which isolates affected tissue from muscle fibers. In the intensive-black tumors the invasion of tumor cells to the adjacent transversal striated musculature is observed. Distinct symptoms of necrosis are revealed in all slides of the new growths. Blood vessels are formed in most tumors, and the blood flow is recorded before the completion of the vessels forming, that apparently supplies the tumors feeding. Metastases in different organs revealed in several minnow specimens. Tumor affected individuals of the minnow has parasite species complex practically identical (by species list and quantity) with the same of the even-aged unaffected fishes. However, the parasite component communities of the affected individuals are characterized by 4 groups of species, while the parasite component communities of the intact individuals--by 3 groups. The parasite communities of affected and unaffected one-year fishes are similar by the number of the groups of species, but differ in the number of species.

  13. Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula)

    PubMed Central

    Al-Lawati, Abbas; Jana, Gerry Aplang; Vishwas Patankar, Himanshu; Glick, Bernard R.

    2016-01-01

    In addition to being a forage crop, Caliph medic (Medicago truncatula) is also a model legume plant and is used for research focusing on the molecular characterization of the interaction between rhizobia and plants. However, the endophytic microbiome in this plant is poorly defined. Endophytic bacteria play a role in supplying plants with the basic requirements necessary for growth and development. Moreover, these bacteria also play a role in the mechanism of salinity stress adaptation in plants. As a prelude to the isolation and utilization of these bacteria in Caliph medic farming, 41 bacterial OTUs were identified in this project from within the interior of the roots of this plant by pyrosequencing of the small ribosomal subunit gene (16S rDNA) using a cultivation-independent approach. In addition, the differential abundance of these bacteria was studied following exposure of the plants to salinity stress. About 29,064 high-quality reads were obtained from the sequencing of six libraries prepared from control and salinity-treated tissues. Statistical analysis revealed that the abundance of ~70% of the OTUs was significantly (p ≤ 0.05) altered in roots that were exposed to salinity stress. Sequence analysis showed a similarity between some of the identified species and other, known, growth-promoting bacteria, marine and salt-stressed soil-borne bacteria, and nitrogen-fixing bacterial isolates. Determination of the amendments to the bacterial community due to salinity stress in Caliph medic provides a crucial step toward developing an understanding of the association of these endophytes, under salt stress conditions, in this model plant. To provide direct evidence regarding their growth promoting activity, a group of endophytic bacteria were isolated from inside of plant roots using a cultivation-dependent approach. Several of these isolates were able to produce ACC-deaminase, ammonia and IAA; and to solubilize Zn+2 and PO4-3. This data is consistent with the

  14. Defining dysbiosis and its influence on host immunity and disease.

    PubMed

    Petersen, Charisse; Round, June L

    2014-07-01

    Mammalian immune system development depends on instruction from resident commensal microorganisms. Diseases associated with abnormal immune responses towards environmental and self antigens have been rapidly increasing over the last 50 years. These diseases include inflammatory bowel disease (IBD), multiple sclerosis (MS), type I diabetes (T1D), allergies and asthma. The observation that people with immune mediated diseases house a different microbial community when compared to healthy individuals suggests that pathogenesis arises from improper training of the immune system by the microbiota. However, with hundreds of different microorganisms on our bodies it is hard to know which of these contribute to health and more importantly how? Microbiologists studying pathogenic organisms have long adhered to Koch's postulates to directly relate a certain disease to a specific microbe, raising the question of whether this might be true of commensal-host relationships as well. Emerging evidence supports that rather than one or two dominant organisms inducing host health, the composition of the entire community of microbial residents influences a balanced immune response. Thus, perturbations to the structure of complex commensal communities (referred to as dysbiosis) can lead to deficient education of the host immune system and subsequent development of immune mediated diseases. Here we will overview the literature that describes the causes of dysbiosis and the mechanisms evolved by the host to prevent these changes to community structure. Building off these studies, we will categorize the different types of dysbiosis and define how collections of microorganisms can influence the host response. This research has broad implications for future therapies that go beyond the introduction of a single organism to induce health. We propose that identifying mechanisms to re-establish a healthy complex microbiota after dysbiosis has occurred, a process we will refer to as rebiosis

  15. Defining dysbiosis and its influence on host immunity and disease

    PubMed Central

    Petersen, Charisse; Round, June L

    2014-01-01

    Mammalian immune system development depends on instruction from resident commensal microorganisms. Diseases associated with abnormal immune responses towards environmental and self antigens have been rapidly increasing over the last 50 years. These diseases include inflammatory bowel disease (IBD), multiple sclerosis (MS), type I diabetes (T1D), allergies and asthma. The observation that people with immune mediated diseases house a different microbial community when compared to healthy individuals suggests that pathogenesis arises from improper training of the immune system by the microbiota. However, with hundreds of different microorganisms on our bodies it is hard to know which of these contribute to health and more importantly how? Microbiologists studying pathogenic organisms have long adhered to Koch's postulates to directly relate a certain disease to a specific microbe, raising the question of whether this might be true of commensal–host relationships as well. Emerging evidence supports that rather than one or two dominant organisms inducing host health, the composition of the entire community of microbial residents influences a balanced immune response. Thus, perturbations to the structure of complex commensal communities (referred to as dysbiosis) can lead to deficient education of the host immune system and subsequent development of immune mediated diseases. Here we will overview the literature that describes the causes of dysbiosis and the mechanisms evolved by the host to prevent these changes to community structure. Building off these studies, we will categorize the different types of dysbiosis and define how collections of microorganisms can influence the host response. This research has broad implications for future therapies that go beyond the introduction of a single organism to induce health. We propose that identifying mechanisms to re-establish a healthy complex microbiota after dysbiosis has occurred, a process we will refer to as rebiosis

  16. Assessing the influence of geographic distance in parasite communities of an exotic lizard.

    PubMed

    Bezerra, Castiele Holanda; Pinheiro, Luan Tavares; de Melo, Gabriela Cavalcante; Zanchi-Silva, Djan; Queiroz, Murilo de Souza; dos Anjos, Luciano Alves; Harris, David James; Borges-Nojosa, Diva Maria

    2016-01-01

    The decay of similarity between biological communities with increasing geographical distance is a well-established pattern in ecology, but there are more complex factors acting on host population connections that influence this association for parasite communities, such as parasites' colonization ability and degree of connectivity between host populations. Here we aim to determine the helminth communities associated with different populations of the host lizard Hemidactylus mabouia, testing if the similarity of parasite communities decreases as the distance between them increases. For this, we collected samples of lizard populations in seven sites from Northeastern coast of Brazil and identified parasite species of helminths and pentastomids in each host, calculated the Sørensen indices of presence/absence and abundance of each pair of communities and related them to the geographical distance. We did not find a relationship of decaying similarity with increasing distance between the parasite communities of the host populations. This can be explained by factors such as the characteristics of the contact between the host populations, and by modes of transmission of most parasite species. Furthermore, it may be related to the exotic nature of the host in Brazil so that parasite communities have not reached equilibrium.

  17. Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers.

    PubMed

    Allard, Sarah M; Walsh, Christopher S; Wallis, Anna E; Ottesen, Andrea R; Brown, Eric W; Micallef, Shirley A

    2016-12-15

    Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. 'BHN602' grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM (R=0.87, p=0.001 in year 1; R=0.93, p=0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil (p<0.05) across the field and corresponding shifts in water activity were positively (R(2)=0.52, p=0.005) and negatively (R(2)=0.48, p=0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field

  18. A Study to Identify the Optimum Method of Providing Biomedical Engineering/Maintenance Support of Radiologic Equipment at General Leonard Wood Army Community Hospital

    DTIC Science & Technology

    1988-01-01

    This study was done to determine the optimum method of providing biomedical engineering /maintenance support of diagnostic radiologic equipment at...General Leonard Wood Army Community Hospital (GLWACH). The study concluded that the optimum method of providing biomedical engineering /maintenance

  19. Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

    PubMed Central

    Hettich, Robert L.; Pan, Chongle; Chourey, Karuna; Giannone, Richard J.

    2013-01-01

    Summary The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. PMID:23469896

  20. A Post Licensing Study of Community Effects at Two Operating Nuclear Power Plants. Final Report.

    ERIC Educational Resources Information Center

    Purdy, Bruce J.; And Others

    In an effort to identify and assess the social, economic, and political effects of nuclear power plant construction and operation upon two host communities (Plymouth, Massachusetts and Waterford, Connecticut), a post-licensing review revealed that the primary impact of the nuclear power plants in both communities was an increase in the property…

  1. Service Learning in Public Health: Exploring the Benefit to Host Agencies in CDC's Public Health Associate Program.

    PubMed

    Wigington, Corinne J; Sobelson, Robyn K; Duncan, Heather L; Young, Andrea C

    2017-02-08

    The "learn by doing" approach to training is common in the public health field and is a core component of service-learning programs. Trainee satisfaction, learning, and application of learning have been studied. What is less understood is the perspective of the agencies that host trainees. This study aimed to identify whether and how the Centers for Disease Control and Prevention's Public Health Associate Program (PHAP) adds value to the agencies that host trainees during 2-year field assignments. An exploratory, qualitative study design consisting of 9 semistructured telephone interviews with PHAP host agency supervisors was used. Results suggested that PHAP increased host agencies' capacity by assigning capable trainees to host agencies. Trainees made quality contributions that led to agency- and/or community-wide improvements and positively affected the agencies' culture. Further evaluation of the host perspective is necessary; as coupled with the trainee's perspective, it will provide a more holistic understanding of program value.

  2. The importance of host age and sex to patterns of reinfection with Ascaris lumbricoides following mass anthelmintic treatment in a South Indian fishing community.

    PubMed

    Elkins, D B; Haswell-Elkins, M; Anderson, R M

    1988-02-01

    Analysis of egg and worm counts of Ascaris recorded at various intervals following a mass anthelmintic treatment programme in a South Indian fishing community is presented. Three indices of infection in the community are compared, namely the prevalence and intensity of egg output (at 2, 6 and 11 months following treatment) and the number of worms expelled following an 11 month period of reinfection. Detailed examination of these measurements revealed significant associations with patient sex and age. The age-prevalence profile of Ascaris infection changed little over time (except immediately following treatment) with the peak prevalence found in the 5-9 year age group. Although 85% of both males and females harboured Ascaris initially, the prevalence following 11 months reinfection was decreased, due to a significantly lower proportion of males being reinfected. By the 11th month of reinfection, the age-intensity profiles of egg output were similar to those observed at initial treatment in the older age groups (10 years and above) and in male children (less than 10 years). However, a dramatic increase in the egg output of female children, greatly exceeding the initial mean, was observed within a 6 month period of reinfection. The intensity of egg output did not accurately reflect the abundance of Ascaris recovered via drug-induced expulsion following an 11 month period of reinfection. Although the egg output attained preintervention levels, the average worm intensity reached only half the initial value. The trends in the sex- and age-intensity profiles were consistent at the two sampling dates and showed similar patterns to the egg output curves. The relevance of the results to helminth control and the monitoring of reinfection is discussed.

  3. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment.

    PubMed

    Macdonald, Catriona A; Crawley, Michael J; Wright, Denis J; Kuczynski, Justin; Robinson, Lucinda; Knight, Rob; Al-Soud, Waleed Abu; Sørensen, Søren J; Deng, Ye; Zhou, Jizhong; Singh, Brajesh K

    2015-03-01

    Herbivory is an important modulator of plant biodiversity and productivity in grasslands, but our understanding of herbivore-induced changes on below-ground processes and communities is limited. Using a long-term (17 years) experimental site, we evaluated impacts of rabbit and invertebrate grazers on some soil functions involved in carbon cycling, microbial diversity, structure and functional composition. Both rabbit and invertebrate grazing impacted soil functions and microbial community structure. All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits. Furthermore, our results suggest that exclusion of invertebrate grazers decreases both microbial biomass and abundance of genes associated with key biogeochemical cycles, and could thus have long-term consequences for ecosystem functions. The mechanism behind these impacts are likely to be driven by both direct effects of grazing altering the pattern of nutrient inputs and by indirect effects through changes in plant species composition. However, we could not entirely discount that the pesticide used to exclude invertebrates may have affected some microbial community measures. Nevertheless, our work illustrates that human activity that affects grazing intensity may affect ecosystem functioning and sustainability, as regulated by multi-trophic interactions between above- and below-ground communities.

  4. Sexual behaviors, sexual health practices, and community engagement among gay and bisexually identified men living in rural areas of the United States.

    PubMed

    Rosenberger, Joshua G; Schick, Vanessa; Schnarrs, Phillip; Novak, David S; Reece, Michael

    2014-01-01

    Limited research has focused on the sexual behaviors of men who have sex with men (MSM) from rural communities. We examined the sexual and health-related behaviors of MSM living in rural areas of the United States in order to understand the sexual health repertoire of this population. A total of 5,357 participants living in rural settings were recruited online and completed an anonymous Internet-based survey that assessed sexual behaviors, condom use, and men's engagement with various community activities and events. These data provide a greater understanding of sexual health profiles that exist among rural MSM and will help inform the design of effective programs for men in these often underserved communities.

  5. Data hosting infrastructure for primary biodiversity data

    PubMed Central

    2011-01-01

    Background Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. Discussion We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. Conclusion The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized. PMID:22373257

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

    USGS Publications Warehouse

    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

  7. Hosting a Katrina Evacuee.

    NASA Astrophysics Data System (ADS)

    Hoagland, David

    2008-03-01

    No individual or institution anticipated the impact on the academic research community of hurricane Katrina. When Tulane physicist Wayne Reed asked me to host his research group just a day or two after the disaster, with no authorization or understanding of the commitment, I agreed immediately and then pondered implications. Fortunately, colleagues helped in making the commitment real, only the bureaucracy of my public university posing small hindrances. Industry was remarkably generous in providing Reed with significant ``loaner'' equipment, and amazingly, a suite of custom Reed experiments was running within weeks. At the end, the most productive collaborations for Reed seemed not to have been with my group, with its similar research, but to other groups at my institution, particularly the synthetic chemists, who gained access to methods previously unique to Tulane while offering samples previously unique to UMass. Quickly designed projects exploiting this match turned out remarkably productive. Although begun with trepidation, hosting of Reed had huge positive benefits to me and UMass, and I believe, also to Reed and Tulane. Some key lessons for the future: (i) industry has capacity and willingness to help academic research during disruption (ii) commitment of a host institution must be immediate, without a wait for formal approvals or arrangement of special funding -- delay leads only to discouragement, (iii) continuing academic progress of displaced students must come first, and (iv) intellectual synergy rather than overlap should be the basis for seeking a host. Lastly, NSF or other funding agency should consider a program directly addressing the research needs of unexpectedly disrupted academic scientists, and most particularly, graduate students who face greatly extended studies.

  8. (13)C metabolic flux analysis of recombinant expression hosts.

    PubMed

    Young, Jamey D

    2014-12-01

    Identifying host cell metabolic phenotypes that promote high recombinant protein titer is a major goal of the biotech industry. (13)C metabolic flux analysis (MFA) provides a rigorous approach to quantify these metabolic phenotypes by applying isotope tracers to map the flow of carbon through intracellular metabolic pathways. Recent advances in tracer theory and measurements are enabling more information to be extracted from (13)C labeling experiments. Sustained development of publicly available software tools and standardization of experimental workflows is simultaneously encouraging increased adoption of (13)C MFA within the biotech research community. A number of recent (13)C MFA studies have identified increased citric acid cycle and pentose phosphate pathway fluxes as consistent markers of high recombinant protein expression, both in mammalian and microbial hosts. Further work is needed to determine whether redirecting flux into these pathways can effectively enhance protein titers while maintaining acceptable glycan profiles.

  9. Identifying the Value of the ACT Score as a Predictor of Student Success in Respiratory Care, Radiography, and Nursing at Southeast Kentucky Community and Technical College

    ERIC Educational Resources Information Center

    Parrott-Robbins, Rebecca Jon

    2010-01-01

    The purpose of this study was to investigate--by utilizing data obtained from the Kentucky Community and Technical College System (KCTCS) PeopleSoft database-- whether the American College Testing (ACT) assessment was a predictor of student success for students who had graduated from respiratory, radiography, and nursing programs at Southeast…

  10. Host Plant Induced Variation in Gut Bacteria of Helicoverpa armigera

    PubMed Central

    Gayatri Priya, Natarajan; Ojha, Abhishek; Kajla, Mayur K.; Raj, Anand; Rajagopal, Raman

    2012-01-01

    Helicoverpa are important polyphagous agricultural insect pests and they have a worldwide distribution. In this study, we report the bacterial community structure in the midgut of fifth instar larvae of Helicoverpa armigera, a species prevalent in the India, China, South Asia, South East Asia, Southern & Eastern Africa and Australia. Using culturable techniques, we isolated and identified members of Bacillus firmus, Bacillus niabense, Paenibacillus jamilae, Cellulomonas variformis, Acinetobacter schindleri, Micrococcus yunnanesis, Enterobacter sp., and Enterococcus cassiliflavus in insect samples collected from host plants grown in different parts of India. Besides these the presence of Sphingomonas, Ralstonia, Delftia, Paracoccus and Bacteriodetes was determined by culture independent molecular analysis. We found that Enterobacter and Enterococcus were universally present in all our Helicoverpa samples collected from different crops and in different parts of India. The bacterial diversity varied greatly among insects that were from different host plants than those from the same host plant of different locations. This result suggested that the type of host plant greatly influences the midgut bacterial diversity of H. armigera, more than the location of the host plant. On further analyzing the leaf from which the larva was collected, it was found that the H. armigera midgut bacterial community was similar to that of the leaf phyllosphere. This finding indicates that the bacterial flora of the larval midgut is influenced by the leaf surface bacterial community of the crop on which it feeds. Additionally, we found that laboratory made media or the artificial diet is a poor bacterial source for these insects compared to a natural diet of crop plant. PMID:22292034

  11. Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques

    SciTech Connect

    McLean, Jeffrey S.; Fansler, Sarah J.; Majors, Paul D.; Mcateer, Kathleen; Allen, Lisa Z.; Shirtliff, Mark E.; Lux, Renate; Shi, Wenyuan

    2012-03-05

    Many human microbial infectious diseases including dental caries are polymicrobial in nature and how these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral microbes have been characterized in vitro, their physiology in vivo in the presence of the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these oral species remain uncultivated to date and little is known except their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated microorganisms will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a novel combination of in vivo Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for temporal monitoring of carbohydrate utilization, organic acid production and identification of metabolically active and inactive bacterial species.

  12. Community Response to a Public Health Threat-VEE

    ERIC Educational Resources Information Center

    McDonald, John L.; Vuturo, Anthony F.

    1975-01-01

    After identifying the mosquito as the Venezuelan equine encephalitis vector, health officials worked with the community to eliminate mosquito breeding sites. By educating the public first, cooperation was received in opening drainage areas and stocking water collection areas with mosquito eating fish t