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Search Results: 1 - 10 of 325440 matches for " S. Reymond "
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QTL for floral stem lignin content and degradability in three recombinant inbred line (RIL) progenies of Arabidopsis thaliana and search for candidate genes involved in cell wall biosynthesis and degradability  [PDF]
H. Chavigneau, N. Goué, S. Delaunay, A. Courtial, L. Jouanin, M. Reymond, V. Méchin, Y. Barrière
Open Journal of Genetics (OJGen) , 2012, DOI: 10.4236/ojgen.2012.21002
Abstract: Deciphering the genetic determinants involved in cell wall assembly is a strategic issue for breeding programs that target both ruminant feeding and biofuel production. The Arabidopsis thaliana model system has great potentials to elucidate the genetic determinants involved in cell wall component biosynthesis and those involved in the regulation cascades allowing their coordinated assembly. QTL for biomass quality related traits (cell wall content, lignin content, and cell wall degradability) were mapped in the three Arabidopsis RIL progenies Bay0 × Shahdara, Bur0 × Col0, and Blh1 × Col0. Overall, 40 QTL were detected for these traits, explaining up to 33 and 12% of the observed phenotypic variation for lignin content and cell wall degradability respectively. Major QTL hotspots were mapped on chromosome 1 (position 5 Mbp), chromosome 4 (position 1 Mbp), and chromosome 5 (position 3 Mbp). A putative candidate gene set (82 genes) was considered including those previously described as involved in cell wall phenolic component biosynthesis, their regulation factors, and genes involved in lignified tissue patterning. Colocalisations observed (according to the reference sequence of Col0) between the detected QTL and these candidate genes did not prioritize any of the three gene groups (monolignol biosynthesis, transcription factors, lignified tissue patterning). Colocalizations were thus observed for 57% of monolignol biosynthesis related genes, 55% of the transcription factors considered, and 66% of genes considered to be involved in lignified tissue patterning and assembly. Colocalizations were observed for at least one member of all investigated gene families, except WRKY transcription factors. Colocalizations were also shown with several miRNA putatively involved in the regulation of lignifying tissue assembly. Taking into account the QTL shown in the Bur0 × Col0 progeny, allelic variations were shown in the MYB32, MYB58, MYB75, GRAS SCARECROW, AtC3H14 zinc finger, SHINE2, and IFL1 genes and in the AtMIR397a. Given that the list of candidate genes is not complete, and because the QTL support intervals encompassed genes of still unknown function, it is still not clear whether one of the selected candidates is responsible for the effect of a detected QTL. Mutant investigation and positional cloning steps are likely essential to clearly determine the causal mechanism involved in cell wall degradability variation.
Multi-axis integrated Hall magnetic sensors
Popovi? Radivoje S.,Kejik Pavel,Reymond Serge,Popovi? Dragana R.
Nuclear Technology and Radiation Protection , 2007, DOI: 10.2298/ntrp0702020p
Abstract: Conventional Hall magnetic sensors respond only to the magnetic field component perpendicular to the surface of the sensor die. Multi-axis sensing capability can be provided in the following two ways: (a) by integrating magnetic flux concentrators on the die, and (b) by using vertical Hall devices. Here we review the most important two-and three-axis integrated Hall magnetic sensors based on these concepts. Their applications include mapping of magnetic fields and sensing angular position.
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
Studies on whole cell fluorescence-based screening for epoxide hydrolases and Baeyer-Villiger monoxygenases
Bicalho, Beatriz;Chen, Lu S.;Grognux, Johann;Reymond, Jean-Louis;Marsaioli, Anita J.;
Journal of the Brazilian Chemical Society , 2004, DOI: 10.1590/S0103-50532004000600019
Abstract: biocatalysis reactions were performed on microtiter plates (200 μl) aiming at the utilization of fluorogenic substrates (100 μmol l-1) for rapid whole cell screening for epoxide hydrolases (ehs) and baeyer-villiger monoxygenases (bvmos). a final protocol was achieved for ehs, with 3 new enzymatic sources being detected (agrobacterium tumefaciens, pichia stipitis, trichosporom cutaneum). the fluorogenic assay for bvmo did not work as expected. however, an approach to possible variables involved (aeration; ph) provided the first detection of a bvmo activity in t. cutaneum.
Anomalous double peak structure in Nb/Ni superconductor/ferromagnet tunneling DOS
P. SanGiorgio,S. Reymond,M. R. Beasley,J. H. Kwon,K. Char
Physics , 2007, DOI: 10.1103/PhysRevLett.100.237002
Abstract: We have experimentally investigated the density of states (DOS) in Nb/Ni (S/F) bilayers as a function of Ni thickness, $d_F$. Our thinnest samples show the usual DOS peak at $\pm\Delta_0$, whereas intermediate-thickness samples have an anomalous ``double-peak'' structure. For thicker samples ($d_F \geq 3.5$ nm), we see an ``inverted'' DOS which has previously only been reported in superconductor/weak-ferromagnet structures. We analyze the data using the self-consistent non-linear Usadel equation and find that we are able to quantitatively fit the features at $\pm\Delta_0$ if we include a large amount of spin-orbit scattering in the model. Interestingly, we are unable to reproduce the sub-gap structure through the addition of any parameter(s). Therefore, the observed anomalous sub-gap structure represents new physics beyond that contained in the present Usadel theory.
Studies of YBCO Strip Lines under Voltage Pulses: Optimisation of the Design of Fault Current Limiters
M. Decroux,L. Antognazza,S. Reymond,W. Paul,M. Chen,O. Fischer
Physics , 2003,
Abstract: We present experimental results on the behaviour of a superconducting YBCO/Au meander of length L submitted to short circuit tests with constant voltage pulses. The meander, at the beginning of the short-circuit, is divided in two regions; one, with a length L1 proportional to the applied voltage, which first switches into a highly dissipative state (HDS) while the rest remains superconducting. Then the rest of the meander will progressively switch into the normal state due to the propagation of this HDS (few m/s) from both ends. The part L1 has to initially support a power density proportional to r.Jp^2 (r is the resistivity of the bilayer and Jp the peak current density). To avoid local excessive dissipation of power and over heating on one part of the wafer in the initial period, we have developed a novel design in order to distribute the dissipating section of the meander into many separated small dissipative zones. Furthermore the apparent propagation velocity of these dissipative zones is increased by the number of propagation fronts. We will show results obtained on 3kW (300V, 10A) FCL on a 2" wafer which confirm the benefits of this new design.
Current-induced highly dissipative domains in high Tc thin films
S. Reymond,L. Antognazza,M. Decroux,E. Koller,P. Reinert,O. Fischer
Physics , 2002, DOI: 10.1103/PhysRevB.66.014522
Abstract: We have investigated the resistive response of high Tc thin films submitted to a high density of current. For this purpose, current pulses were applied into bridges made of Nd(1.15)Ba(1.85)Cu3O7 and Bi2Sr2CaCu2O8. By recording the time dependent voltage, we observe that at a certain critical current j*, a highly dissipative domain develops somewhere along the bridge. The successive formation of these domains produces stepped I-V characteristics. We present evidences that these domains are not regions with a temperature above Tc, as for hot spots. In fact this phenomenon appears to be analog to the nucleation of phase-slip centers observed in conventional superconductors near Tc, but here in contrast they appear in a wide temperature range. Under some conditions, these domains will propagate and destroy the superconductivity within the whole sample. We have measured the temperature dependence of j* and found a similar behavior in the two investigated compounds. This temperature dependence is just the one expected for the depairing current, but the amplitude is about 100 times smaller.
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
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