J. Craig Venter Institute

About: J. Craig Venter Institute is a nonprofit organization based out in La Jolla, California, United States. It is known for research contribution in the topics: Genome & Gene. The organization has 1268 authors who have published 2300 publications receiving 304083 citations. The organization is also known as: JCVI & The Institute for Genomic Research.

Predicting risk of cancer during HIV infection: the role of inflammatory and coagulation biomarkers.

Abstract: Objective: To investigate the relationship between inflammatory [interleukin-6 (IL-6) and C-reactive protein (CRP)] and coagulation (D-dimer) biomarkers and cancer risk during HIV infection. Design: A prospective cohort. Methods: HIV-infected patients on continuous antiretroviral therapy (ART) in the control arms of three randomized trials (N = 5023) were included in an analysis of predictors of cancer (any type, infection-related or infection-unrelated). Hazard ratios for IL-6, CRP and D-dimer levels (log-transformed) were calculated using Cox models stratified by trial and adjusted for demographics and CD4 cell counts and adjusted also for all biomarkers simultaneously. To assess the possibility that biomarker levels were elevated at entry due to undiagnosed cancer, analyses were repeated excluding early cancer events (i.e. diagnosed during first 2 years of follow-up). Results: During approximately 24 000 person-years of follow-up (PYFU), 172 patients developed cancer (70 infection-related; 102 infection-unrelated). The risk of developing cancer was associated with higher levels (per doubling) of IL-6 (hazard ratio 1.38, P<0.001), CRP (hazard ratio 1.16, P=0.001) and D-dimer (hazard ratio 1.17, P=0.03). However, only IL-6 (hazard ratio 1.29, P= 0.003) remained associated with cancer risk when all biomarkers were considered simultaneously. Results for infection-related and infection-unrelated cancers were similar to results for any cancer. Hazard ratios excluding 69 early cancer events were 1.31 (P= 0.007), 1.14 (P=0.02) and 1.07 (P = 0.49) for IL-6, CRP and D-dimer, respectively. Conclusion: Activated inflammation and coagulation pathways are associated with increased cancer risk during HIV infection. This association was stronger for IL-6 and persisted after excluding early cancer. Trials of interventions may be warranted to assess whether cancer risk can be reduced by lowering IL-6 levels in HIV-positive individuals.

Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-Step Model of Paleohexaploidy

Abstract: The genome sequence of the paleohexaploid Brassica rapa shows that fractionation is biased among the three subgenomes and that the least fractionated subgenome has approximately twice as many orthologs as its close (and relatively unduplicated) relative Arabidopsis than had either of the other two subgenomes. One evolutionary scenario is that the two subgenomes with heavy gene losses (I and II) were in the same nucleus for a longer period of time than the third subgenome (III) with the fewest gene losses. This “two-step” hypothesis is essentially the same as that proposed previously for the eudicot paleohexaploidy; however, the more recent nature of the B. rapa paleohexaploidy makes this model more testable. We found that subgenome II suffered recent small deletions within exons more frequently than subgenome I, as would be expected if the genes in subgenome I had already been near maximally fractionated before subgenome III was introduced. We observed that some sequences, before these deletions, were flanked by short direct repeats, a unique signature of intrachromosomal illegitimate recombination. We also found, through simulations, that short—single or two-gene—deletions appear to dominate the fractionation patterns in B. rapa. We conclude that the observed patterns of the triplicated regions in the Brassica genome are best explained by a two-step fractionation model. The triplication and subsequent mode of fractionation could influence the potential to generate morphological diversity—a hallmark of the Brassica genus.

A community-based transcriptomics classification and nomenclature of neocortical cell types

Abstract: To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer

Abstract: Microbial respiration via extracellular electron transfer (EET) is a ubiquitous reaction that occurs throughout anoxic environments and is a driving force behind global biogeochemical cycling of metals. Here we identify specific EET-active microbes and genes in a diverse biofilm using an innovative approach to analyse the dynamic community-wide response to changing EET rates. We find that the most significant gene expression responses to applied EET stimuli occur in only two microbial groups, Desulfobulbaceae and Desulfuromonadales. Metagenomic analyses reveal high coverage draft genomes of these abundant and active microbes. Our metatranscriptomic results show known and unknown genes that are highly responsive to EET stimuli and associated with our identified draft genomes. This new approach yields a comprehensive image of functional microbes and genes related to EET activity in a diverse community, representing the next step towards unravelling complex microbial roles within a community and how microbes adapt to specific environmental stimuli.

New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis

Abstract: Volume 5, no. 1, doi: 10.1128/mBio.00963-13, 2014. In Results, in the paragraph headed “Mobile gene content differences” (PDF page 5), the third sentence should read as follows (revised text is in bold): “A …