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GenBank Database (genbank + database)
Selected AbstractsGSH2, a gene encoding ,-glutamylcysteine synthetase in the methylotrophic yeast Hansenula polymorphaFEMS YEAST RESEARCH, Issue 3 2002Vira M Ubiyvovk Abstract The GSH2 gene, encoding Hansenula polymorpha,-glutamylcysteine synthetase, was cloned by functional complementation of a glutathione (GSH)-deficient gsh2 mutant of H. polymorpha. The gene was isolated as a 4.3-kb XbaI fragment that was capable of restoring GSH synthesis, heavy-metal resistance and cell proliferation when introduced into gsh2 mutant cells. It possesses 53% identical and 69% similar amino acids compared with the Candida albicans homologue (Gcs1p). In comparison to the Saccharomyces cerevisiae homologue (Gsh1p), it possesses 47% identical and 61% similar amino acids. The GSH2 sequence appears in the GenBank database under accession No. AF435121. [source] Identification and characterization of multiple Spidroin 1 genes encoding major ampullate silk proteins in Nephila clavipesINSECT MOLECULAR BIOLOGY, Issue 5 2008W. A. Gaines IV Abstract Spider dragline silk is primarily composed of proteins called major ampullate spidroins (MaSps) that consist of a large repeat array flanked by nonrepetitive N- and C-terminal domains. Until recently, there has been little evidence for more than one gene encoding each of the two major spidroin silk proteins, MaSp1 and MaSp2. Here, we report the deduced N-terminal domain sequences for two distinct MaSp1 genes from Nephila clavipes (MaSp1A and MaSp1B) and for MaSp2. All three MaSp genes are co-expressed in the major ampullate gland. A search of the GenBank database also revealed two distinct MaSp1 C-terminal domain sequences. Sequencing confirmed that both MaSp1 genes are present in all seven Nephila clavipes spiders examined. The presence of nucleotide polymorphisms in these genes confirmed that MaSp1A and MaSp1B are distinct genetic loci and not merely alleles of the same gene. We experimentally determined the transcription start sites for all three MaSp genes and established preliminary pairing between the two MaSp1 N- and C-terminal domains. Phylogenetic analysis of these new sequences and other published MaSp N- and C-terminal domain sequences illustrated that duplications of MaSp genes may be widespread among spider species. [source] cDNA sequence, mRNA expression and genomic DNA of trypsinogen from the Indianmeal moth, Plodia interpunctellaINSECT MOLECULAR BIOLOGY, Issue 1 2000Y. C. Zhu Abstract Trypsin-like enzymes are major insect gut enzymes that digest dietary proteins and proteolytically activate insecticidal proteins produced by the bacterium Bacillus thuringiensis (Bt). Resistance to Bt in a strain of the Indianmeal moth, Plodia interpunctella, was linked to the absence of a major trypsin-like proteinase (Oppert et al., 1997). In this study, trypsin-like proteinases, cDNA sequences, mRNA expression levels and genomic DNAs from Bt-susceptible and -resistant strains of the Indianmeal moth were compared. Proteinase activity blots of gut extracts indicated that the susceptible strain had two major trypsin-like proteinases, whereas the resistant strain had only one. Several trypsinogen-like cDNA clones were isolated and sequenced from cDNA libraries of both strains using a probe deduced from a conserved sequence for a serine proteinase active site. cDNAs of 852 nucleotides from the susceptible strain and 848 nucleotides from the resistant strain contained an open reading frame of 783 nucleotides which encoded a 261-amino acid trypsinogen-like protein. There was a single silent nucleotide difference between the two cDNAs in the open reading frame and the predicted amino acid sequence from the cDNA clones was most similar to sequences of trypsin-like proteinases from the spruce budworm, Choristoneura fumiferana, and the tobacco hornworm, Manduca sexta. The encoded protein included amino acid sequence motifs of serine proteinase active sites, conserved cysteine residues, and both zymogen activation and signal peptides. Northern blotting analysis showed no major difference between the two strains in mRNA expression in fourth-instar larvae, indicating that transcription was similar in the strains. Southern blotting analysis revealed that the restriction sites for the trypsinogen genes from the susceptible and resistant strains were different. Based on an enzyme size comparison, the cDNA isolated in this study corresponded to the gene for the smaller of two trypsin-like proteinases, which is found in both the Bt-susceptible and -resistant strains of the Indianmeal moth. The sequences reported in this paper have been deposited in the GenBank database (accession numbers AF064525 for the RC688 strain and AF064526 for HD198). [source] New computational algorithm for the prediction of protein folding typesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001Nikola, tambuk Abstract We present a new computational algorithm for the prediction of a secondary protein structure. The method enables the evaluation of ,- and ,-protein folding types from the nucleotide sequences. The procedure is based on the reflected Gray code algorithm of nucleotide,amino acid relationships, and represents the extension of Swanson's procedure in Ref. 4. It is shown that six-digit binary notation of each codon enables the prediction of ,- and ,-protein folds by means of the error-correcting linear block triple-check code. We tested the validity of the method on the test set of 140 proteins (70 ,- and 70 ,-folds). The test set consisted of standard ,- and ,-protein classes from Jpred and SCOP databases, with nucleotide sequence available in the GenBank database. 100% accurate classification of ,- and ,-protein folds, based on 39 dipeptide addresses derived by the error-correcting coding procedure was obtained by means of the logistic regression analysis (p<0.00000001). Classification tree and machine learning sequential minimal optimization (SMO) classifier confirmed the results by means 97.1% and 90% accurate classification, respectively. Protein fold prediction quality tested by means of leave-one-out cross-validation was a satisfactory 82.1% for the logistic regression and 81.4% for the SMO classifier. The presented procedure of computational analysis can be helpful in detecting the type of protein folding from the newly sequenced exon regions. The method enables quick, simple, and accurate prediction of ,- and ,-protein folds from the nucleotide sequence on a personal computer. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 13,22, 2001 [source] Expression Profile During the Development of Appressoria Induced by Hydrophobic Surfaces in Magnaporthe grisea Y34JOURNAL OF PHYTOPATHOLOGY, Issue 3 2010Qingchao Jin Abstract To study the gene expression profile during appressorium developmental process of Magnaphorthe grisea strain Y34 isolated from the rich area of Asia cultivated rice resources, expressed sequence tags (ESTs) and cDNA array analysis were performed. A total of 4756 tentative unique transcripts (TUTs) were obtained from 13 057 ESTs of the 3, ends of the strain, which was approximately 25% of the total M. grisea EST sequences deposited in the GenBank database. Approximately 84% of these TUTs matched with the published draft genome sequences of strain 70-15. Southern analyses with 12 TUT probes revealed no obvious DNA polymorphism among strains 70-15, Guy11 and Y34. A cDNA array with 4108 TUTs was used to monitor gene expression patterns during appressorium development of M. grisea. Compared with ungerminated conidia, the number of up-regulated and down-regulated genes was almost consistent at any time-points of 2, 8, 20 and 30 h during appressorium development. More genes were differentially expressed during appressorium maturation (20 and 30 h) than during appressorium induction (2 h) and formation (8 h). During appressorium maturation (20,30 h), genes generally seemed to be most actively expressed. [source] Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequencesLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2007Y.H. Zeng Abstract Aim:, To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments. Methods and Results:, All nucleotide sequences of the APB marker gene pufM from cultures and environmental clones were retrieved from the GenBank database. A set of cutoff values (sequence distances 0·06, 0·15 and 0·48 for species, genus, and (sub)phylum levels, respectively) was established using a distance-based grouping program. Analysis of the environmental clones revealed that current efforts on APB isolation and sampling in natural environments are largely inadequate. Analysis of the average distance between each identified genus and an uncultured environmental pufM sequence indicated that the majority of cultured APB genera lack environmental representatives. Conclusions:, The distance-based grouping method is fast and efficient for bulk functional gene sequences analysis. The results clearly show that we are at a relatively early stage in sampling the global richness of APB species. Periodical assessment will undoubtedly facilitate in-depth analysis of potential biogeographical distribution pattern of APB. Significance and Impact of the Study:, This is the first attempt to assess the present understanding of APB diversity in natural environments. The method used is also useful for assessing the diversity of other functional genes. [source] Bacterial diversity in aphthous ulcersMOLECULAR ORAL MICROBIOLOGY, Issue 4 2007L. Marchini Introduction:, Recurrent aphthous ulcers are common lesions of the oral mucosa of which the etiology is unknown. This study aimed to estimate the bacterial diversity in the lesions and in control mucosa in pooled samples using a culture-independent molecular approach. Methods:, Samples were collected from ten healthy individuals and ten individuals with a clinical history of recurrent aphthous ulcers. After DNA extraction, the 16S ribosomal RNA bacterial gene was amplified by polymerase chain reaction with universal primers; amplicons were cloned, sequenced and matched to the GenBank database. Results:, A total of 535 clones were analyzed, defining 95 bacterial species. We identified 62 putative novel phylotypes. In recurrent aphthous ulcer lesions 57 phylotypes were detected, of which 11 were known species. Control samples had 38 phylotypes, five of which were already known. Only three species or phylotypes were abundant and common to both groups (Gemella haemolysans, Streptococcus mitis strain 209 and Streptococcus pneumoniae R6). One genus was found only in recurrent aphthous ulcer samples (Prevotella) corresponding to 16% of all lesion-derived clones. Conclusion:, The microbiota found in recurrent aphthous ulcers and in the control groups diverged markedly and the rich variety of genera found can provide a new starting point for individual qualitative and quantitative analyses of bacteria associated with this oral condition. [source] Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequencesANIMAL GENETICS, Issue 5 2010T. Revay Summary In this study, we assessed the maternal origin of six Hungarian indigenous chicken breeds using mitochondrial DNA information. Sequences of Hungarian chickens were compared with the D-loop chicken sequences annotated in the GenBank and to nine previously described reference haplotypes representing the main haplogroups of chicken. The first 530 bases of the D-loop region were sequenced in 74 chickens of nine populations. Eleven haplotypes (HIC1 - HIC11) were observed from 17 variable sites. Three sequences (HIC3, HIC8 and HIC9) of our chickens were found as unique to Hungary when searched against the NCBI GenBank database. Hungarian domestic chicken mtDNA sequences could be assigned into three clades and probably two maternal lineages. Results indicated that 86% of the Hungarian haplotypes are related to the reference sequence that likely originated from the Indian subcontinent, while the minor part of our sequences presumably derive from South East Asia, China and Japan. [source] Postnatal transcription profile and polymorphism of the ADIPOR1 gene in five pig breedsANIMAL GENETICS, Issue 1 2010M. Stachowiak Summary As a result of its role in energy homeostasis regulation, the ADIPOR1 gene is a candidate for fat deposition, an important production trait, in the pig. The aim of the study was to conduct a comparative analysis of the ADIPOR1 postnatal transcript level, in order to establish its promoter and 5,UTR sequences and to search the gene for polymorphisms. The transcription level was examined in longissimus dorsi and semimembranosus muscles collected from 180 pigs at 60,210 days of age, representing five pig breeds: Duroc, Polish Large White, Polish Landrace, Pietrain and Pulawska. We calculated highly significant breed by age by muscle interaction (P < 0.0001) and breed by muscle interactions (P < 0.01). The 5,UTR and promoter region of the porcine ADIPOR1 gene were amplified for the first time and their sequences were deposited in the GenBank database. In total, 21 novel and two previously described polymorphisms were found in the ADIPOR1 promoter, coding, intronic, 5, and 3, untranslated regions. The only SNP detected in the coding region was a synonymous substitution. Two polymorphisms in 3,UTR (c.*129A>C and c.*536A>G) showed no significant effect on the transcript level. Our results showed a high polymorphism of the ADIPOR1 and a complexity in its transcription level in the studied muscles. This complexity indicates that conclusions based on such studies should be carefully gradated. [source] A microsatellite linkage map for Atlantic salmon (Salmo salar)ANIMAL GENETICS, Issue 2 2004J. Gilbey Summary A linkage map of the Atlantic salmon is described here consisting of 15 linkage groups containing 50 microsatellite loci with a 14 additional unlinked markers (including three allozymes). The map shows the largest sex-specific recombination rate differences so far found in any vertebrate species (3.92:1 female:male). Homologies with previous linkage mapping studies of Atlantic salmon and rainbow trout are described. An in silico search of the Genbank database carried out using the microsatellites used in the mapping process identified significant matches between the flanking regions of the microsatellite SS11 and the calcium-binding mitochondrial carrier protein, ,Aralar1'. [source] | ||||||||||