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Query Sequence (query + sequence)

Distribution by Scientific Domains

Life Sciences	60%

Selected Abstracts

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes

FEMS MICROBIOLOGY LETTERS, Issue 2 2002
Leda Cummings
Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. [source]

Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application,

JOURNAL OF MOLECULAR RECOGNITION, Issue 2 2005
F. J. Stevens
Abstract Based on a study involving structural comparisons of proteins sharing 25% or less sequence identity, three rounds of Psi-BLAST appear capable of identifying remote evolutionary homologs with greater than 95% confidence provided that more than 50% of the query sequence can be aligned with the target sequence. Since it seems that more than 80% of all homologous protein pairs may be characterized by a lack of significant sequence similarity, the experimental biologist is often confronted with a lack of guidance from conventional homology searches involving pair-wise sequence comparisons. The ability to disregard levels of sequence identity and expect value in Psi-BLAST if at least 50% of the query sequence has been aligned allows for generation of new hypotheses by consideration of matches that are conventionally disregarded. In one example, we suggest a possible evolutionary linkage between the cupredoxin and immunoglobulin fold families. A thermostable hypothetical protein of unknown function may be a circularly permuted homolog to phosphotriesterase, an enzyme capable of detoxifying organophosphate nerve agents. In a third example, the amino acid sequence of another hypothetical protein of unknown function reveals the ATP binding-site, metal binding site, and catalytic sidechain consistent with kinase activity of unknown specificity. This approach significantly expands the utility of existing sequence data to define the primary structure degeneracy of binding sites for substrates, cofactors and other proteins. Copyright © 2004 John Wiley & Sons, Ltd. [source]

Novel Hemoglobins to Enhance Microaerobic Growth and Substrate Utilization in Escherichiacoli,

BIOTECHNOLOGY PROGRESS, Issue 5 2001
Christian J. T. Bollinger
Limited oxygen availability is a prevalent problem in microbial biotechnology. Recombinant Escherichia coli expressing the hemoglobin from Vitreoscilla (VHb) or the flavohemoglobin from Ralstonia eutropha (formerly Alcaligenes eutrophus) (FHP) demonstrate significantly increased cell growth and productivity under microaerobic conditions. We identify novel bacterial hemoglobin-like proteins and examine if these novel bacterial hemoglobins can elicit positive effects similar to VHb and FHP and if these hemoglobins alleviate oxygen limitation under microaerobic conditions when expressed in E. coli. Several finished and unfinished bacterial genomes were screened using R. eutropha FHP as a query sequence for genes (hmp) encoding hemoglobin-like proteins. Novel hmp genes were identified in Pseudomonas aeruginosa, Salmonella typhi, Klebsiellapneumoniae, Deinococcus radiodurans, and Campylobacter jejuni. Previously characterized hmp genes from E. coli and Bacillus subtilis and the novel hmpgenes from P. aeruginosa, S. typhi, C. jejuni, K.pneumoniae, and D. radiodurans were PCR amplified and introduced into a plasmid for expression in E. coli. Biochemically active hemoproteins were expressed in all constructs, as judged by the ability to abduct carbon monoxide. Growth behavior and byproduct formation of E. coli K-12 MG1655 cells expressing various hemoglobins were analyzed in microaerobic fed-batch cultivations and compared to plasmid-bearing control and to E. coli cells expressing VHb. The clones expressing hemoglobins from E. coli, D. radiodurans, P.aeruginosa, and S. typhi reached approximately 10%, 27%, 23%, and 36% higher final optical density values, respectively, relative to the plasmid bearing E. coli control (A600 5.5). E. coli cells expressing hemoproteins from P. aeruginosa, S. typhi, and D. radiodurans grew to similar final cell densities as did the strain expressing VHb (A600 7.5), although none of the novel constructs was able to outgrow the VHb-expressing E. coli strain. Additionally, increased yield of biomass on glucose was measured for all recombinant strains, and an approximately 2-fold yield enhancement was obtained with D.radiodurans hemoprotein-expressing E. colirelative to the E. coli control carrying the parental plasmid without any hemoglobin gene. [source]

Rapid and accurate identification of microorganisms contaminating cosmetic products based on DNA sequence homology

INTERNATIONAL JOURNAL OF COSMETIC SCIENCE, Issue 6 2005
Y. Fujita
Synopsis The aim of this study was to develop rapid and accurate procedures to identify microorganisms contaminating cosmetic products, based on the identity of the nucleotide sequences of the internal transcribed spacer (ITS) region of the ribosomal RNA coding DNA (rDNA). Five types of microorganisms were isolated from the inner portion of lotion bottle caps, skin care lotions, and cleansing gels. The rDNA ITS region of microorganisms was amplified through the use of colony-direct PCR or ordinal PCR using DNA extracts as templates. The nucleotide sequences of the amplified DNA were determined and subjected to homology search of a publicly available DNA database. Thereby, we obtained DNA sequences possessing high similarity with the query sequences from the databases of all the five organisms analyzed. The traditional identification procedure requires expert skills, and a time period of approximately 1 month to identify the microorganisms. On the contrary, 3,7 days were sufficient to complete all the procedures employed in the current method, including isolation and cultivation of organisms, DNA sequencing, and the database homology search. Moreover, it was possible to develop the skills necessary to perform the molecular techniques required for the identification procedures within 1 week. Consequently, the current method is useful for rapid and accurate identification of microorganisms, contaminating cosmetics. Résumé Le but de cette étude est de développer une procédure rapide et fiable pour identifier les micro-organismes contaminant les produits cosmétiques. Cette procédure repose sur l'identification des séquences des nucléotides des espaceurs transcrits internes (Internal Transcribed Spacer ou région ITS), de l'ADN codant pour l'ARN ribosomique (rADN). Cinq types de micro-organismes sont isolés sur la partie intérieure des bouchons des flacons de lotions pour le soin de la peau et de gels lavants. Les régions ITS rADN des micro-organismes sont amplifiées grâce à l'utilisation de la méthode ,colony-direct PCR, ou ,ordinal PCR, en utilisant les extraits d'ADN comme matrices. Les séquences de nucléotides de l'ADN amplifiées sont évaluées et soumises à une recherche homologique dans une librairie d'ADN disponible au public. Ainsi, grâce aux bases de données, nous obtenons des séquences d'ADN qui possèdent une similaritéélevée avec les séquences recherchées des cinq organismes analysés. La procédure d'identification classique exige des compétences d'experts et une période d'environ un mois pour identifier les micro-organismes. D'autre part, il faut 3 à 7 jours pour terminer toutes les procédures utilisées dans la méthode ici décrite, y compris l'isolation et la culture des organismes, le séquençage de l'ADN et la recherche dermatologique dans les bases de données. De plus, il est possible en 1 semaine de développer les compétences nécessaires pour mettre en ,uvre les techniques moléculaires requises pour les procédures d'identification. Cette méthode est donc utile pour une identification rapide et fiable des micro-organismes qui contaminent les cosmétiques. [source]

MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce

NEW PHYTOLOGIST, Issue 4 2010
Igor A. Yakovlev
Summary ,Norway spruce expresses a temperature-dependent epigenetic memory from the time of embryo development, which thereafter influences the timing bud phenology. MicroRNAs (miRNAs)are endogenous small RNAs, exerting epigenetic gene regulatory impacts. We have tested for their presence and differential expression. ,We prepared concatemerized small RNA libraries from seedlings of two full-sib families, originated from seeds developed in a cold and warm environment. One family expressed distinct epigenetic effects while the other not. We used available plant miRNA query sequences to search for conserved miRNAs and from the sequencing we found novel ones; the miRNAs were monitored using relative real time-PCR. ,Sequencing identified 24 novel and four conserved miRNAs. Further screening of the conserved miRNAs confirmed the presence of 16 additional miRNAs. Most of the miRNAs were targeted to unknown genes. The expression of seven conserved and nine novel miRNAs showed significant differences in transcript levels in the full-sib family showing distinct epigenetic difference in bud set, but not in the nonresponding full-sib family. Putative miRNA targets were studied. ,Norway spruce contains a set of conserved miRNAs as well as a large proportion of novel nonconserved miRNAs. The differentially expression of specific miRNAs indicate their putative participation in the epigenetic regulation. [source]