T4SP: A Novel Tool and Database for Type IV Secretion Systems in Bacterial Genomes

Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system （T4SS） is one of the secretion systems and it usually consists of 12 genes： VirB1, VirB2 ...VirB11, and VirD4[2]. The structure and molecular mechanisms of these genes have been well analyzed in Gram-negative strains[3] and Gram-positive strains were once believed to be lack of T4SS. However, some recent studies revealed that one or more virB/D genes also exist in some kinds of Gram-positive bacteria and play similar role, and form a T4SS-like system[3]. The VirBl-like, VirB4, VirB6, and VirD4 genes were identified in the chromosome of Gram-positive bacterium Streptococcus suis in our previous studies and their role as important mobile elements for horizontal transfer to recipients in an 89 K pathogenicity island （PAl） was demonstrated[45]. However, their structure and molecular mechanisms in other strains, especially in Gram-positive strains, are remained unclear.

Phylogenetic analysis of the genomes of two strains of human adenovirus type 3

Human adenovirus type 3 （HAdV-3） is widely prevalent all over the world, especially in Asia. The objective of this study is to carry out complete genomic DNA sequencing and the phylogenetic analysis for two strains （Guangzhou01 and Guangzhou02） of HAdV-3 wild virus isolated from South China. Nasopharyngeal secretion aspirate specimens of sick children were inoculated into HEp-2 and HeLa culture tubes, and the cultures were identified by neutralization assay with type-specific reference rabbit antiserum. Type-specific primers were also utilized to confirm the serotype. The restriction fragments of HAdV genome DNA were cloned into pBlueScript SK （ ＋ ） vectors and sequenced, and the 5＇ and 3＇ ends of the linear HAdV-3 genome were directly sequenced with double purified genomic DNA as templates. General features of the HAdV-3 genome sequences were explored by using several bio-software. Phylogenetic analysis was done with MEGA 3.0 software. The genomic sequences of Guangzhou01 and Guangzhou02 possess the same 4 early regions and 5 late regions and have 39 coding sequences and two RNA coding sequences. Other non-coding regions are conservative. Inverted repeats and palindromes were identified in the genome sequences. The genomes of group B human adenovirus as well as HAdV-3 have close phylogenetic relationship with that of chimpanzee adenovirus type 21. The genomic lengths of these two isolated strains are 35 273 bp and 35 269 bp, respectively. The phylogenetic analysis showed that HAdV-B species has some relationship with certain types of chimpanzee adenovirus.

Relationship between Genomic Types of Escherichia coli and Clinical Diseases

In this study, by analysis of genome structures of E. coli, the relationships between the genomic types of E. coli and the associated diseases were investigated. Samples of sputum, urine and other excretions from patients with different infective diseases were collected. And 62 E. coli strains were isolated from these samples. Intact bacterial genomic DNA was cleaved with I-CeuI, separated by pulsed field gel electrophoresis and then typed on the basis of cleavage map. The results showed that 7 I-CeuI sites were found in all the genome structures of the 62 E. coli, indicating that there were 7 rrn operons in the genomes. The size of genome ranged from 4500 kb to 5000 kb. According to the genome structures, 62 E. coli strains were divided into 30 genome types. It was concluded that genome structures of E. coli isolated from the patients with different infective diseases varied to some extent, suggesting that some genome types of E. coli were closely related to some infective diseases.

Family Competition Pheromone Genetic Algorithm for Comparative Genome Assembly

Genome assembly is a prerequisite step for analyzing next generation sequencing data and also far from being solved. Many assembly tools have been proposed and used extensively. Majority of them aim to assemble sequencing reads into contigs; however, we focus on the assembly of contigs into scaffolds in this paper. This is called scaffolding, which estimates the relative order of the contigs as well as the size of the gaps between these contigs. Pheromone trail-based genetic algorithm （PGA） was previously proposed and had decent performance according to their paper. From our previous study, we found that family competition mechanism in genetic algorithm is able to further improve the results. Therefore, we propose family competition pheromone genetic algorithm （FCPGA） and demonstrate the improvement over PGA.

Confirmation of susceptibility gene loci on chromosome 1 in Northern China Han families with type 2 diabetes

Objective To confirm previous effort to identify type 2 diabetes susceptibility genes in a Northern Chinese population by conducting a new genome scan with both an increased number of type 2 diabetes families and a new set of microsatellite markers within the previously localized regions.Methods A genome scan method was applied. After multiplexed PCR, electrophoreses, genescan and genotyping analysis, we obtained size information for all loci , and then a further study was done by both parametric and non-parametric linkage analysis to investigate the P values and Z values of these loci.Results We surveyed 34 microsatellite markers which distributed within 5 regions along chromosome 1, and a total of 12?000 genotypes were screened. Evidence of linkage with diabetes was identified for 8 of the 34 loci. All P values of the 8 loci were lower than 0.05, and the highest Z value was 2.17. A very interesting finding is that all 5 markers at the p- terminal 1p36.3-1p36.23 region, spanning a long range of 16.9?cM, were identified to have a low P value of less than 0.05, which suggests that this region may contain multiple susceptibility genes. Regions 4 and 5 also confirmed the previous findings, and we narrowed these two regions to a 2.7?cM and 2.5?cM regions, respectively.Conclusions We further confirmed the results gained in the previous genome-wide scan using an increased number of NIDDM families and a new set of microsatellite markers lying within the initially localized regions. The fact that all 5 loci at the p- terminal region displayed a low P value of less than 0.05 suggests that more than 1 susceptibility gene may reside in this region.

Public health implications of Yersinia enterocolitica investigation:an ecological modeling and molecular epidemiology study

Background Yersinia enterocolitica has been sporadically recovered from animals,foods,and human clinical samples in various regions of Ningxia,China.However,the ecological and molecular characteristics of Y.enterocolitica,as well as public health concerns about infection in the Ningxia Hui Autonomous Region,remain unclear.This study aims to analyze the ecological and molecular epidemiological characteristics of Y.enterocolitis in order to inform the public health intervention strategies for the contains of related diseases.Methods A total of 270 samples were collected for isolation[animals(n=208),food(n=49),and patients(n=13)],then suspect colonies were isolated and identified by the API20E biochemical identification system,serological tests,biotyping tests,and 16S rRNA-PCR.Then,we used an ecological epidemiological approach combined with machine learning algorithms(general linear model,random forest model,and eXtreme Gradient Boosting)to explore the associations between ecological factors and the pathogenicity of Y.enterocolitis.Furthermore,average nucleotide identity(ANI)estimation,single nucleotide polymorphism(SNP),and core gene multilocus sequence typing(cgMLST)were applied to characterize the molecular profile of isolates based on whole genome sequencing.The statistical test used single-factor analysis,Chi-square tests,t-tests/ANOVA-tests,Wilcoxon rank-sum tests,and Kruskal–Wallis tests.Results A total of 270 isolates of Yersinia were identified from poultry and livestock(n=191),food(n=49),diarrhoea patients(n=13),rats(n=15),and hamsters(n=2).The detection rates of samples from different hosts were statistically different(χ^(2)=22.636,P<0.001).According to the relatedness clustering results,270 isolates were divided into 12 species,and Y.enterocolitica(n=187)is a predominated species.Pathogenic isolates made up 52.4%(98/187),while non-pathogenic isolates made up 47.6%(89/187).Temperature and precipitation were strongly associated with the pathogenicity of the isolates(P<0.001).The random forest(RF)prediction model showed the best performance.The prediction result shows a high risk of pathogenicity Y.enterocolitica was located in the northern,northwestern,and southern of the Ningxia Hui Autonomous Region.The Y.enterocolitica isolates were classified into 54 sequence types(STs)and 125 cgMLST types(CTs),with 4/O:3 being the dominant bioserotype in Ningxia.The dominant STs and dominant CTs of pathogenic isolates in Ningxia were ST429 and HC100_2571,respectively.Conclusions The data indicated geographical variations in the distribution of STs and CTs of Y.enterocolitica isolates in Ningxia.Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment.CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food.Therefore,strengthening health surveillance on pig farms in high-risk areas and focusing on testing food of pig origin are optional strategies to prevent disease outbreaks.