Microbial & comparative genomics最新文献_第10页

An efficient, automatable template preparation for high throughput sequencing. 一种高效、自动化的高通量测序模板制备方法。

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.237

M Engelstein, T J Aldredge, D Madan, J H Smith, J I Mao, D R Smith, P W Rice

{"title":"An efficient, automatable template preparation for high throughput sequencing.","authors":"M Engelstein, T J Aldredge, D Madan, J H Smith, J I Mao, D R Smith, P W Rice","doi":"10.1089/omi.1.1998.3.237","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.237","url":null,"abstract":"We have developed a 96-well format for DNA template isolation that can be readily automatable. The template isolation protocol involves simple alkaline lysis chemistry and reversible capture on a silica solid phase. After the cells are lysed, no centrifugation is necessary, as lysate purification, DNA binding, washing, and release occur in 96-well filter plates. Large numbers of templates prepared using the silica purification method have been sequenced and analyzed. The quality of sequence resulting from our method has been compared with that generated from several commercial plasmid preparation protocols. We found sequence quality of the silica bead preparations to be equivalent to or, in some cases, better than those prepared by other methods. This method offers many advantages over other protocols we have used. First, the silica purifications have allowed us to more than double overall laboratory throughput while decreasing our template isolation materials cost at least five-fold. Second, because we have eliminated all centrifugation steps in the protocol, automation has been much simpler. The protocol has also been adapted to purify PCR products for use as templates in subsequent sequencing reactions.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20901936","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}

引用次数: 21

Meeting summary. Computational genomics I. 会议总结。计算基因组学1。

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.193

D J Doyle, A R Kerlavage

引用次数: 14

Sequence analysis of the cupin gene family in Synechocystis PCC6803. 聚胞菌PCC6803 cupin基因家族序列分析。

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.141

J M Dunwell

{"title":"Sequence analysis of the cupin gene family in Synechocystis PCC6803.","authors":"J M Dunwell","doi":"10.1089/omi.1.1998.3.141","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.141","url":null,"abstract":"The recently described cupin superfamily of proteins includes the germin and germinlike proteins, of which the cereal oxalate oxidase is the best characterized. This superfamily also includes seed storage proteins, in addition to several microbial enzymes and proteins with unknown function. All these proteins are characterized by the conservation of two central motifs, usually containing two or three histidine residues presumed to be involved with metal binding in the catalytic active site. The present study on the coding regions of Synechocystis PCC6803 identifies a previously unknown group of 12 related cupins, each containing the characteristic two-motif signature. This group comprises 11 single-domain proteins, ranging in length from 104 to 289 residues, and includes two phosphomannose isomerases and two epimerases involved in cell wall synthesis, a member of the pirin group of nuclear proteins, a possible transcriptional regulator, and a close relative of a cytochrome c551 from Rhodococcus. Additionally, there is a duplicated, two-domain protein that has close similarity to an oxalate decarboxylase from the fungus Collybia velutipes and that is a putative progenitor of the storage proteins of land plants.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20613820","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}

引用次数: 14

Pseudomonas aeruginosa PAO1 bacterial artificial chromosomes: strategies for mapping, screening, and sequencing 100 kb loci of the 5.9 Mb genome. 铜绿假单胞菌PAO1细菌人工染色体:5.9 Mb基因组100kb位点的定位、筛选和测序策略

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.105

K Dewar, L Sabbagh, G Cardinal, F Veilleux, F Sanschagrin, B Birren, R C Levesque

{"title":"Pseudomonas aeruginosa PAO1 bacterial artificial chromosomes: strategies for mapping, screening, and sequencing 100 kb loci of the 5.9 Mb genome.","authors":"K Dewar, L Sabbagh, G Cardinal, F Veilleux, F Sanschagrin, B Birren, R C Levesque","doi":"10.1089/omi.1.1998.3.105","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.105","url":null,"abstract":"Pseudomonas aeruginosa is an opportunistic bacterial pathogen frequently found in nosocomial infections and is a major cause of morbidity and mortality in patients with cystic fibrosis. To facilitate molecular studies of this organism, we have generated a bacterial artificial chromosome (BAC) library. Genomic DNA was isolated from the prototype strain PAO1, partially digested with HindIII, size selected after pulsed-field gel electrophoresis, and used to construct a BAC library using the pBeloBAC11 vector. DNAs from approximately 850 clones, representing more than 9.5-fold physical coverage of the 5.9-Mb PAO1 genome, were analyzed after SpeI and HindIII digestions and agarose gel electrophoresis. The BAC library had clones with insert fragments ranging from 20 to more than 290 kb. A subset of 264 BACs having inserts > 80 kb, representing > 4 genome equivalents, were rearrayed into 96-well plates, and a clone pooling and PCR screening strategy was developed. The PCR library screening enabled the identification and recovery of BACs containing genes implicated in cell division and in cell wall biosynthesis, as well as a series of known genes mapping to different regions of the PAO1 chromosome. A physical and genetic map was constructed for the 98-kb pMOC5 BAC clone, which spans the entire fts-mur locus. Chromosome walking from each end of the pMOC5 clone placed it within a contig spanning 243 kb. The BAC library and screening resources now allow a PCR-based screening of a P. aeruginosa genomic library for any gene of interest. The restriction fragment analysis of overlapping clones indicated that BAC clones stably maintain and propagate Pseudomonas DNA, providing evidence that the PAO1 BAC library is an appropriate reagent for genome sequencing.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20613817","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}

引用次数: 26

First report on the systematic sequencing of the small genome of Encephalitozoon cuniculi (Protozoa, Microspora): gene organization of a 4.3 kbp region on chromosome I. cucuuli脑囊虫(原生动物，小孢子目)小基因组系统测序首次报道:1号染色体上4.3 kbp区域的基因组织。

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.1

F Duffieux, P Peyret, B A Roe, C P Vivares

{"title":"First report on the systematic sequencing of the small genome of Encephalitozoon cuniculi (Protozoa, Microspora): gene organization of a 4.3 kbp region on chromosome I.","authors":"F Duffieux, P Peyret, B A Roe, C P Vivares","doi":"10.1089/omi.1.1998.3.1","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.1","url":null,"abstract":"Belonging to a large group of parasitic amitochondrial protozoans (Microspora), Encephalitozoon cuniculi infects humans and other mammals. Because of its medical importance and small genome size (2.9 Mbp), we are systematically sequencing its smallest (217 kbp) chromosome. The shotgun cloning strategy now has produced the sequence of randomly dispersed contigs representing more than 180 kbp of this chromosome. The present report describes analysis of the 4.3 kbp contig, which includes the complete coding regions of dihydrofolate reductase (DHFR), thymidylate synthase (TS), and serine hydroxymethyl transferase (SHMT) genes and the partial coding region of an aminopeptidase (AP) gene. In contrast to the other reported protozoan genes, DHFR and TS are encoded by two different open reading frames (ORFs). The SHMT gene is the first one identified in a protozoan and corresponds to the cytosolic form of the enzyme. No introns were detected, and the intergenic noncoding regions do not exceed 50 bp. The mean GC content is close to 60%, and there is a G or C third-base codon bias. Transcription and translation initiation signals also are analyzed, and a model for the mRNA-ssu rRNA interactions is proposed.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21847045","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}

引用次数: 19

Microbial Genomes III: Sequencing, Functional Characterization and Comparative Genomics. Chantilly, Virginia, USA. January 29-February 1, 1999. Abstracts. 微生物基因组III:测序，功能表征和比较基因组学。尚蒂伊，弗吉尼亚州，美国。一九九九年一月二十九日至二月一日。摘要。

Microbial & comparative genomics Pub Date : 1998-01-01

引用次数: 0

Microbial genomes. II: Sequencing, functional analysis and comparative genomics, Hilton Head Island, South Carolina, January 31-February 3, 1998. 微生物基因组。II:测序、功能分析和比较基因组学，南卡罗来纳州希尔顿黑德岛，1998年1月31日至2月3日。

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.97

D J Doyle

引用次数: 0

On the presence and organization of open reading frames of the nonmotile pathogen Brucella abortus similar to class II, III, and IV flagellar genes and to LcrD virulence superfamily. 与II、III、IV类鞭毛基因和LcrD毒力超家族相似的非运动致病菌流产布鲁氏菌开放阅读框的存在和组织

Microbial & comparative genomics Pub Date : 1998-01-01 DOI: 10.1089/omi.1.1998.3.21

S M Halling

引用次数: 28

G1 and S phase gene expression cannot be analyzed in mammalian cells synchronized by inhibition. G1期和S期基因在哺乳动物细胞中不能通过抑制同步表达。

Microbial & comparative genomics Pub Date : 1997-01-01 DOI: 10.1089/omi.1.1997.2.269

S Cooper

{"title":"G1 and S phase gene expression cannot be analyzed in mammalian cells synchronized by inhibition.","authors":"S Cooper","doi":"10.1089/omi.1.1997.2.269","DOIUrl":"https://doi.org/10.1089/omi.1.1997.2.269","url":null,"abstract":"Sequence analyses of mRNA from cells arrested with either a G1 phase DNA content or an S phase DNA content were interpreted as indicating that these two cell populations differentially expressed particular transcripts (Earle-Hughes et al. Genome Sci Technol 1, 89-128, 1996). Approximately 13% of the total transcript population appeared to be differentially expressed between the G1 and S phases of the cell cycle. The question arises if it is possible, using inhibition methods (double-thymidine block to produce cells with an S phase DNA content and inhibition with dibutyryl adenosine 3'5'-cyclic monophosphate and theophylline to produce cells with a G1 phase DNA content), to truly synchronize cells and obtain cell populations representative of specific phases of the division cycle. Here it is argued that this is not possible. Cells may have specific amounts of DNA (i.e., G1 phase or S phase DNA content) yet not be representative of these particular phases. It is proposed that the differential gene expression observed may be due to the effects of the inhibitors and does not necessarily reflect the actual transcription pattern in unperturbed cells in specific cell cycle phases. This proposal has a wide applicability and should not be confined to the specific article under discussion.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1997.2.269","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20605054","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}

引用次数: 10

Components of Eukaryotic-like Protein Signaling Pathways in Mycobacterium tuberculosis 结核分枝杆菌真核样蛋白信号通路的组成

Microbial & comparative genomics Pub Date : 1997-01-01 DOI: 10.1089/OMI.1.1997.2.63

Y. Av‐Gay, J. Davies

引用次数: 25