Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assist...Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.展开更多
The objectives of the present study were to determine associations between these polymorphisms of PON1 gene and growth and carcass traits. For this purpose, genotyping was performed on males of 18 Angus, 23 Jinnan cat...The objectives of the present study were to determine associations between these polymorphisms of PON1 gene and growth and carcass traits. For this purpose, genotyping was performed on males of 18 Angus, 23 Jinnan cattle, 20 Limousin, 28 Luxi cattle, 26 Qinchuan cattle, 29 Simmental, 29 Charolais. Traits of interest were analyzed using the RFLP-PCR and GLM procedure of SAS 9.1 and least square means of the genotypes were compared by the Tukey＇ s test in the association studies. Association of PONI/ EcoRV genotypes with body weight, average daily gain, rib eye area and tenderness were significant （P〈0.05）, and AG genotype was significant difference with others in average daily gain and tenderness （P〈0.05）, with AA genotype may have higher rib eye area （p〈0.05）. The association analysis of the PONI/Alu I polymorphism showed significant associations between genotypes and growth： body weight and carcass traits net meat weight and tenderness （P〈0.05）. AA genotype was considered more favorable than others in all growth and production traits. There were significant differences among breeds for all associated interests traits and difference between beef breeds and native breeds are obviously in all aspects. And these results may be useful for the breeding selection.展开更多
Calpastatin is an endogenous inhibitor of calpain which is responsible for the breakdown of myofibrillar proteins, The association of Single Nucleotide Polymorphism （SNP） in the calpastatin gene with meat tenderness...Calpastatin is an endogenous inhibitor of calpain which is responsible for the breakdown of myofibrillar proteins, The association of Single Nucleotide Polymorphism （SNP） in the calpastatin gene with meat tenderness is an important topic in meat production. Therefore efficient procedure to investigate the SNP is necessary. The objectives of this study were to detect the SNP of calpastatin gene at domain L marker （G/C transversion） of the Kamphaengsaen beef breed （KPS cattle; n = 26） by the Amplification Refractory Mutation System （ARMS） compared with the Restriction Fragment Length Polymorphism （RFLP） methods and to determine the genotypes of the KPS cattle at that marker. Genomic DNA of calpastatin gene extracted from blood of the KPS cattle was detected with ARMS and RFLP methods. The ARMS system has utilized two primer pairs to amplify the two different alleles of a polymorphism in single PCR reaction to detected single base mutation. In this method, the alleles-specific primers had a mismatch at 3＇ terminal base and a second deliberate mismatch at position -2 from 3＇ terminus. While the RFLP method detected a polymorphism using PCR-base technique follow by RsaI restriction enzyme. Amplification of the ARMS method revealed that the results were not different from the conventional method of RFLP. Analysis of genotypes revealed that the KPS cattle inherited the CC, CG and GG genotypes at domain L marker. These were reliable when verified by nucleotide sequence analysis of PCR products. The animals were genotyped and determined for tenderness phenotype with this marker that predicted variation of an intronic polymorphism at domain L of the calpastatin gene. Therefore, the ARMS method was simple, efficient technique, and suitable for detecting SNP at domain L marker of the calpastatin gene.展开更多
Variable selection is one of the most fundamental problems in regression analysis. By sampling from the posterior distributions of candidate models, Bayesian variable selection via MCMC （Markov chain Monte-Carlo） is...Variable selection is one of the most fundamental problems in regression analysis. By sampling from the posterior distributions of candidate models, Bayesian variable selection via MCMC （Markov chain Monte-Carlo） is effective to overcome the computational burden of all-subset variable selection approaches. However, the convergence of the MCMC is often hard to determine and one is often not sure about if obtained samples are unbiased. This complication has limited the application of Bayesian variable selection in practice. Based on the idea of CFTP （coupling from the past）, perfect sampling schemes have been developed to obtain independent samples from the posterior distribution for a variety of problems. Here the authors propose an efficient and effective perfect sampling algorithm for Bayesian variable selection of linear regression models, which independently and identically sample from the posterior distribution of the model space and can efficiently handle thousands of variables. The effectiveness of the authors＇ algorithm is illustrated by three simulation studies, which have up to thousands of variables, the authors＇ method is further illustrated in SNPs （single nucleotide polymorphisms） association study among RA （rheumatoid arthritis） patients.展开更多
Polymorphisms associated with genes coding for a variety of drug-metabolizing enzymes （DMEs） and associated transport proteins can influence the drug metabolism rate of individuals, potentially affecting the efficac...Polymorphisms associated with genes coding for a variety of drug-metabolizing enzymes （DMEs） and associated transport proteins can influence the drug metabolism rate of individuals, potentially affecting the efficacy of drug and the occurrence of adverse reactions. Single nucleotide polymorphisms （SNPs） are prevalent in all types of genetic variations. Reliable SNP genotyping provides excellent markers for detecting genetic polymolphisms, genetic disorders, and resistance of pathogen to drug, which are needed for the genetic diagnosis of disease and subtle genetic factors. With a large number of SNP genotyping studies being conducted, a lot of novel SNP identifying methods have been developed. Several SNP genotyping methods and techniques have been introduced for clinical test. These include TaqMan drug metabolism genotyping assays, pH-sensing semiconductor system, high-resolution melting curve analysis （HRM） of polymerase chain reaction （PCR） amplicons, novel multiplexed electrochemical biosensor with non-fouling surface, DNA hybridization detection using less than 10-nm gap silicon nanogap structure, tetra-primer ARMS-PCR method, acoustic detection of DNA conformation in genetic assays combined with PCR, microbeads-mass spectrometry （MEMS）-based approach, and liquid chromatography-electrospray ionization mass spectrometry. Personalized medicine has changed the conventional ways of using drugs according to experiences. It focuses on making the individualized pattern for each individual based on their own characteristics. Lots of researchers are using the analysis of clinical samples to explain the relationship between the drug adverse reactions and genetic polymorphisms. But it takes a long time from collecting the blood samples for DNA extraction and genotyping to getting results on the side effect of drug through clinical study. Therefore, it is desirable to develop improved in vitro methods to study the drug metabolizing-enzymes and transport protein genetic polymorphisms.展开更多
Objective： To investigate a possible association between common variations of the P2RY12 and the residual clopidogrel on-treatment platelet reactivity after adjusting for the influence of CYP2C19 tested by thromboe- ...Objective： To investigate a possible association between common variations of the P2RY12 and the residual clopidogrel on-treatment platelet reactivity after adjusting for the influence of CYP2C19 tested by thromboe- lastography （TEG）. Methods： One hundred and eighty patients with acute coronary syndrome （ACS） treated with clopJdogrel and aspJdn were included and platelet function was assessed by TEG. Five selected P2RY12 single nu- cleotide polymorphisms （SNPs; rs6798347, rs6787801, rs6801273, rs6785930, and rs2046934）, which cover the common variations in the P2RY12 gene and its regulatory regions, and three CYP2C19 SNPs （ 2, 3, 17） were geno- typed and possible haplotypes were analyzed. Results： The high on-treatment platelet reactivity （HTPR） prevalence defined by a platelet inhibition rate 〈30% by TEG in adenosine diphosphate （ADP）-channel was 69 （38.33%）. Six common haplotypes were inferred from four of the selected P2RY12 SNPs （denoted H0 to H5） according to the linkage disequilibrium R square （except for rs2046934）. Haplotype H1 showed a significantly lower incidence of HTPR than the reference haplotype （H0） in the total study population while haplotypes H1 and H2 showed significantly lower incidences of HTPR than H0 in the nonsmoker subgroup after adjusting for CYP2Clg effects and demographic characteristics. rs2046934 （T744C） did not show any significant association with HTPR. Conclusions： The combination of common P2RY12 variations including regulatory regions rather than rs2046934 （T744C） that related to pharmacodynamics of clopidogrel in patients with ACS was independently associated with residual on-clopidogrel platelet reactivity. This is apart from the established association of the CYP2C19. This association seemed more important in the subgroup defined by smoking.展开更多
文摘Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.
文摘The objectives of the present study were to determine associations between these polymorphisms of PON1 gene and growth and carcass traits. For this purpose, genotyping was performed on males of 18 Angus, 23 Jinnan cattle, 20 Limousin, 28 Luxi cattle, 26 Qinchuan cattle, 29 Simmental, 29 Charolais. Traits of interest were analyzed using the RFLP-PCR and GLM procedure of SAS 9.1 and least square means of the genotypes were compared by the Tukey＇ s test in the association studies. Association of PONI/ EcoRV genotypes with body weight, average daily gain, rib eye area and tenderness were significant （P〈0.05）, and AG genotype was significant difference with others in average daily gain and tenderness （P〈0.05）, with AA genotype may have higher rib eye area （p〈0.05）. The association analysis of the PONI/Alu I polymorphism showed significant associations between genotypes and growth： body weight and carcass traits net meat weight and tenderness （P〈0.05）. AA genotype was considered more favorable than others in all growth and production traits. There were significant differences among breeds for all associated interests traits and difference between beef breeds and native breeds are obviously in all aspects. And these results may be useful for the breeding selection.
文摘Calpastatin is an endogenous inhibitor of calpain which is responsible for the breakdown of myofibrillar proteins, The association of Single Nucleotide Polymorphism （SNP） in the calpastatin gene with meat tenderness is an important topic in meat production. Therefore efficient procedure to investigate the SNP is necessary. The objectives of this study were to detect the SNP of calpastatin gene at domain L marker （G/C transversion） of the Kamphaengsaen beef breed （KPS cattle; n = 26） by the Amplification Refractory Mutation System （ARMS） compared with the Restriction Fragment Length Polymorphism （RFLP） methods and to determine the genotypes of the KPS cattle at that marker. Genomic DNA of calpastatin gene extracted from blood of the KPS cattle was detected with ARMS and RFLP methods. The ARMS system has utilized two primer pairs to amplify the two different alleles of a polymorphism in single PCR reaction to detected single base mutation. In this method, the alleles-specific primers had a mismatch at 3＇ terminal base and a second deliberate mismatch at position -2 from 3＇ terminus. While the RFLP method detected a polymorphism using PCR-base technique follow by RsaI restriction enzyme. Amplification of the ARMS method revealed that the results were not different from the conventional method of RFLP. Analysis of genotypes revealed that the KPS cattle inherited the CC, CG and GG genotypes at domain L marker. These were reliable when verified by nucleotide sequence analysis of PCR products. The animals were genotyped and determined for tenderness phenotype with this marker that predicted variation of an intronic polymorphism at domain L of the calpastatin gene. Therefore, the ARMS method was simple, efficient technique, and suitable for detecting SNP at domain L marker of the calpastatin gene.
文摘Variable selection is one of the most fundamental problems in regression analysis. By sampling from the posterior distributions of candidate models, Bayesian variable selection via MCMC （Markov chain Monte-Carlo） is effective to overcome the computational burden of all-subset variable selection approaches. However, the convergence of the MCMC is often hard to determine and one is often not sure about if obtained samples are unbiased. This complication has limited the application of Bayesian variable selection in practice. Based on the idea of CFTP （coupling from the past）, perfect sampling schemes have been developed to obtain independent samples from the posterior distribution for a variety of problems. Here the authors propose an efficient and effective perfect sampling algorithm for Bayesian variable selection of linear regression models, which independently and identically sample from the posterior distribution of the model space and can efficiently handle thousands of variables. The effectiveness of the authors＇ algorithm is illustrated by three simulation studies, which have up to thousands of variables, the authors＇ method is further illustrated in SNPs （single nucleotide polymorphisms） association study among RA （rheumatoid arthritis） patients.
基金The Influence of Artesunate on β-catenin Signaling Pathway of Hetatic Atellate Cells(Grant No.2011CDB491)
文摘Polymorphisms associated with genes coding for a variety of drug-metabolizing enzymes （DMEs） and associated transport proteins can influence the drug metabolism rate of individuals, potentially affecting the efficacy of drug and the occurrence of adverse reactions. Single nucleotide polymorphisms （SNPs） are prevalent in all types of genetic variations. Reliable SNP genotyping provides excellent markers for detecting genetic polymolphisms, genetic disorders, and resistance of pathogen to drug, which are needed for the genetic diagnosis of disease and subtle genetic factors. With a large number of SNP genotyping studies being conducted, a lot of novel SNP identifying methods have been developed. Several SNP genotyping methods and techniques have been introduced for clinical test. These include TaqMan drug metabolism genotyping assays, pH-sensing semiconductor system, high-resolution melting curve analysis （HRM） of polymerase chain reaction （PCR） amplicons, novel multiplexed electrochemical biosensor with non-fouling surface, DNA hybridization detection using less than 10-nm gap silicon nanogap structure, tetra-primer ARMS-PCR method, acoustic detection of DNA conformation in genetic assays combined with PCR, microbeads-mass spectrometry （MEMS）-based approach, and liquid chromatography-electrospray ionization mass spectrometry. Personalized medicine has changed the conventional ways of using drugs according to experiences. It focuses on making the individualized pattern for each individual based on their own characteristics. Lots of researchers are using the analysis of clinical samples to explain the relationship between the drug adverse reactions and genetic polymorphisms. But it takes a long time from collecting the blood samples for DNA extraction and genotyping to getting results on the side effect of drug through clinical study. Therefore, it is desirable to develop improved in vitro methods to study the drug metabolizing-enzymes and transport protein genetic polymorphisms.
基金Project supported by the Beijing Higher Education Young Elite Teacher Project(No.YETP0064),China
文摘Objective： To investigate a possible association between common variations of the P2RY12 and the residual clopidogrel on-treatment platelet reactivity after adjusting for the influence of CYP2C19 tested by thromboe- lastography （TEG）. Methods： One hundred and eighty patients with acute coronary syndrome （ACS） treated with clopJdogrel and aspJdn were included and platelet function was assessed by TEG. Five selected P2RY12 single nu- cleotide polymorphisms （SNPs; rs6798347, rs6787801, rs6801273, rs6785930, and rs2046934）, which cover the common variations in the P2RY12 gene and its regulatory regions, and three CYP2C19 SNPs （ 2, 3, 17） were geno- typed and possible haplotypes were analyzed. Results： The high on-treatment platelet reactivity （HTPR） prevalence defined by a platelet inhibition rate 〈30% by TEG in adenosine diphosphate （ADP）-channel was 69 （38.33%）. Six common haplotypes were inferred from four of the selected P2RY12 SNPs （denoted H0 to H5） according to the linkage disequilibrium R square （except for rs2046934）. Haplotype H1 showed a significantly lower incidence of HTPR than the reference haplotype （H0） in the total study population while haplotypes H1 and H2 showed significantly lower incidences of HTPR than H0 in the nonsmoker subgroup after adjusting for CYP2Clg effects and demographic characteristics. rs2046934 （T744C） did not show any significant association with HTPR. Conclusions： The combination of common P2RY12 variations including regulatory regions rather than rs2046934 （T744C） that related to pharmacodynamics of clopidogrel in patients with ACS was independently associated with residual on-clopidogrel platelet reactivity. This is apart from the established association of the CYP2C19. This association seemed more important in the subgroup defined by smoking.
