An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical...An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 com-plex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.展开更多
Gram-negative,facultative intracellular anaerobes of the genus Shigella,the principal etiologic agents of shigellosis,continue to pose a threat to public health.Shigellosis causes 1.1 million deaths with over 164 mill...Gram-negative,facultative intracellular anaerobes of the genus Shigella,the principal etiologic agents of shigellosis,continue to pose a threat to public health.Shigellosis causes 1.1 million deaths with over 164 million annual cases.The Shigella spp.can be divided into four serogroups:Shigella dysenteriae,Shigella flexneri,Shigella boydii and Shigella sonnei.The completion of seven Shigella genome sequences of representative strains from each of the Shigella species has introduced an era of whole-genome study.This paper reviews contemporary understanding of genomics,transcriptomics,proteomics and the structural biology of Shigella.展开更多
Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide.In China,serogroup A strains were responsible for over 95%of the cases,while serogroup B strains were mainly the cause of locali...Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide.In China,serogroup A strains were responsible for over 95%of the cases,while serogroup B strains were mainly the cause of localized outbreaks and sporadic cases.Before 2003,serogroup C strains were only re-covered from a few sporadic cases.However,a sudden increase in the number of cases due to sero-group C strains occurred during 2003—2005 in Anhui Province,China.Many cases were found in other provinces at the same time.Multilocus sequence typing(MLST)results indicated that the unique se-quence type 4821 clone meningococci,a new hyper-virulent lineage,was responsible for the serogroup C meningitis outbreaks.We have completed the project of sequencing the whole genome of the Chi-nese N.meningitidis serogroup C representative isolate 053442.We fabricated a whole-genome mi-croarray of N.meningitidis isolate 053442 and analyzed the genome composition differences among 81 serogroup C isolates which were isolated from 14 provinces of China during 1966—2005.The com-parative genomic hybridization(CGH)result shows that the genome compositions of nearly all sero-group C isolates are similar to that of 053442.The products of many absent open reading frames(ORFs)are conserved hypothetical proteins.The results will provide a valuable resource from which one can analyze the genome composition and genetic background of serogroup C meningococci in China.展开更多
Trichophyton rubrum is a dominating superficial dermatophyte,whose conidial germination is corre-lated to pathopoiesis and a highly important developmental process.To investigate the changes of physiology,biochemistry...Trichophyton rubrum is a dominating superficial dermatophyte,whose conidial germination is corre-lated to pathopoiesis and a highly important developmental process.To investigate the changes of physiology,biochemistry and cytology during the germination,we selected 3364 function identified ESTs from T.rubrum cDNA library to construct cDNA microarrays,and compared the gene expression levels of conidia and germinating phase.Data analysis indicated that 335 genes were up-regulated during the germination,which mainly encoded translated,modified proteins and structural proteins.The constituents of cell wall and cell membrane were synthetized abundantly,suggesting that they are the foundation of cell morphogenesis.The ingredients of the two-component signal transduction sys-tem were up-regulated,presuming that they were important for the conidial germination.Genes of various metabolic pathways were expressed prosperously,especially the genes that participated in glycolysis and oxidative phosphorylation were up-regulated on the whole,demonstrating that in the environment with sufficient oxygen and glucose,conidia obtained energy through aerobic respiration.This paper provides important clues which are helpful to understanding the changes in gene expres-sion,signal conduction and metabolism characteristics during T.rubrum conidial germination,and possess significant meaning to the study of other superficial dermatophytes.展开更多
In this study,we constructed single mutants MTS-1,MTS-2 of IroN and ShuA gene and double mutant MTS of them in Shigella dysenteriae A1 strain 51197 by insert and absence.The functional detection of every mutant was pe...In this study,we constructed single mutants MTS-1,MTS-2 of IroN and ShuA gene and double mutant MTS of them in Shigella dysenteriae A1 strain 51197 by insert and absence.The functional detection of every mutant was performed at the level of culture medium and cell experiment.The gene expression profiles of the mutants and the wild-type strains under iron-enriched and iron-limited conditions were analyzed by the SD51197 whole genomic microarray.The results showed that all the mutants grew obviously less well than the wild-type strains in L broth appending iron chelator DIP.The addition of iron to the cultures can stimulate the growth of mutants back to wild-type levels.In either the experiments on the ability of intracellular multiplication or the cell-to-cell spread in HeLa and U937 cell lines,mutants showed no obvious change in virulence compared with the parental strain SD51197.However when DIP was added to the cultured HeLa cells,the ability of intracellular multiplication of MTS-1,MTS-2,MTS has reduced about 23.4%,25.2%,43.6%respectively.The analysis of expression profiles under the iron-limited condition showed that the mutants were more sensitive for the changes of iron deficiency than the wild-type strains,many genes have been altered.Up-regulated genes mainly involved genes of transcription,coenzyme metabolism,amino acid transport and metabolism,and unknown functional genes,while down-regulated genes mainly involved genes of energy and carbohydrate metabolism and unknown function genes;the expression levels of known iron-transport associated genes generally showed up-regulated.The results demonstrated that iron-transport associated genes IroN,ShuA were likely to have some effects on the virulence and growth of S.dysenteriae.展开更多
Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading fram...Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading frames, ORFs) of E. coli K12 strain MG1655 and spe-cific ORFs of S. dysenteriae A1 strain Sd51197. The CGH results indicated the genomes of the serotypes contain 2654 conserved ORFs originating from E. coli. However, 219 intrinsic genes of E. coli including those prophage genes, molecular chaperones, synthesis of specific O antigen and so on were absent. Moreover, some specific genes such as type II secretion system associ-ated components, iron transport related genes and some others as well were acquired through horizontal transfer. According to phylogenic trees based on genetic composition, it was demon-strated that A1, A2, A8, A10 were distinct from the other S. dysenteriae serotypes. Our results in this report may provide new insights into the physiological process, pathogenicity and evolution of S. dysenteriae.展开更多
We report on the preparation and superconductivity of metastable γ-Ga islands on Si(111) substrate. The Ga grows in a typical Volmer-Weber mode at a low temperature of 110 K, resulting in formation of Ga nanoislands ...We report on the preparation and superconductivity of metastable γ-Ga islands on Si(111) substrate. The Ga grows in a typical Volmer-Weber mode at a low temperature of 110 K, resulting in formation of Ga nanoislands at various sizes with the identical γ-phase. In-situ low temperature scanning tunneling spectra reveal quantized electronic states in ultrathin Ga islands. It is found that both the lateral size and thickness of the Ga islands strongly suppress the superconductivity. Due to substantial surface energy contribution, the transition temperature Tc scales inversely with the island thickness and the minimum thickness for the occurrence of superconductivity is calculated to be two monolayers.展开更多
Comparative Genomic Hybridization (CGH) microarray analysis was used tocompare the genomic compositions of all eighteen Shigella boydii serotype representative strains.The results indicated the genomic ''backb...Comparative Genomic Hybridization (CGH) microarray analysis was used tocompare the genomic compositions of all eighteen Shigella boydii serotype representative strains.The results indicated the genomic ''backbone'' of this subgroup contained 2552 ORFs homologous tononpatho-genic E. coli K12. Compared with the genome of K12199 ORFs were found to be absent in allS. boydii serotype representatives, including mainly outer membrane protein genes and O-antigenbiosynthesis genes. Yet the specific ORFs of S. boydii subgroup contained basically bacteriophagegenes and the function unknown (FUN) genes. Some iron metabolism, transport and type Ⅱ secretionsystem related genes were found in most representative strains. According to the CGH phylogeneticanalysis, the eighteen S. boydii serotype representatives were divided into four groups, in whichserotype C13 strain was remarkably distinguished from the other serotype strains. This groupingresult corresponded to the distribution of some metabolism related genes. Furthermore, the analysisof genome backbone genes, specific genes, and the phylogenetic trees allowed us to discover theevolution laws of S. boydii and to find out important clues to pathogenesis research, vaccinationand the therapeutic medicine development.展开更多
Trichophyton rubrum (T.rubrum) is one of the most common human fungal pathogens that cause chronic infections of the skin and nails. To identify antifungal responsive genes, cDNA microarray analysis was performed for ...Trichophyton rubrum (T.rubrum) is one of the most common human fungal pathogens that cause chronic infections of the skin and nails. To identify antifungal responsive genes, cDNA microarray analysis was performed for T. rubrum to reveal global transcriptional profiles of drug-specific responses to 5-Flucytosine (5-FC). cDNA microarray was constructed from the T. rubrum expressed sequence tag (ESTs) database, the minimum inhibitory concentration (MIC) of 5-FC was determined, and microarray hybridization and data analysis were applied. The expression pattern of 7 genes observed by microarray was confirmed by the quantitative real-time reverser transcription polymerase chain reaction (RT-PCR). Data analysis indicated that a total of 474 genes were found differentially expressed, 196 showed an increase in expression and 278 showed a decrease in expression. Marked down-regulation of genes involved in nucleotide metabolism (such as CDC21), transcription (such as E2F1), and RNA processing (such as SGN1, RIM4 and NOP1) was observed. Other genes involved in signal transduction, chaperones, inorganic ion transport, secondary metabolite biosynthesis, amino acid transport, lipid transport and potential drug resistance mechanism were also affected by 5-FC. Quantitative real-time RT-PCR of the selected genes confirmed the reliability of the microarray results. This is the first analysis of transcriptional profiles in response to 5-FC for T. rubrum. The findings may be valuable for the identification of genes involved in mechanisms of action and mechanisms of antifungal drug resistance of 5-FC.展开更多
基金Supported by the National Key Technologies Research and Development Program (Grant No. 2005BA711A09)from the Ministry of Science and Technology of China
文摘An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 com-plex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.
基金supported by the National Natural Science Foundation of China(Grant No.30700033)National Basic Research Program of China(Grant Nos.2009CB522603 and 2005CB522904)
文摘Gram-negative,facultative intracellular anaerobes of the genus Shigella,the principal etiologic agents of shigellosis,continue to pose a threat to public health.Shigellosis causes 1.1 million deaths with over 164 million annual cases.The Shigella spp.can be divided into four serogroups:Shigella dysenteriae,Shigella flexneri,Shigella boydii and Shigella sonnei.The completion of seven Shigella genome sequences of representative strains from each of the Shigella species has introduced an era of whole-genome study.This paper reviews contemporary understanding of genomics,transcriptomics,proteomics and the structural biology of Shigella.
基金the National High Technology Research and development Program from the Ministry of Science and Technology of China(Grant No.2005BA711A09)
文摘Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide.In China,serogroup A strains were responsible for over 95%of the cases,while serogroup B strains were mainly the cause of localized outbreaks and sporadic cases.Before 2003,serogroup C strains were only re-covered from a few sporadic cases.However,a sudden increase in the number of cases due to sero-group C strains occurred during 2003—2005 in Anhui Province,China.Many cases were found in other provinces at the same time.Multilocus sequence typing(MLST)results indicated that the unique se-quence type 4821 clone meningococci,a new hyper-virulent lineage,was responsible for the serogroup C meningitis outbreaks.We have completed the project of sequencing the whole genome of the Chi-nese N.meningitidis serogroup C representative isolate 053442.We fabricated a whole-genome mi-croarray of N.meningitidis isolate 053442 and analyzed the genome composition differences among 81 serogroup C isolates which were isolated from 14 provinces of China during 1966—2005.The com-parative genomic hybridization(CGH)result shows that the genome compositions of nearly all sero-group C isolates are similar to that of 053442.The products of many absent open reading frames(ORFs)are conserved hypothetical proteins.The results will provide a valuable resource from which one can analyze the genome composition and genetic background of serogroup C meningococci in China.
基金the National High Technology Research and Development Program of China(Grant No.2001AA223021)National Key Technologies R&D Programme(Grant No.2002BA711A14)
文摘Trichophyton rubrum is a dominating superficial dermatophyte,whose conidial germination is corre-lated to pathopoiesis and a highly important developmental process.To investigate the changes of physiology,biochemistry and cytology during the germination,we selected 3364 function identified ESTs from T.rubrum cDNA library to construct cDNA microarrays,and compared the gene expression levels of conidia and germinating phase.Data analysis indicated that 335 genes were up-regulated during the germination,which mainly encoded translated,modified proteins and structural proteins.The constituents of cell wall and cell membrane were synthetized abundantly,suggesting that they are the foundation of cell morphogenesis.The ingredients of the two-component signal transduction sys-tem were up-regulated,presuming that they were important for the conidial germination.Genes of various metabolic pathways were expressed prosperously,especially the genes that participated in glycolysis and oxidative phosphorylation were up-regulated on the whole,demonstrating that in the environment with sufficient oxygen and glucose,conidia obtained energy through aerobic respiration.This paper provides important clues which are helpful to understanding the changes in gene expres-sion,signal conduction and metabolism characteristics during T.rubrum conidial germination,and possess significant meaning to the study of other superficial dermatophytes.
基金supported by the High Technology Research and Development Program of China(Grant No.2004AA223090)the State Key Basic Research Program(Grant No.2005CB522904)Interational Science and Technology Co-operation Project(Grant No.2001AA223116).
文摘In this study,we constructed single mutants MTS-1,MTS-2 of IroN and ShuA gene and double mutant MTS of them in Shigella dysenteriae A1 strain 51197 by insert and absence.The functional detection of every mutant was performed at the level of culture medium and cell experiment.The gene expression profiles of the mutants and the wild-type strains under iron-enriched and iron-limited conditions were analyzed by the SD51197 whole genomic microarray.The results showed that all the mutants grew obviously less well than the wild-type strains in L broth appending iron chelator DIP.The addition of iron to the cultures can stimulate the growth of mutants back to wild-type levels.In either the experiments on the ability of intracellular multiplication or the cell-to-cell spread in HeLa and U937 cell lines,mutants showed no obvious change in virulence compared with the parental strain SD51197.However when DIP was added to the cultured HeLa cells,the ability of intracellular multiplication of MTS-1,MTS-2,MTS has reduced about 23.4%,25.2%,43.6%respectively.The analysis of expression profiles under the iron-limited condition showed that the mutants were more sensitive for the changes of iron deficiency than the wild-type strains,many genes have been altered.Up-regulated genes mainly involved genes of transcription,coenzyme metabolism,amino acid transport and metabolism,and unknown functional genes,while down-regulated genes mainly involved genes of energy and carbohydrate metabolism and unknown function genes;the expression levels of known iron-transport associated genes generally showed up-regulated.The results demonstrated that iron-transport associated genes IroN,ShuA were likely to have some effects on the virulence and growth of S.dysenteriae.
文摘Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading frames, ORFs) of E. coli K12 strain MG1655 and spe-cific ORFs of S. dysenteriae A1 strain Sd51197. The CGH results indicated the genomes of the serotypes contain 2654 conserved ORFs originating from E. coli. However, 219 intrinsic genes of E. coli including those prophage genes, molecular chaperones, synthesis of specific O antigen and so on were absent. Moreover, some specific genes such as type II secretion system associ-ated components, iron transport related genes and some others as well were acquired through horizontal transfer. According to phylogenic trees based on genetic composition, it was demon-strated that A1, A2, A8, A10 were distinct from the other S. dysenteriae serotypes. Our results in this report may provide new insights into the physiological process, pathogenicity and evolution of S. dysenteriae.
基金supported by the National Natural Science Foundation of China(Grant No.11374336)
文摘We report on the preparation and superconductivity of metastable γ-Ga islands on Si(111) substrate. The Ga grows in a typical Volmer-Weber mode at a low temperature of 110 K, resulting in formation of Ga nanoislands at various sizes with the identical γ-phase. In-situ low temperature scanning tunneling spectra reveal quantized electronic states in ultrathin Ga islands. It is found that both the lateral size and thickness of the Ga islands strongly suppress the superconductivity. Due to substantial surface energy contribution, the transition temperature Tc scales inversely with the island thickness and the minimum thickness for the occurrence of superconductivity is calculated to be two monolayers.
文摘Comparative Genomic Hybridization (CGH) microarray analysis was used tocompare the genomic compositions of all eighteen Shigella boydii serotype representative strains.The results indicated the genomic ''backbone'' of this subgroup contained 2552 ORFs homologous tononpatho-genic E. coli K12. Compared with the genome of K12199 ORFs were found to be absent in allS. boydii serotype representatives, including mainly outer membrane protein genes and O-antigenbiosynthesis genes. Yet the specific ORFs of S. boydii subgroup contained basically bacteriophagegenes and the function unknown (FUN) genes. Some iron metabolism, transport and type Ⅱ secretionsystem related genes were found in most representative strains. According to the CGH phylogeneticanalysis, the eighteen S. boydii serotype representatives were divided into four groups, in whichserotype C13 strain was remarkably distinguished from the other serotype strains. This groupingresult corresponded to the distribution of some metabolism related genes. Furthermore, the analysisof genome backbone genes, specific genes, and the phylogenetic trees allowed us to discover theevolution laws of S. boydii and to find out important clues to pathogenesis research, vaccinationand the therapeutic medicine development.
基金Supported by the National High Technology Research and Development Program of China (Grant No. 2006AA020504)
文摘Trichophyton rubrum (T.rubrum) is one of the most common human fungal pathogens that cause chronic infections of the skin and nails. To identify antifungal responsive genes, cDNA microarray analysis was performed for T. rubrum to reveal global transcriptional profiles of drug-specific responses to 5-Flucytosine (5-FC). cDNA microarray was constructed from the T. rubrum expressed sequence tag (ESTs) database, the minimum inhibitory concentration (MIC) of 5-FC was determined, and microarray hybridization and data analysis were applied. The expression pattern of 7 genes observed by microarray was confirmed by the quantitative real-time reverser transcription polymerase chain reaction (RT-PCR). Data analysis indicated that a total of 474 genes were found differentially expressed, 196 showed an increase in expression and 278 showed a decrease in expression. Marked down-regulation of genes involved in nucleotide metabolism (such as CDC21), transcription (such as E2F1), and RNA processing (such as SGN1, RIM4 and NOP1) was observed. Other genes involved in signal transduction, chaperones, inorganic ion transport, secondary metabolite biosynthesis, amino acid transport, lipid transport and potential drug resistance mechanism were also affected by 5-FC. Quantitative real-time RT-PCR of the selected genes confirmed the reliability of the microarray results. This is the first analysis of transcriptional profiles in response to 5-FC for T. rubrum. The findings may be valuable for the identification of genes involved in mechanisms of action and mechanisms of antifungal drug resistance of 5-FC.
