Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and ...Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.展开更多
Single-nucleotide polymorphisms(SNPs)are the third generation of genetic markers,having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite p...Single-nucleotide polymorphisms(SNPs)are the third generation of genetic markers,having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite polymorphisms.SNPs represent a focal point of current studies of Staphylococcus aureus.On one hand,this review aims to summarize common methodologies for detecting SNPs.These methods have typically included DNA genome sequencing methods and PCR-based detection methods.Alternative methods,such as mass spectrometry,denaturing high-performance liquid chromatography,SNaPshot,and SNP array have also been employed for SNP analysis.On the other hand,we enumerate a series of applications of SNP analysis in investigations of Staphylococcus aureus.SNP analysis can be applied to investigate epidemiological outbreaks and transmission of Staphylococcus aureus infections,the transmission and evolution of antimicrobial resistance genes in Staphylococcus aureus isolates,interactions of Staphylococcus aureus with other bacteria,and the links between Staphylococcus aureus in humans and livestock.展开更多
Objective To identify the association of thyroid stimulating hormone receptor(TSHR)gene intron 1 susceptible loci and 4p14 susceptible locus rs6832151 polymorphisms with Graves’disease(GD)in Han Chinese population in...Objective To identify the association of thyroid stimulating hormone receptor(TSHR)gene intron 1 susceptible loci and 4p14 susceptible locus rs6832151 polymorphisms with Graves’disease(GD)in Han Chinese population in Bengbu,Anhui,China.The gene-gene interaction among TSHR intron 1 susceptible loci and 4p14susceptible locus rs6832151 was also investigated.Methods The genotypes of the single-nucleotide polymor-展开更多
BACKGROUND The MBOAT7 rs641738 single-nucleotide polymorphism(SNP)has been proven to influence various liver diseases,but its association with hepatocellular carcinoma(HCC)susceptibility has been debated.To address th...BACKGROUND The MBOAT7 rs641738 single-nucleotide polymorphism(SNP)has been proven to influence various liver diseases,but its association with hepatocellular carcinoma(HCC)susceptibility has been debated.To address this discrepancy,we conducted the current systematic review and meta-analysis.AIM To perform a systematic review and meta-analysis on association of MBOAT7 SNP and HCC susceptibility.METHODS We performed a systematic review in PubMed,Web of Science,Scopus,and EMBASE;applied specific inclusion and exclusion criteria;and extracted the data.Meta-analysis was conducted with the meta package in R.Sensitivity and subgroup analyses were also performed.This meta-analysis was registered in PROSPERO(CRD42023458046).RESULTS Eight studies were included in the systematic review,and 12 cohorts from 6 studies were included in the meta-analysis.Our meta-analysis revealed an association between the MBOAT7 SNP and HCC susceptibility in both the dominant[odds ratio(OR):1.14,95%confidence interval(95%CI):1.02-1.26,P=0.020]and recessive(OR:1.21,95%CI:1.05-1.39,P=0.008)models.Subgroup analysis revealed that stratification of the included patients by geographical origin showed a significant association in Asia(OR:1.20,95%CI:1.03-1.39).CONCLUSION This meta-analysis underscores the contribution of the MBOAT7 rs641738 SNP to hepatocarcinogenesis,especially in Asian populations,which warrants further investigation.展开更多
BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese po...BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese population.AIM To explored associations of two SNPs and haplotypes in the lncRNA NONHSAT102891 promoter region with depression susceptibility in Chinese population.METHODS This this case-control association study was approved by the Ethics Committee of Chengdu Medical College(approval number:201815).Patient diagnosis was based on DSM-IV criteria.We selected a total of 480 patients with depression and 329 healthy controls with no history of psychopathology,and performed genotyping of two SNPs by extracting peripheral venous blood samples from the subjects.The function of the two lncRNA NONHSAT102891 promoter G/C and A/T haplotypes was detected by dual-luciferase reporter assays of human embryonic kidney 293T transfected cells.RESULTS Stratified analysis of clinical and genotypic characteristics of our cohort showed that the degree of mild depressive episodes associated with the rs6230 TC/CC genotype increased by 1.59 times[TC/CC vs TT:odds ratio(OR)=1.59,95%confidence interval(CI):1.08-2.35,P=0.019].The haploid analysis revealed linkage disequilibrium between rs3792747 and rs6230,and the double SNP CG haplotype was more common in the control group compared to case group,indicating that this haplotype significantly reduced the risk of depression(C/G vs T/A:OR=0.42,95%CI:0.21-0.83,P=0.01).There was no significant difference in the dual-luciferase reporter activity of the G/C and A/T haplotypes compared with the control group(P>0.05),indicating that the double SNP haplotype has no transcrip-tional activity.CONCLUSION The rs3792747 and rs6230 CG haplotypes of the lncRNA NONHSA T102891 promoter may be related to a reduced risk of depression in the Han Chinese population.展开更多
Ischemic stroke is a complicated disease, and its pathogenesis has been attributed to the occurrence of genetic polymorphisms.Evidence has suggested that the microRNA let-7a is involved in the pathogenesis of ischemic...Ischemic stroke is a complicated disease, and its pathogenesis has been attributed to the occurrence of genetic polymorphisms.Evidence has suggested that the microRNA let-7a is involved in the pathogenesis of ischemic stroke.Pri-miRNA is the primary transcript, which undergoes several processing steps to generate pre-miRNA and, later, mature miRNAs.In this case-control study, we analyzed the distribution of prilet-7a-2 variants in patients at a high risk for ischemic stroke and the interactions of pri-let-7a-2 variants and environmental factors.Blood samples and clinical information were collected from 1086 patients with ischemic stroke and 836 healthy controls between December 2013 and December 2015 at the First Affiliated Hospital of China Medical University.We found that the rs1143770 CC genotype and the C allele were associated with a decreased risk of ischemic stroke, whereas the rs629367 CC genotype was associated with an increased risk for ischemic stroke.Moreover, these two single-nucleotide polymorphisms were in linkage disequilibrium in this study sample.We analyzed gene-environment interactions and found that rs1143770 exerted a combined effect on the pathogenesis of ischemic stroke, together with alcohol use, smoking, and a history of hypertension.Therefore, the detection of pri-let-7a-2 polymorphisms may increase the awareness of ischemic stroke risk.This study was approved by the Institutional Ethics Committee of the First Affiliated Hospital of China Medical University, China(approval No.2012-38-1) on February 20, 2012, and was registered with the Chinese Clinical Trial Registry(registration number: ChiCTR-COC-17013559) on December 27, 2017.展开更多
BACKGROUND Single-nucleotide polymorphisms(SNPs)of the serotonin type 3 receptor subunit(HTR3)genes have been associated with psychosomatic symptoms,but it is not clear whether these associations exist in irritable bo...BACKGROUND Single-nucleotide polymorphisms(SNPs)of the serotonin type 3 receptor subunit(HTR3)genes have been associated with psychosomatic symptoms,but it is not clear whether these associations exist in irritable bowel syndrome(IBS).AIM To assess the association of HTR3 polymorphisms with depressive,anxiety,and somatization symptoms in individuals with IBS.METHODS In this retrospective study,623 participants with IBS were recruited from five specialty centers in Germany,Sweden,the United States,the United Kingdom,and Ireland.Depressive,anxiety,and somatization symptoms and sociodemographic characteristics were collected.Four functional SNPs—HTR3A c.-42C>T,HTR3B c.386A>C,HTR3C c.489C>A,and HTR3E c.*76G>A—were genotyped and analyzed using the dominant and recessive models.We also performed separate analyses for sex and IBS subtypes.SNP scores were calculated as the number of minor alleles of the SNPs above.The impact of HTR3C c.489C>A was tested by radioligand-binding and calcium influx assays.RESULTS Depressive and anxiety symptoms significantly worsened with increasing numbers of minor HTR3C c.489C>A alleles in the dominant model(F_(depressive)=7.475,P_(depressive)=0.006;F_(anxiety)=6.535,P_(anxiety)=0.011).A higher SNP score(range 0-6)was linked to a worsened depressive symptoms score(F=7.710,P-linear trend=0.006)in IBS.The potential relevance of the HTR3C SNP was corroborated,showing changes in the expression level of 5-HT3AC variant receptors.CONCLUSION We have provided the first evidence that HTR3C c.489C>A is involved in depressive and anxiety symptoms in individuals with IBS.The SNP score indicated that an increasing number of minor alleles is linked to the worsening of depressive symptoms in IBS.展开更多
AIM To investigate the contribution of polymorphisms in the CYP1A1, CYP2E1 and EPHX1 genes on sporadic colorectal cancer(SCRC) risk. METHODS Six hundred forty-one individuals(227 patients with SCRC and 400 controls) w...AIM To investigate the contribution of polymorphisms in the CYP1A1, CYP2E1 and EPHX1 genes on sporadic colorectal cancer(SCRC) risk. METHODS Six hundred forty-one individuals(227 patients with SCRC and 400 controls) were enrolled in the study. The variables analyzed were age, gender, tobacco and alcohol consumption, and clinical and histopathological tumor parameters. The CYP1A1 *2A, CYP1A1 *2C CYP2E1 *5B and CYP2E1 *6 polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). The EPHX1 Tyr113 His, EPHX1 His139 Arg and CYP1A1 *2C polymorphisms were detected by real-time PCR. Chisquared test and binary logistic regression were used in the statistical analysis. Haplotype analysis was conducted using the Haploview program, version 2.05.RESULTS Age over 6 2 years was a risk factor for SCRC development(OR = 7.54, 95%CI: 4.94-11.50, P < 0.01). Male individuals were less susceptible to SCRC(OR = 0.55, 95%CI: 0.35-0.85, P < 0.01). The CYP2E1*5B polymorphism was associated with SCRC in the codominant(heterozygous genotype: OR = 2.66, 95%CI: 1.64-4.32, P < 0.01), dominant(OR = 2.82, 95%CI: 1.74-4.55, P < 0.01), overdominant(OR = 2.58, 95%CI: 1.59-4.19, P < 0.01), and log-additive models(OR = 2.84, 95%CI: 1.78-4.52, P < 0.01). The CYP2E1*6 polymorphism was associated with an increased SCRC risk in codominant(heterozygous genotype: OR = 2.81, 95%CI: 1.84-4.28, P < 0.01; homozygous polymorphic : OR = 7. 3 2, 9 5 % C I : 1.85-28.96, P < 0.01), dominant(OR = 2.97, 95%CI: 1.97-4.50, P < 0.01), recessive(OR = 5.26, 95%CI: 1.35-20.50, P = 0.016), overdominant(OR = 2.64, 95%CI: 1.74-4.01, P < 0.01), and log-additive models(OR = 2.78, 95%CI: 1.91-4.06, P < 0.01). The haplotype formed by the minor alleles of the CYP2E1*5B(C) and CYP2E1*6(A) polymorphisms was associated with SCRC(P = 0.002). However, the CYP1A1 *2A, CYP1A1 *2C, EPHX1 Tyr113 His and EPHX1 His139 Arg polymorphisms were not associated with SCRC.CONCLUSION In conclusion, the results demonstrated that CYP2E1*5B and CYP2E1*6 minor alleles play a role in the development of SCRC.展开更多
BACKGROUND The genetic backgrounds of diabetic kidney disease(DKD)and end-stage kidney disease(ESKD)have not been fully elucidated.AIM To examine the individual and cumulative effects of single-nucleotide polymorphism...BACKGROUND The genetic backgrounds of diabetic kidney disease(DKD)and end-stage kidney disease(ESKD)have not been fully elucidated.AIM To examine the individual and cumulative effects of single-nucleotide polymorphisms(SNPs)previously associated with DKD on the risk for ESKD of diabetic etiology and to determine if any associations observed were specific for DKD.METHODS Fourteen SNPs were genotyped in hemodialyzed 136 patients with diabetic ESKD(DKD group)and 121 patients with non-diabetic ESKD(NDKD group).Patients were also re-classified on the basis of the primary cause of chronic kidney disease(CKD).The distribution of alleles was compared between diabetic and nondiabetic groups as well as between different sub-phenotypes.The weighted multilocus genetic risk score(GRS)was calculated to estimate the cumulative risk conferred by all SNPs.The GRS distribution was then compared between the DKD and NDKD groups as well as in the groups according to the primary cause of CKD.RESULTS One SNP(rs841853;SLC2A1)showed a nominal association with DKD(P=0.048;P>0.05 after Bonferroni correction).The GRS was higher in the DKD group(0.615±0.260)than in the NDKD group(0.590±0.253),but the difference was not significant(P=0.46).The analysis of associations between GRS and individual factors did not show any significant correlation.However,the GRS was significantly higher in patients with glomerular disease than in those with tubulointerstitial disease(P=0.014)and in those with a combined group(tubulointerstitial,vascular,and cystic and congenital disease)(P=0.018).CONCLUSION Our results suggest that selected SNPs that were previously associated with DKD may not be specific for DKD and may confer risk for CKD of different etiology,particularly those affecting renal glomeruli.展开更多
BACKGROUND Dermatologic adverse events(DAEs)are associated with a better outcome in patients with hepatocellular carcinoma(HCC)irrespective of the therapeutic agent received.The exact mechanisms associated with the de...BACKGROUND Dermatologic adverse events(DAEs)are associated with a better outcome in patients with hepatocellular carcinoma(HCC)irrespective of the therapeutic agent received.The exact mechanisms associated with the development of DAEs are unknown although several studies point to direct toxicity of tyrosine kinase inhibitors(TKIs)to the skin or an immune-mediated reaction triggered by the oncologic treatment.As is the case in other conditions,individual genetic variants may partially explain a higher risk of DAEs.AIM To evaluate the contribution of several gene variants to the risk of developing DAEs in HCC patients treated with TKIs.METHODS We first analyzed 27 single-nucleotide polymorphisms(SNPs)from 12 genes selected as potential predictors of adverse event(AE)development in HCC patients treated with sorafenib[Barcelona Clinic Liver Cancer 1(BCLC1)cohort].Three additional cohorts were analyzed for AGT1(rs699)and AGT2(rs4762)polymorphisms-initially identified as predictors of DAEs:BCLC2(n=79),Northern Italy(n=221)and Naples(n=69)cohorts,respectively.The relation between SNPs and DAEs and death were assessed by univariate and multivariate Cox regression models,and presented with hazard ratios and their 95%confidence intervals(95%CI).RESULTS The BCLC1 cohort showed that patients with arterial hypertension(AHT)(HR=1.61;P value=0.007)and/or AGT SNPs had an increased risk of DAEs.Thereafter,AGT2(rs4762)AA genotype was found to be linked to a statistically significant increased probability of DAEs(HR=5.97;P value=0.0201,AA vs GG)in the Northern Italy cohort by multivariate analysis adjusted for BCLC stage,ECOG-PS,diabetes and AHT.The value of this genetic marker was externally validated in the cohort combining the BCLC1,BCLC2 and Naples cohorts[HR=3.12(95%CI:1.2-8.14),P value=0.0199,AGT2(rs4762)AA vs AG genotype and HR=2.73(95%CI:1.18-6.32)P value=0.0188,AGT2(rs4762)AA vs GG genotype].None of the other gene variants tested were found to be associated with the risk of DAE development.CONCLUSION DAE development in HCC patients receiving TKIs could be explained by the AGT2(rs4762)gene variant.If validated in other anti-oncogenic treatments,it might be considered a good prognosis marker.展开更多
<strong>Objective:</strong> To assess the association between circulating C-reactive protein (CRP), and CRP polymorphisms in the diesel engine exhaust (DEE)-exposed workers. <strong>Methods:</stro...<strong>Objective:</strong> To assess the association between circulating C-reactive protein (CRP), and CRP polymorphisms in the diesel engine exhaust (DEE)-exposed workers. <strong>Methods:</strong> In 137 DEE-exposed workers and 127 unexposed comparable control workers, six urinary mono-hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) and serum CRP levels were assayed. Genotyping of four CRP single-nucleotide polymorphisms (SNPs) was measured. <strong>Results: </strong>Serum CRP levels increased in exposed versus control workers (all p < 0.001). In the DEE-exposed workers, two CRP polymorphisms were associated with serum CRP levels, the subjects of rs1205 TT genotype had lower serum CRP levels (p < 0.05 compared to TC or CC). <strong>Conclusions: </strong>Our findings suggest that polymorphisms in CRP and circulating CRP involved in the inflammatory process may play significant roles in human sensitivity to lung function injury caused by DEE exposure. This study will help investigate the underlying mechanisms of adverse respiratory effects induced by DEE.展开更多
Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,ar...Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.展开更多
Objective Evidence from prospective studies on the consumption of tea and risk of gout is conflicting and limited.We aimed to investigate the potential causal effects of tea intake on gout using Mendelian randomizatio...Objective Evidence from prospective studies on the consumption of tea and risk of gout is conflicting and limited.We aimed to investigate the potential causal effects of tea intake on gout using Mendelian randomization(MR).Methods Genome-wide association studies in UK Biobank included 349376 individuals and successfully discovered single-nucleotide polymorphisms linked to consumption of one cup of tea per day.Summary statistics from the Chronic Kidney Disease Genetics consortium included 13179 cases and 750634 controls for gout.Two-sample MR analyses were used to evaluate the relationship between tea consumption and gout risk.The inverse-variance weighted(IVW)method was used for primary analysis,and sensitivity analyses were also conducted to validate the potential causal effect.Results In this study,the genetically predicted increase in tea consumption per cup was associated with a lower risk of gout in the IVW method(OR:0.90;95%CI:0.82–0.98).Similar results were found in weighted median methods(OR:0.88;95%CI:0.78–1.00),while no significant associations were found in MR-Egger(OR:0.89;95%CI:0.71–1.11),weighted mode(OR:0.80;95%CI:0.65–0.99),and simple mode(OR:1.01;95%CI:0.75–1.36).In addition,no evidence of pleiotropy was detected by MR-Egger regression(P=0.95)or MR-PRESSO analysis(P=0.07).Conclusion This study provides evidence for the daily consumption of an extra cup of tea to reduce the risk of gout.展开更多
Background:Chronic obstructive pulmonary disease(COPD)is a leading cause of morbidity and mortality worldwide.Genome-wide association studies in non-Asian population revealed a link between COPD and mutations in the P...Background:Chronic obstructive pulmonary disease(COPD)is a leading cause of morbidity and mortality worldwide.Genome-wide association studies in non-Asian population revealed a link between COPD and mutations in the PTCH1 gene encoding Patched1,a receptor in the Hedgehog signaling pathway important for lung morphogenesis and pulmonary function.The aim of this study was to investigate the association between PTCH1 polymorphisms and the COPD risk in the Chinese Han population.Methods:We performed a case-control study including 296 patients with COPD and 300 healthy individuals.Single-nucleotide polymorphisms in the PTCH1 gene were identified and genotyped based on the linkage disequilibrium analysis in all participants.Odds ratios(ORs)and 95%confidence intervals(95%CIs)were estimated using logistic regression analysis after adjustment for age,gender,and smoking.Results:In total,28 single-nucleotide polymorphisms were identified in patients with COPD.Among them,"A"allele of rs28491365(OR:1.388,95%CI:1.055-1.827,P=0.018),and"G"alleles of rs10512248(OR:1.299,95%CI:1.021-1.653,P=0.033)and rs28705285(OR:1.359,95%CI:1.024-1.803,P=0.033;respectively)were significantly associated with an increased COPD risk.Genetic model analysis revealed that the"T/T"genotype of rs34695652 was associated with a decreased COPD risk under the recessive model(OR:0.490,95%CI:0.270-0.880,P=0.010),whereas rs28504650/rs10512248 haplotype CG was significantly associated with an increased COPD risk after adjustment for age,gender,and smoking status(OR:6.364,95%CI:1.220-33.292,P=0.028).Conclusions:The study provides a new insight into the role of PTCH1 polymorphisms in the susceptibility to COPD in the Chinese Han population.展开更多
谷氨酸棒杆菌是食品安全级菌株,可作为生产高价值产物的优良底盘细胞用于工业生产。它具有良好的分泌系统,是表达重组蛋白的潜在宿主,有极大的研究价值。为优化底盘细胞提高其蛋白表达能力,挖掘并验证谷氨酸棒杆菌中与外源蛋白高表达相...谷氨酸棒杆菌是食品安全级菌株,可作为生产高价值产物的优良底盘细胞用于工业生产。它具有良好的分泌系统,是表达重组蛋白的潜在宿主,有极大的研究价值。为优化底盘细胞提高其蛋白表达能力,挖掘并验证谷氨酸棒杆菌中与外源蛋白高表达相关的基因。在谷氨酸棒杆菌重测序的基础上,应用生物信息学对单核苷酸多态性(single-nucleotide polymorphisms,SNP)基因进行挖掘,分析基因保守结构域。通过构建SNP基因过表达和敲除重组菌株,评估其生长情况以及增强型绿色荧光蛋白(enhanced green fluorescence protein,EGFP)和人重组特立帕肽(recombinant human teriparatide,rtPTH)的外源蛋白表达能力。分析并整理了高产量外源蛋白菌株的重测序数据,共有33个SNP突变位点,主要涉及5个基因。其中SNP重组菌株over-2370和ko-973-974的荧光值最高,并且发酵生产rtPTH,均比野生型(wild type,WT)提高了近1倍。该研究成功挖掘出与蛋白表达相关的基因GL002370和GL000974,这些发现将有助于获得优化的底盘细胞,并为深入研究增加蛋白产量的靶基因提供指导。展开更多
Powdery mildew,caused by Blumeria graminis f.sp.tritici(Bgt),is one of the most damaging diseases to wheat in the world.The cultivation of resistant varieties of wheat is essential for controlling the powdery mildew e...Powdery mildew,caused by Blumeria graminis f.sp.tritici(Bgt),is one of the most damaging diseases to wheat in the world.The cultivation of resistant varieties of wheat is essential for controlling the powdery mildew epidemic.Wheat landraces are important resources of resistance to many diseases.Mapping powdery mildew resistance genes from wheat landraces will promote the development of new varieties with disease resistance.The Chinese wheat landrace Baiyouyantiao possesses characteristic of disease resistance to powdery mildew.To identify the resistance gene in this landrace,Baiyouyantiao was crossed with the susceptible cultivar Jingshuang 16 and seedlings of parents and F_1,BC_1,F_2,and F_(2:3) were tested with Bgt isolate E09.The genetic results showed that the resistance of Baiyouyantiao to E09 was controlled by a single recessive gene,tentatively designated Pm BYYT.An Illumina wheat 90K single-nucleotide polymorphism(SNP)array was applied to screen polymorphisms between F_2-resistant and F_2-susceptible DNA bulks for identifying the chromosomal location of Pm BYYT.A high percentage of polymorphic SNPs between the resistant and susceptible DNA bulks was found on chromosome 7B,indicating that Pm BYYT may be located on this chromosome.A genetic linkage map of Pm BYYT consisting of two simple sequence repeat markers and eight SNP markers was developed.The two flanking markers were SNP markers W7BL-8 and W7BL-15,with genetic distances of 3 and 2.9 c M,respectively.The results of this study demonstrated the rapid characterization of a wheat disease resistance gene and SNP marker development using the 90K SNP assay.The flanking markers of gene Pm BYYT will benefit marker-assisted selection(MAS)and map-based cloning in breeding wheat cultivars with powdery mildew resistance.展开更多
Dramatic progress has been made in the area of germline genetics of prostate cancer(PCa)in the past decade.Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice...Dramatic progress has been made in the area of germline genetics of prostate cancer(PCa)in the past decade.Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice-changing have been identified.For men with high risk PCa,the application of genetic testing for inherited pathogenic mutations is becoming standard of care.A major question exists about which additional populations of men to test,as men at all risk levels can potentially benefit by knowing their unique genetic profile of germline susceptibility variants.This article will provide a brief overview of some current issues in understanding inherited susceptibility for PCa.展开更多
Background:Immune-and inflammation-related genes(IIRGs)play an important role in the pathogenesis of tuberculosis(TB).However,the relationship between IIRG polymorphisms and TB risk remains unknown.In this study,the g...Background:Immune-and inflammation-related genes(IIRGs)play an important role in the pathogenesis of tuberculosis(TB).However,the relationship between IIRG polymorphisms and TB risk remains unknown.In this study,the gene polymorphisms and their association with tuberculosis were determined in a Chinese population.Methods:We performed a case-control study involving 1016 patients with TB and 507 healthy controls of Han Chinese origin.Sixty-four single-nucleotide polymorphisms(SNPs)belonging to 18 IIRGs were genotyped by the PCR-MassArray assay,and the obtained data was analyzed withχ2-test,Bonferroni correction,and unconditional logistic regression analysis.Results:We observed significant differences in the allele frequency of LTA rs2229094*C(P=0.015),MBL2 rs2099902*C(P=0.001),MBL2 rs930507*G(P=0.004),MBL2 rs10824793*G(P=0.004),and IL12RB1 rs2305740*G(P=0.040)between the TB and healthy groups.Increased TB risk was identified in the rs930507 G/G genotype(Padjusted=0.027)under a codominant genetic model as well as in the rs2099902(C/T+C/C)vs T/T genotype(Padjusted=0.020),rs930507(C/G+G/G)vs C/C genotype(Padjusted=0.027),and rs10824793(G/A+G/G)vs A/A genotype(Padjusted=0.017)under a dominant genetic model after Bonferroni correction in the analysis of the overall TB group rather than the TB subgroups.Furthermore,the rs10824793_rs7916582*GT and rs10824793_rs7916582*GC haplotypes were significantly associated with increased TB risk(P=0.001,odds ratio[OR]=1.421,95%confidence interval[CI]:1.152-1.753;and P=0.018,OR=1.364,95%CI:1.055-1.765,respectively).Moreover,the rs10824793_rs7916582*AT/AT or rs10824793_rs7916582*GT/GT diplotype showed a protective(P=0.003,OR=0.530,95%CI:0.349-0.805)or harmful(P=0.009,OR=1.396,95%CI:1.087-1.793)effect against the development of TB.Conclusions:This study indicated that MBL2 polymorphisms,haplotypes,and diplotypes were associated with TB susceptibility in the Han Chinese population.Additionally,larger sample size studies are needed to further confirm these findings in the future.展开更多
Coumarate 3-hydroxylase(C3h)genes participate in the synthesis of lignin and may affect the properties of wood that are important for its commercial value.A better understanding of the natural variation in C3h genes a...Coumarate 3-hydroxylase(C3h)genes participate in the synthesis of lignin and may affect the properties of wood that are important for its commercial value.A better understanding of the natural variation in C3h genes and their associations to wood properties is required to effectively improve wood quality.We used a candidate gene-based association mapping approach to identify CfC3h allelic variants associated with traits that affect the wood properties of Catalpa fargesii.We first isolated the full-length CfC3h cDNA(1825 bp),which was expressed at relatively high levels in xylem according to real time-polymerase chain reaction.In totally,17 common single-nucleotide polymorphisms(minor allele frequency>5%)were identified through cloning and sequencing the CfC3h locus from a mapping population(including 88 unrelated natural C.fargesii individuals collected from main distribution area).Nucleotide diversity and linkage disequilibrium(LD)in CfC3h indicate that CfC3h has low nucleotide diversity(π_(t)=0.0031 andθ_(w)=0.0103)and relatively low LD(within 1800 bp;r^(2)≥0.1).An association analysis identified eight common single-nucleotide polymorphisms(SNPs)(false discovery rate,Q<0.10)and ten haplotypes(Q<0.10)associated with wood properties,explaining 4.92-12.09%of the phenotypic variance in an association population consisted of 125 unrelated natural individuals(The 88 individuals from the mapping population were comprised in the association population).Our study would provide new insight into C3h gene affecting wood quality,and the SNP markers identified would have potential applications in marker-assisted breeding in the future.展开更多
The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in ...The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in chloroplast rbc L and mat K gene sequences in 19 accessions representing C. quinoa and C. album indicated that the accessions IC-411824 and IC-411825,which have white seeds, belong to C. quinoa rather than C. album. This observation was also supported by a time tree that indicated IC-411824 and IC-411825 to be a sister clade to accessions of C. quinoa with an estimated age of 1.2 Mya. Whereas multiple alignments of rbc L gene sequences from the 19 accessions revealed 1.26% parsimony-informative sites with 0.68%interspecific sequence diversity, alignment of nucleotide sequences of amplicons representing the mat K gene revealed 4.97% parsimony-informative sites and 2.81% interspecific sequence diversity. Validation of SNPs in the cp rbc L and mat K regions of 36 accessions belonging to C. quinoa and C. album was performed by allele-specific PCR with primers carrying a single base change at the 3′ end. We report the first C. quinoa-specific SNP-based primer, R1RQ-AFR,designed from rbc L sequences, that could differentiate quinoa from 64 genera including13 species of the genus Chenopodium. With an estimated age of 10.5–4.1 million years(Myr), the Himalayan chenopods are evolutionarily younger than the Andean chenopods. The results establish the paraphyletic origin of the genus Chenopodium.展开更多
文摘Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.
文摘Single-nucleotide polymorphisms(SNPs)are the third generation of genetic markers,having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite polymorphisms.SNPs represent a focal point of current studies of Staphylococcus aureus.On one hand,this review aims to summarize common methodologies for detecting SNPs.These methods have typically included DNA genome sequencing methods and PCR-based detection methods.Alternative methods,such as mass spectrometry,denaturing high-performance liquid chromatography,SNaPshot,and SNP array have also been employed for SNP analysis.On the other hand,we enumerate a series of applications of SNP analysis in investigations of Staphylococcus aureus.SNP analysis can be applied to investigate epidemiological outbreaks and transmission of Staphylococcus aureus infections,the transmission and evolution of antimicrobial resistance genes in Staphylococcus aureus isolates,interactions of Staphylococcus aureus with other bacteria,and the links between Staphylococcus aureus in humans and livestock.
文摘Objective To identify the association of thyroid stimulating hormone receptor(TSHR)gene intron 1 susceptible loci and 4p14 susceptible locus rs6832151 polymorphisms with Graves’disease(GD)in Han Chinese population in Bengbu,Anhui,China.The gene-gene interaction among TSHR intron 1 susceptible loci and 4p14susceptible locus rs6832151 was also investigated.Methods The genotypes of the single-nucleotide polymor-
文摘BACKGROUND The MBOAT7 rs641738 single-nucleotide polymorphism(SNP)has been proven to influence various liver diseases,but its association with hepatocellular carcinoma(HCC)susceptibility has been debated.To address this discrepancy,we conducted the current systematic review and meta-analysis.AIM To perform a systematic review and meta-analysis on association of MBOAT7 SNP and HCC susceptibility.METHODS We performed a systematic review in PubMed,Web of Science,Scopus,and EMBASE;applied specific inclusion and exclusion criteria;and extracted the data.Meta-analysis was conducted with the meta package in R.Sensitivity and subgroup analyses were also performed.This meta-analysis was registered in PROSPERO(CRD42023458046).RESULTS Eight studies were included in the systematic review,and 12 cohorts from 6 studies were included in the meta-analysis.Our meta-analysis revealed an association between the MBOAT7 SNP and HCC susceptibility in both the dominant[odds ratio(OR):1.14,95%confidence interval(95%CI):1.02-1.26,P=0.020]and recessive(OR:1.21,95%CI:1.05-1.39,P=0.008)models.Subgroup analysis revealed that stratification of the included patients by geographical origin showed a significant association in Asia(OR:1.20,95%CI:1.03-1.39).CONCLUSION This meta-analysis underscores the contribution of the MBOAT7 rs641738 SNP to hepatocarcinogenesis,especially in Asian populations,which warrants further investigation.
基金Supported by National Natural Science Foundation of China,No.81901379Chengdu Medical College Graduate Research Innovation Fund Project,No.YCX2023-01-03National Undergraduate Training Program for Innovation and Entrepreneurship,No.202113705034.
文摘BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese population.AIM To explored associations of two SNPs and haplotypes in the lncRNA NONHSAT102891 promoter region with depression susceptibility in Chinese population.METHODS This this case-control association study was approved by the Ethics Committee of Chengdu Medical College(approval number:201815).Patient diagnosis was based on DSM-IV criteria.We selected a total of 480 patients with depression and 329 healthy controls with no history of psychopathology,and performed genotyping of two SNPs by extracting peripheral venous blood samples from the subjects.The function of the two lncRNA NONHSAT102891 promoter G/C and A/T haplotypes was detected by dual-luciferase reporter assays of human embryonic kidney 293T transfected cells.RESULTS Stratified analysis of clinical and genotypic characteristics of our cohort showed that the degree of mild depressive episodes associated with the rs6230 TC/CC genotype increased by 1.59 times[TC/CC vs TT:odds ratio(OR)=1.59,95%confidence interval(CI):1.08-2.35,P=0.019].The haploid analysis revealed linkage disequilibrium between rs3792747 and rs6230,and the double SNP CG haplotype was more common in the control group compared to case group,indicating that this haplotype significantly reduced the risk of depression(C/G vs T/A:OR=0.42,95%CI:0.21-0.83,P=0.01).There was no significant difference in the dual-luciferase reporter activity of the G/C and A/T haplotypes compared with the control group(P>0.05),indicating that the double SNP haplotype has no transcrip-tional activity.CONCLUSION The rs3792747 and rs6230 CG haplotypes of the lncRNA NONHSA T102891 promoter may be related to a reduced risk of depression in the Han Chinese population.
基金supported by the National Natural Science Foundation of China, No.81901189the Natural Science Foundation of Liaoning Province of China, No.2019-BS-147(both to YZW)。
文摘Ischemic stroke is a complicated disease, and its pathogenesis has been attributed to the occurrence of genetic polymorphisms.Evidence has suggested that the microRNA let-7a is involved in the pathogenesis of ischemic stroke.Pri-miRNA is the primary transcript, which undergoes several processing steps to generate pre-miRNA and, later, mature miRNAs.In this case-control study, we analyzed the distribution of prilet-7a-2 variants in patients at a high risk for ischemic stroke and the interactions of pri-let-7a-2 variants and environmental factors.Blood samples and clinical information were collected from 1086 patients with ischemic stroke and 836 healthy controls between December 2013 and December 2015 at the First Affiliated Hospital of China Medical University.We found that the rs1143770 CC genotype and the C allele were associated with a decreased risk of ischemic stroke, whereas the rs629367 CC genotype was associated with an increased risk for ischemic stroke.Moreover, these two single-nucleotide polymorphisms were in linkage disequilibrium in this study sample.We analyzed gene-environment interactions and found that rs1143770 exerted a combined effect on the pathogenesis of ischemic stroke, together with alcohol use, smoking, and a history of hypertension.Therefore, the detection of pri-let-7a-2 polymorphisms may increase the awareness of ischemic stroke risk.This study was approved by the Institutional Ethics Committee of the First Affiliated Hospital of China Medical University, China(approval No.2012-38-1) on February 20, 2012, and was registered with the Chinese Clinical Trial Registry(registration number: ChiCTR-COC-17013559) on December 27, 2017.
基金results in part from collaboration and network activities promoted under the frame of the international network GENIEUR (Genes in Irritable Bowel Syndrome Research Network Europe),which has been funded by the COST program (BM1106, www.GENIEUR.eu)currently supported by the European Society of Neurogastroenterology and Motility (ESNM, www.ESNM.eu)
文摘BACKGROUND Single-nucleotide polymorphisms(SNPs)of the serotonin type 3 receptor subunit(HTR3)genes have been associated with psychosomatic symptoms,but it is not clear whether these associations exist in irritable bowel syndrome(IBS).AIM To assess the association of HTR3 polymorphisms with depressive,anxiety,and somatization symptoms in individuals with IBS.METHODS In this retrospective study,623 participants with IBS were recruited from five specialty centers in Germany,Sweden,the United States,the United Kingdom,and Ireland.Depressive,anxiety,and somatization symptoms and sociodemographic characteristics were collected.Four functional SNPs—HTR3A c.-42C>T,HTR3B c.386A>C,HTR3C c.489C>A,and HTR3E c.*76G>A—were genotyped and analyzed using the dominant and recessive models.We also performed separate analyses for sex and IBS subtypes.SNP scores were calculated as the number of minor alleles of the SNPs above.The impact of HTR3C c.489C>A was tested by radioligand-binding and calcium influx assays.RESULTS Depressive and anxiety symptoms significantly worsened with increasing numbers of minor HTR3C c.489C>A alleles in the dominant model(F_(depressive)=7.475,P_(depressive)=0.006;F_(anxiety)=6.535,P_(anxiety)=0.011).A higher SNP score(range 0-6)was linked to a worsened depressive symptoms score(F=7.710,P-linear trend=0.006)in IBS.The potential relevance of the HTR3C SNP was corroborated,showing changes in the expression level of 5-HT3AC variant receptors.CONCLUSION We have provided the first evidence that HTR3C c.489C>A is involved in depressive and anxiety symptoms in individuals with IBS.The SNP score indicated that an increasing number of minor alleles is linked to the worsening of depressive symptoms in IBS.
基金Supported by Sao Paulo Research Foundation(FAPESP),No.2011/23969-1 and No.2012/02473-0Coordination for the Improvement of Higher Education Personnel(CAPES)(Master grant)and National Council of Technological and Scientific Development(CNPq),No.310582/2014-8
文摘AIM To investigate the contribution of polymorphisms in the CYP1A1, CYP2E1 and EPHX1 genes on sporadic colorectal cancer(SCRC) risk. METHODS Six hundred forty-one individuals(227 patients with SCRC and 400 controls) were enrolled in the study. The variables analyzed were age, gender, tobacco and alcohol consumption, and clinical and histopathological tumor parameters. The CYP1A1 *2A, CYP1A1 *2C CYP2E1 *5B and CYP2E1 *6 polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). The EPHX1 Tyr113 His, EPHX1 His139 Arg and CYP1A1 *2C polymorphisms were detected by real-time PCR. Chisquared test and binary logistic regression were used in the statistical analysis. Haplotype analysis was conducted using the Haploview program, version 2.05.RESULTS Age over 6 2 years was a risk factor for SCRC development(OR = 7.54, 95%CI: 4.94-11.50, P < 0.01). Male individuals were less susceptible to SCRC(OR = 0.55, 95%CI: 0.35-0.85, P < 0.01). The CYP2E1*5B polymorphism was associated with SCRC in the codominant(heterozygous genotype: OR = 2.66, 95%CI: 1.64-4.32, P < 0.01), dominant(OR = 2.82, 95%CI: 1.74-4.55, P < 0.01), overdominant(OR = 2.58, 95%CI: 1.59-4.19, P < 0.01), and log-additive models(OR = 2.84, 95%CI: 1.78-4.52, P < 0.01). The CYP2E1*6 polymorphism was associated with an increased SCRC risk in codominant(heterozygous genotype: OR = 2.81, 95%CI: 1.84-4.28, P < 0.01; homozygous polymorphic : OR = 7. 3 2, 9 5 % C I : 1.85-28.96, P < 0.01), dominant(OR = 2.97, 95%CI: 1.97-4.50, P < 0.01), recessive(OR = 5.26, 95%CI: 1.35-20.50, P = 0.016), overdominant(OR = 2.64, 95%CI: 1.74-4.01, P < 0.01), and log-additive models(OR = 2.78, 95%CI: 1.91-4.06, P < 0.01). The haplotype formed by the minor alleles of the CYP2E1*5B(C) and CYP2E1*6(A) polymorphisms was associated with SCRC(P = 0.002). However, the CYP1A1 *2A, CYP1A1 *2C, EPHX1 Tyr113 His and EPHX1 His139 Arg polymorphisms were not associated with SCRC.CONCLUSION In conclusion, the results demonstrated that CYP2E1*5B and CYP2E1*6 minor alleles play a role in the development of SCRC.
基金Supported by Ministry of Science and Higher Education Grant,No.171/12.
文摘BACKGROUND The genetic backgrounds of diabetic kidney disease(DKD)and end-stage kidney disease(ESKD)have not been fully elucidated.AIM To examine the individual and cumulative effects of single-nucleotide polymorphisms(SNPs)previously associated with DKD on the risk for ESKD of diabetic etiology and to determine if any associations observed were specific for DKD.METHODS Fourteen SNPs were genotyped in hemodialyzed 136 patients with diabetic ESKD(DKD group)and 121 patients with non-diabetic ESKD(NDKD group).Patients were also re-classified on the basis of the primary cause of chronic kidney disease(CKD).The distribution of alleles was compared between diabetic and nondiabetic groups as well as between different sub-phenotypes.The weighted multilocus genetic risk score(GRS)was calculated to estimate the cumulative risk conferred by all SNPs.The GRS distribution was then compared between the DKD and NDKD groups as well as in the groups according to the primary cause of CKD.RESULTS One SNP(rs841853;SLC2A1)showed a nominal association with DKD(P=0.048;P>0.05 after Bonferroni correction).The GRS was higher in the DKD group(0.615±0.260)than in the NDKD group(0.590±0.253),but the difference was not significant(P=0.46).The analysis of associations between GRS and individual factors did not show any significant correlation.However,the GRS was significantly higher in patients with glomerular disease than in those with tubulointerstitial disease(P=0.014)and in those with a combined group(tubulointerstitial,vascular,and cystic and congenital disease)(P=0.018).CONCLUSION Our results suggest that selected SNPs that were previously associated with DKD may not be specific for DKD and may confer risk for CKD of different etiology,particularly those affecting renal glomeruli.
基金the Bayer Grant,No.JBT-SOR 2013-01the Instituto de Salud Carlos III,No.PI18/00768,PI15/00145 and PI18/0358+2 种基金Fondo Europeo de Desarrollo Regional(FEDER)from the European Commission“Una manera de hacer Europa”Pla estratègic de recerca i innovacióen salut(PERIS)Grant,No.PERIS_IPIF19-SLT008/18/00182-RH0Contratos Predoctorales de Formación en Investigación en Salud(PFIS),No.FI19/00222.
文摘BACKGROUND Dermatologic adverse events(DAEs)are associated with a better outcome in patients with hepatocellular carcinoma(HCC)irrespective of the therapeutic agent received.The exact mechanisms associated with the development of DAEs are unknown although several studies point to direct toxicity of tyrosine kinase inhibitors(TKIs)to the skin or an immune-mediated reaction triggered by the oncologic treatment.As is the case in other conditions,individual genetic variants may partially explain a higher risk of DAEs.AIM To evaluate the contribution of several gene variants to the risk of developing DAEs in HCC patients treated with TKIs.METHODS We first analyzed 27 single-nucleotide polymorphisms(SNPs)from 12 genes selected as potential predictors of adverse event(AE)development in HCC patients treated with sorafenib[Barcelona Clinic Liver Cancer 1(BCLC1)cohort].Three additional cohorts were analyzed for AGT1(rs699)and AGT2(rs4762)polymorphisms-initially identified as predictors of DAEs:BCLC2(n=79),Northern Italy(n=221)and Naples(n=69)cohorts,respectively.The relation between SNPs and DAEs and death were assessed by univariate and multivariate Cox regression models,and presented with hazard ratios and their 95%confidence intervals(95%CI).RESULTS The BCLC1 cohort showed that patients with arterial hypertension(AHT)(HR=1.61;P value=0.007)and/or AGT SNPs had an increased risk of DAEs.Thereafter,AGT2(rs4762)AA genotype was found to be linked to a statistically significant increased probability of DAEs(HR=5.97;P value=0.0201,AA vs GG)in the Northern Italy cohort by multivariate analysis adjusted for BCLC stage,ECOG-PS,diabetes and AHT.The value of this genetic marker was externally validated in the cohort combining the BCLC1,BCLC2 and Naples cohorts[HR=3.12(95%CI:1.2-8.14),P value=0.0199,AGT2(rs4762)AA vs AG genotype and HR=2.73(95%CI:1.18-6.32)P value=0.0188,AGT2(rs4762)AA vs GG genotype].None of the other gene variants tested were found to be associated with the risk of DAE development.CONCLUSION DAE development in HCC patients receiving TKIs could be explained by the AGT2(rs4762)gene variant.If validated in other anti-oncogenic treatments,it might be considered a good prognosis marker.
文摘<strong>Objective:</strong> To assess the association between circulating C-reactive protein (CRP), and CRP polymorphisms in the diesel engine exhaust (DEE)-exposed workers. <strong>Methods:</strong> In 137 DEE-exposed workers and 127 unexposed comparable control workers, six urinary mono-hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) and serum CRP levels were assayed. Genotyping of four CRP single-nucleotide polymorphisms (SNPs) was measured. <strong>Results: </strong>Serum CRP levels increased in exposed versus control workers (all p < 0.001). In the DEE-exposed workers, two CRP polymorphisms were associated with serum CRP levels, the subjects of rs1205 TT genotype had lower serum CRP levels (p < 0.05 compared to TC or CC). <strong>Conclusions: </strong>Our findings suggest that polymorphisms in CRP and circulating CRP involved in the inflammatory process may play significant roles in human sensitivity to lung function injury caused by DEE exposure. This study will help investigate the underlying mechanisms of adverse respiratory effects induced by DEE.
基金Supported by the Laoshan Laboratory (No.LSKJ202204005)the Mount Tai Scholar Climbing Plan to Song SUNthe Open Fund of CAS Key Laboratory of Marine Ecology and Environmental Sciences,Institute of Oceanology,Chinese Academy of Sciences (No.KLMEES201801)
文摘Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.
基金supported by grants from the Natural Science Foundation of China(No.82102199)the General Program of Shanghai Municipal Commission of Health and Family Planning(No.202040479).
文摘Objective Evidence from prospective studies on the consumption of tea and risk of gout is conflicting and limited.We aimed to investigate the potential causal effects of tea intake on gout using Mendelian randomization(MR).Methods Genome-wide association studies in UK Biobank included 349376 individuals and successfully discovered single-nucleotide polymorphisms linked to consumption of one cup of tea per day.Summary statistics from the Chronic Kidney Disease Genetics consortium included 13179 cases and 750634 controls for gout.Two-sample MR analyses were used to evaluate the relationship between tea consumption and gout risk.The inverse-variance weighted(IVW)method was used for primary analysis,and sensitivity analyses were also conducted to validate the potential causal effect.Results In this study,the genetically predicted increase in tea consumption per cup was associated with a lower risk of gout in the IVW method(OR:0.90;95%CI:0.82–0.98).Similar results were found in weighted median methods(OR:0.88;95%CI:0.78–1.00),while no significant associations were found in MR-Egger(OR:0.89;95%CI:0.71–1.11),weighted mode(OR:0.80;95%CI:0.65–0.99),and simple mode(OR:1.01;95%CI:0.75–1.36).In addition,no evidence of pleiotropy was detected by MR-Egger regression(P=0.95)or MR-PRESSO analysis(P=0.07).Conclusion This study provides evidence for the daily consumption of an extra cup of tea to reduce the risk of gout.
基金Central South University Clinical Data System for Pulmonary Inflammatory Diseases.
文摘Background:Chronic obstructive pulmonary disease(COPD)is a leading cause of morbidity and mortality worldwide.Genome-wide association studies in non-Asian population revealed a link between COPD and mutations in the PTCH1 gene encoding Patched1,a receptor in the Hedgehog signaling pathway important for lung morphogenesis and pulmonary function.The aim of this study was to investigate the association between PTCH1 polymorphisms and the COPD risk in the Chinese Han population.Methods:We performed a case-control study including 296 patients with COPD and 300 healthy individuals.Single-nucleotide polymorphisms in the PTCH1 gene were identified and genotyped based on the linkage disequilibrium analysis in all participants.Odds ratios(ORs)and 95%confidence intervals(95%CIs)were estimated using logistic regression analysis after adjustment for age,gender,and smoking.Results:In total,28 single-nucleotide polymorphisms were identified in patients with COPD.Among them,"A"allele of rs28491365(OR:1.388,95%CI:1.055-1.827,P=0.018),and"G"alleles of rs10512248(OR:1.299,95%CI:1.021-1.653,P=0.033)and rs28705285(OR:1.359,95%CI:1.024-1.803,P=0.033;respectively)were significantly associated with an increased COPD risk.Genetic model analysis revealed that the"T/T"genotype of rs34695652 was associated with a decreased COPD risk under the recessive model(OR:0.490,95%CI:0.270-0.880,P=0.010),whereas rs28504650/rs10512248 haplotype CG was significantly associated with an increased COPD risk after adjustment for age,gender,and smoking status(OR:6.364,95%CI:1.220-33.292,P=0.028).Conclusions:The study provides a new insight into the role of PTCH1 polymorphisms in the susceptibility to COPD in the Chinese Han population.
文摘谷氨酸棒杆菌是食品安全级菌株,可作为生产高价值产物的优良底盘细胞用于工业生产。它具有良好的分泌系统,是表达重组蛋白的潜在宿主,有极大的研究价值。为优化底盘细胞提高其蛋白表达能力,挖掘并验证谷氨酸棒杆菌中与外源蛋白高表达相关的基因。在谷氨酸棒杆菌重测序的基础上,应用生物信息学对单核苷酸多态性(single-nucleotide polymorphisms,SNP)基因进行挖掘,分析基因保守结构域。通过构建SNP基因过表达和敲除重组菌株,评估其生长情况以及增强型绿色荧光蛋白(enhanced green fluorescence protein,EGFP)和人重组特立帕肽(recombinant human teriparatide,rtPTH)的外源蛋白表达能力。分析并整理了高产量外源蛋白菌株的重测序数据,共有33个SNP突变位点,主要涉及5个基因。其中SNP重组菌株over-2370和ko-973-974的荧光值最高,并且发酵生产rtPTH,均比野生型(wild type,WT)提高了近1倍。该研究成功挖掘出与蛋白表达相关的基因GL002370和GL000974,这些发现将有助于获得优化的底盘细胞,并为深入研究增加蛋白产量的靶基因提供指导。
基金funded by the National Key Research and Development Program of China (2017YFD0201701)the Special Fund for Agro-scientific Research in the Public Interest,China (201303016)the Science and Technology Project for Xingjiang Uygur Autonomous Region,China (2013911092)
文摘Powdery mildew,caused by Blumeria graminis f.sp.tritici(Bgt),is one of the most damaging diseases to wheat in the world.The cultivation of resistant varieties of wheat is essential for controlling the powdery mildew epidemic.Wheat landraces are important resources of resistance to many diseases.Mapping powdery mildew resistance genes from wheat landraces will promote the development of new varieties with disease resistance.The Chinese wheat landrace Baiyouyantiao possesses characteristic of disease resistance to powdery mildew.To identify the resistance gene in this landrace,Baiyouyantiao was crossed with the susceptible cultivar Jingshuang 16 and seedlings of parents and F_1,BC_1,F_2,and F_(2:3) were tested with Bgt isolate E09.The genetic results showed that the resistance of Baiyouyantiao to E09 was controlled by a single recessive gene,tentatively designated Pm BYYT.An Illumina wheat 90K single-nucleotide polymorphism(SNP)array was applied to screen polymorphisms between F_2-resistant and F_2-susceptible DNA bulks for identifying the chromosomal location of Pm BYYT.A high percentage of polymorphic SNPs between the resistant and susceptible DNA bulks was found on chromosome 7B,indicating that Pm BYYT may be located on this chromosome.A genetic linkage map of Pm BYYT consisting of two simple sequence repeat markers and eight SNP markers was developed.The two flanking markers were SNP markers W7BL-8 and W7BL-15,with genetic distances of 3 and 2.9 c M,respectively.The results of this study demonstrated the rapid characterization of a wheat disease resistance gene and SNP marker development using the 90K SNP assay.The flanking markers of gene Pm BYYT will benefit marker-assisted selection(MAS)and map-based cloning in breeding wheat cultivars with powdery mildew resistance.
文摘Dramatic progress has been made in the area of germline genetics of prostate cancer(PCa)in the past decade.Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice-changing have been identified.For men with high risk PCa,the application of genetic testing for inherited pathogenic mutations is becoming standard of care.A major question exists about which additional populations of men to test,as men at all risk levels can potentially benefit by knowing their unique genetic profile of germline susceptibility variants.This article will provide a brief overview of some current issues in understanding inherited susceptibility for PCa.
基金This study was funded by the Beijing Municipal Science&Technology Commission(Grant No.Z181100001718005 and 19 L2152)the National Natural Science Foundation of China(Grant No.81801643)+1 种基金the Army"Twelfth Five"Scientific Research Foundation(Grant No.BWS11J050)the Chinese PLA General Hospital(Grant No.QNC19047)。
文摘Background:Immune-and inflammation-related genes(IIRGs)play an important role in the pathogenesis of tuberculosis(TB).However,the relationship between IIRG polymorphisms and TB risk remains unknown.In this study,the gene polymorphisms and their association with tuberculosis were determined in a Chinese population.Methods:We performed a case-control study involving 1016 patients with TB and 507 healthy controls of Han Chinese origin.Sixty-four single-nucleotide polymorphisms(SNPs)belonging to 18 IIRGs were genotyped by the PCR-MassArray assay,and the obtained data was analyzed withχ2-test,Bonferroni correction,and unconditional logistic regression analysis.Results:We observed significant differences in the allele frequency of LTA rs2229094*C(P=0.015),MBL2 rs2099902*C(P=0.001),MBL2 rs930507*G(P=0.004),MBL2 rs10824793*G(P=0.004),and IL12RB1 rs2305740*G(P=0.040)between the TB and healthy groups.Increased TB risk was identified in the rs930507 G/G genotype(Padjusted=0.027)under a codominant genetic model as well as in the rs2099902(C/T+C/C)vs T/T genotype(Padjusted=0.020),rs930507(C/G+G/G)vs C/C genotype(Padjusted=0.027),and rs10824793(G/A+G/G)vs A/A genotype(Padjusted=0.017)under a dominant genetic model after Bonferroni correction in the analysis of the overall TB group rather than the TB subgroups.Furthermore,the rs10824793_rs7916582*GT and rs10824793_rs7916582*GC haplotypes were significantly associated with increased TB risk(P=0.001,odds ratio[OR]=1.421,95%confidence interval[CI]:1.152-1.753;and P=0.018,OR=1.364,95%CI:1.055-1.765,respectively).Moreover,the rs10824793_rs7916582*AT/AT or rs10824793_rs7916582*GT/GT diplotype showed a protective(P=0.003,OR=0.530,95%CI:0.349-0.805)or harmful(P=0.009,OR=1.396,95%CI:1.087-1.793)effect against the development of TB.Conclusions:This study indicated that MBL2 polymorphisms,haplotypes,and diplotypes were associated with TB susceptibility in the Han Chinese population.Additionally,larger sample size studies are needed to further confirm these findings in the future.
基金This work was supported by the National Key Research and Development Program of China[No.2017YFD0600201]Forestry Industry Research Special Funds for Public Welfare Projects[No.201404101].
文摘Coumarate 3-hydroxylase(C3h)genes participate in the synthesis of lignin and may affect the properties of wood that are important for its commercial value.A better understanding of the natural variation in C3h genes and their associations to wood properties is required to effectively improve wood quality.We used a candidate gene-based association mapping approach to identify CfC3h allelic variants associated with traits that affect the wood properties of Catalpa fargesii.We first isolated the full-length CfC3h cDNA(1825 bp),which was expressed at relatively high levels in xylem according to real time-polymerase chain reaction.In totally,17 common single-nucleotide polymorphisms(minor allele frequency>5%)were identified through cloning and sequencing the CfC3h locus from a mapping population(including 88 unrelated natural C.fargesii individuals collected from main distribution area).Nucleotide diversity and linkage disequilibrium(LD)in CfC3h indicate that CfC3h has low nucleotide diversity(π_(t)=0.0031 andθ_(w)=0.0103)and relatively low LD(within 1800 bp;r^(2)≥0.1).An association analysis identified eight common single-nucleotide polymorphisms(SNPs)(false discovery rate,Q<0.10)and ten haplotypes(Q<0.10)associated with wood properties,explaining 4.92-12.09%of the phenotypic variance in an association population consisted of 125 unrelated natural individuals(The 88 individuals from the mapping population were comprised in the association population).Our study would provide new insight into C3h gene affecting wood quality,and the SNP markers identified would have potential applications in marker-assisted breeding in the future.
基金Financial support received from Department of Biotechnology,Government of India vide grant No.BT/PR-8953/BCE/08/533/2007project sanctioned against grant No.BT/04/NE/2009financial support from Department of Science&Technology,Government of India in the form of a research fellowship under the INSPIRE program
文摘The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in chloroplast rbc L and mat K gene sequences in 19 accessions representing C. quinoa and C. album indicated that the accessions IC-411824 and IC-411825,which have white seeds, belong to C. quinoa rather than C. album. This observation was also supported by a time tree that indicated IC-411824 and IC-411825 to be a sister clade to accessions of C. quinoa with an estimated age of 1.2 Mya. Whereas multiple alignments of rbc L gene sequences from the 19 accessions revealed 1.26% parsimony-informative sites with 0.68%interspecific sequence diversity, alignment of nucleotide sequences of amplicons representing the mat K gene revealed 4.97% parsimony-informative sites and 2.81% interspecific sequence diversity. Validation of SNPs in the cp rbc L and mat K regions of 36 accessions belonging to C. quinoa and C. album was performed by allele-specific PCR with primers carrying a single base change at the 3′ end. We report the first C. quinoa-specific SNP-based primer, R1RQ-AFR,designed from rbc L sequences, that could differentiate quinoa from 64 genera including13 species of the genus Chenopodium. With an estimated age of 10.5–4.1 million years(Myr), the Himalayan chenopods are evolutionarily younger than the Andean chenopods. The results establish the paraphyletic origin of the genus Chenopodium.
