Dataset Information

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

ABSTRACT: Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.

SUBMITTER: Beja O

PROVIDER: S-EPMC126555 | biostudies-literature | 2002 Jan

REPOSITORIES: biostudies-literature

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Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

Béjà Oded O Koonin Eugene V EV Aravind L L Taylor Lance T LT Seitz Heidi H Stein Jefferey L JL Bensen Daniel C DC Feldman Robert A RA Swanson Ronald V RV DeLong Edward F EF

Applied and environmental microbiology 20020101 1

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the ...[more]

PMID: 11772643

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Project description:Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.

Project description:Amidst concerns regarding the capacity of the public health system to respond rapidly and appropriately to threats such as pandemics and terrorism, along with changing population health needs, governments have focused on strengthening public health systems. A key factor in a robust public health system is its workforce. As part of a nationally funded study of public health renewal in Canada, a policy analysis was conducted to compare public health human resources-relevant documents in two Canadian provinces, British Columbia (BC) and Ontario (ON), as they each implement public health renewal activities.A content analysis of policy and planning documents from government and public health-related organizations was conducted by a research team comprised of academics and government decision-makers. Documents published between 2003 and 2011 were accessed (BC?=?27; ON?=?20); documents were either publicly available or internal to government and excerpted with permission. Documentary texts were deductively coded using a coding template developed by the researchers based on key health human resources concepts derived from two national policy documents.Documents in both provinces highlighted the importance of public health human resources planning and policies; this was particularly evident in early post-SARS documents. Key thematic areas of public health human resources identified were: education, training, and competencies; capacity; supply; intersectoral collaboration; leadership; public health planning context; and priority populations. Policy documents in both provinces discussed the importance of an educated, competent public health workforce with the appropriate skills and competencies for the effective and efficient delivery of public health services.This policy analysis identified progressive work on public health human resources policy and planning with early documents providing an inventory of issues to be addressed and later documents providing evidence of beginning policy development and implementation. While many similarities exist between the provinces, the context distinctive to each province has influenced and shaped how they have focused their public health human resources policies.

Project description:Improved awareness of the hepatitis C virus (HCV) transmission has contributed to the overall decline in the HCV infection rate in some developing countries including Thailand. Chronic HCV infection in some rural Thai communities, however, presents a challenge in the efforts to treat and manage HCV-related diseases. Published and unpublished studies have suggested an unusually high incidence of HCV infection in a Thai province of Phetchabun compared to elsewhere in Thailand. To determine the magnitude of HCV infection and identify potential factors contributing to the higher rate of HCV infection in this province, we performed a population-based study in Phetchabun (n = 1667) and the neighboring Khon Kaen province (n = 1410) where HCV prevalence is much lower. Individuals between 30 and 64 years old completed detailed questionnaires designed to identify HCV risk factors and provided blood samples for anti-HCV antibody screening. The anti-HCV seropositive rates were 15.5% (259/1667) in Phetchabun and 3.6% (51/1410) in Khon Kaen. Positive samples were subsequently genotyped for HCV core gene sequence and assessed for the hepatitis B virus surface antigen (HBsAg) and human immunodeficiency virus antigen/antibody (HIV Ag/Ab). More individuals in Phetchabun possessed the combined presence of HBsAg (5.0%) and HIV Ag/Ab (0.4%) than those in Khon Kaen (3.9% HBsAg and 0.0% HIV Ag/Ab). While male gender, intravenous drug use (IVDU) and tattoos were significant HCV risk factors in both provinces (p <0.05), education less than high school and agriculture-related occupation were additionally associated with HCV in Phetchabun. HCV genotypes 6, 3, and 1 were identified in similar frequency in both provinces. We estimated that prevalence of HCV seropositivity and viremic carriers were higher in Phetchabun (143 and 111 per 1000) than in Khon Kaen (34 and 22 per 1000). Finally, we derived a simple risk factor-based scoring system as a useful preclinical tool to screen individuals at risk of chronic HCV infection prior to intervention. Knowledge gained from this study will assist in HCV screening and promote access to anti-viral treatment in high-risk groups.

Dataset Information

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

Publications

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

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