HilA is a central regulator of Salmonella pathogenicity island 1 (SPI1), which is necessary for host invasion by Salmonella and induction of gastroenteritis. The iagB lies downstream of hilA and is thought to be co-transcribed with hilA, but iagB expression has not yet been analyzed directly. In this study, iagB expression in various mutant strains was measured to determine whether the expression pattern was similar to that of hilA. A β-galactosidase assay revealed that iagB expression was greater under shaking than standing culture condition. iagB expression was decreased in relA/spoT and ihfB mutants but not in luxS mutant, in line with previous reports on hilA expression. The hilA and iagB mRNA levels decreased by approximately 2-fold in arcA mutant grown aerobically and increased by approximately 10-fold in fnr mutant grown anaerobically. Although the fold changes in hilA and iagB mRNA level differed in hfq mutant strain, the patterns of time- and Hfq-dependent regulation were similar for both genes. Thus, iagB and hilA exhibited similar expression patterns in various mutational backgrounds and under different growth condition.
Gastroenteritis ; Genomic Islands* ; RNA, Messenger ; Salmonella typhimurium ; Salmonella* ; Virulence*

Bacteria ; genetics ; pathogenicity ; Dental Research ; Genomic Islands ; Periodontitis ; microbiology

Enterotoxigenic B. pagilis (ETBF) strains which produce a 20 kDa zinc metalloprotease toxin (BFI) have been associated with diarrheal disease of animals and young children. Using B. pngilis toxin gene (bfi) from strain 86-5443-2-2 (piglet isolate) as a probe, the gene was identified in 74/77 human and animal ETBF strains but only 2/97 non-toxigenic B. fragilis (NTBF) strains. The region flanking bp was mapped with several restriction enzymes and 8 resriction fragments aacent to bft were used to probe colony blots of 77 KTBF and 97 NTBF strains. All 74 bft-positive ETBF strains hybridized to the 8 probes spanning a ca. 18 kb chromosomal region; however, this 18 kb region was absent in the 3 ETBF strains lacking p, and 47 of the 97 (48%) NTBF strains lacked the entire 18 kb region. Of note, the 2 NTBF strains containing btf did not have a ca. 12 kb region upstream of btfp. A ca. 9 kb fragment flanking the btf gene has been sequenced. Analysis of this data revealed several open reading frames (ORF) of which 3 are of particular interest (ORFs 1, 2 and 3). ORF1 and ORF3 encode proteins with significant homology to mobilization proteins, and ORF2 encodes a protein with significant homology to metalloprotease proteins, but only 50% similarity and 30% identity to BFf. These results suggest: 1) the btf genes are flanked by at least 18 kb of DNA largely unique to ETBF strains indicating a putative pathogenic island, 2) another metalloprotease protein present in ETBF strains may contribute to the pathogenicity and variable virulence of these diarrheagenic strains and 3) the pathogenic island may be mobiTized among different Bacteroides strains, and possibly among different species of intestinal bacteria.
Animals ; Bacteria ; Bacteroides fragilis* ; Bacteroides* ; Child ; DNA ; Genomic Islands* ; Humans ; Open Reading Frames ; Virulence* ; Zinc

OBJECTIVES: An atypical Shigella flexneri strain with a plural agglutination pattern [i.e., reacting not only with serum samples containing type antigen II but also with serum samples containing group antigens (3)4 and 7(8)] was selected for genome sequencing, with the aim of obtaining additional comparative information about such strains. METHODS: The genomic DNA of atypical S. flexneri strain NCCP 15744 was sequenced using an Ion Torrent PGM sequencing machine (Life Technologies, USA). The raw sequence data were preprocessed and reference-assembled in the CLC Assembly Cell software (version 4.0.6; CLC bio, USA). RESULTS: Ion Torrent sequencing produced 1,450,025 single reads with an average length of 144 bp, totaling ~209 Mbp. The NCCP 15744 genome is composed of one chromosome and four plasmids and contains a gtrX gene. Among the published genome sequences of S. flexneri strains, including 2457T, Sf301, and 2002017, strain NCCP 15744 showed high similarity with strain 2002017. The differences between NCCP 15744 and 2002017 are as follows: i) NCCP 15744 carries four plasmids whereas 2002017 carries five; ii) 19 genes (including CI, CII, and cro) were lost in the SHI-O genomic island of NCCP 15744 and six genes were gained as compared with strain 2002017. CONCLUSION: Strain NCCP 15744 is genetically similar to 2002017, but these two strains have different multilocus sequence types and serotypes. The exact reason is unclear, but the 19 lost genes may be responsible for the atypical seroconversion of strain NCCP 15744.
Agglutination ; DNA ; Genome* ; Genomic Islands ; Genomics ; Korea* ; Plasmids ; Sequence Analysis ; Seroconversion ; Serogroup ; Shigella flexneri* ; Shigella*

PURPOSE: The H. pylori cagA gene, vacA gene and iceA gene are considered to be important virurence factors that have been implicated in the development of gastric adenocarcinoma. It was reported that the presence of IS605 elements may be responsible for rearrangements and lead to partial or total deletions of the cag pathogenicity island (PAI) and the virulence of cag PAI may be changed. However, different results regarding the association between these virulence factors and clinical disease have been reported from different geographic regions. This study evaluated the relationship between H. pylori virulence factors such as cagA, vacA, iceA, IS605 and gastric adenocarcinoma. MATERIALS AND METHODS: H. pylori isolates were obtained from 54 infected patients (24 cases of gastric adenocarcinoma, 30 cases of control). H. pylori isolates were identified by PCR with ureC gene and 16S rRNA. PCR was performed to examine cagA, vacA, iceA and IS605 genotypes. RESULTS: Significant difference was found in the negative rates of cagA between gastric adenocarcinoma group and control (62.5% vs. 33.3% P=0.033). No significant difference was found in the prevalence of iceA, vacA between gastric adenocar cinoma and control. The genotype of cagA+ vacA s1-m1 iceA1 was predominant in H. pylori isolates irrespective of the clinical outcome. IS605 in PAI was not found in gastric adenocarcinoma gruop and control. The positive rates of IS605 in genome were 33.3% in gastric adenocarcinoma group and 36.7% in control (P>0.05). In gastric carcinoma, the positive rate of cagA+/IS605- was lower than in control (12.5% vs. 40.0%, P=0.025) and the positive rate of cagA-/IS605- was higher than in control (54.2% vs. 23.3%, P=0.02). CONCLUSION: H. pylori virulence factors had not related significantly with gastric adenocarcinoma. Further study is needed to examine the specificity of H. pylori strains.
Adenocarcinoma* ; Genome ; Genomic Islands ; Genotype ; Helicobacter pylori* ; Helicobacter* ; Humans ; Polymerase Chain Reaction ; Prevalence ; Sensitivity and Specificity ; Virulence Factors ; Virulence*

Two forms of genomic instability have been described in colorectal cancer: chromosomal (CIN) and microsatellite instability (MIN). Colorectal cancer has been considered to progress through one of these two major pathways. However, recently a CpG island methylator pathway (CIMP) has been established among sporadic MIN cancers. Aberrant methylation of a promoter CpG island is associated with inactivation of tumor suppressor genes and is one of the epigenetic alterations identified to be involved in tumorigenesis. Now, several types of epigenetic alterations appear to play roles complementary to genetic mutations in colorectal carcinogenesis and seem to contribute to the progression of cancer. Epigenetic alterations also increase the probability that genetic changes will lead to cancer initiation. So far, major epigenetic alterations have been categorized into four groups of dysregulations: 1) hypomethylation with oncogene activation and chromosomal instability, 2) hypermethylation with tumor suppressor gene silencing, 3) chromatin modifications, and 4) loss of imprinting (LOI). Especially, LOI is a common epigenetic variant and should have a field effect on the colon, making it more vulnerable to genetic insults. Genomic imprinting is parental-origin-specific allele silencing, a form of gene silencing that is epigenetic in origin and does not involving alterations in the DNA sequence but does involve methylation and other modifications that are heritable during cell division. LOI is the loss of parental-origin-specific marks, leading either to aberrant activation of a normally silent allele of a growth promoter gene or to silencing of the growth inhibitor allele. Most of the attention has been focused on LOI of the IGF2 (insulin-like growth factor II) gene in a Wilms' tumor and colorectal cancer. LOI of IGF2 involves abnormal activation of a normally silent maternally inherited allele and has been associated with personal and family history of colorectal cancer, supporting a role for LOI in carcinogenesis. LOI may be a valuable predictive marker of an individual's risk for colorectal cancer. Now, epigenetics and imprinting are emerging areas in the study of human-cancer genetics.
Alleles ; Base Sequence ; Carcinogenesis ; Cell Division ; Chromatin ; Chromosomal Instability ; Colon ; Colorectal Neoplasms* ; CpG Islands ; Epigenomics* ; Gene Silencing ; Genes, Tumor Suppressor ; Genetics ; Genomic Imprinting ; Genomic Instability ; Humans ; Methylation ; Microsatellite Instability ; Oncogenes ; Wilms Tumor

Knowledge regarding molecular events of cancer development has been rapidly accumulated during the last decade. The discovery of tumor suppressor gene-silencing by aberrant promoter CpG island hypermethylation and histone-directed chromatin remodeling has led epigenetics to its recognition as an important alternative mechanism for carcinogenesis. Epigenetics does not involve changes in nucleotide sequences, but it affects on genetic composition in many ways. Cancer cells integratively co-opt genetic and epigenetic mechanisms to acquire different aspects of carcinogenetic phenotypes. Since epigenetic changes can be reversed with relative ease, the research of cancer epigenetics provides great potential for new therapeutic regimens.
Cell Transformation, Neoplastic ; CpG Islands/genetics ; DNA Methylation ; English Abstract ; Gene Silencing ; Genes, Tumor Suppressor ; Genomic Imprinting ; Humans ; Neoplasms/*genetics ; Promoter Regions (Genetics)

OBJECTIVETo study the characteristics of the strains of Salmonella enterica (S. enterica) serovar Senftenberg lacking Salmonella pathogenicity island 1 (SPI-1).

METHODSA total of 10 strains of S. enterica serovar Senftenberg were isolated from 10 cases of diarrhea patients. Pulsed field gel electrophoresis (PFGE), PCR, sequencing techniques and cell invasion test were adapted to study the molecular types and invasiveness of the genes and cells; and made a comparison between the 10 strains and the strains (C02013) isolated in Shenzhen in 2002.

RESULTSThe 10 Senftenberg isolated (S09007-S09012, S09014-S09017) in Shanghai showed three PFGE patterns, which were significantly different from the strains isolated in Shenzhen. PCR-amplified results indicated the invasion gene (invA), secreted effector protein gene (sipA) and gene fragments as fhlA-hilA, hilA-spaP and spaP-invH in the 10 strains of SPI-1 were all negative. The sequencing results revealed that the 10 strains isolated in Shanghai lacked most parts of SPI-1 genes, as fragments from orgA to invH and parts of orgA gene itself; however, compared with strains isolated in Shenzhen, the sprB-orgC gene existed. The missing parts of genes were replaced by a simple insertion sequence (IS) of 1000 bp in the strains isolated both in Shenzhen in 2002 and in Shanghai in 2006. The invasiveness rates of the 10 strains (S09007-S09012, S09014-S09017) towards Hela cells were (0.0053 ± 0.0024)%, (0.0046 ± 0.0006)%, (0.0047 ± 0.0003)%, (0.0064 ± 0.0012)%, (0.0065 ± 0.0011)%, (0.0070 ± 0.0020)%, (0.0115 ± 0.0030)%, (0.0099 ± 0.0039)%, (0.0180 ± 0.0135)% and (0.0031 ± 0.0012)%, respectively; which were all significantly lower than the rate of invA-positive control strain STM1344 ((5.0800 ± 0.6333)%); lower or close to the rate of invA-lacked artificial-mutated strain STMinvA-((0.0193 ± 0.0045)%).

CONCLUSIONSPI-1 genes are not essential for the diarrhea caused by S. enterica serovar Senftenberg.

Adult ; Aged ; Bacterial Typing Techniques ; Diarrhea ; microbiology ; Feces ; microbiology ; Female ; Genes, Bacterial ; Genomic Islands ; HeLa Cells ; Humans ; Male ; Middle Aged ; Salmonella enterica ; genetics ; isolation & purification ; pathogenicity

Herein, we report the pathogenic and phylogenetic characteristics of seven Shiga toxin (Stx)-producing Escherichia coli (STEC) isolates from 434 retail meats collected in Korea during 2006 to 2012. The experimental analyses revealed that all isolates (i) were identified as non-O157 STEC, including O91:H14 (3 isolates), O121:H10 (2 isolates), O91:H21 (1 isolate), and O18:H20 (1 isolate), (ii) carried diverse Stx subtype genes (stx₁, stx(2c), stx(2e), or stx₁ + stx(2b)) whose expression levels varied strain by strain, and (iii) lacked the locus of enterocyte effacement (LEE) pathogenicity island, a major virulence factor of STEC, but they possessed one or more alternative virulence genes encoding cytotoxins (Cdt and SubAB) and/or adhesins (Saa, Iha, and EcpA). Notably, a significant heterogeneity in glutamate-induced acid resistance was observed among the STEC isolates (p < 0.05). In addition, phylogenetic analyses demonstrated that all three STEC O91:H14 isolates were categorized into sequence type (ST) 33, of which two beef isolates were identical in their pulsotypes. Similar results were observed with two O121:H10 pork isolates (ST641; 88.2% similarity). Interestingly, 96.0% of the 100 human STEC isolates collected in Korea during 2003 to 2014 were serotyped as O91:H14, and the ST33 lineage was confirmed in approximately 72.2% (13/18 isolates) of human STEC O91:H14 isolates from diarrheal patients.
Cytotoxins ; Enterocytes ; Escherichia coli ; Genomic Islands ; Humans ; Korea ; Meat ; Population Characteristics ; Red Meat ; Shiga Toxin ; Shiga-Toxigenic Escherichia coli ; Virulence ; Virulence Factors

OBJECTIVE: To establish two methods by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing for genotyping rs220030 (a SNP in the promoter region of small nuclear ribonucleoprotein polypeptide N, SNRPN). To establish an analytical technique for detecting CpG methylation status by pyrosequencing and to further investigate the feasibility of applying rs220030 to the determination of parental origin allele. METHODS: The rs220030 of 97 blood samples from individuals of Shanghai Han population were genotyped by DGGE, meanwhile the rs220030 of 25 blood samples of them were genotyped by pyrosequencing to compare the two methods in genotyping SNP. Pyrosequencing united bisulfite conversion method was applied to detect CpG methylation status of region upstream rs220030 of two random blood genealogical samples and investigate whether the methylation status was parental related. RESULTS: The rs220030 genotyping results of 97 blood samples detected by DGGE were 20 C homozygote, 29 T homozygote, and 48 C/T heterozygote. Twenty-five blood samples genotyped by pyrosequencing showed the same result with DGGE. The CpG methylation status of region upstream rs220030 of the child was similar to the mother. CONCLUSION Compared with DGGE, pyrosequencing is more accurate, convenient, and suitable for large samples and high throughput SNP genotyping. Pyrosequencing united bisulfite conversion can be used to detect CpG methylation status precisely. It is feasible to apply rs220030 to parental origin allele determination.
Asian People/genetics* ; CpG Islands ; DNA/genetics* ; DNA Methylation ; DNA Primers ; Genomic Imprinting ; Genotype ; Heterozygote ; Humans ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sulfites/metabolism* ; snRNP Core Proteins/genetics*