EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegans differential gene expression

BACKGROUND: Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences (e.g. gene promoters) and transcription factors in the nematode Caenorhabditis elegans. We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an upstream regulator. The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration. DESCRIPTION: Here, we report the implementation of a C. elegans differential gene expression database (EDGEdb). This database enables the storage and retrieval of protein-DNA interactions and other data that relate to differential gene expression. Specifically, EDGEdb contains: i) sequence information of regulatory elements, including gene promoters, ii) sequence information of all 934 predicted transcription factors, their DNA binding domains, and, where available, their dimerization partners and consensus DNA binding sites, iii) protein-DNA interactions between regulatory elements and transcription factors, and iv) expression patterns conferred by regulatory elements, and how such patterns are affected by interacting transcription factors. CONCLUSION: EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms. The database is available at

Apoptosis Control in Syncytia Induced by the HIV Type 1–Envelope Glycoprotein Complex: Role of Mitochondria and Caspases

Syncytia arising from the fusion of cells expressing a lymphotropic HIV type 1–encoded envelope glycoprotein complex (Env) with cells expressing the CD4/CXC chemokine receptor 4 complex spontaneously undergo cell death. Here we show that this process is accompanied by caspase activation and signs of mitochondrial membrane permeabilization (MMP), including the release of intermembrane proteins such as cytochrome c (Cyt-c) and apoptosis-inducing factor (AIF) from mitochondria. In Env-induced syncytia, caspase inhibition did not suppress AIF- and Cyt-c translocation, yet it prevented all signs of nuclear apoptosis. Translocation of Bax to mitochondria led to MMP, which was inhibited by microinjected Bcl-2 protein or bcl-2 transfection. Bcl-2 also prevented the subsequent nuclear chromatin condensation and DNA fragmentation. The release of AIF occurred before that of Cyt-c and before caspase activation. Microinjection of AIF into syncytia sufficed to trigger rapid, caspase-independent Cyt-c release. Neutralization of endogenous AIF by injection of an antibody prevented all signs of spontaneous apoptosis occurring in syncytia, including the Cyt-c release and nuclear apoptosis. In contrast, Cyt-c neutralization only prevented nuclear apoptosis, and did not affect AIF release. Our results establish that the following molecular sequence governs apoptosis of Env-induced syncytia: Bax-mediated/Bcl-2–inhibited MMP → AIF release → Cyt-c release → caspase activation → nuclear apoptosis

Two-years of Eddy-covariance CO2 and CH4 measurements in a French peatland dominated Molinia caerulea

International audiencePeatlands act as a powerful carbon (C) sink. This specificity notably results from their particular environment, composed of Shagnum mosses, and the acidic state of the soil combined with a high water saturation that strongly limit organic matter decomposition. Future natural and anthropogenic global changes are expected to modify peatlands functioning and notably their species composition, which could reverse their valuable role in C sequestration and thus in climate change mitigation. However, the response of peatlands to these biotic changes, and thus the variability of greenhouse gas fluxes, remains poorly characterized and understood. We investigated CO2 and CH4 emissions in the La Guette peatland, an acidic fen located in the center of France, thanks to an Eddy-covariance station that was installed in the ecosystem in early 2017. In addition, this site is applying for the ICOS network labelling as an associated site, and follows the ICOS recommendations. Our main concern is that La Guette peatland is submitted to a strong domination by a grass plant, Molinia caerulea, which is suspected to modify the C dynamic of the ecosystem. From January 2017 to date, CO2 and CH4 fluxes to the atmosphere ranged from to -19.46 to 19.73 µmol m-2 s-1 and from -0.10 to 0.10 µmol m-2 s-1, respectively. Mean CO2 flux for 2017 and 2018 were respectively ~ -0.21 and ~ -0.89 µmol m-2 s-1, showing that La Guette peatland acted as a sink of C over these two years. This result suggests that Molinia caerulea did not reverse the C sequestration potential of the fen. In a larger scale, this Eddy-covariance station is a part of a French Peatland Observatory Service, and is included in a network of three tower fluxes deployed in three contrasted French peatlands. This Eddy-covariance network will provide important data that will help to understand the evolution of the C balance in temperate peatlands with global changes

High frequency measurements of CO2 and CH4 fluxes in a temperate peatland dominated by Molinia caerulea (La Guette, France)

International audiencePeatlands act as a powerful carbon (C) sink. This specificity results from their particular environment, composed of Shagnum mosses, and the acidic state of the soil combined with a high water saturation that strongly limit organic matter decomposition. Future natural and anthropogenic global changes are expected to modify peatlands functioning and their species composition, which could reverse their valuable role in C sequestration and thus in climate change mitigation. However, the response of peatlands to these biotic changes, and thus the variability of greenhouse gas fluxes, remains poorly characterized and understood. We investigated CO2 and CH4 emissions in the La Guette peatland, an acidic fen located in the center of France, thanks to an Eddy-covariance station that was installed in the ecosystem in early 2017. In addition, this site is applying for the ICOS network labelling as an associated site, and follows the ICOS recommendations. Our main concern is that La Guette peatland is submitted to a strong domination by a herbaceous plant, Molinia caerulea, and a ericaceous shrub, Erica tetralix, which are suspected to modify the C dynamic of the ecosystem. From January 2017 to September 2019, CO2 and CH4 fluxes to the atmosphere ranged from to -19.46 to 19.73 µmol m-2 s-1 and from -0.12 to 0.42 µmol m-2 s-1, respectively. Mean CO2 flux for 2017, 2018 and 2019 were respectively 1.13, 1.08 and 0.44 µmol m-2 s-1. Carbon balance of the ecosystem since the beginning of 2017 has been evaluated to 982 gC m-², suggesting that the peatland acted as a source of C over these three last years. In a larger scale, this Eddy covariance station is a part of a French Peatland Observatory Service, and is included in a network of three tower fluxes deployed in three contrasted French peatlands. In the long term, this Eddy-covariance network will provide important data that will help to understand the evolution of the C balance in temperate peatlands with global changes

High frequency measurements of CO2 and CH4 in a temperate peatland dominated by Molinia caerulea (La Guette, France)

International audiencePeatlands act as a powerful carbon (C) sink. This specificity results from their particular environment, composed of Shagnum mosses, and the acidic state of the soil combined with a high water saturation that strongly limit organic matter decomposition. Future natural and anthropogenic global changes are expected to modify peatlands functioning and their species composition, which could reverse their valuable role in C sequestration and thus in climate change mitigation. However, the response of peatlands to these biotic changes, and thus the variability of greenhouse gas fluxes, remains poorly characterized and understood. We investigated CO2 and CH4 emissions in the La Guette peatland, an acidic fen located in the center of France, thanks to an Eddy-covariance station that was installed in the ecosystem in early 2017. In addition, this site is applying for the ICOS network labelling as an associated site, and follows the ICOS recommendations. Our main concern is that La Guette peatland is submitted to a strong domination by a herbaceous plant, Molinia caerulea, and a ericaceous shrub, Erica tetralix, which are suspected to modify the C dynamic of the ecosystem. From January 2017 to September 2019, CO2 and CH4 fluxes to the atmosphere ranged from to -19.46 to 19.73 µmol m-2 s-1 and from -0.12 to 0.42 µmol m-2 s-1, respectively. Mean CO2 flux for 2017, 2018 and 2019 were respectively 1.13, 1.08 and 0.44 µmol m-2 s-1. Carbon balance of the ecosystem since the beginning of 2017 has been evaluated to 982 gC m-², suggesting that the peatland acted as a source of C over these three last years. In a larger scale, this Eddy covariance station is a part of a French Peatland Observatory Service, and is included in a network of three tower fluxes deployed in three contrasted French peatlands. In the long term, this Eddy-covariance network will provide important data that will help to understand the evolution of the C balance in temperate peatlands with global changes

Restoration peatland and eLTER, case of France

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Plasma lipoprotein distribution and lipid transfer activities in patients with type IIb hyperlipidemia treated with simvastatin

International audienceThe aim of the present study was to search in type IIb hyperlipidemic patients for putative concomitant effects of simvastatin on the physicochemical characteristics of low density lipoproteins (LDL) and high density lipoproteins (HDL), as well as on the activities of the cholesteryl ester transfer protein (CETP) and the phospholipid transfer protein (PLTP) that were determined in both endogenous lipoprotein-dependent and endogenous lipoprotein-independent assays. In a double-blind, randomized trial, patients received either placebo (one tablet/day; n=12) or simvastatin (20 mg/day; n=12) for a period of 8 weeks after a 5-week run-in period. Simvastatin, unlike placebo, reduced the lipid and apolipoprotein B contents of the most abundant LDL-1, LDL-2, and LDL-3 subfractions without inducing significant changes in the overall size distribution of LDL and HDL. Whereas simvastatin significantly increased PLTP activity in an endogenous lipoprotein-dependent assay (P B 0.01), no variation was observed in a lipoprotein-independent assay. Simvastatin significantly decreased plasma CETP activity in an endogenous lipoprotein-dependent assay (PB0.01), and the reduction in plasma cholesteryl ester transfer rates was explained by a 16% drop in CETP mass concentration (PB0.01). In contrast, the specific activity of CETP was unaffected by the simvastatin treatment reflecting at least in part the lack of significant alteration in plasma triglyceride-rich lipoprotein acceptors. The simvastatin-induced changes in plasma CETP mass levels correlated positively with changes in plasma CETP activity (r=0.483, P=0.0561), in total cholesterol levels (r=0.769; PB0.01), and in LDL-cholesterol levels (r= 0.736; P B0.01). Whereas the observations suggest that simvastatin might exert concomitant beneficial effects on plasma CETP and LDL levels, neither plasma cholesteryl ester transfer activity nor plasma phospholipid transfer activity appeared as the main determinants of the LDL and HDL distribution profiles in type IIb hyperlipidemic patients

Screening New Xylanase Biocatalysts from the Mangrove Soil Diversity

International audienceMangrove sediments from New Caledonia were screened for xylanase sequences. One enzyme was selected and characterized both biochemically and for its industrial potential. Using a specific cDNA amplification method coupled with a MiSeq sequencing approach, the diversity of expressed genes encoding GH11 xylanases was investigated beneath Avicenia marina and Rhizophora stylosa trees during the wet and dry seasons and at two different sediment depths. GH11 xylanase diversity varied more according to tree species and season, than with respect to depth. One complete cDNA was selected (OFU29) and expressed in Pichia pastoris. The corresponding enzyme (called Xyn11-29) was biochemically characterized, revealing an optimal activity at 40–50 °C and at a pH of 5.5. Xyn11-29 was stable for 48 h at 35 °C, with a half-life of 1 h at 40 °C and in the pH range of 5.5–6. Xyn11-29 exhibited a high hydrolysis capacity on destarched wheat bran, with 40% and 16% of xylose and arabinose released after 24 h hydrolysis. Its activity on wheat straw was lower, with a release of 2.8% and 6.9% of xylose and arabinose, respectively. As the protein was isolated from mangrove sediments, the effect of sea salt on its activity was studied and discussed