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21.
Bottolo L Chadeau-Hyam M Hastie DI Langley SR Petretto E Tiret L Tregouet D Richardson S 《Bioinformatics (Oxford, England)》2011,27(4):587-588
SUMMARY: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the 'large p, small n' case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements. AVAILABILITY: C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html. 相似文献
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Lanzarotti E Pellizza L Bercovich A Foti M Coria SH Vazquez SC Ruberto L Hernández EA Dias RL Mac Cormack WP Cicero DO Smal C Nicolas MF Vasconcelos AT Marti MA Turjanski AG 《Journal of bacteriology》2011,193(23):6797-6798
A psychrotolerant marine bacterial strain, designated JUB59(T), was isolated from Antarctic surface seawater and classified as a new species of the genus Bizionia. Here, we present the first draft genome sequence for this genus, which suggests interesting features such as UV resistance, hydrolytic exoenzymes, and nitrogen metabolism. 相似文献
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Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion 总被引:3,自引:2,他引:3
The tethered particle motion (TPM) allows the direct detection of activity of a variety of biomolecules at the single molecule level. First pioneered for RNA polymerase, it has recently been applied also to other enzymes. In this work we employ TPM for a systematic investigation of the kinetics of DNA looping by wild-type Lac repressor (wt-LacI) and by hinge mutants Q60G and Q60 + 1. We implement a novel method for TPM data analysis to reliably measure the kinetics of loop formation and disruption and to quantify the effects of the protein hinge flexibility and of DNA loop strain on such kinetics. We demonstrate that the flexibility of the protein hinge has a profound effect on the lifetime of the looped state. Our measurements also show that the DNA bending energy plays a minor role on loop disruption kinetics, while a strong effect is seen on the kinetics of loop formation. These observations substantiate the growing number of theoretical studies aimed at characterizing the effects of DNA flexibility, tension and torsion on the kinetics of protein binding and dissociation, strengthening the idea that these mechanical factors in vivo may play an important role in the modulation of gene expression regulation. 相似文献
24.
Chaves DF Ferrer PP de Souza EM Gruz LM Monteiro RA de Oliveira Pedrosa F 《Proteomics》2007,7(20):3759-3763
Herbaspirillum seropedicae is an endophytic diazotroph associated with economically important crops such as rice, sugarcane, and wheat. Here, we present a 2-D reference map for H. seropedicae. Using MALDI-TOF-MS we identified 205 spots representing 173 different proteins with a calculated average of 1.18 proteins/gene. Seventeen hypothetical or conserved hypothetical ORFs were shown to code for true gene products. These data will support the genome annotation process and provide a basis on which to undertake comparative proteomic studies. 相似文献
25.
Evolution of GnRH ligands and receptors in gnathostomata 总被引:5,自引:0,他引:5
Guilgur LG Moncaut NP Canário AV Somoza GM 《Comparative biochemistry and physiology. Part A, Molecular & integrative physiology》2006,144(3):272-283
Gonadotropin-releasing hormone (GnRH) is the final common signaling molecule used by the brain to regulate reproduction in all vertebrates. Until now, a total of 24 GnRH structural variants have been characterized from vertebrate, protochordate and invertebrate nervous tissue. Almost all vertebrates already investigated have at least two GnRH forms coexisting in the central nervous system. Furthermore, it is now well accepted that three GnRH forms are present both in early and late evolved teleostean fishes. The number and taxonomic distribution of the different GnRH variants also raise questions about the phylogenetic relationships between them. Most of the GnRH phylogenetic analyses are in agreement with the widely accepted idea that the GnRH family can be divided into three main groups. However, the examination of the gnathostome GnRH phylogenetic relationships clearly shows the existence of two main paralogous GnRH lineages: the 'midbrain GnRH" group and the "forebrain GnRH" group. The first one, represented by chicken GnRH-II forms, and the second one composed of two paralogous lineages, the salmon GnRH cluster (only represented in teleostean fish species) and the hypophysotropic GnRH cluster, also present in tetrapods. This analysis suggests that the two forebrain clades share a common precursor and reinforces the idea that the salmon GnRH branch has originated from a duplication of the hypophysotropic lineage. GnRH ligands exert their activity through G protein-coupled receptors of the rhodopsin-like family. As with the ligands, multiple GnRHRs are expressed in individual vertebrate species and phylogenetic analyses have revealed that all vertebrate GnRHRs cluster into three main receptor types. However, new data and a new phylogenetic analysis propose a two GnRHR type model, in which different rounds of gene duplications may have occurred in different groups within each lineage. 相似文献
26.
Alcantarea martinellii is described and illustrated as a new species endemic to Serra dos Órgãos, Petrópolis, Rio de Janeiro State, Brazil. The presence of a simple and erect inflorescence concomitant with a conspicuous water impounding rosette is an unreported combination of characters for Alcantarea. This new lithophytic taxon is unique, with no obvious close relative, but it is similar to A. benzingii, A. farneyi, and A. hatschbachii, which also have unbranched inflorescences. 相似文献
27.
Patricia L. Fernandez Fabianno F. Dutra Letícia Alves Rodrigo T. Figueiredo Diego Mour?o-Sa Guilherme B. Fortes Sophie Bergstrand David L?nn Ricardo R. Cevallos Renata M. S. Pereira Ulisses G. Lopes Leonardo H. Travassos Claudia N. Paiva Marcelo T. Bozza 《The Journal of biological chemistry》2010,285(43):32844-32851
Infectious diseases that cause hemolysis are among the most threatening human diseases, because of severity and/or global distribution. In these conditions, hemeproteins and heme are released, but whether heme affects the inflammatory response to microorganism molecules remains to be characterized. Here, we show that heme increased the lethality and cytokine secretion induced by LPS in vivo and enhanced the secretion of cytokines by macrophages stimulated with various agonists of innate immune receptors. Activation of nuclear factor κB (NF-κB) and MAPKs and the generation of reactive oxygen species were essential to the increase in cytokine production induced by heme plus LPS. This synergistic effect of heme and LPS was blocked by a selective inhibitor of spleen tyrosine kinase (Syk) and was abrogated in dendritic cells deficient in Syk. Moreover, inhibition of Syk and the downstream molecules PKC and PI3K reduced the reactive oxygen species generation by heme. Our results highlight a mechanism by which heme amplifies the secretion of cytokines triggered by microbial molecule activation and indicates possible pathways for therapeutic intervention during hemolytic infectious diseases. 相似文献
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