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PubMed2026

Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.

BACKGROUND: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean. RESULTS: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses. CONCLUSIONS: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.

Membrane Transport Proteins↗
PubMed2000

[Reduced morbidity of schistosomiasis: report from an expert workshop on the control of schistosomiasis held at CERMES (15-18 February 2000, Niamey, Niger)].

Schistosomiasis remains a problem for public health in sub-Saharan Africa. Despite past efforts, cases have not decreased significantly. Schistosoma haematobium and S. mansoni are endemic in all the West African countries. The distribution of both parasites is focal. During a workshop held at CERMES in Niamey, in February 2000, a group of experts recommended that schistosomiasis control be considered as a public health priority in all the endemic West African countries, and National Control Programmes rapidly implemented. The objective of these control programmes would be to reduce schistosomiasis-related morbidity. Case detection should be based on clinical symptoms such as haematuria or bloody diarrhoea, and be carried out at two levels: health care centres and schools, in order to reach patients and school-age children. Health workers should be trained in case detection and community based control of schistosomiasis. The assembled experts advocated the use of praziquantel dosed at 40 mg.kg-1, which therefore must be made available and accessible in outlying areas. Associated measures consist of sanitation, water supply and health education, especially aimed at improving patients' treatment-seeking behaviour. A West African network for schistosomiasis control was created during the workshop. It runs on the Web site of CERMES as network co-ordinator. (http://www.mpl.ird.fr/cermes/).

Africa South of the Sahara↗
PubMedDate not supplied

Making room in the market-place. 75th annual Catholic Health Assembly.

In a world that is rapidly changing, healthcare stands in the midst of the maelstrom. Yet the one thing that everybody agrees on is the need for more change. The 75th Annual Catholic Health Assembly brought together members of the Catholic healthcare community to reflect on the need to reform the U.S. healthcare system. Together, they examined the problems, the proposals, and the processes for change. At the assembly, marking the 75th anniversary of the founding of CHA, the ministry's leaders reaffirmed their commitment to the founders' values and looked at practical ways to fulfill their mission to serve the poor and most vulnerable among us.

Catholicism↗
PubMed2003

Measuring contextual characteristics for community health.

OBJECTIVE: To conceptualize and measure community contextual influences on population health and health disparities. DATA SOURCES: We use traditional and nontraditional secondary sources of data comprising a comprehensive array of community characteristics. STUDY DESIGN: Using a consultative process, we identify 12 overarching dimensions of contextual characteristics that may affect community health, as well as specific subcomponents relating to each dimension. DATA COLLECTION: An extensive geocoded library of data indicators relating to each dimension and subcomponent for metropolitan areas in the United States is assembled. PRINCIPAL FINDINGS: We describe the development of community contextual health profiles, present the rationale supporting each of the profile dimensions, and provide examples of relevant data sources. CONCLUSIONS: Our conceptual framework for community contextual characteristics, including a specified set of dimensions and components, can provide practical ways to monitor health-related aspects of the economic, social, and physical environments in which people live. We suggest several guiding principles useful for understanding how aspects of contextual characteristics can affect health and health disparities.

Community Health Planning↗
PubMed2026

VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.

MOTIVATION: Metagenomic Hi-C provides in situ proximity signals that can improve genome binning and enable virus-host-association analysis. However, viral genome recovery remains difficult because virus-virus Hi-C contact matrices are extremely sparse. Viral genomes are small, often low-abundance, and frequently assemble into short contigs, leaving many true within-genome links unobserved and causing viral bins to fragment. RESULTS: We present VirBinn, a graph-diffusion framework for viral binning from metagenomic Hi-C. VirBinn enhances virus-virus connectivity through two complementary mechanisms: random-walk-with-restart enhancement on the sparse virus-virus contact graph and host-guided diffusion that propagates viral seeds through the host network to infer indirect virus-virus associations. The enhanced views are integrated and clustered using Leiden community detection to produce viral metagenome-assembled genomes (vMAGs). On dataset-specific simulation benchmarks with ground truth, VirBinn consistently recovers more high-quality vMAGs than Hi-C-based and shotgun-based baselines and substantially increases the number of near-complete genomes. On four real metagenomic Hi-C datasets spanning human gut, pig gut, sheep gut (long-read assembly), and wastewater, VirBinn yields more high-completeness vMAGs under CheckV and produces bins with strong within-cluster contact support. Finally, host linkage analysis using reconstructed host MAGs reveals habitat-specific host-association patterns and plausible host taxonomic profiles. AVAILABILITY AND IMPLEMENTATION: VirBinn is available at https://github.com/dyxstat/VirBinn. The scripts to reproduce the results and figures in this article are available at https://github.com/dyxstat/Reproduce_VirBinn.

Genome, Viral↗
PubMed2005

Comparative metagenomics of microbial communities.

The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.

Animals↗
PubMed1997

What explains rural-urban differentials in child mortality in Brazil?

This paper presents an analysis of differentials in child survival by rural-urban place of residence in Brazil and examines the hypothesis that observed mortality differentials by place of residence are merely manifestations of underlying differences in socioeconomic status and demographic and reproductive behavior. The child mortality data come from the 1986 Demographic and Health Survey of Brazil and supplementary community-level variables are obtained from a database assembled by the Brazilian federal statistical agency. Child mortality rates are substantially and significantly lower in urban areas of Brazil. Our results suggest, however, that the urban advantage does not simply reflect underlying differences in socioeconomic and behavioral characteristics at the individual and household levels; rather, community variables appear to play an independent and important role. We also find that the effects of community characteristics on child survival are moderated by household socioeconomic factors, especially maternal education. Differences in socioeconomic characteristics are therefore important in explaining rural-urban child mortality differentials, but not in the way hypothesized by previous researchers.

Adolescent↗
PubMed1990

Wonderwomen and superman take on AIDS.

Superbarrio is the name given to the folk hero and spokesperson of the Asamblea de Barrios--a democratic assembly of Mexico City's poorer neighborhoods. Dressed like Batman, he is often the central figure in mass demonstrations for better living conditions. Now he is appearing with Superwoman in the Assembly's campaign against AIDS. In February 1990, Superbarrio spoke at the opening of a community AIDS information center, set up and run by women members of the Assembly. A brigade of volunteer educators handed out leaflets and condoms in the surrounding streets and underground stations.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Does private religious activity prolong survival? A six-year follow-up study of 3,851 older adults.

BACKGROUND: Previous studies have linked higher religious attendance and longer survival. In this study, we examine the relationship between survival and private religious activity. METHODS: A probability sample of elderly community-dwelling adults in North Carolina was assembled in 1986 and followed for 6 years. Level of participation in private religious activities such as prayer, meditation, or Bible study was assessed by self-report at baseline, along with a wide variety of sociodemographic and health variables. The main outcome was time (days) to death or censoring. RESULTS: During a median 6.3-year follow-up period, 1,137 subjects (29.5%) died. Those reporting rarely to never participating in private religious activity had an increased relative hazard of dying over more frequent participants, but this hazard did not remain significant for the sample as a whole after adjustment for demographic and health variables. When the sample was divided into activity of daily living (ADL) impaired and unimpaired, the effect did not remain significant for the ADL impaired group after controlling for demographic variables (hazard ratio [RH] 1.11, 95% confidence interval [CI] 0.91-1.35). However, the increased hazard remained significant for the ADL unimpaired group even after controlling for demographic and health variables (RH 1.63, 95% CI 1.20-2.21), and this effect persisted despite controlling for numerous explanatory variables including health practices, social support, and other religious practices (RH 1.47, 95% CI 1.07-2.03). CONCLUSIONS: Older adults who participate in private religious activity before the onset of ADL impairment appear to have a survival advantage over those who do not.

Activities of Daily Living↗
PubMed2025

Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.

Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.

Lakes↗
PubMed1993

Effects of potential aneuploidy inducing agents on microtubule assembly in vitro.

The present study was carried out with the 10 known or suspected spindle poisons of the Commission of the European Communities program to study aneuploidy induction. We have investigated these substances on the assembly of isolated bovine microtubules at 10, 100 and 1000 microM and studied morphology by electron microscopy. The substances could be grouped into two categories, strong and weak inhibitors. Colchicine, vinblastine and thimerosal were strong inhibitors; cadmium chloride, thiabendazole, chloral hydrate, hydroquinone, diazepam and econazole were weak inhibitors, the latter three causing aberrant forms visible on electron microscopy. Pyrimethamine did not inhibit the assembly of microtubules, but produced aberrant forms.

Aneuploidy↗
PubMed2006

Sequence resources at the Candida Genome Database.

The Candida Genome Database (CGD, http://www.candidagenome.org/) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic pathogen Candida albicans. With the recent release of a new assembly of the C.albicans genome, Assembly 20, C.albicans genomics has entered a new era. Although the C.albicans genome assembly continues to undergo refinement, multiple assemblies and gene nomenclatures will remain in widespread use by the research community. CGD has now taken on the responsibility of maintaining the most up-to-date version of the genome sequence by providing the data from this new assembly alongside the data from the previous assemblies, as well as any future corrections and refinements. In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD provides. CGD is freely accessible at http://www.candidagenome.org/ and CGD curators may be contacted by email at candida-curator@genome.stanford.edu.

Candida albicans↗
PubMed2025

A method for authenticating the fidelity of Cryptococcus neoformans knockout collections.

Gene knockout (KO) strain collections are important tools for discovery in microbiology. Cryptococcus neoformans, a human fungal pathogen, has an available genome-wide gene deletion collection that is widely used by the research community. We uncovered mix-ups in the assembly of the commercially available C. neoformans deletion collection of ~4,700 unique strains acquired by our laboratory. Evidence supporting a mix-up includes RNAseq analysis that identified transcripts for the gene listed as the KO. The mystery was soon solved as this same KO strain lacked RNA transcripts for a different KO strain gene found in the same plate position in an earlier partial KO collection, suggesting a plate swap between two KO collections. Therefore, we developed a quick PCR assay to distinguish the two KO collections based on the size differences between their nourseothricin (NAT)-resistance cassettes, confirmed by genome sequencing. Here, we report that nine of the first 15 plates of the 42-plate our KN99ɑ KO collection had been replaced with the corresponding plates from an earlier partial KO collection. We provide additional evidence that the remaining plates are correct, and the simple authentication method presented here serves as a quick check to identify similar mix-ups in the KO collections.IMPORTANCEGene KO strain collections are important tools for discovery in microbiology. The human fungal pathogen Cryptococcus neoformans has an available genome-wide deletion collection that is widely used by the research community. Here, we report that our KN99ɑ collection is comprised of mixed plates from two independent KO libraries and present a simple authentication method that other investigators can use to distinguish the identities of these KO collections. Above all, this article serves as a reminder to users of the 2015 KO library collection to screen the plates before undertaking large phenotyping experiments.

Cryptococcus neoformans↗
PubMedDate not supplied

Building relationships and resilience in the prevention of youth violence.

Self Enhancement, Inc., is a grassroots, community-service organization working in the most disadvantaged high-risk community in Portland, Oregon. Its violence-prevention program targets middle-school and high-school students by providing classroom and community activities to these young people. These activities are designed to enhance protective factors and build resilience in youths to enable them to attain healthy and productive lives and to resist the threats of gangs, violence, and drugs. RMC Research Corporation works in partnership with Self Enhancement, Inc., to conduct research and evaluation on the effectiveness of its programs. The Self Enhancement, Inc., program works primarily at the individual student and interpersonal relationship levels. Resilience Theory and its culturally specific Relationship Model drive the formulation of specific strategies and activities. Program staff mentor each student through his or her preadolescent and adolescent years, promoting positive, prosocial norms and expectations for behavior through their peer group activities. The Self Enhancement, Inc., program consists of three major components: classroom, exposure, and proactive education. Classroom education focuses on anger management, conflict resolution, and problem solving. Exposure education consists of quarterly field trips to agencies and organizations in the Portland area that deal with the causes and consequences of violence in the community. Proactive education includes newsletters, student-run assemblies and conferences, and radio/ television public service announcements that communicate antiviolence messages. The evaluation plan is a longitudinal matched comparison group designed to assess the outcomes of the violence-prevention program. Key outcomes are protective factors, health-risk behaviors, and academic measures. Standardized assessment instruments (the Individual Protective Factors Index and the Youth Risk Behavior Survey) were administered to all students during winter 1994. The instruments will be readministered during the same period in the following two years of the project. School records were extracted to assess students' attendance and progress through their academic programs. Of the 326 seventh-, eighth-, and ninth-grade students participating in this study, 95% are African Americans and 51% are boys. The prevalence of fighting (56%) during the past 12 months is higher than that among African-American high-school students nationally, but weapon carrying (27%), alcohol use (30%), and marijuana use (18%) are the same or lower than national averages for this group. All baseline indicators are equivalent between the program and comparison groups with the exception of weapon carrying. Program students report carrying weapons more than do their comparison group counterparts. Baseline indicators of violence-related behaviors clearly indicate the need for intervention in this highly disadvantaged, African-American community. Through its historical presence and recent program development efforts, Self Enhancement, Inc., is well positioned to make a difference in the lives of these young people. The equivalence of program and comparison group students on baseline indicators of violence bodes well for an unequivocal assessment of program effectiveness over time.

Adolescent↗
PubMed2001

Nested assemblages resulting from host size variation: the case of endoparasite communities in fish hosts.

Nested species subsets are a common pattern in many types of communities found in insular or fragmented habitats. Nestedness occurs in some communities of ectoparasites of fish, as does the exact opposite departure from random assembly, anti-nestedness. Here, we looked for nested and anti-nested patterns in the species composition of communities of internal parasites of 23 fish populations from two localities in Finland. We also compared various community parameters of nested and anti-nested assemblages of parasites, and determined whether nestedness may result simply from a size-related accumulation of parasite species by feeding fish hosts. Nested parasite communities were characterised by higher prevalence (proportion of infected fish) and intensities of infection (number of parasites per fish) than anti-nested communities; the two types of non-random communities did not differ with respect to parasite species richness, however. In addition, the correlation between fish size and the number of parasite species harboured by individual fish was much stronger in nested assemblages than in anti-nested ones, where it was often nil. These results were shown not to be artefacts of sampling effort or host phylogeny. They apply to both assemblages of adult and larval parasites, which were treated separately. Since species of larval parasites are extremely unlikely to interact with one another in fish hosts, the establishment of nestedness appears independent of the potential action of interspecific interactions. The species composition of these parasite communities is not determined from within the community, but rather by the extrinsic influence of host feeding rates and how they amplify differences among parasite species in probabilities of colonisation or extinction. Nested patterns occur in parasite communities whose fish hosts accumulate parasites in a predictable fashion proportional to their size, whereas anti-nested communities occur in parasite communities whose fish hosts do not, possibly because of dietary specialisation preventing them from sampling the entire pool of parasite species available locally. Thus, nestedness in parasite communities may result from processes somewhat different from those generating nested patterns in free-living communities.

Animals↗