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At Molecular Station Bioinformatics, you will find all the bioinformatics programs you will need. We have over 800 bioinformatic tools for DNA bioinformatics, RNA bioinformatics, Protein Bioinformatics, and Proteomic bioinformatic tools. We also provide databses for each of these categories in order to easily find your sequence of interest from several sequence databases.
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Functional Analysis of the Quorum-Sensing Streptococcal Invasion Locus (sil).
PLoS Pathog. 2009 Nov;5(11):e1000651
Authors: Belotserkovsky I, Baruch M, Peer A, Dov E, Ravins M, Mishalian I, Persky M, Smith Y, Hanski E
Group A streptococcus (GAS) causes a wide variety of human diseases, and at the same time, GAS can also circulate without producing symptoms, similar to its close commensal relative, group G streptococcus (GGS). We previously identified, by transposon-tagged mutagenesis, the streptococcal invasion locus (sil). sil is a quorum-sensing regulated locus which is activated by the autoinducer peptide SilCR through the two-component system SilA-SilB. Here we characterize the DNA promoter region necessary for SilA-mediated activation. This site is composed of two direct repeats of 10 bp, separated by a spacer of 11 bp. Fusion of this site to gfp allowed us to systematically introduce single-base substitutions in the repeats region and to assess the relative contribution of various positions to promoter strength. We then developed an algorithm giving different weights to these positions, and performed a chromosome-wide bioinformatics search which was validated by transcriptome analysis. We identified 13 genes, mostly bacteriocin related, that are directly under the control of SilA. Having developed the ability to quantify SilCR signaling via GFP accumulation prompted us to search for GAS and GGS strains that sense and produce SilCR. While the majority of GAS strains lost sil, all GGS strains examined still possess the locus and approximately 63% are able to respond to exogenously added SilCR. By triggering the autoinduction circle using a minute concentration of synthetic SilCR, we identified GAS and GGS strains that are capable of sensing and naturally producing SilCR, and showed that SilCR can be sensed across these streptococci species. These findings suggest that sil may be involved in colonization and establishment of commensal host-bacterial relationships.
PMID: 19893632 [PubMed - in process]
Liver fibrosis causes down-regulation of miRNA-150 and miRNA-194 in hepatic stellate cells and their over-expression causes decreased stellate cell activation.
Am J Physiol Gastrointest Liver Physiol. 2009 Nov 5;
Authors: Venugopal SK, Jiang J, Kim TH, Li Y, Wang SS, Torok NJ, Wu J, Zern MA
Activation of hepatic stellate cells (HSC) results in their proliferation and in the secretion of extracellular matrix (ECM) proteins, which leads to hepatic fibrosis. microRNAs (miRNAs) have been shown to regulate various cell functions, such as proliferation, differentiation and apoptosis. Hence, we have analyzed the miRNAs that were differentially expressed in HSC isolated from sham-operated and bile duct-ligated rats. Expression of two miRNAs, miRNA-150 and miRNA-194, was reduced in HSC isolated from fibrotic rats compared with sham-operated animals. These two miRNAs were over-expressed in LX-2 cells and their ability to inhibit cell proliferation, the expression of smooth muscle alpha-actin (SMA), a marker for activation, and collagen type I, a marker for extra-cellular matrix secretion, were determined. Over-expression of these two miRNAs resulted in a significant inhibition of proliferation (p<0.05), reduced SMA and collagen I levels compared with either untreated cells or non-specific miRNA expressing cells. Next, the protein targets of these two miRNAs were found using bioinformatics approaches. C-myb was found to be a target for miR-150 and rac 1 was found to be one of the targets for miR-194. Therefore, we studied the expression of these two proteins by over-expressing these two miRNAs in LX-2 cells, and found that over-expression of miR-150 and miR-194 resulted in a significant inhibition of c-myb and rac1 expression respectively. We conclude that both miRNA-150 and miRNA-194 inhibit HSC activation and ECM production, at least in part, via inhibition of c-myb and rac 1 expression.
PMID: 19892940 [PubMed - as supplied by publisher]
Use of bioinformatics in planning a protein purification.
Methods Enzymol. 2009;463:21-8
Authors: Burgess RR
Now that many hundreds and even thousands of whole genomes have been sequenced, it is rare to be studying a target protein whose amino acid sequence is not known. However, it is still often necessary to obtain large amounts of the target protein for a variety of purposes including structural studies, drug discovery, enzymology, protein biochemistry, and industrial application. It would seem that knowing the amino acid sequences would make it much easier to design an effective purification of that protein. We examine in this chapter what you can and cannot predict from an amino acid sequence and conclude that protein purification is still largely an empirical science.
PMID: 19892163 [PubMed - in process]
The ClosTron: Mutagenesis in Clostridium refined and streamlined.
J Microbiol Methods. 2009 Nov 2;
Authors: Heap JT, Kuehne SA, Ehsaan M, Cartman ST, Cooksley CM, Scott JC, Minton NP
The recent development of the ClosTron Group II intron directed mutagenesis tool for Clostridium has advanced genetics in this genus, and here we present several significant improvements. We have shown how marker re-cycling can be used to construct strains with multiple mutations, demonstrated using FLP/FRT in Clostridium acetobutylicum; tested the capacity of the system for the delivery of transgenes to the chromosome of Clostridium sporogenes, which proved feasible for 1.0kbp transgenes in addition to a marker; and extended the host range of the system, constructing mutants in Clostridium beijerinckii and, for the first time, in a B1/NAP1/027 'epidemic' strain of Clostridium difficile. Automated intron design bioinformatics are now available free-of-charge at our website http://clostron.com; the out-sourced construction of re-targeted intron plasmids has become cost-effective as well as rapid; and the combination of constitutive intron expression with direct selection for intron insertions has made mutant isolation trivial. These developments mean mutants can now be constructed with very little time and effort for the researcher. Those who prefer to construct plasmids in-house are no longer reliant on a commercial kit, as a mixture of two new plasmids provides unlimited template for intron re-targeting by Splicing by Overlap Extension (SOE) PCR. The new ClosTron plasmids also offer blue-white screening and other options for identification of recombinant plasmids. The improved ClosTron system supersedes the prototype plasmid pMTL007 and the original method, and exploits the potential of Group II introns more fully.
PMID: 19891996 [PubMed - as supplied by publisher]
RNA folding on the 3D triangular lattice.
BMC Bioinformatics. 2009 Nov 5;10(1):369
Authors: Gillespie J, Mayne M, Jiang M
ABSTRACT: BACKGROUND: Difficult problems in structural bioinformatics are often studied in simple exact models to gain insights and to derive general principles. Protein folding, for example, has long been studied in the lattice model. Recently, researchers have also begun to apply the lattice model to the study of RNA folding. RESULTS: We present a novel method for predicting RNA secondary structures with pseudoknots: first simulate the folding dynamics of the RNA sequence on the 3D triangular lattice, next extract and select a set of disjoint base pairs from the best lattice conformation found by the folding simulation. Experiments on sequences from PseudoBase show that our prediction method outperforms the HotKnot algorithm of Ren, Rastegari, Condon and Hoos, a leading method for RNA pseudoknot prediction. Our method for RNA secondary structure prediction can be adapted into an efficient reconstruction method that, given an RNA sequence and an associated secondary structure, finds a conformation of the sequence on the 3D triangular lattice that realizes the base pairs in the secondary structure. We implemented a suite of computer programs for the simulation and visualization of RNA folding on the 3D triangular lattice. These programs come with detailed documentation and are accessible from the companion website of this paper at http://www.cs.usu.edu/~mjiang/rna/DeltaIS/. CONCLUSION: Folding simulation on the 3D triangular lattice is effective method for RNA secondary structure prediction and lattice conformation reconstruction. The visualization software for the lattice conformations of RNA structures is a valuable tool for the study of RNA folding and is a great pedagogic device.
PMID: 19891777 [PubMed - as supplied by publisher]
Functional Genes and Proteins of Clonorchis sinensis.
Korean J Parasitol. 2009 Oct;47(Supplement):S59-S68
Authors: Kim TI, Na BK, Hong SJ
During the past several decades, researches on parasite genetics have progressed from biochemical and serodiagnostic studies to protein chemistry, molecular biology, and functional gene studies. Nowadays, bioinformatics, genomics, and proteomics approaches are being applied by Korean parasitology researchers. As for Clonorchis sinensis, investigations have been carried out to identify its functional genes using forward and reverse genetic approaches and to characterize the biochemical and biological properties of its gene products. The authors review the proteins of cloned genes, which include antigenic proteins, physiologic and metabolic enzymes, and the gene expression profile of Clonorchis sinensis.
PMID: 19885336 [PubMed - as supplied by publisher]
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