JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database—the JASPAR CORE sub-database—has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net

EFEITO DO ÓLEO DE COCO NAS COMPLICAÇÕES DA DOENÇA HEPÁTICA

Background: Prevention of the progression of cirrhosis with dietary supplementation has been in focus Coconut oil has been suggested. Objective: To evaluate the effect of coconut oil supplementation in cirrhotic rats. Method: Forty Wistars were divided: control (CO), control + coconut oil (CO + OC), thioacetamide (TAA) and thioacetamide + coconut oil (TAA + OC). TAA was added to water for 13 weeks and coconut oil was administered by gavage. Blood, liver, muscle and nervous tissue samples were obtained for laboratory and histopathological analyses. Results: AST, ALT, total cholesterol, HDL, LDL, triglycerides were not statistically significant. In histology, even without differences, there was a tendency towards significance regarding the proliferation of bile ducts, fibrotic septa and muscle fiber atrophy between the TAA and TAA + OC groups. Conclusion: No significant protective effect of coconut oil on liver disease was found.Racional: A prevenção da evolução da cirrose com suplementação dietética tem estado em foco óleo de coco tem sido sugerido. Objetivo: Avaliar o efeito da suplementação de óleo de coco em ratos cirróticos. Método: Quarenta Wistar foram divididos: controle (CO); controle + óleo de coco (CO+OC); tioacetamida (TAA) e tioacetamida + óleo de coco (TAA + OC). O TAA foi adicionado à água por 13 semanas e o óleo de coco administrado por gavagem. Amostras de sangue, fígado, tecido muscular e nervoso foram obtidas para análises laboratorial e histopatológica. Resultados: AST, ALT, colesterol total, HDL, LDL, triglicérides não foram estatisticamente significantes. Na histologia, mesmo sem diferenças, houve tendência na significância quanto a proliferação de ductos biliares, septos fibróticos e atrofia da fibra muscular entre os grupos TAA e TAA + OC. Conclusão: Não foi encontrado efeito protetor significativo do óleo de coco na doença hepática

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices

<p>Abstract</p> <p>Background</p> <p>The accurate determination of transcription factor binding affinities is an important problem in biology and key to understanding the gene regulation process. Position weight matrices are commonly used to represent the binding properties of transcription factor binding sites but suffer from low information content and a large number of false matches in the genome. We describe a novel algorithm for the refinement of position weight matrices representing transcription factor binding sites based on experimental data, including ChIP-chip analyses. We present an iterative weight matrix optimization method that is more accurate in distinguishing true transcription factor binding sites from a negative control set. The initial position weight matrix comes from JASPAR, TRANSFAC or other sources. The main new features are the discriminative nature of the method and matrix width and length optimization.</p> <p>Results</p> <p>The algorithm was applied to the increasing collection of known transcription factor binding sites obtained from ChIP-chip experiments. The results show that our algorithm significantly improves the sensitivity and specificity of matrix models for identifying transcription factor binding sites.</p> <p>Conclusion</p> <p>When the transcription factor is known, it is more appropriate to use a discriminative approach such as the one presented here to derive its transcription factor-DNA binding properties starting with a matrix, as opposed to performing <it>de novo </it>motif discovery. Generating more accurate position weight matrices will ultimately contribute to a better understanding of eukaryotic transcriptional regulation, and could potentially offer a better alternative to <it>ab initio </it>motif discovery.</p

Draft genome sequence of <em>Streptococcus equi</em> subsp. <em>zooepidemicus</em> strain S31A1, isolated from equine infectious endometritis

We present the draft genome sequence of Streptococcus equi subsp. zooepidemicus S31A1, a strain isolated from equine infectious endometritis in Denmark. Comparative analyses of this genome were done with four published reference genomes: S. zooepidemicus strains MGCS10565, ATCC 35246, and H70 and S. equi subsp. equi strain 4047

Short-term transcriptomic response to plasma membrane injury

Plasma membrane repair mechanisms are activated within seconds post-injury to promote rapid membrane resealing in eukaryotic cells and prevent cell death. However, less is known about the regeneration phase that follows and how cells respond to injury in the short-term. Here, we provide a genome-wide study into the mRNA expression profile of MCF-7 breast cancer cells exposed to injury by digitonin, a mild non-ionic detergent that permeabilizes the plasma membrane. We focused on the early transcriptional signature and found a time-dependent increase in the number of differentially expressed (> twofold, P < 0.05) genes (34, 114 and 236 genes at 20-, 40- and 60-min post-injury, respectively). Pathway analysis highlighted a robust and gradual three-part transcriptional response: (1) prompt activation of immediate-early response genes, (2) activation of specific MAPK cascades and (3) induction of inflammatory and immune pathways. Therefore, plasma membrane injury triggers a rapid and strong stress and immunogenic response. Our meta-analysis suggests that this is a conserved transcriptome response to plasma membrane injury across different cell and injury types. Taken together, our study shows that injury has profound effects on the transcriptome of wounded cells in the regeneration phase (subsequent to membrane resealing), which is likely to influence cellular status and has been previously overlooked