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Computational prediction and experimental validation of novel markers for detection of STEC O157:H7
  • ISSN号:1007-9327
  • 期刊名称:《世界胃肠病学杂志:英文版》
  • 时间:0
  • 分类:Q987[生物学—遗传学;生物学—人类学] S852.612[农业科学—基础兽医学;农业科学—兽医学;农业科学—畜牧兽医]
  • 作者机构:[1]Department of Pathogenobiology, Norman Bethune Medical College of Jilin University, Changchun 130000, Jilin Province, China, [2]Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, United States, [3]Department of Bioinformatics, College of Computer Science and Technology, Jilin University, Changchun 130000, Jilin Province, China
  • 相关基金:Supported by National Natural Science Foundation of China No. 30872415; National Science Foundation No. DBI-0354771 ITR-IIS-0407204 DBI-0542119 CCF0621700; National Institutes of Health No. 1R01GM075331 and 1R01GM081682; BioEnergy Science Center US Department of Energy BioEnergy Research Center supported by the Office of Biological and Environmental Research in DOE Office of Science
中文摘要:

瞄准:识别并且为 Shiga 的察觉估计新奇制造者毒素生产 Escherichia coli (STEC ) O157 : 有一条综合计算、试验性的途径的 H7。方法:高产量的 NCBI 强风(电子值截止 e-5 ) 被用来在编码为每 STEC O157 的三紧张的每基因的所有定序的原核生物的染色体之中寻找相应基因: 有完全的染色体的 H7,试图在 O157 发现唯一的基因: H7 作为它的潜在的标记。保证从 STEC O157 的三紧张的识别标记: H7 能为所有 STEC O157 用作一般标记: H7 紧张,一条 genomic barcode 途径被用来选择标记最小化选择标记基因为一个 transposable 元素的部分的可能性。预言的标记的有效性然后被在 O157 的 18 紧张上运用聚合酶链反应(PCR ) 验证: 有 5 个另外的染色体的 H7 用作否定控制。结果:分别地,强风搜索在 STEC O157 的三定序的紧张识别了 20, 16 和 20 基因: H7,它没在任何另外的原核生物的染色体有相当或相同的事物。三基因, wzy, Z0372 和 Z0344,对三张基因表普通,基于 genomic barcode 途径被选择。PCR 证明 18 上的 100% 的鉴定精确性测试了紧张和 5 控制。结论:三个识别新奇标记, wzy, Z0372 和 Z0344,为 STEC O157 的察觉是高度有希望的: H7,在里面对已知的标记补足。

英文摘要:

AIM:To identify and assess the novel makers for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 with an integrated computational and experimental approach. METHODS:High-throughput NCBI blast (E-value cutoff e-5) was used to search homologous genes among all sequenced prokaryotic genomes of each gene encoded in each of the three strains of STEC O157:H7 with complete genomes,aiming to find unique genes in O157:H7 as its potential markers. To ensure that the identified markers from the three strains of STEC O157:H7 can serve as general markers for all the STEC O157:H7 strains,a genomic barcode approach was used to select the markers to minimize the possibility of choosing a marker gene as part of a transposable element. Effectiveness of the markers predicted was then validated by running polymerase chain reaction (PCR) on 18 strains of O157:H7 with 5 additional genomes used as negative controls. RESULTS:The blast search identified 20,16 and 20 genes,respectively,in the three sequenced strains of STEC O157:H7,which had no homologs in any of the other prokaryotic genomes. Three genes,wzy,Z0372 and Z0344,common to the three gene lists,were selected based on the genomic barcode approach. PCR showed an identification accuracy of 100% on the 18 tested strains and the 5 controls. CONCLUSION:The three identified novel markers,wzy,Z0372 and Z0344,are highly promising for the detection of STEC O157:H7,in complementary to the known markers.

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  • 《世界胃肠病学杂志:英文版》
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  • 国际标准刊号:ISSN:1007-9327
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