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Search Results: 1 - 10 of 7653 matches for " Philippe Reymond "
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Global gene expression patterns in rice
Philippe Reymond
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-1-reports010
Abstract: The authors used 10 rice cDNA libraries represented in dbEST: database of expressed sequence tags. Each library contained at least 890 ESTs and was, in most cases, prepared from a different tissue or developmental stage. ESTs were organized into clusters and contig sequences, and expression profiles (EST counts) were derived for each of 707 contigs containing five or more constituent ESTs. In order to identify genes exhibiting a similar expression pattern, a statistical method (Pearson correlation coefficient) was used to calculate similarity between pairs of genes. These pairs of contigs were then organized into mutually matching clusters. The authors show, for example, that genes encoding storage proteins are clustered together and are predominantly found in libraries prepared from immature seed and panicle at ripening stage. The method is also successfully used to assess pairwise similarity between whole cDNA libraries and shows that two tissues expressing a similar complement of genes are clustered together. Finally, a two-dimensional graphical representation of expression measurements is presented which allows a rapid visualization of clusters of genes obeying similar expression patterns in different conditions (different libraries).A method for EST quality control and generation of contigs can be found at the Structural and genetic information server.Convincing evidence is provided that a rigorous statistical analysis of EST libraries allows fine-scale identification of sequences with correlated expression profiles. The application of this approach to a large collection of cDNA libraries prepared from different organisms at different developmental stages will certainly provide a valuable alternative to cDNA microarray studies in generating gene expression data. A limitation of such a technique is the need for standardization of the preparation of cDNA libraries to ensure that EST frequency tightly correlates with transcript abundance. As the method relies on t
Finding flavor genes
Philippe Reymond
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-2-reports0057
Abstract: Aharoni et al. randomly isolated 1,701 cDNA clones from a strawberry fruit cDNA library and 480 clones from petunia corolla (as control) and printed the PCR-amplified clones on chemically modified glass slides using a robotic device. They used these microarrays to monitor changes in gene expression at three fruit developmental stages (from green to red). Using a rigorous statistical analysis, the authors found that 401 clones were differentially expressed between all three stages, with 177 clones being upregulated between the green and red stages. Sequences of the latter group of genes revealed that more than 50% were related to primary and secondary metabolism. From the other sequences potentially involved in flavor formation, Aharoni et al. identified a novel gene (SAAT) for an alcohol acetyltransferase, an enzyme that catalyzes the final step in the synthesis of volatile esters. This gene shows 16-fold greater expression during the red stage than the green stage of fruit development. The authors expressed recombinant SAAT in Escherichia coli and confirmed that the enzyme has alcohol acetyltransferase activity. Analysis of a series of potential substrates suggests that SAAT is responsible for formation of the predominant esters found in ripe strawberries.Access to Arabidopsis cDNA microarrays is provided by the Arabidopsis Functional Genomics Consortium (AFGC). Links to information on plant microarrays can also be found via the Virtual library: plant-arrays.Large-scale cDNA microarrays are now used with model systems to investigate global patterns of gene expression at the level of the whole organism. The utility of microarrays that cover a restricted portion of the genome, like that described in this paper, will become increasingly recognized, however. This paper is a first example of the use of customized plant cDNA microarrays from a non-model system. It provides a good example of how a small selected array can be used to study a particular developmental proces
Global Analysis of Extracytoplasmic Stress Signaling in Escherichia coli
Stéphanie Bury-Moné ,Yanoura Nomane,Nancie Reymond,Romain Barbet,Eric Jacquet,Sandrine Imbeaud,Annick Jacq ,Philippe Bouloc
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000651
Abstract: The Bae, Cpx, Psp, Rcs, and σE pathways constitute the Escherichia coli signaling systems that detect and respond to alterations of the bacterial envelope. Contributions of these systems to stress response have previously been examined individually; however, the possible interconnections between these pathways are unknown. Here we investigate the dynamics between the five stress response pathways by determining the specificities of each system with respect to signal-inducing conditions, and monitoring global transcriptional changes in response to transient overexpression of each of the effectors. Our studies show that different extracytoplasmic stress conditions elicit a combined response of these pathways. Involvement of the five pathways in the various tested stress conditions is explained by our unexpected finding that transcriptional responses induced by the individual systems show little overlap. The extracytoplasmic stress signaling pathways in E. coli thus regulate mainly complementary functions whose discrete contributions are integrated to mount the full adaptive response.
Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways
Frédéric G Masclaux, Friederike Bruessow, Fabian Schweizer, Caroline Gouhier-Darimont, Laurent Keller, Philippe Reymond
BMC Plant Biology , 2012, DOI: 10.1186/1471-2229-12-227
Abstract: Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K), perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory.This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.Due to their sessile nature, plants have constantly to adjust to their changing environment. Temperature fluctuations, variation in water content in soil, and pathogen attacks are some of the environmental factors with which plants have to cope. In particular, the presence of plant neighbours often reduces the availability of resources including light, water and nutrients. This struggle for common limited resources, which leads to decrease in growth, survival and fecundity, is defined as ‘competition’. Furthermore, since plants often have passive seed dispersal, competition can occur between plant neighbours from the same species (intraspecific competition) and, even more, from closely related individuals [1].Competition does not only refer to the passive exploitation of limited resources by plants, but also to an active response to interferences caused by neighbours. It is now clearly established that plants are able to detect and interact with neighbours in different manners. Aboveground, the presence of neighbours can lead to a decrease in light intensity and quality available for the plant. Before light resource becomes limiting, plant
A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina
Frédérique Bidard, Sandrine Imbeaud, Nancie Reymond, Olivier Lespinet, Philippe Silar, Corinne Clavé, Hervé Delacroix, Véronique Berteaux-Lecellier, Robert Debuchy
BMC Research Notes , 2010, DOI: 10.1186/1756-0500-3-171
Abstract: We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS.A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.Development of a gene expression microarray comprises several time-consuming and complex steps. Probe libraries are generated by commercial services or specialized design programs [1], which analyze nucleic acid physical parameters to identify probes that offer the best theoretical characteristics, in terms of specificity and sensitivity. Optimal probe design is a compromise between these two latter features, which are predicted by computational methods that assume probes are in solution, while arrays, in fact, consist of surface-immobilized probes. Therefore an empirical approach appears as the optimal strategy to assess the quality of the probe design outcome [2-4]. This experimental step has been long overlooked, due to microarray cost and reluctance to modify a fixed design. In situ synthesized oligomer arrays now offer great flexibility for changing probes, thus promoting the addition of real hybridizations in the probe selection process. Probe design
Natural Variation in Arabidopsis thaliana Revealed a Genetic Network Controlling Germination Under Salt Stress
Navot Galpaz,Matthieu Reymond
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015198
Abstract: Plant responses to environmental stresses are polygenic and complex traits. In this study quantitative genetics using natural variation in Arabidopsis thaliana was used to investigate the genetic architecture of plant responses to salt stress. Eighty seven A. thaliana accessions were screened and showed a large variation for root development and seed germination under 125 and 200 mM NaCl, respectively. Twenty two quantitative trait loci for these traits have been detected by phenotyping two recombinants inbred line populations, Sha x Col and Sha x Ler. Four QTLs controlling germination under salt were detected in the Sha x Col population. Interestingly, only one allelic combination at these four QTLs inhibits germination under salt stress, implying strong epistatic interactions between them. In this interacting context, we confirmed the effect of one QTL by phenotyping selected heterozygous inbred families. We also showed that this QTL is involved in the control of germination under other stress conditions such as KCl, mannitol, cold, glucose and ABA. Our data highlights the presence of a genetic network which consists of four interacting QTLs and controls germination under limiting environmental conditions.
The future is genome-wide
Samuel Deutsch, Alexandre Reymond
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-8-324
Abstract: More than 1,700 human geneticists from 59 countries congregated in Amsterdam in May for this year's meeting of the European Society of Human Genetics, which mainly focused on the use of post-genome analysis tools to dissect the causes of and mechanisms governing complex traits. Many of the exciting studies presented were based on two technologies: array-based methods for genome-wide genotyping or technologies for high-density comparative genome hybridization (CGH). A highlight of the meeting was the keynote lecture by Nobel laureate Sydney Brenner (Salk Institute for Biological Studies, La Jolla, USA) on 'humanity's genes', which focused on the challenges we face in transforming the information from the human genome into concrete benefits for our societies.This year has seen the success of several whole-genome association studies using genotyping for single-nucleotide polymorphisms (SNPs) to identify genes responsible for some common complex phenotypes for both discrete and quantitative traits. A plenary lecture by Kari Stefansson (deCODE Genetics, Reykjavik, Iceland) highlighted the tremendous potential of this approach. Several examples were discussed in which new genes have recently been identified using a combination of linkage and association analysis approaches. One example is a locus on human chromosome 8p12 that confers susceptibility to schizophrenia. Although nucleotide variation around the NRG1 gene has been known to be associated with schizophrenia for the past 4 years, the mechanism of action of the associated SNPs, located in noncoding regions 53 to the gene, has remained unclear. Recent evidence strongly suggests that these variants might influence the level of NRG1 expression. Stefansson suggested that many SNPs involved in the etiology of complex phenotypes are likely to affect gene expression or splicing, and that these variants are under strong selective pressure. A second, more recent, example presented by Stefansson concerns the genetics of myoc
Carto-humeur, Carto humour. Avec mon petit atlas…
Mappemonde , 1989,
The Integration of Formal and Non-formal Education: The Dutch “brede school”
du Bois-Reymond, Manuela
Social Work and Society , 2009,
Abstract: The Dutch “brede school” (BS) development originates in the 1990s and has spread unevenly since: quicker in the primary than secondary educational sector. In 2007, there were about 1000 primary and 350 secondary BS schools and it is the intention of the government as well as the individual municipalities to extend that number and make the BS the dominant school form of the near future. In the primary sector, a BS cooperates with crèche and preschool facilities, besides possible other neighborhood partners. The main targets are, first, to enhance educational opportunities, particularly for children with little (western-) cultural capital, and secondly to increase women’s labor market participation by providing extra familial care for babies and small children. All primary schools are now obliged to provide such care. In the secondary sector, a BS is less neighborhood-orientated than a primary BS because those schools are bigger and more often located in different buildings. As in the primary sector, there are broad and more narrow BS, the first profile cooperating with many non-formal and other partners and facilities and the second with few. On the whole, there is a wide variety of BS schools, with different profiles and objectives, dependent on the needs and wishes of the initiators and the neighborhood. A BS is always the result of initiatives of the respective school and its partners: parents, other neighborhood associations, municipality etc. BS schools are not enforced by the government although the general trend will be that existing school organizations transform into BS. The integration of formal and non-formal education and learning is more advanced in primary than secondary schools. In secondary education, vocational as well as general, there is a clear dominance of formal education; the non-formal curriculum serves mainly two lines and objectives: first, provide attractive leisure activities and second provide compensatory courses and support for under-achievers who are often students with migrant background. In both sectors, primary and secondary, it is the formal school organization with its professionals which determines the character of a BS; there is no full integration of formal and non-formal education resulting in one non-disruptive learning trajectory, nor is there the intention to go in that direction. Non-formal pedagogues are partly professionals, like youth- and social workers, partly volunteers, like parents, partly non-educational partners, like school-police, psycho-medical help or commercial leisure providers. Besides that, t
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
Gert Sclep, Joke Allemeersch, Robin Liechti, Bj?rn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin TR Kuiper, Pierre Hilson
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-400
Abstract: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition.To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA databas
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