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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. Use of lice to identify cowbird hosts

    USGS Publications Warehouse

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

    2000-01-01

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

  4. 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

  5. Using lice to identify cowbird hosts

    USGS Publications Warehouse

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

    1995-01-01

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

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

    PubMed

    Koehler, Anson V; Poulin, Robert

    2010-10-01

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

  7. 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

  8. 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

  9. Impact of host community composition on Lyme disease risk.

    PubMed

    LoGiudice, Kathleen; Duerr, Shannon T K; Newhouse, Michael J; Schmidt, Kenneth A; Killilea, Mary E; Ostfeld, Richard S

    2008-10-01

    The drivers of variable disease risk in complex multi-host disease systems have proved very difficult to identify. Here we test a model that explains the entomological risk of Lyme disease (LD) in terms of host community composition. The model was parameterized in a continuous forest tract at the Cary Institute of Ecosystem Studies (formerly the Institute of Ecosystem Studies) in New York State, U.S.A. We report the results of continuing longitudinal observations (10 years) at the Cary Institute, and of a shorter-term study conducted in forest fragments in LD endemic areas of Connecticut, New Jersey, and New York, USA. Model predictions were significantly correlated with the observed nymphal infection prevalence (NIP) in both studies, although the relationship was stronger in the longer-term Cary Institute study. Species richness was negatively, albeit weakly, correlated with NIP (logistic regression), and there was no relationship between the Shannon diversity index (H') and NIP. Although these results suggest that LD risk is in fact dependent on host diversity, the relationship relies explicitly on the identities and frequencies of host species such that conventional uses of the term biodiversity (i.e., richness, evenness, H') are less appropriate than are metrics that include species identity. This underscores the importance of constructing interaction webs for vertebrates and exploring the direct and indirect effects of anthropogenic stressors on host community composition.

  10. 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.

  11. 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

  12. Inhibitors of bacterial virulence identified in a surrogate host model.

    PubMed

    Benghezal, Mohammed; Adam, Eric; Lucas, Aurore; Burn, Christine; Orchard, Michael G; Deuschel, Christine; Valentino, Emilio; Braillard, Stéphanie; Paccaud, Jean-Pierre; Cosson, Pierre

    2007-05-01

    Antibiotic resistance continues to reduce the number of available antibiotics, increasing the need for novel antibacterial drugs. Since the seminal work of Sir Alexander Fleming, antibiotic identification has been based exclusively on the inhibition of bacterial growth in vitro. Recently, inhibitors of bacterial virulence which interfere with bacterial pathogenesis mechanisms have been proposed as an alternative to antibiotics, and a few were discovered using assays targeting specific virulence mechanisms. Here we designed a simple surrogate host model for the measurement of virulence and systematic discovery of anti-virulence molecules, based on the interaction of Tetrahymena pyriformis and Klebsiella pneumoniae cells. We screened a library of small molecules and identified several inhibitors of virulence. In a mouse pneumonia model we confirmed that an anti-virulence molecule displayed antibacterial activity against Klebsiella pneumoniae and Pseudomonas aeruginosa, by reducing dramatically the bacterial load in the lungs. This molecule did not inhibit bacterial growth in vitro but prevented biosynthesis of the Klebsiella capsule and lipopolysaccharides, a key requirement for virulence. Our results demonstrate that anti-virulence molecules represent an alternative to antibiotics and those can be discovered using non-animal host models.

  13. 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

  14. 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.

  15. 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.

  16. 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.

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

    PubMed

    Wegener Parfrey, Laura

    2015-09-01

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

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

    PubMed

    Wegener Parfrey, Laura

    2015-09-01

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

  19. 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...

  20. 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

  1. 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

  2. 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.

  3. 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

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

    PubMed

    Dallas, Tad; Cornelius, Emily

    2015-08-17

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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. Defining and identifying communities in networks.

    PubMed

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

    2004-03-01

    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.

  10. 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

  11. 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.

  12. Community impacts of anthropogenic disturbance: natural enemies exploit multiple routes in pursuit of invading herbivore hosts

    PubMed Central

    2010-01-01

    Background Biological invasions provide a window on the process of community assembly. In particular, tracking natural enemy recruitment to invading hosts can reveal the relative roles of co-evolution (including local adaptation) and ecological sorting. We use molecular data to examine colonisation of northern Europe by the parasitoid Megastigmus stigmatizans following invasions of its herbivorous oak gallwasp hosts from the Balkans. Local host adaptation predicts that invading gallwasp populations will have been tracked primarily by sympatric Balkan populations of M. stigmatizans (Host Pursuit Hypothesis). Alternatively, ecological sorting allows parasitoid recruitment from geographically distinct populations with no recent experience of the invading hosts (Host Shift Hypothesis). Finally, we test for long-term persistence of parasitoids introduced via human trade of their hosts' galls (Introduction Hypothesis). Results Polymorphism diagnostic of different southern refugial regions was present in both mitochondrial and nuclear microsatellite markers, allowing us to identify the origins of northern European invaded range M. stigmatizans populations. As with their hosts, some invaded range populations showed genetic variation diagnostic of Balkan sources, supporting the Host Pursuit Hypothesis. In contrast, other invading populations had an Iberian origin, unlike their hosts in northern Europe, supporting the Host Shift Hypothesis. Finally, both British and Italian M. stigmatizans populations show signatures compatible with the Introduction Hypothesis from eastern Mediterranean sources. Conclusions These data reveal the continental scale of multi-trophic impacts of anthropogenic disturbance and highlight the fact that herbivores and their natural enemies may face very different constraints on range expansion. The ability of natural enemies to exploit ecologically-similar hosts with which they have had no historical association supports a major role for ecological

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

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

    ERIC Educational Resources Information Center

    Thomas, Lisa Rey; Donovan, Dennis M.; Sigo, Robin L. W.

    2010-01-01

    Indigenous communities have engaged in needs and resources assessments for thousands of years. By blending CBPR/TPR approaches with community-driven assets and needs assessments, academic and community based researchers can work together to better understand and identify community strengths as well as issues of concern in Native communities. This…

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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…

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

    PubMed

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

    2015-03-17

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

  7. 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

  8. 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

  9. 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.

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

    PubMed Central

    Konopka, Allan; Lindemann, Stephen; Fredrickson, Jim

    2015-01-01

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

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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,…

  18. 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...

  19. 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...

  20. The role of transient dynamics in biological pest control: insights from a host-parasitoid community.

    PubMed

    Kidd, David; Amarasekare, Priyanga

    2012-01-01

    1. Identifying natural enemies that can maintain pests at low abundances is a priority in biological control. Here, we show that experiments combined with models generate new insights into identifying effective control agents prior to their release in the field. Using a host-parasitoid community (the harlequin bug and its egg parasitoids) as a model system, we report three key findings. 2. The interplay between the host's self-limitation and the parasitoids' saturating functional response causes the long-term (steady-state) outcomes for pest suppression to differ from those of short-term (transient) dynamics. When the bug's self-limitation is moderately strong, the parasitoid with the higher attack rate and conversion efficiency (Ooencyrtus) achieves greater host suppression in the long term, but its longer handling time causes long periods of transient dynamics during which the bug can reach high abundances; when the bug's self-limitation is weak, host fluctuations amplify over time and Ooencyrtus fails at host suppression altogether. In contrast, the parasitoid with the lower attack rate and conversion efficiency but the shorter handling time (Trissolcus) induces only weak transient fluctuations of short duration and can maintain the host at low abundances regardless of the strength of the bug's self-limitation. 3. Release of multiple enemy species can compromise host suppression if an enemy that induces stronger transient fluctuations excludes one that induces weaker fluctuations. For instance, Ooencyrtus excludes Trissolcus despite having a longer handling time because of its higher conversion efficiency. The model correctly predicts the time to exclusion observed in experiments, suggesting that it captures the key biological features of the host-parasitoid interaction. 4. Intraspecific interference reduces long-term pest suppression but improves short-term pest control by reducing the magnitude and duration of transient fluctuations. 5. These results highlight

  1. The role of transient dynamics in biological pest control: insights from a host-parasitoid community.

    PubMed

    Kidd, David; Amarasekare, Priyanga

    2012-01-01

    1. Identifying natural enemies that can maintain pests at low abundances is a priority in biological control. Here, we show that experiments combined with models generate new insights into identifying effective control agents prior to their release in the field. Using a host-parasitoid community (the harlequin bug and its egg parasitoids) as a model system, we report three key findings. 2. The interplay between the host's self-limitation and the parasitoids' saturating functional response causes the long-term (steady-state) outcomes for pest suppression to differ from those of short-term (transient) dynamics. When the bug's self-limitation is moderately strong, the parasitoid with the higher attack rate and conversion efficiency (Ooencyrtus) achieves greater host suppression in the long term, but its longer handling time causes long periods of transient dynamics during which the bug can reach high abundances; when the bug's self-limitation is weak, host fluctuations amplify over time and Ooencyrtus fails at host suppression altogether. In contrast, the parasitoid with the lower attack rate and conversion efficiency but the shorter handling time (Trissolcus) induces only weak transient fluctuations of short duration and can maintain the host at low abundances regardless of the strength of the bug's self-limitation. 3. Release of multiple enemy species can compromise host suppression if an enemy that induces stronger transient fluctuations excludes one that induces weaker fluctuations. For instance, Ooencyrtus excludes Trissolcus despite having a longer handling time because of its higher conversion efficiency. The model correctly predicts the time to exclusion observed in experiments, suggesting that it captures the key biological features of the host-parasitoid interaction. 4. Intraspecific interference reduces long-term pest suppression but improves short-term pest control by reducing the magnitude and duration of transient fluctuations. 5. These results highlight

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

    PubMed Central

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

    2015-01-01

    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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

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

    PubMed Central

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

    2012-01-01

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

  9. Host-specific assemblages typify gut microbial communities of related insect species.

    PubMed

    Sabree, Zakee L; Moran, Nancy A

    2014-01-01

    Mutualisms between microbes and insects are ubiquitous and facilitate exploitation of various trophic niches by host insects. Dictyopterans (mantids, cockroaches and termites) exhibit trophisms that range from omnivory to strict wood-feeding and maintain beneficial symbioses with the obligate endosymbiont, Blattabacterium, and/or diverse gut microbiomes that include cellulolytic and diazotrophic microbes. While Blattabacterium in omnivorous Periplaneta is fully capable of provisioning essential amino acids, in wood-feeding dictyopterans it has lost many genes for their biosynthesis (Mastotermes and Cryptocercus) or is completely absent (Heterotermes). The conspicuous functional degradation and absence of Blattabacterium in most strict wood-feeding dictyopteran insects suggest that alternative means of acquiring nutrients limited in their diet are being employed. A 16S rRNA gene amplicon resequencing approach was used to deeply sample the composition and diversity of gut communities in related dictyopteran insects to explore the possibility of shifts in symbiont allegiances during termite and cockroach evolution. The gut microbiome of Periplaneta, which has a fully functional Blattabacterium, exhibited the greatest within-sample operational taxonomic unit (OTU) diversity and abundance variability than those of Mastotermes and Cryptocercus, whose Blattabacterium have shrunken genomes and reduced nutrient provisioning capabilities. Heterotermes lacks Blattabacterium and a single OTU that was 95% identical to a Bacteroidia-assigned diazotrophic endosymbiont of an anaerobic cellulolytic protist termite gut inhabitant samples consistently dominates its gut microbiome. Many host-specific OTUs were identified in all host genera, some of which had not been previously detected, indicating that deep sampling by pyrotag sequencing has revealed new taxa that remain to be functionally characterized. Further analysis is required to uncover how consistently detected taxa in the

  10. 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.

  11. 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.

  12. 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

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

    PubMed Central

    Eisen, Jonathan A.; Kopp, Artyom

    2012-01-01

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

  14. Identifying the molecular basis of host-parasite coevolution: merging models and mechanisms.

    PubMed

    Dybdahl, Mark F; Jenkins, Christina E; Nuismer, Scott L

    2014-07-01

    Mathematical models of the coevolutionary process have uncovered consequences of host-parasite interactions that go well beyond the traditional realm of the Red Queen, potentially explaining several important evolutionary transitions. However, these models also demonstrate that the specific consequences of coevolution are sensitive to the structure of the infection matrix, which is embedded in models to describe the likelihood of infection in encounters between specific host and parasite genotypes. Traditional cross-infection approaches to estimating infection matrices might be unreliable because evolutionary dynamics and experimental sampling lead to missing genotypes. Consequently, our goal is to identify the likely structure of infection matrices by synthesizing molecular mechanisms of host immune defense and parasite counterdefense with coevolutionary models. This synthesis reveals that the molecular mechanisms of immune reactions, although complex and diverse, conform to two basic models commonly used within coevolutionary theory: matching infection and targeted recognition. Our synthesis also overturns conventional wisdom, revealing that the general models are not taxonomically restricted but are applicable to plants, invertebrates, and vertebrates. Finally, our synthesis identifies several important areas for future research that should improve the explanatory power of coevolutionary models. The most important among these include empirical studies to identify the molecular hotspots of genotypic specificity and theoretical studies examining the consequences of matrices that more accurately represent multistep infection processes and quantitative defenses.

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

    PubMed

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

    2013-10-15

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

  16. Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation.

    PubMed

    Christian, Natalie; Sullivan, Courtney; Visser, Noelle D; Clay, Keith

    2016-10-01

    All plants form symbioses with endophytic fungi, which affect host plant health and function. Most endophytic fungi are horizontally transmitted, and consequently, local environment and geographic location greatly influence endophyte community composition. Growing evidence also suggests that identity of the plant host (e.g., species, genotype) can be important in shaping endophyte communities. However, little is known about how disturbances to plants affect their fungal symbiont communities. The goal of this study was to test if disturbances, from both natural and anthropogenic sources, can alter endophyte communities independent of geographic location or plant host identity. Using the plant species white snakeroot (Ageratina altissima; Asteraceae), we conducted two experiments that tested the effect of perturbation on endophyte communities. First, we examined endophyte response to leaf mining insect activity, a natural perturbation, in three replicate populations. Second, for one population, we applied fungicide to plant leaves to test endophyte community response to an anthropogenic perturbation. Using culture-based methods and Sanger sequencing of fungal isolates, we then examined abundance, diversity, and community structure of endophytic fungi in leaves subjected to perturbations by leaf mining and fungicide application. Our results show that plant host individual and geographic location are the major determinants of endophyte community composition even in the face of perturbations. Unexpectedly, we found that leaf mining did not impact endophyte communities in white snakeroot, but fungicide treatment resulted in small but significant changes in endophyte community structure. Together, our results suggest that endophyte communities are highly resistant to biotic and anthropogenic disturbances. PMID:27341838

  17. Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation.

    PubMed

    Christian, Natalie; Sullivan, Courtney; Visser, Noelle D; Clay, Keith

    2016-10-01

    All plants form symbioses with endophytic fungi, which affect host plant health and function. Most endophytic fungi are horizontally transmitted, and consequently, local environment and geographic location greatly influence endophyte community composition. Growing evidence also suggests that identity of the plant host (e.g., species, genotype) can be important in shaping endophyte communities. However, little is known about how disturbances to plants affect their fungal symbiont communities. The goal of this study was to test if disturbances, from both natural and anthropogenic sources, can alter endophyte communities independent of geographic location or plant host identity. Using the plant species white snakeroot (Ageratina altissima; Asteraceae), we conducted two experiments that tested the effect of perturbation on endophyte communities. First, we examined endophyte response to leaf mining insect activity, a natural perturbation, in three replicate populations. Second, for one population, we applied fungicide to plant leaves to test endophyte community response to an anthropogenic perturbation. Using culture-based methods and Sanger sequencing of fungal isolates, we then examined abundance, diversity, and community structure of endophytic fungi in leaves subjected to perturbations by leaf mining and fungicide application. Our results show that plant host individual and geographic location are the major determinants of endophyte community composition even in the face of perturbations. Unexpectedly, we found that leaf mining did not impact endophyte communities in white snakeroot, but fungicide treatment resulted in small but significant changes in endophyte community structure. Together, our results suggest that endophyte communities are highly resistant to biotic and anthropogenic disturbances.

  18. 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

  19. 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

  20. 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

  1. Parasite transmission in complex communities: predators and alternative hosts alter pathogenic infections in amphibians.

    PubMed

    Orlofske, Sarah A; Jadin, Robert C; Preston, Daniel L; Johnson, Pieter T J

    2012-06-01

    While often studied in isolation, host-parasite interactions are typically embedded within complex communities. Other community members, including predators and alternative hosts, can therefore alter parasite transmission (e.g., the dilution effect), yet few studies have experimentally evaluated more than one such mechanism. Here, we used data from natural wetlands to design experiments investigating how alternative hosts and predators of parasites mediate trematode (Ribeiroia ondatrae) infection in a focal amphibian host (Pseudacris regilla). In short-term predation bioassays involving mollusks, zooplankton, fish, larval insects, or newts, four of seven tested species removed 62-93% of infectious stages. In transmission experiments, damselfly nymphs (predators) and newt larvae (alternative hosts) reduced infection in P. regilla tadpoles by -50%, whereas mosquitofish (potential predators and alternative hosts) did not significantly influence transmission. Additional bioassays indicated that predators consumed parasites even in the presence of alternative prey. In natural wetlands, newts had similar infection intensities as P. regilla, suggesting that they commonly function as alternative hosts despite their unpalatability to downstream hosts, whereas mosquitofish had substantially lower infection intensities and are unlikely to function as hosts. These results underscore the importance of studying host-parasite interactions in complex communities and of broadly linking research on predation, biodiversity loss, and infectious diseases.

  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. Identifying host genetic risk factors in the context of public health surveillance for invasive pneumococcal disease.

    PubMed

    Lingappa, Jairam R; Dumitrescu, Logan; Zimmer, Shanta M; Lynfield, Ruth; McNicholl, Janet M; Messonnier, Nancy E; Whitney, Cynthia G; Crawford, Dana C

    2011-01-01

    Host genetic factors that modify risk of pneumococcal disease may help target future public health interventions to individuals at highest risk of disease. We linked data from population-based surveillance for invasive pneumococcal disease (IPD) with state-based newborn dried bloodspot repositories to identify biological samples from individuals who developed invasive pneumococcal disease. Genomic DNA was extracted from 366 case and 732 anonymous control samples. TagSNPs were selected in 34 candidate genes thought to be associated with host response to invasive pneumococcal disease, and a total of 326 variants were successfully genotyped. Among 543 European Americans (EA) (182 cases and 361 controls), and 166 African Americans (AA) (53 cases and 113 controls), common variants in surfactant protein D (SFTPD) are consistently underrepresented in IPD. SFTPD variants with the strongest association for IPD are intronic rs17886286 (allelic OR 0.45, 95% confidence interval (CI) [0.25, 0.82], with p = 0.007) in EA and 5' flanking rs12219080 (allelic OR 0.32, 95%CI [0.13, 0.78], with p = 0.009) in AA. Variants in CD46 and IL1R1 are also associated with IPD in both EA and AA, but with effects in different directions; FAS, IL1B, IL4, IL10, IL12B, SFTPA1, SFTPB, and PTAFR variants are associated (p≤0.05) with IPD in EA or AA. We conclude that variants in SFTPD may protect against IPD in EA and AA and genetic variation in other host response pathways may also contribute to risk of IPD. While our associations are not corrected for multiple comparisons and therefore must be replicated in additional cohorts, this pilot study underscores the feasibility of integrating public health surveillance with existing, prospectively collected, newborn dried blood spot repositories to identify host genetic factors associated with infectious diseases.

  5. 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 ...

  6. 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

  7. 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.

  8. 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

  9. 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

  10. Phlebotomus sergenti (Parrot, 1917) identified as Leishmania killicki host in Ghardaïa, south Algeria.

    PubMed

    Boubidi, S C; Benallal, K; Boudrissa, A; Bouiba, L; Bouchareb, B; Garni, R; Bouratbine, A; Ravel, C; Dvorak, V; Votypka, J; Volf, P; Harrat, Z

    2011-07-01

    Since 2005, an outbreak of human cutaneous leishmaniasis (CL) in Ghardaïa, south Algeria, was studied and one output of these investigations was the identification of two Leishmania species, Leishmania major and Leishmania killicki, as the CL causative agents. In the present study, we were curious to focus on sand fly fauna present in this area and detection of Leishmania-positive sand fly females. Sand flies (3717) were collected during two seasons using sticky papers and CDC light traps in urban, rural and sylvatic sites. Twelve Phlebotomus species were identified. Phlebotomus papatasi was dominant in the urban site while Phlebotomus sergenti and Phlebotomus riouxi/chabaudi were dominant in the sylvatic site. Out of 74 P. sergenti females captured by CDC light traps in the sylvatic site populated by Ghardaïas' Gundi (Massoutiera mzabi), three ones were hosting Leishmania promastigotes. PCR-RFLP and sequencing of seven single-copy coding DNA sequences identified the promastigotes as L. killicki. Furthermore, laboratory experiments revealed that L. killicki isolate sampled from a CL patient inhabiting the studied region develop well in P. sergenti females. Our findings strongly suggest that the human cutaneous leishmaniases caused by L. killicki is a zoonotic disease with P. sergenti sand flies acting as hosts and vectors and gundi rodents as reservoirs.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. Relationships between Host Phylogeny, Host Type and Bacterial Community Diversity in Cold-Water Coral Reef Sponges

    PubMed Central

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

    2013-01-01

    Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level), as well as sponge type (high versus low microbial abundance), and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that as many as 345 (79%) of the 437 different bacterial operational taxonomic units (OTUs) detected in the dataset were shared between sponges and sediments, while only 70 (16%) appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation), sponge family (52%) or sponge type (30%), whereas mesoscale geographic distances and water depth showed comparatively small effects (<5% each). In addition, a highly significant, positive relationship between bacterial community dissimilarity and sponge phylogenetic distance was observed within the ancient family of the Geodiidae. Overall, the high diversity of sponges in cold-water coral reefs, combined with the observed sponge-related variation in bacterial community structure, support the idea that sponges represent heterogeneous, yet structured microbial habitats that contribute significantly to enhancing bacterial diversity in deep-sea ecosystems. PMID:23393586

  17. 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.

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

    PubMed

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

    2010-07-22

    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.

  19. 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.

  20. 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

  1. 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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  4. 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

  5. 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.

  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. Comparative definition of community and corresponding identifying algorithm

    NASA Astrophysics Data System (ADS)

    Hu, Yanqing; Chen, Hongbin; Zhang, Peng; Li, Menghui; di, Zengru; Fan, Ying

    2008-08-01

    A comparative definition for community in networks is proposed, and the corresponding detecting algorithm is given. A community is defined as a set of nodes, which satisfies the requirement that each node’s degree inside the community should not be smaller than the node’s degree toward any other community. In the algorithm, the attractive force of a community to a node is defined as the connections between them. Then employing an attractive-force-based self-organizing process, without any extra parameter, the best communities can be detected. Several artificial and real-world networks, including the Zachary karate club, college football, and large scientific collaboration networks, are analyzed. The algorithm works well in detecting communities, and it also gives a nice description of network division and group formation.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. Temporal SILAC-based quantitative proteomics identifies host factors involved in chikungunya virus replication.

    PubMed

    Treffers, Emmely E; Tas, Ali; Scholte, Florine E M; Van, Myrthe N; Heemskerk, Matthias T; de Ru, Arnoud H; Snijder, Eric J; van Hemert, Martijn J; van Veelen, Peter A

    2015-07-01

    Chikungunya virus (CHIKV) is an arthropod-borne reemerging human pathogen that generally causes a severe persisting arthritis. Since 2005, the virus has infected millions of people during outbreaks in Africa, Indian Ocean Islands, Asia, and South/Central America. Many steps of the replication and expression of CHIKV's 12-kb RNA genome are highly dependent on cellular factors, which thus constitute potential therapeutic targets. SILAC and LC-MS/MS were used to define the temporal dynamics of the cellular response to infection. Using samples harvested at 8, 10, and 12 h postinfection, over 4700 proteins were identified and per time point 2800-3500 proteins could be quantified in both biological replicates. At 8, 10, and 12 h postinfection, 13, 38, and 106 proteins, respectively, were differentially expressed. The majority of these proteins showed decreased abundance. Most subunits of the RNA polymerase II complex were progressively degraded, which likely contributes to the transcriptional host shut-off observed during CHIKV infection. Overexpression of four proteins that were significantly downregulated (Rho family GTPase 3 (Rnd3), DEAD box helicase 56 (DDX56), polo-like kinase 1 (Plk1), and ubiquitin-conjugating enzyme E2C (UbcH10) reduced susceptibility of cells to CHIKV infection, suggesting that infection-induced downregulation of these proteins is beneficial for CHIKV replication. All MS data have been deposited in the ProteomeXchange with identifier PXD001330 (http://proteomecentral.proteomexchange.org/dataset/PXD001330).

  13. 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…

  14. 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…

  15. 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:…

  16. Defining and identifying cograph communities in complex networks

    NASA Astrophysics Data System (ADS)

    Jia, Songwei; Gao, Lin; Gao, Yong; Nastos, James; Wang, Yijie; Zhang, Xindong; Wang, Haiyang

    2015-01-01

    Community or module detection is a fundamental problem in complex networks. Most of the traditional algorithms available focus only on vertices in a subgraph that are densely connected among themselves while being loosely connected to the vertices outside the subgraph, ignoring the topological structure of the community. However, in most cases one needs to make further analysis on the interior topological structure of communities to obtain various meaningful subgroups. We thus propose a novel community referred to as a cograph community, which has a well-understood structure. The well-understood structure of cographs and their corresponding cotree representation allows for an immediate identification of structurally-equivalent subgroups. We develop an algorithm called the Edge P4 centrality-based divisive algorithm (EPCA) to detect these cograph communities; this algorithm is efficient, free of parameters and independent of additional measures mainly due to the novel local edge P4 centrality measure. Further, we compare the EPCA with algorithms from the existing literature on synthetic, social and biological networks to show it has superior or competitive performance in accuracy. In addition to the computational advantages over other community-detection algorithms, the EPCA provides a simple means of discovering both dense and sparse subgroups based on structural equivalence or homogeneous roles which may otherwise go undetected by other algorithms which rely on edge density measures for finding subgroups.

  17. Identifying Schistosoma japonicum excretory/secretory proteins and their interactions with host immune system.

    PubMed

    Liao, Qi; Yuan, Xiongying; Xiao, Hui; Liu, Changning; Lv, Zhiyue; Zhao, Yi; Wu, Zhongdao

    2011-01-01

    Schistosoma japonicum is a major infectious agent of schistosomiasis. It has been reported that large number of proteins excreted and secreted by S. japonicum during its life cycle are important for its infection and survival in definitive hosts. These proteins can be used as ideal candidates for vaccines or drug targets. In this work, we analyzed the protein sequences of S. japonicum and found that compared with other proteins in S. japonicum, excretory/secretory (ES) proteins are generally longer, more likely to be stable and enzyme, more likely to contain immune-related binding peptides and more likely to be involved in regulation and metabolism processes. Based on the sequence difference between ES and non-ES proteins, we trained a support vector machine (SVM) with much higher accuracy than existing approaches. Using this SVM, we identified 191 new ES proteins in S. japonicum, and further predicted 7 potential interactions between these ES proteins and human immune proteins. Our results are useful to understand the pathogenesis of schistosomiasis and can serve as a new resource for vaccine or drug targets discovery for anti-schistosome.

  18. Caenorhabditis elegans-based screen identifies Salmonella virulence factors required for conserved host-pathogen interactions.

    PubMed

    Tenor, Jennifer L; McCormick, Beth A; Ausubel, Frederick M; Aballay, Alejandro

    2004-06-01

    A Caenorhabditis elegans-Salmonella enterica host-pathogen model was used to identify both novel and previously known S. enterica virulence factors (HilA, HilD, InvH, SptP, RhuM, Spi4-F, PipA, VsdA, RepC, Sb25, RfaL, GmhA, LeuO, CstA, and RecC), including several related to the type III secretion system (TTSS) encoded in Salmonella pathogenicity island 1 (SPI-1). Mutants corresponding to presumptive novel virulence-related genes exhibited diminished ability to invade epithelial cells and/or to induce polymorphonuclear leukocyte migration in a tissue culture model of mammalian enteropathogenesis. When expressed in C. elegans intestinal cells, the S. enterica TTSS-exported effector protein SptP inhibited a conserved p38 MAPK signaling pathway and suppressed the diminished pathogenicity phenotype of an S. enterica sptP mutant. These results show that C. elegans is an attractive model to study the interaction between Salmonella effector proteins and components of the innate immune response, in part because there is a remarkable overlap between Salmonella virulence factors required for human and nematode pathogenesis.

  19. Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling

    PubMed Central

    2010-01-01

    Background There was a large scale outbreak of the highly pathogenic porcine reproductive and respiratory syndrome (PRRS) in China and Vietnam during 2006 and 2007 that resulted in unusually high morbidity and mortality among pigs of all ages. The mechanisms underlying the molecular pathogenesis of the highly virulent PRRS virus (H-PRRSV) remains unknown. Therefore, the relationship between pulmonary gene expression profiles after H-PRRSV infection and infection pathology were analyzed in this study using high-throughput deep sequencing and histopathology. Results H-PRRSV infection resulted in severe lung pathology. The results indicate that aberrant host innate immune responses to H-PRRSV and induction of an anti-apoptotic state could be responsible for the aggressive replication and dissemination of H-PRRSV. Prolific rapid replication of H-PRRSV could have triggered aberrant sustained expression of pro-inflammatory cytokines and chemokines leading to a markedly robust inflammatory response compounded by significant cell death and increased oxidative damage. The end result was severe tissue damage and high pathogenicity. Conclusions The systems analysis utilized in this study provides a comprehensive basis for better understanding the pathogenesis of H-PRRSV. Furthermore, it allows the genetic components involved in H-PRRSV resistance/susceptibility in swine populations to be identified. PMID:20929578

  20. 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

  1. 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

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

    PubMed Central

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

    2011-01-01

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

  3. 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.

  4. 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)

  5. 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.

  6. 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

  7. Host specificity and seasonality of helminth component communities in central European grebes (Podicipediformes) and loons (Gaviiformes).

    PubMed

    Sitko, Jiljí; Heneberg, Petr

    2015-10-01

    Structure and pattern of helminth component communities parasitizing grebes and loons are poorly understood. Here we analyze the prevalence, intensity and diversity of helminths in 505 Czech grebes (Podiceps cristatus, Podiceps nigricollis, Tachybaptus ruficollis) and loons (Gavia arctica, Gavia stellata) collected between 1962 and 2014. The species richness of helminth component communities ranged from 31±8 (P. cristatus) to 50±4 (G. stellata) species, with helminth load similar in all five host species, but with strong differences in prevalence and intensity of infection at a helminth species-specific level. The dominance was low, ranging from 0.11 (P. cristatus and G. stellata) to 0.21 (P. nigricollis). Dominant species (>25% prevalence) in P. cristatus were Confluaria sp., Tylodelphys clavata, Echinochasmus coaxatus, Petasiger neocomense and Ligula colymbi; in P. nigricollis and T. ruficollis: Confluaria sp. and Tatria sp.; in G. arctica and G. stellata: Tetrabothrius microcephalus, Stephanoprora denticulata, Cryptocotyle concava, Diplostomum gavium and Ichthyocotylurus erraticus; in G. stellata only: Echinochasmus (Monilifer) spinulosus. Four (12%) of the grebe digenean species were not locally acquired (with non-sympatric intermediate hosts) despite the fact that they represented 25% of digenean individuals found. In loons, five (28%) of digenean species and striking 38% of individuals found used the non-sympatric intermediate host species. Component communities of grebes were similar to each other (Sørensen similarity index 0.47-0.65) but differed strongly from those hosted by loons (0.00-0.20). We present the first systematically collected evidence of intra-annual changes of helminth component communities in grebes, and provide 20 new host records. PMID:26008120

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

    PubMed

    Kleinschmidt, Ross; Black, Jeffrey; Akber, Riaz

    2011-03-01

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

  9. 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

  10. 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.

  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. 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

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

    PubMed

    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

    2015-11-09

    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.

  14. 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

  15. 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.

  16. Analysis of the Staphylococcus aureus abscess proteome identifies antimicrobial host proteins and bacterial stress responses at the host-pathogen interface

    PubMed Central

    Attia, Ahmed S.; Cassat, James E.; Aranmolate, Sheg O.; Zimmerman, Lisa J.; Boyd, Kelli L.; Skaar, Eric P.

    2013-01-01

    Abscesses are a hallmark of invasive staphylococcal infections and the site of a dynamic struggle between pathogen and host. However, the precise host and bacterial factors that contribute to abscess formation and maintenance have not been completely described. In this work, we define the Staphylococcus aureus abscess proteome from both wildtype and neutropenic mice to elucidate the host response to staphylococcal infection and uncover novel S. aureus virulence factors. Among the proteins identified, the mouse protein histone H4 was enriched in the abscesses of wildtype compared to neutropenic animals. Histone H4 inhibits staphylococcal growth in vitro demonstrating a role for this protein in the innate immune response to staphylococcal infection. These analyses also identified staphylococcal proteins within the abscess, including known virulence factors and proteins with previously unrecognized roles in pathogenesis. Within the latter group was the universal stress protein Usp2, which was enriched in kidney lesions from neutropenic mice and required for the S. aureus response to stringent stress. Taken together, these data describe the S. aureus abscess proteome and lay the foundation for the identification of contributors to innate immunity and bacterial pathogenesis. PMID:23847107

  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. 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.

  19. 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

  20. 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

  1. 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

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

    PubMed

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

    2014-11-11

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

  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. 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

  5. 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

  6. Deciphering bartonella diversity, recombination, and host specificity in a rodent community.

    PubMed

    Buffet, Jean-Philippe; Pisanu, Benoît; Brisse, Sylvain; Roussel, Sophie; Félix, Benjamin; Halos, Lénaïg; Chapuis, Jean-Louis; Vayssier-Taussat, Muriel

    2013-01-01

    Host-specificity is an intrinsic feature of many bacterial pathogens, resulting from a long history of co-adaptation between bacteria and their hosts. Alpha-proteobacteria belonging to the genus Bartonella infect the erythrocytes of a wide range of mammal orders, including rodents. In this study, we performed genetic analysis of Bartonella colonizing a rodent community dominated by bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus) in a French suburban forest to evaluate their diversity, their capacity to recombine and their level of host specificity. Following the analysis of 550 rodents, we detected 63 distinct genotypes related to B. taylorii, B. grahamii, B. doshiae and a new B. rochalimae-like species. Investigating the most highly represented species, we showed that B. taylorii strain diversity was markedly higher than that of B. grahamii, suggesting a possible severe bottleneck for the latter species. The majority of recovered genotypes presented a strong association with either bank voles or wood mice, with the exception of three B. taylorii genotypes which had a broader host range. Despite the physical barriers created by host specificity, we observed lateral gene transfer between Bartonella genotypes associated with wood mice and Bartonella adapted to bank voles, suggesting that those genotypes might co-habit during their life cycle.

  7. 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

  8. Community participatory research with deaf sign language users to identify health inequities.

    PubMed

    Barnett, Steven; Klein, Jonathan D; Pollard, Robert Q; Samar, Vincent; Schlehofer, Deirdre; Starr, Matthew; Sutter, Erika; Yang, Hongmei; Pearson, Thomas A

    2011-12-01

    Deaf people who use American Sign Language (ASL) are medically underserved and often excluded from health research and surveillance. We used a community participatory approach to develop and administer an ASL-accessible health survey. We identified deaf community strengths (e.g., a low prevalence of current smokers) and 3 glaring health inequities: obesity, partner violence, and suicide. This collaborative work represents the first time a deaf community has used its own data to identify health priorities.

  9. The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks

    PubMed Central

    Hawlena, Hadas; Rynkiewicz, Evelyn; Toh, Evelyn; Alfred, Andrew; Durden, Lance A; Hastriter, Michael W; Nelson, David E; Rong, Ruichen; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith

    2013-01-01

    Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment. PMID:22739493

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

    PubMed Central

    2012-01-01

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

  11. 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

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

    PubMed

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

    2013-10-21

    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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    1993-01-01

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

  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. Concordance of bacterial communities of two tick species and blood of their shared rodent host.

    PubMed

    Rynkiewicz, Evelyn C; Hemmerich, Chris; Rusch, Douglas B; Fuqua, Clay; Clay, Keith

    2015-05-01

    High-throughput sequencing is revealing that most macro-organisms house diverse microbial communities. Of particular interest are disease vectors whose microbiome could potentially affect pathogen transmission and vector competence. We investigated bacterial community composition and diversity of the ticks Dermacentor variabilis (n = 68) and Ixodes scapularis (n = 15) and blood of their shared rodent host, Peromyscus leucopus (n = 45) to quantify bacterial diversity and concordance. The 16S rRNA gene was amplified from genomic DNA from field-collected tick and rodent blood samples, and 454 pyrosequencing was used to elucidate their bacterial communities. After quality control, over 300 000 sequences were obtained and classified into 118 operational taxonomic units (OTUs, clustered at 97% similarity). Analysis of rarefied communities revealed that the most abundant OTUs were tick species-specific endosymbionts, Francisella and Rickettsia, and the commonly flea-associated bacterium Bartonella in rodent blood. An Arsenophonus and additional Francisella endosymbiont were also present in D. variabilis samples. Rickettsia was found in both tick species but not in rodent blood, suggesting that it is not transmitted during feeding. Bartonella was present in larvae and nymphs of both tick species, even those scored as unengorged. Relatively, few OTUs (e.g. Bartonella, Lactobacillus) were found in all sample types. Overall, bacterial communities from each sample type were significantly different and highly structured, independent of their dominant OTUs. Our results point to complex microbial assemblages inhabiting ticks and host blood including infectious agents, tick-specific endosymbionts and environmental bacteria that could potentially affect arthropod-vectored disease dynamics. PMID:25847197

  17. Concordance of bacterial communities of two tick species and blood of their shared rodent host.

    PubMed

    Rynkiewicz, Evelyn C; Hemmerich, Chris; Rusch, Douglas B; Fuqua, Clay; Clay, Keith

    2015-05-01

    High-throughput sequencing is revealing that most macro-organisms house diverse microbial communities. Of particular interest are disease vectors whose microbiome could potentially affect pathogen transmission and vector competence. We investigated bacterial community composition and diversity of the ticks Dermacentor variabilis (n = 68) and Ixodes scapularis (n = 15) and blood of their shared rodent host, Peromyscus leucopus (n = 45) to quantify bacterial diversity and concordance. The 16S rRNA gene was amplified from genomic DNA from field-collected tick and rodent blood samples, and 454 pyrosequencing was used to elucidate their bacterial communities. After quality control, over 300 000 sequences were obtained and classified into 118 operational taxonomic units (OTUs, clustered at 97% similarity). Analysis of rarefied communities revealed that the most abundant OTUs were tick species-specific endosymbionts, Francisella and Rickettsia, and the commonly flea-associated bacterium Bartonella in rodent blood. An Arsenophonus and additional Francisella endosymbiont were also present in D. variabilis samples. Rickettsia was found in both tick species but not in rodent blood, suggesting that it is not transmitted during feeding. Bartonella was present in larvae and nymphs of both tick species, even those scored as unengorged. Relatively, few OTUs (e.g. Bartonella, Lactobacillus) were found in all sample types. Overall, bacterial communities from each sample type were significantly different and highly structured, independent of their dominant OTUs. Our results point to complex microbial assemblages inhabiting ticks and host blood including infectious agents, tick-specific endosymbionts and environmental bacteria that could potentially affect arthropod-vectored disease dynamics.

  18. 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.

  19. 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

  20. 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

  1. Anthelmintic treatment alters the parasite community in a wild mouse host.

    PubMed

    Pedersen, Amy B; Antonovics, Janis

    2013-08-23

    Individuals are often co-infected with several parasite species, yet the consequences of drug treatment on the dynamics of parasite communities in wild populations have rarely been measured. Here, we experimentally reduced nematode infection in a wild mouse population and measured the effects on other non-target parasites. A single oral dose of the anthelmintic, ivermectin, significantly reduced nematode infection, but resulted in a reciprocal increase in other gastrointestinal parasites, specifically coccidial protozoans and cestodes. These results highlight the possibility that drug therapy may have unintended consequences for non-target parasites and that host-parasite dynamics cannot always be fully understood in the framework of single host-parasite interactions.

  2. 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

  3. A novel cause of community-acquired pneumonia in a young immunocompetent host.

    PubMed

    James, Nicholas; Gilman, Matthew; Duncan, Robert; Gray, Anthony

    2016-09-01

    Diffuse pulmonary infiltrates represent a common problem encountered by pulmonologists. The differential diagnosis is extensive and includes infectious, inflammatory, environmental and malignant conditions. Appropriate evaluation, aside from a thorough history and physical examination, includes serologic, radiographic and procedural elements. We describe a case of a healthy male with diffuse pulmonary infiltrates. Work up revealed a novel infectious etiology. Although this particular microorganism has been described to cause native valve endocarditis, recurrent breast abscesses, osteomyelitis and bacteremia, it has to date not been described as a cause for community acquired pneumonia in immunocompetent hosts.

  4. 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

  5. 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

  6. 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

  7. 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

  8. Cell-type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy

    PubMed Central

    Inkeles, Megan S.; Teles, Rosane M.B.; Pouldar, Delila; Andrade, Priscila R.; Madigan, Cressida A.; Ambrose, Mike; Sarno, Euzenir N.; Rea, Thomas H.; Ochoa, Maria T.; Iruela-Arispe, M. Luisa; Swindell, William R.; Ottenhoff, Tom H.M.; Geluk, Annemieke; Bloom, Barry R.

    2016-01-01

    Transcriptome profiles derived from the site of human disease have led to the identification of genes that contribute to pathogenesis, yet the complex mixture of cell types in these lesions has been an obstacle for defining specific mechanisms. Leprosy provides an outstanding model to study host defense and pathogenesis in a human infectious disease, given its clinical spectrum, which interrelates with the host immunologic and pathologic responses. Here, we investigated gene expression profiles derived from skin lesions for each clinical subtype of leprosy, analyzing gene coexpression modules by cell-type deconvolution. In lesions from tuberculoid leprosy patients, those with the self-limited form of the disease, dendritic cells were linked with MMP12 as part of a tissue remodeling network that contributes to granuloma formation. In lesions from lepromatous leprosy patients, those with disseminated disease, macrophages were linked with a gene network that programs phagocytosis. In erythema nodosum leprosum, neutrophil and endothelial cell gene networks were identified as part of the vasculitis that results in tissue injury. The present integrated computational approach provides a systems approach toward identifying cell-defined functional networks that contribute to host defense and immunopathology at the site of human infectious disease. PMID:27699251

  9. Cell-type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy

    PubMed Central

    Inkeles, Megan S.; Teles, Rosane M.B.; Pouldar, Delila; Andrade, Priscila R.; Madigan, Cressida A.; Ambrose, Mike; Sarno, Euzenir N.; Rea, Thomas H.; Ochoa, Maria T.; Iruela-Arispe, M. Luisa; Swindell, William R.; Ottenhoff, Tom H.M.; Geluk, Annemieke; Bloom, Barry R.

    2016-01-01

    Transcriptome profiles derived from the site of human disease have led to the identification of genes that contribute to pathogenesis, yet the complex mixture of cell types in these lesions has been an obstacle for defining specific mechanisms. Leprosy provides an outstanding model to study host defense and pathogenesis in a human infectious disease, given its clinical spectrum, which interrelates with the host immunologic and pathologic responses. Here, we investigated gene expression profiles derived from skin lesions for each clinical subtype of leprosy, analyzing gene coexpression modules by cell-type deconvolution. In lesions from tuberculoid leprosy patients, those with the self-limited form of the disease, dendritic cells were linked with MMP12 as part of a tissue remodeling network that contributes to granuloma formation. In lesions from lepromatous leprosy patients, those with disseminated disease, macrophages were linked with a gene network that programs phagocytosis. In erythema nodosum leprosum, neutrophil and endothelial cell gene networks were identified as part of the vasculitis that results in tissue injury. The present integrated computational approach provides a systems approach toward identifying cell-defined functional networks that contribute to host defense and immunopathology at the site of human infectious disease.

  10. Identifying host species driving transmission of schistosomiasis japonica, a multihost parasite system, in China.

    PubMed

    Rudge, James W; Webster, Joanne P; Lu, Da-Bing; Wang, Tian-Ping; Fang, Guo-Ren; Basáñez, María-Gloria

    2013-07-01

    Understanding disease transmission dynamics in multihost parasite systems is a research priority for control and potential elimination of many infectious diseases. In China, despite decades of multifaceted control efforts against schistosomiasis, the indirectly transmitted helminth Schistosoma japonicum remains endemic, partly because of the presence of zoonotic reservoirs. We used mathematical modeling and conceptual frameworks of multihost transmission ecology to assess the relative importance of various definitive host species for S. japonicum transmission in contrasting hilly and marshland areas of China. We examine whether directing control interventions against zoonotic reservoirs could further reduce incidence of infection in humans or even eliminate transmission. Results suggest that, under current control programs, infections in humans result from spillover of transmission among zoonotic reservoirs. Estimates of the basic reproduction number within each species suggest that bovines (water buffalo and cattle) maintained transmission in the marshland area and that the recent removal of bovines from this area could achieve local elimination of transmission. However, the sole use of antifecundity S. japonicum vaccines for bovines, at least at current efficacies, may not achieve elimination in areas of comparable endemicity where removal of bovines is not a feasible option. The results also suggest that rodents drive transmission in the hilly area. Therefore, although targeting bovines could further reduce and potentially interrupt transmission in marshland regions of China, elimination of S. japonicum could prove more challenging in areas where rodents might maintain transmission. In conclusion, we show how mathematical modeling can give important insights into multihost transmission of indirectly transmitted pathogens.

  11. Non-invasive methods for identifying oocysts of Sarcocystis spp. from definitive hosts.

    PubMed

    Xiang, Zheng; Chen, Xinwen; Yang, Lijun; He, Yongshu; Jiang, Runsheng; Rosenthal, Benjamin M; Luan, Pengtao; Attwood, S W; Zuo, Yangxian; Zhang, Ya-ping; Yang, Zhaoqing

    2009-09-01

    Because the excreted sporocysts and/or oocysts of various species of Sarcocystis may not be discriminated morphologically, we sought to validate a diagnostic technique based on variation in the 18S rDNA sequence. Oocysts and/or sporocysts from three taxa of Sarcocystis were collected from human, feline, and canine definitive hosts that had fed upon meats infected with the muscle cysts of Sarcocystis hominis, Sarcocystis fusiformis and a species of Sarcocystis from water buffalo that could not be distinguished from Sarcocystis cruzi. Using a new collection method employing filter paper, these excreted oocysts and sporocysts were subjected to DNA extraction, as were the corresponding muscle cysts. Methods employing PCR-RFLP and DNA sequencing of a partial 18S rDNA gene (ssrRNA) sequence were then used to successfully distinguish among the three taxa. The same, unique restriction digestion pattern characterizes the tissue cysts and oocysts and/or sporocysts of each parasite taxon. The technique makes possible amplification and identification of species specific gene sequences based on DNA extracted from as few as 7 excreted sporocysts (the equivalent of 3 and 1/2 oocysts) from freshly prepared material, or as few as 50 sporocysts from feces samples that had been stored in potassium dichromate (K2Cr2O7) for as long as 6 years. This represents the first report using molecular diagnostic procedures to diagnose oocysts of Sarcocystis in faecal samples, describing a valuable new tool for studying the epidemiology of various Sarcocystis species.

  12. 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…

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

    SciTech Connect

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

    2013-03-20

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

  14. Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity

    NASA Astrophysics Data System (ADS)

    He, Dan; Ren, Lijuan; Wu, Qinglong

    2012-03-01

    Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species. However, the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood. We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes: Vallisneria natans and Hydrilla verticillata in Taihu Lake, Jiangsu, China, using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes. The results show that: (1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria, and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria, including Burkholderiales, was the most abundant bacterial group on both plants. Cyanobacteria and Gammaproteobacteria were the second largest groups on V. natans and H. verticillata, respectively. Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations. Both ANOSIM of the T-RFLP data and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants. Therefore, the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific, which may aid in understanding the ecological functions of submerged macrophytes in general.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  16. 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.

  17. 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

  18. 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

  19. 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

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

    PubMed

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

    2013-09-01

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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

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

    PubMed

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

    2015-03-01

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

  9. 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

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

    DOE PAGES

    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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Clinical deterioration in community acquired infections associated with lymphocyte upsurge in immunocompetent hosts.

    PubMed

    Cheng, Vincent C C; Wu, Alan K L; Hung, Ivan F N; Tang, Bone S F; Lee, Rodney A; Lau, Susanna K P; Woo, Patrick C Y; Yuen, Kwok-Yung

    2004-01-01

    Clinical deterioration during the course of community-acquired infections can occur as a result of an exaggerated immune response of the host towards the inciting pathogens, leading to immune-mediated tissue damage. Whether a surge in the peripheral lymphocyte count can be used as a surrogate marker indicating the onset of immunopathological tissue damage is not known. In this study, we report the clinical presentations and outcomes of a cohort of immunocompetent patients with non-tuberculous community acquired infections who experienced clinical deterioration during hospital stay (n=85). 12 (14.1%) patients had a surge in lymphocyte count preceding their clinical deteriorations, and their diagnoses included viral pneumonitis , viral encephalitis , scrub typhus , leptospirosis , brucellosis , and dengue haemorrhagic fever . The clinical manifestations during deterioration ranged from interstitial pneumonitis , airway obstruction , CNS disturbances , and systemic capillary leak syndrome , all of which were thought to represent immunopathological tissue damages. When compared with patients without lymphocyte surge, these patients were more likely to be infected with fastidious/viral pathogens (0 vs 12; p<0.05), in addition to having lower mean baseline lymphocyte counts (403+/-181 vs 1143+/-686 cells/microl; p<0.05). We postulate that the peripheral lymphocyte count may be a useful surrogate marker indicating the presence of immunopathological damage during clinical deterioration in certain infectious diseases.

  18. A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

    PubMed Central

    2011-01-01

    Background Metabolic interactions involve the exchange of metabolic products among microbial species. Most microbes live in communities and usually rely on metabolic interactions to increase their supply for nutrients and better exploit a given environment. Constraint-based models have successfully analyzed cellular metabolism and described genotype-phenotype relations. However, there are only a few studies of genome-scale multi-species interactions. Based on genome-scale approaches, we present a graph-theoretic approach together with a metabolic model in order to explore the metabolic variability among bacterial strains and identify and describe metabolically interacting strain communities in a batch culture consisting of two or more strains. We demonstrate the applicability of our approach to the bacterium E. coli across different single-carbon-source conditions. Results A different diversity graph is constructed for each growth condition. The graph-theoretic properties of the constructed graphs reflect the inherent high metabolic redundancy of the cell to single-gene knockouts, reveal mutant-hubs of unique metabolic capabilities regarding by-production, demonstrate consistent metabolic behaviors across conditions and show an evolutionary difficulty towards the establishment of polymorphism, while suggesting that communities consisting of strains specifically adapted to a given condition are more likely to evolve. We reveal several strain communities of improved growth relative to corresponding monocultures, even though strain communities are not modeled to operate towards a collective goal, such as the community growth and we identify the range of metabolites that are exchanged in these batch co-cultures. Conclusions This study provides a genome-scale description of the metabolic variability regarding by-production among E. coli strains under different conditions and shows how metabolic differences can be used to identify metabolically interacting strain

  19. Express Path Analysis Identifies a Tyrosine Kinase Src-centric Network Regulating Divergent Host Responses to Mycobacterium tuberculosis Infection*

    PubMed Central

    Karim, Ahmad Faisal; Chandra, Pallavi; Chopra, Aanchal; Siddiqui, Zaved; Bhaskar, Ashima; Singh, Amit; Kumar, Dhiraj

    2011-01-01

    Global gene expression profiling has emerged as a major tool in understanding complex response patterns of biological systems to perturbations. However, a lack of unbiased analytical approaches has restricted the utility of complex microarray data to gain novel system level insights. Here we report a strategy, express path analysis (EPA), that helps to establish various pathways differentially recruited to achieve specific cellular responses under contrasting environmental conditions in an unbiased manner. The analysis superimposes differentially regulated genes between contrasting environments onto the network of functional protein associations followed by a series of iterative enrichments and network analysis. To test the utility of the approach, we infected THP1 macrophage cells with a virulent Mycobacterium tuberculosis strain (H37Rv) or the attenuated non-virulent strain H37Ra as contrasting perturbations and generated the temporal global expression profiles. EPA of the results provided details of response-specific and time-dependent host molecular network perturbations. Further analysis identified tyrosine kinase Src as the major regulatory hub discriminating the responses between wild-type and attenuated Mtb infection. We were then able to verify this novel role of Src experimentally and show that Src executes its role through regulating two vital antimicrobial processes of the host cells (i.e. autophagy and acidification of phagolysosome). These results bear significant potential for developing novel anti-tuberculosis therapy. We propose that EPA could prove extremely useful in understanding complex cellular responses for a variety of perturbations, including pathogenic infections. PMID:21953458

  20. 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

  1. 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

  2. Genetic differences between blight-causing Erwinia species with differing host specificities, identified by suppression subtractive hybridization.

    PubMed

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

    2006-11-01

    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.

  3. 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

  4. 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.

  5. Exploring perceptions of community health policy in Kenya and identifying implications for policy change

    PubMed Central

    McCollum, Rosalind; Otiso, Lilian; Mireku, Maryline; Theobald, Sally; de Koning, Korrie; Hussein, Salim; Taegtmeyer, Miriam

    2016-01-01

    Background: Global interest and investment in close-to-community health services is increasing. Kenya is currently revising its community health strategy (CHS) alongside political devolution, which will result in revisioning of responsibility for local services. This article aims to explore drivers of policy change from key informant perspectives and to study perceptions of current community health services from community and sub-county levels, including perceptions of what is and what is not working well. It highlights implications for managing policy change. Methods: We conducted 40 in-depth interviews and 10 focus group discussions with a range of participants to capture plural perspectives, including those who will influence or be influenced by CHS policy change in Kenya (policymakers, sub-county health management teams, facility managers, community health extension worker (CHEW), community health workers (CHWs), clients and community members) in two purposively selected counties: Nairobi and Kitui. Qualitative data were digitally recorded, transcribed, translated and coded before framework analysis. Results: There is widespread community appreciation for the existing strategy. High attrition, lack of accountability for voluntary CHWs and lack of funds to pay CHW salaries, combined with high CHEW workload were seen as main drivers for strategy change. Areas for change identified include: lack of clear supervisory structure including provision of adequate travel resources, current uneven coverage and equity of community health services, limited community knowledge about the strategy revision and demand for home-based HIV testing and counselling. Conclusion: This in-depth analysis which captures multiple perspectives results in robust recommendations for strategy revision informed by the Five Wonders of Change Framework. These recommendations point towards a more people-centred health system for improved equity and effectiveness and indicate priority

  6. 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.

  7. 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.

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

    ERIC Educational Resources Information Center

    Brock, Kishia R.

    2014-01-01

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

  9. 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…

  10. The impact of refugees on the health status and health services of host communities: Compounding bad with worse?

    PubMed

    Dick, B

    1985-12-01

    Although there have been a number of recent developments in our understanding of refugee health problems that have influenced policies and action, the effects of refugees on the health status and services of host communities remain relatively neglected. This article sets out to explain why this is an important issue with implications for policy, planning surveillance and evaluation, training and research. The first sections outline some of the problems facing host governments and communities in Africa and discuss the changing rhetoric between the first and second International Conferences for Assistance to Refugees in Africa. A number of possible ways in which refugees could affect the individual, agent and environmental causes of disease are considered, as are the characteristics of the refugees, the host communities and the response which may all modify this impact. Policy implications of the impact of the refugees, both negative and positive, are discussed, and detailed consideration is given to the pros and cons of integrated and parallel approaches to health care provision. The need to monitor carefully the health status and services of host communities is emphasized and recommendations are made for this and other essential developments relating to training and research.

  11. 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...

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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...

  4. 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

  5. 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.

  6. 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

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

    PubMed Central

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

    2016-01-01

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

  8. [Identifying and solving drug-related problems in terms of the community pharmacist].

    PubMed

    Masaryková, Lucia; Fulmeková, Magdaléna; Lehocká, Lubica; Fazekaš, Tomáš

    2014-02-01

    The issue of drug related problems (DRPs) has been known and dealt with in many studies for a long time. It is primarily due to the fact that drug-related problems have the potential to increase patients morbidity and mortality in particular. The issue of identifying and solving drug-related problems in the area of pharmacotherapy by community pharmacists in the Slovak Republic, unlike in other European countries such as the Netherlands and the United Kingdom, is still at the beginning and gradually developing. The aim of the survey was to obtain information from pharmacy practice concerning the current state and possible solutions of potential risks of medicines in the form of drug-related problems of patients from community pharmacists point of view as well as to find out the role and status of community pharmacists in identifying and solving drug-related problems. A questionnaire survey using a sample of 237 respondents, its statistical processing and evaluation revealed the drug-related problems frequency met at their patients (the most common types of DRPs, their causes and subsequent intervention), as well as the opinions of community pharmacists on their current possibilities of (legislative, material, personnel, time) solving and risk-rating therapies for patients.

  9. Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient

    PubMed Central

    Gosling, Paul; Mead, Andrew; Proctor, Maude; Hammond, John P; Bending, Gary D

    2013-01-01

    High soil phosphorus (P) concentration is frequently shown to reduce root colonization by arbuscular mycorrhizal (AM) fungi, but the influence of P on the diversity of colonizing AM fungi is uncertain. We used terminal restriction fragment length polymorphism (T-RFLP) of 18S rDNA and cloning to assess diversity of AM fungi colonizing maize (Zea mays), soybean (Glycene max) and field violet (Viola arvensis) at three time points in one season along a P gradient of 10–280 mg l−1 in the field. Percentage AM colonization changed between sampling time points but was not reduced by high soil P except in maize. There was no significant difference in AM diversity between sampling time points. Diversity was reduced at concentrations of P > 25 mg l−1, particularly in maize and soybean. Both cloning and T-RFLP indicated differences between AM communities in the different host species. Host species was more important than soil P in determining the AM community, except at the highest P concentration. Our results show that the impact of soil P on the diversity of AM fungi colonizing plants was broadly similar, despite the fact that different plants contained different communities. However, subtle differences in the response of the AM community in each host were evident. PMID:23421495

  10. 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

  11. 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

  12. 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

  13. 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

  14. Analyzing the Role of Community and Individual Factors in Food Insecurity: Identifying Diverse Barriers Across Clustered Community Members.

    PubMed

    Jablonski, Becca B R; McFadden, Dawn Thilmany; Colpaart, Ashley

    2016-10-01

    This paper uses the results from a community food security assessment survey of 684 residents and three focus groups in Pueblo County, Colorado to examine the question: what community and individual factors contribute to or alleviate food insecurity, and are these factors consistent throughout a sub-county population. Importantly, we use a technique called cluster analysis to endogenously determine the key factors pertinent to food access and fruit and vegetable consumption. Our results show significant heterogeneity among sub-population clusters in terms of the community and individual factors that would make it easier to get access to fruits and vegetables. We find two distinct clusters of food insecure populations: the first was significantly less likely to identify increased access to fruits and vegetables proximate to where they live or work as a way to improve their household's healthy food consumption despite being significantly less likely to utilize a personal vehicle to get to the store; the second group did not report significant challenges with access, rather with affordability. We conclude that though interventions focused on improving the local food retail environment may be important for some subsamples of the food insecure population, it is unclear that proximity to a store with healthy food will support enhanced food security for all. We recommend that future research recognizes that determinants of food insecurity may vary within county or zip code level regions, and that multiple interventions that target sub-population clusters may elicit better improvements in access to and consumption of fruits and vegetables.

  15. Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem.

    PubMed

    Guo, Xiaohong; Gong, Jun

    2014-02-01

    Arbuscular mycorrhizal fungi (AMF) were investigated in roots of 18 host plant species in a salinized south coastal plain of Laizhou Bay, China. From 18 clone libraries of 18S rRNA genes, all of the 22 AMF phylotypes were identified into Glomus, of which 18 and 4 were classified in group A and B in the phylogenetic tree, respectively. The phylotypes related to morphologically defined Glomus species occurred generally in soil with higher salinity. AMF phylotype richness, Shannon index, and evenness were not significantly different between root samples from halophytes vs. non-halophytes, invades vs. natives, or annuals vs. perennials. However, AMF diversity estimates frequently differed along the saline gradient or among locations, but not among pH gradients. Moreover, UniFrac tests showed that both plant traits (salt tolerance, life style or origin) and abiotic factors (salinity, pH, or location) significantly affected the community composition of AMF colonizers. Redundancy and variation partitioning analyses revealed that soil salinity and pH, which respectively explained 6.9 and 4.2 % of the variation, were the most influential abiotic variables in shaping the AMF community structure. The presented data indicate that salt tolerance, life style, and origin traits of host species may not significantly affect the AMF diversity in roots, but do influence the community composition in this salinized ecosystem. The findings also highlight the importance of soil salinity and pH in driving the distribution of AMF in plant and soil systems.

  16. Same host-plant, different sterols: variation in sterol metabolism in an insect herbivore community.

    PubMed

    Janson, Eric M; Grebenok, Robert J; Behmer, Spencer T; Abbot, Patrick

    2009-11-01

    Insects lack the ability to synthesize sterols de novo, which are required as cell membrane inserts and as precursors for steroid hormones. Herbivorous insects typically utilize cholesterol as their primary sterol. However, plants rarely contain cholesterol, and herbivorous insects must, therefore, produce cholesterol by metabolizing plant sterols. Previous studies have shown that insects generally display diversity in phytosterol metabolism. Despite the biological importance of sterols, there has been no investigation of their metabolism in a naturally occurring herbivorous insect community. Therefore, we determined the neutral sterol profile of Solidago altissima L., six taxonomically and ecologically diverse herbivorous insect associates, and the fungal symbiont of one herbivore. Our results demonstrated that S. altissima contained Delta(7)-sterols (spinasterol, 22-dihydrospinasterol, avenasterol, and 24-epifungisterol), and that 85% of the sterol pool existed in a conjugated form. Despite feeding on a shared host plant, we observed significant variation among herbivores in terms of their qualitative tissue sterol profiles and significant variation in the cholesterol content. Cholesterol was absent in two dipteran gall-formers and present at extremely low levels in a beetle. Cholesterol content was highly variable in three hemipteran phloem feeders; even species of the same genus showed substantial differences in their cholesterol contents. The fungal ectosymbiont of a dipteran gall former contained primarily ergosterol and two ergosterol precursors. The larvae and pupae of the symbiotic gall-former lacked phytosterols, phytosterol metabolites, or cholesterol, instead containing an ergosterol metabolite in addition to unmetabolized ergosterol and erogsterol precursors, thus demonstrating the crucial role that a fungal symbiont plays in their nutritional ecology. These data are discussed in the context of sterol physiology and metabolism in insects, and the

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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.

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

    PubMed Central

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

    2016-01-01

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

  3. 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…

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

    PubMed Central

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

    2016-01-01

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

  5. 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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Montanari, Alberto

    2010-05-01

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

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

    ERIC Educational Resources Information Center

    Bronfman, B. H.

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

  9. Disentangling vector-borne transmission networks: a universal DNA barcoding method to identify vertebrate hosts from arthropod bloodmeals.

    PubMed

    Alcaide, Miguel; Rico, Ciro; Ruiz, Santiago; Soriguer, Ramón; Muñoz, Joaquín; Figuerola, Jordi

    2009-01-01

    Emerging infectious diseases represent a challenge for global economies and public health. About one fourth of the last pandemics have been originated by the spread of vector-borne pathogens. In this sense, the advent of modern molecular techniques has enhanced our capabilities to understand vector-host interactions and disease ecology. However, host identification protocols have poorly profited of international DNA barcoding initiatives and/or have focused exclusively on a limited array of vector species. Therefore, ascertaining the potential afforded by DNA barcoding tools in other vector-host systems of human and veterinary importance would represent a major advance in tracking pathogen life cycles and hosts. Here, we show the applicability of a novel and efficient molecular method for the identification of the vertebrate host's DNA contained in the midgut of blood-feeding arthropods. To this end, we designed a eukaryote-universal forward primer and a vertebrate-specific reverse primer to selectively amplify 758 base pairs (bp) of the vertebrate mitochondrial Cytochrome c Oxidase Subunit I (COI) gene. Our method was validated using both extensive sequence surveys from the public domain and Polymerase Chain Reaction (PCR) experiments carried out over specimens from different Classes of vertebrates (Mammalia, Aves, Reptilia and Amphibia) and invertebrate ectoparasites (Arachnida and Insecta). The analysis of mosquito, culicoid, phlebotomie, sucking bugs, and tick bloodmeals revealed up to 40 vertebrate hosts, including 23 avian, 16 mammalian and one reptilian species. Importantly, the inspection and analysis of direct sequencing electropherograms also assisted the resolving of mixed bloodmeals. We therefore provide a universal and high-throughput diagnostic tool for the study of the ecology of haematophagous invertebrates in relation to their vertebrate hosts. Such information is crucial to support the efficient management of initiatives aimed at reducing

  10. 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

  11. 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

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

    PubMed

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

    2016-01-01

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

  13. 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

  14. 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

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

    PubMed

    Weimer, P J; Stevenson, D M; Mantovani, H C; Man, S L C

    2010-12-01

    The purpose of this study was to examine the stability and host specificity of a cow's ruminal bacterial community following massive challenge with ruminal microflora from another cow. In each of 2 experiments, 1 pair of cows was selected on the basis of differences in ruminal bacterial community composition (BCC), determined by automated ribosomal intergenic spacer analysis (ARISA), a culture-independent "community fingerprinting" technique. Each pair of cows was then subjected to a 1-time exchange of >95% of ruminal contents without changing the composition of a corn silage/alfalfa haylage-based TMR. In experiment 1, the 2 cows differed (P<0.01) in prefeed ruminal pH (mean = 6.88 vs. 6.14) and prefeed total VFA concentration (mean = 57 vs. 77 mM), averaged over 3 d. Following exchange of ruminal contents, ruminal pH and total VFA concentration in both cows returned to their preexchange values within 24h. Ruminal BCC also returned to near its original profile, but this change required 14 d for 1 cow and 61 d for the other cow. In experiment 2, the 2 other cows differed in prefeed ruminal pH (mean = 6.69 vs. 6.20) and total VFA concentration (mean = 101 vs. 136 mM). Following exchange of ruminal contents, the first cow returned to its preexchange pH and VFA values within 24h; the second cow's rumen rapidly stabilized to a higher prefeed pH (mean = 6.47) and lower prefeed VFA concentration (mean = 120 mM) that was retained over the 62-d test period. Both cows reached somewhat different BCC than before the exchange. However, the BCC of both cows remained distinct and were ultimately more similar to that of the preexchange BCC than of the donor animal BCC. The data indicate that the host animal can quickly reestablish its characteristic ruminal pH and VFA concentration despite dramatic perturbation of its ruminal microbial community. The data also suggest that ruminal BCC displays substantial host specificity that can reestablish itself with varying success when

  16. 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

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

    PubMed Central

    Messier, Christian; Kembel, Steven W.

    2016-01-01

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

  18. 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

  19. 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...

  20. 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.

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

    SciTech Connect

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

    2015-04-23

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

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

    DOE PAGES

    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

  3. 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

  4. 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

  5. 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

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

    PubMed Central

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

    2012-01-01

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

  7. 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

  8. 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.

  9. 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.

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

    ERIC Educational Resources Information Center

    Orum, Anthony M.

    2005-01-01

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

  12. 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

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  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.

  16. 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

  17. 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

  18. Tritrophic interactions at a community level: effects of host plant species quality on bird predation of caterpillars.

    PubMed

    Singer, Michael S; Farkas, Timothy E; Skorik, Christian M; Mooney, Kailen A

    2012-03-01

    Effects of plant traits on herbivore-carnivore interactions are well documented in component communities but are not well understood at the level of large, complex communities. We report on a 2-year field experiment testing mechanisms by which variation in food quality among eight temperate forest tree species alters avian suppression of an assemblage of dietary generalist caterpillars. Plant quality and bird effects varied dramatically among tree species; high-quality plants yielded herbivores of 50% greater mass than those on low-quality plants, and bird effects ranged from near 0% to 97% reductions in caterpillar density. We also find evidence for two mechanisms linking host plant quality to bird effects. If caterpillar density was statistically controlled for, birds had relatively strong effects on the herbivores of low-quality plants, as predicted by the slow-growth/high-mortality hypothesis. At the same time, caterpillar density increased with plant quality, and bird effects were density dependent. Consequently, the net effect of birds was strongest on the herbivores of high-quality plants, a dynamic we call the high-performance/high-mortality hypothesis. Host plant quality thus changes highly generalized herbivore-carnivore interactions by two complementary but opposing mechanisms. These results highlight the interrelatedness of plant-herbivore and herbivore-carnivore interactions and thus the importance of a tritrophic perspective.

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

    PubMed

    Smith, R Scott

    2008-12-01

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

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

    PubMed

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

    2015-09-01

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

  1. 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

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

    PubMed

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

    2015-09-01

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

  3. 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 ...

  4. 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.

  5. 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

  6. 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

  7. 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…

  8. 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,…

  9. 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

  10. 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

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

    PubMed

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

    2015-01-01

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

  12. [A system of indicators for identifying the specific healthcare needs of communities by large health departments].

    PubMed

    Ciaralli, Fabrizio; D'Ascanio, Italo; Saffioti, Concetto; Spunticchia, Giorgio; Perria, Carla; Vicario, Gianni; Zega, Maurizio; Panà, Augusto

    2012-01-01

    Clinical governance of healthcare and community services by healthcare organizations requires the use of validated tools for identifying the specific healthcare needs of the local population. The population served by a local health organization may be large and although data regarding this population as a whole is useful for a preliminary evaluation, it may be too generic for an accurate estimation of the healthcare needs at the district level since different districts may face different challenges and have profoundly different realities. In this context, it can be strategically useful to use a system of indicators targeted at districts, the latter regarded as the basic unit of the health care system and characterized by a relatively constant structure and size.A set of district indicators has been developed and adopted by a local health authority in Rome (Italy) "ASL Roma B", as part of a collaborative project with the Public Health Agency of the Lazio region. In this paper, we present the main results of the first four years of implementation of the system (from 2007 to 2010).The data shows that even within a metropolitan health organization serving an apparently homogeneous population, health needs, provision of services and outcomes may vary greatly between different districts suggesting the adoption of diverse operational strategies. PMID:23064091

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

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

    PubMed

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

    2014-10-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. 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.

  4. 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.

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

    PubMed

    George-Nascimento, Mario; Oliva, Marcelo

    2015-01-01

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

  6. 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

  7. 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.

  8. 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.

  9. Using AlphaScreen(®) to Identify Small-Molecule Inhibitors Targeting a Conserved Host-Pathogen Interaction.

    PubMed

    Austin, Sisley; Taouji, Saïd; Chevet, Eric; Wodrich, Harald; Rayne, Fabienne

    2016-01-01

    AlphaScreen(®) is a technology particularly suitable for bi-molecular inhibitor screening assays, e.g. using protein-protein interactions with purified recombinant proteins. Each binding partner of the bi-molecular interaction is coupled either to donor or to acceptor beads. The technology is based on the quantifiable transfer of oxygen singlets from donor to acceptor microbeads brought together by a specific interaction between the partners. We identified the conserved interaction between WW domains of cellular ubiquitin ligases of the Nedd4 family and a short peptide motif (PPxY) present in several structural and non-structural viral proteins as a potential drug target. Using an AlphaScreen assay recapitulating the interaction between Nedd4.2 and the PPxY motif of the adenoviral capsid protein VI, we screened a library of small molecules and identified specific inhibitors of this interaction. PMID:27613056

  10. 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

  11. 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.

  12. 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…

  13. 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…

  14. 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…

  15. 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…

  16. 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…

  17. 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 ...

  18. 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

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

    PubMed

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

    2011-07-01

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

  20. 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.

  1. 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.

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

    PubMed Central

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

    2016-01-01

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

  3. Anthelmintic treatment alters the parasite community in a wild mouse host

    PubMed Central

    Pedersen, Amy B.; Antonovics, Janis

    2013-01-01

    Individuals are often co-infected with several parasite species, yet the consequences of drug treatment on the dynamics of parasite communities in wild populations have rarely been measured. Here, we experimentally reduced nematode infection in a wild mouse population and measured the effects on other non-target parasites. A single oral dose of the anthelmintic, ivermectin, significantly reduced nematode infection, but resulted in a reciprocal increase in other gastrointestinal parasites, specifically coccidial protozoans and cestodes. These results highlight the possibility that drug therapy may have unintended consequences for non-target parasites and that host–parasite dynamics cannot always be fully understood in the framework of single host–parasite interactions. PMID:23658004

  4. 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

    2016-08-31

    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.

  5. 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

  6. 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.

  7. 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…

  8. Word Frequency and Content Analysis Approach to Identify Demand Patterns in a Virtual Community of Carriers of Hepatitis C

    PubMed Central

    Carvalho, Darlinton; Lucena, Carlos

    2013-01-01

    Background Orkut, a Brazilian virtual social network, is responsible for popularization of the Internet among people of low income and educational level. It’s observed that rapid growth of virtual communities can be reached by low cost Internet access in community local area network houses. Orkut poses an important social resource for Brazilian patients with chronic conditions like hepatitis C virus (HCV) carriers, who face several obstacles in adapting to everyday difficulties. Objective Identify Patterns of Recurring Demands (PRD) expressed in messages posted by members of virtual communities dedicated to HCV carriers. Methods Pre-selection: we identified terms commonly associated to HCV on generic Internet searches (primary Keywords - Kps); Kps were used to identify the most representative HCV communities in a virtual community site (Orkut); all messages published along 8 years on all topics of the community were collected and tabulated; the word frequency was used to construct a “word cloud” (graphic representation of the word frequency) on which was applied a content analysis technique. Results The most cited terms expressed: search for information about medications (prescribed and “forbidden”); emphasis on counting time, which were interpreted as surviving expectations; frequent mention of God, doctors, and “husbands” (female carriers were 68%). These elements provided material for further research – they will be useful in the construction of categories in discourse analysis. Conclusions The present work is a disclosure of preliminary findings considered original and promising. The word frequency/content analysis approach expressed needs of social support and material assistance that may provide subsidies for further qualitative approach and public health policies aimed to HCV carriers. The study of PRD by word frequency may be useful in identifying demands underestimated by other means. PMID:23827772

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. Immigrant community leaders identify four dimensions of trust for culturally appropriate diabetes education and care.

    PubMed

    Dahal, Govinda; Qayyum, Adnan; Ferreyra, Mariella; Kassim, Hussein; Pottie, Kevin

    2014-10-01

    This paper explores immigrant community leaders' perspectives on culturally appropriate diabetes education and care. We conducted exploratory workshops followed by focus groups with Punjabi, Nepali, Somali, and Latin American immigrant communities in Ottawa, Ontario. We used the constant comparative method of grounded theory to explore issues of trust and its impact on access and effectiveness of care. Detailed inquiry revealed the cross cutting theme of trust at the "entry" level and in relation to "accuracy" of diabetes information, as well as the influence of trust on personal "privacy" and on the "uptake" of recommendations. These four dimensions of trust stood out among immigrant community leaders: entry level, accuracy level, privacy level, and intervention level and were considered important attributes of culturally appropriate diabetes education and care. These dimensions of trust may promote trust at the patient-practitioner level and also may help build trust in the health care system.

  17. Adaptation of a community-based participatory research model to gain community input on identifying indicators of successful parenting.

    PubMed

    Zlotnick, Cheryl; Wright, Marguerite; Sanchez, Roberto Macias; Kusnir, Rosario Murga; Te'o-Bennett, Iemaima

    2010-01-01

    Parenting models are generally based on families in stable homes, rather than in transitional situations such as in foster care, homeless shelters, and other temporary, at-risk residences. Consequently, these models do not recognize the unique challenges of families in transition. This study explored the domains of the Circumplex Model and examined its fit for transitional families using tenets from community-based participatory research. Findings suggest that in addition to the Circumplex Model's components, caregivers with children living in transition believe that managing the scrutiny of external authority systems and countering the negative influences of poverty and racism are two indicators that contribute to parenting success. Obtaining consumer-informed views of parenting not only is an important contributor to standards of practice, but also a promising avenue for future research.

  18. 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.…

  19. 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…

  20. 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…

  1. 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…

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

    PubMed

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

    2006-02-01

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

  3. 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…

  4. 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.

  5. 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…

  6. 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.

  7. Spatial and temporal structuring of arbuscular mycorrhizal communities is differentially influenced by abiotic factors and host crop in a semi-arid prairie agroecosystem.

    PubMed

    Bainard, Luke D; Bainard, Jillian D; Hamel, Chantal; Gan, Yantai

    2014-05-01

    Agroecosystems are dynamic systems that experience frequent chemical inputs and changes in plant cover. The objective of this study was to test whether abiotic (soil chemical properties and climate) and biotic (plant host identity) factors influence the spatial and temporal structuring of arbuscular mycorrhizal fungal (AMF) communities in a semi-arid prairie agroecosystem. 454 GS FLX+ high-throughput sequencing technology was successfully utilized to characterize the AMF communities based on long reads (mean length: 751.7 bp) and generated high-resolution data with excellent taxonomic coverage. The composition of the AMF community colonizing roots of the three crops (pea, lentil, and wheat) significantly differed, but plant host identity had a minimal effect on the composition of the AMF community in the soil. We observed a temporal shift in the composition of AMF communities in the roots and surrounding soil of the crops during the growing season. This temporal shift was particularly evident in the root-associated AMF community and was correlated with soil phosphate flux and climatic variables. In contrast, the spatial structuring of the AMF community in the site was correlated with soil pH and electrical conductivity. Individual AMF taxa were significantly correlated with pH, electrical conductivity, and phosphate flux, and these relationships were phylogenetically conserved at the genus level within the Glomeromycota.

  8. 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.

  9. 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

  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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. Response of a gall wasp community to genetic variation in the host plant Quercus crispula: a test using half-sib families

    NASA Astrophysics Data System (ADS)

    Ito, Masato; Ozaki, Kenichi

    2005-02-01

    The structure of a herbivore community may change consistently along the genetic cline of a host plant, change at particular points along the cline, or respond independently of the cline. To reveal such relationships between a gall wasp community and genetic variation in the host plant Quercus crispula, we examined patterns in the species richness and abundance of gall wasps along a genetic cline of the host plant, using 12 half-sib families from six different regions. The genetic relationships among the half-sib families of Q. crispula were quantified on the basis of leaf morphology, which represented a morphological cline from leaves typical of Q. crispula to leaves resembling another oak species, Q. dentata. The morphological cline could be regarded as a genetic cline caused by a history of hybridization with Q. dentata. The mean numbers of gall types varied among the half-sib families, but did not show a consistent increase or decrease along the genetic cline. This pattern could be explained by the fact that responses to host plant variation differed among the gall wasp species. The half-sib families were classified into three groups based on an ordination analysis of the species composition of the gall wasp community that to some extent also reflected the genetic cline of Q. crispula. This suggests that the species composition of gall wasps changed intermittently along the genetic cline, rather than gradually and consistently along the cline.

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

    PubMed

    Nissinen, Riitta M; Männistö, Minna K; van Elsas, Jan Dirk

    2012-11-01

    Endophytic bacteria inhabit internal plant tissues, and have been isolated from a large diversity of plants, where they form nonpathogenic relationships with their hosts. This study combines molecular and culture-dependent approaches to characterize endophytic bacterial communities of three arcto-alpine plant species (Oxyria digyna, Diapensia lapponica and Juncus trifidus) sampled in the low Arctic (69°03'N). Analyses of a 325 bacterial endophyte isolates, as well as seven clone libraries, revealed a high diversity. In particular, members of the Actinobacteria, Bacteroidetes, Firmicutes, Acidobacteria, and Proteobacteria were found. The compositions of the endophytic bacterial communities were dependent on host-plant species as well as on snow cover at sampling sites. Several bacterial genera were found to be associated tightly with specific host-plant species. In particular, Sphingomonas spp. were characteristic for D. lapponica and O. digyna, and their phylogenetic grouping corresponded to the host plant. Most of the endophyte isolates grew well and retained activity at +4 °C, and isolate as well as clone library sequences were often highly similar to sequences from bacteria from cold environments. Taken together, this study shows that arctic plants harbour a diverse community of bacterial endophytes, a portion of which seems to be tightly associated with specific plant species.

  20. Urbanization breaks up host-parasite interactions: a case study on parasite community ecology of rufous-bellied thrushes (Turdus rufiventris) along a rural-urban gradient.

    PubMed

    Calegaro-Marques, Cláudia; Amato, Suzana B

    2014-01-01

    Urbanization drastically alters natural ecosystems and the structure of their plant and animal communities. Whereas some species cope successfully with these environmental changes, others may go extinct. In the case of parasite communities, the expansion of urban areas has a critical effect by changing the availability of suitable substrates for the eggs or free-larval stages of those species with direct life cycles or for the range of hosts of those species with complex cycles. In this study we investigated the influence of the degree of urbanization and environmental heterogeneity on helminth richness, abundance and community structure of rufous-bellied thrushes (Turdus rufiventris) along a rural-urban gradient in the metropolitan region of Porto Alegre, State of Rio Grande do Sul, Brazil. This common native bird species of southern Brazil hosts 15 endoparasite species at the study region. A total of 144 thrushes were collected with mist nets at 11 sites. The degree of urbanization and environmental heterogeneity were estimated by quantifying five landscape elements: buildings, woodlands, fields, bare lands, and water. Landscape analyses were performed at two spatial scales (10 and 100 ha) taking into account home range size and the potential dispersal distance of thrushes and their prey (intermediate hosts). Mean parasite richness showed an inverse relationship with the degree of urbanization, but a positive relationship with environmental heterogeneity. Changes in the structure of component communities along the rural-urban gradient resulted from responses to the availability of particular landscape elements that are compatible with the parasites' life cycles. We found that the replacement of natural environments with buildings breaks up host-parasite interactions, whereas a higher environmental (substrate) diversity allows the survival of a wider range of intermediate hosts and vectors and their associated parasites.

  1. Urbanization Breaks Up Host-Parasite Interactions: A Case Study on Parasite Community Ecology of Rufous-Bellied Thrushes (Turdus rufiventris) along a Rural-Urban Gradient

    PubMed Central

    Calegaro-Marques, Cláudia; Amato, Suzana B.

    2014-01-01

    Urbanization drastically alters natural ecosystems and the structure of their plant and animal communities. Whereas some species cope successfully with these environmental changes, others may go extinct. In the case of parasite communities, the expansion of urban areas has a critical effect by changing the availability of suitable substrates for the eggs or free-larval stages of those species with direct life cycles or for the range of hosts of those species with complex cycles. In this study we investigated the influence of the degree of urbanization and environmental heterogeneity on helminth richness, abundance and community structure of rufous-bellied thrushes (Turdus rufiventris) along a rural-urban gradient in the metropolitan region of Porto Alegre, State of Rio Grande do Sul, Brazil. This common native bird species of southern Brazil hosts 15 endoparasite species at the study region. A total of 144 thrushes were collected with mist nets at 11 sites. The degree of urbanization and environmental heterogeneity were estimated by quantifying five landscape elements: buildings, woodlands, fields, bare lands, and water. Landscape analyses were performed at two spatial scales (10 and 100 ha) taking into account home range size and the potential dispersal distance of thrushes and their prey (intermediate hosts). Mean parasite richness showed an inverse relationship with the degree of urbanization, but a positive relationship with environmental heterogeneity. Changes in the structure of component communities along the rural-urban gradient resulted from responses to the availability of particular landscape elements that are compatible with the parasites' life cycles. We found that the replacement of natural environments with buildings breaks up host-parasite interactions, whereas a higher environmental (substrate) diversity allows the survival of a wider range of intermediate hosts and vectors and their associated parasites. PMID:25068271

  2. 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

  3. Multi-element fingerprinting and high throughput sequencing identify multiple elements that affect fungal communities in Quercus macrocarpa foliage.

    PubMed

    Jumpponen, Ari; Keating, Karen; Gadbury, Gary; Jones, Kenneth L; Mattox, J David

    2010-09-01

    Diverse fungal mutualists, pathogens and saprobes colonize plant leaves. These fungi face a complex environment, in which stochastic dispersal interplays with abiotic and biotic filters. However, identification of the specific factors that drive the community assembly seems unattainable. We mined two broad data sets and identified chemical elements, to which dominant molecular operational taxonomic units (OTUs) in the foliage of a native tree respond most extremely. While many associations could be identified, potential complicating issues emerged. Those were related to unevenly distributed OTU frequency data, a large number of potentially explanatory variables, and the disproportionate effects of outlier observations.

  4. Parasitism rate, parasitoid community composition and host specificity on exposed and semi-concealed caterpillars from a tropical rainforest.

    PubMed

    Hrcek, Jan; Miller, Scott E; Whitfield, James B; Shima, Hiroshi; Novotny, Vojtech

    2013-10-01

    The processes maintaining the enormous diversity of herbivore-parasitoid food webs depend on parasitism rate and parasitoid host specificity. The two parameters have to be evaluated in concert to make conclusions about the importance of parasitoids as natural enemies and guide biological control. We document parasitism rate and host specificity in a highly diverse caterpillar-parasitoid food web encompassing 266 species of lepidopteran hosts and 172 species of hymenopteran or dipteran parasitoids from a lowland tropical forest in Papua New Guinea. We found that semi-concealed hosts (leaf rollers and leaf tiers) represented 84% of all caterpillars, suffered a higher parasitism rate than exposed caterpillars (12 vs. 5%) and their parasitoids were also more host specific. Semi-concealed hosts may therefore be generally more amenable to biological control by parasitoids than exposed ones. Parasitoid host specificity was highest in Braconidae, lower in Diptera: Tachinidae, and, unexpectedly, the lowest in Ichneumonidae. This result challenges the long-standing view of low host specificity in caterpillar-attacking Tachinidae and suggests higher suitability of Braconidae and lower suitability of Ichneumonidae for biological control of caterpillars. Semi-concealed hosts and their parasitoids are the largest, yet understudied component of caterpillar-parasitoid food webs. However, they still remain much closer in parasitism patterns to exposed hosts than to what literature reports on fully concealed leaf miners. Specifically, semi-concealed hosts keep an equally low share of idiobionts (2%) as exposed caterpillars.

  5. 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

  6. 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

  7. Identifying unprotected and potentially at risk plant communities in the western USA

    USGS Publications Warehouse

    Wright, R.G.; Scott, J.M.; Mann, S.; Murray, M.

    2001-01-01

    We analyzed the conservation status of 73 vegetation cover types distributed across a 1.76 million km2 region in 10 states of the western USA. We found that 25 vegetation cover types had at least 10% of their area in nature reserves. These were generally plant communities located at higher elevations and thus more commonly associated with national parks and wilderness areas. All but three of the remaining 48 cover types occurred with sufficient area on publically owned lands in the region to imply that transforming land management intent on these lands could also increase their protection. We also analyzed the level of protection afforded each cover type across its entire geographic distribution in the region. Most cover types that were at least minimally protected in total across the region were also at least minimally protected in most areas of their occurrence. Our results show that there is a realistic opportunity to design a system of biodiversity reserves in this region that represent the full range of environmental conditions in which the various plant communities occur. Conducting this type of broad-scale analysis is a necessary first step in that process and provides a database for others to work from. Published by Elsevier Science Ltd.

  8. Identifying pious and heretical citizens in a permanent supported housing community.

    PubMed

    Wright, Anthony

    2015-01-01

    This article offers an analysis of the impact of recovery-oriented treatment discourses and practices on tenant-staff relationships in the context of the Pinewood Apartments, a Texas-based permanent supported housing community. Drawing on 6 months of ethnographic research and personal experience of working as a caregiver at Pinewood, I demonstrate how tenant-staff relationships were compromised by service providers' negative evaluations of certain tenants in the context of emotionally charged service interactions. These negative evaluations, I argue, stem from deeply held ideas about valuable citizenship that are embedded in the philosophy and practices of recovery, which emphasizes client choice, self-sufficiency, and autonomy. It should be noted, though, that negative evaluations were not necessarily definitive; both tenants and service providers at times exhibited sympathy and forgiveness for each other. PMID:25918775

  9. 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…

  10. 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

  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 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

  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.

  14. 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.

  15. Identifying Risk Factors Associated with Inappropriate Use of Acid Suppressive Therapy at a Community Hospital

    PubMed Central

    Bodukam, Vijay; Saigal, Kirit; Bahl, Jaya; Wang, Yvette; Hanlon, Alexandra; Lu, Yinghui; Davis, Michael

    2016-01-01

    Purpose. By examining the prescribing patterns and inappropriate use of acid suppressive therapy (AST) during hospitalization and at discharge we sought to identify the risk factors associated with such practices. Methods. In this retrospective observational study, inpatient records were reviewed from January 2011 to December 2013. Treatment with AST was considered appropriate if the patient had a known specific indication or met criteria for stress ulcer prophylaxis. Results. In 2011, out of 58 patients who were on AST on admission, 32 were newly started on it and 23 (72%) were inappropriate cases. In 2012, out of 97 patients on AST, 61 were newly started on it and 51 (84%) were inappropriate cases. In 2013, 99 patients were on AST, of which 48 were newly started on it and 36 (75%) were inappropriate cases. 19% of the patients inappropriately started on AST were discharged on it in three years. Younger age, female sex, and 1 or more handoffs between services were significantly associated with increased risk of inappropriate AST. Conclusion. Our findings reflect inappropriate prescription of AST which leads to increase in costs of care and unnecessarily puts the patient at risk for potential adverse events. The results of this study emphasize the importance of examining the patient's need for AST at each level of care especially when the identified risk factors are present.

  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. 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

  18. 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.

  19. 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

  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. Using a service sector segmented approach to identify community stakeholders who can improve access to suicide prevention services for veterans.

    PubMed

    Matthieu, Monica M; Gardiner, Giovanina; Ziegemeier, Ellen; Buxton, Miranda

    2014-04-01

    Veterans in need of social services may access many different community agencies within the public and private sectors. Each of these settings has the potential to be a pipeline for attaining needed health, mental health, and benefits services; however, many service providers lack information on how to conceptualize where Veterans go for services within their local community. This article describes a conceptual framework for outreach that uses a service sector segmented approach. This framework was developed to aid recruitment of a provider-based sample of stakeholders (N = 70) for a study on improving access to the Department of Veterans Affairs and community-based suicide prevention services. Results indicate that although there are statistically significant differences in the percent of Veterans served by the different service sectors (F(9, 55) = 2.71, p = 0.04), exposure to suicidal Veterans and providers' referral behavior is consistent across the sectors. Challenges to using this framework include isolating the appropriate sectors for targeted outreach efforts. The service sector segmented approach holds promise for identifying and referring at-risk Veterans in need of services.

  2. 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

  3. 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

  4. Identifying barriers to healthcare to reduce health disparity in Zuni Indians using focus group conducted by community health workers.

    PubMed

    Shah, Vallabh O; Ghahate, Donica M; Bobelu, Jeanette; Sandy, Phillip; Newman, Sara; Helitzer, Deborah L; Faber, Thomas; Zager, Philip

    2014-02-01

    The Zuni Pueblo is home to an economically disadvantaged population, which faces a public health challenge from the interrelated epidemics of obesity, diabetes and kidney disease. Efforts to decrease the impact of these epidemics have been complicated by historical, economic and cultural barriers, which may limit healthcare utilization. The NIH supported Zuni Health Initiative (ZHI) conducted a study to identify barriers to healthcare in the Zuni Pueblo. Community health representatives (CHRs) led 14 one-hour focus group sessions at which a total of 112 people participated posed unique questions that took into account the Zuni culture to elicit information on perceived barriers to healthcare. Audiotapes were translated and transcribed by bilingual ZHI staff. We reduced the text to thematic categories, constructed a coding dictionary and inserted the text into NVivo 9 program. We identified nine themes emerged regarding the barriers experienced in receiving healthcare and adhering to medical advice. These included distance; transportation; embarrassment; relating to healthcare professionals; navigating the medical system; awareness of available resources; waiting times; adhering to medication; and incentives in health promotion. In conclusion the implementation of culturally appropriate community-based health promotion programs and preventive screening techniques will improve access to healthcare and diminish health disparities.

  5. 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.

  6. 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

  7. West Nile Virus Prevalence across Landscapes Is Mediated by Local Effects of Agriculture on Vector and Host Communities

    PubMed Central

    Crowder, David W.; Dykstra, Elizabeth A.; Brauner, Jo Marie; Duffy, Anne; Reed, Caitlin; Martin, Emily; Peterson, Wade; Carrière, Yves; Dutilleul, Pierre; Owen, Jeb P.

    2013-01-01

    Arthropod-borne viruses (arboviruses) threaten the health of humans, livestock, and wildlife. West Nile virus (WNV), the world’s most widespread arbovirus, invaded the United States in 1999 and rapidly spread across the county. Although the ecology of vectors and hosts are key determinants of WNV prevalence across landscapes, the factors shaping local vector and host populations remain unclear. Here, we used spatially-explicit models to evaluate how three land-use types (orchards, vegetable/forage crops, natural) and two climatic variables (temperature, precipitation) influence the prevalence of WNV infections and vector/host distributions at landscape and local spatial scales. Across landscapes, we show that orchard habitats were associated with greater prevalence of WNV infections in reservoirs (birds) and incidental hosts (horses), while increased precipitation was associated with fewer infections. At local scales, orchard habitats increased the prevalence of WNV infections in vectors (mosquitoes) and the abundance of mosquitoes and two key reservoir species, the American robin and the house sparrow. Thus, orchard habitats benefitted WNV vectors and reservoir hosts locally, creating focal points for the transmission of WNV at landscape scales in the presence of suitable climatic conditions. PMID:23383032

  8. Suicidal ideation: Are refugees more at risk compared to host population? Findings from a preliminary assessment in a refugee community in Nigeria.

    PubMed

    Akinyemi, O O; Atilola, O; Soyannwo, T

    2015-12-01

    Among the serious mental health problems that may be associated with being a refugee is suicidal behavior. This study aimed to assess the prevalence and correlates of suicidal ideation among African refugees in Oru-Ijebu Nigeria. Suicidal ideation was assessed using appropriate section in the Mini-International Neuropsychiatric Interview while the brief version of the WHO Quality of Life was used to assess quality of life as a clinical variable. Study involved 444 refugees and 527 non-refugee member of host community. Result showed that the prevalence of suicidal ideation was significantly higher among the refugees than the non-refugee comparison group (27.3% vs. 17.3%; p<0.001). Social status and quality of life was significantly poorer among the refugees compared with their non-refugee members of same community. Quality of life was the only factor independently associated with suicidal ideations among refugees. In conclusion, the study shows that the prevalence of suicidal ideation is significantly higher among the refugees than the non-refugee members of the host community and calls for innovative ways of extending mental health services to refugees at the study site.

  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. Unraveling the complexity of the zoo community: identifying the variables related to conservation performance in zoological parks.

    PubMed

    Fàbregas, María C; Guillén-Salazar, Federico; Garcés-Narro, Carlos

    2012-01-01

    Zoological parks make up a highly heterogeneous community. Ranging from small collections at shopping malls to highly developed bioparks, their contribution to conservation is expected to vary enormously. Although several studies have focused on assessing such contribution, the parameters used frequently do not apply when considering more modest zoos. The goals of this study are to determine, within the wide range of zoos, which type tend to fulfill the conservation mission of modern zoos and to identify the variables associated to their conservation performance. We used the requirements demanded by the European Community Zoos Directive 1999/22/EC, relating to the keeping of wild animals in zoological parks, to assess conservation performance in 72% of officially registered Spanish zoos. Sampled zoos were classified into groups according to their common characteristics, and then the variables related to how they met each of the Directive's requirements in the groups were assessed. We found that private zoological parks with large zoological collections, located within metropolitan areas, and members of a zoo association tended to fulfill the requirements. Being a member of a zoo association was the variable that better explained fulfillment of the requirements among the evaluated zoos. Data revealed that zoos not meeting any requirement were few, although those meeting all of them were not frequent. The requirement related to adequate record keeping showed the lowest level of fulfillment. We discuss the implications of our results and propose measures of change in order to promote the contribution of zoos to biodiversity conservation.

  11. 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

  12. 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.

  13. 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…

  14. 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…

  15. Species diversity reduces parasite infection through cross-generational effects on host abundance.

    PubMed

    Johnson, Pieter T J; Preston, Daniel L; Hoverman, Jason T; Henderson, Jeremy S; Paull, Sara H; Richgels, Katherine L D; Redmond, Miranda D

    2012-01-01

    With growing interest in the effects of biodiversity on disease, there is a critical need for studies that empirically identify the mechanisms underlying the diversity-disease relationship. Here, we combined wetland surveys of host community structure with mechanistic experiments involving a multi-host parasite to evaluate competing explanations for the dilution effect. Sampling of 320 wetlands in California indicated that snail host communities were strongly nested, with competent hosts for the trematode Ribeiroia ondatrae predominating in low-richness assemblages and unsuitable hosts increasingly present in more diverse communities. Moreover, competent host density was negatively associated with increases in snail species richness. These patterns in host community assembly support a key prerequisite underlying the dilution effect. Results of multigenerational mesocosm experiments designed to mimic field-observed community assemblages allowed us to evaluate the relative importance of host density and diversity in influencing parasite infection success. Increases in snail species richness (from one to four species) had sharply negative effects on the density of infected hosts (-90% reduction). However, this effect was indirect; competition associated with non-host species led to a 95% reduction in host density (susceptible host regulation), owing primarily to a reduction in host reproduction. Among susceptible hosts, there were no differences in infection prevalence as a function of community structure, indicating a lack of support for a direct effect of diversity on infection (encounter reduction). In monospecific conditions, higher initial host densities increased infection among adult hosts; however, compensatory reproduction in the low-density treatments equalized the final number of infected hosts by the next generation, underscoring the relevance of multigenerational studies in understanding the dilution effect. These findings highlight the role of

  16. Dyspepsia in the community: value of a community-based mailed survey to identify potential participants for a randomized clinical trial

    PubMed Central

    Herrick, Linda M.; Locke, G. Richard; Schleck, Cathy D.; Zinsmeister, Alan R.; Treder, Vickie; Talley, Nicholas, J.

    2015-01-01

    Objective To assess the usefulness of a community-based mailed survey to identify participants with functional dyspepsia (FD) for a clinical trial. Material and Methods In 2008, a valid self-report questionnaire of gastrointestinal (GI) symptoms required for diagnosis of FD was mailed to randomly selected cohorts of Olmsted County, Minnesota residents. From survey responses (54%), FD cases and controls were identified. Phone calls were completed in 2010 and 2011 to 54% of respondents offering participation to those meeting criteria. Results Of 937 people identified from the survey, 189 cases and 265 controls were contacted by phone using four questions similar to the written survey resulting in a moderate level of agreement (Kappa 0.43, 95% CI: 0.35 to 0.51; p =0.11). The proportion reporting FD symptoms by survey was 42% while the proportion by phone was 38%. Comparing classification of cases and controls, 118 (62%) survey cases had dyspepsia symptoms on phone screening while 53 (20%) of the survey controls reported FD symptoms. Of 171 who had symptoms, 60 (35%) declined, 33 (19%) were over study age limit, 24 (14%) had inadequate symptom levels, and 36 (21%) had co-morbidities. Of survey respondents contacted, 6 (3%) people were enrolled with 2 screen fails resulting in 4 (1%) randomized. Conclusions Agreement between survey and phone questions was modest. Classifications between case and control changed. People eligible and willing to participate were a fraction of people reporting symptoms. People participating in clinical trials do not broadly represent those in the population. PMID:25761431

  17. 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…

  18. 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 ...

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

    PubMed

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

    2016-10-01

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

  20. 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.

  1. 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

  2. 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

  3. Identifying Temporal Changes and Topics that Promote Growth Within Online Communities: A Prospective Study of Six Online Cancer Forums

    PubMed Central

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

    2011-01-01

    In this paper the authors have extended the methodology for temporal analysis of online forums and applied the methodology to six online cancer forums (melanoma, prostate cancer, testicular cancer, ovarian cancer and breast cancer). The goal was to develop, apply and improve methods that quantify the responsiveness of the interactions in online forums in order to identify the users and topics that promote use and usefulness of these online medical communities. The evolutional stages that gauge when a forum is expanding, contracting, or in a state of equilibrium were considered. The response function was thought to be an approximation of a discussion group’s utility to its members. By applying the evolutionary phase algorithm, it was determined that two out of six of the forums are in contracting phases, while four are in their largest growth phase. By analyzing the topics of the influential threads, the authors conclude that cancer treatment discussions as well as stage IV cancer discussions promote growth in the forums. It is observed that the discussion of treatment rather than diagnosis is important to help a cancer forum thrive. PMID:22022636

  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. An Exploration of Strategic Planning Perspectives and Processes within Community Colleges Identified as Being Distinctive in Their Strategic Planning Practices

    ERIC Educational Resources Information Center

    Augustyniak, Lisa J.

    2015-01-01

    Community college leaders face unprecedented change, and some have begun reexamining their institutional strategic planning processes. Yet, studies in higher education strategic planning spend little time examining how community colleges formulate their strategic plans. This mixed-method qualitative study used an expert sampling method to identify…

  7. 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…

  8. Empowering Youth to Change Their World: Identifying Key Components of a Community Service Program to Promote Positive Development

    ERIC Educational Resources Information Center

    Lakin, Rebecca; Mahoney, Annette

    2006-01-01

    Prior to graduating from high school, the vast majority of youth in the United States will take part in at least one community service activity. Although it is frequently assumed that community service is inherently beneficial to those that take part, the activities and processes of youth service programs tend to be unsystematic and vary widely.…

  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. Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host.

    PubMed

    Hongoh, Yuichi; Deevong, Pinsurang; Inoue, Tetsushi; Moriya, Shigeharu; Trakulnaleamsai, Savitr; Ohkuma, Moriya; Vongkaluang, Charunee; Noparatnaraporn, Napavarn; Kudo, Toshiaki

    2005-11-01

    We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic "termite clusters" comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites. PMID:16269686

  11. Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host.

    PubMed

    Hongoh, Yuichi; Deevong, Pinsurang; Inoue, Tetsushi; Moriya, Shigeharu; Trakulnaleamsai, Savitr; Ohkuma, Moriya; Vongkaluang, Charunee; Noparatnaraporn, Napavarn; Kudo, Toshiaki

    2005-11-01

    We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic "termite clusters" comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.

  12. The invasive spider mite Tetranychus evansi (Acari: Tetranychidae) alters community composition and host-plant use of native relatives.

    PubMed

    Ferragut, Francisco; Garzón-Luque, Eva; Pekas, Apostolos

    2013-07-01

    The tomato spider mite Tetranychus evansi Baker and Pritchard (Acari: Tetranychidae), is a worldwide pest of solanaceous crops that has recently invaded many parts of the world. In the present study we examined the ecological impact of its arrival in the Mediterranean region. The spider mite and phytoseiid mite assemblages in various crop and non-crop plants in three areas of Valencia (Spain) were studied a few months before and 10 years after the invasion of T. evansi. According to rarefaction analyses, the invasion of T. evansi did not affect neither the total number of species in the mite community examined (spider mite and phytoseiid species) nor the number of species when the two communities were examined separately. However, after the invasion, the absolute and relative abundance of the native Tetranychus species was significantly reduced. Before the invasion, T. urticae and T. turkestani were the most abundant spider mites, accounting for 62.9 and 22.8 % of the specimens. After the invasion, T. evansi became the most abundant species, representing 60 % of the total spider mites recorded, whereas the abundance of T. urticae was significantly reduced (23 %). This reduction took place principally on non-crop plants, where native species were replaced by the invader. Null model analyses provided evidence for competition structuring the spider mite community on non-crop plants after the invasion of T. evansi. Resistance to acaricides, the absence of efficient native natural enemies, manipulation of the plant defenses and the web type produced by T. evansi are discussed as possible causes for the competitive displacement.

  13. 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

  14. Global sensitivity analysis of a mathematical model of acute inflammation identifies nonlinear dependence of cumulative tissue damage on host interleukin-6 responses.

    PubMed

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

    2014-10-01

    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 from IL-10 and the activation of positive feedback sustained by IL-6. At high AUCIL6, damage recovery was interestingly restored in some population of simulated animals due to the NO-mediated anti-inflammatory responses. These observations suggest that the host's health status during acute inflammation depends in a nonlinear fashion on the magnitude of the inflammatory stimulus

  15. Effects of host species and life stage on the helminth communities of sympatric northern leopard frogs (Lithobates pipiens) and wood frogs (Lithobates sylvaticus) in the Sheyenne National Grasslands, North Dakota.

    PubMed

    Gustafson, Kyle D; Newman, Robert A; Tkach, Vasyl V

    2013-08-01

    We studied helminth communities in sympatric populations of leopard frogs (Lithobates pipiens) and wood frogs (Lithobates sylvaticus) and assessed the effects of host species and life stage on helminth community composition and helminth species richness. We examined 328 amphibians including 218 northern leopard frogs and 110 wood frogs collected between April and August of 2009 and 2010 in the Sheyenne National Grasslands of southeastern North Dakota. Echinostomatid metacercariae were the most common helminths found, with the highest prevalence in metamorphic wood frogs. Host species significantly influenced helminth community composition, and host life stage significantly influenced the component community composition of leopard frogs. In these sympatric populations, leopard frogs were common hosts for adult trematodes whereas wood frogs exhibited a higher prevalence of nematodes with direct life cycles. Metamorphic frogs were commonly infected with echinostomatid metacercariae and other larval trematodes whereas juvenile and adult frogs were most-frequently infected with directly transmitted nematodes and trophically transmitted trematodes. Accordingly, helminth species richness increased with the developmental life stage of the host.

  16. 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

  17. 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

  18. Both host plant and ecosystem engineer identity influence leaf-tie impacts on the arthropod community of Quercus.

    PubMed

    Wang, H George; Marquis, Robert J; Baer, Christina S

    2012-10-01

    Many insect herbivores build shelters on plants, which are then colonized by other arthropod species. To understand the impacts of such ecosystem engineering on associated species, the contributions of ecosystem engineer and host-plant identities must be understood. We investigated these contingencies at the patch scale using two species of leaf-tying caterpillars, which vary in size and tie construction mode, on eight species of oak (Quercus) trees, which vary in leaf size and leaf chemistry. We created three types of artificial leaf ties by clipping together pairs of adjacent leaves using metal hair clips. We left the first type of leaf tie empty while adding individuals of the leaf-tying caterpillars of either Pseudotelphusa quercinigracella or Psilocorsis cryptolechiella to the other two. We also created a control treatment of untied leaves by affixing clips to single leaves. Leaf ties increased occupancy in the early season and arthropod alpha diversity throughout the experiment, on average fourfold. Furthermore, the presence of leaf ties increased arthropod species density on average three times and abundance 10-35 times, depending on the plant species. The mean phenolic content of the leaves of each oak species was positively correlated with the leaf-tie effect on abundance and negatively correlated with the leaf-tie effect on species diversity. Species diversity, but not abundance, was affected by the identity of the tie-maker. Arthropod species composition differed between untied leaves and artificial leaf ties, and between ties made by the two leaf-tier species. Our results demonstrate that the presence of leaf ties adds to habitat diversity within the oak-herbivore system, not only by creating a new kind of microhabitat (the leaf tie) within trees, but also by exacerbating differences among the eight oak species in apparent habitat quality. The identity of the leaf-tying caterpillar adds to this heterogeneity by creating leaf ties of different size, thus

  19. 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…

  20. 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

  1. Using community-based participatory research to identify potential interventions to overcome barriers to adolescents’ healthy eating and physical activity

    PubMed Central

    Goh, Ying-Ying; Sipple-Asher, Bessie Ko; Uyeda, Kimberly; Hawes-Dawson, Jennifer; Olarita-Dhungana, Josephina; Ryan, Gery W.; Schuster, Mark A.

    2010-01-01

    Using a community-based participatory research approach, we explored adolescent, parent, and community stakeholder perspectives on barriers to healthy eating and physical activity, and intervention ideas to address adolescent obesity. We conducted 14 adolescent focus groups (n = 119), 8 parent focus groups (n = 63), and 28 interviews with community members (i.e., local experts knowledgeable about youth nutrition and physical activity). Participants described ecological and psychosocial barriers in neighborhoods (e.g., lack of accessible nutritious food), in schools (e.g., poor quality of physical education), at home (e.g., sedentary lifestyle), and at the individual level (e.g., lack of nutrition knowledge). Participants proposed interventions such as nutrition classes for families, addition of healthy school food options that appeal to students, and non-competitive physical education activities. Participants supported health education delivered by students. Findings demonstrate that community-based participatory research is useful for revealing potentially feasible interventions that are acceptable to community members. PMID:19544091

  2. 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

  3. Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system.

    PubMed

    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

    2006-09-19

    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 (>10(9) cm(-3)) of microbial cells in sediment pavements above the CO2 lake, decreasing to strikingly low cell numbers (10(7) 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.

  4. The metazoan parasite communities of the Argentinean sandperch Pseudopercis semifasciata (Pisces: Perciformes) and their use to elucidate the stock structure of the host.

    PubMed

    Timi, J T; Lanfranchi, A L

    2009-09-01

    The use of parasites as biological tags allowed the identification of 3 stocks of Argentinean sandperch, Pseudopercis semifasciata (Cuvier), in the Argentine Sea. A total of 100 specimens caught in 3 zones: Villa Gesell (37 degrees 15'S, 57 degrees 23'W; n=20), Miramar (38 degrees 03'S, 57 degrees 30'W-38 degrees 44'S, 58 degrees 44'W; n=30) and Península Valdes (42 degrees 00'-42 degrees 45'S; n=50), were examined and 28 parasite species were found, 15 of them being new host records. Both univariate and multivariate analyses identified discrete stocks in each zone. The observed differences were not related to the host size or sex. Each locality was characterized by its own indicator species. Villa Gesell was typified by unidentified cestode plerocercoids, Corynosoma cetaceum and Hysterothylacium sp., Miramar by Heterosentis sp. and Pseudoterranova sp. and Península Valdes by A. simplex s.l. Fishes from both northern localities shared gnathiid pranizae, Corynosoma australe and Grillotia sp. as indicators, whereas Miramar and Península Valdes shared only Trifur tortuosus. The most distant localities showed no indicator species in common. Discriminant analyses of parasite assemblages agreed with populational comparisons in identifying the same set of biological tags, whereas some differences in the identity of indicator species were obtained by similarity analysis. However, the 3 approaches were congruent in identifying Grillotia sp., C. australe and C. cetaceum as indicators of northern localities, and A. simplex s.l. as related to Patagonian waters. Differences among zones could be enhanced by the sedentary habits, limited dispersal and high site fidelity of P. semifasciata, and their spawning in rocky outcrops, which are isolated environments. PMID:19627631

  5. 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…

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Community.

    ERIC Educational Resources Information Center

    Grauer, Kit, Ed.

    1995-01-01

    Art in context of community is the theme of this newsletter. The theme is introduced in an editorial "Community-Enlarging the Definition" (Kit Grauer). Related articles include: (1) "The Children's Bridge is not Destroyed: Heart in the Middle of the World" (Emil Robert Tanay); (2) "Making Bridges: The Sock Doll Project" (Anami Naths); (3)…

  11. A novel human enterovirus C (EV-C118) identified in two children hospitalised because of acute otitis media and community-acquired pneumonia in Israel.

    PubMed

    Daleno, Cristina; Greenberg, David; Piralla, Antonio; Scala, Alessia; Baldanti, Fausto; Principi, Nicola; Esposito, Susanna

    2013-02-01

    We report the discovery of a novel enterovirus C (EV-C118) identified in two Israeli children hospitalised for acute otitis media and community-acquired pneumonia. The highest pair-wise sequence identity scores with the EV-C109 and EV-C117 reference strains were, respectively, 63.5% and 63.6% nucleotide identity, and 82.5% and 79.9% amino acid identity.

  12. 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

  13. 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.

  14. 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

  15. Microbial metaproteomics: Identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

    SciTech Connect

    Hettich, Robert {Bob} L; Sharma, Ritin; Chourey, Karuna; Giannone, Richard J

    2012-01-01

    The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics - the characterization of the complement of proteins expressed by a microbial community in an environmental sample

  16. 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…

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. Uncertainty Analysis of Runoff Simulations and Parameter Identifiability in the Community Land Model – Evidence from MOPEX Basins

    SciTech Connect

    Huang, Maoyi; Hou, Zhangshuan; Leung, Lai-Yung R.; Ke, Yinghai; Liu, Ying; Fang, Zhufeng; Sun, Yu

    2013-12-01

    With the emergence of earth system models as important tools for understanding and predicting climate change and implications to mitigation and adaptation, it has become increasingly important to assess the fidelity of the land component within earth system models to capture realistic hydrological processes and their response to the changing climate and quantify the associated uncertainties. This study investigates the sensitivity of runoff simulations to major hydrologic parameters in version 4 of the Community Land Model (CLM4) by integrating CLM4 with a stochastic exploratory sensitivity analysis framework at 20 selected watersheds from the Model Parameter Estimation Experiment (MOPEX) spanning a wide range of climate and site conditions. We found that for runoff simulations, the most significant parameters are those related to the subsurface runoff parameterizations. Soil texture related parameters and surface runoff parameters are of secondary significance. Moreover, climate and soil conditions play important roles in the parameter sensitivity. In general, site conditions within water-limited hydrologic regimes and with finer soil texture result in stronger sensitivity of output variables, such as runoff and its surface and subsurface components, to the input parameters in CLM4. This study demonstrated the feasibility of parameter inversion for CLM4 using streamflow observations to improve runoff simulations. By ranking the significance of the input parameters, we showed that the parameter set dimensionality could be reduced for CLM4 parameter calibration under different hydrologic and climatic regimes so that the inverse problem is less ill posed.

  2. 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.

  3. 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.

  4. 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

  5. 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 chicken