Tissue Resources for the Functional Annotation of Animal Genomes

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles

Algorithmic Decision Systems in the Health and Justice Sectors: Certification and Explanations for Algorithms in European and French Law

International audienceAlgorithmic decision systems are already used in many everyday tools and services on the Internet. They also play an increasing role in many situations in which people’s lives and rights are strongly affected, such as job and loans applications, but also medical diagnosis and therapeutic choices, or legal advice and court decisions. This evolution gives rise to a whole range of questions. In this paper, we argue that certification and explanation are two complementary means of strengthening the European legal framework and enhancing trust in algorithmic decision systems. The former can be seen as the delegation of the task of checking certain criteria to an authority, while the latter allows the stakeholders themselves (for example, developers, users and decision-subjects) to understand the results or the logic of the system. We explore potential legal requirements of accountability in this sense and their effective implementation. These two aspects are tackled from the perspective of the European and French legal frameworks. We focus on two particularly sensitive application domains, namely the medical and legal sectors

Algorithmic Decision Systems in the Health and Justice Sectors: Certification and Explanations for Algorithms in European and French Law

International audienceAlgorithmic decision systems are already used in many everyday tools and services on the Internet. They also play an increasing role in many situations in which people’s lives and rights are strongly affected, such as job and loans applications, but also medical diagnosis and therapeutic choices, or legal advice and court decisions. This evolution gives rise to a whole range of questions. In this paper, we argue that certification and explanation are two complementary means of strengthening the European legal framework and enhancing trust in algorithmic decision systems. The former can be seen as the delegation of the task of checking certain criteria to an authority, while the latter allows the stakeholders themselves (for example, developers, users and decision-subjects) to understand the results or the logic of the system. We explore potential legal requirements of accountability in this sense and their effective implementation. These two aspects are tackled from the perspective of the European and French legal frameworks. We focus on two particularly sensitive application domains, namely the medical and legal sectors

Utilisation périphérique du glucose chez le poulet et le canard : implications pour la croissance et la qualité de la viande

Birds have developed original adaptive mechanisms ensuring them an active energy metabolism characterized by a high basal temperature and glycaemia (42 degrees C and 2g/L). Studies completed mostly on agronomic species (chicken, duck) emphasize a specific regulation of glucose homeostasis. In a first part we report some general data on glucose metabolism characteristics and its regulation by insulin in poultry. In a second part we present recent work concerning glucose uptake, its use and storage by the 3 major tissues implied in glucose homeostasis regulation (liver, muscle and fat). The purpose of this fundamental knowledge is to direct applied programs aimed at improving growth and quality of poultry productions.Les Oiseaux ont développé des mécanismes adaptatifs originaux leur assurant un métabolisme énergétique actif caractérisé par une température et une glycémie basales élevées (42°C et 2 g/L). Les travaux réalisés en majorité sur les espèces d’intérêt agronomique (poulet, canard) font ressortir une régulation particulière de l’homéostasie glucidique et notamment du système insulinique, hormone majeure contrôlant le métabolisme. Dans une première partie, nous rapportons quelques données générales concernant les particularités du métabolisme glucidique et de sa régulation par l’insuline chez les espèces avicoles. Dans une deuxième partie, nous présentons les travaux récents concernant la captation de glucose, son utilisation et son stockage par les trois tissus majeurs impliqués dans le maintien de l’homéostasie glucidique à savoir le foie, le muscle et le tissu adipeux. Ces connaissances fondamentales ont pour but d’orienter les programmes de recherche appliquée visant à améliorer la croissance et la qualité des viandes de volailles

Algorithmic Decision Systems in the Health and Justice Sectors: Certification and Explanations for Algorithms in European and French Law

International audienceAlgorithmic decision systems are already used in many everyday tools and services on the Internet. They also play an increasing role in many situations in which people’s lives and rights are strongly affected, such as job and loans applications, but also medical diagnosis and therapeutic choices, or legal advice and court decisions. This evolution gives rise to a whole range of questions. In this paper, we argue that certification and explanation are two complementary means of strengthening the European legal framework and enhancing trust in algorithmic decision systems. The former can be seen as the delegation of the task of checking certain criteria to an authority, while the latter allows the stakeholders themselves (for example, developers, users and decision-subjects) to understand the results or the logic of the system. We explore potential legal requirements of accountability in this sense and their effective implementation. These two aspects are tackled from the perspective of the European and French legal frameworks. We focus on two particularly sensitive application domains, namely the medical and legal sectors

The effect of albumen removal before incubation (embryonic protein under-nutrition) on the post-hatch performance, regulators of protein translation activation and proteolysis in neonatal broilers.

Albumen was removed from broiler eggs before the start of incubation to induce prenatal protein under-nutrition in chicken embryos. With this method, the direct effect of protein deficiency was investigated, differing from mammalian models manipulating the maternal diet where indirect, hormonal effects can interfere. Based on the estimated albumen/egg weight ratio, 10 % of albumen was removed with an 18G needle, after making a hole at the sharp end of the egg with another 18G needle. Eggs were taped thereafter. The sham group underwent the same procedure, except that no albumen was removed. Control eggs did not receive any treatment. The removal of albumen decreased both embryonic and post-hatch body weight up to day 7 compared with the control group. On embryonic day 18, embryos from the albumen-deprived group had higher plasma uric acid levels compared with the sham (P= 0.016) and control (P= 0.009) groups. Moreover, a lower plasma amino acid concentration was observed at hatch compared with the sham (P= 0.038) and control (P= 0.152) groups. These findings indicate an altered protein metabolism. At hatch, a higher mRNA expression of muscle ring finger-1 (MuRF1), a gene related to proteolysis, was observed in albumen-deprived chicks compared with the control and sham chicks, together with an up-regulated expression of atrogin-1 (another atrogene) at this time point in the male protein-deficient chicks. These findings suggest that muscle proteolysis is transiently increased by the removal of albumen before the start of incubation. No evidence was found for altered protein synthesis capacity and translational efficiency in albumen-deprived chicks

Ontogeny of hepatic metabolism in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle

International audienceAbstract Background Nutrient availability during early stages of development (embryogenesis and the first week post-hatch) can have long-term effects on physiological functions and bird metabolism. The embryo develops in a closed structure and depends entirely on the nutrients and energy available in the egg. The aim of this study was to describe the ontogeny of pathways governing hepatic metabolism that mediates many physiological functions in the pHu + and pHu- chicken lines, which are divergently selected for the ultimate pH of meat, a proxy for muscle glycogen stores, and which differ in the nutrient content and composition of eggs. Results We identified eight clusters of genes showing a common pattern of expression between embryonic day 12 (E12) and day 8 (D8) post-hatch. These clusters were not representative of a specific metabolic pathway or function. On E12 and E14, the majority of genes differentially expressed between the pHu + and pHu- lines were overexpressed in the pHu + line. Conversely, the majority of genes differentially expressed from E18 were overexpressed in the pHu- line. During the metabolic shift at E18, there was a decrease in the expression of genes linked to several metabolic functions (e.g. protein synthesis, autophagy and mitochondrial activity). At hatching (D0), there were two distinct groups of pHu + chicks based on hierarchical clustering; these groups also differed in liver weight and serum parameters (e.g. triglyceride content and creatine kinase activity). At D0 and D8, there was a sex effect for several metabolic pathways. Metabolism appeared to be more active and oriented towards protein synthesis ( RPS6 ) and fatty acid β-oxidation ( ACAA2 , ACOX1 ) in males than in females. In comparison, the genes overexpressed in females were related to carbohydrate metabolism ( SLC2A1, SLC2A12 , FoxO1 , PHKA2 , PHKB , PRKAB2 and GYS2 ). Conclusions Our study provides the first detailed description of the evolution of different hepatic metabolic pathways during the early development of embryos and post-hatching chicks. We found a metabolic orientation for the pHu + line towards proteolysis, glycogen degradation, ATP synthesis and autophagy, likely in response to a higher energy requirement compared with pHu- embryos. The metabolic orientations specific to the pHu + and pHu- lines are established very early, probably in relation with their different genetic background and available nutrients