Multiple single nucleotide polymorphisms may contribute to cognitive decline in Parkinson’s disease. However, the mechanism by which these single nucleotide polymorphisms modify brain imaging phenotype remains unclea...Multiple single nucleotide polymorphisms may contribute to cognitive decline in Parkinson’s disease. However, the mechanism by which these single nucleotide polymorphisms modify brain imaging phenotype remains unclear. The aim of this study was to investigate the potential effects of multiple single nucleotide polymorphisms on brain imaging phenotype in Parkinson’s disease. Forty-eight Parkinson’s disease patients and 39 matched healthy controls underwent genotyping and 7 T magnetic resonance imaging. A cognitive-weighted polygenic risk score model was designed, in which the effect sizes were determined individually for 36 single nucleotide polymorphisms. The correlations between polygenic risk score, neuroimaging features, and clinical data were analyzed. Furthermore, individual single nucleotide polymorphism analysis was performed to explore the main effects of genotypes and their interactive effects with Parkinson’s disease diagnosis. We found that, in Parkinson’s disease, the polygenic risk score was correlated with the neural activity of the hippocampus, parahippocampus, and fusiform gyrus, and with hippocampal-prefrontal and fusiform-temporal connectivity, as well as with gray matter alterations in the orbitofrontal cortex. In addition, we found that single nucleotide polymorphisms in α-synuclein(SNCA) were associated with white matter microstructural changes in the superior corona radiata, corpus callosum, and external capsule. A single nucleotide polymorphism in catechol-O-methyltransferase was associated with the neural activities of the lingual, fusiform, and occipital gyri, which are involved in visual cognitive dysfunction. Furthermore, DRD3 was associated with frontal and temporal lobe function and structure. In conclusion, imaging genetics is useful for providing a better understanding of the genetic pathways involved in the pathophysiologic processes underlying Parkinson’s disease. This study provides evidence of an association between genetic factors, cognitive functions, and multi-modality neuroimaging biomarkers in Parkinson’s disease.展开更多
AIM:To explore the association of single nucleotide polymorphisms(SNPs)in the IL33/IL1RL1 gene region with the susceptibility to Behcet’s disease(BD)in a Chinese Han population.METHODS:A total of eight SNPs in the ca...AIM:To explore the association of single nucleotide polymorphisms(SNPs)in the IL33/IL1RL1 gene region with the susceptibility to Behcet’s disease(BD)in a Chinese Han population.METHODS:A total of eight SNPs in the candidate gene region(rs11792633,rs7025417,rs10975519 and rs1048274 in IL33;rs2310220,rs12712142,rs13424006 and rs3821204 in IL1RL1)were genotyped in783 BD patients and 701 healthy controls by the Sequenom Mass Array i PLEX platform.RESULTS:A statistically significant association was observed between IL1RL1 rs12712142 and BD patients.The frequency of IL1RL1 rs12712142 variant allele A was significantly lower in BD patients than that in controls(OR=0.8,95%CI:0.69-0.94,Pc=0.039);the genotype distribution(Pc=0.043)and additive and dominant genetic model analyses(OR=0.8,95%CI:0.69-0.94,Pc=0.040 and OR=0.72,95%CI:0.58-0.88,Pc=0.011)also indicated a strong association between rs12712142 and BD patients.CONCLUSION:This is the first study to reveal the association between IL1RL1 rs12712142 variant allele A and the decreased risk of BD in the Chinese Han population,indicating a protective role of IL1RL1 in the pathogenesis of BD.展开更多
The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy...The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.展开更多
AIM:To access the association of forty-eight single nucleotide polymorphisms(SNPs)identified from Caucasian population with steroid-induced ocular hypertension(OHT)in India population.METHODS:Fifty-four triamcinolone-...AIM:To access the association of forty-eight single nucleotide polymorphisms(SNPs)identified from Caucasian population with steroid-induced ocular hypertension(OHT)in India population.METHODS:Fifty-four triamcinolone-acetonide(TA)and for ty-seven dexamethasone(Dex)administered subjects were enrolled in the study after a written consent.Intraocular pressure(IOP)values were recorded for a period of 6-month post steroid injections and patients were grouped as steroid-responders(SR:IOP≥21 mm Hg)and non-responders(NR:IOP≤20 mm Hg).Genomic DNA was isolated from peripheral venous blood.Forty-eight SNPs identified in TA treated Caucasian patients by genome wide association study(GWAS)were genotyped using iPLEXTM MassA RRAY among TA as well as Dex administered Indian patients.Genotyping data of 48 general subjects from a previous study were considered as reference controls for statistical analysis.Genotypic frequencies were calculated and P-value,Chi-square and odds ratio at 95%confidenceinterval of group A(steroid treated vs controls),group B(SR vs NR),group C(phenotype correlation:influence of time,severity and gender on IOP rise),were calculated.P<0.05 was considered to be statistically significant.RESULTS:OHT was observed in 50%of TA and 26%of Dex administered patients,respectively.IOP rise was mostly severe(>30 mm Hg)and immediate(<1 wk)among TA-SR patients while it was noticed to be mild(<30 mm Hg)and between 1-2 mo among Dex-SR patients.Logistic regression for risk factor correlation with OHT remained non-significant,hence these factors were not considered as confounding parameters for further analysis.rs133,rs34016742,rs274554,rs10936746,rs274547,rs804854,rs7751500,rs359498,and rs7547448 SNPs significantly varied even after Bonferroni corrections(P<0.0025;group A).rs1879370(TA)and rs6559662(Dex)were significantly(P<0.05)associated with OHT(group B).rs133(severe IOP rise),rs11047639 and rs1879370(male gender),and rs11171569(immediate IOP rise)significantly(P<0.05)influenced the phenotype correlation only among TAOHT patients.However,the significance of these SNPs in group B and phenotype analysis(group C)was lost upon Bonferroni corrections(P<0.0025).CONCLUSION:Prevalence of OHT in study population is observed to be similar to other studies both in TA and Dex treated patients.We can correlate rs34016742 involved in diabetes signaling pathway to the occurrence of ocular edematous and inflammatory conditions.Except rs133 that is involved in neuro-degeneration and myopia occurrence,none of the other SNPs identified in Caucasian population possess any correlation with OHT incidence in TA and Dex administered Indian subjects.展开更多
AIM:To investigate relationship between refractive errors and eleven single nucleotide polymorphisms(SNPs)in HGF,GC,MFN1,GNB4,and VDR genes in Turkish population.METHODS:A group of 212 participants with myopia(n=91),h...AIM:To investigate relationship between refractive errors and eleven single nucleotide polymorphisms(SNPs)in HGF,GC,MFN1,GNB4,and VDR genes in Turkish population.METHODS:A group of 212 participants with myopia(n=91),hyperopia(n=45),and emmetropia(n=76)were investigated in this study.SNPs in HGF,GC,MFN1,GNB4 and VDR genes were studied by Snap Shot technique.RESULTS:The patients in this study consists of 47 female/44 male(age:23.47±4.30)patients with myopia,20 female/25 male(age:31.20±8.02)with hyperopia and 33 female/43 male(age:25.22±6.60)with emmetropia.The genotype distribution of the rs7618348 polymorphism,which was the only statistically significant one between myopia and emmetropia group.The genotype distribution of the rs3819545,rs3735520,rs7041,and rs2239182 polymorphisms,which were statistically significant between hyperopia and emmetropia groups.CONCLUSION:The importance of genetic predisposition to refractive errors with respect to etiology of the disease is revealed.It is known that polymorphism studies may differ because of genetic diversity among populations so larger cohort studies are required in different populations to enlighten the etiology of the refractive errors.展开更多
Residual ridge resorption(RRR)is the decrease in the jaw structure that follows tooth extraction.It is a multifactorial disorder,but reports on the associated genetic factors are scarce,particularly amongst the Saudis...Residual ridge resorption(RRR)is the decrease in the jaw structure that follows tooth extraction.It is a multifactorial disorder,but reports on the associated genetic factors are scarce,particularly amongst the Saudis.This study aimed to investigate the role of single nucleotide polymorphisms(SNPs)in fibroblast growth factor receptor 1 oncogene partner 2(FGFR1OP2)in RRR development in Saudis.The study included 192 individuals(RRR=96;controls=96)attending outpatient clinics at the College of Dentistry,King Saud University.Demographic and clinical data were collected,the digital panoramic dental radiograph was obtained,and mandibular residual ridge height was measured.DNA was extracted from saliva and genotyping was conducted on“Sequenom MassARRAY iPLEX”.Genotype and allele frequencies of three SNPs were calculated and compared.The age at first diagnosis and bone height were compared in the three genotypes of each SNP.The age of the patients,age at first edentulism,and bone height ranged 21-80 years,12-70 years,and 13-34.6 mm,respectively.All three genotypes of the studied SNPs(rs2279351,rs78054962 and rs2306852)were identified.SNP rs2279351 associated significantly with RRR,and the mutant C allele was highly predisposing.No association was observed for the other two SNPs.The genotypes of all SNPs had an influence on age at first edentulism and bone height,but the results were not statistically different.Since FGFR1OP2 plays a role in the process of rapid wound healing in the oral cavity,it may be playing a role in the development of RRR by influencing the rate of resorption of the jawbone.SNP rs2279351 may alter its expression and hence RRR development.This study is limited due to small a sample size,and further large-scale studies are required to confirm this association and to consider rs2279351 as a possible marker of RRR development.展开更多
Bamboos are one of the most beautiful and useful plants on Earth.The genetic background and population structure of bamboos are well known,which helps accelerate the process of artificial domestication of bamboo.Parti...Bamboos are one of the most beautiful and useful plants on Earth.The genetic background and population structure of bamboos are well known,which helps accelerate the process of artificial domestication of bamboo.Partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species were analyzed for occurrence of single nucleotide polymorphisms(SNPs).The nucleotide diversityθw and total nucleotide polymorphismsπT of the sequenced DNA regions was 0.05137 and 0.03332,respectively.Bothπnonsyn/πsyn and Ka/Ks values were<1.The nucleotide sequences of these six genes were inferred to be relatively conserved,and the haplotype diversity was relatively high.The results of evolutionary neutrality tests showed that the six genes were in line with neutral evolution,and that the NRT2.1 and AMT2.1 gene sequences may have experienced negative selection.An inter-SNP recombination event at the NRT2.1 gene in the all pooled sample,of all 32 bamboo species was the lowest at 0.0645,whereas the AMT gene recombination events were all>0.1.Estimation and analysis of linkage disequilibrium of five genes revealed that with the increase in nucleotide sequence length,the degree of SNP linkage disequilibrium decreased rapidly.We inferred the population genetic structure of 32 bamboo species based on the SNP loci of six genes with frequencies>18%.32 bamboo species were divided into five categories,which indicated that the combined population of all bamboo species had obvious multivariate characteristics and was heterogeneous;red(Group 1)and green(Group 2)were the main groups.展开更多
Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objec...Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.展开更多
Vitamin D is a fat-soluble vitamin.It is an essential vitamin for human body.It has a classical effect on regulating calcium and phosphorus metabolism.Participate in cellular and humoral immune processes by regulating...Vitamin D is a fat-soluble vitamin.It is an essential vitamin for human body.It has a classical effect on regulating calcium and phosphorus metabolism.Participate in cellular and humoral immune processes by regulating the growth,differentiation and metabolism of immune cells.A large number of studies in recent years have shown that vitamin D deficiency increases the incidence of respiratory diseases.Respiratory diseases mainly include bronchial asthma,chronic obstructive pulmonary disease,tuberculosis,acute upper respiratory tract infection and pneumonia.Vitamin D metabolic pathway genes play a very important regulatory role in the transformation of vitamin D into active vitamin D,including CYP2R1,CYP27B1,CYP24A1,VDBP,VDR five genes.Genetic polymorphism of genes is the molecular basis of individual differences and disease development.Therefore,this paper summarizes the research on single nucleotide polymorphism of vitamin D metabolic pathway gene and respiratory diseases.In order to provide a new idea for future treatment.展开更多
Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression t...Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. The status of the CCR5Δ32 gene has not been reported in Nigeria. Aim: This study was aimed at analyzing single nucleotide polymorphism of CCR5 gene among the Ijaws resident in Yenagoa, Nigeria. Methods: 100 subjects (75 HIV negative and 25 HIV positive control) were recruited for this study. The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. Results: The results showed that 75 (100%) of the HIV negative subjects had 189 base pair in their CCR5 gene. Nucleotide of the 20 (100%) of the sequenced samples were conservatively same and no SNP was observed. Conclusion: This study documented no SNPs in CCR5 gene of the study population hence;the study population has no protection from HIV infection.展开更多
Inflammation plays a significant role in the etiology of type 2 diabetes mellitus(T2DM).The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury,o...Inflammation plays a significant role in the etiology of type 2 diabetes mellitus(T2DM).The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury,oxidative stress and beta cell apoptosis in T2 DM.Among the recognized markers are interleukin(IL)-6,IL-1,IL-10,IL-18,tissue necrosis factor-alpha(TNF-α),C-reactive protein,resistin,adiponectin,tissue plasminogen activator,fibrinogen and heptoglobins.Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance.Many single nucleotide polymorphisms(SNPs) in various genes including those of pro and antiinflammatory cytokines have been reported as a risk for T2 DM.Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups.The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene,gene-environment and gene-nutrient interactions.This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6,TNF-α,resistin and adiponectin in pathogenesis of T2 DM.展开更多
AIM: To investigate the relationship between low molecular polypeptide-7 (LMP-7) gene polymorphism and response to interferon (IFN) therapy in chronic hepatitis C virus (HCV) patients. METHODS: LMP-7 polymorphism at c...AIM: To investigate the relationship between low molecular polypeptide-7 (LMP-7) gene polymorphism and response to interferon (IFN) therapy in chronic hepatitis C virus (HCV) patients. METHODS: LMP-7 polymorphism at codon 49 with nucleotide substitution from A to C was amplified in 104 chronic HCV patients of genotype 4. The amplicons were digested with restriction endonuclease Bsm I and the produced restriction fragment length polymorphism was analyzed. Patients received IFN + regional blood volume therapy for 48 wk and the frequency of thissingle nucleotide polymorphism (SNP) was statistically correlated with treatment response. The exclusion criteria for these patients were stated by the national health program for treating viral hepatitis. Main exclusion criteria included co-infection with hepatitis B virus or schistosomiasis, thyroid dysfunction, uncontrolled diabetes mellitus, history of long term drug or alcohol intake and autoimmune hepatitis. Multivariate analyses were done to correlate LMP-7 SNP plus several factors such as age, gender, weight, serum alpha-fetoprotein (AFP) and alanine aminotransferase levels, liver activity, fibrosis score and viral load with response to therapy. RESULTS: The data presented in this study clearly demonstrated statistically significant differences between sustained virological response (SVR) (defined as the absence of HCV RNA levels in the patient's sera at least 6 mo after discontinuation of treatment) and non-response (NR) (where HCV RNA levels in the patient's sera never become undetectable for 6 mo during or after treatment). Variables were described as odds ratio with 95%CI. The data were considered significant if P values were ≤ 0.05; highly significant if P < 0.01 and very highly significant if P < 0.001. Current data showed that 91.7% of patients carrying LMP-7 C/C allele were associated with SVR, while the other two genotypes C/A and A/A were associated with NR patients, 83.3% and 64.3% respectively, showing that genotype CC was strongly associated with response to interferon (95%CI: 12.0719-134.6572, P = 0.0001). The majority of parameters recorded in SVR and NR patients included higher values of mean age (P = 0.004), alanine aminotransferase (P = 0.001), AFP (P = 0.001), body weight (P = 0.025), viral load (P = 0.025), higher fibrosis and histological activity index indices among NR vs SVR patients. Also, the multivariate statistical analysis of the different factors of fibro-sis score, liver activity grade, genotypes and alleles of LMP-7 gene polymorphism in responders and NRs of HCV patients in this study showed that HCV patients with A allele had a very highly significant association with the NRs, high fibrosis and higher liver activity, while the C allele had a very highly significant association with the responders, low fibrosis and lower liver activity (95%CI: 3.5800-13.2519, P = 0.0001).CONCLUSION: LMP-7 SNP is a candidate gene that should be considered when designing a mathematical model for predicting response to therapy and disease progression in HCV patients.展开更多
Objective:To discuss the association between single nucleotide polymorphism(SNP) of rs3811047 in IL-1 F7 gene and rheumatoid arthritis(RA) susceptibility among the Han population in central plains of China.Methods:A t...Objective:To discuss the association between single nucleotide polymorphism(SNP) of rs3811047 in IL-1 F7 gene and rheumatoid arthritis(RA) susceptibility among the Han population in central plains of China.Methods:A total of 276 RA patients admitted to our hospital from December 2009 to December 2011 together with 276 healthy physical examinees in the same period were chosen as the subjects.The typing for rs3811047 SNP in IL-1 F7 gene was carried out by using ligase detection reaction and polymerase chain reaction technique.And the frequency of each allele and genotypes distribution was calculated so as to evaluate the association between genotype distribution and RA susceptibility.Results:The frequency of A allele of rs3811047 in IL-1 F7 gene in RA group and control group was 16.27%and 17.68%,respectively,and that of G allele in two groups was 83.73%and 82.32%,respectively.The difference between two groups wasn’t statistical significant(P 】0.05).The frequency of genotype AA,AG and GG in RA group was 2.19%,27.84%and 69.97%,respectively,while that in control group was 2.94%,29.78%and 67.28%, respectively.The difference of distribution of three genotypes was not statistically significant (P 】0.05).RA patients with A allele were better than those without A allele in joint swelling index, rest pain,HAQ scoring and blood sedimentation.There was significant difference between two groups in above indexes(P【0.05/P【0.01).Conclusions:No significant correlation between RA susceptibility among the Han population in central plains of China and rs3811047 SNP inIL-1 F7 gene is observed.However,A allele of rs3811047 has certain influence on the condition of RA patients.展开更多
Nucleotide diversity(π) and linkage disequilibrium(LD) analysis based on SNP marker could provide a sound basis for choosing an association analysis method.Japanese larch(Larix kaempferi) is an important timber conif...Nucleotide diversity(π) and linkage disequilibrium(LD) analysis based on SNP marker could provide a sound basis for choosing an association analysis method.Japanese larch(Larix kaempferi) is an important timber coniferous tree species for pulping and papermaking,but its high lignin content has significantly restricted it application potential.In this study,the LACCASE gene,that plays an important regulatory role for lignin biosynthesis,was selected as research target.The full-length c DNA and genomic sequences of the encoding Lk LAC8 gene were isolated from the LACCASE expressed sequence tags of the Japanese larch transcriptome database using the rapid amplification of c DNA ends-polymerase chain reaction(RACE-PCR).The c DNA was determined to be 1940 bp,with an open reading frame(ORF,1734 bp) that encoded a protein of 577 AA.This protein contains four highly specific Cu^(2+) binding sites and 11 glycosylation sites,thus belonging to the LACCASE family.The deduced protein sequence shared an 89% identity with the Pta LAC from Pinus taeda.A real-time PCR analysis showed that the Lk LAC8 transcript was expressed predominantly in mature xylem,with moderate levels in the immature xylem,cambium and mature leaves,the lowest in the roots.Lastly,the genomic sequences of Lk LAC8 in 40 individuals from six naturally distributed populations of Japanese larch were amplified,and a total of 201 SNPs(103 and 98 mutation types of transition and transversion,respectively) were detected;the frequency of the SNPs was 1/19 bp.Nucleotide diversity among the six populations ranged from 0.0034 to 0.0053,which suggested that there were no significant differences among the populations.The LD analysis showed that the LD level decayed rapidly within the increasing length of the Lk LAC8 gene.These results implied that LD mapping and association analysis based on candidate gene may be feasible for the marker-assisted breeding of new germplasms with low lignin in Japanese larch.展开更多
AIM: To investigate the association between single nucleotide polymorphism (SNP)in promoter of the DNA methyltransferase 3B (DNNT3B) gene and risk for development and lymphatic metastasis of gastric cardiac adenocarci...AIM: To investigate the association between single nucleotide polymorphism (SNP)in promoter of the DNA methyltransferase 3B (DNNT3B) gene and risk for development and lymphatic metastasis of gastric cardiac adenocarcinoma (GCA).METHODS: The hospital based case-control study included 212 GCA patients and 294 control subjects without overt cancer. The DNMT3B SNP was genotyped by PCR and restriction fragment length polymorphism (RFLP) analysis. RESULTS: The C/C genotype was not detected in both GCA patients and controls. In control subjects, the frequency of T/T and C/T genotypes was 94.9% and 5.1% respectively,and that of T and C alleles was 97.4% and 2.6%, respectively.The genotype and allelotype distribution in the GCA patients was not significantly different from that in controls (P = 0.34 and 0.33, respectively). When stratified by smoking status and family history of upper gastrointestinal cancer, significant difference in the genotype distribution was not observed between GCA patients and controls. The distribution of DNMT3Bgenotypes in GCA patients with or without lymphatic metastasis did not show significant difference (P = 0.42). CONCLUSION: The distribution of DNMT3BSNP in North China is distinct from that in Caucasians. Although this SNP has been associated with susceptibility to lung, head, neck and breast cancer, it may not be used as a stratification marker to predict susceptibility and lymphatic metastasis of GCA, at least in the population of North China.展开更多
Objective To identify the genetic defects of the the adiponectin (APM1) gene that contribute to the development of type 2 diabetes (T2DM) and determine the functional single nucleotide polymorphisms (SNPs) in the APM1...Objective To identify the genetic defects of the the adiponectin (APM1) gene that contribute to the development of type 2 diabetes (T2DM) and determine the functional single nucleotide polymorphisms (SNPs) in the APM1 gene associated with T2DM in Han nationality. Methods The APM1 gene 5’-UTR was screened by direct sequencing to identify common polymorphisms. Identified SNPs were genotyped in 585 nondiabetic controls, 278 subjects with impaired glucose intolerance (IGT) and 212 patients with T2DM. The functions of SNPs in the regulatory region were assessed by reporter gene assay. Possible association between SNPs and plasma APM1 levels or metabolic parameters was statistically assessed. Results Three SNPs were identified in the APM1 gene 5’-UTR. A case-control study revealed that SNP -11377 G/C had significant differences in allele frequencies between T2DM patients and nondiabetic controls (G 0.314/C 0.686 vs. G 0.265/C 0.735, P=0.03). Haplotype analysis of three SNPs in the APM1 gene showed that no significant association of haplotypes with T2DM. IGT was detected in the present study. Reporter gene assay showed that SNP did not influence the transcription efficiency in the 3T3-L1 cell line. Conclusion SNP -11377 G/C in the proximal promoter region of the APM1 gene contributes to the development of T2DM in Han nationality but may not be a functional SNP in the APM1 gene.展开更多
The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron re...The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.展开更多
Silent information regulator 2(Sir2) proteins, or sirtuins, are nicotine adenine dinucleotide(NAD)-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Sir2 hom...Silent information regulator 2(Sir2) proteins, or sirtuins, are nicotine adenine dinucleotide(NAD)-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Sir2 homologs, namely, silent information regulators(SIRT1–7). SIRT4 and SIRT7 genes play a crucial role in regulating lipid metabolism, cellular growth and metabolism. This suggests that they are potential candidate genes for affecting body size and meat quality traits in animals. Hence, this study aimed to detect genetic variations of both SIRT4 and SIRT7 bovine genes in Qinchuan cattle, and to evaluate the effect of these variations on economically important body size and meat quality traits. Expression analysis using quantitative real-time PCR(q PCR) indicated that SIRT4 and SIRT7 were broadly expressed in all thirteen studied tissues. The expression of SIRT4 was higher in liver, muscle, and in subcutaneous fat tissue. In the case of SIRT7, the expression was higher in lung, abomasum, and subcutaneous fat. Using DNA sequencing, a total of three single nucleotide polymorphisms(SNPs) were identified within SIRT4 and SIRT7 genes in 468 Qinchuan cattle. These included one novel SNP within 3′ untranslated regions(UTR) of SIRT4(SNP1: g.13915A>G) and two novel synonymous substitutions in SIRT7(SNP2: g.3587C>T and SNP3: g.3793T>C). Statistical analyses indicated that all three SNPs could significantly influence some body size and meat quality traits in Qinchuan cattle. These novel findings will provide a background for application of bovine SIRT4 and SIRT7 genes in the selection program of Chinese cattle.展开更多
In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide as...In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide association study.In Japanese populations,the correlation between 2 SNPs on 17q and the risk of prostate cancer and tumor aggressiveness was also confirmed by a large-scale experiment.However,whether 17q is associated with prostate cancer and its clinical manifestations in Chinese populations is still unknown.Therefore,we conducted a case-control study in a northern Chinese population and tested 2 SNPs,rs4430796 and rs1859962,on 17q in 124 prostate cancer patients and 111 controls using polymerase chain reaction-high resolution melting curve(PCR-HRM) combined with sequencing.We analyzed the association of the 2 SNPs with the risk of prostate cancer as well as patients' lifestyles,onset ages,Gleason scores,PSA levels,and pathologic stages.We found a significant difference in the G allele of SNP rs1859962(P = 0.035,OR = 1.51,95% CI = 1.03-2.21) but not in the rs4430796 genotype frequency or allele frequency distribution between prostate cancer patients and the controls(P > 0.05).Neither of the SNPs was significantly associated with the onset age,Gleason score,PSA level,pathologic stage,or other clinical indicators of patients with prostate cancer(P > 0.05).Our results show that polymorphism of the G allele of SNP rs1859962 is associated with the risk of prostate cancer in a Chinese population.展开更多
基金supported by grants from the National Natural Science Foundation of China,Nos. 81771216 (to JLP), 81520108010 (to BRZ),and 82101323 (to TS)the National Key R&D Program of China,No. 2018YFA0701400 (to HYL)+3 种基金the Primary Research and Development Plan of Zhejiang Province,No. 2020C03020 (to BRZ)the Key Project of Zhejiang Laboratory,No. 2018EB0ZX01 (to HYL)the Fundamental Research Funds for the Central Universities,No. 2019XZZX001-01-21 (to HYL)Preferred Foundation of Zhejiang Postdoctors,No. ZJ2021152 (to TS)。
文摘Multiple single nucleotide polymorphisms may contribute to cognitive decline in Parkinson’s disease. However, the mechanism by which these single nucleotide polymorphisms modify brain imaging phenotype remains unclear. The aim of this study was to investigate the potential effects of multiple single nucleotide polymorphisms on brain imaging phenotype in Parkinson’s disease. Forty-eight Parkinson’s disease patients and 39 matched healthy controls underwent genotyping and 7 T magnetic resonance imaging. A cognitive-weighted polygenic risk score model was designed, in which the effect sizes were determined individually for 36 single nucleotide polymorphisms. The correlations between polygenic risk score, neuroimaging features, and clinical data were analyzed. Furthermore, individual single nucleotide polymorphism analysis was performed to explore the main effects of genotypes and their interactive effects with Parkinson’s disease diagnosis. We found that, in Parkinson’s disease, the polygenic risk score was correlated with the neural activity of the hippocampus, parahippocampus, and fusiform gyrus, and with hippocampal-prefrontal and fusiform-temporal connectivity, as well as with gray matter alterations in the orbitofrontal cortex. In addition, we found that single nucleotide polymorphisms in α-synuclein(SNCA) were associated with white matter microstructural changes in the superior corona radiata, corpus callosum, and external capsule. A single nucleotide polymorphism in catechol-O-methyltransferase was associated with the neural activities of the lingual, fusiform, and occipital gyri, which are involved in visual cognitive dysfunction. Furthermore, DRD3 was associated with frontal and temporal lobe function and structure. In conclusion, imaging genetics is useful for providing a better understanding of the genetic pathways involved in the pathophysiologic processes underlying Parkinson’s disease. This study provides evidence of an association between genetic factors, cognitive functions, and multi-modality neuroimaging biomarkers in Parkinson’s disease.
基金the National Natural Science Foundation of China (No.81770917)。
文摘AIM:To explore the association of single nucleotide polymorphisms(SNPs)in the IL33/IL1RL1 gene region with the susceptibility to Behcet’s disease(BD)in a Chinese Han population.METHODS:A total of eight SNPs in the candidate gene region(rs11792633,rs7025417,rs10975519 and rs1048274 in IL33;rs2310220,rs12712142,rs13424006 and rs3821204 in IL1RL1)were genotyped in783 BD patients and 701 healthy controls by the Sequenom Mass Array i PLEX platform.RESULTS:A statistically significant association was observed between IL1RL1 rs12712142 and BD patients.The frequency of IL1RL1 rs12712142 variant allele A was significantly lower in BD patients than that in controls(OR=0.8,95%CI:0.69-0.94,Pc=0.039);the genotype distribution(Pc=0.043)and additive and dominant genetic model analyses(OR=0.8,95%CI:0.69-0.94,Pc=0.040 and OR=0.72,95%CI:0.58-0.88,Pc=0.011)also indicated a strong association between rs12712142 and BD patients.CONCLUSION:This is the first study to reveal the association between IL1RL1 rs12712142 variant allele A and the decreased risk of BD in the Chinese Han population,indicating a protective role of IL1RL1 in the pathogenesis of BD.
基金Supported by the National Key R&D Program of China(Nos.2018YFD0900106,2018YFC1406700)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)the MOA Modern Agricultural Talents Support Project。
文摘The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.
基金Supported by equally the Department of Biotechnology under the grant(No.BT/PR3580/PID/6/625/2011)Indian Council of Medical Research(ICMR)under grant[No.82/19/2012/PHGEN(TF)/BMS]。
文摘AIM:To access the association of forty-eight single nucleotide polymorphisms(SNPs)identified from Caucasian population with steroid-induced ocular hypertension(OHT)in India population.METHODS:Fifty-four triamcinolone-acetonide(TA)and for ty-seven dexamethasone(Dex)administered subjects were enrolled in the study after a written consent.Intraocular pressure(IOP)values were recorded for a period of 6-month post steroid injections and patients were grouped as steroid-responders(SR:IOP≥21 mm Hg)and non-responders(NR:IOP≤20 mm Hg).Genomic DNA was isolated from peripheral venous blood.Forty-eight SNPs identified in TA treated Caucasian patients by genome wide association study(GWAS)were genotyped using iPLEXTM MassA RRAY among TA as well as Dex administered Indian patients.Genotyping data of 48 general subjects from a previous study were considered as reference controls for statistical analysis.Genotypic frequencies were calculated and P-value,Chi-square and odds ratio at 95%confidenceinterval of group A(steroid treated vs controls),group B(SR vs NR),group C(phenotype correlation:influence of time,severity and gender on IOP rise),were calculated.P<0.05 was considered to be statistically significant.RESULTS:OHT was observed in 50%of TA and 26%of Dex administered patients,respectively.IOP rise was mostly severe(>30 mm Hg)and immediate(<1 wk)among TA-SR patients while it was noticed to be mild(<30 mm Hg)and between 1-2 mo among Dex-SR patients.Logistic regression for risk factor correlation with OHT remained non-significant,hence these factors were not considered as confounding parameters for further analysis.rs133,rs34016742,rs274554,rs10936746,rs274547,rs804854,rs7751500,rs359498,and rs7547448 SNPs significantly varied even after Bonferroni corrections(P<0.0025;group A).rs1879370(TA)and rs6559662(Dex)were significantly(P<0.05)associated with OHT(group B).rs133(severe IOP rise),rs11047639 and rs1879370(male gender),and rs11171569(immediate IOP rise)significantly(P<0.05)influenced the phenotype correlation only among TAOHT patients.However,the significance of these SNPs in group B and phenotype analysis(group C)was lost upon Bonferroni corrections(P<0.0025).CONCLUSION:Prevalence of OHT in study population is observed to be similar to other studies both in TA and Dex treated patients.We can correlate rs34016742 involved in diabetes signaling pathway to the occurrence of ocular edematous and inflammatory conditions.Except rs133 that is involved in neuro-degeneration and myopia occurrence,none of the other SNPs identified in Caucasian population possess any correlation with OHT incidence in TA and Dex administered Indian subjects.
基金Eskisehir Osmangazi University Scientific Research Projects Commission,Eskisehir,Turkey(No.2016-1234)。
文摘AIM:To investigate relationship between refractive errors and eleven single nucleotide polymorphisms(SNPs)in HGF,GC,MFN1,GNB4,and VDR genes in Turkish population.METHODS:A group of 212 participants with myopia(n=91),hyperopia(n=45),and emmetropia(n=76)were investigated in this study.SNPs in HGF,GC,MFN1,GNB4 and VDR genes were studied by Snap Shot technique.RESULTS:The patients in this study consists of 47 female/44 male(age:23.47±4.30)patients with myopia,20 female/25 male(age:31.20±8.02)with hyperopia and 33 female/43 male(age:25.22±6.60)with emmetropia.The genotype distribution of the rs7618348 polymorphism,which was the only statistically significant one between myopia and emmetropia group.The genotype distribution of the rs3819545,rs3735520,rs7041,and rs2239182 polymorphisms,which were statistically significant between hyperopia and emmetropia groups.CONCLUSION:The importance of genetic predisposition to refractive errors with respect to etiology of the disease is revealed.It is known that polymorphism studies may differ because of genetic diversity among populations so larger cohort studies are required in different populations to enlighten the etiology of the refractive errors.
文摘Residual ridge resorption(RRR)is the decrease in the jaw structure that follows tooth extraction.It is a multifactorial disorder,but reports on the associated genetic factors are scarce,particularly amongst the Saudis.This study aimed to investigate the role of single nucleotide polymorphisms(SNPs)in fibroblast growth factor receptor 1 oncogene partner 2(FGFR1OP2)in RRR development in Saudis.The study included 192 individuals(RRR=96;controls=96)attending outpatient clinics at the College of Dentistry,King Saud University.Demographic and clinical data were collected,the digital panoramic dental radiograph was obtained,and mandibular residual ridge height was measured.DNA was extracted from saliva and genotyping was conducted on“Sequenom MassARRAY iPLEX”.Genotype and allele frequencies of three SNPs were calculated and compared.The age at first diagnosis and bone height were compared in the three genotypes of each SNP.The age of the patients,age at first edentulism,and bone height ranged 21-80 years,12-70 years,and 13-34.6 mm,respectively.All three genotypes of the studied SNPs(rs2279351,rs78054962 and rs2306852)were identified.SNP rs2279351 associated significantly with RRR,and the mutant C allele was highly predisposing.No association was observed for the other two SNPs.The genotypes of all SNPs had an influence on age at first edentulism and bone height,but the results were not statistically different.Since FGFR1OP2 plays a role in the process of rapid wound healing in the oral cavity,it may be playing a role in the development of RRR by influencing the rate of resorption of the jawbone.SNP rs2279351 may alter its expression and hence RRR development.This study is limited due to small a sample size,and further large-scale studies are required to confirm this association and to consider rs2279351 as a possible marker of RRR development.
基金This study was financially supported by the National Natural Science Foundation of China(41301346)the Natural Science Foundation of Fujian Province(2020J01375)the Natural Science Foundation of Fujian Province(2015N0034).
文摘Bamboos are one of the most beautiful and useful plants on Earth.The genetic background and population structure of bamboos are well known,which helps accelerate the process of artificial domestication of bamboo.Partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species were analyzed for occurrence of single nucleotide polymorphisms(SNPs).The nucleotide diversityθw and total nucleotide polymorphismsπT of the sequenced DNA regions was 0.05137 and 0.03332,respectively.Bothπnonsyn/πsyn and Ka/Ks values were<1.The nucleotide sequences of these six genes were inferred to be relatively conserved,and the haplotype diversity was relatively high.The results of evolutionary neutrality tests showed that the six genes were in line with neutral evolution,and that the NRT2.1 and AMT2.1 gene sequences may have experienced negative selection.An inter-SNP recombination event at the NRT2.1 gene in the all pooled sample,of all 32 bamboo species was the lowest at 0.0645,whereas the AMT gene recombination events were all>0.1.Estimation and analysis of linkage disequilibrium of five genes revealed that with the increase in nucleotide sequence length,the degree of SNP linkage disequilibrium decreased rapidly.We inferred the population genetic structure of 32 bamboo species based on the SNP loci of six genes with frequencies>18%.32 bamboo species were divided into five categories,which indicated that the combined population of all bamboo species had obvious multivariate characteristics and was heterogeneous;red(Group 1)and green(Group 2)were the main groups.
文摘Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.
基金National College Student Innovation and Entrepreneurship Training Project(Project No.:202011810001).
文摘Vitamin D is a fat-soluble vitamin.It is an essential vitamin for human body.It has a classical effect on regulating calcium and phosphorus metabolism.Participate in cellular and humoral immune processes by regulating the growth,differentiation and metabolism of immune cells.A large number of studies in recent years have shown that vitamin D deficiency increases the incidence of respiratory diseases.Respiratory diseases mainly include bronchial asthma,chronic obstructive pulmonary disease,tuberculosis,acute upper respiratory tract infection and pneumonia.Vitamin D metabolic pathway genes play a very important regulatory role in the transformation of vitamin D into active vitamin D,including CYP2R1,CYP27B1,CYP24A1,VDBP,VDR five genes.Genetic polymorphism of genes is the molecular basis of individual differences and disease development.Therefore,this paper summarizes the research on single nucleotide polymorphism of vitamin D metabolic pathway gene and respiratory diseases.In order to provide a new idea for future treatment.
文摘Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. The status of the CCR5Δ32 gene has not been reported in Nigeria. Aim: This study was aimed at analyzing single nucleotide polymorphism of CCR5 gene among the Ijaws resident in Yenagoa, Nigeria. Methods: 100 subjects (75 HIV negative and 25 HIV positive control) were recruited for this study. The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. Results: The results showed that 75 (100%) of the HIV negative subjects had 189 base pair in their CCR5 gene. Nucleotide of the 20 (100%) of the sequenced samples were conservatively same and no SNP was observed. Conclusion: This study documented no SNPs in CCR5 gene of the study population hence;the study population has no protection from HIV infection.
文摘Inflammation plays a significant role in the etiology of type 2 diabetes mellitus(T2DM).The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury,oxidative stress and beta cell apoptosis in T2 DM.Among the recognized markers are interleukin(IL)-6,IL-1,IL-10,IL-18,tissue necrosis factor-alpha(TNF-α),C-reactive protein,resistin,adiponectin,tissue plasminogen activator,fibrinogen and heptoglobins.Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance.Many single nucleotide polymorphisms(SNPs) in various genes including those of pro and antiinflammatory cytokines have been reported as a risk for T2 DM.Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups.The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene,gene-environment and gene-nutrient interactions.This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6,TNF-α,resistin and adiponectin in pathogenesis of T2 DM.
文摘AIM: To investigate the relationship between low molecular polypeptide-7 (LMP-7) gene polymorphism and response to interferon (IFN) therapy in chronic hepatitis C virus (HCV) patients. METHODS: LMP-7 polymorphism at codon 49 with nucleotide substitution from A to C was amplified in 104 chronic HCV patients of genotype 4. The amplicons were digested with restriction endonuclease Bsm I and the produced restriction fragment length polymorphism was analyzed. Patients received IFN + regional blood volume therapy for 48 wk and the frequency of thissingle nucleotide polymorphism (SNP) was statistically correlated with treatment response. The exclusion criteria for these patients were stated by the national health program for treating viral hepatitis. Main exclusion criteria included co-infection with hepatitis B virus or schistosomiasis, thyroid dysfunction, uncontrolled diabetes mellitus, history of long term drug or alcohol intake and autoimmune hepatitis. Multivariate analyses were done to correlate LMP-7 SNP plus several factors such as age, gender, weight, serum alpha-fetoprotein (AFP) and alanine aminotransferase levels, liver activity, fibrosis score and viral load with response to therapy. RESULTS: The data presented in this study clearly demonstrated statistically significant differences between sustained virological response (SVR) (defined as the absence of HCV RNA levels in the patient's sera at least 6 mo after discontinuation of treatment) and non-response (NR) (where HCV RNA levels in the patient's sera never become undetectable for 6 mo during or after treatment). Variables were described as odds ratio with 95%CI. The data were considered significant if P values were ≤ 0.05; highly significant if P < 0.01 and very highly significant if P < 0.001. Current data showed that 91.7% of patients carrying LMP-7 C/C allele were associated with SVR, while the other two genotypes C/A and A/A were associated with NR patients, 83.3% and 64.3% respectively, showing that genotype CC was strongly associated with response to interferon (95%CI: 12.0719-134.6572, P = 0.0001). The majority of parameters recorded in SVR and NR patients included higher values of mean age (P = 0.004), alanine aminotransferase (P = 0.001), AFP (P = 0.001), body weight (P = 0.025), viral load (P = 0.025), higher fibrosis and histological activity index indices among NR vs SVR patients. Also, the multivariate statistical analysis of the different factors of fibro-sis score, liver activity grade, genotypes and alleles of LMP-7 gene polymorphism in responders and NRs of HCV patients in this study showed that HCV patients with A allele had a very highly significant association with the NRs, high fibrosis and higher liver activity, while the C allele had a very highly significant association with the responders, low fibrosis and lower liver activity (95%CI: 3.5800-13.2519, P = 0.0001).CONCLUSION: LMP-7 SNP is a candidate gene that should be considered when designing a mathematical model for predicting response to therapy and disease progression in HCV patients.
文摘Objective:To discuss the association between single nucleotide polymorphism(SNP) of rs3811047 in IL-1 F7 gene and rheumatoid arthritis(RA) susceptibility among the Han population in central plains of China.Methods:A total of 276 RA patients admitted to our hospital from December 2009 to December 2011 together with 276 healthy physical examinees in the same period were chosen as the subjects.The typing for rs3811047 SNP in IL-1 F7 gene was carried out by using ligase detection reaction and polymerase chain reaction technique.And the frequency of each allele and genotypes distribution was calculated so as to evaluate the association between genotype distribution and RA susceptibility.Results:The frequency of A allele of rs3811047 in IL-1 F7 gene in RA group and control group was 16.27%and 17.68%,respectively,and that of G allele in two groups was 83.73%and 82.32%,respectively.The difference between two groups wasn’t statistical significant(P 】0.05).The frequency of genotype AA,AG and GG in RA group was 2.19%,27.84%and 69.97%,respectively,while that in control group was 2.94%,29.78%and 67.28%, respectively.The difference of distribution of three genotypes was not statistically significant (P 】0.05).RA patients with A allele were better than those without A allele in joint swelling index, rest pain,HAQ scoring and blood sedimentation.There was significant difference between two groups in above indexes(P【0.05/P【0.01).Conclusions:No significant correlation between RA susceptibility among the Han population in central plains of China and rs3811047 SNP inIL-1 F7 gene is observed.However,A allele of rs3811047 has certain influence on the condition of RA patients.
基金Acknowledgment This work was supported by the National High Tech- nology Research and Development Program of China （Grants 2004AA216090 and 2002BA711A08）, National Basic Research Program of China （Grant 2004Cb518805）, the Natural National Science Foundation of China （Grant 30470960） and the China Medical Board of New York.
文摘瞄准：分析单个核苷酸多型性(SNP ) 的分发在 methylenetetrahydrofolate reductase (MTHFR ) 的 C677T 在有自发的精子缺乏或严重 oligozoospermia 和是的 252 个肥沃的中国人的 355 个不肥沃的中国病人的基因控制探索 SNP 和男不孕的可能的协会。方法：用聚合酶链反应(PCR ) ，限制碎片长度多型性技术，等位基因和在 MTHFR 基因的 SNP C677T 的遗传型分发在病人和 controls.Results 被调查：等位基因 T 的频率(40.9% 对 30.4% ， P = 0.002，机会定量[或]= 1.58， 95%confidence 间隔[CI ] ：1.24-2.02 ) 并且变异的同质接合体(TT )(18.3% 对 11.5% ， P = 0.023，或 =1.72， 95% CI：1.07-2.76 ) 象有等位基因(TT + CT ) 的搬运人一样(63.4% 对 49.2% ， P = 0.0005，或 =1.79， 95% CI：1.29-2.48 ) 在不肥沃的病人比在控制的那些显著地高。在耐心的层化以后，在在每耐心的亚群和控制组之间的 SNP 的分发的重要差别尚待。结论：我们的调查结果显示有在有男不孕的 MTHFR 基因的 SNP C677T 的一个协会，建议这多型性可能是为在中国人的男不孕的一个基因风险因素。
基金financially supported by the Fundamental Research Funds for the Central Non-profit Research Institution of CAF(RIF2014-06)the Forestry Industry Research special funds for Public Welfare Projects(201504104)
文摘Nucleotide diversity(π) and linkage disequilibrium(LD) analysis based on SNP marker could provide a sound basis for choosing an association analysis method.Japanese larch(Larix kaempferi) is an important timber coniferous tree species for pulping and papermaking,but its high lignin content has significantly restricted it application potential.In this study,the LACCASE gene,that plays an important regulatory role for lignin biosynthesis,was selected as research target.The full-length c DNA and genomic sequences of the encoding Lk LAC8 gene were isolated from the LACCASE expressed sequence tags of the Japanese larch transcriptome database using the rapid amplification of c DNA ends-polymerase chain reaction(RACE-PCR).The c DNA was determined to be 1940 bp,with an open reading frame(ORF,1734 bp) that encoded a protein of 577 AA.This protein contains four highly specific Cu^(2+) binding sites and 11 glycosylation sites,thus belonging to the LACCASE family.The deduced protein sequence shared an 89% identity with the Pta LAC from Pinus taeda.A real-time PCR analysis showed that the Lk LAC8 transcript was expressed predominantly in mature xylem,with moderate levels in the immature xylem,cambium and mature leaves,the lowest in the roots.Lastly,the genomic sequences of Lk LAC8 in 40 individuals from six naturally distributed populations of Japanese larch were amplified,and a total of 201 SNPs(103 and 98 mutation types of transition and transversion,respectively) were detected;the frequency of the SNPs was 1/19 bp.Nucleotide diversity among the six populations ranged from 0.0034 to 0.0053,which suggested that there were no significant differences among the populations.The LD analysis showed that the LD level decayed rapidly within the increasing length of the Lk LAC8 gene.These results implied that LD mapping and association analysis based on candidate gene may be feasible for the marker-assisted breeding of new germplasms with low lignin in Japanese larch.
基金Supported by the National Natural Science Foundation of China,No.30371591the Natural Science Foundation of Hebei Province,No.C20040062
文摘AIM: To investigate the association between single nucleotide polymorphism (SNP)in promoter of the DNA methyltransferase 3B (DNNT3B) gene and risk for development and lymphatic metastasis of gastric cardiac adenocarcinoma (GCA).METHODS: The hospital based case-control study included 212 GCA patients and 294 control subjects without overt cancer. The DNMT3B SNP was genotyped by PCR and restriction fragment length polymorphism (RFLP) analysis. RESULTS: The C/C genotype was not detected in both GCA patients and controls. In control subjects, the frequency of T/T and C/T genotypes was 94.9% and 5.1% respectively,and that of T and C alleles was 97.4% and 2.6%, respectively.The genotype and allelotype distribution in the GCA patients was not significantly different from that in controls (P = 0.34 and 0.33, respectively). When stratified by smoking status and family history of upper gastrointestinal cancer, significant difference in the genotype distribution was not observed between GCA patients and controls. The distribution of DNMT3Bgenotypes in GCA patients with or without lymphatic metastasis did not show significant difference (P = 0.42). CONCLUSION: The distribution of DNMT3BSNP in North China is distinct from that in Caucasians. Although this SNP has been associated with susceptibility to lung, head, neck and breast cancer, it may not be used as a stratification marker to predict susceptibility and lymphatic metastasis of GCA, at least in the population of North China.
基金supported by the Capital Development Fund Project (Grant No. 2002-1017).
文摘Objective To identify the genetic defects of the the adiponectin (APM1) gene that contribute to the development of type 2 diabetes (T2DM) and determine the functional single nucleotide polymorphisms (SNPs) in the APM1 gene associated with T2DM in Han nationality. Methods The APM1 gene 5’-UTR was screened by direct sequencing to identify common polymorphisms. Identified SNPs were genotyped in 585 nondiabetic controls, 278 subjects with impaired glucose intolerance (IGT) and 212 patients with T2DM. The functions of SNPs in the regulatory region were assessed by reporter gene assay. Possible association between SNPs and plasma APM1 levels or metabolic parameters was statistically assessed. Results Three SNPs were identified in the APM1 gene 5’-UTR. A case-control study revealed that SNP -11377 G/C had significant differences in allele frequencies between T2DM patients and nondiabetic controls (G 0.314/C 0.686 vs. G 0.265/C 0.735, P=0.03). Haplotype analysis of three SNPs in the APM1 gene showed that no significant association of haplotypes with T2DM. IGT was detected in the present study. Reporter gene assay showed that SNP did not influence the transcription efficiency in the 3T3-L1 cell line. Conclusion SNP -11377 G/C in the proximal promoter region of the APM1 gene contributes to the development of T2DM in Han nationality but may not be a functional SNP in the APM1 gene.
基金Supported by the National Basic Research Program of China(973Program)(No.2010CB126304)the Special Fund for Agro-scientific Research in the Public Interest(No.200903046)the Project from the Ministry of Science and Technology of China(No.2006DKA30470017)
文摘The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.
基金supported by the National 863 Program of China (2013 AA102505)the National Natural Science Foundation of China (31272411 and 31402044)+2 种基金the National Beef and Yak Industrial Technology System,China (CARS-38)the China Postdoctoral Science Foundation (2016M590976)the Key Technologies R&D Program of Henan Province,China (122102110062)
文摘Silent information regulator 2(Sir2) proteins, or sirtuins, are nicotine adenine dinucleotide(NAD)-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Sir2 homologs, namely, silent information regulators(SIRT1–7). SIRT4 and SIRT7 genes play a crucial role in regulating lipid metabolism, cellular growth and metabolism. This suggests that they are potential candidate genes for affecting body size and meat quality traits in animals. Hence, this study aimed to detect genetic variations of both SIRT4 and SIRT7 bovine genes in Qinchuan cattle, and to evaluate the effect of these variations on economically important body size and meat quality traits. Expression analysis using quantitative real-time PCR(q PCR) indicated that SIRT4 and SIRT7 were broadly expressed in all thirteen studied tissues. The expression of SIRT4 was higher in liver, muscle, and in subcutaneous fat tissue. In the case of SIRT7, the expression was higher in lung, abomasum, and subcutaneous fat. Using DNA sequencing, a total of three single nucleotide polymorphisms(SNPs) were identified within SIRT4 and SIRT7 genes in 468 Qinchuan cattle. These included one novel SNP within 3′ untranslated regions(UTR) of SIRT4(SNP1: g.13915A>G) and two novel synonymous substitutions in SIRT7(SNP2: g.3587C>T and SNP3: g.3793T>C). Statistical analyses indicated that all three SNPs could significantly influence some body size and meat quality traits in Qinchuan cattle. These novel findings will provide a background for application of bovine SIRT4 and SIRT7 genes in the selection program of Chinese cattle.
文摘In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide association study.In Japanese populations,the correlation between 2 SNPs on 17q and the risk of prostate cancer and tumor aggressiveness was also confirmed by a large-scale experiment.However,whether 17q is associated with prostate cancer and its clinical manifestations in Chinese populations is still unknown.Therefore,we conducted a case-control study in a northern Chinese population and tested 2 SNPs,rs4430796 and rs1859962,on 17q in 124 prostate cancer patients and 111 controls using polymerase chain reaction-high resolution melting curve(PCR-HRM) combined with sequencing.We analyzed the association of the 2 SNPs with the risk of prostate cancer as well as patients' lifestyles,onset ages,Gleason scores,PSA levels,and pathologic stages.We found a significant difference in the G allele of SNP rs1859962(P = 0.035,OR = 1.51,95% CI = 1.03-2.21) but not in the rs4430796 genotype frequency or allele frequency distribution between prostate cancer patients and the controls(P > 0.05).Neither of the SNPs was significantly associated with the onset age,Gleason score,PSA level,pathologic stage,or other clinical indicators of patients with prostate cancer(P > 0.05).Our results show that polymorphism of the G allele of SNP rs1859962 is associated with the risk of prostate cancer in a Chinese population.
