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BLAST Analysis (blast + analysis)
Selected AbstractsIdentification of the ornithine decarboxylase gene in the putrescine-producer Oenococcus oeni BIFI-83FEMS MICROBIOLOGY LETTERS, Issue 2 2004Angela Marcobal Abstract We report here the identification of an ornithine decarboxylase (ODC) gene in the putrescine-producer Oenococcus oeni BIFI-83 strain. The gene contains a 2,235-nucleotide open reading frame encoding a 745-amino acid residues protein with a deduced molecular mass of 81 kDa. The primary structure of the ODC deduced from the nucleotide sequence has a consensus sequence containing the pyridoxal-5-phosphate (PLP) binding domain, and the critical amino acids residues involved in enzymatic activity are also conserved. As determined by BLAST analysis, the deduced amino acid sequence of the odc gene shares a 67% identity with the ODC protein from Lactobacillus 30a. The odc gene appears to be rarely present in the genome of O. oeni, since in a screening for the presence of this gene in 42 oenococcal strains none of the strains possessed an odc gene copy. [source] Phenotypic and genotypic characterization of competitive exclusion products for use in poultryJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2003R.D. Wagner Abstract Aims: Phenotypic and genotypic bacteria identification methods were compared for their efficacy in determining the composition of competitive exclusion (CE) products. Methods and Results: Phenotypic methods used for bacterial identification were fatty acid methyl ester profiles, biochemical assays and carbohydrate utilization profiles. Genotypic methods were MicroSeq16S rRNA sequence analysis and BLAST searches of the GenBank sequence database. Agreement between phenotypic and genotypic methods for identification of bacteria isolated from the Preempt CE product was 20%. A defined test mixture of bacteria was identified to the species level 100% by BLAST analysis, 64% by MicroSeq and 36% by phenotypic techniques. Conclusions: The wide range of facultative and obligate anaerobic bacteria present in a CE product are more accurately identified with 16S rRNA sequence analyses than with phenotypic identification techniques. Significance and Impact of the Study: These results will provide guidelines for manufacturers of CE products to submit more reliable product information for market approval by regulatory agencies. [source] Construction and identification of a recombinant live attenuated Salmonella typhimurium vaccine strain carrying Helicobacter pylori heat shock protein subunit B geneJOURNAL OF DIGESTIVE DISEASES, Issue 4 2003Guo Qing LI OBJECTIVE: Because Helicobacter pylori is the principal cause of chronic active gastritis and peptic ulcer disease, the present study explored the possibility of constructing a recombinant live attenuated S. typhimurium vaccine strain carrying H. pylori heat shock protein subunit B (HspB) gene. METHODS: A 1640-bp HspB gene was cloned into a prokaryotic expression plasmid pTrc99A. After sequence analysis, the result was compared with the sequence of H. pylori -HspB gene and protein provided by the Genebank using BLAST analysis. The identified recombinant plasmid was then introduced into a live attenuated S. typhimurium strain SL3261. RESULTS: Using polymerase chain reaction (PCR) and restriction enzyme digestion, a recombinant prokaryotic expression plasmid pTrc99A-HspB harboring the HspB gene was constructed and successfully introduced into a live attenuated S. typhimurium strain SL3261. Most of the H. pylori -HspB in the recombinant plasmid pTrc99A-HspB was consistent with the H. pylori -HspB sequence provided by the Genebank. The exchange of A/T or C/G in the cloned sequence hardly changed the encoded amino acids; the homology for both the genes and proteins of H. pylori SS1 strain was 97%; the homology with other common H. pylori strains J99 and 26695 was 96% for both. CONCLUSION: A recombinant live attenuated S. typhimurium vaccine strain harboring H. pylori -HspB gene was successfully constructed and verified, which may help in the development of an oral vaccine against H. pylori infection. [source] Detection of the Sm31 antigen in sera of Schistosoma mansoni, infected patients from a low endemic areaPARASITE IMMUNOLOGY, Issue 1 2010G. S. SULBARÁN Summary Schistosoma mansoni cathepsin B (Sm31) is a major antigen from adult worms that circulates in the blood of infected patients (Li et al., Parasitol Res 1996; 82: 14,18). An analysis of the Sm31 sequence (Klinkert et al., Mol Biochem Parasitol 1989; 33: 113,122) allowed the prediction of seven hydrophilic regions that were confirmed to be exposed on the surface of a 3D model of Sm31; the species specificity of these regions was checked using BLAST analysis. The corresponding peptides were chemically synthesized in polymerazible forms using the t-Boc technique. Rabbits developed a high humoral response against these peptides as tested by a multiple antigen blot assay; it recognized native Sm31 in crude S. mansoni extracts and as circulating antigen in sera of S. mansoni-infected patients by western blot. Relevant antigenic determinants were located at the N- and C-terminus sequences. Antibodies against these regions recognized the native enzyme in an ELISA-like assay called cysteine protease immuno assay in which the immunocaptured enzyme was revealed by the intrinsic cathepsin B hydrolytic activity of Sm31. The method successfully and specifically detected Sm31 in sera of infected individuals, most of them (83ˇ3%) with light infections, offering a rationale for the development of parasite enzyme capture assays using anti-synthetic peptide antibodies for possible use in the diagnosis of schistoso,iasis. [source] Expression of Ht2 -related genes in response to the HT-Toxin of Exserohilum turcicum in MaizeANNALS OF APPLIED BIOLOGY, Issue 1 2010H. Wang Complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis was conducted to analyze differential expression of Ht2 -related genes between maize (Zea mays) near-isogenic lines (NILs), Huangzaosi (HZS) and HuangzaosiHt2 (HZSHt2), following treatment with a crude extract of the HT-toxin. Twenty-one transcript-derived fragments (TDFs), designated H1 to H21, were specifically expressed or upregulated in HZSHt2 following exposure to the HT-toxin. Among them, 4, 7, 4, 2, 2 and 2 TDFs were detected at 3, 6, 12, 24, 48 and 72 h after treatment, respectively. BLAST analysis showed that H1, H11, H13 and H15 are related to regulation of the defence response to environmental stresses. H3, H6 and H10 are associated with energy metabolism. H5, H17 and H18 are involved in photosynthesis. H9 is similar to ubiquitin-like domain containing CTD phosphatase. H8, H9, H16 and H20 are probably transcription factors. The genes associated with basal energy metabolism and signal of stress tolerance were mainly expressed at 3 h after treatment. Transcription factor and most genes for stress tolerance were expressed at 6 h after treatment. RT-PCR analysis demonstrated that H8 was upregulated in HZSHt2 only at 6 h after exposure to the HT-toxin and H13 was upregulated at 6 and 12 h. The full length cDNAs of H8 (GenBank accession number FJ600319) and H13 (FJ600320) were cloned. The deduced protein encoded by H8 cDNA showed 77% homology to the Plus-3 domain containing protein, which is found in yeast gene Rtf1. H13 cDNA encodes a QM-like protein, which is an important protein in plant tolerance to environmental stress. The mechanism regulating the resistance of Ht2 to the HT-toxin might involve a translation elongation factor or an upregulated QM-like protein. [source] Characterization of Wheat Random Amplified Polymorphic DNA Markers Associated with the H11 Hessian Fly Resistance GeneJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 8 2006Dhia Bouktila Abstract In Tunisia, the Hessian fly Mayetiola destructor Say is a major pest of durum wheat (Triticum durum Desf.) and bread wheat (T. aestivum L.). Genetic resistance is the most efficient and economical method of control of this pest. To date, 31 resistance genes, designated H1,H31, have been identified in wheat. These genes condition resistance to the insect genes responsible for virulence. Using wheat cultivars differing for the presence of an individual Hessian fly resistance gene and random amplified polymorphic DNA (RAPD) analysis, we have identified a polymorphic 386-bp DNA marker (Xgmib1-1A.1) associated with the H11 Hessian fly resistance gene. Blast analysis showed a high identity with a short region in the wild wheat (T. monococcum) genome, adjacent to the leaf rust resistance Lr10 gene. A genetic linkage was reported between this gene (Lr10) and Hessian fly response in wheat. These data were used for screening Hessian fly resistance in Tunisian wheat germplasm. Xgmib1-1A.1-like fragments were detected in four Tunisian durum and bread wheat varieties. Using these varieties in Hessian fly breeding programs in Tunisia would be of benefit in reducing the damage caused by this fly. (Managing editor: Li-Hui Zhao) [source] | |||||||||||||