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Amplification biases: possible differences among deviating gene expressions Inra
Degrelle, S.A.; Hennequet-Antier, C.; Chiapello, H.; Piot-Kaminski, K.; Piumi, F.; Robin, S.; Renard, J.P.; Hue, I..
BackgroundGene expression profiling has become a tool of choice to study pathological or developmental questions but in most cases the material is scarce and requires sample amplification. Two main procedures have been used: in vitro transcription (IVT) and polymerase chain reaction (PCR), the former known as linear and the latter as exponential. Previous reports identified enzymatic pitfalls in PCR and IVT protocols; however the possible differences between the sequences affected by these amplification defaults were only rarely explored.ResultsScreening a bovine cDNA array dedicated to embryonic stages with embryonic (n = 3) and somatic tissues (n = 2), we proceeded to moderate amplifications starting from 1 μg of total RNA (global PCR or IVT one round)....
Tipo: Journal Article Palavras-chave: AMPLIFICATION; IN VITRO TRANSCRIPTION (IVT); POLYMERASE CHAIN REACTION (PCR); GENE EXPRESSION; MICROARRAY.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200839ed8f6c&uri=/notices/prodinra1/2009/11/
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Analysis of a simulated microarray dataset : Comparison of methods for data normalisation and detection of differential expression Inra
Watson, M.; Pérez-Alegre, M.; Baron, M.D.; Delmas, C.; Dovc, P.; Duval, M.; Foulley, J.L.; Garrido-Pavon, J.J.; Hulsegge, I.; Jaffrézic, F.; Jiménez-Marin, A.; Lavric, M.; Lê Cao, K.A.; Marot, G.; Mouzaki, D.; Pool, M.H.; Robert-Granié, C.; San Cristobal, M.; Tosser-Klopp, G.; Waddington, D.; Koning, D.J. de.
Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed.Methods of comparing the normalised data are also abundant, and no clear consensus has yetbeen reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively.Use of an intensity-dependent normalisation procedure was common, as was correction formultiple testing. Most variety in performance...
Tipo: Journal Article Palavras-chave: GENE EXPRESSION; STATISTICAL ANALYSIS; SIMULATION; TWO COLOUR MICROARRAY.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008dce3eba7&uri=/notices/prodinra1/2011/04/
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Analysis of the transcript levels of VvAdh1, VvAdh2 and VvGrip4, three genes highly expressed during Vitis vinifera L. berry development Inra
Tesniere, C.; Davies, C.; Sreekantan, L.; Bogs, J.; Thomas, M.; Torregrosa, L..
Well defined promoter sequences are required for the targeted expression of genes in transgenic grapevines. This paper describes a detailed study of the expression of three genes with potentially useful promoters. We have used real-time RT-PCR to evaluate the transcript levels of VvAdh1, VvAdh2 and VvGrip4 genes in various tissues (root, bud, tendril, inflorescence, fruit and embryogenic callus) of Vitis vinifera L. at different stages of development. Transcript levels of the three genes were highest in berry tissues but each had a distinct pattern of expression. VvAdh1 showed higher transcript levels during the early stages of berry development, while levels of VvAdh2 and VvGrip4 were higher during ripening. However, none of these genes was expressed in a...
Tipo: Journal Article Palavras-chave: BAIE; DEVELOPPEMENT DU FRUIT ALCOHOL DESHYDROGENASE; GENE EXPRESSION; FRUIT DEVELOPMENT; PROMOTER.
Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2006e5329af6&uri=/notices/prodinra1/2008/08/
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Development and activity of Glomus intraradices as affected by co-existence with Glomus claroideum in one root system Inra
Janoušková, M.; Seddas, P.; Mrnka, L.; Van Tuinen, D.; Dvořáčková, A.; Tollot, M.; Gianinazzi-Pearson, V.; Vosátka, M.; Gollotte, A..
The co-existence of two arbuscular mycorrhizal fungal (AMF) species, Glomus intraradices and Glomus claroideum, in the root systems of plants was investigated in a greenhouse experiment aimed at reconstructing interactions during an early stage of primary succession on a coal-mine spoil bank in Central Europe. Two plant species, Tripleurospermum inodorum and Calamagrostis epigejos, were inoculated either with one or both AMF species. Fungal development, determined by trypan blue and alkaline phosphatase staining as well as by PCR amplification of rRNA genes with species-specific primers, and the expression of five genes with different metabolic functions in the intraradical structures of G. intraradices were followed after 6 and 9 weeks of cultivation. The...
Tipo: Journal Article Palavras-chave: MYCORHIZES A ARBUSCULES; PHOSPHATASE ALCALINE; MYCELIUM INTRARADICAL ALKALINE PHOSPHATASE; ARBUSCULAR MYCORRHIZA; GENE EXPRESSION; INTRARADICAL MYCELIUM; NESTED PCR.
Ano: 2009 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20119c7b67f7&uri=/notices/prodinra1/2011/05/
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Dietary vitamin mix levels influence the ossification process in European sea bass (Dicentrarchus labrax) larvae Inra
Mazurais, D.; Darias, M.J.; Gouillou-Coustans, M.F.; Le Gall, M.M.; Huelvan, C.; Desbruyères, E.; Quazuguel, P.; Cahu, C.; Zambonino Infante, J.L..
Tipo: Journal Article Palavras-chave: MORPHOGENESIS; BONE DIFFERENTIATION; DIETARY VITAMIN; GENE EXPRESSION.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200844338209&uri=/notices/prodinra1/2010/09/
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Differential activities of four Lactobacillus casei promoters during bacterial transit through the gastrointestinal tracts of human-microbiota-associated mice Inra
Oozeer, R.; Furet, J.P.; Goupil-Feuillerat, N.; Anba, J.; Mengaud, J.; Corthier, G..
In a previous study using fusion of the deregulated lactose promoter lacTp* and reporter genes, we suggested that Lactobacillus casei could initiate de novo protein synthesis during intestinal transit. In order to confirm this finding and extend it to other promoters, we adopted a reverse transcriptase quantitative PCR (RT-QPCR) approach combined with a transcriptional fusion system consisting of luciferase genes under the control of four promoters (ccpA, dlt, ldh, and lacT*) from L. casei DN-114 001. Promoter expression was monitored during cell growth, and variable luciferase activities were detected. In 3-day cultures, all the genetically modified strains survived but without exhibiting luciferase activity. Luciferase mRNA levels determined by RT-QPCR...
Tipo: Journal Article Palavras-chave: HUMAN; MOUSE; GENE EXPRESSION; INTESTINAL MICROBIOTA; FECES; RT-QPCR; PROBIOTIC; GASTROINTESTINAL TRACT.
Ano: 2005 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008ec5c541b&uri=/notices/prodinra1/2008/06/
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Expression of phenol oxidase and heat-shock genes during the development of Agaricus bisporus fruiting bodies, healthy and infected by Lecanicillium fungicola Inra
Largeteau, M.; Latapy, C.; Minvielle, N.; Regnault-Roger, C.; Savoie, J.M..
The fungal pathogen Lecanicillium fungicola (formerly Verticillium fungicola) is responsible for severe losses worldwide in the mushroom (Agaricus bisporus) industry. Infected crops are characterised by masses of undifferentiated tissue (bubbles) growing in place of sporophores. The expression of three laccase genes (lcc1, lcc2 and lcc3), two tyrosinase genes (AbPPO1 and AbPPO2) and the hspA gene encoding a heat-shock protein known to be potentially associated with host–pathogen interaction was investigated in mycelial aggregates and during the development of healthy sporophores and bubbles of a susceptible cultivar. The lcc3, AbPPO2 and hspA genes were each expressed at different levels at the different stages of sporophore morphogenesis, whilst they...
Tipo: Journal Article Palavras-chave: SPOROPHORE; EXPRESSION DES GÈNES; FRUCTIFICATION BUBBLE DISEASE; FUNGAL PATHOGEN; MUSHROOM; GENE EXPRESSION; HSP70; LACCASE; TYROSINASE.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200968262c91&uri=/notices/prodinra1/2010/09/
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Functional analysis and expression characteristics of chloroplastic Prx IIE Inra
Gama, F.; Bréhélin, C; Gelhaye, É.; Meyer, Y; Jacquot, J.P.; Rey, P; Rouhier, N..
Peroxiredoxins (Prxs) are ubiquitous thiol-dependent peroxidases capable of eliminating a variety of peroxides through reactive catalytic cysteines, which are regenerated by reducing systems. Based on amino acid sequences and their mode of catalysis, five groups of thiol peroxidases have been distinguished in plants, and type II Prx is one of them with representatives in many sub-cellular compartments. The mature form of poplar chloroplastic Prx IIE was expressed as a recombinant protein in Escherichia coli. The protein is able to reduce H2O2 and tert-butyl hydroperoxide and is regenerated by both glutaredoxin (Grx) and thioredoxin (Trx) systems. Nevertheless, compared with Trxs, Grxs, and more especially chloroplastic Grx S12, are far more efficient...
Tipo: Journal Article Palavras-chave: CHLOROPLAST GENETICS; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENES; ARABIDOPSIS THALIANA; PLANTS.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010720c64a1&uri=/notices/prodinra1/2011/02/
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Fungi have three tetraspanin families with distinct functions Inra
Lambou, K; Tharreau, D.; Kohler, A.; Sirven, C; Marguerettaz, M; Barbisan, C; Sexton, A; Kellner, E; Martin, F.; Howlett, B; Orbach, M; Lebrun, MH.
Background: Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human andmouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin families have beenidentified in fungi. These are Pls1, which is required for pathogenicity of the plant pathogenic ascomycetes, Magnaporthe grisea,Botrytis cinerea and Colletotrichum lindemuthianum, and Tsp2, whose function is unknown. In this report, we describe a third familyof tetraspanins (Tsp3) and a new family of tetraspanin-like proteins (Tpl1) in fungi. We also describe expression of some of thesegenes in M. grisea and a basidiomycete, Laccaria bicolor, and also their functional analysis in M. grisea. Results: The exhaustive search...
Tipo: Journal Article Palavras-chave: BASIDIOMYCETES; ASCOMYCETES; COPRINUS CINEREUS; LACCARIA BICOLOR; MAGNAPORTHE GRISEA; PROTEINE MEMBRANAIRE; TETRASPANINE; PATHOGENIE; POUVOIR PATHOGENE; INFECTION RICE; BARLEY; GENE EXPRESSION; MYCELIUM; PATHOGENICITY; PLANT PATHOGENIC FUNGI; SURFACE PROTEINS; TRANSCRIPTION; DNA TRANSCRIPTION; MEMBRANE PROTEINS.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20101f8edf6&uri=/notices/prodinra1/2010/11/
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Gene transcription in Lactarius quietus-Quercus petraea ectomycorrhizas from a forest soil Inra
Courty, P.E.; Poletto, M; Duchaussoy, F.; Buee, M.; Garbaye, J.; Martin, F..
Extracting fungal mRNA from ectomycorrhizas (ECMs) and forest soil samples for monitoring in situ metabolic activities is a significant challenge when studying the role of ECMs in biogeochemical cycles. A robust, simple, rapid, and effective method was developed for extracting RNA from rhizospheric soil and ECMs by adapting previous grinding and lysis methods. The quality and yield of the extracted RNA were sufficient to be used for reverse transcription. RNA extracted from ECMs of Lactarius quietus in a 100-year-old oak stand was used to construct a cDNA library and sequence expressed sequence tags. The transcripts of many genes involved in primary metabolism and in the degradation of organic matter were found. The transcription levels of four...
Tipo: Journal Article Palavras-chave: ECTOMYCORHIZE AMINO ACIDS; ECTOMYCORRHIZAS; FOREST SOILS; GENE EXPRESSION; GLUTAMATE-AMMONIA LIGASE; METABOLISM; MYCORRHIZAL FUNGI; N-ACETYL-BETA-GLUCOSAMINIDASE; RHIZOSPHERE; RNA; SOIL TYPES; BETA-N-ACETYLGLUCOSAMINIDASE; DNA TRANSCRIPTION; GLUTAMINE SYNTHETASE; RIBONUCLEIC ACID; TYROSINASE.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010e4344c33&uri=/notices/prodinra1/2010/11/
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Hepatic glucokinase and glucose-6-phosphatase responses to dietary glucose and starch in gilthead sea bream (Sparus aurata) juveniles reared at two temperatures Inra
Enes, P.; Panserat, S.; Kaushik, S.; Oliva-Teles, A..
Tipo: Journal Article Palavras-chave: CARBOHYDRATE; GENE EXPRESSION; GILTHEAD SEA BREAM; GLUCOKINASE; GLUCOSE-6-PHOSPHATASE.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2007c34ac6ff&uri=/notices/prodinra1/2007/12/
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Impact of chloroplastic- and extracellular-sourced ROS on high light-responsive gene expression in Arabidopsis Inra
Bechtold, U.; Richard, O.; Zamboni, A.; Gapper, C.; Geisler, M.; Pogson, B.; Karpinski, S.; Mullineaux, P.M..
The expression of 28 high light (HL)-responsive genes of Arabidopsis was analysed in response to environmental and physiological factors known to influence the expression of the HL-responsive gene, ASCORBATE PEROXIDASE2 (APX2). Most (81%) of the HL-responsive genes, including APX2, required photosynthetic electron transport for their expression, and were responsive to abscisic acid (ABA; 68%), strengthening the impression that these two signals are crucial in the expression of HL-responsive genes. Further, from the use of mutants altered in reactive oxygen species (ROS) metabolism, it was shown that 61% of these genes, including APX2, may be responsive to chloroplast-sourced ROS. In contrast, apoplastic/plasma membrane-sourced H2O2, in part directed by the...
Tipo: Journal Article Palavras-chave: CHLOROPLAST; EXCESS LIGHT; GENE EXPRESSION; PLASMA MEMBRANE; REACTIVE OXYGEN SPECIES; SIGNALLING.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200950d31e9d&uri=/notices/prodinra1/2010/08/
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Liver and muscle metabolic changes induced by dietary energy content and genetic selection in rainbow trout (Oncorhynchus mykiss) Inra
Kolditz, C.; Borthaire, M.; Richard, N.; Corraze, G.; Panserat, S.; Vachot, C.; Lefèvre, F.; Medale, F..
Tipo: Journal Article Palavras-chave: ACTIVITE ENZYMATIQUE FISH NUTRITION; METABOLISM; ENZYME ACTIVITY; GENE EXPRESSION.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20089604c1dd&uri=/notices/prodinra1/2010/09/
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Molecular characterization of a second copy of holocarboxylase synthetase gene (hcs2) in Arabidopsis thaliana Inra
Denis, L.; Grossemy, M.; Douce, R.; Alban, C.. (Coordinateur).
Tipo: Journal Article Palavras-chave: CELLULE VEGETALE; HOLOCARBOXYLASE SYNTHETASE; EPISSAGE ALTERNATIF; BIOTINYLATION DES PROTEINES PLANTE; PLANT; PLANT CELL; HOLOCARBOXYLASE SYNTHETASE; METABOLISM; BIOCHEMISTRY; VITAMIN; BIOTIN; ENZYME; GENE EXPRESSION; MRNA; ALTERNATIVE SPLICING; PROTEIN BIOTINYLATION.
Ano: 2002 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2007210a015e&uri=/notices/prodinra1/2010/11/
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Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism Inra
Merret, R.; Moulia, B.; Hummel, I.; Cohen, D.; Dreyer, E.; Bogeat, M.B..
Background: Technological advances have enabled the accurate quantification of gene expression, even within single cell types. While transcriptome analyses are routinely performed, most experimental designs only provide snapshots of gene expression. Molecular mechanisms underlying cell fate or positional signalling have been revealed through these discontinuous datasets. However, in developing multicellular structures, temporal and spatial cues, known to directly influence transcriptional networks, get entangled as the cells are displaced and expand. Access to an unbiased view of the spatiotemporal regulation of gene expression occurring duringdevelopment requires a specific framework that properly quantifies the rate of change of a property in a moving...
Tipo: Journal Article Palavras-chave: POPULUS DELTOIDES × NIGRA CV 'SOLIGO'); GENE EXPRESSION; MONITORING; REAL-TIME POLYMERASE CHAIN REACTION; KINEMATICS; GROWTH REGULATION; VELOCITY; RNA.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2011c2f24ced&uri=/notices/prodinra1/2011/01/
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Pheromones in a Superorganism : From Gene to Social Regulation Inra
ALAUX, C.; Maisonnasse, A.; Le Conte, Y..
Analogous to the importance of hormones in controlling organism homoeostasis, pheromones play a major role in the regulation of group homoeostasis at the social level. In social insects, pheromones coordinate the association of “unitary” organisms into a coherent social unit or so called “superorganism.” For many years, honey bees have been a convincing model for studying pheromone regulation of social life. In addition, with the recent sequencing of its genome, a global view of pheromone communication is starting to emerge, and it is now possible to decipher this complex chemical language from the molecular to the social level. We review here the different pheromones regulating the main biological functions of the superorganism and detail their respective...
Tipo: Journal Article Palavras-chave: SOCIETE ANIMALE; INSECTE SOCIAL; DIVISION DU TRAVAIL; REGULATION PHYSIOLOGIQUE; REPRODUCTION; LONGEVITE; REGULATION COMPORTEMENTALE; DEFENCE; REGULATION GENIQUE; PHEROMONE; EXPRESSION GENIQUE HONEY BEE; DIVISION OF LABOR; SOCIAL REGULATION; GENE EXPRESSION; TRANSCRIPTION FACTOR; CIS-REGULATORY ELEMENT; JUVENILE HORMONE; VITELLOGENIN.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2011fb3b2963&uri=/notices/prodinra1/2011/04/
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Population transcriptomics of life-history variation in the genus Salmo Inra
Giger, T.; Excoffier, L.; Amstutz, U.; Day, P.; Champigneulle, A.; Hansen, M; Kelso, J.; Largiadèr, C.R..
Tipo: Journal Article Palavras-chave: EXPRESSION DU GENE; SALMONIDES; ADN cDNA MICROARRAY; GENE EXPRESSION; LIFE HISTORY; POPULATION TRANSCRIPTONIC SALMONIDS.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200914bd7e3d&uri=/notices/prodinra1/2009/03/
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Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate Inra
Krouk, G.; Mirowski, P.; LeCun, Y.; Shasha, D.E.; Coruzzi, G.M..
BackgroundNitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified.ResultsHere we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes...
Tipo: Journal Article Palavras-chave: ROOT ; GENE EXPRESSION.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2011b2779f64&uri=/notices/prodinra1/2011/05/
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R-spondin1 is required for normal epithelial morphogenesis during mammary gland development Inra
Chadi, S.; Buscara, L.; Péchoux, C.; Costa, J.; Laubier, J.; Chaboissier, M-C; Pailhoux, E.; Vilotte, J.L.; Chanat, E.; Le Provost, F..
The R-spondin (Rspo) proteins constitute a novel class of ligands that induce Wnt signalling. Rspo1 knockout XX mice were previously shown to be sex-reversed, but some remain sub-fertile. These last were unable to feed their pups for some unknown reason. Using these mice and transplanted mammary tissues from Rspo1(-/-) virgin mice in nude mice, we report that the lack of Rspo1 expression results in the absence of duct side-branching development and subsequent alveolar formation, explaining the above mentioned phenotype. Our data demonstrate that local epithelial Rspo1 signalling is required for normal development of the mammary gland.
Tipo: Journal Article Palavras-chave: MAMMARY GLAND; EPITHELIAL CELL; DEVELOPMENT; R-SPONDIN; DUCT FORMATION; GENE EXPRESSION.
Ano: 2009 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD201088080799&uri=/notices/prodinra1/2010/05/
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Site-specific antiphagocytic function of the Photorhabdus luminescens type III secretion system during insect colonization Inra
Brugirard-Ricaud, K.; Duchaud, E.; Givaudan, A.; Girard, P.A.; Kunst, F.; Boemare, N.; Brehélin, M.; Zumbihl, R..
Photorhabdus is an entomopathogenic bacterium belonging to the Enterobacteriaceae. The genome of the TT01 strain of Photorhabdus luminescens was recently sequenced and a large number of toxin-encoding genes were found. Genomic analysis predicted the presence on the chromosome of genes encoding a type three secretion system (TTSS), the main role of which is the delivery of effector proteins directly into eukaryotic host cells. We report here the functional characterization of the TTSS. The locus identified encodes the secretion/translocation apparatus, gene expression regulators and an effector protein - LopT - homologous to the Yersinia cysteine protease cytotoxin YopT. Heterologous expression in Yersinia demonstrated that LopT was translocated into mammal...
Tipo: Journal Article Palavras-chave: ENTOMOPATHOGENIC BACTERIUM; GENE EXPRESSION; ENTOMOPATHOGENIC NEMATODE; INSECT CELL MEMBRANE.
Ano: 2005 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008e8fb85eb&uri=/notices/prodinra1/2009/03/
Registros recuperados: 24
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