DNA sequence : the journal of DNA sequencing and mapping最新文献

{"title":"Nucleotide sequence of a G/11 family xylanase encoding gene in Scytalidium thermophilum.","authors":"Sophon Boonlue,&nbsp;Tadanori Aimi,&nbsp;Yutaka Kitamoto,&nbsp;Tsutomu Morinaga","doi":"10.1080/10425170701606250","DOIUrl":"https://doi.org/10.1080/10425170701606250","url":null,"abstract":"<p><p>The nucleotide sequence of the xylanase encoding gene in Scytalidium thermophilum Af101-3 was determined. The gene encodes a family G/11 xylanase, and the coding region is interrupted by a 72 bp intron. Transcription of the gene was investigated by reverse transcription PCR (RT-PCR). Transcription of the gene was not affected by the presence of 2% glucose in the medium. Xylanase production in S. thermophilum Af101-3 was also affected by concentration of glucose in the medium (modified Czapek's supplemented with 2% corn cob powder and 0.1% glucose). Therefore, xylanase expression in this fungus may not be regulated by the carbon source in the medium.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":"19 3","pages":"366-70"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701606250","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27032894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bluetongue virus serotype 17 sequence variation associated with neutralization.","authors":"William C Wilson,&nbsp;Kristen A Bernard,&nbsp;Babara A Israel,&nbsp;James O Mecham","doi":"10.1080/10425170701550524","DOIUrl":"https://doi.org/10.1080/10425170701550524","url":null,"abstract":"<p><p>Bluetongue virus (BTV) is an insect-transmitted orbivirus of importance to the cattle and sheep industry. The VP2 protein, encoded by L2, contains neutralizing epitopes. Previously, a panel of neutralizing monoclonal antibodies (MAbs) to the BTV serotype 17 (BTV-17) prototype strain was generated and it was determined that the neutralization domain consists of three overlapping epitopes. Over 30 amino acid changes were found between a neutralized BTV-17 prototype strain and a non-neutralized BTV-17 198 strain. In this study, the L2 genes from eight additional strains, representing both the neutralized and non-neutralized groups of BTV-17, were sequenced to determine the degree of conservation of the previously characterized differences. Comparison of the deduced amino acid sequences showed that 91% (30/33) of the previously noted changes were conserved within each group. The sequence of the M5 gene that encodes VP5 was also examined, since this surface protein has also been shown to affect neutralization. No consistent changes were noted between the neutralized and non-neutralized groups of BTV-17 by analysis of the VP5 protein. Finally, the L2 sequences of five MAb neutralization escape mutants were determined to identify specific amino acids involved in neutralization and perhaps virulence. All five mutants contained 1-3 amino acid changes that were in close proximity to a previously described variable region. These amino acid changes likely define critical sites in the overlapping neutralization domains previously described. This is the first description of two BT virus populations that have distinct neutralization characteristics co-circulating in a defined geographical region.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"237-40"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701550524","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40959612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution and expression of gamma-aminobutyric acid type A receptor-associated protein from the amphioxus Branchiostoma belcheri.","authors":"Jianxiao Tian,&nbsp;Shicui Zhang,&nbsp;Zhenhui Liu,&nbsp;Yongjun Wang","doi":"10.1080/10425170701606144","DOIUrl":"https://doi.org/10.1080/10425170701606144","url":null,"abstract":"<p><p>The cDNA encoding a gamma-aminobutyric acid type A (GABA(A)) receptor-associated protein (GABARAP) was identified from the gut cDNA library of amphioxus Branchiostoma belcheri. It consisted of 1246 bp with a 354 bp open reading frame coding for a 117 amino acids protein of 13.9 kDa. The phylogenetic tree analysis showed that amphioxus GABARAP clustered with GABARAPs, separating from GABARAP-like proteins including amphioxus GABARAPL2. Amphioxus GABARAP gene had an exon-intron organization similar to human, mouse, zebrafish and sea squirt GABARAP homologs in terms of both exon number and sequence homology of each exon, hinting at the clue that GABARAP gene transcription is regulated similarly in all the chordates. In situ hybridization histochemistry revealed a ubiquitous expression pattern of amphioxus GABARAP gene, although it was temporally expressed specifically in the primitive gut of 2- to 10-day larvae, suggesting a conserved role of GABARAP in amphioxus as well as in mammalian species.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"319-25"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701606144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41034489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cloning and characterization of farnesyl pyphosphate synthase gene from the ABA-producing fungi Botrytis cinerea.","authors":"Hong-Yuan Deng,&nbsp;Xin-Rong Ma,&nbsp;Zhi-Dong Li,&nbsp;Hong Tan","doi":"10.1080/10425170701606052","DOIUrl":"https://doi.org/10.1080/10425170701606052","url":null,"abstract":"<p><p>Farnesyl pyphosphate synthase (FPPS) catalyzes the systhesis of farnesyl pyphosphate and appears to be a promising regulation site of Abscisic acid (ABA) biosynthesis pathway in fungi. Here we reported the isolation and characterization of Botrytis cinerea (FPPS) gene. The cloned FPPS gene carries an open reading frame of 1044-bp encoding a deduced protein of 347 amino acids with a molecular weight of 39.83 kDa, and the coding region is interrupted with a 63-bp intron. Comparison analysis showed that the deduced amino acids sequence share high similarity with other known FPPS gene. Southern blot revealed a single copy of FPPS gene in the genomic DNA. The result of transcription analysis indicated that the cloned FPPS gene expressed constitutively and was not induced in ABA accumulation phase.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":"19 3","pages":"313-8"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701606052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27429494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular cloning and characterization of the gene encoding squalene epoxidase in Panax notoginseng.","authors":"Fengmei He,&nbsp;Yongping Zhu,&nbsp;Mingxiong He,&nbsp;Yizheng Zhang","doi":"10.1080/10425170701575026","DOIUrl":"https://doi.org/10.1080/10425170701575026","url":null,"abstract":"<p><p>Squalene epoxidase (SE) is one of the rate-limiting enzymes in the triterpene saponins biosynthetic pathway. Panax notoginseng, one of the famous medicinal plants in China, produces bioactive triterpene saponins. Here we report the P. notoginseng SE, which was cloned from the root of P. notoginseng by PCR. The nucleotide sequence of the ORF (GenBank accession no. DQ386734) contains 1611 nucleotides and encodes 537 amino acid residues with molecular weight of 59.14 kDa and pI of 8.81. The gene has 98% identity with P. ginseng but different identities with other SE families. P. notoginseng SE has a FAD function domain, NAD(P)-binding Rossmann-fold domains, hydrophobicity and 4 transmembrane helices. This SE may be a microsomal membrane-associated enzyme. Real time quantitative PCR shows that the cDNA has different expression pattern and is highly expressed in root, especially in 3-year-old root.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"270-3"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701575026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40959614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of promoter regions of SOX3, SOX14 and SOX18 orthologs in mammals.","authors":"Natasa Kovacevic-Grujicic,&nbsp;Marija Mojsin,&nbsp;Jelena Djurovic,&nbsp;Isidora Petrovic,&nbsp;Milena Stevanovic","doi":"10.1080/10425170701462092","DOIUrl":"https://doi.org/10.1080/10425170701462092","url":null,"abstract":"<p><p>SOX proteins constitute a large family of diverse and well conserved transcription factors implicated in the control of various developmental processes. Previously we have cloned and characterized human SOX3, SOX14 and SOX18 genes and performed functional characterization of their promoter regions. To better understand organization and function of SOX3, SOX14 and SOX18 promoters and to determine evolutionary conserved regulatory regions, we performed comparative genomic analyses of orthologous genes promoters. Mammalian orthologs of the human SOX3, SOX14 and SOX18 genes show high sequence identity in their promoter regions, particularly within basal promoters of the respective human genes. Binding sites for transcription factors NF-Y, Sp1 and USF1, previously shown to play critical roles in transcriptional regulation of these human genes, are highly conserved in sequence and position among diverse mammalian species. Conservation of binding sites might indicate their highly significant roles in maintaining the transcriptional regulation of these genes among different species.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"185-94"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701462092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40961181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of cDNA encoding B. taurus cathelicidin-7 like antibiotic peptide from bone marrow cells of Bubalus bubalis.","authors":"Hemen Das,&nbsp;Shahaj Uddin Ahmed,&nbsp;Tukaram More","doi":"10.1080/10425170701606219","DOIUrl":"https://doi.org/10.1080/10425170701606219","url":null,"abstract":"<p><p>Cathelicidins represent a diverse family of endogenous cationic antibiotic peptide present in all mammalian species. In the present study, a novel cathelicidin cDNA was identified and characterized from bone marrow cells of buffalo (Bubalus bubalis) using RT-PCR based approach. The cDNA encodes a propeptide of 1.18 kDa with net positive charge at neutral pH. The precursor peptide possesses a signal peptide of 29 amino acids and a biologically active peptide of 34 residues. Comparison of sequences indicates only 66.1 and 64.1% identity at nucleotides and amino acids level respectively, with the already reported cathelicidin congener from the same species. However, high degree of similarity (92.8% nucleotides and 81.9% amino acids) was noticed with cathelicidin 7 sequence of Bos taurus suggesting interspecies conservation of cathelicidin peptides rather than intra-species within bovidae family. Phylogenetic trees analyses also support these data. Our findings, further justify the cloned cDNA as a unique cathelicidin member of B. bubalis, and may reasonably considered to be another example of structural diversity exhibited by cathelicidin-derived peptides as reported from other mammals.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"347-56"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701606219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40960310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cloning and characterization of TsMT3, a type 3 metallothionein gene from salt cress (Thellungiella salsuginea).","authors":"Xian Q Quan,&nbsp;Zeng L Wang,&nbsp;Hui Zhang,&nbsp;Yu P Bi","doi":"10.1080/10425170701606201","DOIUrl":"https://doi.org/10.1080/10425170701606201","url":null,"abstract":"<p><p>A full-length type 3 plant metallothionein cDNA was isolated from 200 mM NaCl stressed shoots of the salt cress (Thellungiella salsuginea). The 447 bp TsMT3 cDNA sequence has a 207 bp open reading frame (ORF) and encodes a deduced 69 residue peptide of molecular weight 7.52 kDa. Southern blot analysis indicates that, there is only one copy of TsMT3 in the T. salsuginea genome. The accumulation of TsMT3 mRNA is enhanced by the stress imposed by PEG6000, 200 mM NaCl, 50 microM ABA, 4 degrees C, 40 microM CuSO(4) or 25 microM CdCl2. The expression vector pET28-TsMT3 was heterologously expressed in Escherichia coli to define the contribution of TsMT3 to heavy metal tolerance. In the presence of 2 mM CuSO4, 0.3 mM Pb(NO3)2 or 0.4 mM CdCl2, TsMT3 expressing cells exhibited enhanced metal tolerance and accumulated more metal than the controls. We believe that TsMT3 is probably involved in the processes of metal homeostasis, tolerance, and reactive oxygen species (ROS) scavenging.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"340-6"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701606201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40959613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Title change announcement - DNA Sequence to Mitochondrial DNA.","authors":"","doi":"10.1080/19401730802110558","DOIUrl":"https://doi.org/10.1080/19401730802110558","url":null,"abstract":"We are pleased to announce that with the publication of issue 19:4 (July 2008) DNA Sequence: the Journal of DNA Mapping, Sequencing and Analysis will change its title to Mitochondrial DNA. The title change also heralds the introduction of a new Editor-in-Chief for the Journal: Professor Rob de Salle of the American Museum of Natural History in New York. Professor de Salle has worked in conjunction with the former Editor, the Publisher and a new Editorial Board to provide a new direction for the Journal. Mitochondrial DNA will accept original high quality reports based on mapping, sequencing and analysis of mitochondrial DNA and RNA. Descriptive papers on DNA sequences from mitochondrial genomes, and also analytical papers in the areas of population genetics, medical genetics, phylogenetics and human evolution that use mitochondrial DNA as a source of evidence for studies will be considered for publication. The Editorial Board will also consider manuscripts that examine population genetic and systematic theory that specifically address the use of mitochondrial DNA sequences, as well as papers that discuss the utility of mitochondrial DNA information in medical studies and in human evolutionary biology. The Journal is supported by a specially selected Editorial Board consisting of representatives from the fields of Human and Medical Mitochondrial DNA, MitoGenomics, Population Genetics and Mitochondrial Parasitology. To coincide with the launch of the new title we have also introduced a fully electronic, online submission system. To view instructions on how to prepare your manuscript or to make a submission please visit http:// mc.manuscriptcentral.com/gdna For more information on Mitochondrial DNA please visit the Journal website at www.informaworld. com/MitochondrialDNA We wish to thank all of those that have supported DNA Sequence since its launch in 1990. In particular we would like to thanks Dr Bart Barrell of the Sanger Institute, Cambridge, who first launched the Journal and Professor Stephan Beck, the departing Editor, who has done so much work to ensure quality and regularity of publication since he took the editorship in 2003. We trust that you find the new incarnation of the Journal every bit as edifying as DNA Sequence.","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":"19 3","pages":"158"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19401730802110558","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27429490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of phosphatidylinositol-glycan biosynthesis protein class F gene in rice.","authors":"Dong Hoon Lee,&nbsp;Sang Gu Kang","doi":"10.1080/10425170701575364","DOIUrl":"https://doi.org/10.1080/10425170701575364","url":null,"abstract":"<p><p>The glycosylphosphatidylinositol (GPI) anchors are linked to glycosylphosphatidylinositol-anchored proteins (GAPs) which are essential for the growth of mammalian, yeast and protozoan cells. The GPI anchor is covalently linked to GAP by amide bond formation between the carboxyl terminus and phosphoethanolamine attached at the third mannose and mediated by a transamidase complex. Mediation of GPI synthesis is by the sequential additions of GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex, the GlcN-PI de-N-acetylase, the GlcN-PI mannosyltransferases and the GPI lipid anchor phosphoethanolamine transferase complexes. We report a rice gene OsPIG-F that encodes a homolog to the human PIG-F protein, one of GPI lipid anchor phosphoethanolamine transferase complexes. The amino acid sequences of rice PIG-F consisted of six helix transmembrane domains, one glycosaminoglycan attachment site, one cGMP-dependent protein kinase phosphorylation site and a protein C phosphorylation site at the C-terminus. This unique structure of rice PIG-F indicates the typical membrane bound structure of a protein. Polyclonal antibody for rice PIG-F was found to be cross-reactive with a protein extracted from the leaves of rice. The levels of rice PIG-F transcripts were found to be abundant in leaves, moderately in the milky stage of seed development and less in the floral spikelet, indicating that the rice PIG-F gene was differentially regulated in specific tissues. Furthermore, the levels of rice PIG-F transcription were up-regulated by growth hormones including GA(3), NAA and kinetin. These results indicated that the rice PIG-F gene expression may medicated by these growth regulators.</p>","PeriodicalId":11197,"journal":{"name":"DNA sequence : the journal of DNA sequencing and mapping","volume":" ","pages":"282-90"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10425170701575364","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40959611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}