GOHTAM: a website for ‘Genomic Origin of Horizontal Transfers, Alignment and Metagenomics’

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies

High levels of mercury and low levels of persistent organic pollutants in a tropical seabird in French Guiana, the Magnificent frigatebird, Fregata magnificens

In the present study, trace elements and persistent organic pollutants (POPs) were quantified from Magnificent frigatebirds (Fregata magnificens) breeding at a southern Atlantic island. Stable isotope ratio of carbon (δ13C) and nitrogen (δ15N) were also measured to infer the role of foraging habitat on the contamination. For another group from the same colony, GPS tracks were recorded to identify potential foraging areas where the birds may get contaminated. Fourteen trace elements were targeted as well as a total of 40 individual POPs, including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). The concentration of Hg in the blood was up to 6 times higher in adults (5.81 ± 1.27 μg g−1 dw.) than in nestlings (0.99 ± 0.23 μg g−1 dw.). A similar pattern was found for POPs. ∑PCBs was the prevalent group both in adults (median 673, range 336–2801 pg g−1 ww.) and nestlings (median 41, range 19–232 pg g−1 ww.), followed by the sum of dichlorodiphenyltrichloroethanes and metabolites (∑DDTs), showing a median value of 220 (range 75–2342 pg g−1 ww.) in adults and 25 (range 13–206 pg g−1 ww.) in nestlings. The isotope data suggested that the accumulation of trace elements and POPs between adults and nestlings could be due to parental foraging in two different areas during incubation and chick rearing, respectively, or due to a shift in the feeding strategies along the breeding season. In conclusion, our work showed high Hg concentration in frigatebirds compared to non-contaminated seabird populations, while other trace elements showed lower values within the expected range in other seabird species. Finally, POP exposure was found generally lower than that previously measured in other seabird specie

Editorial:T cell regulation by the environment

International audienc

Human and Mouse CD8+CD25+FOXP3+ Regulatory T Cells at Steady State and during Interleukin-2 Therapy

International audienceIn addition to CD4+ regulatory T cells (Tregs), CD8+ suppressor T cells are emerging as an important subset of regulatory T cells. Diverse populations of CD8+ T cells with suppressive activities have been described. Among them, a small population of CD8+CD25+FOXP3+ T cells is found both in mice and humans. In contrast to thymic-derived CD4+CD25+FOXP3+ Tregs, their origin and their role in the pathophysiology of autoimmune diseases (AIDs) are less understood. We report here the number, phenotype, and function of CD8+ Tregs cells in mice and humans, at the steady state and in response to low-dose interleukin-2 (IL-2). CD8+ Tregs represent approximately 0.4 and 0.1% of peripheral blood T cells in healthy humans and mice, respectively. In mice, their frequencies are quite similar in lymph nodes (LNs) and the spleen, but two to threefold higher in Peyer patches and mesenteric LNs. CD8+ Tregs express low levels of CD127. CD8+ Tregs express more activation or proliferation markers such as CTLA-4, ICOS, and Ki-67 than other CD8+ T cells. In vitro, they suppress effector T cell proliferation as well as or even better than CD4+ Tregs. Owing to constitutive expression of CD25, CD8+ Tregs are 20- to 40-fold more sensitive to in vitro IL-2 stimulation than CD8+ effector T cells, but 2–4 times less than CD4+ Tregs. Nevertheless, low-dose IL-2 dramatically expands and activates CD8+ Tregs even more than CD4+ Tregs, in mice and humans. Further studies are warranted to fully appreciate the clinical relevance of CD8+ Tregs in AIDs and the efficacy of IL-2 treatment

Suppressing miR-21 activity in tumor-associated macrophages promotes an antitumor immune response

microRNA-21 (miR-21) is the most commonly upregulated miRNA in solid tumors. This cancer-associated microRNA (oncomiR) regulates various downstream effectors associated with tumor pathogenesis during all stages of carcinogenesis. In this study, we analyzed the function of miR-21 in noncancer cells of the tumor microenvironment to further evaluate its contribution to tumor progression. We report that the expression of miR-21 in cells of the tumor immune infiltrate, and in particular in macrophages, was responsible for promoting tumor growth. Absence of miR-21 expression in tumor- associated macrophages (TAMs), caused a global rewiring of their transcriptional regulatory network that was skewed toward a proinflammatory angiostatic phenotype. This promoted an antitumoral immune response characterized by a macrophage-mediated improvement of cytotoxic T-cell responses through the induction of cytokines and chemokines, including IL-12 and C-X-C motif chemokine 10. These effects translated to a reduction in tumor neovascularization and an induction of tumor cell death that led to decreased tumor growth. Additionally, using the carrier peptide pH (low) insertion peptide, we were able to target miR-21 in TAMs, which decreased tumor growth even under conditions where miR-21 expression was deficient in cancer cells. Consequently, miR-21 inhibition in TAMs induced an angiostatic and immunostimulatory activation with potential therapeutic implications

A Benchmark of Parametric Methods for Horizontal Transfers Detection

Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity