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Bioaccessibility and associated concepts: Terminology in the context of in vitro food digestion studies
No full textInternational audienceIn vitro gastrointestinal models are widely used to study food digestion, in combination with analytical methods to determine the physicochemical and biochemical fate of food compounds. The in vitro bioaccessibility determined with these models is often used as an indicator of the in vivo bioavailability. However, the bioaccessibility concept is not used consistently within the scientific literature, leading to confusion and making it difficult to compare the results from different studies.The aim of this article is to provide standardized definitions of in vitro digestibility and bioaccessibility, detailing the main processes involved, including physical release, solubilization, and biochemical/metabolic reactions. The terminology of complementary cellular, ex vivo, and animal/human in vivo experiments is also given. Application of the in vitro terminology to different nutrients is discussed, including lipids, proteins, carbohydrates, vitamins, and other bioactive compounds. The proposed definitions unify most concepts related to the gastrointestinal fate of ingested food compounds.</p
Genetic regulation of gene expression across multiple tissues in chickens
No full textAll raw data analyzed in this study are publicly available for download without restrictions from SRA (https://www.ncbi.nlm.nih.gov/sra/) and NGDC BioProject(https://bigd.big.ac.cn/bioproject/) databases. Details of RNA-Seq, WGS, ChIP-Seq peaks and single-cell RNA-Seq can be found in Supplementary Tables,respectively. The GRCg6a chicken reference genome (v102) is available at Ensembl (https://www.ensembl.org). All processed data and the full summary statistics ofmolQTL mapping and genotype imputation reference panel are available at http://chicken.farmgtex.org.International audienceThe chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3 '-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits
Establishing Trends in Trophic Functioning of the Sélune River Megatidal Estuary Prior to Dam Removal
No full textInternational audienceRestoration of the ecological continuity of rivers has become a strong ecological issue. In some cases, it may lead to the dismantling of dams, but ecological consequences for estuarine ecosystems are poorly known. Notably, by increasing sediment and nutrient retention in reservoirs, dams can alter the influx of terrestrial subsidies to estuarine food webs. Here, we assessed the trophic functioning of the megatidal estuary of the river Sélune (bay of Mont-Saint-Michel, France) before the removal of two large dams on the river. Both estuarine benthic invertebrate and bentho-demersal fish faunas were characterized at two periods (spring and autumn 2017) and food web described by means of stable isotope (nitrogen and carbon) and fish gut analyses. Macrobenthic fauna was typical of European estuaries, with low species richness because of high physical constraints (highly variable salinity, strong currents, high altitude) prevailing in the area. High abundances and biomasses were observed in the two downstream sectors under the marine influence providing them a feeding interest for juvenile fish. Two species of gobies (Pomatoschistus microps and Pomatoschistus minutus), juvenile sea bass (Dicentrarchus labrax) and juvenile flounder (Platichthys flesus) dominated the fish fauna. Food web was mostly fueled by local primary production, predominantly microphytobenthos. Macrobenthic invertebrates (Corophium arenarium or Bathyporeia pilosa) and harpacticoid copepods and mysids in autumn were the major prey (primary consumer level) for secondary consumers. The analysis of the trophic niche of fish and their overlaps gave elements on the respective feeding strategies and inter-specific competitions. Expected long-term effects of dam removal on food web, benthic estuarine ecosystem and nursery function are clarified and discussed
Effects of polysaccharide-based edible coatings on the shelf life of fresh-cut carrots with different pigmentations
No full textInternational audiencePromoting the consumption of purple carrots, particularly in ready-to-eat products, is justified due to their peculiar composition and health benefits for consumers. However, there is limited literature on the shelf life of ready-to-eat purple carrots and the potential role of edible coatings in mitigating their quality decay. This study examined the postharvest behavior of sliced carrots 'Dordogne' (orange) and 'Purple Sun' (purple), both uncoated and coated with chitosan (CH) or locust bean gum (LBG), stored for 0 (S 0 ), 4 (S 4 ), and 8 (S 8 ) days at 4.0 • C. 'Purple Sun' proved a high fresh weight loss (up to 7.57 g 100 g -1 FW) and respiration metabolism. Compared to controls, CH reduced total color difference in 'Dordogne' (-70 %) but increased it in 'Purple Sun' (+68 %) due to the occurrence of tissue browning. Compared to uncoated controls, at the end of storage, total phenolic and ascorbic acid contents were lower in CH-coated 'Purple Sun' (-14 % and -20 %, respectively), while CH preserved total carotenoid content in 'Dordogne' (up to 1000 mg kg -1 DW). Moreover, compared to controls, LBG promoted Pseudomonas spp. (+23 % and +22 % in 'Dordogne' and 'Purple Sun', respectively) and yeasts and molds (+26 % and +24 %, respectively). Overall, these results indicate that issues of ready-to-eat carrots are significantly affected by carrot type, with the gas-barrier effect (in the case of CH for 'Purple Sun') and the antimicrobial properties of LBG (for both cultivars) seeming the most critical aspects to enhance the shelf life of the tested carrots
The INRAE Biological Resource Center ‘BrACySol’: a French centre of valuable Brassica, Allium and Solanum genetic resources for breeding
No full textInternational audienceThe INRAE Biological Resource Center 'BrACySol' belongs to BRC4Plants, the plant network of the French Research Infrastructure of Agronomic Biological Resource Centers (AgroBRC-RARe). It preserves more than 15,000 accessions belonging to different cultivated genera: Brassica (cabbage, turnip, rape and mustard), Allium (shallot and garlic) and Solanum (potato and crop wild relatives). The Brassica genetic resources are conserved as seeds in freezers or liquid nitrogen. The Allium resources are maintained by vegetative propagation in fields or greenhouses and the Solanum resources are maintained by vegetative propagation in fields, greenhouses, in vitro or in liquid nitrogen. These collections include old landraces, widespread cultivars, crop wild relatives and original scientific material. The accessions are described with passport, morphological or agronomic descriptors or traits. They have been included in various research programmes, at the national or international level, aiming at characterizing the diversity of these collections, studying the genetics of agronomic traits, developing molecular tools and creating pre-breeding lines helpful for breeding programmes
Empowering bioinformatics communities with Nextflow and nf-core
No full textInternational audienceStandardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia
Favorable alleles for early plant vigor related traits display unbalanced occurrence within rapeseed germplasms
No full textInternational audienceDuring early plant development, rapeseed is subjected to a number of biotic and abiotic stresses, which can compromise the crop's establishment and yield potential. Therefore, early vigor, defined here as a rapid early development of leaf area and above-ground biomass from emergence to the 4-5 leaf stage, is an essential factor to consider for a successful establishment. However, early plant vigor is an integrative trait that can be defined as the result of a combination of shoot, root and whole-plant traits. To date, there has been a limited focus on the genetic control of traits involved in early vigor in rapeseed, particularly when the whole plant is considered. A diversity panel was developed, including winter, spring and Asian rapeseed as well as winter fodder and swede accessions. This panel was phenotyped for early plant vigor related traits to allow QTL detection through genome-wide association studies. Young plants were phenotyped on the basis of leaf area dynamics, biomass and surface developmental traits at the 4-5 leaf stage, as well as carbon and nitrogen fluxes, at the scale of shoot, root and whole plant compartments. Our results revealed that the diversity panel consisted in three different genomic clusters that exhibited distinct patterns of leaf area and biomass development. These observations can be attributed to variations in carbon and nitrogen acquisition and utilization efficiencies. Twenty-four loci with low to moderate effects involved in early vigor traits were identified. The majority of the favorable alleles at the detected QTL presented a high frequency (>0.5) only in a specific genomic cluster. The favorable allele frequency modulation according to the considered genomic cluster demonstrates the need to integrate genetic diversity from the whole panel (i.e. the three distinct genomic clusters) to improve the elite material for early vigor traits. The results provide further insight into the genetic control of early vigor in rapeseed at the whole-plant level
PPARγ, a key modulator of metabolic reprogramming, stemness and chemoresistance associated with retrodifferentiation in human hepatocellular carcinomas
No full textInternational audienceHuman hepatocellular carcinomas (HCCs) with cancer stem cell (CSC) features are a subclass of therapeutically challenging cancers. We recently showed that retrodifferentiation of hepatic cancer cells into CSC-like cells leads to metabolic reprogramming and chemoresistance. The molecular mechanisms whereby differentiated cancer cells switch towards a CSC phenotype are poorly understood. By studying metabolic reprogramming associated with HCC cell plasticity, we identified an unsuspected role of peroxisome proliferator-activated receptor (PPAR)γ in hepatic CSC phenotype acquisition. Gene expression and metabolic analyses performed throughout the cell differentiation/retrodifferentiation process of human HepaRG and HBG-BC2 HCC cells show that metabolic reprogramming in hepatic CSCs is associated with a fragmented mitochondrial network, decreased respiration, de novo lipogenesis, and fatty acid oxidation, but increased glycolysis and lipid storage. Mitochondrial genes downregulated in HepaRG-CSCs are also downregulated in the STEM HCC subclass. While PPARα is the main isoform in differentiated hepatic cells, we find high PPARγ expression in hepatic CSCs. Accordingly, nuclear localization of PPARγ is detected in human HCC tumors, and PPARγ high /PPARα low expression is associated with the STEM HCC subclass and a poor outcome in human HCC cohorts. PPARγ silencing or/and inhibition of its target gene pyruvate dehydrogenase kinase 4 reactivates cell respiration, increases reactive oxygen species production and sensitizes hepatic CSCs to chemotherapy. Conversely, PPARα activation synergizes with chemotherapy to induce cell death. Targeting PPARγ, a key regulator of metabolic reprogramming and stemness in hepatic CSCs, or modulating the PPARγ/PPARα balance that finely tunes the differentiation/retrodifferentiation process in HCC deserves further investigation for anti-tumor therapy.</div
An Identification Method for Two Types of Particular Behaviours in Stream Temperature Time Series: Application to a National Dataset in Mainland France
No full textInternational audienceThe measurement of the stream water temperature signal is subject to various issues and environmental phenomena. Accurate interpretations of the data composing water temperature time series (WTS) often require a high‐level human expertise during data preprocessing steps to sort out meaningful temperature signals. This study proposes a method to highlight two main types of particular behaviours encountered in WTS, apart from outliers: intensified data and buffered data. The method uses a metric based on the WTS itself to identify periods with particular data. It enables the identification and the visualisation of regular and irregular particular behaviours in a given WTS. The method was applied to a large national dataset collected in mainland France. The dataset contains 993 WTS with a wide range of data quality and environmental measurement conditions. Data identified as particular behaviour accounts for up to 7% of the dataset. Depending on the measurement conditions, up to 25% of a given WTS data can be considered as ‘occasional particular behaviour’ and potentially not exploitable. Buffered data mostly occur during winter months with no apparent spatial pattern. Intensified data occur mainly in summer months and a spatial pattern shows WTS containing the highest percentage of intensified data in the south‐east part of the study area. The identification method was also applied to several known situations where a high‐level human expertise was available. It provided robust identification performances at regional scale confronted with human expertise as well as at national scale, on a large dataset. Such methods can facilitate the selection of exploitable data in large datasets which are more widely available today. Potentially problematic data becomes straightforward and subsequent data qualification or correction is facilitated