Objective： To explore the role of transcription-coupled repair （TCR） pathway in the UVC-induced SupF gene mutation in Tet-on 293 cell line, we designed and constructed a Tet-responsive plasmid DNA pTCR-C1, and util...Objective： To explore the role of transcription-coupled repair （TCR） pathway in the UVC-induced SupF gene mutation in Tet-on 293 cell line, we designed and constructed a Tet-responsive plasmid DNA pTCR-C1, and utilized this pTCR-C 1 plasmid to obtain the mutation frequency of SupF reporter gene induced by UVC in Tet-on 293 cell line. Methods： SupF gene was cloned into a Tet-responsive plamid pBI-L, which include a bidirectional Tet-responsive promoter, and was named pTCR-C1. The pTCR-C1 plasmid was transfected into Tet-on 293 cell line, and the mutation frequency of SupF reporter gene was detected in the presence and absence of DOX. Results： The pTCR-C1 plasmid was identified with the methods of restriction digestion and DNA sequencing. The mutation frequency of SupF reporter gene in the presence of DOX was higher than in the absence of DOX. Conclusion： The TCR pathway takes part in the UVC-induced SupF gene mutation in Tet-on 293 cell line.展开更多
The aim of this study was to analyze the point mutation of the exon 1 at codon 54 of the mannose (or mannan)-binding lectin (MBL) gene in healthy individuals of Chinese Hans and Mongolian population, and to find out a...The aim of this study was to analyze the point mutation of the exon 1 at codon 54 of the mannose (or mannan)-binding lectin (MBL) gene in healthy individuals of Chinese Hans and Mongolian population, and to find out any association between the plasma levels of MBL and the gene mutation frequency in both groups of individuals. Blood samples were collected randomly from 56 healthy individuals of Chinese Hans and 37 Mongolian. The detection of the point mutations of the MBL gene was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and detections for plasma levels of MBL were determined by using MBL ELISA kits. A MBL PCR method of assay was established with high specificity, and good reproducibility. By optimizing the PCR condition, the optimal annealing temperature was 55℃, and the lowest detection limit was 160 pg. No bands were found in non-specificity samples (HAV, HBV, HCV and TB), and the sequences of PCR products were the same as the expected ones. Also a MBL PCR-RFLP was established. Upon electrophoresis of the digested products in 3% agarose gel, there were 3 patterns: in which 2 bands correspond to molecule weight 232 bp and 93 bp; 1 band, corresponds to molecule weight 325 bp and 3 bands correspond to molecule weight 325 bp, 232 bp and 93 bp, respectively. Three bands of 325 bp, 232 bp and 93 bp of point mutations were found at codon 54 of MBL coding gene. Frequencies in healthy Han and Mongolian population were 0.2321 and 0.1757 respectively. The average plasma MBL concentration was 1998.750 μg/L, with SD of 1505.152 in 56 healthy Han population and 2525.676 μg/L, with SD of 1955.188 in 37 Mongolian. A negative correlation between MBL concentration and gene mutation frequency was found in healthy Han population. Frequency of point mutation was 1.00 when the MBL concentrations were below 100 μg/L; frequency of point mutation was 0.4524 when the concentration was 100 μg/L to 1000 μg/L; and the frequency of point mutation was 0.0156 when the concentration was over 1000 μg/L. Analysis of association between MBL concentration and gene frequency in healthy Mongolian population showed that frequency of point mutation was 1.00 when the MBL concentrations were below 100 μg/L and the frequency of point mutation was 0.4583 when the MBL concentrations were 100 μg/L to 1000 μg/L; no point mutation was found when the concentration was over 1000 μg/L. It is concluded that the frequencies of mutation at codon 54 of MBL coding gene had been determined in both healthy Hans and Mongolian population, and the frequency was higher in healthy Hans than that of Mongolian, but no statistical significance (χ 2=0.8574, P >0.05). The MBL level was lower in healthy Hans than in Mongolian population, but there was no statistical significance( t =1.448, 0.1< P <0.2). There was a negative correlation between frequency of point mutation and MBL concentrations in both Hans and Mongolian population( r =-0.62, r =-0.641).展开更多
The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine th...The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic.In this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes.All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation efficiency.As a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation frequency.Furthermore,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons usage.In addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐2.Finally,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.展开更多
Objective To evaluate the frequencies and polymorphisms of CCR5-△32,CCR2-641 and SDF1-3'A alleles conferring resistance to HIV-1 infection in Chinese population from Han ethnic origin.Methods This cohort was comp...Objective To evaluate the frequencies and polymorphisms of CCR5-△32,CCR2-641 and SDF1-3'A alleles conferring resistance to HIV-1 infection in Chinese population from Han ethnic origin.Methods This cohort was comprised of 1251 subjects(915 men and 336 women)aged 15 -80 years and none was HIV-1 positive.Genotyping of allelic CCR5-△32,CCR2-641 and SDF1-3' A variants was performed using PCR or PCR/RFLP assay,and further confirmed by direct DNA sequencing.Results Our finding shows that the△32 deletion mutation in the CCR5 gene does occur in this population and can be inherited in a Mendelian fashion in indigenous Han Chinese at a very low frequency of 0.00119(n= 1254).The frequencies of mutant CCR2-641 and SDF1-3'A alleles were 0.20023(n = 1251)and 0.2873(n = 893),in this population,which are higher than those found in American Caucasians.Furthermore the polymorphisms of CCR2-641 and SDF1-3' A alleles in the Han Chinese population were different from those in American Caucasians.Statistical analysis showed that the genotype distribution of CCR5-△32,CCR2-641 and SDF1-3' A alleles was in equilibrium according to the Hardy-Weinberg equation.Conclusion The CCR5-△32 mutation may not be a major resistant factor against HIV-1 infection in indigenous Han Chinese.The significance of higher frequencies of CCR2-641 and SDF1-3' A alleles (0.20023 and 0.2791)in the Han population remains to be clarified in HIV-1-positive carriers and AIDS patients.展开更多
Objective:To study the ecology of antibiotic resistant bacteria with emphasis on sucrose negative vibrios in water and sediments samples of traditional shrimp farming system(bhery)in West Bengal,India.Methods:The vibr...Objective:To study the ecology of antibiotic resistant bacteria with emphasis on sucrose negative vibrios in water and sediments samples of traditional shrimp farming system(bhery)in West Bengal,India.Methods:The vibrios were isolated from traditional shrimp farm samples on thiosulphate citrate bile salt sucrose agar and sucrose negative bacterial strains were used as biomarkers to assess the frequency of antibiotic resistance.Results:The incoming water brought presumptive vibrios ranging from 5.50×10^(1)to 1.00×10^(3)mL in to the bhery,and there appeared to build up vibrios in the culture system with days of culture,as there was about 9 fold increase in vibrios.The levels of vibrios were observed to be moderately higher in outlet water and ranged between 4.15×10^(2)and 4.15x10^(3)mL.The counts of vibrios in pond sediment was found to be 1.00x10^(2)-4.90×10^(3)g;while in inlet(2.00×10^(2)-4.20×10^(4)g)and outlet(3.00×10^(2)-6.85×10^(3)g)their levels were observed to be higher than the pond sediment.Thirteen different Vibrio species were encountered in traditional shrimp culture system and all vibrios were sensitive to chloramphenicol,followed by ciprofloxacin and gatifloxacin(98.24%),gentamicin(95.61%)and other antibiotics.The multiple antibiotic resistance(MAR),i.e.,resistance to at least two antibiotics,was noticed among 43.85%of the sucrose negative vibrios and 41.86%of the sucrose negative non--vibrios.All vibrios harveyi strains exhibited MAR.Although no antibiotic was used in the bhery,the prevalence of MAR in 44%of the sucrose negative vibrios and nonvibrios is a cause of concern.The MAR index was higher in inlet water and sediment samples.The MAR observed in biomarker strains of pond water and sediment(40%)was comparable to those of inlet samples,thus confirming the fact that incoming water was the major source of antibiotic resistant bacteria.Conclusions:It seems that the shrimp culture in bhery does not favour the proliferation and spread of antibiotic resistant bacteria.展开更多
基金the National Natural Science Foundation of China(30471958)the Natural Science Foundation of Chongqing(No.2006BB5045)
文摘Objective： To explore the role of transcription-coupled repair （TCR） pathway in the UVC-induced SupF gene mutation in Tet-on 293 cell line, we designed and constructed a Tet-responsive plasmid DNA pTCR-C1, and utilized this pTCR-C 1 plasmid to obtain the mutation frequency of SupF reporter gene induced by UVC in Tet-on 293 cell line. Methods： SupF gene was cloned into a Tet-responsive plamid pBI-L, which include a bidirectional Tet-responsive promoter, and was named pTCR-C1. The pTCR-C1 plasmid was transfected into Tet-on 293 cell line, and the mutation frequency of SupF reporter gene was detected in the presence and absence of DOX. Results： The pTCR-C1 plasmid was identified with the methods of restriction digestion and DNA sequencing. The mutation frequency of SupF reporter gene in the presence of DOX was higher than in the absence of DOX. Conclusion： The TCR pathway takes part in the UVC-induced SupF gene mutation in Tet-on 293 cell line.
文摘The aim of this study was to analyze the point mutation of the exon 1 at codon 54 of the mannose (or mannan)-binding lectin (MBL) gene in healthy individuals of Chinese Hans and Mongolian population, and to find out any association between the plasma levels of MBL and the gene mutation frequency in both groups of individuals. Blood samples were collected randomly from 56 healthy individuals of Chinese Hans and 37 Mongolian. The detection of the point mutations of the MBL gene was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and detections for plasma levels of MBL were determined by using MBL ELISA kits. A MBL PCR method of assay was established with high specificity, and good reproducibility. By optimizing the PCR condition, the optimal annealing temperature was 55℃, and the lowest detection limit was 160 pg. No bands were found in non-specificity samples (HAV, HBV, HCV and TB), and the sequences of PCR products were the same as the expected ones. Also a MBL PCR-RFLP was established. Upon electrophoresis of the digested products in 3% agarose gel, there were 3 patterns: in which 2 bands correspond to molecule weight 232 bp and 93 bp; 1 band, corresponds to molecule weight 325 bp and 3 bands correspond to molecule weight 325 bp, 232 bp and 93 bp, respectively. Three bands of 325 bp, 232 bp and 93 bp of point mutations were found at codon 54 of MBL coding gene. Frequencies in healthy Han and Mongolian population were 0.2321 and 0.1757 respectively. The average plasma MBL concentration was 1998.750 μg/L, with SD of 1505.152 in 56 healthy Han population and 2525.676 μg/L, with SD of 1955.188 in 37 Mongolian. A negative correlation between MBL concentration and gene mutation frequency was found in healthy Han population. Frequency of point mutation was 1.00 when the MBL concentrations were below 100 μg/L; frequency of point mutation was 0.4524 when the concentration was 100 μg/L to 1000 μg/L; and the frequency of point mutation was 0.0156 when the concentration was over 1000 μg/L. Analysis of association between MBL concentration and gene frequency in healthy Mongolian population showed that frequency of point mutation was 1.00 when the MBL concentrations were below 100 μg/L and the frequency of point mutation was 0.4583 when the MBL concentrations were 100 μg/L to 1000 μg/L; no point mutation was found when the concentration was over 1000 μg/L. It is concluded that the frequencies of mutation at codon 54 of MBL coding gene had been determined in both healthy Hans and Mongolian population, and the frequency was higher in healthy Hans than that of Mongolian, but no statistical significance (χ 2=0.8574, P >0.05). The MBL level was lower in healthy Hans than in Mongolian population, but there was no statistical significance( t =1.448, 0.1< P <0.2). There was a negative correlation between frequency of point mutation and MBL concentrations in both Hans and Mongolian population( r =-0.62, r =-0.641).
基金This study was supported by funding from the Foundation of the Committee on Science and Technology of Tianjin(19YFZCSN00080)the State Key Research and Development Plan(2019YFC1605004)the National Key Programs for Infectious Diseases of China(2017ZX10303405‐001).
文摘The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic.In this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes.All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation efficiency.As a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation frequency.Furthermore,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons usage.In addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐2.Finally,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.
基金ThisprojectwassupportedbyagrantfromNationalNaturalSciencesFoundationofthePRChina (No 3 9770 683 )
文摘Objective To evaluate the frequencies and polymorphisms of CCR5-△32,CCR2-641 and SDF1-3'A alleles conferring resistance to HIV-1 infection in Chinese population from Han ethnic origin.Methods This cohort was comprised of 1251 subjects(915 men and 336 women)aged 15 -80 years and none was HIV-1 positive.Genotyping of allelic CCR5-△32,CCR2-641 and SDF1-3' A variants was performed using PCR or PCR/RFLP assay,and further confirmed by direct DNA sequencing.Results Our finding shows that the△32 deletion mutation in the CCR5 gene does occur in this population and can be inherited in a Mendelian fashion in indigenous Han Chinese at a very low frequency of 0.00119(n= 1254).The frequencies of mutant CCR2-641 and SDF1-3'A alleles were 0.20023(n = 1251)and 0.2873(n = 893),in this population,which are higher than those found in American Caucasians.Furthermore the polymorphisms of CCR2-641 and SDF1-3' A alleles in the Han Chinese population were different from those in American Caucasians.Statistical analysis showed that the genotype distribution of CCR5-△32,CCR2-641 and SDF1-3' A alleles was in equilibrium according to the Hardy-Weinberg equation.Conclusion The CCR5-△32 mutation may not be a major resistant factor against HIV-1 infection in indigenous Han Chinese.The significance of higher frequencies of CCR2-641 and SDF1-3' A alleles (0.20023 and 0.2791)in the Han population remains to be clarified in HIV-1-positive carriers and AIDS patients.
基金supported by Department of Aquatic Animal Health,Faculty of Fishery Sciences,West Bengal University of Animal and Fishery Sciences,West Bengal,India.(FFS/Adm-21/323)
文摘Objective:To study the ecology of antibiotic resistant bacteria with emphasis on sucrose negative vibrios in water and sediments samples of traditional shrimp farming system(bhery)in West Bengal,India.Methods:The vibrios were isolated from traditional shrimp farm samples on thiosulphate citrate bile salt sucrose agar and sucrose negative bacterial strains were used as biomarkers to assess the frequency of antibiotic resistance.Results:The incoming water brought presumptive vibrios ranging from 5.50×10^(1)to 1.00×10^(3)mL in to the bhery,and there appeared to build up vibrios in the culture system with days of culture,as there was about 9 fold increase in vibrios.The levels of vibrios were observed to be moderately higher in outlet water and ranged between 4.15×10^(2)and 4.15x10^(3)mL.The counts of vibrios in pond sediment was found to be 1.00x10^(2)-4.90×10^(3)g;while in inlet(2.00×10^(2)-4.20×10^(4)g)and outlet(3.00×10^(2)-6.85×10^(3)g)their levels were observed to be higher than the pond sediment.Thirteen different Vibrio species were encountered in traditional shrimp culture system and all vibrios were sensitive to chloramphenicol,followed by ciprofloxacin and gatifloxacin(98.24%),gentamicin(95.61%)and other antibiotics.The multiple antibiotic resistance(MAR),i.e.,resistance to at least two antibiotics,was noticed among 43.85%of the sucrose negative vibrios and 41.86%of the sucrose negative non--vibrios.All vibrios harveyi strains exhibited MAR.Although no antibiotic was used in the bhery,the prevalence of MAR in 44%of the sucrose negative vibrios and nonvibrios is a cause of concern.The MAR index was higher in inlet water and sediment samples.The MAR observed in biomarker strains of pond water and sediment(40%)was comparable to those of inlet samples,thus confirming the fact that incoming water was the major source of antibiotic resistant bacteria.Conclusions:It seems that the shrimp culture in bhery does not favour the proliferation and spread of antibiotic resistant bacteria.
