The availability of a large number of sequenced bacterial genomes allows researchers not only to derive functional and regulation information about specific organisms but also to study the fundamental properties of th...The availability of a large number of sequenced bacterial genomes allows researchers not only to derive functional and regulation information about specific organisms but also to study the fundamental properties of the organization of a genome. Here we address an important and chal- lenging question regarding the global arrangement of operons in a bacterial genome： why operons in a bacterial genome are arranged in the way they are. We have previously studied this question and found that operons of more frequently activated pathways tend to be more clustered together in a genome. Specifically, we have developed a simple sequential distance-based pseudo energy func- tion and found that the arrangement of operons in a bacterial genome tend to minimize the clus- teredness function （C value） in comparison with artificially-generated alternatives, for a variety of bacterial genomes. Here we extend our previous work, and report a number of new observations： （a） operons of the same pathways tend to group into a few clusters rather than one; and （b） the global arrangement of these operon clusters tend to minimize a new ＂energy＂ function （C＋ value） that reflects the efficiency of the transcriptional activation of the encoded pathways. These obser- vations provide insights into further study of the genomic organization of genes in bacteria.展开更多
近年来,多种新型耐药基因的出现和全球性流行,严重威胁了全球公众健康。CRISPR-Cas9系统(clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 system)是细菌的一种适应性免疫系统,可切割耐药基因...近年来,多种新型耐药基因的出现和全球性流行,严重威胁了全球公众健康。CRISPR-Cas9系统(clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 system)是细菌的一种适应性免疫系统,可切割耐药基因、抵御外来核酸入侵,现已作为一种新型基因编辑工具应用于防控细菌耐药性研究。本团队已建立了一种单质粒介导靶向mcr-1基因的CRISPR-Cas9系统,能有效并特异性消除黏菌素耐药大肠杆菌中的mcr-1,恢复其对黏菌素的敏感性。同时也发现在临床中应用还需要优化其递送方式。本文对近几年该技术在细菌耐药性防控方面的研究进展进行了综述,包括CRISPR-Cas9系统的发现过程、作用机制、递送方式、在体外检测实验结果的进展以及当前存在的问题等方面,以期为防控细菌耐药性提供新思路。展开更多
目的:比较并优化2种试剂盒提取以巨型球菌为代表的难提取细菌基因组DNA的方法,以获得高质量的DNA用于高通量测序,探索高通量测序样品的前期处理方法。方法:用Life Technologies公司的Charge Switchg DNA Mini Bacteria Kit和Roche公司的...目的:比较并优化2种试剂盒提取以巨型球菌为代表的难提取细菌基因组DNA的方法,以获得高质量的DNA用于高通量测序,探索高通量测序样品的前期处理方法。方法:用Life Technologies公司的Charge Switchg DNA Mini Bacteria Kit和Roche公司的High Pure PCR Template Preparation Kit提取制备困难的巨型球菌基因组DNA,然后通过添加溶葡球菌酶和增加溶菌酶、RNase A、Protein K的投入量及延长消化时间优化2个试剂盒,对4种方法提取的细菌基因组DNA进行浓度、纯度和基因组完整性测定,选取质量良好的基因组进行高通量测序。结果:改良后的2个试剂盒提取的巨型球菌DNA浓度较高,分别达到78.4和67.8 ng/μL,可满足高通量测序的需求,并获得基因组全序列。结论:改良后的2种方法是提取制备困难的巨型球菌基因组DNA更好的方法。展开更多
In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding at...In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions （IGRs） and in the analysis of those ＂junk＂ regions for ge- nomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http：//pranag.physics.iisc.ernet.in/junker/.展开更多
基金supported in part by National Science Foundation (Grant No. NSF DEB-0830024 and NSF MCB-0958172)by Grant from the BioEnergy Science Center(BESC) of US Department of Energy through the Office of Biological and Environmental Research
文摘The availability of a large number of sequenced bacterial genomes allows researchers not only to derive functional and regulation information about specific organisms but also to study the fundamental properties of the organization of a genome. Here we address an important and chal- lenging question regarding the global arrangement of operons in a bacterial genome： why operons in a bacterial genome are arranged in the way they are. We have previously studied this question and found that operons of more frequently activated pathways tend to be more clustered together in a genome. Specifically, we have developed a simple sequential distance-based pseudo energy func- tion and found that the arrangement of operons in a bacterial genome tend to minimize the clus- teredness function （C value） in comparison with artificially-generated alternatives, for a variety of bacterial genomes. Here we extend our previous work, and report a number of new observations： （a） operons of the same pathways tend to group into a few clusters rather than one; and （b） the global arrangement of these operon clusters tend to minimize a new ＂energy＂ function （C＋ value） that reflects the efficiency of the transcriptional activation of the encoded pathways. These obser- vations provide insights into further study of the genomic organization of genes in bacteria.
文摘近年来,多种新型耐药基因的出现和全球性流行,严重威胁了全球公众健康。CRISPR-Cas9系统(clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 system)是细菌的一种适应性免疫系统,可切割耐药基因、抵御外来核酸入侵,现已作为一种新型基因编辑工具应用于防控细菌耐药性研究。本团队已建立了一种单质粒介导靶向mcr-1基因的CRISPR-Cas9系统,能有效并特异性消除黏菌素耐药大肠杆菌中的mcr-1,恢复其对黏菌素的敏感性。同时也发现在临床中应用还需要优化其递送方式。本文对近几年该技术在细菌耐药性防控方面的研究进展进行了综述,包括CRISPR-Cas9系统的发现过程、作用机制、递送方式、在体外检测实验结果的进展以及当前存在的问题等方面,以期为防控细菌耐药性提供新思路。
文摘目的:比较并优化2种试剂盒提取以巨型球菌为代表的难提取细菌基因组DNA的方法,以获得高质量的DNA用于高通量测序,探索高通量测序样品的前期处理方法。方法:用Life Technologies公司的Charge Switchg DNA Mini Bacteria Kit和Roche公司的High Pure PCR Template Preparation Kit提取制备困难的巨型球菌基因组DNA,然后通过添加溶葡球菌酶和增加溶菌酶、RNase A、Protein K的投入量及延长消化时间优化2个试剂盒,对4种方法提取的细菌基因组DNA进行浓度、纯度和基因组完整性测定,选取质量良好的基因组进行高通量测序。结果:改良后的2个试剂盒提取的巨型球菌DNA浓度较高,分别达到78.4和67.8 ng/μL,可满足高通量测序的需求,并获得基因组全序列。结论:改良后的2种方法是提取制备困难的巨型球菌基因组DNA更好的方法。
文摘In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions （IGRs） and in the analysis of those ＂junk＂ regions for ge- nomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http：//pranag.physics.iisc.ernet.in/junker/.
