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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. 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

  4. 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

  5. Dissecting host-associated communities with DNA barcodes.

    PubMed

    Baker, Christopher C M; Bittleston, Leonora S; Sanders, Jon G; Pierce, Naomi E

    2016-09-01

    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

  6. Identifying hosts of families of viruses: a machine learning approach.

    PubMed

    Raj, Anil; Dewar, Michael; Palacios, Gustavo; Rabadan, Raul; Wiggins, Christopher H

    2011-01-01

    Identifying emerging viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to an epidemic. Phylogenetics, though currently the most popular tool used to characterize the likely host of a virus, can be ambiguous when studying species very distant to known species and when there is very little reliable sequence information available in the early stages of the outbreak of disease. Motivated by an existing framework for representing biological sequence information, we learn sparse, tree-structured models, built from decision rules based on subsequences, to predict viral hosts from protein sequence data using popular discriminative machine learning tools. Furthermore, the predictive motifs robustly selected by the learning algorithm are found to show strong host-specificity and occur in highly conserved regions of the viral proteome. PMID:22174744

  7. 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.

  8. Identifying and managing malnutrition in the community.

    PubMed

    McEvilly, Aimee

    2016-01-01

    Malnutrition affects more than 3 million people in the UK, most of whom live in the community. Malnutrition is both a cause and consequence of disease and can lead to increased mortality and morbidity, delayed recovery from illness and impaired body function which can make carrying out activities of daily living difficult. Managing malnutrition in the community involves identifying malnutrition using a universally validated screening tool and implementing appropriate care plans according to the degree of malnutrition. Regional and local guidance can be used to assist healthcare professionals to prescribe appropriate oral nutritional supplements and monitor nutritional aims and goals. PMID:27396860

  9. 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

  10. 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

  11. 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.

  12. 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. PMID:23407539

  13. Ecology of insect host-parasitoid communities.

    PubMed

    Force, D C

    1974-05-10

    Although conclusive evidence is lacking for its establishment, the thesis that complexity adds stability to communities is probably accepted by the majority of ecologists. I believe this attitude found its origins in the indisputable fact that there are latitudinal and altitudinal changes in community complexity. As one progresses northward or southward from the equator, or higher in altitude in most parts of the world, one cannot help but notice that communities tend to become simpler, that is, there are fewer species per community. At the same time, these communities appear to become less stable. But perhaps this change in stability is in appearance only; they appear to be less stable because of the relatively greater number of individuals comprising each species population in temperate areas. Each population, because of its greater numbers, is therefore conspicuous, and changes in these numbers are noticed. We are particularly aware of such changes because populations in these areas of the world have been comparatively well studied. Many of the most studied populations include species of economic importance where changes in population numbers are vital to agricultural or forestry practices. Equatorial populations, on the other hand, contain smaller numbers of individuals of each species because of the greater number of species present. Number changes are simply not as noticeable because the population itself is not as obvious among the other populations. It may be that when (if ever) we have as much data on equatorial populations as we have on those of temperate climates, we will find fluctuations of equal relative magnitude (but not of equal numbers, of course). If, on the other hand, we really do find a correlation between complexity and stability, the suggestion by May (12) that stability permits complexity may be well worth investigating. Because of its organization and physical setting, the Rhopalomyia community I have studied might be expected to have

  14. 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...

  15. Identifying a key host in an acanthocephalan-amphipod system.

    PubMed

    Bauer, Alexandre; Rigaud, Thierry

    2015-11-01

    Trophically transmitted parasites may use multiple intermediate hosts, some of which may be 'key-hosts', i.e. contributing significantly more to the completion of the parasite life cycle, while others may be 'sink hosts' with a poor contribution to parasite transmission. Gammarus fossarum and Gammarus roeseli are sympatric crustaceans used as intermediate hosts by the acanthocephalan Pomphorhynchus laevis. Gammarus roeseli suffers higher field prevalence and is less sensitive to parasite behavioural manipulation and to predation by definitive hosts. However, no data are available on between-host differences in susceptibility to P. laevis infection, making it difficult to untangle the relative contributions of these hosts to parasite transmission. Based on results from estimates of prevalence in gammarids exposed or protected from predation and laboratory infections, G. fossarum specimens were found to be more susceptible to P. laevis infection. As it is more susceptible to both parasite infection and manipulation, G. fossarum is therefore a key host for P. laevis transmission. PMID:26303006

  16. Competitive Metagenomic DNA Hybridization Identifies Host-Specific Microbial Genetic Markers in Cow Fecal Samples†

    PubMed Central

    Shanks, Orin C.; Santo Domingo, Jorge W.; Lamendella, Regina; Kelty, Catherine A.; Graham, James E.

    2006-01-01

    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 (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities. PMID:16751515

  17. Phylogenetic structure and host abundance drive disease pressure in communities.

    PubMed

    Parker, Ingrid M; Saunders, Megan; Bontrager, Megan; Weitz, Andrew P; Hendricks, Rebecca; Magarey, Roger; Suiter, Karl; Gilbert, Gregory S

    2015-04-23

    Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a 'rare-species advantage'. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry. PMID:25903634

  18. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species

    PubMed Central

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Background Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. Methodology and Results To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. Conclusions The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation. PMID:27008327

  19. 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

  20. Identifying and Leading Effective Professional Learning Communities

    ERIC Educational Resources Information Center

    Stoll, Louise; McMahon, Agnes; Thomas, Sally

    2006-01-01

    This article reports key findings from a 2-1/2-year mixed methodological study of professional learning communities, the first of its kind in England. In particular, the concept of effectiveness is explored as it relates to professional learning communities. We describe three ways in which effectiveness can be construed, arguing that any…

  1. The bacterial community of entomophilic nematodes and host beetles.

    PubMed

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. PMID:26992100

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

    PubMed

    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. 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

  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. PMID:25640965

  5. Defining and identifying communities in networks

    PubMed Central

    Radicchi, Filippo; Castellano, Claudio; Cecconi, Federico; Loreto, Vittorio; Parisi, Domenico

    2004-01-01

    The investigation of community structures in networks is an important issue in many domains and disciplines. This problem is relevant for social tasks (objective analysis of relationships on the web), biological inquiries (functional studies in metabolic and protein networks), or technological problems (optimization of large infrastructures). Several types of algorithms exist for revealing the community structure in networks, but a general and quantitative definition of community is not implemented in the algorithms, leading to an intrinsic difficulty in the interpretation of the results without any additional nontopological information. In this article we deal with this problem by showing how quantitative definitions of community are implemented in practice in the existing algorithms. In this way the algorithms for the identification of the community structure become fully self-contained. Furthermore, we propose a local algorithm to detect communities which outperforms the existing algorithms with respect to computational cost, keeping the same level of reliability. The algorithm is tested on artificial and real-world graphs. In particular, we show how the algorithm applies to a network of scientific collaborations, which, for its size, cannot be attacked with the usual methods. This type of local algorithm could open the way to applications to large-scale technological and biological systems. PMID:14981240

  6. 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.

  7. 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

  8. Panamanian frog species host unique skin bacterial communities.

    PubMed

    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

  9. Body size and meta-community structure: the allometric scaling of parasitic worm communities in their mammalian hosts.

    PubMed

    DE Leo, Giulio A; Dobson, Andrew P; Gatto, Marino

    2016-06-01

    In this paper we derive from first principles the expected body sizes of the parasite communities that can coexist in a mammal of given body size. We use a mixture of mathematical models and known allometric relationships to examine whether host and parasite life histories constrain the diversity of parasite species that can coexist in the population of any host species. The model consists of one differential equation for each parasite species and a single density-dependent nonlinear equation for the affected host under the assumption of exploitation competition. We derive threshold conditions for the coexistence and competitive exclusion of parasite species using invasion criteria and stability analysis of the resulting equilibria. These results are then used to evaluate the range of parasites species that can invade and establish in a target host and identify the 'optimal' size of a parasite species for a host of a given body size; 'optimal' is defined as the body size of a parasite species that cannot be outcompeted by any other parasite species. The expected distributions of parasites body sizes in hosts of different sizes are then compared with those observed in empirical studies. Our analysis predicts the relative abundance of parasites of different size that establish in the host and suggests that increasing the ratio of parasite body size to host body size above a minimum threshold increases the persistence of the parasite population. PMID:27001526

  10. Acute community acquired Aspergillus pneumonia in a presumed immunocompetent host

    PubMed Central

    Sridhar, Varun; Rajagopalan, Natarajan; C, Shivaprasad; Patil, Mahantesh; Varghese, Jaicob

    2012-01-01

    Infection from Aspergillus results in a wide range of diseases from simple Aspergillus pneumonia to fatal invasive Aspergillosis. Though the fungus is known to predominantly affect the immunocompromised host, it has also been known to cause acute pneumonia in immunocompetent hosts which is invariably fatal. It presents as an acute pneumonia with bilateral chest infiltrates on radiograph. Early clinical suspicion and microbiological identification by measures such as broncho alveolar lavage and initiation of therapy with voricanozole significantly increase the chances of survival. In this article the authors discuss a case of acute community acquired Aspergillus pneumonia in an immunocompetent host who survived due to early identification and prompt treatment with appropriate antifungal medication. PMID:22605848

  11. Effects of basic human values on host community acculturation orientations.

    PubMed

    Sapienza, Irene; Hichy, Zira; Guarnera, Maria; Nuovo, Santo Di

    2010-08-01

    Although literature provides evidence for the relationship between values and acculturation, the relationship between host community acculturation orientations has not yet been investigated. In this study we tested the effects of four high-order values (openness to change, self-transcendence, conservation, and self-enhancement, devised according to Schwartz's model) on host community acculturation orientations towards immigrants (devised according the interactive acculturation model) in the public domain of employment and the private domain of endogamy/exogamy. Participants were 264 Italian University students, who completed a questionnaire containing the Portrait Values Questionnaire, a measure of personal values, and the Host Community Acculturation Scale, aimed at measuring Italian acculturation strategies towards three groups of immigrants: Immigrants (the general category), Chinese (the valued immigrant group), and Albanians (the devalued immigrant group). Results showed that personal values are related to the adoption of acculturation orientations: In particular, the values that mostly impacted on acculturation orientations were self-transcendence and conservation. Values concerning self-transcendence encourage the adoption of integrationism, integrationism-transformation, and individualism and reduce the adoption of assimilationism, segregationism, and exclusionism. Values concerning conservation encourage the adoption of assimilation, segregation and exclusion orientations and reduce the adoption of both types of integrationism and individualism. Minor effects were found regarding self-enhancement and openness to change. PMID:22044017

  12. Feeding guild of non-host community members affects host-foraging efficiency of a parasitic wasp.

    PubMed

    De Rijk, Marjolein; Yang, Daowei; Engel, Bas; Dicke, Marcel; Poelman, Erik H

    2016-06-01

    Interactions between predator and prey, or parasitoid and host, are shaped by trait- and density-mediated processes involving other community members. Parasitoids that lay their eggs in herbivorous insects locate their hosts through infochemicals such as herbivore-induced plant volatiles (HIPVs) and host-produced kairomones. Hosts are frequently accompanied by non-host herbivores that are unsuitable for the parasitoid. These non-hosts may interfere with host location primarily through trait-mediated processes, by their own infochemicals, and their induction of the emission of plant volatiles. Although it is known that single non-hosts can interfere with parasitoid host location, it is still unknown whether the observed effects are due to species specific characteristics or to the feeding habits of the non-host herbivores. Here we addressed whether the feeding guild of non-host herbivores differentially affects foraging of the parasitoid Cotesia glomerata for its common host, caterpillars of Pieris brassicae feeding on Brassica oleracea plants. We used different phloem-feeding and leaf-chewing non-hosts to study their effects on host location by the parasitoid when searching for host-infested plants based on HIPVs and when searching for hosts on the plant using infochemicals. To evaluate the ultimate effect of these two phases in host location, we studied parasitism efficiency of parasitoids in small plant communities under field-tent conditions. We show that leaf-chewing non-hosts primarily affected host location through trait-mediated effects via plant volatiles, whereas phloem-feeding non-hosts exerted trait-mediated effects by affecting foraging efficiency of the parasitoid on the plant. These trait-mediated effects resulted in associational susceptibility of hosts in environments with phloem feeders and associational resistance in environments with non-host leaf chewers. PMID:27459770

  13. 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.

  14. 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. PMID:26148974

  15. 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. PMID:24750488

  16. Developing Communities of Innovation by Identifying Innovation Champions

    ERIC Educational Resources Information Center

    Coakes, Elayne; Smith, Peter

    2007-01-01

    Purpose: The purpose of this paper is to propose that a form of communities of practice (CoP), a community of innovation (CoInv), is the best support for sustainable innovation. It aims to outline a method for identifying champions of innovation in organisation. Design/methodology/approach: The paper draws on extant research to argue that…

  17. 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. PMID:23607753

  18. Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges

    PubMed Central

    Easson, Cole G.; Thacker, Robert W.

    2014-01-01

    Sponges (Porifera) can host diverse and abundant communities of microbial symbionts that make crucial contributions to host metabolism. Although these communities are often host-specific and hypothesized to co-evolve with their hosts, correlations between host phylogeny and microbiome community structure are rarely tested. As part of the Earth Microbiome Project (EMP), we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range. We tested whether (1) univariate metrics of microbiome diversity displayed significant phylogenetic signal across the host phylogeny; (2) host identity and host phylogeny were significant factors in multivariate analyses of taxonomic and phylogenetic dissimilarity; and (3) different minimum read thresholds impacted these results. We observed significant differences in univariate metrics of diversity among host species for all read thresholds, with strong phylogenetic signal in the inverse Simpson's index of diversity (D). We observed a surprisingly wide range of variability in community dissimilarity within host species (4–73%); this variability was not related to microbial abundance within a host species. Taxonomic and phylogenetic dissimilarity were significantly impacted by host identity and host phylogeny when these factors were considered individually; when tested together, the effect of host phylogeny was reduced, but remained significant. In our dataset, this outcome is largely due to closely related host sponges harboring distinct microbial taxa. Host identity maintained a strong statistical signal at all minimum read thresholds. Although the identity of specific microbial taxa varied substantially among host sponges, closely related hosts tended to harbor microbial communities with similar patterns of relative abundance. We hypothesize that microbiomes with low D might be structured by regulation of the microbial community by the host or by the presence of

  19. 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

  20. Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography.

    PubMed

    Scordato, Elizabeth S C; Kardish, Melissa R

    2014-11-01

    Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species and the geographical scale of comparisons. In this study, we asked whether these factors also predict diversity and turnover in parasite communities. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked whether parasite prevalence and community structure varied with host population, host phylogeography or geographical distance. We used PCR to screen birds for infections and then used Bayesian methods to determine phylogenetic relationships among malaria strains. Metrics of both community and phylogenetic beta diversity were used to examine patterns of malaria strain turnover between host populations, and partial Mantel tests were used determine the correlation between malaria beta diversity and geographical distance. Finally, we developed microsatellite markers to describe the genetic structure of host populations and assess the relationship between host phylogeography and parasite beta diversity. We found that different genera of malaria parasites infect the two hosts at different rates. Within hosts, parasite communities in one population were phylogenetically clustered, but there was otherwise no correlation between metrics of parasite beta diversity and geographical or genetic distance between host populations. Patterns of parasite turnover among host populations are consistent with malaria transmission occurring in the winter rather than on the breeding grounds. Our results indicate greater turnover in parasite communities between different hosts than between different study sites. Differences in host species, as well as transmission location and vector ecology, seem to be more important in structuring malaria communities than the distance-decay relationships frequently found in macroorganisms. Determining the factors

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

    PubMed

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

    2016-03-01

    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

  2. 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.

  3. 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. PMID:25963605

  4. 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. PMID:18194146

  5. Effect of host species diversity on multiparasite systems in rodent communities.

    PubMed

    Rendón-Franco, Emilio; Muñoz-García, Claudia I; Romero-Callejas, Evangelina; Moreno-Torres, Karla I; Suzán, Gerardo

    2014-01-01

    Reduced species diversity has been suggested to increase transmission rates and prevalence of infectious diseases. While this theory has been studied mostly in single pathogen systems, little is known regarding multiple pathogens systems in vertebrates at the community level. The aim of this study was to evaluate the effect of host richness and diversity on multiple parasite systems on a local scale. We captured small rodents and collected feces in three different vegetation types in a natural protected area in Janos, Chihuahua, Mexico. The flotation technique was used to identify parasite eggs or oocysts. Analysis of linear correlations was conducted between parasite prevalence and host and parasite diversity and richness. Negative correlation was detected between parasite prevalence and host diversity (p = 0.02 r(2) =-0.86), but no significant correlations was detected between parasite prevalence and host richness or parasite diversity or richness. Our study shows that at local scale, host diversity could affect multiple parasite systems in the same way that single pathogens do. Further studies should be performed on larger temporal and spatial scales to more thoroughly investigate the correlation observed in our analysis. PMID:24337614

  6. 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. PMID:24579829

  7. 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. PMID:26915079

  8. 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

  9. Integrative Functional Genomics of Hepatitis C Virus Infection Identifies Host Dependencies in Complete Viral Replication Cycle

    PubMed Central

    Li, Qisheng; Zhang, Yong-Yuan; Chiu, Stephan; Hu, Zongyi; Lan, Keng-Hsin; Cha, Helen; Sodroski, Catherine; Zhang, Fang; Hsu, Ching-Sheng; Thomas, Emmanuel; Liang, T. Jake

    2014-01-01

    Recent functional genomics studies including genome-wide small interfering RNA (siRNA) screens demonstrated that hepatitis C virus (HCV) exploits an extensive network of host factors for productive infection and propagation. How these co-opted host functions interact with various steps of HCV replication cycle and exert pro- or antiviral effects on HCV infection remains largely undefined. Here we present an unbiased and systematic strategy to functionally interrogate HCV host dependencies uncovered from our previous infectious HCV (HCVcc) siRNA screen. Applying functional genomics approaches and various in vitro HCV model systems, including HCV pseudoparticles (HCVpp), single-cycle infectious particles (HCVsc), subgenomic replicons, and HCV cell culture systems (HCVcc), we identified and characterized novel host factors or pathways required for each individual step of the HCV replication cycle. Particularly, we uncovered multiple HCV entry factors, including E-cadherin, choline kinase α, NADPH oxidase CYBA, Rho GTPase RAC1 and SMAD family member 6. We also demonstrated that guanine nucleotide binding protein GNB2L1, E2 ubiquitin-conjugating enzyme UBE2J1, and 39 other host factors are required for HCV RNA replication, while the deubiquitinating enzyme USP11 and multiple other cellular genes are specifically involved in HCV IRES-mediated translation. Families of antiviral factors that target HCV replication or translation were also identified. In addition, various virologic assays validated that 66 host factors are involved in HCV assembly or secretion. These genes included insulin-degrading enzyme (IDE), a proviral factor, and N-Myc down regulated Gene 1 (NDRG1), an antiviral factor. Bioinformatics meta-analyses of our results integrated with literature mining of previously published HCV host factors allows the construction of an extensive roadmap of cellular networks and pathways involved in the complete HCV replication cycle. This comprehensive study of HCV host

  10. Distance decay of similarity among parasite communities of three marine invertebrate hosts.

    PubMed

    Thieltges, David W; Ferguson, MacNeill A D; Jones, Cathy S; Krakau, Manuela; de Montaudouin, Xavier; Noble, Leslie R; Reise, Karsten; Poulin, Robert

    2009-05-01

    The similarity in species composition between two communities generally decays as a function of increasing distance between them. Parasite communities in vertebrate definitive hosts follow this pattern but the respective relationship in intermediate invertebrate hosts of parasites with complex life cycles is unknown. In intermediate hosts, parasite communities are affected not only by the varying vagility of their definitive hosts (dispersing infective propagules) but also by the necessary coincidence of all their hosts in environmentally suitable localities. As intermediate hosts often hardly move they do not contribute to parasite dispersal. Hence, their parasite assemblages may decrease faster in similarity with increasing distance than those in highly mobile vertebrate definitive hosts. We use published field survey data to investigate distance decay of similarity in trematode communities from three prominent coastal molluscs of the Eastern North-Atlantic: the gastropods Littorina littorea and Hydrobia ulvae, and the bivalve Cerastoderma edule. We found that the similarity of trematode communities in all three hosts decayed with distance, independently of local sampling effort, and whether or not the parasites used the mollusc as first or second intermediate host in their life cycle. In H. ulvae, the halving distance (i.e. the distance that halves the similarity from its initial similarity at 1 km distance) for the trematode species using birds as definitive hosts was approximately two to three times larger than for species using fish. The initial similarities (estimated at 1 km distance) among trematode communities were relatively higher, whereas mean halving distances were lower, compared to published values for parasite communities in vertebrate hosts. We conclude that the vagility of definitive hosts accounts for a high similarity at the local scale, while the strong decay of similarity across regions is a consequence of the low probability that all

  11. 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,…

  12. 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...

  13. 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...

  14. Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis.

    PubMed

    Scholz, Roland; Imami, Koshi; Scott, Nichollas E; Trimble, William S; Foster, Leonard J; Finlay, B Brett

    2015-07-01

    Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation

  15. Modeling Relapsing Disease Dynamics in a Host-Vector Community

    PubMed Central

    Stone, Emily F.

    2016-01-01

    Vector-borne diseases represent a threat to human and wildlife populations and mathematical models provide a means to understand and control epidemics involved in complex host-vector systems. The disease model studied here is a host-vector system with a relapsing class of host individuals, used to investigate tick-borne relapsing fever (TBRF). Equilibrium analysis is performed for models with increasing numbers of relapses and multiple hosts and the disease reproduction number, R0, is generalized to establish relationships with parameters that would result in the elimination of the disease. We show that host relapses in a single competent host-vector system is needed to maintain an endemic state. We show that the addition of an incompetent second host with no relapses increases the number of relapses needed for maintaining the pathogen in the first competent host system. Further, coupling of the system with hosts of differing competencies will always reduce R0, making it more difficult for the system to reach an endemic state. PMID:26910884

  16. Modeling Relapsing Disease Dynamics in a Host-Vector Community.

    PubMed

    Johnson, Tammi L; Landguth, Erin L; Stone, Emily F

    2016-02-01

    Vector-borne diseases represent a threat to human and wildlife populations and mathematical models provide a means to understand and control epidemics involved in complex host-vector systems. The disease model studied here is a host-vector system with a relapsing class of host individuals, used to investigate tick-borne relapsing fever (TBRF). Equilibrium analysis is performed for models with increasing numbers of relapses and multiple hosts and the disease reproduction number, R0, is generalized to establish relationships with parameters that would result in the elimination of the disease. We show that host relapses in a single competent host-vector system is needed to maintain an endemic state. We show that the addition of an incompetent second host with no relapses increases the number of relapses needed for maintaining the pathogen in the first competent host system. Further, coupling of the system with hosts of differing competencies will always reduce R0, making it more difficult for the system to reach an endemic state. PMID:26910884

  17. 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

  18. 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

  19. Tandem immunoprecipitation approach to identify HIV-1 Gag associated host factors.

    PubMed

    Gao, Wei; Li, Min; Zhang, Jingxin

    2014-07-01

    HIV-1 Gag by itself is able to assemble and release from host cells and thus serves as a simplified model to identify host factors involved in this stage of the HIV-1 life cycle. In this study, a tandem immunoprecipitation approach is taken to immunoprecipitate Gag-interacting host proteins from transfected 293T cells. It is demonstrated that with the tandem immunoprecipitation method Gag-interacting host factors can be precipitated more efficiently than by single-step immunoprecipitation. Gag proteins are found to interact with multiple RNA-binding proteins such as hnRNPs, nucleolin, EF1a and ribosomal proteins. Such interactions are mediated by cellular RNAs and the Gag Nuclear Capsid (NC) domain. Deletion of the NC domain results in removal of most of the RNA-binding proteins, as well as a reduction of the Gag releasing capability, which can be restored by replacing the deleted NC domain with another multimerization motif. Importantly, interactions between Gag and host factors are relevant functionally, as evidenced by significantly increased nucleolin protein in the cytoplasm where it is recruited into the Gag complex, and enhanced Gag release when nucleolin is over-expressed. PMID:24690621

  20. 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. PMID:27278778

  1. 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.

  2. 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

  3. Identifying Naturally Occurring Retirement Communities: A Spatial Analysis

    PubMed Central

    Rivera-Hernandez, Maricruz; Yamashita, Takashi; Kinney, Jennifer M.

    2016-01-01

    Objectives Guided by the concept of “aging in place” and potential policy implications, the study analyzed naturally occurring retirement communities (NORCs; 40% or greater house owners and renters aged 65 years and older) and whether there were spatiotemporal patterns in Ohio between 2000 and 2010. Method Data were derived from the 2000 and 2010 census tracts. Geovisualization was used to visually examine the distribution of NORCs in 2000 and 2010. Global Moran’s I was used to quantify the spatial distribution of NORCs in Ohio and Local Moran’s I was used to identify clusters of NORCs (i.e., hot spots). Results The number of NORCs slightly decreased despite the overall increase of the older population from 2000 to 2010. NORCs were identified in one of the 3 most populous counties (i.e., Cuyahoga) and its neighboring counties. A number of hot spots were identified in Cuyahoga County (among Ohio’s most populous and NORC-rich counties), both in 2000 and 2010. There were different patterns including emerging, disappearing, and enduring NORCs and disproportionate distributions of NORCs across the state between 2000 and 2010. Discussion Locating NORCs could aid governments to create “aging in place” sensitive policies to address issues of independence, social care, health care, volunteerism, and community participation. PMID:24958694

  4. 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

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

    PubMed

    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

    2015-09-01

    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

  6. 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. PMID:23724731

  7. 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 ...

  8. 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. PMID:27044639

  9. Spatial variation in an avian host community: implications for disease dynamics.

    PubMed

    States, Sarah L; Hochachka, Wesley M; Dhondt, André A

    2009-12-01

    Because many pathogens can infect multiple host species within a community, disease dynamics in a focal host species can be affected by the composition of the host community. We examine the extent to which spatial variation in species' abundances in an avian host community may contribute to geographically varying prevalence of a recently emerged wildlife pathogen. Mycoplasma gallisepticum is a pathogen novel to songbirds that has caused substantial mortality in house finches (Carpodacus mexicanus) in eastern North America. Though the house finch is the primary host species for M. gallisepticum, the American goldfinch (Spinus tristis) and northern cardinal (Cardinalis cardinalis) are alternate hosts, and laboratory experiments have demonstrated M. gallisepticum transmission between house finches and goldfinches. Still unknown is the real world impact on disease dynamics of variation in abundances of the three hosts. We analyzed data from winter-long bird and disease surveys in the northeastern United States. We found that higher disease prevalence in house finches was associated with higher numbers of northern cardinals and American goldfinches, although only the effect of cardinal abundance was statistically significant. Nevertheless, our results indicate that spatial variation in bird communities has the potential to cause geographic variation in disease prevalence in house finches. PMID:20130959

  10. Compensation for risks: host community benefits in siting locally unwanted facilities

    NASA Astrophysics Data System (ADS)

    Himmelberger, Jeffery J.; Ratick, Samuel J.; White, Allen L.

    1991-09-01

    This article analyzes the recent negotiations connected with siting 24 solid-waste landfills in Wisconsin. We examine the association between the type and amount of compensation paid to host communities by facility developers and the size of facilities, certain facility characteristics, the timing of negotiated agreements, the size of the host community, and the socioeconomic status of the host area. Our findings suggest that the level of compensation after adjusting for landfill capacity is positively associated with the percentage of total facility capacity dedicated to host community use, positively associated with the percentage of people of the host area who are in poverty, and larger for public facilities that accept municipal wastes. Other explanatory variables we examined, whose association with levels of compensation proved statistically insignificant, were facility size, facility status (new vs expansion), facility use (countyonly vs multicounty), timing of negotiation, host community size, and the host area education level, population density, and per capita income. We discuss the policy implications of our principal findings and future research questions in light of the persistent opposition surrounding the siting of solid-waste and other waste-management facilities.

  11. Dual Myxovirus Screen Identifies a Small-Molecule Agonist of the Host Antiviral Response

    PubMed Central

    Yan, Dan; Krumm, Stefanie A.; Sun, Aiming; Steinhauer, David A.; Luo, Ming; Moore, Martin L.

    2013-01-01

    As we are confronted with an increasing number of emerging and reemerging viral pathogens, the identification of novel pathogen-specific and broad-spectrum antivirals has become a major developmental objective. Targeting of host factors required for virus replication presents a tangible approach toward obtaining novel hits with a broadened indication range. However, the identification of developable host-directed antiviral candidates remains challenging. We describe a novel screening protocol that interrogates the myxovirus host-pathogen interactome for broad-spectrum drug candidates and simultaneously probes for conventional, pathogen-directed hits. With resource efficiency and pan-myxovirus activity as the central developmental parameters, we explored coscreening against two distinct, independently traceable myxoviruses in a single-well setting. Having identified a pair of unrelated pathogenic myxoviruses (influenza A virus and measles virus) with comparable replication kinetics, we observed unimpaired coreplication of both viruses, generated suitable firefly and Renilla luciferase reporter constructs, respectively, and validated the protocol for up to a 384-well plate format. Combined with an independent counterscreen using a recombinant respiratory syncytial virus luciferase reporter, implementation of the protocol identified candidates with a broadened antimyxovirus profile, in addition to pathogen-specific hits. Mechanistic characterization revealed a newly discovered broad-spectrum lead that does not block viral entry but stimulates effector pathways of the innate cellular antiviral response. In summary, we provide proof of concept for the efficient discovery of broad-spectrum myxovirus inhibitors in parallel to para- and orthomyxovirus-specific hit candidates in a single screening campaign. The newly identified compound provides a basis for the development of a novel broad-spectrum small-molecule antiviral class. PMID:23926334

  12. 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

  13. 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. PMID:25343259

  14. 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

  15. 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

  16. Quantifying dilution and amplification in a community of hosts for tick-borne pathogens.

    PubMed

    Levi, Taal; Keesing, Felicia; Holt, Robert D; Barfield, Michael; Ostfeld, Richard S

    2016-03-01

    Recent controversy over whether biodiversity reduces disease risk (dilution effect) has focused on the ecology of Lyme disease, a tick-borne zoonosis. A criticism of the dilution effect is that increasing host species richness might amplify disease risk, assuming that total host abundance, and therefore feeding opportunities for ticks, increase with species richness. In contrast, a dilution effect is expected when poor quality hosts for ticks and pathogens (dilution hosts) divert tick blood meals away from competent hosts. Even if host densities are additive, the relationship between host density and tick encounters can be nonlinear if the number of ticks that encounter a host is a saturating function of host density, which occurs if ticks aggregate on the remaining hosts rather than failing to find a host before death. Both dilution and amplification are theoretical possibilities, and assessing which is more prevalent required detailed analyses of empirical systems. We used field data to explore the degree of tick redistribution onto fewer individuals with variation in intraspecific host density and novel data-driven models for tick dynamics to determine how changes in vertebrate community composition influence the density of nymphs infected with the Lyme bacterium. To be conservative, we allowed total host density to increase additively with species richness. Our long-term field studies found that larval and nymphal ticks redistribute onto fewer individuals as host densities decline, that a large proportion of nymphs and adults find hosts, and that mice and chipmunks feed a large proportion of nymphs. White-footed mice, eastern chipmunks, short-tailed shrews, and masked shrews were important amplification hosts that greatly increased the density of infected nymphs. Gray squirrels and Virginia opossums were important dilution hosts. Removing these two species increased the maximum number of larvae attached to amplification hosts by 57%. Raccoons and birds were

  17. Community trees: Identifying codiversification in the Páramo dipteran community.

    PubMed

    Carstens, Bryan C; Gruenstaeudl, Michael; Reid, Noah M

    2016-05-01

    Groups of codistributed species that responded in a concerted manner to environmental events are expected to share patterns of evolutionary diversification. However, the identification of such groups has largely been based on qualitative, post hoc analyses. We develop here two methods (posterior predictive simulation [PPS], Kuhner-Felsenstein [K-F] analysis of variance [ANOVA]) for the analysis of codistributed species that, given a group of species with a shared pattern of diversification, allow empiricists to identify those taxa that do not codiversify (i.e., "outlier" species). The identification of outlier species makes it possible to jointly estimate the evolutionary history of co-diversifying taxa. To evaluate the approaches presented here, we collected data from Páramo dipterans, identified outlier species, and estimated a "community tree" from species that are identified as having codiversified. Our results demonstrate that dipteran communities from different Páramo habitats in the same mountain range are more closely related than communities in other ranges. We also conduct simulation testing to evaluate this approach. Results suggest that our approach provides a useful addition to comparative phylogeographic methods, while identifying aspects of the analysis that require careful interpretation. In particular, both the PPS and K-F ANOVA perform acceptably when there are one or two outlier species, but less so as the number of outliers increases. This is likely a function of the corresponding degradation of the signal of community divergence; without a strong signal from a codiversifying community, there is no dominant pattern from which to detect an outlier species. For this reason, both the magnitude of K-F distance distribution and outside knowledge about the phylogeographic history of each putative member of the community should be considered when interpreting the results. PMID:27061575

  18. New Hosts of Simplicimonas similis and Trichomitus batrachorum Identified by 18S Ribosomal RNA Gene Sequences

    PubMed Central

    Dimasuay, Kris Genelyn B.; Lavilla, Orlie John Y.; Rivera, Windell L.

    2013-01-01

    Trichomonads are obligate anaerobes generally found in the digestive and genitourinary tract of domestic animals. In this study, four trichomonad isolates were obtained from carabao, dog, and pig hosts using rectal swab. Genomic DNA was extracted using Chelex method and the 18S rRNA gene was successfully amplified through novel sets of primers and undergone DNA sequencing. Aligned isolate sequences together with retrieved 18S rRNA gene sequences of known trichomonads were utilized to generate phylogenetic trees using maximum likelihood and neighbor-joining analyses. Two isolates from carabao were identified as Simplicimonas similis while each isolate from dog and pig was identified as Pentatrichomonas hominis and Trichomitus batrachorum, respectively. This is the first report of S. similis in carabao and the identification of T. batrachorum in pig using 18S rRNA gene sequence analysis. The generated phylogenetic tree yielded three distinct groups mostly with relatively moderate to high bootstrap support and in agreement with the most recent classification. Pathogenic potential of the trichomonads in these hosts still needs further investigation. PMID:23936631

  19. Interactions between the Powdery Mildew Effector BEC1054 and Barley Proteins Identify Candidate Host Targets.

    PubMed

    Pennington, Helen G; Gheorghe, Dana M; Damerum, Annabelle; Pliego, Clara; Spanu, Pietro D; Cramer, Rainer; Bindschedler, Laurence V

    2016-03-01

    There are over 500 candidate secreted effector proteins (CSEPs) or Blumeria effector candidates (BECs) specific to the barley powdery mildew pathogen Blumeria graminis f.sp. hordei. The CSEP/BEC proteins are expressed and predicted to be secreted by biotrophic feeding structures called haustoria. Eight BECs are required for the formation of functional haustoria. These include the RNase-like effector BEC1054 (synonym CSEP0064). In order to identify host proteins targeted by BEC1054, recombinant BEC1054 was expressed in E. coli, solubilized, and used in pull-down assays from barley protein extracts. Many putative interactors were identified by LC-MS/MS after subtraction of unspecific binders in negative controls. Therefore, a directed yeast-2-hybrid assay, developed to measure the effectiveness of the interactions in yeast, was used to validate putative interactors. We conclude that BEC1054 may target several host proteins, including a glutathione-S-transferase, a malate dehydrogenase, and a pathogen-related-5 protein isoform, indicating a possible role for BEC1054 in compromising well-known key players of defense and response to pathogens. In addition, BEC1054 interacts with an elongation factor 1 gamma. This study already suggests that BEC1054 plays a central role in barley powdery mildew virulence by acting at several levels. PMID:26813582

  20. 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.

  1. 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. PMID:26900749

  2. A general method of community detection by identifying community centers with affinity propagation

    NASA Astrophysics Data System (ADS)

    Guo, Wei-Feng; Zhang, Shao-Wu

    2016-04-01

    Detection of community structures is beneficial to analyzing the structures and properties of networks. It is of theoretical interest and practical significance in modern science. So far, a large number of algorithms have been proposed to detect community structures in complex networks, but most of them are suitable for a specific network structure. In this paper, a novel method (called CDMIC) is proposed to detect the communities in un-weighted, weighted, un-directed, directed and signed networks by constructing a dissimilarity distance matrix of network and identifying community centers with maximizing modularity. For a given network, we first estimate the distance between all pairs of nodes for constructing the dissimilarity distance matrix of the network. Then, this distance matrix is input to the affinity propagation (AP) algorithm to extract a candidate center set of community. Thirdly, we rank these centers in descending order according to the sum of their availability and responsibility. Finally, we determine the community structure by selecting the center subset from the candidate center set in an incremental manner to make the modularity maximization. On three real-world networks and some synthetic networks, experimental results show that our CDMIC method has higher performance in terms of classification accuracy and normalized mutual information (NMI), and ability to tolerate the resolution limitation.

  3. Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment

    PubMed Central

    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. PMID:23967097

  4. 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. PMID:26661903

  5. Determinants of parasitoid communities of willow-galling sawflies: habitat overrides physiology, host plant and space.

    PubMed

    Nyman, Tommi; Leppänen, Sanna A; Várkonyi, Gergely; Shaw, Mark R; Koivisto, Reijo; Barstad, Trond Elling; Vikberg, Veli; Roininen, Heikki

    2015-10-01

    Studies on the determinants of plant-herbivore and herbivore-parasitoid associations provide important insights into the origin and maintenance of global and local species richness. If parasitoids are specialists on herbivore niches rather than on herbivore taxa, then alternating escape of herbivores into novel niches and delayed resource tracking by parasitoids could fuel diversification at both trophic levels. We used DNA barcoding to identify parasitoids that attack larvae of seven Pontania sawfly species that induce leaf galls on eight willow species growing in subarctic and arctic-alpine habitats in three geographic locations in northern Fennoscandia, and then applied distance- and model-based multivariate analyses and phylogenetic regression methods to evaluate the hierarchical importance of location, phylogeny and different galler niche dimensions on parasitoid host use. We found statistically significant variation in parasitoid communities across geographic locations and willow host species, but the differences were mainly quantitative due to extensive sharing of enemies among gallers within habitat types. By contrast, the divide between habitats defined two qualitatively different network compartments, because many common parasitoids exhibited strong habitat preference. Galler and parasitoid phylogenies did not explain associations, because distantly related arctic-alpine gallers were attacked by a species-poor enemy community dominated by two parasitoid species that most likely have independently tracked the gallers' evolutionary shifts into the novel habitat. Our results indicate that barcode- and phylogeny-based analyses of food webs that span forested vs. tundra or grassland environments could improve our understanding of vertical diversification effects in complex plant-herbivore-parasitoid networks. PMID:26340615

  6. 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

  7. 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. PMID:26441854

  8. Perceived intergroup threat and attitudes of host community members toward immigrant acculturation.

    PubMed

    Florack, Arnd; Piontkowski, Ursula; Rohmann, Anette; Balzer, Tanja; Perzig, Steffi

    2003-10-01

    The authors expected the extent to which host community members (a) perceive immigrants as threatening, (b) believe that the immigrants are able to assimilate to the host community (permeability), and (c) consider their presence in the host community as legitimate to predict attitudes towards immigrant acculturation. The authors designed Study 1 to examine attitudes of Germans toward Turkish immigrants. Participants were 227 German white-collar and blue-collar workers. As expected, ethnocentric acculturation attitudes positively correlated with perceived threat and negatively correlated with perceived legitimacy and perceived permeability. However, only perceived threat contributed uniquely to the prediction of the attitudes. In Study 2, the authors applied an experimental manipulation of perceived threat. Before answering attitude questions, participants read magazine articles with a threatening, enriching, or irrelevant content. The manipulation had the predicted impact on the self-reported attitudes toward immigrants. However, the salience of threatening or enriching aspects of the Turkish culture did not affect implicitly measured attitudes. PMID:14609057

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

    PubMed

    Budischak, Sarah A; Hoberg, Eric P; Abrams, Art; Jolles, Anna E; Ezenwa, Vanessa O

    2015-09-01

    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, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity of lethal sampling severely restricts the host species that can be studied, the adequacy of sample sizes to assess diversity, the geographic scope of collections and the research questions that can be addressed. Focusing on gastrointestinal nematodes of wild African buffalo, we evaluated whether accurate characterization of nematode communities could be made using a noninvasive technique that combined conventional parasitological approaches with molecular barcoding. To establish the reliability of this new method, we compared estimates of gastrointestinal nematode abundance, prevalence, richness and community composition derived from lethal sampling with estimates derived from our noninvasive approach. Our noninvasive technique accurately estimated total and species-specific worm abundances, as well as worm prevalence and community composition when compared to the lethal sampling method. Importantly, the rate of parasite species discovery was similar for both methods, and only a modest number of barcoded larvae (n = 10) were needed to capture key aspects of parasite community composition. Overall, this new noninvasive strategy offers numerous advantages over lethal sampling methods for studying nematode-host interactions in wildlife and can readily be applied to a range of study systems. PMID:25644900

  10. Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands.

    PubMed

    Jones, Ryan T; Bressan, Alberto; Greenwell, April M; Fierer, Noah

    2011-12-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants. PMID:21965398

  11. Identifying Host Sources of Fecal Pollution: Diversity of Escherichia coli in Confined Dairy and Swine Production Systems

    PubMed Central

    Lu, Zexun; Lapen, David; Scott, Andrew; Dang, Angela; Topp, Edward

    2005-01-01

    Repetitive extragenic palindromic PCR fingerprinting of Escherichia coli is one microbial source tracking approach for identifying the host source origin of fecal pollution in aquatic systems. The construction of robust known-source libraries is expensive and requires an informed sampling strategy. In many types of farming systems, waste is stored for several months before being released into the environment. In this study we analyzed, by means of repetitive extragenic palindromic PCR using the enterobacterial repetitive intergenic consensus primers and comparative analysis using the Bionumerics software, collections of E. coli obtained from a dairy farm and from a swine farm, both of which stored their waste as a slurry in holding tanks. In all fecal samples, obtained from either barns or holding tanks, the diversity of the E. coli populations was underrepresented by collections of 500 isolates. In both the dairy and the swine farms, the diversity of the E. coli community was greater in the manure holding tank than in the barn, when they were sampled on the same date. In both farms, a comparison of stored manure samples collected several months apart suggested that the community composition changed substantially in terms of the detected number, absolute identity, and relative abundance of genotypes. Comparison of E. coli populations obtained from 10 different locations in either holding tank suggested that spatial variability in the E. coli community should be accounted for when sampling. Overall, the diversity in E. coli populations in manure slurry storage facilities is significant and likely is problematic with respect to library construction for microbial source tracking applications. PMID:16204513

  12. Influence of host species on ectomycorrhizal communities associated with two co-occurring oaks (Quercus spp.) in a tropical cloud forest.

    PubMed

    Morris, Melissa H; Pérez-Pérez, Miguel A; Smith, Matthew E; Bledsoe, Caroline S

    2009-08-01

    Interactions between host tree species and ectomycorrhizal fungi are important in structuring ectomycorrhizal communities, but there are only a few studies on host influence of congeneric trees. We investigated ectomycorrhizal community assemblages on roots of deciduous Quercus crassifolia and evergreen Quercus laurina in a tropical montane cloud forest, one of the most endangered tropical forest ecosystems. Ectomycorrhizal fungi were identified by sequencing internal transcribed spacer and partial 28S rRNA gene. We sampled 80 soil cores and documented high ectomycorrhizal diversity with a total of 154 taxa. Canonical correspondence analysis indicated that oak host was significant in explaining some of the variation in ectomycorrhizal communities, despite the fact that the two Quercus species belong to the same red oak lineage (section Lobatae). A Tuber species, found in 23% of the soil cores, was the most frequent taxon. Similar to oak-dominated ectomycorrhizal communities in temperate forests, Thelephoraceae, Russulaceae and Sebacinales were diverse and dominant. PMID:19508503

  13. 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....

  14. 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

  15. 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

  16. 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: teacher…

  17. Identifying Value Indicators and Social Capital in Community Health Partnerships

    ERIC Educational Resources Information Center

    Hausman, Alice J.; Becker, Julie; Brawer, Rickie

    2005-01-01

    Increasingly, public health practice is turning to the application of community collaborative models to improve population health status. Despite the growth of these activities, however, evaluations of the national demonstrations have indicated that community health partnerships fail to achieve measurable results and struggle to maintain integrity…

  18. Identifying Rural Health Care Needs Using Community Conversations

    ERIC Educational Resources Information Center

    Moulton, Patricia L.; Miller, Marlene E.; Offutt, Sue M.; Gibbens, Brad P.

    2007-01-01

    Context: Community input can lead to better-defined goals in an organization. With this in mind, the Center for Rural Health at the University of North Dakota School of Medicine and Health Sciences embarked on a series of 13 meetings with representatives of organizations serving rural communities, including 5 Native American reservations. Purpose:…

  19. 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…

  20. 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. PMID:27190163

  1. 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. PMID:27033168

  2. Phylogenetic isolation of host trees affects assembly of local Heteroptera communities

    PubMed Central

    Vialatte, A.; Bailey, R. I.; Vasseur, C.; Matocq, A.; Gossner, M. M.; Everhart, D.; Vitrac, X.; Belhadj, A.; Ernoult, A.; Prinzing, A.

    2010-01-01

    A host may be physically isolated in space and then may correspond to a geographical island, but it may also be separated from its local neighbours by hundreds of millions of years of evolutionary history, and may form in this case an evolutionarily distinct island. We test how this affects the assembly processes of the host's colonizers, this question being until now only invoked at the scale of physically distinct islands or patches. We studied the assembly of true bugs in crowns of oaks surrounded by phylogenetically more or less closely related trees. Despite the short distances (less than 150 m) between phylogenetically isolated and non-isolated trees, we found major differences between their Heteroptera faunas. We show that phylogenetically isolated trees support smaller numbers and fewer species of Heteroptera, an increasing proportion of phytophages and a decreasing proportion of omnivores, and proportionally more non-host-specialists. These differences were not due to changes in the nutritional quality of the trees, i.e. species sorting, which we accounted for. Comparison with predictions from meta-community theories suggests that the assembly of local Heteroptera communities may be strongly driven by independent metapopulation processes at the level of the individual species. We conclude that the assembly of communities on hosts separated from their neighbours by long periods of evolutionary history is qualitatively and quantitatively different from that on hosts established surrounded by closely related trees. Potentially, the biotic selection pressure on a host might thus change with the evolutionary proximity of the surrounding hosts. PMID:20335208

  3. 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

  4. Identifying etiological agents causing diarrhea in low income Ecuadorian communities.

    PubMed

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

    2014-09-01

    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

  5. 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

  6. 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. PMID:26913026

  7. 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.

  8. Market Analysis Identifies Community and School Education Goals.

    ERIC Educational Resources Information Center

    Lindle, Jane C.

    1989-01-01

    Principals must realize the positive effects that marketing can have on improving schools and building support for them. Market analysis forces clarification of the competing needs and interests present in the community. The four marketing phases are needs assessment, analysis, goal setting, and public relations and advertising. (MLH)

  9. 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. PMID:25447830

  10. 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. PMID:24424507

  11. 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.

  12. 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

  13. Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering

    PubMed Central

    Gaiteri, Chris; Chen, Mingming; Szymanski, Boleslaw; Kuzmin, Konstantin; Xie, Jierui; Lee, Changkyu; Blanche, Timothy; Chaibub Neto, Elias; Huang, Su-Chun; Grabowski, Thomas; Madhyastha, Tara; Komashko, Vitalina

    2015-01-01

    Biological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological components are involved in multiple functions. However, traditional clustering methods detect non-overlapping communities. These detected communities may also be unstable and difficult to replicate, because traditional methods are sensitive to noise and parameter settings. These aspects of traditional clustering methods limit our ability to detect biological communities, and therefore our ability to understand biological functions. To address these limitations and detect robust overlapping biological communities, we propose an unorthodox clustering method called SpeakEasy which identifies communities using top-down and bottom-up approaches simultaneously. Specifically, nodes join communities based on their local connections, as well as global information about the network structure. This method can quantify the stability of each community, automatically identify the number of communities, and quickly cluster networks with hundreds of thousands of nodes. SpeakEasy shows top performance on synthetic clustering benchmarks and accurately identifies meaningful biological communities in a range of datasets, including: gene microarrays, protein interactions, sorted cell populations, electrophysiology and fMRI brain imaging. PMID:26549511

  14. Quantitative Mass Spectrometry Identifies Novel Host Binding Partners for Pathogenic Escherichia coli Type III Secretion System Effectors.

    PubMed

    Law, Robyn J; Law, Hong T; Scurll, Joshua M; Scholz, Roland; Santos, Andrew S; Shames, Stephanie R; Deng, Wanyin; Croxen, Matthew A; Li, Yuling; de Hoog, Carmen L; van der Heijden, Joris; Foster, Leonard J; Guttman, Julian A; Finlay, B Brett

    2016-05-01

    Enteropathogenic and enterohemorrhagic Escherichia coli cause enteric diseases resulting in significant morbidity and mortality worldwide. These pathogens remain extracellular and translocate a set of type III secreted effector proteins into host cells to promote bacterial virulence. Effectors manipulate host cell pathways to facilitate infection by interacting with a variety of host targets, yet the binding partners and mechanism of action of many effectors remain elusive. We performed a mass spectrometry screen to identify host targets for a library of effectors. We found five known effector targets and discovered four novel interactions. Interestingly, we identified multiple effectors that interacted with the microtubule associated protein, ensconsin. Using co-immunoprecipitations, we confirmed that NleB1 and EspL interacted with ensconsin in a region that corresponded to its microtubule binding domain. Ensconsin is an essential cofactor of kinesin-1 that is required for intracellular trafficking, and we demonstrated that intracellular trafficking was severely disrupted during wild type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants. Our findings demonstrate the efficacy of quantitative proteomics for identifying effector-host protein interactions and suggest that vesicular trafficking is a crucial cellular process that may be targeted by NleB1 and EspL through their interaction with ensconsin. PMID:27018634

  15. 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. PMID:27267931

  16. Infection and transmission heterogeneity of a multi-host pathogen (Batrachochytrium dendrobatidis) within an amphibian community.

    PubMed

    Fernández-Beaskoetxea, S; Bosch, J; Bielby, J

    2016-02-11

    The majority of parasites infect multiple hosts. As the outcome of the infection is different in each of them, most studies of wildlife disease focus on the few species that suffer the most severe consequences. However, the role that each host plays in the persistence and transmission of infection can be crucial to understanding the spread of a parasite and the risk it poses to the community. Current theory predicts that certain host species can modulate the infection in other species by amplifying or diluting both infection prevalence and infection intensity, both of which have implications for disease risk within those communities. The fungus Batrachochytrium dendrobatidis (Bd), the causal agent of the disease chytridiomycosis, has caused global amphibian population declines and extinctions. However, not all infected species are affected equally, and thus Bd is a good example of a multi-host pathogen that must ultimately be studied with a community approach. To test whether the common midwife toad Alytes obstetricans is a reservoir and possible amplifier of infection of other species, we used experimental approaches in captive and wild populations to determine the effect of common midwife toad larvae on infection of other amphibian species found in the Peñalara Massif, Spain. We observed that the most widely and heavily infected species, the common midwife toad, may be amplifying the infection loads in other species, all of which have different degrees of susceptibility to Bd infection. Our results have important implications for performing mitigation actions focused on potential 'amplifier' hosts and for better understanding the mechanisms of Bd transmission. PMID:26865231

  17. Juxtaposition between host population structures: implications for disease transmission in a sympatric cervid community

    PubMed Central

    Vander Wal, Eric; Edye, Iain; Paquet, Paul C; Coltman, David W; Bayne, Erin; Brook, Ryan K; Andrés, José A

    2013-01-01

    Sympatric populations of phylogenetically related species are often vulnerable to similar communicable diseases. Although some host populations may exhibit spatial structure, other hosts within the community may have unstructured populations. Thus, individuals from unstructured host populations may act as interspecific vectors among discrete subpopulations of sympatric alternate hosts. We used a cervid-bovine tuberculosis (Mycobacterium bovis) system to investigate the landscape-scale potential for bovine tuberculosis transmission within a nonmigratory white-tailed deer (Odocoileus virginianus) and elk (Cervus canadensis) community. Using landscape population genetics, we tested for genetic and spatial structure in white-tailed deer. We then compared these findings with the sympatric elk population that is structured and which has structure that correlates spatially and genetically to physiognomic landscape features. Despite genetic structure that indicates the white-tailed deer population forms three sympatric clusters, the absence of spatial structure suggested that intraspecific pathogen transmission is not likely to be limited by physiognomic landscape features. The potential for intraspecific transmission among subpopulations of elk is low due to spatial population structure. Given that white-tailed deer are abundant, widely distributed, and exhibit a distinct lack of spatial population structure, white-tailed deer likely pose a greater threat as bovine tuberculosis vectors among elk subpopulations than elk. PMID:24187583

  18. 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

  19. Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape.

    PubMed

    Lothamer, K; Brown, S P; Mattox, J D; Jumpponen, A

    2014-05-01

    Non-native tree species are often used as ornamentals in urban landscapes. However, their root-associated fungal communities remain yet to be examined in detail. Here, we compared richness, diversity and community composition of ectomycorrhizosphere fungi in general and ectomycorrhizal (EcM) fungi in particular between a non-native Pinus nigra and a native Quercus macrocarpa across a growing season in urban parks using 454-pyrosequencing. Our data show that, while the ectomycorrhizosphere community richness and diversity did not differ between the two host, the EcM communities associated with the native host were often more species rich and included more exclusive members than those of the non-native hosts. In contrast, the ectomycorrhizosphere communities of the two hosts were compositionally clearly distinct in nonmetric multidimensional ordination analyses, whereas the EcM communities were only marginally so. Taken together, our data suggest EcM communities with broad host compatibilities and with a limited numbers of taxa with preference to the non-native host. Furthermore, many common fungi in the non-native Pinus were not EcM taxa, suggesting that the fungal communities of the non-native host may be enriched in non-mycorrhizal fungi at the cost of the EcM taxa. Finally, while our colonization estimates did not suggest a shortage in EcM inoculum for either host in urban parks, the differences in the fungi associated with the two hosts emphasize the importance of using native hosts in urban environments as a tool to conserve endemic fungal diversity and richness in man-made systems. PMID:24221903

  20. Iterated tabu search for identifying community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Lü, Zhipeng; Huang, Wenqi

    2009-08-01

    This paper presents an iterated tabu search (denoted by ITS) algorithm for optimizing the modularity of community structure in complex networks. The proposed algorithm follows a general framework composed of two phases: basic optimization and postrefinement. When the basic optimization cannot improve the modularity any more, a postrefinement procedure is employed to further optimize the objective function with a global view. For both these two phases, iterated tabu search algorithm is employed to optimize the objective function. Computational results show the high effectiveness of the proposed ITS algorithm compared with six state-of-the-art algorithms in the literature. In particular, our ITS algorithm improves the previous best known modularity for several small and medium size networks.

  1. Iterated tabu search for identifying community structure in complex networks.

    PubMed

    Lü, Zhipeng; Huang, Wenqi

    2009-08-01

    This paper presents an iterated tabu search (denoted by ITS) algorithm for optimizing the modularity of community structure in complex networks. The proposed algorithm follows a general framework composed of two phases: basic optimization and postrefinement. When the basic optimization cannot improve the modularity any more, a postrefinement procedure is employed to further optimize the objective function with a global view. For both these two phases, iterated tabu search algorithm is employed to optimize the objective function. Computational results show the high effectiveness of the proposed ITS algorithm compared with six state-of-the-art algorithms in the literature. In particular, our ITS algorithm improves the previous best known modularity for several small and medium size networks. PMID:19792223

  2. 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

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

    PubMed

    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

  4. An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance.

    PubMed

    Leiss, Kirsten A; Choi, Young H; Verpoorte, Robert; Klinkhamer, Peter G L

    2011-06-01

    Secondary metabolites provide a potential source for the generation of host plant resistance and development of biopesticides. This is especially important in view of the rapid and vast spread of agricultural and horticultural pests worldwide. Multiple pests control tactics in the framework of an integrated pest management (IPM) programme are necessary. One important strategy of IPM is the use of chemical host plant resistance. Up to now the study of chemical host plant resistance has, for technical reasons, been restricted to the identification of single compounds applying specific chemical analyses adapted to the compound in question. In biological processes however, usually more than one compound is involved. Metabolomics allows the simultaneous detection of a wide range of compounds, providing an immediate image of the metabolome of a plant. One of the most universally used metabolomic approaches comprises nuclear magnetic resonance spectroscopy (NMR). It has been NMR which has been applied as a proof of principle to show that metabolomics can constitute a major advancement in the study of host plant resistance. Here we give an overview on the application of NMR to identify candidate compounds for host plant resistance. We focus on host plant resistance to western flower thrips (Frankliniella occidentalis) which has been used as a model for different plant species. PMID:21765818

  5. 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. PMID:26811357

  6. 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

  7. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter.

    PubMed

    Sheppard, Samuel K; Didelot, Xavier; Meric, Guillaume; Torralbo, Alicia; Jolley, Keith A; Kelly, David J; Bentley, Stephen D; Maiden, Martin C J; Parkhill, Julian; Falush, Daniel

    2013-07-16

    Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192 Campylobacter isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B5-depleted media and propose that this difference may be an adaptation to host diet. PMID:23818615

  8. Host Response to Respiratory Bacterial Pathogens as Identified by Integrated Analysis of Human Gene Expression Data

    PubMed Central

    Smith, Steven B.; Magid-Slav, Michal; Brown, James R.

    2013-01-01

    Respiratory bacterial pathogens are one of the leading causes of infectious death in the world and a major health concern complicated by the rise of multi-antibiotic resistant strains. Therapeutics that modulate host genes essential for pathogen infectivity could potentially avoid multi-drug resistance and provide a wider scope of treatment options. Here, we perform an integrative analysis of published human gene expression data generated under challenges from the gram-negative and Gram-positive bacteria pathogens, Pseudomonas aeruginosa and Streptococcus pneumoniae, respectively. We applied a previously described differential gene and pathway enrichment analysis pipeline to publicly available host mRNA GEO datasets resulting from exposure to bacterial infection. We found 72 canonical human pathways common between four GEO datasets, representing P. aeruginosa and S. pneumoniae. Although the majority of these pathways are known to be involved with immune response, we found several interesting new interactions such as the SUMO1 pathway that might have a role in bacterial infections. Furthermore, 36 host-bacterial pathways were also shared with our previous results for respiratory virus host gene expression. Based on our pathway analysis we propose several drug-repurposing opportunities supported by the literature. PMID:24086587

  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. 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

  12. Identifying overlapping communities as well as hubs and outliers via nonnegative matrix factorization

    PubMed Central

    Cao, Xiaochun; Wang, Xiao; Jin, Di; Cao, Yixin; He, Dongxiao

    2013-01-01

    Community detection is important for understanding networks. Previous studies observed that communities are not necessarily disjoint and might overlap. It is also agreed that some outlier vertices participate in no community, and some hubs in a community might take more important roles than others. Each of these facts has been independently addressed in previous work. But there is no algorithm, to our knowledge, that can identify these three structures altogether. To overcome this limitation, we propose a novel model where vertices are measured by their centrality in communities, and define the identification of overlapping communities, hubs, and outliers as an optimization problem, calculated by nonnegative matrix factorization. We test this method on various real networks, and compare it with several competing algorithms. The experimental results not only demonstrate its ability of identifying overlapping communities, hubs, and outliers, but also validate its superior performance in terms of clustering quality. PMID:24129402

  13. Emergency rabies control in a community of two high-density hosts

    PubMed Central

    2012-01-01

    Background Rabies is a fatal viral disease that potentially can affect all mammals. Terrestrial rabies is not present in the United Kingdom and has been eliminated from Western Europe. Nevertheless the possibility remains that rabies could be introduced to England, where it would find two potentially suitable hosts, red foxes and badgers. With the aim to analyse the spread and emergency control of rabies in this two species host community, a simulation model was constructed. Different control strategies involving anti-rabies vaccination and population culling were developed, considering control application rates, spatial extent and timing. These strategies were evaluated for efficacy and feasibility to control rabies in hypothetical rural areas in the South of England immediately after a disease outbreak. Results The model confirmed that both fox and badger populations, separately, were competent hosts for the spread of rabies. Realistic vaccination levels were not sufficient to control rabies in high-density badger populations. The combined species community was a very strong rabies host. However, disease spread within species appeared to be more important than cross-species infection. Thus, the drivers of epidemiology depend on the potential of separate host species to sustain the disease. To control a rabies outbreak in the two species, both species had to be targeted. Realistic and robust control strategies involved vaccination of foxes and badgers, but also required badger culling. Although fox and badger populations in the UK are exceptionally dense, an outbreak of rabies can be controlled with a higher than 90% chance, if control response is quick and follows a strict regime. This requires surveillance and forceful and repeated control campaigns. In contrast, an uncontrolled rabies outbreak in the South of England would quickly develop into a strong epizootic involving tens of thousands of rabid foxes and badgers. Conclusions If populations of both host

  14. 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

  15. 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

  16. 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. PMID:27172891

  17. 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. PMID:24400863

  18. Comparisons of AM fungal spore communities with the same hosts but different soil chemistries over local and geographic scales.

    PubMed

    Ji, Baoming; Bentivenga, Stephen P; Casper, Brenda B

    2012-01-01

    Arbuscular mycorrhizal (AM) fungi are ubiquitous and ecologically important microbes in grasslands. Both the host plant species and soil properties have been suggested as potentially important factors structuring AM fungal communities based on studies within local field sites. However, characterizations of the communities in relation to both host plant identity and soil properties in natural plant communities across both local and broader geographic scales are rare. We examined the AM fungal spore communities associated with the same C(4) grasses in two Eastern serpentine grasslands, where soils have elevated heavy metals, and two Iowa tallgrass prairie sites. We compared AM fungal spore communities among host plants within each site, looked for correlations between fungal communities and local soil properties, and then compared communities among sites. Spore communities did not vary with host plant species or correlate with local soil chemical properties at any site. They did not differ between the two serpentine sites or between the two prairie sites, despite geographic separation, but they did differ between serpentine and prairie. Soil characteristics are suggested as a driving force because spore communities were strongly correlated with soil properties when data from all four sites are considered, but climatic differences might also play a role. PMID:21769630

  19. Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data

    PubMed Central

    Illingworth, Christopher J. R.; Fischer, Andrej; Mustonen, Ville

    2014-01-01

    The within-host evolution of influenza is a vital component of its epidemiology. A question of particular interest is the role that selection plays in shaping the viral population over the course of a single infection. We here describe a method to measure selection acting upon the influenza virus within an individual host, based upon time-resolved genome sequence data from an infection. Analysing sequence data from a transmission study conducted in pigs, describing part of the haemagglutinin gene (HA1) of an influenza virus, we find signatures of non-neutrality in six of a total of sixteen infections. We find evidence for both positive and negative selection acting upon specific alleles, while in three cases, the data suggest the presence of time-dependent selection. In one infection we observe what is potentially a specific immune response against the virus; a non-synonymous mutation in an epitope region of the virus is found to be under initially positive, then strongly negative selection. Crucially, given the lack of homologous recombination in influenza, our method accounts for linkage disequilibrium between nucleotides at different positions in the haemagglutinin gene, allowing for the analysis of populations in which multiple mutations are present at any given time. Our approach offers a new insight into the dynamics of influenza infection, providing a detailed characterisation of the forces that underlie viral evolution. PMID:25080215

  20. 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

  1. 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. PMID:24367253

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

    PubMed

    Wilkinson, David A; 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

  3. 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

  4. 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

  5. Quantitative Proteomics Identifies Serum Response Factor Binding Protein 1 as a Host Factor for Hepatitis C Virus Entry.

    PubMed

    Gerold, Gisa; Meissner, Felix; Bruening, Janina; Welsch, Kathrin; Perin, Paula M; Baumert, Thomas F; Vondran, Florian W; Kaderali, Lars; Marcotrigiano, Joseph; Khan, Abdul G; Mann, Matthias; Rice, Charles M; Pietschmann, Thomas

    2015-08-01

    Hepatitis C virus (HCV) enters human hepatocytes through a multistep mechanism involving, among other host proteins, the virus receptor CD81. How CD81 governs HCV entry is poorly characterized, and CD81 protein interactions after virus binding remain elusive. We have developed a quantitative proteomics protocol to identify HCV-triggered CD81 interactions and found 26 dynamic binding partners. At least six of these proteins promote HCV infection, as indicated by RNAi. We further characterized serum response factor binding protein 1 (SRFBP1), which is recruited to CD81 during HCV uptake and supports HCV infection in hepatoma cells and primary human hepatocytes. SRFBP1 facilitates host cell penetration by all seven HCV genotypes, but not of vesicular stomatitis virus and human coronavirus. Thus, SRFBP1 is an HCV-specific, pan-genotypic host entry factor. These results demonstrate the use of quantitative proteomics to elucidate pathogen entry and underscore the importance of host protein-protein interactions during HCV invasion. PMID:26212323

  6. Influence of Host Community on Industrial Relations Practices and Policies: A Survey of Agbara Community and Power Holding Company of Nigeria (PHCN)

    ERIC Educational Resources Information Center

    Chidi, Christopher O.; Shadare, Oluseyi A.

    2011-01-01

    This study investigated the influence of host community on industrial relations practices and policies using Agbara community and Power Holding Company of Nigeria PLC as a case. The study adopted both the qualitative and quantitative methods. A total of 120 samples were drawn from the population using the simple random sampling technique in which…

  7. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

    PubMed

    Heidelberg, John F; Nelson, William C; Schoenfeld, Thomas; Bhaya, Devaki

    2009-01-01

    CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B') as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities. PMID:19132092

  8. Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton.

    PubMed

    Bagatini, Inessa Lacativa; Eiler, Alexander; Bertilsson, Stefan; Klaveness, Dag; Tessarolli, Letícia Piton; Vieira, Armando Augusto Henriques

    2014-01-01

    Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways. PMID:24465807

  9. Activity-based protein profiling identifies a host enzyme, carboxylesterase 1, which is differentially active during hepatitis C virus replication.

    PubMed

    Blais, David R; Lyn, Rodney K; Joyce, Michael A; Rouleau, Yanouchka; Steenbergen, Rineke; Barsby, Nicola; Zhu, Lin-Fu; Pegoraro, Adrian F; Stolow, Albert; Tyrrell, David L; Pezacki, John Paul

    2010-08-13

    Hepatitis C virus (HCV) relies on many interactions with host cell proteins for propagation. Successful HCV infection also requires enzymatic activity of host cell enzymes for key post-translational modifications. To identify such enzymes, we have applied activity-based protein profiling to examine the activity of serine hydrolases during HCV replication. Profiling of hydrolases in Huh7 cells replicating HCV identified CES1 (carboxylesterase 1) as a differentially active enzyme. CES1 is an endogenous liver protein involved in processing of triglycerides and cholesterol. We observe that CES1 expression and activity were altered in the presence of HCV. The knockdown of CES1 with siRNA resulted in lower levels of HCV replication, and up-regulation of CES1 was observed to favor HCV propagation, implying an important role for this host cell protein. Experiments in HCV JFH1-infected cells suggest that CES1 facilitates HCV release because less intracellular HCV core protein was observed, whereas HCV titers remained high. CES1 activity was observed to increase the size and density of lipid droplets, which are necessary for the maturation of very low density lipoproteins, one of the likely vehicles for HCV release. In transgenic mice containing human-mouse chimeric livers, HCV infection also correlates with higher levels of endogenous CES1, providing further evidence that CES1 has an important role in HCV propagation. PMID:20530478

  10. 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.

  11. 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

  12. 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. PMID:25088929

  13. Parasite Communities of Icefish (Chionodraco hamatus) in the Ross Sea (Antarctica): Influence of the Host Sex on the Helminth Infracommunity Structure

    PubMed Central

    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. PMID:24558440

  14. 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.

  15. In Silico Designing and Analysis of Inhibitors against Target Protein Identified through Host-Pathogen Protein Interactions in Malaria

    PubMed Central

    Samant, Monika; Chadha, Nidhi; Tiwari, Anjani K.; Hasija, Yasha

    2016-01-01

    Malaria, a life-threatening blood disease, has been a major concern in the field of healthcare. One of the severe forms of malaria is caused by the parasite Plasmodium falciparum which is initiated through protein interactions of pathogen with the host proteins. It is essential to analyse the protein-protein interactions among the host and pathogen for better understanding of the process and characterizing specific molecular mechanisms involved in pathogen persistence and survival. In this study, a complete protein-protein interaction network of human host and Plasmodium falciparum has been generated by integration of the experimental data and computationally predicting interactions using the interolog method. The interacting proteins were filtered according to their biological significance and functional roles. α-tubulin was identified as a potential protein target and inhibitors were designed against it by modification of amiprophos methyl. Docking and binding affinity analysis showed two modified inhibitors exhibiting better docking scores of −10.5 kcal/mol and −10.43 kcal/mol and an improved binding affinity of −83.80 kJ/mol and −98.16 kJ/mol with the target. These inhibitors can further be tested and validated in vivo for their properties as an antimalarial drug. PMID:27057354

  16. Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage.

    PubMed

    Anderson, Rika E; Brazelton, William J; Baross, John A

    2011-07-01

    Metagenomic analyses of viruses have revealed widespread diversity in the viriosphere, but it remains a challenge to identify specific hosts for a viral assemblage. To address this problem, we analyze the viral metagenome of a northeast Pacific hydrothermal vent with a comprehensive database of spacers derived from the clustered regularly interspaced short palindromic repeat (CRISPR) putative immune system. CRISPR spacer matches to the marine vent virome suggest that viruses infecting hosts from diverse taxonomic groups are present in this vent environment. Comparative virome analyses show that CRISPR spacers from vent isolates and from thermophiles in general have a higher percentage of matches to the vent virome than to other marine or terrestrial hot spring viromes. However, a high percentage of hits to spacers from mesophilic hosts, combined with a moderately high modeled alpha diversity, suggest that the marine vent virome is comprised of viruses that have the potential to infect diverse taxonomic groups of multiple thermal regimes in both the bacterial and the archaeal domains. PMID:21410492

  17. Quantitative Proteomics Identifies Host Factors Modulated during Acute Hepatitis E Virus Infection in the Swine Model

    PubMed Central

    Rogée, Sophie; Le Gall, Morgane; Chafey, Philippe; Bouquet, Jérôme; Cordonnier, Nathalie; Frederici, Christian

    2014-01-01

    ABSTRACT Hepatitis E virus (HEV) causes acute enterically transmitted hepatitis. In industrialized countries, it is a zoonotic disease, with swine being the major reservoir of human HEV contamination. The occurrence and severity of the disease are variable, with clinical symptoms ranging from asymptomatic to self-limiting acute hepatitis, chronic infection, or fulminant hepatitis. In the absence of a robust cell culture system or small-animal models, the HEV life cycle and pathological process remain unclear. To characterize HEV pathogenesis and virulence mechanisms, a quantitative proteomic analysis was carried out to identify cellular factors and pathways modulated during acute infection of swine. Three groups of pigs were inoculated with three different strains of swine HEV to evaluate the possible role of viral determinants in pathogenesis. Liver samples were analyzed by a differential proteomic approach, two-dimensional difference in gel electrophoresis, and 61 modulated proteins were identified by mass spectroscopy. The results obtained show that the three HEV strains replicate similarly in swine and that they modulate several cellular pathways, suggesting that HEV impairs several cellular processes, which can account for the various types of disease expression. Several proteins, such as heterogeneous nuclear ribonucleoprotein K, apolipoprotein E, and prohibitin, known to be involved in other viral life cycles, were upregulated in HEV-infected livers. Some differences were observed between the three strains, suggesting that HEV's genetic variability may induce variations in pathogenesis. This comparative analysis of the liver proteome modulated during infection with three different strains of HEV genotype 3 provides an important basis for further investigations on the factors involved in HEV replication and the mechanism of HEV pathogenesis. IMPORTANCE Hepatitis E virus (HEV) is responsible for acute hepatitis, with clinical symptoms ranging from asymptomatic

  18. 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

  19. Genetic host-tree effects on the ectomycorrhizal community and root characteristics of Norway spruce.

    PubMed

    Velmala, S M; Rajala, T; Haapanen, M; Taylor, A F S; Pennanen, T

    2013-01-01

    A greenhouse experiment was used to study the effects of host genotype on short root formation and ectomycorrhizal (ECM) fungal community structure in Norway spruce (Picea abies (L.) Karst.). Rooted cuttings representing 55 clones were inoculated with a mix of vegetative hyphae of five ECM fungal species (Laccaria sp., Amphinema byssoides, Piloderma sp., Cadophora finlandia, Paxillus involutus). After one growing season, the ECM fungal community structure was determined by amplifying the fungal internal transcribed spacer (ITS) of ribosomal DNA directly from ECM root tips. Restriction profiles of obtained amplicons were then compared to those of the inoculated strains. Spruce clones differed in their ECM fungal community composition; we found a statistically significant clone-specific effect on ECM fungal diversity and dominating fungal species. Nevertheless, the broad sense heritabilities of the levels of Laccaria sp., Piloderma sp. and A. byssoides colonisations as well as the ECM fungal community structure were low (H(2) = 0.04-0.11), owing to the high within-clone variation. As nitrogen concentration of needles correlated negatively with ECM fungal richness, our results imply that in the experimental conditions nutrient acquisition of young trees may benefit from colonisation with only one or two ECM fungal species. The heritability of short root density was moderate (H(2) = 0.41) and highest among all the measured shoot and root growth characteristics of Norway spruce cuttings. We suggest that the genetic component determining root growth and short root formation is significant for the performance of young trees in natural environments as these traits drive the formation of the below-ground symbiotic interactions. PMID:22644394

  20. 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. PMID:27031835

  1. 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

  2. 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.

  3. 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

  4. 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

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

    PubMed

    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

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

    DOE PAGESBeta

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; et al

    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

  7. Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities

    PubMed Central

    Aleklett, Kristin; Leff, Jonathan W.; Fierer, Noah

    2015-01-01

    Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed–Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy–Leucanthemum vulgare and Alsike clover–Trifolium hybridum). Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca) still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition. PMID:25755932

  8. Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities.

    PubMed

    Aleklett, Kristin; Leff, Jonathan W; Fierer, Noah; Hart, Miranda

    2015-01-01

    Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed-Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy-Leucanthemum vulgare and Alsike clover-Trifolium hybridum). Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca) still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition. PMID:25755932

  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. PMID:26148979

  10. Identifying the core competencies of community support providers working with people with psychiatric disabilities.

    PubMed

    Aubry, Tim D; Flynn, Robert J; Gerber, Gary; Dostaler, Theresa

    2005-01-01

    The study was intended to identify core competencies for community support providers working with people with psychiatric disabilities. Using multiple methods developed from previous research in the field of developmental disabilities, 18 consumers receiving services and 16 staff members from two mental health community support programs identified a list of 68 competencies that included personal attributes, knowledge, and skills. Based on a card sort task, 34 consumers receiving services and 34 support workers from six mental health community support programs rated 59 of the 68 competencies as being either absolutely necessary or desirable. Results of a second card sort task found that a majority of competencies identified as being needed pre-employment were personal attributes consistent with adopting a person-centered approach. Competencies categorized as to be learned on the job involved special knowledge and skills specific to working with people with psychiatric disabilities. The range of personal attributes, knowledge, skills represented in the identified competencies reflects the complexity of contemporary mental health community support. Findings are indicative of the need for specialized training and supervision that has not been typically available in the community mental health sector. PMID:15895918

  11. 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. PMID:26626912

  12. Development and Use of a Selectable, Broad-Host-Range Reporter Transposon for Identifying Environmentally Regulated Promoters in Bacteria

    PubMed Central

    Spinler, Jennifer K.; Zajdowicz, Sheryl L. W.; Haller, Jon C.; Oram, Diana Marra; Gill, Ronald E.; Holmes, Randall K.

    2009-01-01

    This report describes the development and use of TnKnXSp, a selectable broad-host-range reporter transposon with a promoterless aphA gene. Insertion of TnKnXSp into the chromosome of a kanamycin-susceptible bacterium confers resistance to kanamycin only if aphA is transcribed from an active promoter adjacent to the insertion site. We designed TnKnXSp as a tool for identifying environmentally regulated promoters in bacteria and developed general methods for initial characterization of any TnKnXSp integrant. To identify putative iron-regulated promoters in Corynebacterium diphtheriae, we constructed TnKnXSp integrants and identified a subgroup that expressed kanamycin resistance under low-iron, but not high-iron, conditions. We characterized representative integrants with this phenotype, located the TnKnXSp insertion in each, and demonstrated that transcription of aphA was repressed under high-iron vs. low-iron growth conditions. We also demonstrated that TnKnXSp can be used in bacteria other than C. diphtheriae, including Escherichia coli and Bacillus subtilus. Our findings validate TnKnXSp as a useful tool for identifying environmentally regulated promoters in bacteria. PMID:19146571

  13. 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. PMID:25901117

  14. 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

  15. Identifying barriers to mental health system improvements: an examination of community participation in assertive community treatment programs

    PubMed Central

    2011-01-01

    Background Integrating the best available evidence into program standards is essential if system-wide improvements in the delivery of community-based mental health services are to be achieved. Since the beginning of the Assertive Community Treatment (ACT) program movement, program standards have included a role for the community. In particular, ACT program standards have sought to ensure that members of the local community are involved in governance and that former clients participate in service delivery as "Peer Support Specialists". This paper reports on the extent to which ACT program standards related to community participation have been implemented and identifies barriers to full compliance. Methods Qualitative and quantitative data were collected through a telephone survey of ACT Program Coordinators in Ontario, Canada, using a census sample of the existing 66 ACT programs. A thematic approach to content analysis was used to analyze respondents' qualitative comments. Quantitative data were analyzed using SPSS 16.0 and included means, frequencies, independent t-tests and Pearson Correlations. Results An 85% response rate was achieved. Of the 33 program standards, the two that received the lowest perceived compliance ratings were the two standards directly concerning community participation. Specifically, the standard to have a functioning Community Advisory Body and the standard requiring the inclusion of a Peer Support Specialist. The three major themes that emerged from the survey data with respect to the barriers to fully implementing the Community Advisory Body were: external issues; standard related issues; and, organizational/structural related issues. The three major themes concerning barriers to implementing the Peer Support Specialist role were: human resource related issues; organizational/structural related issues; and, standard related issues. Conclusions The reasons for low compliance of ACT programs with community participation standards are

  16. 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. PMID:25227989

  17. Engaging Communities in Identifying Local Strategies for Expanding Integrated Employment During and After High School.

    PubMed

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

    2016-09-01

    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 conversation" events held in 6 geographically and economically diverse locales. Each event used an asset-based dialogue approach called the World Café ( Brown & Isaacs, 2005 ) to solicit ideas from a broad cross-section of community members on improving integrated employment that reflect local priorities and possibilities. Six key themes encapsulated the 1,556 strategies generated by the almost 400 attendees. Although considerable consistency was found among the categories of strategies raised across events, the manner in which those individual strategies would be implemented locally reflected the unique accent of each community. Attendees also viewed these events as promising and productive pathways for identifying next steps for their community. We offer recommendations for community-level intervention efforts and suggest directions for future research. PMID:27611351

  18. 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.

  19. Genetic Differences between Blight-Causing Erwinia Species with Differing Host Specificities, Identified by Suppression Subtractive Hybridization▿

    PubMed Central

    Triplett, Lindsay R.; Zhao, Youfu; Sundin, George W.

    2006-01-01

    PCR-based subtractive hybridization was used to isolate sequences from Erwinia amylovora strain Ea110, which is pathogenic on apples and pears, that were not present in three closely related strains with differing host specificities: E. amylovora MR1, which is pathogenic only on Rubus spp.; Erwinia pyrifoliae Ep1/96, the causal agent of shoot blight of Asian pears; and Erwinia sp. strain Ejp556, the causal agent of bacterial shoot blight of pear in Japan. In total, six subtractive libraries were constructed and analyzed. Recovered sequences included type III secretion components, hypothetical membrane proteins, and ATP-binding proteins. In addition, we identified an Ea110-specific sequence with homology to a type III secretion apparatus component of the insect endosymbiont Sodalis glossinidius, as well as an Ep1/96-specific sequence with homology to the Yersinia pestis effector protein tyrosine phosphatase YopH. PMID:16963554

  20. Using Community-Based Participatory Research to Identify Environmental Justice Issues in an Inner-City Community and Inform Urban Planning.

    PubMed

    Mansyur, Carol Leler; Jeng, Hueiwang Anna; Holloman, Erica; DeBrew, Linwood

    2016-01-01

    The Southeast CARE Coalition has been using community-based participatory research to examine environmental degradation in the Southeast Community, Newport News, Virginia. A survey was developed to collect assessment data. Up to 66% of respondents were concerned about environmental problems in their community. Those with health conditions were significantly more likely to identify specific environmental problems. The top 5 environmental concerns included coal dust, air quality, crime, water quality, and trash. The community-based participatory research process is building community capacity and participation, providing community input into strategic planning, and empowering community members to take control of environmental justice issues in their community. PMID:27214672

  1. Host specificity of the ruminal bacterial community in the dairy cow followng near-total exchange of ruminal contents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The purpose of this study was to examine the stability and host specificity of a cow’s ruminal bacterial community following massive challenge with the ruminal microflora from another cow. In each of two experiments, one pair of cows was selected on the basis of differences in ruminal bacterial comm...

  2. A Study To Identify Academic Personnel Replacement Needs in SUNY Community Colleges and Technical Colleges.

    ERIC Educational Resources Information Center

    Winter, Gene M.; And Others

    In 1990, a study was conducted of full-time faculty, deans, chairpersons, and academic administrators at the State University of New York (SUNY) community and technical colleges. The purpose of the study was to profile these groups and to identify future academic personnel replacement needs. A survey questionnaire mailed to SUNY's 30 community…

  3. Identifying Pedophiles "Eligible" for Community Notification under Megan's Law: A Multivariate Model for Actuarially Anchored Decisions.

    ERIC Educational Resources Information Center

    Pallone, Nathaniel J.; Hennessy, James J.; Voelbel, Gerald T.

    1998-01-01

    A scientifically sound methodology for identifying offenders about whose presence the community should be notified is demonstrated. A stepwise multiple regression was calculated among incarcerated pedophiles (N=52) including both psychological and legal data; a precision-weighted equation produced 90.4% "true positives." This methodology can be…

  4. Identifying, Recruiting, Developing, and Retaining Quality Adjunct Faculty in Rural Community Colleges in Ohio

    ERIC Educational Resources Information Center

    Wise, Jessica L.

    2013-01-01

    The purpose of this research was to determine how to identify, recruit, develop, and retain suitable adjunct faculty in rural community colleges in Ohio. The research problem resulted from a limited availability of potential faculty possessing the required credentials and andragogical training in Ohio's rural and Appalachian areas. Research…

  5. 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. PMID:26788724

  6. 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

  7. Tick parasites of rodents in Romania: host preferences, community structure and geographical distribution

    PubMed Central

    2012-01-01

    Background Ticks are among the most important vectors of zoonotic diseases in temperate regions of Europe, with widespread distribution and high densities, posing an important medical risk. Most ticks feed on a variety of progressively larger hosts, with a large number of small mammal species typically harbouring primarily the immature stages. However, there are certain Ixodidae that characteristically attack micromammals also during their adult stage. Rodents are widespread hosts of ticks, important vectors and competent reservoirs of tick-borne pathogens. Micromammal-tick associations have been poorly studied in Romania, and our manuscript shows the results of a large scale study on tick infestation epidemiology in rodents from Romania. Methods Rodents were caught using snap-traps in a variety of habitats in Romania, between May 2010 and November 2011. Ticks were individually collected from these rodents and identified to species and development stage. Frequency, mean intensity, prevalence and its 95% confidence intervals were calculated using the EpiInfo 2000 software. A p value of <0.05 was considered statistically significant. Results We examined 423 rodents (12 species) collected from six counties in Romania for the presence of ticks. Each collected tick was identified to species level and the following epidemiological parameters were calculated: prevalence, mean intensity and mean abundance. The total number of ticks collected from rodents was 483, with eight species identified: Ixodes ricinus, I. redikorzevi, I. apronophorus, I. trianguliceps, I. laguri, Dermacentor marginatus, Rhipicephalus sanguineus and Haemaphysalis sulcata. The overall prevalence of tick infestation was 29.55%, with a mean intensity of 3.86 and a mean abundance of 1.14. Only two polyspecific infestations were found: I. ricinus + I. redikorzevi and I. ricinus + D. marginatus. Conclusions Our study showed a relatively high diversity of ticks parasitizing rodents in Romania. The most

  8. Cytochrome B Analysis of Mosquito Blood Meals: Identifying Wildlife Hosts of West Nile Virus Mosquito Vectors in Wyoming, USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Female mosquitoes commonly exhibit patterns of blood feeding from vertebrate hosts, a behavior that strongly influences mosquito pathogen infection and transmission. The vertebrate host dynamics of the mosquito transmitted arbovirus, West Nile virus (family Flaviviridae, genus Flavivirus, WNV) in sa...

  9. 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

  10. 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

    2015-01-01

    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

  11. 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

  12. Host and habitat filtering in seedling root-associated fungal communities: taxonomic and functional diversity are altered in 'novel' soils.

    PubMed

    Pickles, Brian J; Gorzelak, Monika A; Green, D Scott; Egger, Keith N; Massicotte, Hugues B

    2015-10-01

    Climatic and land use changes have significant consequences for the distribution of tree species, both through natural dispersal processes and following management prescriptions. Responses to these changes will be expressed most strongly in seedlings near current species range boundaries. In northern temperate forest ecosystems, where changes are already being observed, ectomycorrhizal fungi contribute significantly to successful tree establishment. We hypothesised that communities of fungal symbionts might therefore play a role in facilitating, or limiting, host seedling range expansion. To test this hypothesis, ectomycorrhizal communities of interior Douglas-fir and interior lodgepole pine seedlings were analysed in a common greenhouse environment following growth in five soils collected along an ecosystem gradient. Currently, Douglas-fir's natural distribution encompasses three of the five soils, whereas lodgepole pine's extends much further north. Host filtering was evident amongst the 29 fungal species encountered: 7 were shared, 9 exclusive to Douglas-fir and 13 exclusive to lodgepole pine. Seedlings of both host species formed symbioses with each soil fungal community, thus Douglas-fir did so even where those soils came from outside its current distribution. However, these latter communities displayed significant taxonomic and functional differences to those found within the host distribution, indicative of habitat filtering. In contrast, lodgepole pine fungal communities displayed high functional similarity across the soil gradient. Taxonomic and/or functional shifts in Douglas-fir fungal communities may prove ecologically significant during the predicted northward migration of this species; especially in combination with changes in climate and management operations, such as seed transfer across geographical regions for forestry purposes. PMID:25694036

  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. Molecular and lipid biomarker analysis of a gypsum-hosted endoevaporitic microbial community.

    PubMed

    Jahnke, L L; Turk-Kubo, K A; N Parenteau, M; Green, S J; Kubo, M D Y; Vogel, M; Summons, R E; Des Marais, D J

    2014-01-01

    Modern evaporitic microbial ecosystems are important analogs for understanding the record of earliest life on Earth. Although mineral-depositing shallow-marine environments were prevalent during the Precambrian, few such environments are now available today for study. We investigated the molecular and lipid biomarker composition of an endoevaporitic gypsarenite microbial mat community in Guerrero Negro, Mexico. The 16S ribosomal RNA gene-based phylogenetic analyses of this mat corroborate prior observations indicating that characteristic layered microbial communities colonize gypsum deposits world-wide despite considerable textural and morphological variability. Membrane fatty acid analysis of the surface tan/orange and lower green mat crust layers indicated cell densities of 1.6 × 10(9) and 4.2 × 10(9)  cells cm(-3) , respectively. Several biomarker fatty acids, ∆7,10-hexadecadienoic, iso-heptadecenoic, 10-methylhexadecanoic, and a ∆12-methyloctadecenoic, correlated well with distributions of Euhalothece, Stenotrophomonas, Desulfohalobium, and Rhodobacterales, respectively, revealed by the phylogenetic analyses. Chlorophyll (Chl) a and cyanobacterial phylotypes were present at all depths in the mat. Bacteriochlorophyl (Bchl) a and Bchl c were first detected in the oxic-anoxic transition zone and increased with depth. A series of monomethylalkanes (MMA), 8-methylhexadecane, 8-methylheptadecane, and 9-methyloctadecane were present in the surface crust but increased in abundance in the lower anoxic layers. The MMA structures are similar to those identified previously in cultures of the marine Chloroflexus-like organism 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., and may represent the Bchl c community. Novel 3-methylhopanoids were identified in cultures of marine purple non-sulfur bacteria and serve as a probable biomarker for this group in the lower anoxic purple and olive-black layers. Together microbial culture and environmental analyses

  16. Community Health Advocate-Identified Enablers of HIV Testing for Latina Immigrant Women.

    PubMed

    Massengale, Kelley E; Morrison, Sharon D; Sudha, S

    2016-08-01

    This study aims to identify enablers or facilitators of HIV testing among Latina immigrant women through qualitative interviews with five community health advocates (CHAs). CHAs act as cultural bridges between Latinos and service providers. We employed a single case-study design using the PEN-3 model as a conceptual framework for situating HIV testing behaviors within cultural and structural contexts of Latina immigrant women's lives. A cross-case analysis of themes revealed that intrinsic enablers of HIV testing included individual trust, confidentiality, intergenerational family participation, and peers. The extrinsic enablers were local community outreach, bicultural/bilingual testing staff, service location and mass media outlets. These results have implications for the cultural competency of health and social service providers, instituting and revising HIV testing outreach interventions, and the earlier identification of women who may have been infected. They offer important insights for promoting other health behaviors among the Latino communities. PMID:27427927

  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. The Predictability of Phytophagous Insect Communities: Host Specialists as Habitat Specialists

    PubMed Central

    Müller, Jörg; Stadler, Jutta; Jarzabek-Müller, Andrea; Hacker, Hermann; ter Braak, Cajo; Brandl, Roland

    2011-01-01

    The difficulties specialized phytophagous insects face in finding habitats with an appropriate host should constrain their dispersal. Within the concept of metacommunities, this leads to the prediction that host-plant specialists should sort into local assemblages according to the local environmental conditions, i.e. habitat conditions, whereas assemblages of host-plant generalists should depend also on regional processes. Our study aimed at ranking the importance of local environmental factors and species composition of the vegetation for predicting the species composition of phytophagous moth assemblages with either a narrow or a broad host range. Our database consists of 351,506 specimens representing 820 species of nocturnal Macrolepidoptera sampled between 1980 and 2006 using light traps in 96 strict forest reserves in southern Germany. Species were grouped as specialists or generalists according to the food plants of the larvae; specialists use host plants belonging to one genus. We used predictive canonical correspondence and co-correspondence analyses to rank the importance of local environmental factors, the species composition of the vegetation and the role of host plants for predicting the species composition of host-plant specialists and generalists. The cross-validatory fit for predicting the species composition of phytophagous moths was higher for host-plant specialists than for host-plant generalists using environmental factors as well as the composition of the vegetation. As expected for host-plant specialists, the species composition of the vegetation was a better predictor of the composition of these assemblages than the environmental variables. But surprisingly, this difference for specialized insects was not due to the occurrence of their host plants. Overall, our study supports the idea that owing to evolutionary constraints in finding a host, host-plant specialists and host-plant generalists follow two different models of metacommunities: the

  19. Direct and indirect costs of co-infection in the wild: Linking gastrointestinal parasite communities, host hematology, and immune function☆

    PubMed Central

    Budischak, Sarah A.; Jolles, Anna E.; Ezenwa, Vanessa O.

    2012-01-01

    Most animals are concurrently infected with multiple parasites, and interactions among these parasites may influence both disease dynamics and host fitness. However, the sublethal costs of parasite infections are difficult to measure and the effects of concomitant infections with multiple parasite species on individual physiology and fitness are poorly described for wild hosts. To understand the direct and indirect physiological costs of co-infection, we investigated the relationships among gastrointestinal parasite richness, species identity, and abundance and host hematological parameters, body condition, and investment in lymphocyte defenses. Using aggregate-scale parasite data from African buffalo (Syncerus caffer), we found few direct or indirect associations between infection and hematology in male hosts, and no significant associations were observed in female hosts or with respect to body condition in either sex. These results suggest that only strong physiological effects are detectable with aggregate-scale parasite data, and that hematological variables may be more sensitive to changes in condition than standard body fat condition indices. Analyses accounting for parasite species identity in female buffalo revealed that different parasites show distinct relationships with host hematology, body condition, and immune investment. However, four of six species-specific associations were obscured when parasites were considered in combination. Overall, fitness-related physiological mediators such as hematological indices may provide assessments of direct and indirect effects of parasite infection, particularly when parasite species identity and community composition are considered. PMID:24533308

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

    PubMed

    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. 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

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

    PubMed

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

    2016-05-01

    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

  3. 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

  4. 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. PMID:26067836

  5. 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

  6. 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

  7. 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. PMID:27114882

  8. Searching Usenet for Virtual Communities of Practice: Using Mixed Methods to Identify the Constructs of Wenger's Theory

    ERIC Educational Resources Information Center

    Murillo, Enrique

    2008-01-01

    Introduction: This research set out to determine whether communities of practice can be entirely Internet-based by formally applying Wenger's theoretical framework to Internet collectives. Method: A model of a virtual community of practice was developed which included the constructs Wenger identified in co-located communities of practice: mutual…

  9. 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

  10. 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.

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

    PubMed

    Vannucci, Fabio A; Kelley, Molly R; Gebhart, Connie J

    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

  12. 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

  13. 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…

  14. 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

  15. Bacteriophages with Potential for Inactivation of Fish Pathogenic Bacteria: Survival, Host Specificity and Effect on Bacterial Community Structure

    PubMed Central

    Pereira, Carla; Silva, Yolanda J.; Santos, Ana L.; Cunha, Ângela; 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. PMID:22163184

  16. Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing.

    PubMed

    Jeong, Ju-Yong; Park, Hee-Deung; Lee, Kyong-Hee; Weon, Hang-Yeon; Ka, Jong-Ok

    2011-08-01

    It is important to know the comprehensive microbial communities of fecal pollution sources and receiving water bodies for microbial source tracking. Pyrosequencing targeting the V1-V3 hypervariable regions of the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities in the bacterial and Bacteroidales group followed by the pig sample, with human feces having the lowest value. The Bacteroidales, one of the potential fecal indicators, totally dominated in the fecal samples accounting for 31%-52% of bacterial sequences, but much less (0.6%) in the river water. Clustering and Venn diagram analyses showed that the human sample had a greater similarity to the pig sample in the bacterial and Bacteroidales communities than to samples from other hosts. Traditional fecal indicators, i.e., Escherichia coli, were detected in the human and river water samples at very low rates and Clostridium perfringens and enterococci were not detected in any samples. Besides the Bacteroidales group, some microorganisms detected in the specific hosts, i.e., Parasutterella excrementihominis, Veillonella sp., Dialister invisus, Megamonas funiformis, and Ruminococcus lactaris for the human and Lactobacillus amylovorus and Atopostipes sp. for the pig, could be used as potential host-specific fecal indicators. These microorganisms could be used as multiple fecal indicators that are not dependent on the absence or presence of a single indicator. Monitoring for multiple indicators that are highly abundant and host-specific would greatly enhance the effectiveness of fecal pollution source tracking. PMID:21887641

  17. Discrete particle swarm optimization for identifying community structures in signed social networks.

    PubMed

    Cai, Qing; Gong, Maoguo; Shen, Bo; Ma, Lijia; Jiao, Licheng

    2014-10-01

    Modern science of networks has facilitated us with enormous convenience to the understanding of complex systems. Community structure is believed to be one of the notable features of complex networks representing real complicated systems. Very often, uncovering community structures in networks can be regarded as an optimization problem, thus, many evolutionary algorithms based approaches have been put forward. Particle swarm optimization (PSO) is an artificial intelligent algorithm originated from social behavior such as birds flocking and fish schooling. PSO has been proved to be an effective optimization technique. However, PSO was originally designed for continuous optimization which confounds its applications to discrete contexts. In this paper, a novel discrete PSO algorithm is suggested for identifying community structures in signed networks. In the suggested method, particles' status has been redesigned in discrete form so as to make PSO proper for discrete scenarios, and particles' updating rules have been reformulated by making use of the topology of the signed network. Extensive experiments compared with three state-of-the-art approaches on both synthetic and real-world signed networks demonstrate that the proposed method is effective and promising. PMID:24856248

  18. 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. PMID:27093638

  19. Identifying Patients with Bacteremia in Community-Hospital Emergency Rooms: A Retrospective Cohort Study

    PubMed Central

    Takeshima, Taro; Yamamoto, Yosuke; Noguchi, Yoshinori; Maki, Nobuyuki; Gibo, Koichiro; Tsugihashi, Yukio; Doi, Asako; Fukuma, Shingo; Yamazaki, Shin; Kajii, Eiji; Fukuhara, Shunichi

    2016-01-01

    Objectives (1) To develop a clinical prediction rule to identify patients with bacteremia, using only information that is readily available in the emergency room (ER) of community hospitals, and (2) to test the validity of that rule with a separate, independent set of data. Design Multicenter retrospective cohort study. Setting To derive the clinical prediction rule we used data from 3 community hospitals in Japan (derivation). We tested the rule using data from one other community hospital (validation), which was not among the three “derivation” hospitals. Participants Adults (age ≥ 16 years old) who had undergone blood-culture testing while in the ER between April 2011 and March 2012. For the derivation data, n = 1515 (randomly sampled from 7026 patients), and for the validation data n = 467 (from 823 patients). Analysis We analyzed 28 candidate predictors of bacteremia, including demographic data, signs and symptoms, comorbid conditions, and basic laboratory data. Chi-square tests and multiple logistic regression were used to derive an integer risk score (the “ID-BactER” score). Sensitivity, specificity, likelihood ratios, and the area under the receiver operating characteristic curve (i.e., the AUC) were computed. Results There were 241 cases of bacteremia in the derivation data. Eleven candidate predictors were used in the ID-BactER score: age, chills, vomiting, mental status, temperature, systolic blood pressure, abdominal sign, white blood-cell count, platelets, blood urea nitrogen, and C-reactive protein. The AUCs was 0.80 (derivation) and 0.74 (validation). For ID-BactER scores ≥ 2, the sensitivities for derivation and validation data were 98% and 97%, and specificities were 20% and 14%, respectively. Conclusions The ID-BactER score can be computed from information that is readily available in the ERs of community hospitals. Future studies should focus on developing a score with a higher specificity while maintaining the desired sensitivity

  20. 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

  1. A Review of Research on Health Outcomes for Workers, Home and Host Communities of Population Mobility Associated with Extractive Industries.

    PubMed

    Carney, Jason G; Gushulak, Brian D

    2016-06-01

    With a growing awareness of the association between extractive industries, the nature of work in remote locations, population mobility and health status, there is a need to advance an evidence-based approach to ensuring the health of migrant and mobile populations, and the home and host communities with whom they interact. Through a narrative synthesis of peer-reviewed and grey literature, this review examines what is known, and the nature of research activity concerning the range of health impacts determined by the social conditions inherent with population mobility alongside mining and extractive industries; and the extent to which health outcomes impact on workers, and home and host communities. While much of the literature reviewed in the study considered health in a traditional disease or illness based approach, it is clear that many risk factors for the health of mobile workers in the sector reflect broader social determinants. To support the mitigation of individual and population vulnerability to infectious disease endemics, consideration of both the etiology and the social conditions that give rise to adverse health outcomes is required, including an improvement to workers' living conditions, the expansion of diagnostic and medical services, and an approach that ensures the right to health for mobile populations. To further improve upon the rich body of research, resources are required to implement robust data collection including epidemiological surveillance, outbreak monitoring and investigation, and the long term tracking of standardized health information at both origin locations and destination communities. PMID:26902231

  2. 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...

  3. Disentangling the relative importance of host tree community, abiotic environment and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient.

    PubMed

    Matsuoka, Shunsuke; Mori, Akira S; Kawaguchi, Eri; Hobara, Satoru; Osono, Takashi

    2016-05-01

    Recent studies have shown that changes in community compositions of ectomycorrhizal (ECM) fungi along elevation gradients are mainly affected by changes in host tree communities and/or in abiotic environments. However, few studies have taken the effects of processes related to fungal dispersal (i.e. spatial processes) into account and distinguished the effects of host community, abiotic environment and spatial processes on community composition along elevation gradients. This has left unclear the relative importance of these factors in structuring the ECM community assemblages. To address this, we investigated the community composition of ECM fungi along an elevation gradient in northern Japan with 454 meta-barcoding. We found that the community composition of ECM fungi changed along the elevation and that all three factors jointly affected the compositional changes. We separated the magnitude of importance of the three factors in structuring ECM fungal communities and found that most of the spatial variation in ECM fungal community was explained by host communities and abiotic environments. Our results suggest that while biotic and/or abiotic environments can be important factors in determining the ECM fungal community composition along an elevation gradient, spatial processes may also be a primary determinant. PMID:26917782

  4. 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. PMID:26284630

  5. 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

  6. 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.

  7. 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

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

    DOE PAGESBeta

    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)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

  9. 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. PMID:25954263

  10. Multiple independent transmission cycles of a tick-borne pathogen within a local host community.

    PubMed

    Jacquot, Maude; Abrial, David; Gasqui, Patrick; Bord, Severine; Marsot, Maud; Masseglia, Sébastien; Pion, Angélique; Poux, Valérie; Zilliox, Laurence; Chapuis, Jean-Louis; Vourc'h, Gwenaël; Bailly, Xavier

    2016-01-01

    Many pathogens are maintained by multiple host species and involve multiple strains with potentially different phenotypic characteristics. Disentangling transmission patterns in such systems is often challenging, yet investigating how different host species contribute to transmission is crucial to properly assess and manage disease risk. We aim to reveal transmission cycles of bacteria within the Borrelia burgdorferi species complex, which include Lyme disease agents. We characterized Borrelia genotypes found in 488 infected Ixodes ricinus nymphs collected in the Sénart Forest located near Paris (France). These genotypes were compared to those observed in three sympatric species of small mammals and network analyses reveal four independent transmission cycles. Statistical modelling shows that two cycles involving chipmunks, an introduced species, and non-sampled host species such as birds, are responsible for the majority of tick infections. In contrast, the cycle involving native bank voles only accounts for a small proportion of infected ticks. Genotypes associated with the two primary transmission cycles were isolated from Lyme disease patients, confirming the epidemiological threat posed by these strains. Our work demonstrates that combining high-throughput sequence typing with networks tools and statistical modeling is a promising approach for characterizing transmission cycles of multi-host pathogens in complex ecological settings. PMID:27498685

  11. Multiple independent transmission cycles of a tick-borne pathogen within a local host community

    PubMed Central

    Jacquot, Maude; Abrial, David; Gasqui, Patrick; Bord, Severine; Marsot, Maud; Masseglia, Sébastien; Pion, Angélique; Poux, Valérie; Zilliox, Laurence; Chapuis, Jean-Louis; Vourc’h, Gwenaël; Bailly, Xavier

    2016-01-01

    Many pathogens are maintained by multiple host species and involve multiple strains with potentially different phenotypic characteristics. Disentangling transmission patterns in such systems is often challenging, yet investigating how different host species contribute to transmission is crucial to properly assess and manage disease risk. We aim to reveal transmission cycles of bacteria within the Borrelia burgdorferi species complex, which include Lyme disease agents. We characterized Borrelia genotypes found in 488 infected Ixodes ricinus nymphs collected in the Sénart Forest located near Paris (France). These genotypes were compared to those observed in three sympatric species of small mammals and network analyses reveal four independent transmission cycles. Statistical modelling shows that two cycles involving chipmunks, an introduced species, and non-sampled host species such as birds, are responsible for the majority of tick infections. In contrast, the cycle involving native bank voles only accounts for a small proportion of infected ticks. Genotypes associated with the two primary transmission cycles were isolated from Lyme disease patients, confirming the epidemiological threat posed by these strains. Our work demonstrates that combining high-throughput sequence typing with networks tools and statistical modeling is a promising approach for characterizing transmission cycles of multi-host pathogens in complex ecological settings. PMID:27498685

  12. 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

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

    PubMed

    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

  14. Identifying Gender-Preferred Communication Styles within Online Cancer Communities: A Retrospective, Longitudinal Analysis

    PubMed Central

    Durant, Kathleen T.; McCray, Alexa T.; Safran, Charles

    2012-01-01

    Background The goal of this research is to determine if different gender-preferred social styles can be observed within the user interactions at an online cancer community. To achieve this goal, we identify and measure variables that pertain to each gender-specific social style. Methods and Findings We perform social network and statistical analysis on the communication flow of 8,388 members at six different cancer forums over eight years. Kruskal-Wallis tests were conducted to measure the difference between the number of intimate (and highly intimate) dyads, relationship length, and number of communications. We determine that two patients are more likely to form an intimate bond on a gender-specific cancer forum (ovarian P = <0.0001, breast P = 0.0089, prostate P = 0.0021). Two female patients are more likely to form a highly intimate bond on a female-specific cancer forum (Ovarian P<0.0001, Breast P<0.01). Typically a male patient communicates with more members than a female patient (Ovarian forum P = 0.0406, Breast forum P = 0.0013). A relationship between two patients is longer on the gender-specific cancer forums than a connection between two members not identified as patients (ovarian forum P = 0.00406, breast forum P = 0.00013, prostate forum P = .0.0003). Conclusion The high level of interconnectedness among the prostate patients supports the hypothesis that men prefer to socialize in large, interconnected, less-intimate groups. A female patient is more likely to form a highly intimate connection with another female patient; this finding is consistent with the hypothesis that woman prefer fewer, more intimate connections. The relationships of same-gender cancer patients last longer than other relationships; this finding demonstrates homophily within these online communities. Our findings regarding online communication preferences are in agreement with research findings from person-to-person communication preference studies

  15. Arbuscular mycorrhizal fungal community divergence within a common host plant in two different soils in a subarctic Aeolian sand area.

    PubMed

    Francini, Gaia; Männistö, Minna; Alaoja, Vilhelmiina; Kytöviita, Minna-Maarit

    2014-10-01

    There is rising awareness that different arbuscular mycorrhizal (AM) fungi have different autoecology and occupy different soil niches and that the benefits they provide to the host plant are dependent on plant-AM fungus combination. However, the role and community composition of AM fungi in succession are not well known and the northern latitudes remain poorly investigated ecosystems. We studied AM fungal communities in the roots of the grass Deschampsia flexuosa in two different, closely located, successional stages in a northern Aeolian sand area. The AM fungal taxa richness in planta was estimated by cloning and sequencing small subunit ribosomal RNA genes. AM colonization, shoot δ (13)C signature, and %N and %C were measured. Soil microbial community structure and AM fungal mycelium abundance were estimated using phospholipid (PLFA) and neutral lipid (NLFA) analyses. The two successional stages were characterized by distinct plant, microbial, and fungal communities. AM fungal species richness was very low in both the early and late successional stages. AM frequency in D. flexuosa roots was higher in the early successional stage than in the late one. The AM fungal taxa retrieved belonged to the genera generally adapted to Arctic or extreme environments. AM fungi seemed to be important in the early stage of the succession, suggesting that AM fungi may help plants to better cope with the harsh environmental conditions, especially in an early successional stage with more extreme environmental fluctuations. PMID:24687606

  16. Identifying the biting species in snakebite by clinical features: an epidemiological tool for community surveys.

    PubMed

    Pathmeswaran, A; Kasturiratne, A; Fonseka, M; Nandasena, S; Lalloo, D G; de Silva, H J

    2006-09-01

    The outcome of snakebite is related to the biting species but it is often difficult to identify the biting snake, particularly in community settings. We have developed a clinical scoring system suitable for use in epidemiological surveys, with the main aim of identifying the presumed biting species in those with systemic envenoming who require treatment. The score took into account ten features relating to bites of the five medically important snakes in Sri Lanka, and an algorithm was developed applying different weightings for each feature for different species. A systematically developed artificial data set was used to fine tune the score and to develop criteria for definitive identification. The score was prospectively validated using 134 species-confirmed snakebites. It correctly differentiated the bites caused by the three snakes that commonly cause major clinical problems (Russell's viper (RV), kraits and cobra) from other snakes (hump-nosed viper (HNV) and saw-scaled viper (SSV)) with 80% sensitivity and 100% specificity. For individual species, sensitivity and specificity were, respectively: cobra 76%, 99%; kraits 85%, 99%; and RV 70%, 99%. As anticipated, the score was insensitive in the identification of bites due to HNV and SSV. PMID:16412486

  17. 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

  18. 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. PMID:22970260

  19. Sulfur Metabolizing Microbes Dominate Microbial Communities in Andesite-Hosted Shallow-Sea Hydrothermal Systems

    PubMed Central

    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 (CH4) 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 CH4 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 CH4 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. PMID:22970260

  20. 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 ...

  1. 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…

  2. 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,…

  3. 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

  4. [The host community of a child with food allergies: the personalized care project (PCP)].

    PubMed

    Rancé, F

    2010-12-01

    The personalized care project (PCP) can manage allergic emergencies that may occur during school hours. Other objectives are to facilitate academic achievement, social and professional integration of children and adolescents with chronic illness such as food allergy, by promoting education through certain changes. The PCP is derived from official files including Circular N(o) 2003-135 of September 8 and the inter-ministerial circular of 25 June 2001. The family must request a protocol with the host school principal or school head. Then, the doctor of Education organizes the drafting of the document based on information provided by the physician (or allergist). PMID:21074388

  5. Low haemosporidian diversity and one key-host species in a bird malaria community on a mid-Atlantic island (São Miguel, Azores).

    PubMed

    Hellgren, Olof; Križanauskienė, Asta; Hasselquist, Dennis; Bensch, Staffan

    2011-10-01

    When host species colonize new areas, the parasite assemblage infecting the hosts might change, with some parasite species being lost and others newly acquired. These changes would likely lead to novel selective forces on both host and its parasites. We investigated the avian blood parasites in the passerine bird community on the mid-Atlantic island of São Miguel, Azores, a bird community originating from continental Europe. The presence of haemosporidian blood parasites belonging to the genera Haemoproteus, Plasmodium, and Leucocytozoon was assessed using polymerase chain reaction. We found two Plasmodium lineages and two Leucocytozoon lineages in 11 bird species (84% of all breeding passerine species) on the island. These lineages were unevenly distributed across bird species. The Eurasian Blackbird (Turdus merula) was the key-host species (total parasite prevalence of 57%), harboring the main proportion of parasite infections. Except for Eurasian Blackbirds, all bird species had significantly lower prevalence and parasite diversity compared to their continental populations. We propose that in evolutionary novel bird communities, single species may act as key hosts by harboring the main part of the parasite fauna from which parasites "leak" into the other species. This would create very different host-parasite associations in areas recently colonized by hosts as compared to in their source populations. PMID:22102655

  6. 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

  7. 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. PMID:23542624

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

    PubMed

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

    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

  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. 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

  11. 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

  12. 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. PMID:26414063

  13. 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.

  14. Evidence for alteration of fungal endophyte community assembly by host defense compounds.

    PubMed

    Saunders, Megan; Kohn, Linda Myra

    2009-01-01

    * Plant defense compounds are common stressors encountered by endophytes. Fungi readily evolve tolerance to these compounds, yet few studies have addressed the influence of intraspecific variation in defense compound production on endophyte colonization. We compared the influence of defense compound production on the composition of fungal endophyte communities in replicated field experiments. * Maize (Zea mays) produces benzoxazinoids (BXs), compounds with antifungal byproducts persistent in the environment. Fungi were isolated from leaf and root tissue of two maize genotypes that produce BXs, and a natural mutant that does not. Isolates representing the species recovered were tested for tolerance to 2-benzoxazolinone (BOA), a toxic BX byproduct. * In seedling roots and mature leaves, the community proportion with low BOA tolerance was significantly greater in BX nonproducers than producers. Mean isolation frequency of Fusarium species was up to 35 times higher in mature leaves of BX producers than nonproducers. * Fungal species with relatively high tolerance to BOA are more abundant in BX producing than BX nonproducing maize. Production of BXs may increase colonization by Fusarium species in maize, including agents of animal toxicosis and yield-reducing disease in maize. Overall, results indicate that production of defense compounds can significantly alter endophyte community assembly. PMID:19170900

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

    PubMed Central

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

    2014-01-01

    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. PMID:24978929

  16. 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.

  17. 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. PMID:25874424

  18. 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.

  19. 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. PMID:19132518

  20. Metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities.

    PubMed

    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 (H(2)). In order to assess the potential for microbial H(2) 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 H(2)-oxidizers. Both sites also yielded metagenomic evidence for microbial H(2) 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 H(2)-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 H(2)-powered primary production in serpentinite-hosted subsurface habitats. PMID:22232619

  1. 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

  2. Geographic structure and host specificity shape the community composition of symbiotic dinoflagellates in corals from the Northwestern Hawaiian Islands

    NASA Astrophysics Data System (ADS)

    Stat, Michael; Yost, Denise M.; Gates, Ruth D.

    2015-12-01

    How host-symbiont assemblages vary over space and time is fundamental to understanding the evolution and persistence of mutualistic symbioses. In this study, the diversity and geographic structure of coral-algal partnerships across the remote Northwestern Hawaiian Islands archipelago was investigated. The diversity of symbionts in the dinoflagellate genus Symbiodinium was characterised using the ribosomal internal transcribed spacer 2 (ITS2) gene in corals sampled at ten reef locations across the Northwestern Hawaiian Islands. Symbiodinium diversity was reported using operational taxonomic units and the distribution of Symbiodinium across the island archipelago investigated for evidence of geographic structure using permutational MANOVA. A 97 % sequence similarity of the ITS2 gene for characterising Symbiodinium diversity was supported by phylogenetic and ecological data. Four of the nine Symbiodinium evolutionary lineages (clades A, C, D, and G) were identified from 16 coral species at French Frigate Shoals, and host specificity was a dominant feature in the symbiotic assemblages at this location. Significant structure in the diversity of Symbiodinium was also found across the archipelago in the three coral species investigated. The latitudinal gradient and subsequent variation in abiotic conditions (particularly sea surface temperature dynamics) across the Northwestern Hawaiian Islands encompasses an environmental range that decouples the stability of host-symbiont assemblages across the archipelago. This suggests that local adaptation to prevailing environmental conditions by at least one partner in coral-algal mutualism occurs prior to the selection pressures associated with the maintenance of a symbiotic state.

  3. Evaluation of PCR-DGGE as a method to recapitulate host phylogeny by fecal microbial community fingerprint

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Recent studies indicate that host animal could be the primary factor determining the composition of the gastrointestinal microbiome. If host phenotype dictates microbiome composition, then composition should recapitulate host phylogeny. Polymerase chain reaction-denaturing gradient gel ...

  4. 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…

  5. Identifying Fit of Mission and Environment: Applying the American Community College Model Internationally

    ERIC Educational Resources Information Center

    Spangler, Mary S.; Tyler, Arthur Q., Jr.

    2011-01-01

    The two-year community college is a hundred-year-old phenomenon, locally funded and distinctly American, yet increasingly exportable. Serving ever more varied roles while being challenged economically, legislatively, and academically to meet progressively higher expectations in the United States, the American community college has been discovered…

  6. Identifying Success Factors of ICT in Developing a Learning Community: Case Study Charles Sturt University

    ERIC Educational Resources Information Center

    Campbell, Matthew; Uys, Philip

    2007-01-01

    Purpose: A learning community has been developing in a distributed environment amongst the members of the Centre for Enhancing of Learning and Teaching (CELT) located in the Bathurst, Goulburn and Orange campuses of Charles Sturt University. This group is known by the acronym of GDMOB, with the purpose of the community to facilitate the…

  7. The Community College Transfer Calculator: Identifying the Course-Taking Patterns that Predict Transfer

    ERIC Educational Resources Information Center

    Hagedorn, Linda Serra; Cabrera, Alberto; Prather, George

    2011-01-01

    Using a newly developed software application entitled "The Community College Transfer Calculator"[C], this article both quantifies the effect of specific course-taking patterns and stresses the need for an easy to understand tool for community college academic advisors, faculty, and students. The "Calculator" calculates the likelihood of transfer…

  8. 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…

  9. Multiscale assemblage of an ectomycorrhizal fungal community: the influence of host functional traits and soil properties in a 10-ha miombo forest.

    PubMed

    Bauman, David; Raspé, Olivier; Meerts, Pierre; Degreef, Jérôme; Ilunga Muledi, Jonathan; Drouet, Thomas

    2016-10-01

    Ectomycorrhizal fungi (EMF) are highly diversified and dominant in a number of forest ecosystems. Nevertheless, their scales of spatial distribution and the underlying ecological processes remain poorly understood. Although most EMF are considered to be generalists regarding host identity, a preference toward functional strategies of host trees has never been tested. Here, the EMF community was characterised by DNA sequencing in a 10-ha tropical dry season forest-referred to as miombo-an understudied ecosystem from a mycorrhizal perspective. We used 36 soil parameters and 21 host functional traits (FTs) as candidate explanatory variables in spatial constrained ordinations for explaining the EMF community assemblage. Results highlighted that the community variability was explained by host FTs related to the 'leaf economics spectrum' (adjusted R(2) = 11%; SLA, leaf area, foliar Mg content), and by soil parameters (adjusted R(2) = 17%), notably total forms of micronutrients or correlated available elements (Al, N, K, P). Both FTs and soil generated patterns in the community at scales ranging from 75 to 375 m. Our results indicate that soil is more important than previously thought for EMF in miombo woodlands, and show that FTs of host species can be better predictors of symbiont distribution than taxonomical identity. PMID:27402715

  10. 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.

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

    PubMed

    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

  12. Identifying Success Factors in Community College Grants Awarded under the U.S. Department of Labor's Community-Based Job Training Grants Program, 2005-2008

    ERIC Educational Resources Information Center

    Garrison, Debra Linley

    2010-01-01

    This study provides an in-depth analysis of the Community-Based Job Training Grants awarded by the U.S. Department of Labor from 2005 to 2008. The primary research question is designed to identify the most important factors in meeting grant-training outcomes; however, numerous secondary questions were addressed to provide the reader with in-depth…

  13. Identifying the Achilles heel of multi-host pathogens: the concept of keystone ‘host’ species illustrated by Mycobacterium ulcerans transmission

    NASA Astrophysics Data System (ADS)

    Roche, Benjamin; Benbow, M. Eric; Merritt, Richard; Kimbirauskas, Ryan; McIntosh, Mollie; Small, Pamela L. C.; Williamson, Heather; Guégan, Jean-François

    2013-12-01

    Pathogens that use multiple host species are an increasing public health issue due to their complex transmission, which makes them difficult to mitigate. Here, we explore the possibility of using networks of ecological interactions among potential host species to identify the particular disease-source species to target to break down transmission of such pathogens. We fit a mathematical model on prevalence data of Mycobacterium ulcerans in western Africa and we show that removing the most abundant taxa for this category of pathogen is not an optimal strategy to decrease the transmission of the mycobacterium within aquatic ecosystems. On the contrary, we reveal that the removal of some taxa, especially Oligochaeta worms, can clearly reduce rates of pathogen transmission, and these should be considered as keystone organisms for its transmission because they lead to a substantial reduction in pathogen prevalence regardless of the network topology. Besides their potential application for the understanding of M. ulcerans ecology, we discuss how networks of species interactions can modulate transmission of multi-host pathogens.

  14. Host Selection of Microbiota via Differential Adhesion.

    PubMed

    McLoughlin, Kirstie; Schluter, Jonas; Rakoff-Nahoum, Seth; Smith, Adrian L; Foster, Kevin R

    2016-04-13

    The host epithelium is the critical interface with microbial communities, but the mechanisms by which the host regulates these communities are poorly understood. Here we develop the hypothesis that hosts use differential adhesion to select for and against particular members of their microbiota. We use an established computational, individual-based model to study the impact of host factors that regulate adhesion at the epithelial surface. Our simulations predict that host-mediated adhesion can increase the competitive advantage of microbes and create ecological refugia for slow-growing species. We show how positive selection via adhesion can be transformed into negative selection if the host secretes large quantities of a matrix such as mucus. Our work predicts that adhesion is a powerful mechanism for both positive and negative selection within the microbiota. We discuss molecules-mucus glycans and IgA-that affect microbe adhesion and identify testable predictions of the adhesion-as-selection model. PMID:27053168

  15. 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. PMID:25522815

  16. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

    PubMed

    Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

    2016-10-01

    Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. PMID:27402713

  17. Identifying the community structure of the international-trade multi-network

    NASA Astrophysics Data System (ADS)

    Barigozzi, Matteo; Fagiolo, Giorgio; Mangioni, Giuseppe

    2011-06-01

    We study the community structure of the multi-network of commodity-specific trade relations among world countries over the 1992-2003 period. We compare structures across commodities and time by means of the normalized mutual information index (NMI). We also compare them with exogenous community structures induced by geography and regional trade agreements. We find that commodity-specific community structures are very heterogeneous and much more fragmented than that characterizing the aggregate ITN. This shows that the aggregate properties of the ITN may result (and be very different) from the aggregation of very diverse commodity-specific layers of the multi-network. We also show that commodity-specific community structures, especially those related to the chemical sector, are becoming more and more similar to the aggregate one. Finally, our findings suggest that geography-induced partitions of our set of countries are much more correlated with observed community structures than partitions induced by regional-trade agreements. This result strengthens previous findings from the empirical literature on trade.

  18. 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. PMID:23835426

  19. Identifying barriers and catalysts to fostering pro-environmental behavior: opportunities and challenges for community psychology.

    PubMed

    Quimby, Christine C; Angelique, Holly

    2011-06-01

    In this paper, we report on an exploratory study of perceived barriers and catalysts to increasing pro-environmental behavior among people associated with the environmental movement. Perceived barriers include time, money, low efficacy and hopelessness. Catalysts focus on changing social norms, especially through education and institutional support. We discuss the tragedy of the commons and free-riding as impediments to change. We use this study as an entryway to hypothesize opportunities and challenges that community psychologists face in motivating and supporting actions to reduce the impact of global climate change. We provide examples of how community psychologists can foster these changes. In short, we argue that community psychology is well positioned to take a leading role in the fight for a carbon neutral future. PMID:21203832

  20. 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

  1. 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…

  2. 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…

  3. 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.…

  4. The Evolution of a Teacher Community of Practice: Identifying Facilitating and Constraining Factors

    ERIC Educational Resources Information Center

    Borg, Tracey

    2012-01-01

    This paper presents findings from a larger, qualitative study that explored the potential of a school-based teacher community of practice as a model for a transformative form of teacher professional development. This paper reports on initial findings from a grounded theory exploration of the factors that facilitated and constrained the evolution…

  5. Identify in a Canadian Urban Community. A Process Report of the Brunskill Subproject. Project Canada West.

    ERIC Educational Resources Information Center

    Burke, M.; And Others

    The purpose of this subproject is to guide students to meet and interact with individuals from the many subcultures in a community (see ED 055 011). This progress report of the second year's activities includes information on the process of curriculum development, the materials developed, evaluation, roles of supporting agencies, behavioral…

  6. A Student Outcomes Typology for Community Colleges: Identifying Achievers with Longitudinal Cohort Analysis.

    ERIC Educational Resources Information Center

    Boughan, Karl; Clagett, Craig A.

    A study was conducted by Prince George's Community College, in Maryland, to determine outcomes after 4 years for the 2,643 first-time students who entered the college in fall 1990. The analysis was based on an outcomes typology developed at the college which defines outcomes as award and transfer; transfer without an award; award without transfer;…

  7. 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…

  8. 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.

  9. 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. PMID:25066007

  10. Photovoice in Kenya: Using a Community-Based Participatory Research Method to Identify Health Needs.

    PubMed

    Kingery, Francesca P; Naanyu, Violet; Allen, William; Patel, Pradip

    2016-01-01

    Photovoice, a community-based participatory research method, was utilized to delineate the health-related needs of a small rural community in Kenya. Within the Cherangany Constituency, 13 women were recruited and trained in digital photography and appropriate ethical conduct in photography (respect for privacy, consent, and confidentiality). Both individual and group interviews were conducted with the participants, and data were transcribed and analyzed for common themes by both the participants and the researcher. Common themes present in the photos were coded and prioritized in order of importance: (a) school fees, (b) water, (c) hospital fees, (d) sanitation, (e) orphans, (f) widows, (g) lack of jobs/capital, (h) disabilities, and (i) presence of disease. Data from this study will be utilized for (a) development of culturally competent health education, (b) site-specific education/training of incoming medical teams, and (c) informative meetings with local leaders regarding health and associated challenges. PMID:26679942

  11. 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.

  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. PMID:26467674

  13. A Genetic Screen for Pathogenicity Genes in the Hemibiotrophic Fungus Colletotrichum higginsianum Identifies the Plasma Membrane Proton Pump Pma2 Required for Host Penetration.

    PubMed

    Korn, Martin; Schmidpeter, Johannes; Dahl, Marlis; Müller, Susanne; Voll, Lars M; Koch, Christian

    2015-01-01

    We used insertional mutagenesis by Agrobacterium tumefaciens mediated transformation (ATMT) to isolate pathogenicity mutants of Colletotrichum higginsianum. From a collection of 7200 insertion mutants we isolated 75 mutants with reduced symptoms. 19 of these were affected in host penetration, while 17 were affected in later stages of infection, like switching to necrotrophic growth. For 16 mutants the location of T-DNA insertions could be identified by PCR. A potential plasma membrane H(+)-ATPase Pma2 was targeted in five independent insertion mutants. We genetically inactivated the Ku80 component of the non-homologous end-joining pathway in C. higginsianum to establish an efficient gene knockout protocol. Chpma2 deletion mutants generated by homologous recombination in the ΔChku80 background form fully melanized appressoria but entirely fail to penetrate the host tissue and are non-pathogenic. The ChPMA2 gene is induced upon appressoria formation and infection of A. thaliana. Pma2 activity is not important for vegetative growth of saprophytically growing mycelium, since the mutant shows no growth penalty under these conditions. Colletotrichum higginsianum codes for a closely related gene (ChPMA1), which is highly expressed under most growth conditions. ChPMA1 is more similar to the homologous yeast genes for plasma membrane pumps. We propose that expression of a specific proton pump early during infection may be common to many appressoria forming fungal pathogens as we found ChPMA2 orthologs in several plant pathogenic fungi. PMID:25992547

  14. A Genetic Screen for Pathogenicity Genes in the Hemibiotrophic Fungus Colletotrichum higginsianum Identifies the Plasma Membrane Proton Pump Pma2 Required for Host Penetration

    PubMed Central

    Dahl, Marlis; Müller, Susanne; Voll, Lars M.; Koch, Christian

    2015-01-01

    We used insertional mutagenesis by Agrobacterium tumefaciens mediated transformation (ATMT) to isolate pathogenicity mutants of Colletotrichum higginsianum. From a collection of 7200 insertion mutants we isolated 75 mutants with reduced symptoms. 19 of these were affected in host penetration, while 17 were affected in later stages of infection, like switching to necrotrophic growth. For 16 mutants the location of T-DNA insertions could be identified by PCR. A potential plasma membrane H+-ATPase Pma2 was targeted in five independent insertion mutants. We genetically inactivated the Ku80 component of the non-homologous end-joining pathway in C. higginsianum to establish an efficient gene knockout protocol. Chpma2 deletion mutants generated by homologous recombination in the ΔChku80 background form fully melanized appressoria but entirely fail to penetrate the host tissue and are non-pathogenic. The ChPMA2 gene is induced upon appressoria formation and infection of A. thaliana. Pma2 activity is not important for vegetative growth of saprophytically growing mycelium, since the mutant shows no growth penalty under these conditions. Colletotrichum higginsianum codes for a closely related gene (ChPMA1), which is highly expressed under most growth conditions. ChPMA1 is more similar to the homologous yeast genes for plasma membrane pumps. We propose that expression of a specific proton pump early during infection may be common to many appressoria forming fungal pathogens as we found ChPMA2 orthologs in several plant pathogenic fungi. PMID:25992547

  15. Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution.

    PubMed

    Do, Lien Anh Ha; Wilm, Andreas; Van Doorn, H Rogier; Lam, Ha Minh; Sim, Shuzhen; Sukumaran, Rashmi; Tran, Anh Tuan; Nguyen, Bach Hue; Tran, Thi Thu Loan; Tran, Quynh Huong; Vo, Quoc Bao; Dac, Nguyen Anh Tran; Trinh, Hong Nhien; Nguyen, Thi Thanh Hai; Binh, Bao Tinh Le; Le, Khanh; Nguyen, Minh Tien; Thai, Quang Tung; Vo, Thanh Vu; Ngo, Ngoc Quang Minh; Dang, Thi Kim Huyen; Cao, Ngoc Huong; Tran, Thu Van; Ho, Lu Viet; Farrar, Jeremy; Jong, Menno de; Chen, Swaine; Nagarajan, Niranjan; Bryant, Juliet E; Hibberd, Martin L

    2015-12-01

    Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children ,2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites inG were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance. PMID:26407694

  16. 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.

  17. 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. PMID:25068271

  18. 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

  19. Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants.

    PubMed

    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

  20. 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

  1. 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. PMID:23463243

  2. 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

    Hosking, Christopher G; McWilliam, Hamish E G; Driguez, Patrick; Piedrafita, David; Li, Yuesheng; McManus, Donald P; Ilag, Leodevico L; Meeusen, Els N T; Veer, Michael J de

    2015-12-01

    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

  3. 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

  4. Using community-based participatory research to identify health issues for Cambodian American youth.

    PubMed

    Sangalang, Cindy C; Ngouy, Suely; Lau, Anna S

    2015-01-01

    Lack of data disaggregated by ethnic group and the widespread perception of Asian Americans as "model minorities" often masks the health needs of specific groups within the Asian American population. Limited research focuses on health and psychological well-being among Cambodian American youth despite risk of negative educational and behavioral outcomes as well as high levels of trauma and psychiatric symptoms among first-generation Cambodian refugee adults. This article describes the development of a health survey with Cambodian American youth using community-based participatory research (and illustrates how youth can actively engage in research to inform change in health-related programs and policies. PMID:25423244

  5. Molecular insights into a molluscan transferrin homolog identified from disk abalone (Haliotis discus discus) evidencing its detectable role in host antibacterial defense.

    PubMed

    Herath, H M L P B; Elvitigala, Don Anushka Sandaruwan; Godahewa, G I; Whang, Ilson; Lee, Jehee

    2015-11-01

    The basic function of transferrin is to bind iron (III) ions in the medium and to deliver them to the locations where they are required for metabolic processes. It also takes part in the host immune defense mainly via its ability to bind to iron (III) ions. Hence, transferrin is also identified as an important acute-phase protein in host immunity. Abalones are major shellfish aquaculture crops that are susceptible to a range of marine microbial infections. Since transferrin is known to be a major player in innate immunity, in the present study we sought to identify, and molecularly and functionally characterize a transferrin-like gene from disk abalone (Haliotis discus discus) named as AbTrf. AbTrf consisted of a 2187-bp open reading frame (ORF) which encodes a 728 amino acid (aa) protein. The putative amino acid sequence of AbTrf harbored N- and C-terminal transferrin-like domains, active sites for iron binding, and conserved cysteine residues. A constitutive tissue specific AbTrf expression pattern was detected by qPCR in abalones where mantle and muscle showed high AbTrf expression levels. Three immune challenge experiments were conducted using Vibrio parahaemolyticus, Listeria monocytogenes and LPS as stimuli and, subsequently, AbTrf mRNA expression levels were quantified in gill and hemocytes in a time-course manner. The mRNA expression was greatly induced in both tissues in response to both challenges. Evidencing the functional property of transferrins, recombinant AbTrf N-terminal domain (AbTrf-N) showed dose-dependent iron (III) binding activity detected by chrome azurol S (CAS) assay system. Moreover, recombinant AbTrf-N could significantly inhibit the growth of iron-dependent bacterium, Escherichia coli in a dose-dependent manner. However, AbTrf-N was unable to show any detectable bacteriostatic activity against iron-independent bacterium Lactobacillus plantarum (L. plantarum) even at its highest concentration. Collectively, our results suggest that Ab

  6. 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. PMID:25918775

  7. 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

  8. Bacterial community assemblages associated with the phyllosphere, dermosphere, and rhizosphere of tree species of the Atlantic forest are host taxon dependent.

    PubMed

    Lambais, Marcio R; Lucheta, Adriano R; Crowley, David E

    2014-10-01

    Bacterial communities associated with tree canopies have been shown to be specific to their plant hosts, suggesting that plant species-specific traits may drive the selection of microbial species that comprise their microbiomes. To further examine the degree to which the plant taxa drive the assemblage of bacterial communities in specific plant microenvironments, we evaluated bacterial community structures associated with the phyllosphere, dermosphere, and rhizosphere of seven tree species representing three orders, four families and four genera of plants from a pristine Dense Ombrophilous Atlantic forest in Brazil, using a combination of PCR-DGGE of 16S rRNA genes and clone library sequencing. Results indicated that each plant species selected for distinct bacterial communities in the phyllosphere, dermosphere, and rhizosphere, and that the bacterial community structures are significantly related to the plant taxa, at the species, family, and order levels. Further characterization of the bacterial communities of the phyllosphere and dermosphere of the tree species showed that they were inhabited predominantly by species of Gammaproteobacteria, mostly related to Pseudomonas. In contrast, the rhizosphere bacterial communities showed greater species richness and evenness, and higher frequencies of Alphaproteobacteria and Acidobacteria Gp1. With individual tree species each selecting for their specific microbiomes, these findings greatly increase our estimates of the bacterial species richness in tropical forests and provoke questions concerning the ecological functions of the microbial communities that exist on different plant parts. PMID:24889284

  9. Subtype analysis of Blastocystis sp. isolates from human and canine hosts in an urban community in the Philippines.

    PubMed

    Belleza, Maria Luz B; Reyes, John Carlo B; Tongol-Rivera, Pilarita N; Rivera, Windell L

    2016-06-01

    Blastocystis sp. is a common gut-dwelling protist of both humans and animals. A cross-sectional survey among humans and their dogs was conducted to determine the prevalence of Blastocystis infection and to characterize the subtype (ST) distribution in an urban community in the Philippines. Fecal specimens from 1,271 humans and 145 dogs were collected and inoculated in diphasic culture medium. Prevalence of Blastocystis by culture was 13.0% (95% CI=11.2-15.0) and 14.5% (95% CI=9.6-21.2) for humans and dogs, respectively. A total of 168 culture isolates were genotyped using polymerase chain reaction (PCR) with seven pairs of ST-specific sequence-tagged-site (STS) primers. In humans, the ST present in this study were ST1 with 22.6% (95% CI=17.2-29.0), ST2 with 3.1% (95% CI=1.3-6.7), ST3 with 41.4% (95% CI=34.9-48.6), ST4 with 14.8% (95% CI=10.5-20.6), ST5 with 4.1% (95% CI=2.0-8.0), and unknown ST with 13.9% (95% CI=9.6-19.4). In dogs, the ST present in this study were ST1 with 4.3% (95% CI=0.0-29.0), ST2 with 8.7% (95% CI=1.3-28.0), ST3 with 17.4% (95% CI=6.4-37.7), ST4 with 13.0% (95% CI=3.7-33.0), ST5 with 13.0% (95% CI=3.7-33.0), and unknown ST with 47.8% (95% CI=29.2-67.0). This is the first study that reported Blastocystis ST4 in human and canine hosts in the Philippines. PMID:26902433

  10. 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…

  11. The use of concept mapping to identify community-driven intervention strategies for physical and mental health.

    PubMed

    Vaughn, Lisa M; Jacquez, Farrah; McLinden, Daniel

    2013-09-01

    Research that partners with youth and community stakeholders increases contextual relevance and community buy-in and therefore maximizes the chance for intervention success. Concept mapping is a mixed-method participatory research process that accesses the input of the community in a collaborative manner. After a school-wide health needs assessment at a low-income, minority/immigrant K-8 school identified bullying and obesity as the most important health issues, concept mapping was used to identify and prioritize specific strategies to address these two areas. Stakeholders including 160 K-8 students, 33 college students working in the school, 35 parents, 20 academic partners, and 22 teachers/staff brainstormed strategies to reduce and prevent obesity and bullying. A smaller group of stakeholders worked individually to complete an unstructured sorting of these strategies into groups of similar ideas, once for obesity and again for bullying. Multidimensional scaling and cluster analysis was applied to the sorting data to produce a series of maps that illustrated the stakeholders' conceptual thinking about obesity and bullying prevention strategies. The maps for both obesity and bullying organized specific strategies into themes that included education, parental role, teacher/school supervision, youth role, expert/professional role, and school structure/support. PMID:23099661

  12. 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. PMID:22717756

  13. 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. PMID:26383053

  14. Self-Management Goal Setting: Identifying the Practice Patterns of Community-Based Physical Therapists

    PubMed Central

    Peng, Karen; Bourret, Drew; Khan, Usman; Truong, Henry; Nixon, Stephanie; McKay, Sandra

    2014-01-01

    ABSTRACT Purpose: To describe the collaborative goal-setting practices of community-based physical therapists trained in a self-management (SM) approach who work with clients with chronic conditions and to describe clients' goal-achievement rates. Methods: A retrospective chart review was conducted for 296 randomly selected home-care clients from July 2009 through July 2010 using a chart-abstraction form created to capture demographic data and information related to goal setting and achievement. Data were analyzed using frequencies, percentages, and Pearson's chi-square tests. Results: There was no significant relationship between sex, age, or number of chronic conditions and setting SM or non-self-management (NSM) goals or the type of SM goal set. The majority of goals set were “action” as opposed to “verbal” goals. A high proportion (89–100%) of both SM and NSM goals were met. Conclusions: Clinicians should be aware that it is possible to set SM goals regardless of the client's sex, age, or number of chronic conditions. Other possible influences on goal setting, such as severity of chronic conditions and challenges of the health care system, should be further investigated. PMID:24799753

  15. 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.

  16. 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

  17. Increasing community participation after brain injury: strategies for identifying and reducing the risks.

    PubMed

    Durgin, C J

    2000-12-01

    This article describes the complex processes involved in evaluating safety, judgment, and risk after brain injury. Starting with a review of common risk factors after onset, the article then moves to a discussion of the dilemmas faced by family members and clinicians alike when determining the individual's level of risk. Numerous suggestions are offered to identify support system concerns and to establish specific barriers to independence. The need to adopt a systematized approach to empirically verifying concerns about safety is emphasized, in addition to utilizing therapeutic interventions that are sensitive to the individual's learning capacity, psychological status, and environmental influences. The article concludes with examples of how to structure support for individuals who present with ongoing risk factors but still need to experience greater levels of personal freedom. PMID:11056403

  18. Search for Improved Host Architectures: Application of de Novo Structure-Based Design and High-Throughput Screening Methods to Identify Optimal Building Blocks for Multidentate Ethers.

    SciTech Connect

    Hay, Benjamin P.; Oliferenko, Alex A.; Uddin, Jamal; Zhang, Cungen; Firman, Timothy K.

    2005-12-07

    This paper presents a computational approach to the deliberate design of improved host architectures. The approach, which involves the use of computer-aided design software, is illustrated by application to cation hosts containing multiple aliphatic ether oxygen binding sites. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential bidentate building block structures. Enhanced cation binding affinity can be achieved when highly organized building blocks are used to construct macrocyclic hosts.

  19. 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

  20. Identifying Care Coordination Interventions Provided to Community-Dwelling Older Adults Using Electronic Health Records.

    PubMed

    Kim, Tae Youn; Marek, Karen D; Coenen, Amy

    2016-07-01

    Although care coordination is a popular intervention, there is no standard method of delivery. Also little is known about who benefits most, or characteristics that predict the amount of care coordination needed, especially with chronically ill older adults. The purpose of this study was to identify types and amount of nurse care coordination interventions provided to 231 chronically ill older adults who participated in a 12-month home care medication management program in the Midwest. For each participant, the nurse care coordinator spent an average of 134 min/mo providing in-person home care, 48 min/mo of travel, and 18 min/mo of indirect care occurring outside the home visit. This accounted for 67.2%, 23.8%, and 9.0% of nursing time, respectively, for home visits, travel, and indirect care. Four of 11 nursing interventions focused on medication management were provided to all participants. Seven of the 11 main interventions were individualized according to each person's special needs. Wide variations were observed in time provided with in-person home care and communications with multiple stakeholders. Study findings indicate the importance of individualizing interventions and the variability in the amount of nursing time needed to provide care coordination to chronically ill older adults. PMID:26985762

  1. 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

  2. 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

    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

  3. 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

  4. 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

  5. PREDICT-PD: Identifying risk of Parkinson's disease in the community: methods and baseline results

    PubMed Central

    Noyce, Alastair J; Bestwick, Jonathan P; Silveira-Moriyama, Laura; Hawkes, Christopher H; Knowles, Charles H; Hardy, John; Giovannoni, Gavin; Nageshwaran, Saiji; Osborne, Curtis; Lees, Andrew J; Schrag, Anette

    2014-01-01

    Objectives To present methods and baseline results for an online screening tool to identify increased risk for Parkinson's disease (PD) in the UK population. Methods Risk estimates for future PD were derived from the results of a systematic review of risk factors and early features of PD. Participants aged 60–80 years without PD were recruited by self-referral. They completed an online survey (including family history, non-motor symptoms and lifestyle factors), a keyboard-tapping task and the University of Pennsylvania Smell Identification Test. Risk scores were calculated based on survey answers. Preliminary support for the validity of this algorithm was assessed by comparing those estimated to be higher risk for PD with those at lower risk using proxies, including smell loss, REM-sleep behaviour disorder and reduced tapping speed, and by assessing associations in the whole group. Results 1324 eligible participants completed the survey and 1146 undertook the keyboard-tapping task. Smell tests were sent to 1065 participants. Comparing the 100 highest-risk participants and 100 lowest-risk participants, median University of Pennsylvania Smell Identification Test scores were 30/40 versus 33/40 (p<0.001), mean number of key taps in 30 s were 55 versus 58 (p=0.045), and 24% versus 10% scored above cut-off for REM-sleep behaviour disorder (p=0.008). Regression analyses showed increasing risk scores were associated with worse scores in the three proxies across the whole group (p≤0.001). Conclusions PREDICT-PD is the first study to systematically combine risk factors for PD in the general population. Validity to predict risk of PD will be tested through longitudinal follow-up of incident PD diagnosis. PMID:23828833

  6. Identifying risk factors for tungiasis and heavy infestation in a resource-poor community in northeast Brazil.

    PubMed

    Muehlen, Marion; Feldmeier, Hermann; Wilcke, Thomas; Winter, Benedikt; Heukelbach, Jörg

    2006-04-01

    Tungiasis is a neglected parasitic skin disease caused by penetration of female sand fleas into the epidermis. The ectoparasitosis is widespread in resource-poor communities in South America, the Caribbean and sub-Saharan Africa. To identify risk factors for the presence of sand fleas and severe infestation in an endemic community, we examined the entire population of a traditional fishing village for the presence of embedded sand fleas and determined the number and type of lesions. Demographic, behavioural and environmental characteristics of the population were assessed using a structured questionnaire. Multivariable analysis showed that both occurrence of tungiasis and heavy infestation were significantly related to poor housing conditions (odds ratio [OR]=4.7, 95% CI 1.4-15.8), lack of health education (OR=4.1, 95% CI 2.0-8.6) and presence of animals on the compound (OR=1.9, 95% CI 1.1-3.4). Contrary to common belief, a protective effect of frequent use of closed footwear could not be demonstrated. Based on the population attributable fractions calculated for the major risk factors identified, we conclude that several low-cost interventions would have a considerable impact on the occurrence of tungiasis and heavy infestation. PMID:16297946

  7. 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. PMID:25401987

  8. 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. PMID:23748862

  9. Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria

    PubMed Central

    Shen, Hongzhang; Ye, Fuqiang; Xie, Lu; Yang, Jianfeng; Li, Zhen; Xu, Peisong; Meng, Fei; Li, Lei; Chen, Ying; Bo, Xiaochen; Ni, Ming; Zhang, Xiaofeng

    2015-01-01

    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. PMID:26625708

  10. 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…

  11. 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…

  12. Identifying community risk factors for HIV among South African adolescents with mental health problems: a qualitative study of parental perceptions.

    PubMed

    Kagee, Ashraf; Donenberg, Geri; Davids, Alicia; Vermaak, Redwaan; Simbayi, Leickness; Ward, Catherine; Naidoo, Pamela; Mthembu, Jacky

    2014-01-01

    High risk sexual behaviour, alcohol and drug use, and mental health problems combine to yield high levels of HIV-risk behaviour among adolescents with mental health problems. In South Africa, little research has been conducted on parental perspectives of HIV-risk among this population. We conducted a series of focus group discussions with 28 mothers of adolescents receiving services at two mental health clinics in South Africa to identify, from their perspectives, the key community problems facing their children. Participants indicated that HIV remained a serious threat to their adolescent children's well-being, in addition to substance abuse, early sexual debut, and teenage pregnancy. These social problems were mentioned as external to their household dynamics, and thus seemingly beyond the purview of the parent-adolescent relationship. These data have implications for the design of family-based interventions to ameliorate the factors associated with HIV-risk among youth receiving mental health services. PMID:25533404

  13. Identifying Reference Conditions and Quantifying Biological Variability Within Benthic Macroinvertebrate Communities in Perennial and Non-perennial Northern California Streams

    NASA Astrophysics Data System (ADS)

    Lunde, Kevin B.; Cover, Matthew R.; Mazor, Raphael D.; Sommers, Christopher A.; Resh, Vincent H.

    2013-06-01

    Identification of minimally disturbed reference sites is a critical step in developing precise and informative ecological indicators. We tested procedures to select reference sites, and quantified natural variation (inter-site and -annual variability) among reference conditions using a macroinvertebrate data set collected from 429 mediterranean-climate stream reaches in the San Francisco Bay Area, California (USA). We determined that a landscape GIS-based stressor screen followed by a local field-based stressor screen effectively identified least-disturbed reference sites that, based on NMS ordination results, supported different biological communities than sites identified with only landscape (GIS) or local (field) stressors. An examination of least-disturbed reference sites indicated that inter-site variability was strongly associated with stream hydrology (i.e., perennial vs. non-perennial flow) and annual precipitation, which highlights the need to control for such variation when developing biological indicators through natural gradient modeling or using unique biological indicators for both non-perennial and perennial streams. Metrics were more variable among non-perennial streams, indicating that additional modeling may be needed to develop precise biological indicators for non-perennial streams. Among 192 sites sampled two to six times over the 8-year study period, the biological community showed moderate inter-annual variability, with the 100 point index of biotic integrity scores varying from 0 to 51 points (mean = 11.5). Variance components analysis indicated that inter-annual variability explained only a fraction (5-18 %) of the total variation when compared against site-level variation; thus efforts to understand causes of natural variation between sites will produce more precise and accurate biological indicators.

  14. 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. PMID:19926223

  15. Community behavior and spatial regulation within a bacterial microcolony in deep tissue sites serves to protect against host attack

    PubMed Central

    Davis, Kimberly M.; Mohammadi, Sina; Isberg, Ralph R.

    2015-01-01

    Summary Bacterial pathogens express virulence-specific transcriptional programs that allow tissue colonization. Although phenotypic variation has been noted in the context of antibiotic exposure, no direct evidence exists for heterogeneity in virulence-specific transcriptional programs within tissues. In a mouse model of Yersinia pseudotuberculosis infection, we show that at least three subpopulations of bacteria develop within a single tissue site in response to distinct host signals. Bacteria growing on the exterior of spleen microcolonies responded to soluble signals and induced the nitric oxide (NO)-detoxifying gene, hmp. Hmp effectively eliminated NO diffusion and protected the interior bacterial population from exposure to NO-derived inducing signals. A third subpopulation, constituting the most peripherally-localized bacteria, directly contacted neutrophils and transcriptionally upregulated a virulence factor. These studies demonstrate that growth within tissues results in transcriptional specialization within a single focus of microbial replication, facilitating directed pathogen counterattack against the host response. PMID:25500192

  16. Studying Microbial Communities In Vivo: A Model of Host-mediated Interaction Between Candida Albicans and Pseudomonas Aeruginosa in the Airways.

    PubMed

    Faure, Emmanuel; Bortolotti, Perrine; Kipnis, Eric; Faure, Karine; Guery, Benoit

    2016-01-01

    Studying host-pathogen interaction enables us to understand the underlying mechanisms of the pathogenicity during microbial infection. The prognosis of the host depends on the involvement of an adapted immune response against the pathogen. Immune response is complex and results from interaction of the pathogens and several immune or non-immune cellular types. In vitro studies cannot characterise these interactions and focus on cell-pathogen interactions. Moreover, in the airway, particularly in patients with suppurative chronic lung disease or in mechanically ventilated patients, polymicrobial communities are present and complicate host-pathogen interaction. Pseudomonas aeruginosa and Candida albicans are both problem pathogens, frequently isolated from tracheobronchial samples, and associated to severe infections, especially in intensive care unit. Microbial interactions have been reported between these pathogens in vitro but the clinical impact of these interactions remains unclear. To study the interactions between C. albicans and P. aeruginosa, a murine model of C. albicans airways colonization, followed by a P. aeruginosa-mediated acute lung infection was performed. PMID:26863066

  17. 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 ...

  18. 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 incorporates…

  19. 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. PMID:25116591

  20. A GHF7 cellulase from the protist symbiont community of Reticulitermes flavipes enables more efficient lignocellulose processing by host enzymes.

    PubMed

    Sethi, Amit; Kovaleva, Elena S; Slack, Jeffrey M; Brown, Susan; Buchman, George W; Scharf, Michael E

    2013-12-01

    Termites and their gut microbial symbionts efficiently degrade lignocellulose into fermentable monosaccharides. This study examined three glycosyl hydrolase family 7 (GHF7) cellulases from protist symbionts of the termite Reticulitermes flavipes. We tested the hypotheses that three GHF7 cellulases (GHF7-3, GHF7-5, and GHF7-6) can function synergistically with three host digestive enzymes and a fungal cellulase preparation. Full-length cDNA sequences of the three GHF7s were assembled and their protist origins confirmed through a combination of quantitative PCR and cellobiohydrolase (CBH) activity assays. Recombinant versions of the three GHF7s were generated using a baculovirus-insect expression system and their activity toward several model substrates compared with and without metallic cofactors. GHF7-3 was the most active of the three cellulases; it exhibited a combination of CBH, endoglucanase (EGase), and β-glucosidase activities that were optimal around pH 7 and 30°C, and enhanced by calcium chloride and zinc sulfate. Lignocellulose saccharification assays were then done using various combinations of the three GHF7s along with a host EGase (Cell-1), beta-glucosidase (β-glu), and laccase (LacA). GHF7-3 was the only GHF7 to enhance glucose release by Cell-1 and β-glu. Finally, GHF7-3, Cell-1, and β-glu were individually tested with a commercial fungal cellulase preparation in lignocellulose saccharification assays, but only β-glu appreciably enhanced glucose release. Our hypothesis that protist GHF7 cellulases are capable of synergistic interactions with host termite digestive enzymes is supported only in the case of GHF7-3. These findings suggest that not all protist cellulases will enhance saccharification by cocktails of other termite or fungal lignocellulases. PMID:24186432

  1. 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

  2. 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

  3. 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. PMID:23496338

  4. siRNA Screening Identifies the Host Hexokinase 2 (HK2) Gene as an Important Hypoxia-Inducible Transcription Factor 1 (HIF-1) Target Gene in Toxoplasma gondii-Infected Cells

    PubMed Central

    Menendez, Matthew T.; Teygong, Crystal; Wade, Kristin; Florimond, Celia

    2015-01-01

    ABSTRACT Although it is established that oxygen availability regulates cellular metabolism and growth, little is known regarding how intracellular pathogens use host factors to grow at physiological oxygen levels. Therefore, large-scale human small interfering RNA screening was performed to identify host genes important for growth of the intracellular protozoan parasite Toxoplasma gondii at tissue oxygen tensions. Among the genes identified by this screen, we focused on the hexokinase 2 (HK2) gene because its expression is regulated by hypoxia-inducible transcription factor 1 (HIF-1), which is important for Toxoplasma growth. Toxoplasma increases host HK2 transcript and protein levels in a HIF-1-dependent manner. In addition, parasite growth at 3% oxygen is restored in HIF-1-deficient cells transfected with HK2 expression plasmids. Both HIF-1 activation and HK2 expression were accompanied by increases in host glycolytic flux, suggesting that enhanced HK2 expression in parasite-infected cells is functionally significant. Parasite dependence on host HK2 and HIF-1 expression is not restricted to transformed cell lines, as both are required for parasite growth in nontransformed C2C12 myoblasts and HK2 is upregulated in vivo following infection. While HK2 is normally associated with the cytoplasmic face of the outer mitochondrial membrane at physiological O2 levels, HK2 relocalizes to the host cytoplasm following infection, a process that is required for parasite growth at 3% oxygen. Taken together, our findings show that HIF-1-dependent expression and relocalization of HK2 represent a novel mechanism by which Toxoplasma establishes its replicative niche at tissue oxygen tensions. PMID:26106078

  5. 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…

  6. 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…

  7. 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…

  8. Identifying the Irritability Dimension of ODD: Application of a Modified Bifactor Model Across Five Large Community Samples of Children

    PubMed Central

    Burke, Jeffrey D.; Boylan, Khrista; Rowe, Richard; Duku, Eric; Stepp, Stephanie D.; Hipwell, Alison E.; Waldman, Irwin D.

    2014-01-01

    The importance of irritability as measured among the symptoms of oppositional defiant disorder (ODD) has dramatically come to the fore in recent years. New diagnostic categories rely on the distinct clinical utility of irritability, and models of psychopathology suggest it plays a key role in explaining developmental pathways within and between disorders into adulthood. However, only a few studies have tested multidimensional models of ODD, and the results have been conflicting. Further, consensus has not been reached regarding which symptoms best identify irritability. The present analyses use data from five large community data sets with five different measures of parent-reported ODD, comprising 16,280 youth in total, to help resolve these questions. Across the samples, ages ranged from 5 to 18, and included both boys and girls. Confirmatory factor analyses demonstrated that a modified bifactor model showed the best fit in each of the five data sets. The structure of the model included two correlated specific factors (irritability and oppositional behavior) in addition to a general ODD factor. In four of the five models, the best fit was obtained using the items of being touchy, angry and often losing temper as indicators of irritability. Given the structure of the models and the generally high correlation between the specific dimensions, the results suggest that irritability may not be sufficiently distinct from oppositional behavior to support an entirely independent diagnosis. Rather, irritability may be better understood as a dimension of psychopathology that can be distinguished within ODD, and which may be related to particular forms of psychopathology apart from ODD. PMID:25314267

  9. 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.

  10. 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

  11. Global Sensitivity Analysis of a Mathematical Model of Acute Inflammation Identifies Nonlinear Dependence of Cumulative Tissue Damage on Host Interleukin-6 Responses

    PubMed Central

    Mathew, Shibin; Bartels, John; Banerjee, Ipsita; Vodovotz, Yoram

    2014-01-01

    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 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, on the

  12. 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

  13. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities.

    PubMed

    Henschel, Andreas; Anwar, Muhammad Zohaib; Manohar, Vimitha

    2015-10-01

    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

  14. Strength-based well-being indicators for Indigenous children and families: A literature review of Indigenous communities' identified well-being indicators.

    PubMed

    Rountree, Jennifer; Smith, Addie

    2016-01-01

    Mainstream child and family well-being indicators frequently are based on measuring health, economic, and social deficits, and do not reflect Indigenous holistic and strength-based definitions of health and well-being. The present article is a review of literature that features Indigenous communities' self-identified strength-based indicators of child and family well-being. The literature search included Indigenous communities from across the world, incorporating findings from American Indians and Alaska Natives, First Nations, Native Hawaiians, Māori, Aboriginal Australians, and Sámi communities. Sorting the identified indicators into the quadrants of the Relational Worldview, an Indigenous framework for well-being based on medicine wheel teachings that views health and well-being as a balance among physical, mental, contextual, and spiritual factors, the authors discuss the findings. PMID:27383093

  15. An Analysis of Assessment Instruments in Use by the California Community Colleges to Identify and Assess Students with Specific Learning Disabilities.

    ERIC Educational Resources Information Center

    Ostertag, Bruce A.; Baker, Ronald E.

    In 1982, a survey of California community colleges was conducted to determine the formal and informal devices used to identify and assess learning disabled average (LDA) students; the characteristics, skills, and behaviors measured; the personnel who administered the assessment instruments; and the intake process and identification and assessment…

  16. 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

  17. 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

  18. Professional Development for Information Communication Technology Integration: Identifying and Supporting a Community of Practice through Design-Based Research

    ERIC Educational Resources Information Center

    MacDonald, Ronald J.

    2008-01-01

    Research suggests effective classroom ICT integration occurs through needs-based, collaborative professional development (Chandra-Handa, 2001; Cuttance, 2001; Figg, 2000; Gibson, Oberg, & Pelz, 1999; Gross, 2000; Haughey, 2002). A community of practice (CoP) (Wenger, 1998; Wenger, McDermott, & Snyder, 2002) can be an effective mode of such…

  19. 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. PMID:23869991

  20. Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion

    PubMed Central

    2013-01-01

    Background As a strong fermentator, Saccharomyces cerevisiae has the potential to be an excellent host for ethanol production by consolidated bioprocessing. For this purpose, it is necessary to transform cellulose genes into the yeast genome because it contains no cellulose genes. However, heterologous protein expression in S. cerevisiae often suffers from hyper-glycosylation and/or poor secretion. Thus, there is a need to genetically engineer the yeast to reduce its glycosylation strength and to increase its secretion ability. Results Saccharomyces cerevisiae gene-knockout strains were screened for improved extracellular activity of a recombinant exocellulase (PCX) from the cellulose digesting fungus Phanerochaete chrysosporium. Knockout mutants of 47 glycosylation-related genes and 10 protein-trafficking-related genes were transformed with a PCX expression construct and screened for extracellular cellulase activity. Twelve of the screened mutants were found to have a more than 2-fold increase in extracellular PCX activity in comparison with the wild type. The extracellular PCX activities in the glycosylation-related mnn10 and pmt5 null mutants were, respectively, 6 and 4 times higher than that of the wild type; and the extracellular PCX activities in 9 protein-trafficking-related mutants, especially in the chc1, clc1 and vps21 null mutants, were at least 1.5 times higher than the parental strains. Site-directed mutagenesis studies further revealed that the degree of N-glycosylation also plays an important role in heterologous cellulase activity in S. cerevisiae. Conclusions Systematic screening of knockout mutants of glycosylation- and protein trafficking-associated genes in S. cerevisiae revealed that: (1) blocking Golgi-to-endosome transport may force S. cerevisiae to export cellulases; and (2) both over- and under-glycosylation may alter the enzyme activity of cellulases. This systematic gene-knockout screening approach may serve as a convenient means for

  1. 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

  2. Targeting accuracy and impact of a community-identified waiver card scheme for primary care user fees in Afghanistan

    PubMed Central

    2010-01-01

    Background User fees are a known common barrier to using health services, particularly among the poor. When fees are present, many facilities have waiver systems for poor patients to exempt them from paying. Targeting waivers to patients who need them most has been a challenge, especially in fragile states, where relevant data are limited and trust in institutions is low. Methods Community-based targeting of vulnerable households was piloted in Afghanistan and evaluated for its feasibility, accuracy and effect on care-seeking. Waiver cards were distributed to very poor and female-headed households in catchment areas of 26 facilities in 10 provinces of Afghanistan in 2005 as one component of a larger health financing study. Households were nominated by community leaders using general guidelines to support 15% of the poorest members. In most cases, waiver cards were pro-actively distributed to them. Targeting accuracy, perceptions, as well the cards' effects on utilization were evaluated in 2007 through household surveys, health facility data, and in-depth interviews and focus group discussions with facility staff and community leaders. Results The waiver system was implemented quickly at all but one facility charging fees. Facility staff and community leaders reported favorable perceptions of implementation and targeting accuracy. However, an analysis of the asset index of beneficiaries indicated that although targeting was progressive, significant leakage and high levels of under-coverage occurred; 42% of cards were used by people in the wealthiest three quintiles, and only 19% of people in the poorest quintile received a card. Households with waiver cards reported higher rates of care-seeking for recent illnesses compared to those without cards (p = 0.02). Conclusions Community identification of beneficiaries is feasible in a fragile state. Several recommendations are discussed to improve targeting accuracy of a waiver card system in the future, in light of this

  3. Parasite communities of the elongate tigerfish Hydrocynus forskahlii (Cuvier 1819) and redbelly tilapia Tilapia zillii (Gervais 1848) from Lake Turkana, Kenya: influence of host sex and size.

    PubMed

    Otachi, Elick O; Szostakowska, Beata; Jirsa, Franz; Fellner-Frank, Christine

    2014-03-01

    Fish is an important food source for an estimated 300,000 people inhabiting the shores of Lake Turkana, Kenya. Despite its large size (7560 km2) and importance, the lake remains one of the least studied in the Great Lakes Region of Africa. This study describes the parasite community of the elongate tigerfish Hydrocynus forskahlii (Cuvier, 1819) and the redbelly tilapia Tilapia zillii (Gervais, 1848). A total of 87 individuals (43 H. forskahlii and 44 T. zillii) were dissected and examined for parasites. Two taxa infected H. forskahlii, the dominant one being an anisakid nematode Contracaecum sp. (L3) (P = 83.7%, mean intensity (MI) = 46.0, abundance (A) = 38.5). Twelve parasite taxa were recovered from T. zillii, with metacestodes of the gryporhynchid cestode Amirthalingamia macracantha being dominant (P = 79.5, MI = 10.3, A = 8.2). This was the first report of a mixture of merocercoids and plerocercoids in the same host. Fish size was positively correlated with the major parasite infection levels, but, the prevalence of Contracaecum sp. in H. forskahlii was negatively correlated with size, probably reflecting ontogenetic shifts in habitats and diets with age. Fish sex was not a significant influencing factor, with the exception of Contracaecum sp. in H. forskahlii, where prevalence differed significantly between sexes (p<0.05), with the females having a higher prevalence than the males. We conclude that H. forskahlii had a poor parasitic community but that the infection levels with Contracaecum sp. were high. T. zillii had a rich parasite fauna, although, most parasites occurred at low intensities. PMID:26204015

  4. Referral outcomes of individuals identified at high risk of cardiovascular disease by community health workers in Bangladesh, Guatemala, Mexico, and South Africa

    PubMed Central

    Levitt, Naomi S.; Puoane, Thandi; Denman, Catalina A.; Abrahams-Gessel, Shafika; Surka, Sam; Mendoza, Carlos; Khanam, Masuma; Alam, Sartaj; Gaziano, Thomas A.

    2015-01-01

    Background We have found that community health workers (CHWs) with appropriate training are able to accurately identify people at high cardiovascular disease (CVD) risk in the community who would benefit from the introduction of preventative management, in Bangladesh, Guatemala, Mexico, and South Africa. This paper examines the attendance pattern for those individuals who were so identified and referred to a health care facility for further assessment and management. Design Patient records from the health centres in each site were reviewed for data on diagnoses made and treatment commenced. Reasons for non-attendance were sought from participants who had not attended after being referred. Qualitative data were collected from study coordinators regarding their experiences in obtaining the records and conducting the record reviews. The perspectives of CHWs and community members, who were screened, were also obtained. Results Thirty-seven percent (96/263) of those referred attended follow-up: 36 of 52 (69%) were urgent and 60 of 211 (28.4%) were non-urgent referrals. A diagnosis of hypertension (HTN) was made in 69% of urgent referrals and 37% of non-urgent referrals with treatment instituted in all cases. Reasons for non-attendance included limited self-perception of risk, associated costs, health system obstacles, and lack of trust in CHWs to conduct CVD risk assessments and to refer community members into the health system. Conclusions The existing barriers to referral in the health care systems negatively impact the gains to be had through screening by training CHWs in the use of a simple risk assessment tool. The new diagnoses of HTN and commencement on treatment in those that attended referrals underscores the value of having persons at the highest risk identified in the community setting and referred to a clinic for further evaluation and treatment. PMID:25854780

  5. 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

  6. Host genetic and environmental effects on mouse intestinal microbiota

    PubMed Central

    Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana; Campbell, Alisha G; Yang, Zamin K; Wymore, Ann; Palumbo, Anthony V; Chesler, Elissa J; 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. PMID:22695862

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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…

  12. 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.

  13. Wife battering in Asian American communities. Identifying the service needs of an overlooked segment of the U.S. population.

    PubMed

    Huisman, K A

    1996-09-01

    This study examined the specific needs of Asian women who are battered, and explored the various structural and cultural constraints that inhibit these women from securing help from mainstream social service providers in the US. Data were gathered from interviews that were conducted with 18 Asian community activists and service providers throughout the US. The results showed that Asian women who were battered, particularly recently arrived immigrant and refugee women, have needs that differ markedly from most battered women in the general US population. The needs of the refugee women center on language issues, cultural issues, immigration issues, and structural issues. Moreover, there are several internal and external forces that work in tandem to keep the needs of Asian women from being formally included in the mainstream battered women's movement. The internal forces include cultural beliefs and practices, while the external forces include stereotype about Asians, such as the ¿model minority myth,¿ lack of funding for programs for battered Asian women, US immigration laws, the historical exclusion of women of color from the mainstream feminist movement in the US, and the prevalence of sexism and racism in the American society. Finally, recommendations for social providers to better meet these needs are provided. PMID:12295885

  14. 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

  15. Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing

    PubMed Central

    Sadsad, Rosemarie; Martinez, Elena; Jelfs, Peter; Hill-Cawthorne, Grant A.; Gilbert, Gwendolyn L.; Marais, Ben J.; Sintchenko, Vitali

    2016-01-01

    Background Improved tuberculosis control and the need to contain the spread of drug-resistant strains provide a strong rationale for exploring tuberculosis transmission dynamics at the population level. Whole-genome sequencing provides optimal strain resolution, facilitating detailed mapping of potential transmission pathways. Methods We sequenced 22 isolates from a Mycobacterium tuberculosis cluster in New South Wales, Australia, identified during routine 24-locus mycobacterial interspersed repetitive unit typing. Following high-depth paired-end sequencing using the Illumina HiSeq 2000 platform, two independent pipelines were employed for analysis, both employing read mapping onto reference genomes as well as de novo assembly, to control biases in variant detection. In addition to single-nucleotide polymorphisms, the analyses also sought to identify insertions, deletions and structural variants. Results Isolates were highly similar, with a distance of 13 variants between the most distant members of the cluster. The most sensitive analysis classified the 22 isolates into 18 groups. Four of the isolates did not appear to share a recent common ancestor with the largest clade; another four isolates had an uncertain ancestral relationship with the largest clade. Conclusion Whole genome sequencing, with analysis of single-nucleotide polymorphisms, insertions, deletions, structural variants and subpopulations, enabled the highest possible level of discrimination between cluster members, clarifying likely transmission pathways and exposing the complexity of strain origin. The analysis provides a basis for targeted public health intervention and enhanced classification of future isolates linked to the cluster. PMID:26938641

  16. The Role of Host Phylogeny Varies in Shaping Microbial Diversity in the Hindguts of Lower Termites

    PubMed Central

    James, Erick R.; Nalepa, Christine A.; Scheffrahn, Rudolf H.; Perlman, Steve J.; Keeling, Patrick J.

    2014-01-01

    The hindguts of lower termites and Cryptocercus cockroaches are home to a distinct community of archaea, bacteria, and protists (primarily parabasalids and some oxymonads). Within a host species, the composition of these hindgut communities appears relatively stable, but the evolutionary and ecological factors structuring community composition and stability are poorly understood, as are differential impacts of these factors on protists, bacteria, and archaea. We analyzed the microbial composition of parabasalids and bacteria in the hindguts of Cryptocercus punctulatus and 23 species spanning 4 families of lower termites by pyrosequencing variable regions of the small-subunit rRNA gene. Especially for the parabasalids, these data revealed undiscovered taxa and provided a phylogenetic basis for a more accurate understanding of diversity, diversification, and community composition. The composition of the parabasalid communities was found to be strongly structured by the phylogeny of their hosts, indicating the importance of historical effects, although exceptions were also identified. Particularly, spirotrichonymphids and trichonymphids likely were transferred between host lineages. In contrast, host phylogeny was not sufficient to explain the majority of bacterial community composition, but the compositions of the Bacteroidetes, Elusimicrobia, Tenericutes, Spirochaetes, and Synergistes were structured by host phylogeny perhaps due to their symbiotic associations with protists. All together, historical effects probably resulting from vertical inheritance have had a prominent role in structuring the hindgut communities, especially of the parabasalids, but dispersal and environmental acquisition have played a larger role in community composition than previously expected. PMID:25452280

  17. The role of host phylogeny varies in shaping microbial diversity in the hindguts of lower termites.

    PubMed

    Tai, Vera; James, Erick R; Nalepa, Christine A; Scheffrahn, Rudolf H; Perlman, Steve J; Keeling, Patrick J

    2015-02-01

    The hindguts of lower termites and Cryptocercus cockroaches are home to a distinct community of archaea, bacteria, and protists (primarily parabasalids and some oxymonads). Within a host species, the composition of these hindgut communities appears relatively stable, but the evolutionary and ecological factors structuring community composition and stability are poorly understood, as are differential impacts of these factors on protists, bacteria, and archaea. We analyzed the microbial composition of parabasalids and bacteria in the hindguts of Cryptocercus punctulatus and 23 species spanning 4 families of lower termites by pyrosequencing variable regions of the small-subunit rRNA gene. Especially for the parabasalids, these data revealed undiscovered taxa and provided a phylogenetic basis for a more accurate understanding of diversity, diversification, and community composition. The composition of the parabasalid communities was found to be strongly structured by the phylogeny of their hosts, indicating the importance of historical effects, although exceptions were also identified. Particularly, spirotrichonymphids and trichonymphids likely were transferred between host lineages. In contrast, host phylogeny was not sufficient to explain the majority of bacterial community composition, but the compositions of the Bacteroidetes, Elusimicrobia, Tenericutes, Spirochaetes, and Synergistes were structured by host phylogeny perhaps due to their symbiotic associations with protists. All together, historical effects probably resulting from vertical inheritance have had a prominent role in structuring the hindgut communities, especially of the parabasalids, but dispersal and environmental acquisition have played a larger role in community composition than previously expected. PMID:25452280

  18. Evolution of host range in Coleosporium ipomoeae, a plant pathogen with multiple hosts.

    PubMed

    Chappell, Thomas M; Rausher, Mark D

    2016-05-10

    Plants and their pathogens coevolve locally. Previous investigations of one host-one pathogen systems have demonstrated that natural selection favors pathogen genotypes that are virulent on a broad range of host genotypes. In the present study, we examine a system consisting of one pathogen species that infects three host species in the morning glory genus Ipomoea. We show that many pathogen genotypes can infect two or three of the host species when tested on plants from nonlocal communities. By contrast, pathogen genotypes are highly host-specific, infecting only one host species, when tested on host species from the local community. This pattern indicates that within-community evolution narrows the host breadth of pathogen genotypes. Possible evolutionary mechanisms include direct selection for narrow host breadth due to costs of virulence and evolution of ipomoea resistance in the host species. PMID:27114547

  19. 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. PMID:24976050

  20. 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

  1. Comparative genomic analysis identifies divergent genomic features of pathogenic Enterococcus cecorum including a type IC CRISPR-Cas system, a capsule locus, an epa-like locus, and putative host tissue binding proteins.

    PubMed

    Borst, Luke B; Suyemoto, M Mitsu; Scholl, Elizabeth H; Fuller, Fredrick J; Barnes, H John

    2015-01-01

    Enterococcus cecorum (EC) is the dominant enteric commensal of adult chickens and contributes to the gut consortia of many avian and mammalian species. While EC infection is an uncommon zoonosis, like other enterococcal species it can cause life-threating nosocomial infection in people. In contrast to other enterococci which are considered opportunistic pathogens, emerging pathogenic strains of EC cause outbreaks of musculoskeletal disease in broiler chickens. Typical morbidity and mortality is comparable to other important infectious diseases of poultry. In molecular epidemiologic studies, pathogenic EC strains were found to be genetically clonal. These findings suggested acquisition of specific virulence determinants by pathogenic EC. To identify divergent genomic features and acquired virulence determinants in pathogenic EC; comparative genomic analysis was performed on genomes of 3 pathogenic and 3 commensal strains of EC. Pathogenic isolates had smaller genomes with a higher GC content, and they demonstrated large regions of synteny compared to commensal isolates. A molecular phylogenetic analysis demonstrated sequence divergence in pathogenic EC genomes. At a threshold of 98% identity, 414 predicted proteins were identified that were highly conserved in pathogenic EC but not in commensal EC. Among these, divergent CRISPR-cas defense loci were observed. In commensal EC, the type IIA arrangement typical for enterococci was present; however, pathogenic EC had a type IC locus, which is novel in enterococci but commonly observed in streptococci. Potential mediators of virulence identified in this analysis included a polysaccharide capsular locus similar to that recently described for E. faecium, an epa-like locus, and cell wall associated proteins which may bind host extracellular matrix. This analysis identified specific genomic regions, coding sequences, and predicted proteins which may be related to the divergent evolution and increased virulence of emerging

  2. Comparative Genomic Analysis Identifies Divergent Genomic Features of Pathogenic Enterococcus cecorum Including a Type IC CRISPR-Cas System, a Capsule Locus, an epa-Like Locus, and Putative Host Tissue Binding Proteins

    PubMed Central

    Borst, Luke B.; Suyemoto, M. Mitsu; Scholl, Elizabeth H.; Fuller, Fredrick J.; Barnes, H. John

    2015-01-01

    Enterococcus cecorum (EC) is the dominant enteric commensal of adult chickens and contributes to the gut consortia of many avian and mammalian species. While EC infection is an uncommon zoonosis, like other enterococcal species it can cause life-threating nosocomial infection in people. In contrast to other enterococci which are considered opportunistic pathogens, emerging pathogenic strains of EC cause outbreaks of musculoskeletal disease in broiler chickens. Typical morbidity and mortality is comparable to other important infectious diseases of poultry. In molecular epidemiologic studies, pathogenic EC strains were found to be genetically clonal. These findings suggested acquisition of specific virulence determinants by pathogenic EC. To identify divergent genomic features and acquired virulence determinants in pathogenic EC; comparative genomic analysis was performed on genomes of 3 pathogenic and 3 commensal strains of EC. Pathogenic isolates had smaller genomes with a higher GC content, and they demonstrated large regions of synteny compared to commensal isolates. A molecular phylogenetic analysis demonstrated sequence divergence in pathogenic EC genomes. At a threshold of 98% identity, 414 predicted proteins were identified that were highly conserved in pathogenic EC but not in commensal EC. Among these, divergent CRISPR-cas defense loci were observed. In commensal EC, the type IIA arrangement typical for enterococci was present; however, pathogenic EC had a type IC locus, which is novel in enterococci but commonly observed in streptococci. Potential mediators of virulence identified in this analysis included a polysaccharide capsular locus similar to that recently described for E. faecium, an epa-like locus, and cell wall associated proteins which may bind host extracellular matrix. This analysis identified specific genomic regions, coding sequences, and predicted proteins which may be related to the divergent evolution and increased virulence of emerging

  3. Measuring newborn foot length to identify small babies in need of extra care: a cross sectional hospital based study with community follow-up in Tanzania

    PubMed Central

    2010-01-01

    Background Neonatal mortality because of low birth weight or prematurity remains high in many developing country settings. This research aimed to estimate the sensitivity and specificity, and the positive and negative predictive values of newborn foot length to identify babies who are low birth weight or premature and in need of extra care in a rural African setting. Methods A cross-sectional study of newborn babies in hospital, with community follow-up on the fifth day of life, was carried out between 13 July and 16 October 2009 in southern Tanzania. Foot length, birth weight and gestational age were estimated on the first day and foot length remeasured on the fifth day of life. Results In hospital 529 babies were recruited and measured within 24 hours of birth, 183 of whom were also followed-up at home on the fifth day. Day one foot length <7 cm at birth was 75% sensitive (95%CI 36-100) and 99% specific (95%CI 97-99) to identify very small babies (birth weight <1500 grams); foot length <8 cm had sensitivity and specificity of 87% (95%CI 79-94) and 60% (95%CI 55-64) to identify those with low birth weight (<2500 grams), and 93% (95%CI 82-99) and 58% (95%CI 53-62) to identify those born premature (<37 weeks). Mean foot length on the first day was 7.8 cm (standard deviation 0.47); the mean difference between first and fifth day foot lengths was 0.1 cm (standard deviation 0.3): foot length measured on or before the fifth day of life identified more than three-quarters of babies who were born low birth weight. Conclusion Measurement of newborn foot length for home births in resource poor settings has the potential to be used by birth attendants, community volunteers or parents as a screening tool to identify low birth weight or premature newborns in order that they can receive targeted interventions for improved survival PMID:20959008

  4. Using multi-scale distribution and movement effects along a montane highway to identify optimal crossing locations for a large-bodied mammal community

    PubMed Central

    Römer, Heinrich; Germain, Ryan R.

    2013-01-01

    Roads are a major cause of habitat fragmentation that can negatively affect many mammal populations. Mitigation measures such as crossing structures are a proposed method to reduce the negative effects of roads on wildlife, but the best methods for determining where such structures should be implemented, and how their effects might differ between species in mammal communities is largely unknown. We investigated the effects of a major highway through south-eastern British Columbia, Canada on several mammal species to determine how the highway may act as a barrier to animal movement, and how species may differ in their crossing-area preferences. We collected track data of eight mammal species across two winters, along both the highway and pre-marked transects, and used a multi-scale modeling approach to determine the scale at which habitat characteristics best predicted preferred crossing sites for each species. We found evidence for a severe barrier effect on all investigated species. Freely-available remotely-sensed habitat landscape data were better than more costly, manually-digitized microhabitat maps in supporting models that identified preferred crossing sites; however, models using both types of data were better yet. Further, in 6 of 8 cases models which incorporated multiple spatial scales were better at predicting preferred crossing sites than models utilizing any single scale. While each species differed in terms of the landscape variables associated with preferred/avoided crossing sites, we used a multi-model inference approach to identify locations along the highway where crossing structures may benefit all of the species considered. By specifically incorporating both highway and off-highway data and predictions we were able to show that landscape context plays an important role for maximizing mitigation measurement efficiency. Our results further highlight the need for mitigation measures along major highways to improve connectivity between mammal

  5. 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

  6. Genome-wide association study of Arabidopsis thaliana's leaf microbial community

    PubMed Central

    Horton, Matthew W.; Bodenhausen, Natacha; Beilsmith, Kathleen; Meng, Dazhe; Muegge, Brian D.; Subramanian, Sathish; Vetter, M. Madlen; Vilhjálmsson, Bjarni J.; Nordborg, Magnus; Gordon, Jeffrey I.; Bergelson, Joy

    2014-01-01

    Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses, and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host's genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbes’ numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis. PMID:25382143

  7. Host Responses to Biofilm.

    PubMed

    Watters, C; Fleming, D; Bishop, D; Rumbaugh, K P

    2016-01-01

    From birth to death the human host immune system interacts with bacterial cells. Biofilms are communities of microbes embedded in matrices composed of extracellular polymeric substance (EPS), and have been implicated in both the healthy microbiome and disease states. The immune system recognizes many different bacterial patterns, molecules, and antigens, but these components can be camouflaged in the biofilm mode of growth. Instead, immune cells come into contact with components of the EPS matrix, a diverse, hydrated mixture of extracellular DNA (bacterial and host), proteins, polysaccharides, and lipids. As bacterial cells transition from planktonic to biofilm-associated they produce small molecules, which can increase inflammation, induce cell death, and even cause necrosis. To survive, invading bacteria must overcome the epithelial barrier, host microbiome, complement, and a variety of leukocytes. If bacteria can evade these initial cell populations they have an increased chance at surviving and causing ongoing disease in the host. Planktonic cells are readily cleared, but biofilms reduce the effectiveness of both polymorphonuclear neutrophils and macrophages. In addition, in the presence of these cells, biofilm formation is actively enhanced, and components of host immune cells are assimilated into the EPS matrix. While pathogenic biofilms contribute to states of chronic inflammation, probiotic Lactobacillus biofilms cause a negligible immune response and, in states of inflammation, exhibit robust antiinflammatory properties. These probiotic biofilms colonize and protect the gut and vagina, and have been implicated in improved healing of damaged skin. Overall, biofilms stimulate a unique immune response that we are only beginning to understand. PMID:27571696

  8. Host diversity begets parasite diversity: Bird final hosts and trematodes in snail intermediate hosts

    USGS Publications Warehouse

    Hechinger, R.F.; Lafferty, K.D.

    2005-01-01

    An unappreciated facet of biodiversity is that rich communities and high abundance may foster parasitism. For parasites that sequentially use different host species throughout complex life cycles, parasite diversity and abundance in 'downstream' hosts should logically increase with the diversity and abundance of 'upstream' hosts (which carry the preceding stages of parasites). Surprisingly, this logical assumption has little empirical support, especially regarding metazoan parasites. Few studies have attempted direct tests of this idea and most have lacked the appropriate scale of investigation. In two different studies, we used time-lapse videography to quantify birds at fine spatial scales, and then related bird communities to larval trematode communities in snail populations sampled at the same small spatial scales. Species richness, species heterogeneity and abundance of final host birds were positively correlated with species richness, species heterogeneity and abundance of trematodes in host snails. Such community-level interactions have rarely been demonstrated and have implications for community theory, epidemiological theory and ecosystem management. ?? 2005 The Royal Society.

  9. 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. PMID:24171844

  10. 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. PMID:24987989

  11. 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

  12. 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. PMID:24043557

  13. Involving Communities in Deciding What Benefits They Receive in Multinational Research.

    PubMed

    Wendler, David; Shah, Seema

    2015-10-01

    There is wide agreement that communities in lower-income countries should benefit when they participate in multinational research. Debate now focuses on how and to what extent these communities should benefit. This debate has identified compelling reasons to reject the claim that whatever benefits a community agrees to accept are necessarily fair. Yet, those who conduct clinical research may conclude from this rejection that there is no reason to involve communities in the process of deciding how they benefit. Against this possibility, the present manuscript argues that involving host communities in this process helps to promote four important goals: (1) protecting host communities, (2) respecting host communities, (3) promoting transparency, and (4) enhancing social value. PMID:26224724

  14. 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. PMID:26603858

  15. 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

  16. Host introduction and parasites: a case study on the parasite community of the peacock grouper Cephalopholis argus (Serranidae) in the Hawaiian Islands.

    PubMed

    Vignon, Matthias; Sasal, Pierre; Galzin, René

    2009-03-01

    The peacock grouper (Cephalopholis argus) was intentionally introduced to the Hawaiian coastal waters 50 years ago to enhance the local fisheries. Following introduction, this species spread rapidly and became extremely abundant. A comparison of the metazoan parasite community of C. argus was performed between its native range (Moorea Island, French Polynesia) and its introduced range (Oahu and Big Island, Hawaii). Polynesian groupers were infected with a highly diversified parasite community whereas Hawaiian groupers exhibited a depauperate ensemble of parasite species, C. argus having lost most of the parasites common in their native range. Interestingly, the grouper has not acquired new parasites present in Hawaiian waters. This study provides the first field evidence of significant parasite release in a wild but previously introduced fish in coral reefs and is discussed in relation to the Enemy-Release Hypothesis which has never been assessed in those ecosystems. PMID:19002714

  17. 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.…

  18. 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…

  19. Chain of demand. A host of former Triad execs are landing plum jobs in the wake of company's sale to Community--who's next in line?

    PubMed

    Galloro, Vince

    2007-10-22

    Community Health System's $6.97 billion acquisition of competitor Triad Hospitals this past summer left many former Triad executives wealthy but out of work. Some are enjoying a respite while others are being plucked up by CHS competitors. By letting so many Triad executives go, according to management guru Tim Vogus, right, CHS sent a clear message that its newly acquired business will be run its way. PMID:18020042

  20. 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

  1. 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

  2. Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula).

    PubMed

    Yaish, Mahmoud W; 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

  3. Multiple effects of host-species diversity on coexisting host-specific and host-opportunistic microbes.

    PubMed

    Kedem, Hadar; Cohen, Carmit; Messika, Irit; Einav, Monica; Pilosof, Shai; Hawlena, Hadas

    2014-05-01

    While host-species diversity often influences microbial prevalence, there may be multiple mechanisms causing such effects that may also depend on the foraging strategy of the microbes. We employed a natural gradient of rodent-species richness to examine competing hypotheses describing possible mechanisms mediating the relationship between host-species richness and the prevalence of the most dominant microbes, along with microbe specificity to the different rodent host species. We sampled blood from three gerbil species in plots differing in terms of the proportion of the different species and screened for the most dominant bacteria. Two dominant bacterial lineages were detected: host-specific bacteria and host-opportunistic bacteria. Using a model selection approach, we detected evidence for both direct and indirect effects of host-species richness on the prevalence of these bacteria. Infection probability of the host-specific lineage was lower in richer host communities, most likely due to increased frequency and density of the least suitable host species. In contrast, field observations suggest that the effect of host-species richness on infection probability of the opportunistic lineage was both direct and indirect, mostly mediated by changes in flea densities on the host and by the presence of the host-specific lineage. Our results thus suggest that host-species richness has multiple effects on microbial prevalence, depending on the degree of host-specificity of the microbe in question. PMID:25000749

  4. Bayou virus detected in non-oryzomyine rodent hosts: an assessment of habitat composition, reservoir community structure, and marsh rice rat social dynamics.

    PubMed

    Holsomback, Tyla S; McIntyre, Nancy E; Nisbett, Richard A; Strauss, Richard E; Chu, Yong-Kyu; Abuzeineh, Alisa A; de la Sancha, Noé; Dick, Carl W; Jonsson, Colleen B; Morris, Brandon E L

    2009-06-01

    In the United States, Bayou virus (BAYV) ranks second only to Sin Nombre virus (SNV) in terms of hantavirus pulmonary syndrome (HPS) incidents, having been confirmed in cases from Texas and Louisiana since its discovery in 1994. This study on BAYV infection among sympatric, non-oryzomyine rodents ("spillover") in Freeport, TX, is the first to link patterns of hantavirus interspecific spillover with the spatiotemporal ecology of the primary host (marsh rice rat, Oryzomys palustris). Mark-recapture and/or harvest methods were employed from March 2002 through May 2004 in two macrohabitat types. Rodent blood samples were screened for the presence of IgG antibody to BAYV antigen by IFA after which Ab-positive blood, saliva, and urine were analyzed for the presence of viral RNA by nested RT-PCR. From 727 non-oryzomyine captures, five seropositive (but not viral RNA positive) individuals were detected: one each of Baiomys taylori, Peromyscus leucopus, and Reithrodontomys fulvescens; and two Sigmodon hispidus. Spillover hosts were not associated with macrohabitat where O. palustris abundance, density, or seroprevalence was highest. Rather, spillover occurred in the macrohabitat indicative of greater overall disturbance (as indicated by grazing and exotic plant diversity) and overall biodiversity. Spillover occurred during periods of high seroprevalence detected elsewhere within the study region. Spillover locations differed significantly from all other capture locations in terms of percent water, shrub, and grass cover. Although greater habitat and mammal diversity of old-fields may serve to reduce seroprevalence levels by tempering intraspecific contacts between rice rats, greater diversity also may create an ecologically opportunistic setting for BAYV spillover. Impacts of varying levels of disturbance and biodiversity on transmission dynamics represent a vastly uncharacterized component of the evolutionary ecology of hantaviruses. PMID:20836801

  5. Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems

    PubMed Central

    Gerber, Georg K.; Onderdonk, Andrew B.; Bry, Lynn

    2012-01-01

    The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology. Standard approaches for analyzing time-series data of the microbiota involve computation of measures of ecological community diversity at each time-point, or measures of dissimilarity between pairs of time-points. Although these approaches, which treat data as static snapshots of microbial communities, can identify shifts in overall community structure, they fail to capture the dynamic properties of individual members of the microbiota and their contributions to the underlying time-varying behavior of host ecosystems. To address the limitations of current methods, we present a computational framework that uses continuous-time dynamical models coupled with Bayesian dimensionality adaptation methods to identify time-dependent signatures of individual microbial taxa within a host as well as across multiple hosts. We apply our framework to a publicly available dataset of 16S rRNA gene sequences from stool samples collected over ten months from multiple human subjects, each of whom received repeated courses of oral antibiotics. Using new diversity measures enabled by our framework, we discover groups of both phylogenetically close and distant bacterial taxa that exhibit consensus responses to antibiotic exposure across multiple human subjects. These consensus responses reveal a timeline for equilibration of sub-communities of micro-organisms with distinct physiologies, yielding insights into the successive changes that occur in microbial populations in the human gut after antibiotic treatments. Additionally, our framework leverages microbial signatures shared among human subjects to automatically design optimal experiments to interrogate dynamic properties of the microbiota in new studies. Overall, our approach provides a powerful, general-purpose framework for understanding the dynamic behaviors of complex microbial ecosystems, which we believe

  6. Differential sources of host species heterogeneity influence the transmission and control of multihost parasites

    PubMed Central

    Streicker, Daniel G; Fenton, Andy; Pedersen, Amy B

    2013-01-01

    Controlling parasites that infect multiple host species often requires targeting single species that dominate transmission. Yet, it is rarely recognised that such ‘key hosts’ can arise through disparate mechanisms, potentially requiring different approaches for control. We identify three distinct, but not mutually exclusive, processes that underlie host species heterogeneity: infection prevalence, population abundance and infectiousness. We construct a theoretical framework to isolate the role of each process from ecological data and to explore the outcome of different control approaches. Applying this framework to data on 11 gastrointestinal parasites in small mammal communities across the eastern United States reveals variation not only in the magnitude of transmission asymmetries among host species but also in the processes driving heterogeneity. These differences influence the efficiency by which different control strategies reduce transmission. Identifying and tailoring interventions to a specific type of key host may therefore enable more effective management of multihost parasites. PMID:23714379

  7. 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…

  8. 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

  9. 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. PMID:24935069

  10. Specification and installation of a MILNET host

    SciTech Connect

    George, M.

    1986-04-01

    A MILNET host computer was specified and installed to meet the needs of the growing user community at Sandia. The configuration of this host is described from specification through installation and testing. Also included are descriptions of the MILNET network and administrative procedures for the system. 5 figs.

  11. 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.

  12. The relationship between variable host grouping and functional responses among parasitoids of Antispila nysaefoliella (Lepidoptera: Heliozelidae).

    PubMed

    Low, Candace; Scheffer, Sonja J; Lewis, Matthew L; Gates, Michael W

    2012-12-01

    Our study investigated the importance of variability in the parasitoid community as a source of selection on host group size using a field population of the tupelo leafminer, Antispila nysaefoliella Clemens, which specializes on tupelo, Nyssa sylvatica Marsh. Larvae were collected from leaves with variable numbers of larvae and screened for parasitism using polymerase chain reaction of mitochondrial cytochrome oxidase I using markers designed specifically for amplifying parasitoid DNA while excluding host DNA. This method of selective PCR was effective for detecting the presence and identifying species of immature stages of three hymenopteran superfamilies: Chalcidoidea, Ichneumonoidea and Platygastroidea, which represented 83.4%, 16.0% and 0.6% of the total detectable parasitism, respectively. Our resulting sequences were then calibrated with sequences from identified adult parasitoids that had been either reared or field-captured. A cluster analysis revealed 10 distinct clades that showed differences in attack patterns with respect to host traits and season. Total parasitism followed an inverse density-dependent or density-independent pattern with respect to host density (number per leaf). However, when parasitoid taxa were considered separately, one clade, which could be a cryptic species of Pnigalio maculipes Crawford (Chalcidoidea: Eulophidae), was found to increase its per leaf attack rate with host density. Our results suggest that parasitoid community composition and differences among species in their attack strategies can play a large role in determining the adaptive advantage of host grouping. PMID:23094653

  13. 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

  14. Host Density and Competency Determine the Effects of Host Diversity on Trematode Parasite Infection

    PubMed Central

    Wojdak, Jeremy M.; Edman, Robert M.; Wyderko, Jennie A.; Zemmer, Sally A.; Belden, Lisa K.

    2014-01-01

    Variation in host species composition can dramatically alter parasite transmission in natural communities. Whether diverse host communities dilute or amplify parasite transmission is thought to depend critically on species traits, particularly on how hosts affect each other’s densities, and their relative competency as hosts. Here we studied a community of potential hosts and/or decoys (i.e. non-competent hosts) for two trematode parasite species, Echinostoma trivolvis and Ribeiroia ondatrae, which commonly infect wildlife across North America. We manipulated the density of a focal host (green frog tadpoles, Rana clamitans), in concert with manipulating the diversity of alternative species, to simulate communities where alternative species either (1) replace the focal host species so that the total number of individuals remains constant (substitution) or (2) add to total host density (addition). For E. trivolvis, we found that total parasite transmission remained roughly equal (or perhaps decreased slightly) when alternative species replaced focal host individuals, but parasite transmission was higher when alternative species were added to a community without replacing focal host individuals. Given the alternative species were roughly equal in competency, these results are consistent with current theory. Remarkably, both total tadpole and per-capita tadpole infection intensity by E. trivolvis increased with increasing intraspecific host density. For R. ondatrae, alternative species did not function as effective decoys or hosts for parasite infective stages, and the diversity and density treatments did not produce clear changes in parasite transmission, although high tank to tank variation in R. ondatrae infection could have obscured patterns. PMID:25119568

  15. Host plant induced variation in gut bacteria of Helicoverpa armigera.

    PubMed

    Priya, Natarajan Gayatri; 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

  16. 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…

  17. 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.

  18. Local host specialization, host-switching, and dispersal shape the regional distributions of avian haemosporidian parasites

    PubMed Central

    Ellis, Vincenzo A.; Collins, Michael D.; Medeiros, Matthew C. I.; Sari, Eloisa H. R.; Coffey, Elyse D.; Dickerson, Rebecca C.; Lugarini, Camile; Stratford, Jeffrey A.; Henry, Donata R.; Merrill, Loren; Matthews, Alix E.; Hanson, Alison A.; Roberts, Jackson R.; Joyce, Michael; Kunkel, Melanie R.; Ricklefs, Robert E.

    2015-01-01

    The drivers of regional parasite distributions are poorly understood, especially in comparison with those of free-living species. For vector-transmitted parasites, in particular, distributions might be influenced by host-switching and by parasite dispersal with primary hosts and vectors. We surveyed haemosporidian blood parasites (Plasmodium and Haemoproteus) of small land birds in eastern North America to characterize a regional parasite community. Distributions of parasite populations generally reflected distributions of their hosts across the region. However, when the interdependence between hosts and parasites was controlled statistically, local host assemblages were related to regional climatic gradients, but parasite assemblages were not. Moreover, because parasite assemblage similarity does not decrease with distance when controlling for host assemblages and climate, parasites evidently disperse readily within the distributions of their hosts. The degree of specialization on hosts varied in some parasite lineages over short periods and small geographic distances independently of the diversity of available hosts and potentially competing parasite lineages. Nonrandom spatial turnover was apparent in parasite lineages infecting one host species that was well-sampled within a single year across its range, plausibly reflecting localized adaptations of hosts and parasites. Overall, populations of avian hosts generally determine the geographic distributions of haemosporidian parasites. However, parasites are not dispersal-limited within their host distributions, and they may switch hosts readily. PMID:26305975

  19. 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 to interrupt the host-vector-recipient cycle.…

  20. Examining the Process of University-School-Community Collaboration in an Irish Sports Studies and Physical Education Context

    ERIC Educational Resources Information Center

    Crawford, Susan

    2015-01-01

    University-school-community collaborations are little documented despite being advocated across third-level institutes. Researchers identify the need for quality university-school-community collaborations to tackle a host of social inequalities while also addressing innovative approaches to teaching and learning. This study involved the…

  1. Research and Demonstration for a Comprehensive Package of Computer Programs to Serve Community College Learning Resource Centers. Final Report.

    ERIC Educational Resources Information Center

    Weiss, Jack A.

    One of 15 members of the Northern Illinois Learning Resources Cooperative (NILRC), Elgin Community College served as host institution for a project to design, develop, test, and install computer programs in a community college resource center environment. The service functions identified for systems development included circulation, serial…

  2. Parasite-host interactions of bat flies (Diptera: Hippoboscoidea) in Brazilian tropical dry forests.

    PubMed

    de Vasconcelos, Pedro Fonseca; Falcão, Luiz Alberto Dolabela; Graciolli, Gustavo; Borges, Magno Augusto Zazá

    2016-01-01

    Studies on the parasitology of ectoparasitic bat flies are scarce, and they are needed to identify patterns in parasitism. Hence, in the present study, we assessed community composition, prevalence, average infestation intensity, and specificity in the fly-bat associations in Brazilian tropical dry forests. In order to do that, we used the parasitological indices known as prevalence and average infestation intensity, along with an index of host specificity. We collected 1098 bat flies of 38 species. Five of the associations found are new to Brazil, 9 are new to southeastern Brazil, and 10 are new to science. Average infestation intensity varied from 1 to 9 and prevalence 0 to 100 %. In terms of specificity, 76 % of the bat flies were associated to a single host (monoxenic). These results highlight the low capacity of bat flies to survive on a not usual host especially due to an immunological incompatibility between parasites and hosts and dispersal barriers. PMID:26475479

  3. Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals

    NASA Astrophysics Data System (ADS)

    La Rivière, Marie; Garrabou, Joaquim; Bally, Marc

    2015-12-01

    Gorgonian corals serve as key engineering species within Mediterranean rocky-shore communities that have recently suffered from repeated mortality events during warm temperature anomalies. Among the factors that may link thermal conditions with disease outbreaks, a number of bacterial pathogens have been implicated; they may take advantage of decreases in the defenses and/or overall health of the gorgonian hosts. Considering the beneficial role of the resident bacteria in tropical coral holobionts, a detailed characterization of the gorgonian-associated microbial populations is required to better understand the relationships among native microbiota, host fitness, and pathogen susceptibility. In this study, the bacterial communities associated with three sympatric gorgonian species, Eunicella singularis, Eunicella cavolini, and Corallium rubrum, were investigated to provide insight into the stability and the specificity of host-microbe interactions. Natural variations in bacterial communities were detected using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal DNA. No major differences were identified between individual colonies sampled in winter or in summer within each gorgonian species. Although hierarchical cluster analysis of the T-RFLP profiles revealed that the three species harbor distinct communities, comparison of the T-RFLP peaks indicated the presence of common bacterial ribotypes. From phylogenetic analysis of 16S rDNA clone libraries, we identified a bacterial lineage related to the Hahellaceae family within the Oceanospirillales that is shared among E. singularis, E. cavolini, and C. rubrum and that dominates the communities of both species of Eunicella. However, distinct clades of Hahellaceae are harbored by various gorgonian species from Mediterranean and tropical waters, suggesting that these bacteria have formed host-specific symbiotic relationships with gorgonian octocorals. In addition, the relatedness of symbionts

  4. Host genotype is an important determinant of the cereal phyllosphere mycobiome.

    PubMed

    Sapkota, Rumakanta; Knorr, Kamilla; Jørgensen, Lise Nistrup; O'Hanlon, Karen A; Nicolaisen, Mogens

    2015-09-01

    The phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking. Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum × Secale) was studied using next-generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored. In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo-cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified. Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host-specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host-specific pathogens live in a 'sea' of nonspecific fungi. PMID:25898906

  5. Farmers’ markets and the local food environment: Identifying perceived accessibility barriers for SNAP consumers receiving Temporary Assistance for Needy Families (TANF) in an urban Oklahoma community

    PubMed Central

    Wetherill, Marianna; Gray, Karen A.

    2015-01-01

    Objective To examine barriers to farmer’s market (FM) use by Supplemental Nutrition Assistance Program (SNAP) consumers receiving TANF. Design Focus groups. Setting An urban community in Oklahoma. Participants SNAP beneficiaries receiving TANF (n = 64, across 8 focus groups). Phenomenon of Interest Perceptions about FM foods and barriers to FM use. Analysis Transcript-based content analysis using the five dimensions of access framework. Results Few participants ate fresh produce regularly and most appreciated the convenience of shopping at a supermarket. FMs were not perceived as available or accommodating to shopping needs and affordability and acceptability concerns were expressed. Few were aware of FMs that accepted SNAP. Emerging themes suggested residential segregation and cultural barriers to FM use. Conclusions and Implications FM managers, community nutritionists, and researchers should develop interventions that correct common misperceptions about FM products, minimize access barriers, and increase awareness of SNAP payment options. Residential segregation and cultural barriers may play a role in FM use and should be explored further. PMID:25754298

  6. National and Regional Assessment of Antimicrobial Resistance among Community-Acquired Respiratory Tract Pathogens Identified in a 2005-2006 U.S. Faropenem Surveillance Study▿

    PubMed Central

    Critchley, Ian A.; Brown, Steven D.; Traczewski, Maria M.; Tillotson, Glenn S.; Janjic, Nebojsa

    2007-01-01

    Surveillance studies conducted in the United States over the last decade have revealed increasing resistance among community-acquired respiratory pathogens, especially Streptococcus pneumoniae, that may limit future options for empirical therapy. The objective of this study was to assess the scope and magnitude of the problem at the national and regional levels during the 2005-2006 respiratory season (the season when community-acquired respiratory pathogens are prevalent) in the United States. Also, since faropenem is an oral penem being developed for the treatment of community-acquired respiratory tract infections, another study objective was to provide baseline data to benchmark changes in the susceptibility of U.S. respiratory pathogens to the drug in the future. The in vitro activities of faropenem and other agents were determined against 1,543 S. pneumoniae isolates, 978 Haemophilus influenzae isolates, and 489 Moraxella catarrhalis isolates collected from 104 U.S. laboratories across six geographic regions during the 2005-2006 respiratory season. Among S. pneumoniae isolates, the rates of resistance to penicillin, amoxicillin-clavulanate, and cefdinir were 16, 6.4, and 19.2%, respectively. The least effective agents were trimethoprim-sulfamethoxazole (SXT) and azithromycin, with resistance rates of 23.5 and 34%, respectively. Penicillin resistance rates for S. pneumoniae varied by region (from 8.7 to 22.5%), as did multidrug resistance rates for S. pneumoniae (from 8.8 to 24.9%). Resistance to β-lactams, azithromycin, and SXT was higher among S. pneumoniae isolates from children than those from adults. β-Lactamase production rates among H. influenzae and M. catarrhalis isolates were 27.4 and 91.6%, respectively. Faropenem MICs at which 90% of isolates are inhibited were 0.5 μg/ml for S. pneumoniae, 1 μg/ml for H. influenzae, and 0.5 μg/ml for M. catarrhalis, suggesting that faropenem shows promise as a treatment option for respiratory infections caused

  7. National and regional assessment of antimicrobial resistance among community-acquired respiratory tract pathogens identified in a 2005-2006 U.S. Faropenem surveillance study.

    PubMed

    Critchley, Ian A; Brown, Steven D; Traczewski, Maria M; Tillotson, Glenn S; Janjic, Nebojsa

    2007-12-01

    Surveillance studies conducted in the United States over the last decade have revealed increasing resistance among community-acquired respiratory pathogens, especially Streptococcus pneumoniae, that may limit future options for empirical therapy. The objective of this study was to assess the scope and magnitude of the problem at the national and regional levels during the 2005-2006 respiratory season (the season when community-acquired respiratory pathogens are prevalent) in the United States. Also, since faropenem is an oral penem being developed for the treatment of community-acquired respiratory tract infections, another study objective was to provide baseline data to benchmark changes in the susceptibility of U.S. respiratory pathogens to the drug in the future. The in vitro activities of faropenem and other agents were determined against 1,543 S. pneumoniae isolates, 978 Haemophilus influenzae isolates, and 489 Moraxella catarrhalis isolates collected from 104 U.S. laboratories across six geographic regions during the 2005-2006 respiratory season. Among S. pneumoniae isolates, the rates of resistance to penicillin, amoxicillin-clavulanate, and cefdinir were 16, 6.4, and 19.2%, respectively. The least effective agents were trimethoprim-sulfamethoxazole (SXT) and azithromycin, with resistance rates of 23.5 and 34%, respectively. Penicillin resistance rates for S. pneumoniae varied by region (from 8.7 to 22.5%), as did multidrug resistance rates for S. pneumoniae (from 8.8 to 24.9%). Resistance to beta-lactams, azithromycin, and SXT was higher among S. pneumoniae isolates from children than those from adults. beta-Lactamase production rates among H. influenzae and M. catarrhalis isolates were 27.4 and 91.6%, respectively. Faropenem MICs at which 90% of isolates are inhibited were 0.5 mug/ml for S. pneumoniae, 1 mug/ml for H. influenzae, and 0.5 mug/ml for M. catarrhalis, suggesting that faropenem shows promise as a treatment option for respiratory infections

  8. Repeated targeting of the same hosts by a brood parasite compromises host egg rejection

    PubMed Central

    Stevens, Martin; Troscianko, Jolyon; Spottiswoode, Claire N.

    2013-01-01

    Cuckoo eggs famously mimic those of their foster parents to evade rejection from discriminating hosts. Here we test whether parasites benefit by repeatedly parasitizing the same host nest. This should make accurate rejection decisions harder, regardless of the mechanism that hosts use to identify foreign eggs. Here we find strong support for this prediction in the African tawny-flanked prinia (Prinia subflava), the most common host of the cuckoo finch (Anomalospiza imberbis). We show experimentally that hosts reject eggs that differ from an internal template, but crucially, as the proportion of foreign eggs increases, hosts are less likely to reject them and require greater differences in appearance to do so. Repeated parasitism by the same cuckoo finch female is common in host nests and likely to be an adaptation to increase the probability of host acceptance. Thus, repeated parasitism interacts with egg mimicry to exploit cognitive and sensory limitations in host defences. PMID:24064931

  9. Remedial Learners in a Community College Setting Contribute to Their Own Academic Success: Identifying Effective Teaching and Learning Strategies, Delivery Methods and Instructional Technologies for Remedial Learners

    ERIC Educational Resources Information Center

    Bollash, Mary C.

    2013-01-01

    The purpose of this research was to expand on previous research surrounding remedial education at the college level. This research was conducted in four phases and identified common traits for a population of remedial learners and then determined how these common elements, when implemented, positively impacted the academic success for learners in…

  10. The Gut Bacterial Community of Mammals from Marine and Terrestrial Habitats

    PubMed Central

    Nelson, Tiffanie M.; Rogers, Tracey L.; Brown, Mark V.

    2013-01-01

    After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness. PMID:24386245

  11. Polymicrobial-Host Interactions during Infection.

    PubMed

    Tay, Wei Hong; Chong, Kelvin Kian Long; Kline, Kimberly A

    2016-08-28

    Microbial pathogenesis research has, historically, focused on the study of infections as monomicrobial events. However, the advent of next generation sequencing and culture-independent identification methods has revealed that many, if not most, infections are polymicrobial either in origin or in manifestation. Polymicrobial infections are often associated with increased infection severity and poorer patient outcome. Multiple infecting microbes can interact synergistically to induce virulence traits, alter the infected niche, or modulate the host immune response, all of which can promote polymicrobial infection. Importantly, a polymicrobial environment at the time of inoculation, consisting of multiple pathogens or pathogens in combination with the native microbiota, can contribute to the pathogenic progression of a single predominant organism at the time of diagnosis. Hence, in order to completely understand and elucidate the impact of these polymicrobial interactions on infection outcomes, a thorough examination of the entire microbial community present throughout the pathogenic cascade is required: from the time of inoculation to symptomology to resolution. In this review, we highlight the themes of metabolite exploitation, immune modulation, niche optimization, and virulence induction that contribute to polymicrobial infections. We focus on recent literature about microbe-microbe and microbe-host interactions that promote polymicrobial infections with an emphasis on understanding these interactions to identify better interventions for these sometimes complex infections. PMID:27170548

  12. Multifaceted determinants of host specificity in an aphid parasitoid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The host specificity of insect parasitoids and herbivores is thought to be shaped by a suite of behavioral and physiological factors that mediate host acceptance and host suitability. We conducted laboratory experiments to identify mechanisms shaping the host specificity of the aphid parasitoid Bin...

  13. Housekeeping Gene Sequencing and Multilocus Variable-Number Tandem-Repeat Analysis To Identify Subpopulations within Pseudomonas syringae pv. maculicola and Pseudomonas syringae pv. tomato That Correlate with Host Specificity

    PubMed Central

    Gironde, S.

    2012-01-01

    Pseudomonas syringae pv. maculicola causes bacterial spot on Brassicaceae worldwide, and for the last 10 years severe outbreaks have been reported in the Loire Valley, France. P. syringae pv. maculicola resembles P. syringae pv. tomato in that it is also pathogenic for tomato and causes the same types of symptoms. We used a collection of 106 strains of P. syringae to characterize the relationships between P. syringae pv. maculicola and related pathovars, paying special attention to P. syringae pv. tomato. Phylogenetic analysis of gyrB and rpoD gene sequences showed that P. syringae pv. maculicola, which causes diseases in Brassicaceae, forms six genetic lineages within genomospecies 3 of P. syringae strains as defined by L. Gardan et al. (Int. J. Syst. Bacteriol. 49[Pt 2]:469–478, 1999), whereas P. syringae pv. tomato forms two distinct genetic lineages. A multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) conducted with eight minisatellite loci confirmed the genetic structure obtained with rpoD and gyrB sequence analyses. These results provide promising tools for fine-scale epidemiological studies on diseases caused by P. syringae pv. maculicola and P. syringae pv. tomato. The two pathovars had distinct host ranges; only P. syringae pv. maculicola strains were pathogenic for Brassicaceae. A subpopulation of P. syringae pv. maculicola strains that are pathogenic for Pto-expressing tomato plants were shown to lack avrPto1 and avrPtoB or to contain a disrupted avrPtoB homolog. Taking phylogenetic and pathological features into account, our data suggest that the DC3000 strain belongs to P. syringae pv. maculicola. This study shows that P. syringae pv. maculicola and P. syringae pv. tomato appear multiclonal, as they did not diverge from a single common ancestral group within the ancestral P. syringae genomospecies 3, and suggests that pathovar specificity within P. syringae may be due to independent genetic events. PMID:22389364

  14. Sequencing and beyond: integrating molecular ‘omics for microbial community profiling

    PubMed Central

    Franzosa, Eric A.; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C.

    2016-01-01

    High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring additional multi'omic data types that better capture community functional activity, such as transcriptomics, proteomics, and metabolomics; and combining multiple forms of multi'omic data in an integrated framework. We highlight studies in which the multi'omics approach has led to improved mechanistic models of microbial community structure and function. PMID:25915636

  15. ConStrains identifies microbial strains in metagenomic datasets

    PubMed Central

    Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, Dirk

    2015-01-01

    An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived data sets provides insights into microbial community dynamics. PMID:26344404

  16. ConStrains identifies microbial strains in metagenomic datasets.

    PubMed

    Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, Dirk

    2015-10-01

    An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics. PMID:26344404

  17. Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques

    PubMed Central

    McLean, Jeffrey S.; Fansler, Sarah J.; Majors, Paul D.; McAteer, Kathleen; Allen, Lisa Z.; Shirtliff, Mark E.; Lux, Renate; Shi, Wenyuan

    2012-01-01

    Background Many human microbial infectious diseases including dental caries are polymicrobial in nature. 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 bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species. Methodology/Principal Findings Supragingival plaque samples from caries-free children incubated with 13C-substrates under imposed healthy (buffered, pH 7) and diseased states (pH 5.5 and pH 4.5) produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children. Conclusions/Significance Our approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within healthy subjects that

  18. Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community

    PubMed Central

    DeRito, Christopher M.; Pumphrey, Graham M.; Madsen, Eugene L.

    2005-01-01

    The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that 13C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of α-, β-, and γ-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food

  19. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

    PubMed

    Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

    2015-09-01

    A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures. PMID:25998815

  20. Could a brief assessment of negative emotions and self-esteem identify adolescents at current and future risk of self-harm in the community? A prospective cohort analysis

    PubMed Central

    2013-01-01

    Background Self-harm is common in adolescents, but it is often unreported and undetected. Available screening tools typically ask directly about self-harm and suicidal ideation. Although in an ideal world, direct enquiry and open discussion around self-harm would be advocated, non-psychiatric professionals in community settings are often reluctant to ask about this directly and disclosure can be met with feeling of intense anxiety. Training non-specialist staff to directly ask about self-harm has limited effects suggesting that alternative approaches are required. This study investigated whether a targeted analysis of negative emotions and self-esteem could identify young adolescents at risk of self-harm in community settings. Methods Data were collected as part of a clinical trial from young people in school years 8–11 (aged 12–16) at eight UK secondary schools (N = 4503 at baseline, N = 3263 in prospective analysis). The Short Mood and Feelings Questionnaire, Revised Child Anxiety and Depression Scale, Rosenberg Self-Esteem Scale, personal failure (Children’s Automatic Thoughts Scale), and two items on self-harm were completed at baseline, 6 and 12 months. Results Following a process of Principal Components Analysis, item reduction, and logistic regression analysis, three internally reliable factors were identified from the original measures that were independently associated with current and future self-harm; personal failure (3 items), physical symptoms of depression/anxiety (6 items), positive self-esteem (5 items). The summed score of these 14 items had good accuracy in identifying current self-harm (AUC 0.87 girls, 0.81 boys) and at six months for girls (0.81), and fair accuracy at six months for boys (AUC 0.74) and 12 months for girls (AUC 0.77). Conclusions A brief and targeted assessment of negative emotions and self-esteem, focusing on factors that are strongly associated with current and future self-harm, could potentially be used to

  1. Plague outbreaks in prairie dog populations explained by percolation thresholds of alternate host abundance

    PubMed Central

    Salkeld, Daniel J.; Salathé, Marcel; Stapp, Paul; Jones, James Holland

    2010-01-01

    Highly lethal pathogens (e.g., hantaviruses, hendra virus, anthrax, or plague) pose unique public-health problems, because they seem to periodically flare into outbreaks before disappearing into long quiescent phases. A key element to their possible control and eradication is being able to understand where they persist in the latent phase and how to identify the conditions that result in sporadic epidemics or epizootics. In American grasslands, plague, caused by Yersinia pestis, exemplifies this quiescent–outbreak pattern, because it sporadically erupts in epizootics that decimate prairie dog (Cynomys ludovicianus) colonies, yet the causes of outbreaks and mechanisms for interepizootic persistence of this disease are poorly understood. Using field data on prairie community ecology, flea behavior, and plague-transmission biology, we find that plague can persist in prairie-dog colonies for prolonged periods, because host movement is highly spatially constrained. The abundance of an alternate host for disease vectors, the grasshopper mouse (Onychomys leucogaster), drives plague outbreaks by increasing the connectivity of the prairie dog hosts and therefore, permitting percolation of the disease throughout the primary host population. These results offer an alternative perspective on plague's ecology (i.e., disease transmission exacerbated by alternative hosts) and may have ramifications for plague dynamics in Asia and Africa, where a single main host has traditionally been considered to drive Yersinia ecology. Furthermore, abundance thresholds of alternate hosts may be a key phenomenon determining outbreaks of disease in many multihost-disease systems. PMID:20660742

  2. The epidemiological feedbacks critical to the evolution of host immunity.

    PubMed

    Donnelly, R; White, A; Boots, M

    2015-11-01

    We examine in detail how epidemiological feedbacks combine with costs and benefits to determine the evolution of resistance by systematically analysing continuously stable strategies (CSS) for different host-parasite frameworks. The mode of resistance (innate versus acquired), the nature of the host (i.e. life-history and immunological memory) and the nature of the disease (effects on fertility or mortality) all impact on the feedbacks that are critical to the evolution of resistance. By identifying relationships between CSS investment and the underlying epidemiological feedback for each mode of resistance in each framework, we distil complex feedbacks into simple combinations of selection pressures. When the parasite does not affect fertility, CSS investment reflects only the benefit of resistance and we explain why this is markedly different for innate and acquired resistance. If infection has no effect on host fertility, CSS investment in acquired immunity increases with the square of disease prevalence. While in contrast for evolving innate resistance, CSS investment is greatest at intermediate prevalence. When disease impacts fertility, only a fraction of the host population reproduce, and this introduces new ecological feedbacks to both the cost of resistance and the damage from infection. The multiple feedbacks in this case lead to the alternative result that the higher the abundance of infecteds, the higher the investment in innate resistance. A key insight is that maximal investment occurs at intermediate lifespans in a range of different host-parasite interactions, but for disparate reasons which can only be understood by a detailed analysis of the feedbacks. We discuss the extension of our approach to structured host populations and parasite community dynamics. PMID:26285917

  3. Measuring Health Information Dissemination and Identifying Target Interest Communities on Twitter: Methods Development and Case Study of the @SafetyMD Network

    PubMed Central

    2016-01-01

    Background Little is known about the ability of individual stakeholder groups to achieve health information dissemination goals through Twitter. Objective This study aimed to develop and apply methods for the systematic evaluation and optimization of health information dissemination by stakeholders through Twitter. Methods Tweet content from 1790 followers of @SafetyMD (July-November 2012) was examined. User emphasis, a new indicator of Twitter information dissemination, was defined and applied to retweets across two levels of retweeters originating from @SafetyMD. User interest clusters were identified based on principal component analysis (PCA) and hierarchical cluster analysis (HCA) of a random sample of 170 followers. Results User emphasis of keywords remained across levels but decreased by 9.5 percentage points. PCA and HCA identified 12 statistically unique clusters of followers within the @SafetyMD Twitter network. Conclusions This study is one of the first to develop methods for use by stakeholders to evaluate and optimize their use of Twitter to disseminate health information. Our new methods provide preliminary evidence that individual stakeholders can evaluate the effectiveness of health information dissemination and create content-specific clusters for more specific targeted messaging. PMID:27151100

  4. The rules for symbiont community assembly change along a mutualism-parasitism continuum.

    PubMed

    Skelton, James; Doak, Sam; Leonard, Meredith; Creed, Robert P; Brown, Bryan L

    2016-05-01

    Symbiont community assembly is driven by host-symbiont and symbiont-symbiont interactions. The effects that symbionts exert on their hosts are often context-dependent, and existing theoretical frameworks of symbiont community assembly do not consider the implications of variable outcomes to assembly processes. We hypothesized that symbiont-symbiont interactions become increasingly important along a parasitism/mutualism continuum because; (i) negative outcomes favour host resistance which in turn reduces symbiont colonization and subsequently reduce symbiont-symbiont interactions, whereas (ii) positive host outcomes favour tolerance and consequently higher symbiont colonization rates, leading to stronger interactions among symbionts. We found support for this hypothesis in the cleaning symbiosis between crayfish and ectosymbiotic branchiobdellidan worms. The symbiosis between crayfish and their worms can shift from parasitism/commensalism to mutualism as crayfish age. Here, field surveys identified changes in worm density, diversity and composition that were concomitant to changing symbiosis outcomes. We conducted several laboratory experiments and behavioural assays to relate patterns from the field to their likely causal processes. Young crayfish typically hosted only two relatively small worm species. Older crayfish hosted two additional larger species. In laboratory experiments, young crayfish exhibited a directed grooming response to all worm species, but were unable to remove small species. Conversely, adult crayfish did not exhibit grooming responses to any worm species. Relaxed grooming allowed the colonization of large worm species and initiated symbiont-symbiont intraguild predation that reduced the abundance and altered the behaviour of small worm species. Thus, the dominant processes of symbiont community assembly shifted from host resistance to symbiont-symbiont interactions through host ontogeny and a concomitant transition towards mutualism. This work

  5. Validation of a rapid type 1 diabetes autoantibody screening assay for community-based screening of organ donors to identify subjects at increased risk for the disease.

    PubMed

    Wasserfall, C; Montgomery, E; Yu, L; Michels, A; Gianani, R; Pugliese, A; Nierras, C; Kaddis, J S; Schatz, D A; Bonifacio, E; Atkinson, M A

    2016-07-01

    The Network for Pancreatic Organ donors with Diabetes (nPOD) programme was developed in response to an unmet research need for human pancreatic tissue obtained from individuals with type 1 diabetes mellitus and people at increased risk [i.e. autoantibody (AAb)-positive] for the disease. This necessitated the establishment of a type 1 diabetes-specific AAb screening platform for organ procurement organizations (OPOs). Assay protocols for commercially available enzyme-linked immunosorbent assays (elisas) determining AAb against glutamic acid decarboxylase (GADA), insulinoma-associated protein-2 (IA-2A) and zinc transporter-8 (ZnT8A) were modified to identify AAb-positive donors within strict time requirements associated with organ donation programmes. These rapid elisas were evaluated by the international islet AAb standardization programme (IASP) and used by OPO laboratories as an adjunct to routine serological tests evaluating donors for organ transplantation. The rapid elisas performed well in three IASPs (2011, 2013, 2015) with 98-100% specificity for all three assays, including sensitivities of 64-82% (GADA), 60-64% (IA-2A) and 62-68% (ZnT8A). Since 2009, nPOD has screened 4442 organ donors by rapid elisa; 250 (5·6%) were identified as positive for one AAb and 14 (0.3%) for multiple AAb with 20 of these cases received by nPOD for follow-up studies (14 GADA+, two IA-2A(+) , four multiple AAb-positive). Rapid screening for type 1 diabetes-associated AAb in organ donors is feasible, allowing for identification of non-diabetic, high-risk individuals and procurement of valuable tissues for natural history studies of this disease. PMID:27029857

  6. A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS)

    PubMed Central

    2009-01-01

    Background Asthma and atopy are complex phenotypes with shared genetic component. In this study we attempt to identify genes related to these traits performing a two-stage DNA pooling genome-wide analysis in order to reduce costs. First, we assessed all markers in a subset of subjects using DNA pooling, and in a second stage we evaluated the most promising markers at an individual level. Methods For the genome-wide analysis, we constructed DNA pools from 75 subjects with atopy and asthma, 75 subjects with atopy and without asthma and 75 control subjects without atopy or asthma. In a second stage, the most promising regions surrounding significant markers after correction for false discovery rate were replicated with individual genotyping of samples included in the pools and an additional set of 429 atopic subjects and 222 controls from the same study centres. Results Homo sapiens protein kinase-like protein SgK493 (SGK493) was found to be associated with atopy. To lesser extent mitogen-activated protein kinase 5 (MAP3K5), collagen type XVIII alpha 1 (COL18A1) and collagen type XXIX alpha 1 (COL29A1) were also found to be associated with atopy. Functional evidences points out a role for MAP3K5, COL18A1 and COL29A1 but the function of SGK493 is unknown. Conclusion In this analysis we have identified new candidate regions related to atopy and suggest SGK493 as an atopy locus, although these results need further replication. PMID:19961619

  7. Science for Managing Riverine Ecosystems: Actions for the USGS Identified in the Workshop "Analysis of Flow and Habitat for Instream Aquatic Communities"

    USGS Publications Warehouse

    Bencala, Kenneth E.; Hamilton, David B.; Petersen, James H.

    2006-01-01

    Federal and state agencies need improved scientific analysis to support riverine ecosystem management. The ability of the USGS to integrate geologic, hydrologic, chemical, geographic, and biological data into new tools and models provides unparalleled opportunities to translate the best riverine science into useful approaches and usable information to address issues faced by river managers. In addition to this capability to provide integrated science, the USGS has a long history of providing long-term and nationwide information about natural resources. The USGS is now in a position to advance its ability to provide the scientific support for the management of riverine ecosystems. To address this need, the USGS held a listening session in Fort Collins, Colorado in April 2006. Goals of the workshop were to: 1) learn about the key resource issues facing DOI, other Federal, and state resource management agencies; 2) discuss new approaches and information needs for addressing these issues; and 3) outline a strategy for the USGS role in supporting riverine ecosystem management. Workshop discussions focused on key components of a USGS strategy: Communications, Synthesis, and Research. The workshop identified 3 priority actions the USGS can initiate now to advance its capabilities to support integrated science for resource managers in partner government agencies and non-governmental organizations: 1) Synthesize the existing science of riverine ecosystem processes to produce broadly applicable conceptual models, 2) Enhance sel