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Search Results: 1 - 10 of 6155 matches for " Ruiting Lan "
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Molecular Basis of Ribotype Variation in the Seventh Pandemic Clone and its O139 Variant of Vibrio cholerae
Lan, Ruiting;Reeves, Peter R;
Memórias do Instituto Oswaldo Cruz , 1998, DOI: 10.1590/S0074-02761998000500007
Abstract: ribotyping has been widely used to characterise the seventh pandemic clone including south american and o139 variants which appeared in 1991 and 1992 respectively. to reveal the molecular basis of ribotype variation we analysed the rrn operons and their flanking regions. all but one variation detected by bgli, the most discriminatory enzyme, was found to be due to changes within the rrn operons, resulting from recombination between operons. the recombinants are detected because of the presence of a bgli site in the 16s gene in three of the nine rrn operons and/or changes of intergenic spacer types of which four variants were identified. as the frequency of rrn recombination is high, ribotyping becomes a less useful tool for evolutionary studies and long term monitoring of the pathogenic clones of vibrio cholerae as variation could undergo precise reversion by the same recombination event.
Molecular Basis of Ribotype Variation in the Seventh Pandemic Clone and its O139 Variant of Vibrio cholerae
Lan Ruiting,Reeves Peter R
Memórias do Instituto Oswaldo Cruz , 1998,
Abstract: Ribotyping has been widely used to characterise the seventh pandemic clone including South American and O139 variants which appeared in 1991 and 1992 respectively. To reveal the molecular basis of ribotype variation we analysed the rrn operons and their flanking regions. All but one variation detected by BglI, the most discriminatory enzyme, was found to be due to changes within the rrn operons, resulting from recombination between operons. The recombinants are detected because of the presence of a BglI site in the 16S gene in three of the nine rrn operons and/or changes of intergenic spacer types of which four variants were identified. As the frequency of rrn recombination is high, ribotyping becomes a less useful tool for evolutionary studies and long term monitoring of the pathogenic clones of Vibrio cholerae as variation could undergo precise reversion by the same recombination event.
Conditions for the Evolution of Gene Clusters in Bacterial Genomes
Sara Ballouz,Andrew R. Francis,Ruiting Lan,Mark M. Tanaka
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1000672
Abstract: Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters.
In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles
Frank PY Lin, Enrico Coiera, Ruiting Lan, Vitali Sintchenko
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-86
Abstract: Using gene occurrence patterns in sample genomes, we developed two CGP methods (statistical and inductive CGP) to assist with the discovery of bacterial gene functions. Statistical CGP exploits the differences in gene frequency against phenotypic groups, while inductive CGP applies supervised machine learning to identify gene occurrence pattern across genomes. Three rediscovery experiments were designed to evaluate the CGP frameworks. The first experiment attempted to rediscover peptidoglycan genes with 417 published genome sequences. Both CGP methods achieved best areas under receiver operating characteristic curve (AUC) of 0.911 in Escherichia coli K-12 (EC-K12) and 0.978 Streptococcus agalactiae 2603 (SA-2603) genomes, with an average improvement in precision of >3.2-fold and a maximum of >27-fold using statistical CGP. A median AUC of >0.95 could still be achieved with as few as 10 genome examples in each group of genome examples in the rediscovery of the peptidoglycan metabolism genes. In the second experiment, a maximum of 109-fold improvement in precision was achieved in the rediscovery of anaerobic fermentation genes in EC-K12. The last experiment attempted to rediscover genes from 31 metabolic pathways in SA-2603, where 14 pathways achieved AUC >0.9 and 28 pathways achieved AUC >0.8 with the best inductive CGP algorithms.Our results demonstrate that the two CGP methods can assist with the study of functionally uncategorised genomic regions and discovery of bacterial gene-function relationships. Our rediscovery experiments also provide a set of standard tasks against which future methods may be compared.Identifying gene functions is an important task in biology. The exponential growth of genome sequences has placed greater importance on the use of computational approaches for sequence analysis and annotation. With the development of high-throughput technology, methods of comparative genomics are increasingly used to assist with the identification of gene fun
Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae
Connie Lam, Sophie Octavia, Peter R Reeves, Ruiting Lan
BMC Microbiology , 2012, DOI: 10.1186/1471-2180-12-82
Abstract: MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP) typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus.MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing.
Computational Bacterial Genome-Wide Analysis of Phylogenetic Profiles Reveals Potential Virulence Genes of Streptococcus agalactiae
Frank Po-Yen Lin,Ruiting Lan,Vitali Sintchenko,Gwendolyn L. Gilbert,Fanrong Kong,Enrico Coiera
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017964
Abstract: The phylogenetic profile of a gene is a reflection of its evolutionary history and can be defined as the differential presence or absence of a gene in a set of reference genomes. It has been employed to facilitate the prediction of gene functions. However, the hypothesis that the application of this concept can also facilitate the discovery of bacterial virulence factors has not been fully examined. In this paper, we test this hypothesis and report a computational pipeline designed to identify previously unknown bacterial virulence genes using group B streptococcus (GBS) as an example. Phylogenetic profiles of all GBS genes across 467 bacterial reference genomes were determined by candidate-against-all BLAST searches,which were then used to identify candidate virulence genes by machine learning models. Evaluation experiments with known GBS virulence genes suggested good functional and model consistency in cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively). Inspection of the top-10 genes in each of the 15 virulence functional groups revealed at least 15 (of 119) homologous genes implicated in virulence in other human pathogens but previously unrecognized as potential virulence genes in GBS. Among these highly-ranked genes, many encode hypothetical proteins with possible roles in GBS virulence. Thus, our approach has led to the identification of a set of genes potentially affecting the virulence potential of GBS, which are potential candidates for further in vitro and in vivo investigations. This computational pipeline can also be extended to in silico analysis of virulence determinants of other bacterial pathogens.
Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population
Chin Tay, Hazel Mitchell, Quanjiang Dong, Khean-Lee Goh, Ian W Dawes, Ruiting Lan
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-126
Abstract: Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates.The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations.Helicobacter pylori may have infected humans since their origin and currently is believed to infect more than half the population in the world [1,2]. Infection is usually acquired during childhood by intrafamilial transmission and in the majority of cases infection is lifelong unless eradication by antibiotic treatment is undertaken [3,4]. The prevalence of H. pylori infection ranges from 25% in developed countries to more than 80% in the developing regions [3,5,6]. H. pylori is commonly transmitted from mother to child [3].H. pylori is well known for being highly diverse and recombining frequently. DNA sequence analysis of housekeeping and virulence associated genes all have illustrated the unusually high degree of genetic variability in this species [2,7-12]. Comparison of isolates within a single host sampled over an average of 1.8 years has revealed that an average of ~100 DNA imports occur between bacteria, corresponding to 3% of the genome or 50 kb [11] and by extrapolation from these data, it was predicted that with
Development of Multiplex PCR Assays for the Identification of the 33 Serotypes of Streptococcus suis
Zhijie Liu, Han Zheng, Marcelo Gottschalk, Xuemei Bai, Ruiting Lan, Shaobo Ji, Haican Liu, Jianguo Xu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072070
Abstract: Streptococcus suis is an important zoonotic agent causing severe diseases in pigs and humans. To date, 33 serotypes of S. suis have been identified based on antigenic differences in the capsular polysaccharide. The capsular polysaccharide synthesis (cps) locus encodes proteins/enzymes that are responsible for capsular production and variation in the capsule structures are the basis of S. suis serotyping. Multiplex and/or simplex PCR assays have been developed for 15 serotypes based on serotype-specific genes in the cps gene cluster. In this study, we developed a set of multiplex PCR (mPCR) assays to identify the 33 currently known S. suis serotypes. To identify serotype-specific genes for mPCR, the entire genomes of reference strains for the 33 serotypes were sequenced using whole genome high-throughput sequencing, and the cps gene clusters from these strains were identified and compared. We developed a set of 4 mPCR assays based on the polysaccharide polymerase gene wzy, one of the serotype-specific genes. The assays can identify all serotypes except for two pairs of serotypes: 1 and 14, and 2 and 1/2, which have no serotype-specific genes between them. The first assay identifies 12 serotypes (serotypes 1 to 10, 1/2, and 14) that are the most frequently isolated from diseased pigs and patients; the second identifies 10 serotypes (serotypes 11 to 21 except 14); the third identifies the remaining 11 serotypes (serotypes 22 to 31, and 33); and the fourth identifies a new cps cluster of S. suis discovered in this study in 16 isolates that agglutinated with antisera for serotypes 29 and 21. The multiplex PCR assays developed in this study provide a rapid and specific method for molecular serotyping of S. suis.
Population Structure and Evolution of Non-O1/Non-O139 Vibrio cholerae by Multilocus Sequence Typing
Sophie Octavia, Anna Salim, Jacob Kurniawan, Connie Lam, Queenie Leung, Sunjukta Ahsan, Peter R. Reeves, G. Balakrish Nair, Ruiting Lan
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065342
Abstract: Pathogenic non-O1/non-O139 Vibrio cholerae strains can cause sporadic outbreaks of cholera worldwide. In this study, multilocus sequence typing (MLST) of seven housekeeping genes was applied to 55 non-O1/non-O139 isolates from clinical and environmental sources. Data from five published O1 isolates and 17 genomes were also included, giving a total of 77 isolates available for analysis. There were 66 sequence types (STs), with the majority being unique, and only three clonal complexes. The V. cholerae strains can be divided into four subpopulations with evidence of recombination among the subpopulations. Subpopulations I and III contained predominantly clinical strains. PCR screening for virulence factors including Vibrio pathogenicity island (VPI), cholera toxin prophage (CTXΦ), type III secretion system (T3SS), and enterotoxin genes (rtxA and sto/stn) showed that combinations of these factors were present in the clinical isolates with 85.7% having rtxA, 51.4% T3SS, 31.4% VPI, 31.4% sto/stn (NAG-ST) and 11.4% CTXΦ. These factors were also present in environmental isolates but at a lower frequency. Five strains previously mis-identified as V. cholerae serogroups O114 to O117 were also analysed and formed a separate population with V. mimicus. The MLST scheme developed in this study provides a framework to identify sporadic cholera isolates by genetic identity.
Comparative Genomic Hybridization Identifies Virulence Differences in Streptococcus suis
Han Zheng, Ruiting Lan, Xiao Zheng, Zhigang Cui, Zhijie Liu, Xuemei Bai, Shaobo Ji, Marcelo Gottschalk, Jianguo Xu
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0087866
Abstract: Streptococcus suis is an important zoonotic pathogen. However, identification of virulent S. suis strains is complicated because of the high diversity of the species. Here we evaluated the genetic difference among S. suis strains using comparative genomic hybridization (CGH) and virulence variation in vivo and in vitro. We showed that different clades differed in their ability to activate TLR2/6 in vitro and their capacity to induce cytokine production in vivo as well as their resistance to phagocytosis and survival in vivo. Our data showed the S. suis strains tested can be classified into three groups having differing levels of virulence: epidemic and highly virulent strains were clustered into clade Ia (epidemic and highly virulent group, E/HV group), virulent strains were clustered into clade Ib (virulent group, V group), and intermediately or weakly virulent strains were clustered into other clades (intermediately or weakly virulent group, I/WV group). Our study provided further insight into the genomic and virulence variation of S. suis.
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