Cotranscription and intergenic splicing of the PPARG and TSEN2 genes in cattle

BACKGROUND: Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptional termination bypass. RESULTS: We identified bovine chimeric transcripts resulting from cotranscription and intergenic splicing of two neighboring genes, PPARG and TSEN2. These two genes encode the Peroxisome Proliferator Activated Receptors γ1 and γ2 and the tRNA Splicing Endonuclease 2 homolog and are situated in the same orientation about 50 kb apart on bovine chromosome 22q24. Their relative position is conserved in human and mouse. We identified two types of chimeric transcripts containing all but the last exon of the PPARG gene followed by all but the first exon of the TSEN2 gene. The two chimers differ by the presence/absence of an intermediate exon resulting from transcription of a LINE L2 sequence situated between the two genes. Both transcripts use canonical splice sites for all exons coming from both genes, as well as for the LINE L2 sequence. One of these transcripts harbors a premature STOP codon and the other encodes a putative chimeric protein combining most of the PPARγ protein and the entire TSEN2 protein, but we could not establish the existence of this protein. CONCLUSION: By showing that both individual and chimeric transcripts are transcribed from PPARG and TSEN2, we demonstrated regulation of transcription termination. Further, the existence and functionality of a chimeric protein harboring active motifs that are a priori unrelated is hypothesized

Maternal Protein Restriction in Rats Alters Postnatal Growth and Brain Lipid Sensing in Female Offspring

Perinatal nutrition is a key player in the susceptibility to developing metabolic diseases in adulthood, leading to the concept of “metabolic programming”. The aim of this study was to assess the impact of maternal protein restriction during gestation and lactation on glucose homeostasis and eating behaviour in female offspring. Pregnant rats were fed a normal or protein-restricted (PR) diet and followed throughout gestation and lactation. Body weight, glucose homeostasis, and eating behaviour were evaluated in offspring, especially in females. Body weight gain was lower in PR dams during lactation only, despite different food and water intakes throughout gestation and lactation. Plasma concentration of leptin, adiponectin and triglycerides increased drastically before delivery in PR dams in relation to fat deposits. Although all pups had identical birth body weight, PR offspring body weight differed from control offspring around postnatal day 10 and remained lower until adulthood. Offspring glucose homeostasis was mildly impacted by maternal PR, although insulin secretion was reduced for PR rats at adulthood. Food intake, satiety response, and cerebral activation were examined after a lipid preload and demonstrated some differences between the two groups of rats. Maternal PR during gestation and lactation does induce extrauterine growth restriction, accompanied by alterations in maternal plasma leptin and adiponectin levels, which may be involved in programming the alterations in eating behaviour observed in females at adulthood

SKOS Sources Transformations for Ontology Engineering: Agronomical Taxonomy Use Case

Sources like thesauri or taxonomies are already used as input in ontology development process. Some of them are also published on the LOD using the SKOS format. Reusing this type of sources to build an ontology is not an easy task. The ontology developer has to face different syntax and different modelling goals. We propose in this paper a new methodology to transform several non-ontological sources into a single ontology. We take into account: the redundancy of the knowledge extracted from sources in order to discover the consensual knowledge and Ontology Design Patterns (ODPs) to guide the transformation process. We have evaluated our methodology by creating an ontology on wheat taxonomy from three sources: Agrovoc thesaurus, TaxRef taxonomy, NCBI taxonomy

Maternal Protein Restriction in Rats Alters Postnatal Growth and Brain Lipid Sensing in Female Offspring

Perinatal nutrition is a key player in the susceptibility to developing metabolic diseases in adulthood, leading to the concept of “metabolic programming”. The aim of this study was to assess the impact of maternal protein restriction during gestation and lactation on glucose homeostasis and eating behaviour in female offspring. Pregnant rats were fed a normal or protein-restricted (PR) diet and followed throughout gestation and lactation. Body weight, glucose homeostasis, and eating behaviour were evaluated in offspring, especially in females. Body weight gain was lower in PR dams during lactation only, despite different food and water intakes throughout gestation and lactation. Plasma concentration of leptin, adiponectin and triglycerides increased drastically before delivery in PR dams in relation to fat deposits. Although all pups had identical birth body weight, PR offspring body weight differed from control offspring around postnatal day 10 and remained lower until adulthood. Offspring glucose homeostasis was mildly impacted by maternal PR, although insulin secretion was reduced for PR rats at adulthood. Food intake, satiety response, and cerebral activation were examined after a lipid preload and demonstrated some differences between the two groups of rats. Maternal PR during gestation and lactation does induce extrauterine growth restriction, accompanied by alterations in maternal plasma leptin and adiponectin levels, which may be involved in programming the alterations in eating behaviour observed in females at adulthood

Enrichissement d'un module ontologique : proposition d'une méthode pour le cas de l'agriculture

National audienceAfin de contribuer au Web de données pour l'agriculture, nous souhaitons construireune ontologie de ce domaine. Les classes de haut niveau d'un module ontologiqueont déjà été définies ; la problématique maintenant est de réussir à l'enrichir. Noussouhaitons exploiter un point fort de ce domaine qui est l'existence de nombreusessources d'information. Nous avons posé l'hypothèse que l'utilisation de plusieurssources lors d'un processus d'extraction et de transformation permet une extractionsimplifiée et plus efficace que l'utilisation d'une unique source. Par rapport à cettehypothèse, nous avons défini quatre étapes d'une méthode de transformation quipermettrait l'enrichissement de notre module ontologique

Rewriting SELECT SPARQL queries from 1:n complex correspondences

This paper presents a mechanism for rewriting SPARQL queries based on complex ontology correspondences. While the usefulness of simple correspondences, involving single entities from both source and target ontologies, has long been recognized, query rewriting requires more expressive links between ontology entities expressing the true relationships between them. Here, complex correspondences, in the format 1:n, between overlapping ontologies are exploited for rewriting SELECT SPARQL queries, so that they can be expressed over different RDF data sets in the Linked Open Data. Our approach has been evaluated using two data sets, one from the agriculture domain and another based on a reduced set involving the ontologies from the OAEI Conference track

Web de données agricole : transformation de sources pour une ontologie modulaire

National audienceNous souhaitons développer une ontologie pour annoter des corpus de documents sur la surveillance des cultures, la prévention des risques, la protection des cultures et les bonnes pratiques agricoles. Notre ontologie permettra aussi de stocker des données spatio-temporelles relatives aux observations faites sur le développement des cultures et les attaques des bio-agresseurs sur ces mêmes cultures. Le but étant de publier l’ensemble de ces données sur le web de données. Nous allons présenter dans ce document notre intention de développement d’une méthodologie de construction d’ontologie

Traitement des incompatibilités de candidats issus d'alignements entre plusieurs bases de connaissances

26es Journées Francophones d'Ingénierie des Connaissances IC 2015 @PFIA 2015, Rennes, FRA, 29-/06/2015 - 03/07/2015National audienceDe nombreux travaux ont été proposés dans la littérature dans le but de construire des ontologies à partir de sources telles que les thesaurus ou les classifications. Certaines de ces sources sont disponibles sur le Web de données, au format SKOS. Dans nos travaux, nous proposons de construire une base de connaissances destinée à un besoin applicatif particulier, en exploitant un ensemble de sources disponibles sur le domaine considéré. L'originalité de notre approche réside dans le fait d'exploiter la redondance entre les sources afin d'en extraire des candidats (classes, individus, propriétés...). Nous présentons dans cet article la notion d'incompatibilité entre candidats, qui résulte de l'hypothèse de travail selon laquelle nous ne considérons que des relations d'équivalence simple entre les sources. Nous présentons également la génération de sous-ensembles de candidats compatibles afin d'obtenir un consensus cohérent entre les sources. Cette approche a été évaluée sur un cas d'étude réel concernant le domaine de la taxonomie du blé, réalisée en collaboration avec un expert