Search results for "Array"
showing 10 items of 1264 documents
Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experim…
2013
© 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited. The binarization of consensus partition matrices (Bi-CoPaM) method has, among its unique features, the ability to perform ensemble clustering over the same set of genes from multiple microarray datasets by using various clustering methods in order to generate tunable tight clusters. Therefore, we have used the Bi-CoPaM method to the most synchronized 500 cell-cycle-regulated yeast genes from different microarray datasets to produce four tight, specific …
A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification
2007
This article is available from: http://www.biomedcentral.com/1471-2105/8/442
The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes
2003
Regulation of gene expression by mitogen-activated protein kinases (MAPKs) is essential for proper cell adaptation to extracellular stimuli. Exposure of yeast cells to high osmolarity results in rapid activation of the MAPK Hog1, which coordinates the transcriptional programme required for cell survival on osmostress. The mechanisms by which Hog1 and MAPKs in general regulate gene expression are not completely understood, although Hog1 can modify some transcription factors. Here we propose that Hog1 induces gene expression by a mechanism that involves recruiting a specific histone deacetylase complex to the promoters of genes regulated by osmostress. Cells lacking the Rpd3-Sin3 histone deac…
Molecular response of Saccharomyces cerevisiae wine and laboratory strains to high sugar stress conditions.
2010
One of the stress conditions that can affect Saccharomyces cerevisiae cells during their growth is osmotic stress. Under particular environments (for instance, during the production of alcoholic beverages) yeasts have to cope with osmotic stress caused by high sugar concentrations. Although the molecular changes and pathways involved in the response to saline or sorbitol stress are widely understood, less is known about how cells respond to high sugar concentrations. In this work we present a comprehensive study of the response to this form of stress which indicates important transcriptomic changes, especially in terms of the genes involved in both stress response and respiration, and the i…
Saccharomyces cerevisiae Glutaredoxin 5-deficient Cells Subjected to Continuous Oxidizing Conditions Are Affected in the Expression of Specific Sets …
2004
The Saccharomyces cerevisiae GRX5 gene codes for a mitochondrial glutaredoxin involved in the synthesis of iron/sulfur clusters. Its absence prevents respiratory growth and causes the accumulation of iron inside cells and constitutive oxidation of proteins. Null ⌬grx5 mu- tants were used as an example of continuously oxidized cells, as opposed to situations in which oxidative stress is instantaneously caused by addition of external oxi- dants. Whole transcriptome analysis was carried out in the mutant cells. The set of genes whose expression was affected by the absence of Grx5 does not significantly overlap with the set of genes affected in respiratory petite mutants. Many Aft1-dependent ge…
The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.
2010
In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3'/5' RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in …
Salmonella bongori Provides Insights into the Evolution of the Salmonellae
2011
The genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori…
TileCal optical multiplexer board 9U prototype
2007
This paper presents the architecture and the status of the optical multiplexer board (OMB) for the ATLAS/LHC Tile hadronic calorimeter (TileCal). This board will analyze the front-end data CRC to prevent bit and burst errors produced by radiation. Besides, due to its position within the data acquisition chain it will be used to emulate front-end data for tests. The first two prototypes of the final OMB 9U version have been produced at CERN. Detailed design issues and manufacture features of these prototypes are described. These prototypes are being validated whereas some firmware developments are being implemented in the programmable devices of the board. Functional descriptions of the boar…
Performance analysis of the out-of-band signaling scheme for high speed wireless LANs
2005
In this paper, we study the performance of our earlier proposed out-of-band signaling (OBS) scheme for high speed wireless local area networks (WLANs). We employ the system approximation technique for modeling of the OBS scheme. An equivalent state dependent single server queue, that describes the OBS scheme, is constructed for the analysis of the throughput and delay performances. Moreover, we study the throughput optimization of the OBS scheme, which provides a means for optimizing the performance of the OBS scheme, given a particular network environment. Finally, we conduct several simulation experiments to validate our analytical results.
Comprehensive Analysis of Gene Expression Profiles of the Beet Armyworm Spodoptera exigua Larvae Challenged with Bacillus thuringiensis Vip3Aa Toxin
2013
Made available in DSpace on 2014-12-03T13:11:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-12-02Bitstream added on 2014-12-03T13:22:24Z : No. of bitstreams: 1 WOS000327944500105.pdf: 2100332 bytes, checksum: 71ea7616e9a7949eed19cff4ce56111f (MD5) Spanish Ministerio de Ciencia e Innovacion European FEDER funds Generalitat Valenciana Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Host-pathogen interactions result in complex relationship, many aspects of which are not completely understood. Vip proteins, which are Bacillus thuringensis (Bt) insecticidal toxins produced during the vegetative stage, are selectively effective against specific insect pests. This ne…