Objective To optimize the performance of Pulsed-Field Gel Electrophoresis （PFGE） for the comparison of inter-laboratory results and information exchange of Borrelia burgdorferi subtypingo Methods A panel of 34 strai...Objective To optimize the performance of Pulsed-Field Gel Electrophoresis （PFGE） for the comparison of inter-laboratory results and information exchange of Borrelia burgdorferi subtypingo Methods A panel of 34 strains of B. burgdorferi were used to optimize PFGE for subtyping. In order to optimize the electrophoretic parameters （EPs）, all 34 strains of B. burgdorferi were analyzed using four EPs, yielding different Simpson diversity index （D） values and the epidemiological concordance was also evaluated. Results The EP of a switch time of l s to 25 s for13 h and l s to10 s for 6 h produced the highest D value and was declared to be optimal for Mlul and 5mal PFGE of B. burgdorferi. Mlul and Smal were selected as the first and second restriction enzymes for PFGE subtyping of B. burgdorferi according to discrimination and consistency with epidemiological data. Conclusion PFGE can be used as a valuable test for routine genospecies identification of B burgdorferi.展开更多
The actinomycete populations and functions in cadmium （Cd） contaminated soil were investigated by the cultivation- independent molecular methods. The genomic DNA was extracted and purified from soil adulterated with...The actinomycete populations and functions in cadmium （Cd） contaminated soil were investigated by the cultivation- independent molecular methods. The genomic DNA was extracted and purified from soil adulterated with various con- centrations of Cd in the laboratory. The partial 16S rDNA genes were amplified by polymerase chain reaction （PCR） using specific primers bound to evolutionarily conserved regions within these actinomycete genes. The diversity in PCR- amplified products, as measured by denaturing gradient gel electrophoresis （EGGE）, was used as a genetic fingerprint of the population. Principle component analysis and Shannon-Weaver diversity index （H） analyses were used to analyze the DGGE results. Results showed that the two principal components accounted for only a low level of the total variance. The value H in contaminated soil was lower than that in the control at later stages of cultivation, whereas at earlier stages it was higher. Among the six sampling time points, the first, fifth and sixth weeks had the highest values of H. Significantly negative correlations between bioavallable Cd concentration and H values existed in the samples from weeks 2 （R = 0.929, P 〈 0.05） and 4 （R = 0.909, P 〈 0.05）. These results may shed light on the effect of Cd on the soil environment and the chemical behavior and toxicity of Cd to actinomycetes.展开更多
This study is first to investigate proteomic changes in sheep sperm induced by carbon ion radiation using two-dimensional electrophoresis （2-DE） analysis in the project of breeding a new variety of sheep. Differenti...This study is first to investigate proteomic changes in sheep sperm induced by carbon ion radiation using two-dimensional electrophoresis （2-DE） analysis in the project of breeding a new variety of sheep. Differential expression proteins were detected using the PDQuest 8.0 software after staining with Coomassie blue. Valid spots were then analyzed through liquid chromatography tandem mass spectrometry （LC-MS/MS）. Among the 480 total protein spots displayed in 2-D gels, 6 specific protein spots were observed in sperm gels. A search against protein sequences in the National Center for Biotechnology Information databases （NCBI） indicated that differentially expressed proteins correspond to two proteins, identified to be enolase and transcription factor AP-2-alpha （TFAP-2c0. The two proteins were up-regulated in the irradiated sperm. To the best of our knowledge, this study is the first to identify proteomic changes induced by carbon ion radiation in sheep sperm. The analysis of differential expression protein may be useful in identifying new breeding markers in sheep reproduction and in clarifying the mechanisms involved in irradiation or space breeding.展开更多
Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be ne...Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing.highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.展开更多
目的对一起因食用肠炎沙门氏菌污染的熏肉大饼引起的食源性疾病暴发事件进行溯源分析。方法对8例患者进行流行病学调查,采集相关环境、食品及粪便等样本,根据国家标准进行实验室检测,经增菌后挑取可疑菌落进行生化鉴定,对检出的6株沙门...目的对一起因食用肠炎沙门氏菌污染的熏肉大饼引起的食源性疾病暴发事件进行溯源分析。方法对8例患者进行流行病学调查,采集相关环境、食品及粪便等样本,根据国家标准进行实验室检测,经增菌后挑取可疑菌落进行生化鉴定,对检出的6株沙门氏菌株采用标准诊断血清进行血清凝集试验,药敏试验及脉冲场凝胶电泳。结果该起事件发病8例,6份样本中,分离出肠炎沙门氏菌,沙门氏菌检出率食品、环境和病人粪便样本均为100%,药敏试验结果显示,耐药谱为多粘菌素E(Colistin,CT)―头孢噻肟(Cefotaxime,CTX)―四环素(Tetracycline,TET)―环丙沙星(Ciprofloxacin,CIP)―氨苄西林(Ampicillin,AMP)―氨苄西林/舒巴坦(Ampicillin/Sulbactam,AMS),均呈现6重耐药现象,对氯霉素(Chloramphenicol,CHL)、复方新诺明(Sulfamethoxazole,SXT)、厄他培南(Ertapenem,ETP)、美罗培南(Meropenem,MEM)、头孢他啶(Ceftazidime,CAZ)、头孢他啶/阿维巴坦(Ceftazidime/avibactam,CZA)、替加环素(Tigecycline,TIG)、阿奇霉素(Azithromycin,AZM)、阿米卡星(Amikacin,AMI)敏感,6株菌的脉冲场凝胶电泳(Pulse Field Gel Electrophoresis,PFGE)条带一致,同源性100%,显示为同一克隆。结论该起事件为市民食用被肠炎沙门氏菌污染的熏肉大饼引起的食源性疾病暴发事件。展开更多
采用变性梯度凝胶电泳（DGGE）技术对内蒙古河套灌区三种不同盐碱程度土壤（盐土,强度盐化土,轻度盐化土）不同深度（0~20cm和20~30cm）土壤细菌16S r DNA V3~V6可变区扩增片段进行分析,并对土壤理化性质进行了测定.结果表明：细菌群落...采用变性梯度凝胶电泳（DGGE）技术对内蒙古河套灌区三种不同盐碱程度土壤（盐土,强度盐化土,轻度盐化土）不同深度（0~20cm和20~30cm）土壤细菌16S r DNA V3~V6可变区扩增片段进行分析,并对土壤理化性质进行了测定.结果表明：细菌群落多样性随土壤盐碱化程度的加深而减少（轻度盐化土〉强度盐化土〉盐土）,随土壤深度的增加而降低（细菌群落多样性0~20cm土层大于20~30cm土层）.细菌Shannon-Wiener指数在轻度盐化土中最大为3.36,在强度盐化土和盐土分别为3.05和2.49.不同盐碱程度土壤以细菌相似系数聚类,分为0~20cm层与20~30cm层两大族群,土壤细菌群落Shannon-Wiener指数在0~20cm层中（盐土为3.04,强度盐化土为3.29,轻度盐化土为3.36）均大于在20~30cm层（盐土为2.49,强度盐化土为3.05,轻度盐化土为3.14）.相关性分析和典范对应分析表明,土壤w（EC）、p H值、w（SOC）、w（TP）是土壤细菌群落结构多样性的显著影响因素,不同盐碱程度土壤中细菌群落的Shannon-Wiener指数与土壤w（EC）（r=-0.542,P〈0.05）、p H（r=-0.526,P〈0.05）呈显著负相关,与土壤w（SOC）（r=0.700,P〈0.01）和w（TP）（r=0.805,P〈0.01）呈极显著正相关.w（EC）和p H对盐碱土壤细菌群落结构的影响力最大.回收DGGE图谱中20个优势条带进行测序分析,结果显示,变形菌纲（α-变形菌纲、β-变形菌纲、γ-变形菌纲和δ-变形菌纲）是盐碱土壤的主要类群.展开更多
In recent years,great progress has been made in the theory and technology of proteomics.As embranchment of proteomics,serum proteomics has been payed more and more attention also.The advanced techniques have been appl...In recent years,great progress has been made in the theory and technology of proteomics.As embranchment of proteomics,serum proteomics has been payed more and more attention also.The advanced techniques have been applied in serum proteomics research,which promote the development of the methodology.A great advance has been made in serum proteomics research for seeking associated tumor markers,pharmacy and some non-cancer diseases.展开更多
基金supported by the National Natural Science Foundation of China (NSFC)(31100105)the 12th Five-Year Major National Science and Technology Projects of China(No.2012ZX10004219-007)
文摘Objective To optimize the performance of Pulsed-Field Gel Electrophoresis （PFGE） for the comparison of inter-laboratory results and information exchange of Borrelia burgdorferi subtypingo Methods A panel of 34 strains of B. burgdorferi were used to optimize PFGE for subtyping. In order to optimize the electrophoretic parameters （EPs）, all 34 strains of B. burgdorferi were analyzed using four EPs, yielding different Simpson diversity index （D） values and the epidemiological concordance was also evaluated. Results The EP of a switch time of l s to 25 s for13 h and l s to10 s for 6 h produced the highest D value and was declared to be optimal for Mlul and 5mal PFGE of B. burgdorferi. Mlul and Smal were selected as the first and second restriction enzymes for PFGE subtyping of B. burgdorferi according to discrimination and consistency with epidemiological data. Conclusion PFGE can be used as a valuable test for routine genospecies identification of B burgdorferi.
基金Project supported by the National Natural Science Foundation of China (Nos. 30570053 and 40501037)the National High Technology Research and Development Program (863 Program) of China (No. 2007AA10Z409)+1 种基金the National"Eleventh Five Years Plan" Key Project on Science and Technology of China (No. 2006BAJ08B01)the Research Fund of Science and Technology Bureau of Zhejiang Province,China (No. 2008C23088)
文摘The actinomycete populations and functions in cadmium （Cd） contaminated soil were investigated by the cultivation- independent molecular methods. The genomic DNA was extracted and purified from soil adulterated with various con- centrations of Cd in the laboratory. The partial 16S rDNA genes were amplified by polymerase chain reaction （PCR） using specific primers bound to evolutionarily conserved regions within these actinomycete genes. The diversity in PCR- amplified products, as measured by denaturing gradient gel electrophoresis （EGGE）, was used as a genetic fingerprint of the population. Principle component analysis and Shannon-Weaver diversity index （H） analyses were used to analyze the DGGE results. Results showed that the two principal components accounted for only a low level of the total variance. The value H in contaminated soil was lower than that in the control at later stages of cultivation, whereas at earlier stages it was higher. Among the six sampling time points, the first, fifth and sixth weeks had the highest values of H. Significantly negative correlations between bioavallable Cd concentration and H values existed in the samples from weeks 2 （R = 0.929, P 〈 0.05） and 4 （R = 0.909, P 〈 0.05）. These results may shed light on the effect of Cd on the soil environment and the chemical behavior and toxicity of Cd to actinomycetes.
基金supported by the Key Scientific Technology Research Projects of Gans u Province, China (1102NKDA022)the Major Program of Ministry of Agriculture to Cultivate New Varieties of Genetically ModifiedOrganisms of China (2008ZX08008-003)+1 种基金the National Basic Research Program of Chinathe National Natural Science Foundation of China (2010CB834202)
文摘This study is first to investigate proteomic changes in sheep sperm induced by carbon ion radiation using two-dimensional electrophoresis （2-DE） analysis in the project of breeding a new variety of sheep. Differential expression proteins were detected using the PDQuest 8.0 software after staining with Coomassie blue. Valid spots were then analyzed through liquid chromatography tandem mass spectrometry （LC-MS/MS）. Among the 480 total protein spots displayed in 2-D gels, 6 specific protein spots were observed in sperm gels. A search against protein sequences in the National Center for Biotechnology Information databases （NCBI） indicated that differentially expressed proteins correspond to two proteins, identified to be enolase and transcription factor AP-2-alpha （TFAP-2c0. The two proteins were up-regulated in the irradiated sperm. To the best of our knowledge, this study is the first to identify proteomic changes induced by carbon ion radiation in sheep sperm. The analysis of differential expression protein may be useful in identifying new breeding markers in sheep reproduction and in clarifying the mechanisms involved in irradiation or space breeding.
基金funded by the Valle d’Aosta Regional Government (http://www.regione.vda.it/) in the frame of the regional law n.84-07/12/1993 (project ParIS-Parkinson Informative System)
文摘Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing.highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.
文摘目的对一起因食用肠炎沙门氏菌污染的熏肉大饼引起的食源性疾病暴发事件进行溯源分析。方法对8例患者进行流行病学调查,采集相关环境、食品及粪便等样本,根据国家标准进行实验室检测,经增菌后挑取可疑菌落进行生化鉴定,对检出的6株沙门氏菌株采用标准诊断血清进行血清凝集试验,药敏试验及脉冲场凝胶电泳。结果该起事件发病8例,6份样本中,分离出肠炎沙门氏菌,沙门氏菌检出率食品、环境和病人粪便样本均为100%,药敏试验结果显示,耐药谱为多粘菌素E(Colistin,CT)―头孢噻肟(Cefotaxime,CTX)―四环素(Tetracycline,TET)―环丙沙星(Ciprofloxacin,CIP)―氨苄西林(Ampicillin,AMP)―氨苄西林/舒巴坦(Ampicillin/Sulbactam,AMS),均呈现6重耐药现象,对氯霉素(Chloramphenicol,CHL)、复方新诺明(Sulfamethoxazole,SXT)、厄他培南(Ertapenem,ETP)、美罗培南(Meropenem,MEM)、头孢他啶(Ceftazidime,CAZ)、头孢他啶/阿维巴坦(Ceftazidime/avibactam,CZA)、替加环素(Tigecycline,TIG)、阿奇霉素(Azithromycin,AZM)、阿米卡星(Amikacin,AMI)敏感,6株菌的脉冲场凝胶电泳(Pulse Field Gel Electrophoresis,PFGE)条带一致,同源性100%,显示为同一克隆。结论该起事件为市民食用被肠炎沙门氏菌污染的熏肉大饼引起的食源性疾病暴发事件。
文摘采用变性梯度凝胶电泳（DGGE）技术对内蒙古河套灌区三种不同盐碱程度土壤（盐土,强度盐化土,轻度盐化土）不同深度（0~20cm和20~30cm）土壤细菌16S r DNA V3~V6可变区扩增片段进行分析,并对土壤理化性质进行了测定.结果表明：细菌群落多样性随土壤盐碱化程度的加深而减少（轻度盐化土〉强度盐化土〉盐土）,随土壤深度的增加而降低（细菌群落多样性0~20cm土层大于20~30cm土层）.细菌Shannon-Wiener指数在轻度盐化土中最大为3.36,在强度盐化土和盐土分别为3.05和2.49.不同盐碱程度土壤以细菌相似系数聚类,分为0~20cm层与20~30cm层两大族群,土壤细菌群落Shannon-Wiener指数在0~20cm层中（盐土为3.04,强度盐化土为3.29,轻度盐化土为3.36）均大于在20~30cm层（盐土为2.49,强度盐化土为3.05,轻度盐化土为3.14）.相关性分析和典范对应分析表明,土壤w（EC）、p H值、w（SOC）、w（TP）是土壤细菌群落结构多样性的显著影响因素,不同盐碱程度土壤中细菌群落的Shannon-Wiener指数与土壤w（EC）（r=-0.542,P〈0.05）、p H（r=-0.526,P〈0.05）呈显著负相关,与土壤w（SOC）（r=0.700,P〈0.01）和w（TP）（r=0.805,P〈0.01）呈极显著正相关.w（EC）和p H对盐碱土壤细菌群落结构的影响力最大.回收DGGE图谱中20个优势条带进行测序分析,结果显示,变形菌纲（α-变形菌纲、β-变形菌纲、γ-变形菌纲和δ-变形菌纲）是盐碱土壤的主要类群.
文摘In recent years,great progress has been made in the theory and technology of proteomics.As embranchment of proteomics,serum proteomics has been payed more and more attention also.The advanced techniques have been applied in serum proteomics research,which promote the development of the methodology.A great advance has been made in serum proteomics research for seeking associated tumor markers,pharmacy and some non-cancer diseases.
