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Introduction
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January 2013 - December 2020
Biogenouest (http://www.biogenouest.org/)
Position
- Managing Director
January 2012 - present
Publications
Publications (83)
Duck species are known to have different ability to fatty liver production in response to overfeeding and gene expression analyses can help to characterize mechanisms involved in these differences. This data article reports the sequencing of RNAs extracted from the liver of Pekin and Muscovy duck species and of their reciprocal hybrids, Mule and Hi...
Background:
Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from diff...
Background
Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from differ...
Background: Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from diffe...
Background: Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from diffe...
Background
Duck species are known to have different susceptibility to fatty liver production in response to overfeeding. In order to better describe mechanisms involved in the development of hepatic steatosis and differences between species, transcriptome analyses were conducted on RNAs extracted from the livers of Pekin and Muscovy duck species an...
Some studies have shown that expression of peroxisome proliferator-activated receptor gamma ( PPARG ), a key regulator of adipogenesis, and of some adipocyte-specific genes or adipokines are expressed in hepatic steatosis, leading to the concept of ‘adipogenic hepatic steatosis’ or ‘hepatic adiposis.’ Most of these studies were conducted in genetic...
Background:
The analysis of gene annotations referencing back to Gene Ontology plays an important role in the interpretation of high-throughput experiments results. This analysis typically involves semantic similarity and particularity measures that quantify the importance of the Gene Ontology annotations. However, there is currently no sound meth...
Genetic and genomic data analyses are outputting large sets of genes. Functional comparison of these gene sets is a key part of the analysis, as it identifies their shared functions, and the functions that distinguish each set. The Gene Ontology (GO) initiative provides a unified reference for analyzing the genes molecular functions, biological pro...
Le foie gras des palmipèdes gavés est l’expression d’une stéatose hépatique d’origine nutritionnelle, hypertrophique, réversible et caractérisée par une accumulation de triglycérides dans les hépatocytes. Cette aptitude est favorisée par certaines particularités physiologiques et métaboliques des oiseaux en particulier un site prépondérant de synth...
As DNA sequencing throughputs increase and genomics becomes commonplace, more and more animal species are studied. Thus, the duck genome sequence was published recently. However, although this is an important step and will drastically increase our knowledge on the biology of this species, complementary projects are needed. Some have been initiated,...
The fatty liver of overfed waterfowl results from a hepatic steatosis induced by specific nutritional conditions. This steatosis is hypertrophic, reversible and characterised by an accumulation of triglycerides in the hepatocytes. This ability is favoured by different physiological and metabolic peculiarities of birds such as the main site of lipid...
RÉSUMÉ La connaissance et la maîtrise des mécanismes mis en oeuvre lors de la stéatose hépatique sont des préalables essentiels à la définition de prédicteurs précoces expliquant une part de la variabilité des caractères exprimés chez le mulard. C'est dans ce contexte que le projet DLiverS a été entrepris. Il visait à analyser les transcriptomes hé...
RÉSUMÉ Avec la démocratisation des outils de la génomique et plus particulièrement du séquençage à haut débit, la séquence du génome du canard commun a été réalisée et va bientôt être publiée. Cependant, bien que ce soit une étape importante et un tournant dans les connaissances de la biologie de cette espèce, des projets complémentaires sont néces...
Session : Génétique, sélection et reproduction
The fatty liver of overfed waterfowl results from a hepatic steatosis induced by specific nutritional conditions. This steatosis is hypertrophic, reversible and characterised by an accumulation of triglycerides in the hepatocytes. This ability is favoured by different physiological and metabolic peculiarities of birds such as the main site of lipid...
As DNA sequencing throughputs increase and genomics becomes commonplace, more and more animal species are studied. Thus, the duck genome sequence was published recently. However, although this is an important step and will drastically increase our knowledge on the biology of this species, complementary projects are needed. Some have been initiated,...
Background:
There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression o...
Proportion of IEA according to duplicated gene number in the groups in nine species.
(TIF)
Description of DGD groups annotated for Gene Ontology. For each species, the number of groups, the number of annotated groups with GO terms and the percentage of groups annotated are indicated.
(DOC)
Background
As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of...
Figure S2. Distribution of the trait in both AIL populations. TI : Tonic Immobility.
Table S2. List of the genes localized in the candidate interval. Source : Biomart, Ensembl Genes 61 (Sanger UK), Gallus Gallus Genes (WASHUCS52).
Figure S3. Quail in a tonic immobility state. Immobilization is induced by keeping the animal on its back in a U-shaped cradle for 10 seconds.
Figure S1. Distribution of the functional annotation of the detected SNP (log scale). Annotations are from the Ensembl APIs (Application Programme Interface): the functional consequence of each SNP in each transcript has been predicted using the Variant Effect Predictor (VEP). All the non intergenic consequences are represented.
Table S1. List of the 384 SNP used in this study.
Background:
With the development of high throughput methods of gene analyses, there is a growing need for mining tools to retrieve relevant articles in PubMed. As PubMed grows, literature searches become more complex and time-consuming. Automated search tools with good precision and recall are necessary. We developed GO2PUB to automatically enrich...
This text file contents the experts selections for the query Q3.
GO2PUB results file for query Q1.
This text file contents the experts selections for the query Q2.
This text file contents the experts selections for the query Q1.
Bettembourg, C., Diot, C., Burgun, A., Dameron, O. (2012). GO2PUB: Querying PubMed with semantic expansion of gene ontology terms. Journal of Biomedical Semantics, 3, online (september), Non paginé. DOI : 10.1186/2041-1480-3-7 http://prodinra.inra.fr/record/168767
De nombreux progrès ont été réalisés ces dernières années en génomique. Le développement de technologies à base de supports miniaturisés, permet aujourd’hui d’explorer les génomes tant au niveau de leur structure que de leur expression. Les puces à ADN permettent ainsi de génotyper plusieurs milliers de marqueurs SNP d’un génome ou encore de mesure...
Session : Exploiting Genomics to Dissect the Genetic Control of Complex Traits
Much progress has been made in recent years in the genomics field. The development of technologies -based on miniaturized arrays makes it possible to explore genomes at both structural and functional levels. DNA microarrays allow to genotype several thousands of SNP in a genome, or measure the expression level of several thousands of genes in a tis...
The susceptibility to development of hepatic steatosis is known to differ between Muscovy and Pekin ducks. Although some experiments were conducted to decipher these differences, few data have been produced to analyse the role of specific genes in this process. For this purpose, expression levels of genes involved in lipid (ATP citrate lyase, malic...
List of the 1162 genes differentially expressed in the chicken liver after 16 h or 48 h of starvation ordered according to their HCA cluster. These 1162 genes i) were significantly differentially expressed between fasting and fed states (pvalue < 0.01), ii) exhibited at least an expression difference between two conditions exceeding an absolute 1.4...
Starvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression and in which the liver plays a central role. The present study aimed to describe the evolution of global gene expression profiles in liver of 4-week-old male chickens d...
Few genomic tools are available in ducks. To produce some new resources, we have designed Pekin (Anas platyrhynchos) and Muscovy (Cairina moschata) duck-specific primers for 22 genes involved mainly in lipid metabolism, and to a lesser extent in carbohydrate metabolism and other functions. Primers were designed according to duck sequences when avai...
Profils transcriptomiques de foies de poulet soumis au jeûne : utilisation d'une puce à ADN de 20000 oligonucléotides
RÉSUMÉ Le but du programme est de combler les déficits en marqueurs observés pour trois espèces aviaires : la caille, le canard et la poule. La stratégie choisie est l'obtention, à partir de plusieurs individus de lignées d'intérêt, de SNP (Single Nucleotide Polymorphism, polymorphisme d'un nucléotide) par une nouvelle technologie de séquençage à h...
Résumé : Starvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression profiles. In the chicken, liver is a major organ controlling energy metabolism. The present study aimed to describe the evolution of global gene expression pro...
Whereas many QTL for various traits were mapped in livestock, the identification of causal mutations remains laborious. In this study, we propose to combine transcriptomic data and linkage analysis for refining a chicken QTL region previously detected on GGA5 with a strong effect on abdominal fatness. Transcriptome profiles for 46 offspring of a si...
Excessive adiposity has become a major drawback in meat-type chicken production. However, few studies were conducted to analyze the liver expression of genes involved in pathways and mechanisms leading to adiposity. A previous study performed by differential display on RNAs extracted from chicken livers from lean and fat lines allowed us to isolate...
Polyunsaturated fatty acids (PUFA) are known to repress SCD-1 gene expression, key enzyme of monounsaturated fatty acid biosynthesis. Alterations of the monounsaturated/saturated fatty acids ratio have been implicated in various diseases related to the metabolic syndrome, including hypertension. We previously evidenced that lipogenesis end-products...
Sterol regulatory element binding protein-1 and -2 (SREBP-1 and -2) are key transcription factors involved in the biosynthesis
of cholesterol and fatty adds. The SREBP have mainly been studied in rodents in which lipogenesis is regulated in both liver
and adipose tissue. There is, however, a paucity of information on birds, in which lipogenesis occ...
Although excessive adiposity has become a major drawback in meat type chicken production, few of the genes involved in this process have been characterized so far. In order to identify putative genes involved in adiposity, we performed differential display analysis of RNAs extracted from the liver of divergently selected lean and fat chickens. Twen...
In order to provide information on chicken genome expression, expressed sequence tags (ESTs) were developed from chicken liver RNAs using a method based on arbitrarily primed reverse transcription-polymerase chain reaction (RT-PCR) of total RNAs. The method is similar to differential display, using one base anchored oligo-d(T) reverse-primers and 2...
In chicken, adiposity is influenced by hepatic stearoyl-CoA desaturase (SCD) 1. This gene is up-regulated by low-fat high-carbohydrate diet and down-regulated by addition of polyunsaturated fatty acids (PUFA). In this study, we present evidence for an inhibition of chicken SCD1 expression by PUFA using reporter gene constructs in transient transfec...
Hepatic stearoyl CoA desaturase (SCD) activity in chickens from a fat line is higher than that of chickens from a lean line and correlates with plasma triacylglycerol concentrations. Furthermore, in these lines, the hepatic SCD1 mRNA level is positively correlated with the adipose tissue weight. To analyze the contribution of the SCD1 gene in the r...
Increase in adipose tissues in meat-chicken carcasses has prompted investigations in order to control this unfavourable trait, to the benefit of both producers and consumers. Comparisons between experimental lean and fat chicken strains have pointed out the main metabolic differences between lean and fat birds. The main results are recalled. In add...
Peroxisome proliferator-activated receptors (PPAR) belong to the superfamily of the nuclear hormone receptors that play an important role in lipid homeostasis. A partial complementary deoxyribonucleic acid clone encoding a PPAR alpha from chicken liver was isolated and sequenced. Comparison with human, mouse, rat, and Xenopus PPAR alpha cDNA indica...
Previous studies have provided evidence for the important role of liver stearoyl-CoA desaturase (SCD) in excessive adiposity in the chicken and suggest that the difference in SCD activity between fat and lean chickens could be explained by a difference in SCD1 gene expression. In the present study, the regulation of SCD1 gene expression was analyze...
L’augmentation du poids de tissus adipeux présents dans les carcasses de poulet de chair a incité à en rechercher les causes, afin de pouvoir maîtriser ce caractère défavorable, tant pour les producteurs que pour les consommateurs. La comparaison de lignées expérimentales génétiquement grasses et maigres a permis d’identifier les différences métabo...
Avian lipogenesis was studied in the chicken hepatocarcinoma LMH cell line. The differentiated and lipogenic status of these cells was evidenced by the presence of the albumin mRNA as well as of some mRNA coding for enzymes involved in lipogenesis (acetyl-CoA carboxylase, fatty acid synthase, delta 9 desaturase) and for apoproteins (apoprotein B an...
Fatty acid synthase activity has been shown to be regulated mainly at the transcriptional level under both dietary and hormonal influences. As a first step towards elucidating the factors involved, we isolated and characterized chicken genomic clones encompassing the 5' part of the chicken fatty acid synthase gene and its flanking region. The entir...
A panel of four novel human hepatoma cell lines was isolated from a single tumor from a male individual. BC1, B16 and B16A2 lines were well differentiated, while cells of the B9 line were only poorly differentiated, being essentially negative for the functions analyzed. These cell lines have been surveyed for expression of a large set of plasma pro...
Acetyl-CoA carboxylase is a rate-limiting enzyme in the biogenesis of long-chain fatty acids. In the present study, the 5' end and flanking region of the acetyl-CoA carboxylase (ACC) gene was analysed in the chicken. A genomic clone was isolated containing the first three exons, the third one containing the ATG codon. Using nuclease-mapping experim...
We have previously succeeded in infecting normal human hepatocyte primary cultures with hepatitis B virus (HBV). However, infection was subject to individual variations even in the presence of dimethyl sulfoxide (DMSO), which appeared to increase the amounts of viral DNA associated with the cells. In this study, we have defined conditions which enh...
The possibility of obtaining expression of human hepatitis B virus (HBV) genes and production of virus particles in normal liver cells from heterologous species like normal adult rat hepatocytes, by transfecting the complete HBV genome, was investigated. Various techniques for hepatocyte transfection were assayed including the usual calcium-phospha...
Transient expression in a hepatoma cell line of an HBV variant with a defective pre-C region suggested its ability to undergo full replication cycles except for the lack of HBeAg synthesis.
The possibility of obtaining expression of human hepatitis B virus (HBV) genes and production of virus particles in normal liver cells from heterologous species like normal adult rat hepatocytes, by transfecting the complete HBV genome, was investigated. Various techniques for hepatocyte transfection were assayed including the usual calcium-phospha...
Hepatitis B virus (HBV) variants with a nonsense mutation in the distal pre-C region have been detected in patients positive for anti-HBe, and the complete nucleotide sequence of one cloned pre-C variant has been determined. Transfection of this HBV variant clone into the human hepatoma cell line HepG2 resulted in the appearance of major HBV transc...
A human hepatoblastoma cell clone E4 was obtained by transfection of HepG2 cells with a plasmid DNA containing four tandem copies of hepatitis B virus (HBV) genome. Analysis of both intracellular and extracellular viral DNA revealed that this clone exhibited the main steps of the replication process previously found in normal hepatocyte primary cul...
We investigated the possibility of infecting normal adult human hepatocytes maintained in pure cultures or in cocultures with hepatitis B virus (HBV). Several assays with different infectious sera and hepatocyte populations from various donors identified only limited HBV replication, with significant variations from one cell preparation to another....
Sterol regulatory element binding protein- 1 and -2 (SREBP-1 and -2) are key transcription factors involved in the biosynthesis of cholesterol and fatty acids. The SREBP have mainly been studied in rodents in which lipogenesis is regulated in both liver and adipose tissue. There is, however, a paucity of information on birds, in which lipogenesis o...
