Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals

Statut en fluor et nutrition parentérale à domicile

LYON1-BU Santé (693882101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Mixing and Formation of Layers by Internal Wave Forcing

International audienceThe energy pathways from propagating internal waves to the scales of irreversible mixing in the ocean are not fully described. In the ocean interior, the triadic resonant instability is an intrinsic destabilization process that may enhance the energy cascade away from topographies. The present study focuses on the integrated impact of mixing processes induced by a propagative normal mode-1 over long-term experiments in an idealized setup. The internal wave dynamics and the evolution of the density profile are followed using the light attenuation technique. Diagnostics of the turbulent diffusivity KT and background potential energy BPE are provided. Mixing effects result in a partially mixed layer colocated with the region of maximum shear induced by the forcing normal mode. The maximum measured turbulent diffusivity is 250 times larger than the molecular value, showing that diapycnal mixing is largely enhanced by small-scale turbulent processes. Intermittency and reversible energy transfers are discussed to bridge the gap between the present diagnostic and the larger values measured in Dossmann et al. (2016a). The mixing efficiency η is assessed by relating the BPE growth to the linearized KE input. One finds a value of math formula, larger than the mixing efficiency in the case of breaking interfacial wave. After several hours of forcing, the development of staircases in the density profile is observed. This mechanism has been previously observed in experiments with weak homogeneous turbulence and explained by Phillips (1972) argument. The present experiments suggest that internal wave forcing could also induce the formation of density interfaces in the ocean

Properties of the various Botmar1 transcripts in imagoes of the bumble bee, Bombus terrestris (Hymenoptera: Apidae).

Botmar1 elements are mariner-like elements (MLEs), class II transposable elements that occur in the genome of the bumble bee, Bombus terrestris. Each haploid B. terrestris genome contains about 230 Botmar1, consisting entirely of 1.3-kb and 0.85-kb elements. During their evolution in the B. terrestris genome, two Botmar1 lineages have been differentiated in terms of their nucleic acid sequences and the differences found in their 5' untranslated regions suggest that they could be transcribed differently in B. terrestris. Here, we show that small amounts of Botmar1 mRNA occur in RNA extracts purified from B. terrestris imagoes. This indicates that the Botmar1 transcription is either weak in imagoes, or is restricted to very few cells. The cloning of several mRNAs reveals that only lineage-2 Botmar1 elements are transcribed. This transcription is specific, and uses cardinal initiators and terminators of eukaryotic elements in the Botmar1 elements. The intrastrand stem-loop folds in the mRNA theoretically synthesized by elements of the first lineage suggest that mRNA maintenance in cells might be self-regulated by RNA interference

RNA silencing-targeted transcriptome of porcine alveolar macrophages upon infection with porcine reproductive and respiratory syndrome viruses (PRRSV) of different virulence

International audienc

Biochemical composition is not the main factor influencing variability in carbon isotope composition of tree rings

International audienceFrom June to December, we determined the effects of variations in biochemical composition on δ13C of tree rings of 2-year-old oaks (Quercus petraea (Matt.) Liebl.) growing under semi-natural conditions, and the dependence of these effects of water stress during the growth season. Percent abundance, carbon concentration and δ13C were measured in holocellulose, lignin, extractive-free wood, starch and a water-soluble fraction. Relative concentrations of lignin and holocellulose in the extractive-free wood varied little during the season or in response to water stress, indicating that these compounds could not quantitatively explain the variations in whole-wood δ13C. Among all sampled tree rings, the relative concentration of each structural compound (holocellulose and lignin) accounted for less than 5% of the δ13C variability in whole wood. Variations in holocellulose and extractive-free wood δ13C between tree rings were almost identical (r > 0.95), whereas variations in lignin δ13C were less well correlated to these compounds. Whole-wood δ13C had a slightly altered isotopic signal compared with that of the structural compounds because of the presence of the extractive component. These results showed that variations in lignin δ13C and lignin concentration have little influence on extractive-free wood δ13C and whole-wood δ13C. Rather, holocellulose influences δ13C the most. Thus, we confirmed that, for climatic reconstruction from tree rings, removal of extractives by soxhlet is generally sufficient and sometimes unnecessary. Our findings also indicate that, in the case of rapid and severe water stress, the structural component did not accurately record the associated increase in δ13C because of dilution with previously formed organic matter and cessation of trunk growth. The effect of drought on carbon isotope ratios was more pronounced in the extractive compounds, making them good water stress indicators but only on a scale of days to months

Oral Intake of EPA:DHA 6:1 by Middle-Aged Rats for One Week Improves Age-Related Endothelial Dysfunction in Both the Femoral Artery and Vein: Role of Cyclooxygenases

International audienceIn humans, aging is associated with endothelial dysfunction and an increased risk of venous thromboembolism. Although intake of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) at a ratio of 6:1 by old rats improved the endothelial dysfunction in arteries, the impact on veins remains unclear. Eight-month-old male Wistar rats were either untreated or orally administered corn oil, EPA:DHA 1:1, or EPA:DHA 6:1 (500 mg/kg/d) for seven days. Vascular reactivity was studied by myography. In middle-aged femoral artery rings, acetylcholine caused a partial relaxation at low concentrations and a contractile response at high concentrations, whereas in the old femoral vein only a partial relaxation was observed. The EPA:DHA 6:1 treatment blunted the contractile response to acetylcholine in the middle-aged femoral artery and both EPA:DHA 6:1 and 1:1 increased the relaxation to acetylcholine in the old femoral vein. No such effects were observed with corn oil. Both the non-selective cyclooxygenase inhibitor indomethacin and the COX-1 inhibitor SC-560 increased the relaxation to acetylcholine in the middle-aged femoral artery whereas the COX-2 inhibitor NS-398 increased that in the middle-aged femoral vein. In conclusion, our results indicate that aging is associated with an endothelial dysfunction in the femoral artery and vein, which can be improved by EPA:DHA 6:1 treatment-most likely via a cyclooxygenase-dependent mechanism

Long Term Use of Boosted Atazanavir (ATV/r) in Real Life: A 5 Year Retrospective Observational Belgian Cohort of 2264 HIV Patients

For the Belgian HIV Research Consortium BREACHinfo:eu-repo/semantics/nonPublishe