Objective To set up a rapid and simple method for identificating bacteria by 16S 23SrDNA intergenic spacer regions (ISRs) Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced ...Objective To set up a rapid and simple method for identificating bacteria by 16S 23SrDNA intergenic spacer regions (ISRs) Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced directly using purified fragments by excising the gel without cloning Nucleotide sequences were compared with GenBank databases and analyzed by DNAMAN program Results There was only a single product in streptococcus genus after PCR amplification of 16S 23SrDNA ISRs Five streptococcal species were obtained from 7 strains of streptococcus Two major amplicons were consistently generated for 8 strains of Haemophilus influenzae (H influenzae) The sequence data showed that they all belonged to H influenzae type b on GenBank databases Conclusion PCR and direct sequencing of 16S 23SrDNA ISRs were very successful methods for bacterial species identification展开更多
The novelty and suitability of the mitochondrial gene CO1 in DNA barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochond...The novelty and suitability of the mitochondrial gene CO1 in DNA barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochondrial cytochrome c oxidase-1 gene (CO1) which has the necessary universality and variability making it a generally acceptable barcode region. CO1 is a haploid single locus that is uniparentally-inherited. Protein-coding regions are present in high-copy numbers making it an ideal barcode. The mitochondrial oxidase subunit I (COI) gene is a robust barcode with a suitable threshold for delineating animals and is not subject to drastic length variation, frequent mononucleotide repeats or microinversions. However, a low nucleotide substitution rate of plant mitochondrial genome [mtDNA] precludes the use of CO1 as a universal plant DNA barcode and makes the search for alternative barcode regions necessary. Currently, there exists no universal barcode for plants. The plastid region reveals leading candidate loci as appropriate DNA barcodes yet to be explored in biodiversity studies in Kenya. Four of these plastid regions are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and three noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbL) which emerge as ideal candidate DNA loci. While different research groups propose various combinations of these loci, there exists no consensus;the lack thereof impedes progress in getting a suitable universal DNA barcode. Little research has attempted to investigate and document the applicability and extend of effectiveness of different DNA regions as barcodes to delineate cowpea at subspecies level. In this study we sought to test feasibility of the seven putative candidate DNA loci singly and in combination in order to establish a suitable single and multi-locus barcode regions that can have universal application in delineating diverse phylogeographic groups of closely related Kenyan cowpea variants. In this study, our focus was based on genetic parameters including analyses of intra- and infra-specific genetic divergence based on intra- and infra-specific K2P distances;calculation of Wilcoxon signed rank tests of intra-specific divergence among loci and coalescence analyses to delineate independent genetic clusters. Knowledge of DNA candidate loci that are informative will reveal the suitability of DNA barcoding as a tool in biodiversity studies. Results of this study indicate that: matK, trnH-psbA, psbK-psbL, and rbcL are good barcodes for delineating intra and infraspecific distances at single loci level. However, among the combinations, matK + trnH-psbA, rpoB + atpF-atpH + matK are the best barcodes in delineating cowpea subvariants. rbcL gene can be a suitable barcode marker at single locus level, but overall, multi locus approach appears more informative than single locus approach. The present study hopes to immensely contribute to the scanty body of knowledge on the novelty of DNA barcoding in cataloguing closely related cowpea variants at molecular level and hopes to open up future research on genomics and the possibility of use of conserved regions within DNA in inferring phylogenetic relationships among Kenyan cowpea variants.展开更多
根据GenBank中乳酸杆菌16 S^23 S rRNA基因间沉默区序列设计引物,进一步鉴定猪源乳酸杆菌分离株HZ521;并通过体外试验,以嗜酸乳酸杆菌ATCC 4356为参考菌株,探讨HZ521株的益生素作用。部分16 S^23 S rRNA基因序列同源性分析结果表明,该...根据GenBank中乳酸杆菌16 S^23 S rRNA基因间沉默区序列设计引物,进一步鉴定猪源乳酸杆菌分离株HZ521;并通过体外试验,以嗜酸乳酸杆菌ATCC 4356为参考菌株,探讨HZ521株的益生素作用。部分16 S^23 S rRNA基因序列同源性分析结果表明,该分离株属于瑞士乳酸杆菌。HZ521株具有较强的产酸能力,能耐受强酸,对Hela细胞的黏附率为87.2%,显著高于ATCC4356株(P<0.01)。表明瑞士乳酸杆菌HZ521株具有益生素特性,可作为肠道益生素的候选菌株。展开更多
文摘Objective To set up a rapid and simple method for identificating bacteria by 16S 23SrDNA intergenic spacer regions (ISRs) Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced directly using purified fragments by excising the gel without cloning Nucleotide sequences were compared with GenBank databases and analyzed by DNAMAN program Results There was only a single product in streptococcus genus after PCR amplification of 16S 23SrDNA ISRs Five streptococcal species were obtained from 7 strains of streptococcus Two major amplicons were consistently generated for 8 strains of Haemophilus influenzae (H influenzae) The sequence data showed that they all belonged to H influenzae type b on GenBank databases Conclusion PCR and direct sequencing of 16S 23SrDNA ISRs were very successful methods for bacterial species identification
文摘The novelty and suitability of the mitochondrial gene CO1 in DNA barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochondrial cytochrome c oxidase-1 gene (CO1) which has the necessary universality and variability making it a generally acceptable barcode region. CO1 is a haploid single locus that is uniparentally-inherited. Protein-coding regions are present in high-copy numbers making it an ideal barcode. The mitochondrial oxidase subunit I (COI) gene is a robust barcode with a suitable threshold for delineating animals and is not subject to drastic length variation, frequent mononucleotide repeats or microinversions. However, a low nucleotide substitution rate of plant mitochondrial genome [mtDNA] precludes the use of CO1 as a universal plant DNA barcode and makes the search for alternative barcode regions necessary. Currently, there exists no universal barcode for plants. The plastid region reveals leading candidate loci as appropriate DNA barcodes yet to be explored in biodiversity studies in Kenya. Four of these plastid regions are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and three noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbL) which emerge as ideal candidate DNA loci. While different research groups propose various combinations of these loci, there exists no consensus;the lack thereof impedes progress in getting a suitable universal DNA barcode. Little research has attempted to investigate and document the applicability and extend of effectiveness of different DNA regions as barcodes to delineate cowpea at subspecies level. In this study we sought to test feasibility of the seven putative candidate DNA loci singly and in combination in order to establish a suitable single and multi-locus barcode regions that can have universal application in delineating diverse phylogeographic groups of closely related Kenyan cowpea variants. In this study, our focus was based on genetic parameters including analyses of intra- and infra-specific genetic divergence based on intra- and infra-specific K2P distances;calculation of Wilcoxon signed rank tests of intra-specific divergence among loci and coalescence analyses to delineate independent genetic clusters. Knowledge of DNA candidate loci that are informative will reveal the suitability of DNA barcoding as a tool in biodiversity studies. Results of this study indicate that: matK, trnH-psbA, psbK-psbL, and rbcL are good barcodes for delineating intra and infraspecific distances at single loci level. However, among the combinations, matK + trnH-psbA, rpoB + atpF-atpH + matK are the best barcodes in delineating cowpea subvariants. rbcL gene can be a suitable barcode marker at single locus level, but overall, multi locus approach appears more informative than single locus approach. The present study hopes to immensely contribute to the scanty body of knowledge on the novelty of DNA barcoding in cataloguing closely related cowpea variants at molecular level and hopes to open up future research on genomics and the possibility of use of conserved regions within DNA in inferring phylogenetic relationships among Kenyan cowpea variants.
文摘根据GenBank中乳酸杆菌16 S^23 S rRNA基因间沉默区序列设计引物,进一步鉴定猪源乳酸杆菌分离株HZ521;并通过体外试验,以嗜酸乳酸杆菌ATCC 4356为参考菌株,探讨HZ521株的益生素作用。部分16 S^23 S rRNA基因序列同源性分析结果表明,该分离株属于瑞士乳酸杆菌。HZ521株具有较强的产酸能力,能耐受强酸,对Hela细胞的黏附率为87.2%,显著高于ATCC4356株(P<0.01)。表明瑞士乳酸杆菌HZ521株具有益生素特性,可作为肠道益生素的候选菌株。
