PCR-RFLP和MLPA两种技术方法对脊髓性肌萎缩症的诊断

目的应用PCR-RFLP和多重连接依赖式探针扩增法(MLPA)技术对临床诊断为脊髓性肌萎缩症(SMA)患儿进行基因诊断,并比较两种方法检测SMN基因缺失改变的效果。方法应用DNA抽提试剂盒抽提3个SMA家系成员的外周血样品DNA,电泳检测,定量,常规PCR法扩增SMN基因的7、8号外显子,Dra I、Dde I酶切PCR产物,常规聚丙烯胺凝胶电泳法分离酶切后PCR产物,Genefinder染色检测。同时应用M LPA检测试剂盒P021进行检测。结果 PCR-RFLP显示3个家系中的患儿均纯合缺失SMN1的第7、8号外显子,MLPA检测结果与之完全相符。结论与PCR-RFLP相比,MLPA更加简便、快捷、可靠,是一种高效的遗传病基因诊断手段。     

广州管圆线虫GAMMA—BBH基因的克隆表达鉴定和荧光定量检测

目的亚克隆和表达广州管圆线虫γ-丁基甜菜碱羟化酶（γ-butyrobetaine hydroxylase，GAMMA-BBH）基因．对该蛋白属性进行鉴定，定量检测不同虫龄该目的基因表达量。方法PCR扩增GAMMA—BBH cDNA基因．产物经Nco Ⅰ和HindⅢ限制性内切酶酶切后连接至原核表达载体重组为pET—BBH，在B121（DE3）中用IPTG诱导表达．SDS—PAGE、Westernblot和酶活性测定鉴定表达产物，用荧光定量PCR方法检测广州管圆线虫不同虫龄GAMMA—BBH的表达量。结果PCR和核苷酸序列测定结果表明pET—BBH构建正确并能在IPTG诱导下表达，SDS—PAGE和Western blot鉴定表明表达产物分子量与预期分子量（Mr=48500）一致，酶学测定显示表达产物有GAMMA—BBH的酶活性，荧光定量PCR方法检测结果显示GAMMA—BBH在虫体不同虫龄期表达量不一致。结论目的基因能正确编码并表达具有酶活性的GAMMA—BBH，该酶的表达量与虫龄和寄生部位可能有关。     

载脂蛋白E基因PCR-RFLP分析方法的建立

目的为研究新疆地区老龄人群载脂蛋白E(ApoE)基因多态性与阿尔茨海默病发病之间的关系而建立一种快速、简便、敏感的对ApoE基因进行多态性分析的方法.方法从抗凝血中提取人全基因组DNA,聚合酶链式反应(PCR)高效扩增ApoE基因,酶切后进行8%非变性聚丙烯酰胺凝胶电泳,凝胶银染色后进行ApoE基因型分析.结果限制性内切酶酶切图谱证实可特异性对ApoE基因进行分型,PCR-RFLP方法在ApoE基因型检测中得到成功建立.     

人蛋氨酸合成酶还原酶A66G基因突变频率的检测

目的 建立一种简便、准确、实用的人蛋氨酸合成酶还原酶(MSR)A66G基因突变频率的检测方法,并了解汉族人MSR基因的分布特点。方法 应用聚合酶链反应(PCR)特异性扩增蛋氨酸合成酶还原酶(MSR)A66G基因序列,扩增产物用限制性内切酶NdeI酶切,聚丙烯酰胺凝胶电泳后,观察酶切位点的限制性片段长度多态性(RFLP)图谱。结果 运用PCR-RFLP法检测了150名汉族人蛋氨酸合成酶还原酶(MSR)A66G基因点突变,其中野生型纯合子频率为25.33％,杂合子频率为52.00％,突变型纯合子频率为22.67％。突变等位基因频率为0.4867。结论 该方法简便、快速、准确,适合于一般实验室检测及大规模的人群调查,汉族人MSR基因的分布与其他地区人群的分布无明显差异。     

采用通用引物PCR配合SSCP及RFLP技术快速检测常见病原菌

目的 建立一种快速检测病原菌的方法以利于临床诊断。方法 选取10种具有代表性的病原菌，采用通用引物PCR（UPPCR）对其16SrRNA基因进行扩增，并对PCR产物进行限制性酶切片段长度多态性分析（RFLP）和单链构象多态性分析（SSCP）。结果 RFLP电泳图谱呈现多态性，但半数菌的图谱两两相同或相似；SSCP电泳图谱各异，可以相互区分。结论 UPPCR-SSCP技术能快速简便地检测病原菌。     

汉族人维生素D受体基因TruⅠ酶切位点多态性及其对BsmⅠ酶切位点多态性测定的影响

目的测定汉族人维生素D受体基因TruⅠ酶切位点多态性分布并探讨其对BsmⅠ酶切位点多态性分布测定的影响。方法收集80名健康汉族人外周静脉血标本,提取基因组DNA,用限制性片段多态性长度酶切法测定80名汉族人维生素D受体基因TruⅠ、BsmⅠ酶切位点多态性;换用常规引物再次测定上述标本BsmⅠ酶切位点多态性;分析维生素D受体基因TruⅠ、BsmⅠ酶切位点多态性及两次测定的BsmⅠ位点的一致性。结果测得TruⅠ基因型频率为TT68.7%,Tt26.3%,tt5.0%;同一PCR片段上测得BsmⅠ位点基因型频率为BB6.2%,Bb52.5%,bb41.3%,多态性分布均符合Hardy-Weinberg平衡;换用常规引物测定同批标本BsmⅠ位点多态性,基因型分布为BB20.0%,Bb26.2%,bb53.8%,不符合Hardy-Weinberg平衡（r=13.29,P〈0.01）。与第1次测定相比,有22个标本基因型由Bb型变成BB型或bb型,发生基因型丢失。结论汉族人VDR基因存在TruⅠ多态性,其多态性分布与其它种族不同;TruⅠ酶切位点多态性可引起BsmⅠ位点多态性测定时等位基因的丢失。     

TaqMan探针实时PCR检测人MTHFR基因C677T多态性方法的建立

目的建立TaqMan探针实时PCR检测人MTHFR基因C677T多态性的方法。方法设计一对MTHFR基因C677T多态位点的引物及TaqMan探针,采用TaqMan探针实时PCR扩增SNP分型方法检测唇腭裂患者及其父母共100人的MTHFR基因C677T多态性,与常规PCR-RFLP方法进行一致率比较,并对其特异性、敏感性和重复性以及成本-效益等进行评价,同时对部分实时PCR产物样本进行测序验证。结果运用TaqMan探针实时荧光PCR技术对MTHFR基因C677T多态性检测结果准确,特异性好,与常规PCR-RFLP方法结果具有高度一致性,Kappa=0.922>0.75(P=0.000);检测灵敏度可达2×103拷贝;重复性好、高通量、无污染、安全性好;随机样品TaqMan探针分型结果与测序结果完全一致。结论成功建立了TaqMan探针实时PCR检测人MTHFR基因C677T多态性的方法;此方法是常规临床诊断及大规模群体研究的良好平台。     

异基因骨髓移植中PCR-SSP和RFLP对HLA-DRB、DPB1分型的应用

目的:探讨序列特异性引物聚合酶链反应（PCR-SSP）和聚合酶链反应限制性片段长度多态性分析（PCR-RFLP）对HLA-DRB、DPB1分型在异基因骨髓移植中应用的可行性。方法:应用19对不同的DRB抗原所对应等位基因序列特异性的引物,PCR扩增供受者各20个样本DRB,产物直接琼脂糖凝胶电泳分析;同时用另一对引物PCR扩增DPB1第二外显子,产物10种限制性内切酶酶切分析。结果:各DRB带清晰可辨,直接确定为该型;DPB1的多态性片段编码转换后确定其基因型;4例找到供者。结论:它们是异基因骨髓植前快速、精确和可靠的基因分型手段。     

嗜人按蚊rDNA—ITS2基因的克隆鉴定及SNP分析

目的克隆和分析嗜人按蚊核糖体DNA（rDNA）第2内转录间隔区（ITS2）序列，研究嗜人按蚊rDNA-ITS2序列的种属特异性及不同个体rDNA-ITS2序列的单核苷酸多态性（Single Nuclear Polymorphism，SNP）。方法用DNA提取试剂盒从嗜人按蚊中提取DNA摸板，利用蚊虫5．8s和28S序列的保守性设计特异引物进行聚合酶链反应以扩增嗜人按蚊rDNA-ITS2基因，扩增产物经回收纯化后连接到TA载体，经amp^＋LB固体平板筛选的阳性克隆。经amp^＋LB液体培养基培养后进行PCR鉴定、EcoRI酶切鉴定和序列分析。结果经PCR反应扩增出全长556bp的嗜人按蚊rDNA-ITS2基因。纯化后重组克隆经PCB鉴定可重现556bp的特异性条带，其酶切产物亦与目的基因PCR产物位置相同。嗜人按蚊6个克隆的同一性为99．6％，其rDNA-ITS2基因单核苷酸存在颠换和插入，在556的范围内有一个A→T，一个G→T的颠换；一个T的插入。结论嗜人按蚊rDNA-ITS2序列在种间高度保守，但不同个体间也存在一定的SNP多态性。     

内皮素—1基因内含子4Taq I片段多态性的研究

根据EDN1第4内含子设计相应引物,建立检测EDN1第4内含子TaqI多态性PCR＋RFLP技术。利用该技术,扩增到具有特异性的PCR产物,长为358bp。经限制性核酸内切酶TaqI酶酶切检测中国汉族人群该片段多态性状况。实验显示中国汉人群中存在该位点的多态性。基因T1的频率为0．664;T2基因型频率为0．336;T1T1基因型频率为0．418;T1T2基因型频率为0．492;T2T2基因型频率为0．090。该位点可作为遗传标记探讨中国人群中与EDN1相关遗传病的关系。     

Association of vitamin D receptor genotypes with early onset rheumatoid arthritis.

The presence of certain vitamin D receptor (VDR) genotypes has been associated with low bone mineral density (BMD) in elderly populations as well as with accelerated bone loss in patients with rheumatoid arthritis (RA). In the present study, VDR genotypes from 120 Spanish patients with RA were investigated. Three VDR gene polymorphisms (BsmI, ApaI and TaqI) were investigated using polymerase chain reaction followed by enzymatic digestion. The distributions of VDR allelic frequencies were similar in patients and controls and therefore no influence of VDR polymorphisms on rheumatoid arthritis susceptibility could be demonstrated. However, in an analysis of the clinical features of the different VDR-related genetic subgroups, the BB/tt genotype, defined by the BsmI and TaqI restriction site polymorphisms, was identified to be weakly associated with an early onset RA in female patients. This VDR genotype has been associated with a low BMD level in various studies. When patients were stratified according to the presence of the shared HLA epitope SE, it was found that SE + female patients bearing the BB/tt genotype showed the earliest disease onset. The mechanisms by which the VDR polymorphism is associated with RA is unknown, but they could be related to the immunoregulatory properties of vitamin D.     

Detection of Mycoplasma species in cell culture by PCR and RFLP based method: effect of BM-cyclin to cure infections

PURPOSE: A two-stage nested polymerase chain reaction (PCR) assay system was described that amplifies the 16S-23S rRNA spacer region sequences of Mycoplasma and Acholeplasma infections in cell cultures and virus stocks. METHODS: Established cell lines and virus stocks were screened for the presence of Mycoplasma by using nested PCR using two sets of outer and inner primers, amplifies 16S-23S rRNA. PCR and restriction fragment length polymorphism (RFLP) assay was used to detect and identify most of the species-specific Mycoplasmas involved in cell cultures and virus stock contaminants. Infected cultures detected by PCR-RFLP were further treated with BM-cyclin (5 microg/mL) and passaged for three times and tested for Mycoplasma infections by PCR-RFLP. RESULTS: Mycoplasma pirum and Mycoplasma orale infections were detected by nested PCR. Species specificity was identified by using RFLP of Vsp I, Cla I and Hin dIII restriction enzymes. Mycoplasma infections were cured by treatment with BM-cyclin. This was further confirmed by non-amplification of PCR amplimers in BM-cyclin treated vs. non-treated cultures. CONCLUSIONS: Regular monitoring of cell cultures for Mycoplasma infections and identification of species-specific Mollicutes will identify the source of contaminations. This approach can be used for quality control of the biological reagents used in cell culture and virology laboratories.     

Vitamin D receptor gene polymorphism and its association with Parkinson's disease in Chinese Han population

Vitamin D plays an important role in neurodegenerative disorders as a crucial neuro-immunomodulator, and accumulating data have provided evidence for that vitamin D receptor (VDR) gene is a candidate gene for susceptibility to Parkinson's disease (PD). In this study, we performed a case-control study to demonstrate whether the risk for the development of onset of sporadic PD might be influenced by VDR gene polymorphisms in a Chinese cohort. Two hundred and sixty PD patients and 282 matched-healthy controls were genotyped for two representative single nucleotide polymorphisms (SNPs) in VDR gene (FokI C/T and BsmI G/A) by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis in. Results from our study revealed that FokI C allele carriers were likely to associate with an increased risk of PD (P = 0.004) as well as early-onset PD (EOPD) (P = 0.010). Moreover, the frequency of FokI C allele was significantly increased in PD group and late-onset PD (LOPD) group relative to the control groups respectively (P = 0.023 and P = 0.033, respectively). For BsmI polymorphisms, no significant difference in genotype or allele distribution was found between PD patients and the controls, as well as gender- and age-related differences between PD patients and the controls subgroup. This study demonstrated a possible association between the VDR FokI T/C polymorphism and PD, indicating that VDR polymorphisms may well change genetic susceptibility to sporadic PD in a Han Chinese population.     

Lack of association between body weight, bone mineral density and vitamin D receptor gene polymorphism in normal and osteoporotic women

In an ethnically homogeneous population of women living in Tuscany, Italy, the relationships between age, body weight, bone mineral density and the vitamin D receptor (VDR) gene polymorphism were studied, with the objective of recognizing patients at risk for osteoporosis. In 275 women bone mineral density was measured by Dual Energy X-rays Absorptiometry (DEXA). In 50 of them the individual genetic pattern for VDR was evaluated by DNA extraction followed by PCR amplification of the VDR gene, and digestion with the restriction enzyme BsmI. Age and bone mineral density were inversely related (R2 = 0.298). Body weight was associated with bone mineral density (R2 = 0.059), but not with age. In osteoporotic women, mean (+/- SD) body weight was 59.9 +/- 6.5 Kg, lower than that recorded in non osteoporotic women (64.2 +/- 9.4 Kg), even though not significantly different (p = 0.18). No association was found between VDR gene polymorphism, bone density or body weight. The performance of anthropometric and genetic components appear to be poor, and, at least for the time being, bone mineral density measurement by means of MOC-DEXA represents the optimal method to detect women at risk for postmenopausal osteoporosis.     

Lack of association of vitamin D receptor gene polymorphisms with susceptibility to type 1 diabetes mellitus in the Portuguese population

The vitamin D receptor (VDR) gene is a candidate gene for susceptibility to autoimmune disorders. Association studies of VDR polymorphisms and risk of type 1 diabetes often produced conflicting results in different ethnic backgrounds. The aim of this study was to test for association between common VDR polymorphisms and the genetic susceptibility to type 1 diabetes in the Portuguese population. We genotyped 207 patients with type 1 diabetes and 249 controls for the FokI T>C (rs10735810), BsmI A>G (rs1544410), ApaI G>T (rs7975232), and TaqI C>T (rs731236) single nucleotide polymorphisms by polymerase chain reaction and restriction fragment length polymorphism analysis. The distribution of VDR genotype, allele, and haplotype frequencies did not differ significantly between patients and controls. These data suggest that the single nucleotide polymorphisms of the VDR gene are unlikely to contribute significantly to type 1 diabetes susceptibility in the Portuguese population.     

Raloxifene administration in post-menopausal women with osteoporosis: effect of different BsmI vitamin D receptor genotypes

BACKGROUND: The vitamin D receptor (VDR) gene polymorphism has been considered a factor influencing the effectiveness of the anti-osteoporotic treatments. The aim of this study was to correlate the effectiveness of raloxifene treatment in post-menopausal women with osteoporosis to BsmI VDR genotypes. METHODS: Between January and August 2000, 75 Italian osteoporotic women were enrolled and treated with raloxifene at a dose of 60 mg/day. At entry and after 1 year of treatment, lumbar bone mineral density (BMD), serum osteocalcin (OC) and urinary creatinine-corrected free deoxypyridinoline (DPD) levels were evaluated. DNA was extracted from blood and analysed with restriction endonuclease BsmI for VDR gene. RESULTS: After treatment, a significant increase in lumbar BMD and a significant reduction in serum OC and urinary DPD levels were observed. The percentage of change (mean +/- SD) in lumbar BMD, and in serum OC and urinary DPD levels was significantly different in homozygous bb (1.58 +/- 0.80, -5.15 +/- 2.36 and -7.71 +/- 2.89 for BMD, OC and DPD respectively) in comparison with BB (4.13 +/- 2.26, -13.59 +/- 4.68 and -15.16 +/- 4.65 for BMD, OC and DPD respectively) BsmI VDR genotypes. Heterozygous Bb VDR patients showed an intermediate percentage (mean +/- SD) of BMD, serum OC and urinary DPD change (2.49 +/- 1.54, -8.69 +/- 2.60 and -10.52 +/- 2.56 for BMD, OC and DPD respectively) not significantly different in comparison with homozygous BB and bb. CONCLUSIONS: In post-menopausal women with osteoporosis the effectiveness of raloxifene treatment on bone metabolism seems to be controlled by different BsmI VDR genotypes.     

DETERMINATION OF DRB ALLELES USING PCR AMPLIFICATION AND ALLELE-SPECIFIC PRIMERS

HLA class-II allelic diversity is commonly defined using polymerase chain reaction (PCR) in combination with sequence-specific oligotyping (PCR-SSO) or the combination of PCR and restriction fragment length polymorphism methods (PCR-RFLP). Nevertheless, the identification of the DRB polymorphism by PCR-SSO is a time-consuming procedure and the PCR-RFLP is cumbersome. A rapid technique which allows a precise and extensive HLA-DRB typing is required, particularly in order to study the role of class-II matching in organ transplantation. A DRB typing method based on the detection and length of PCR products amplified using combination of allele specific primers has been developed. Thirty-four DRB alleles (29 DRB1, 4DRB3, 1DRB4) can be detected using 29 primers distributed into 19 amplification mixtures.     

Association of estrogen and vitamin D receptor gene polymorphisms with tooth loss and oral bone loss in Japanese postmenopausal women

OBJECTIVE: To investigate the relationship between estrogen receptor (ER) and vitamin D receptor (VDR) gene polymorphisms and tooth loss, oral bone loss, and postcranial bone mineral density (BMD) in Japanese postmenopausal women. DESIGN: Polymorphisms at the ER PvuII and XbaI and VDR BsmI gene sites, number of teeth remaining, oral bone mass, and BMD of the lumbar spine and the hip were evaluated in 149 Japanese postmenopausal women. RESULTS: The distribution of ER PvuII and XbaI and VDR BsmI restriction fragment length polymorphisms was as follows: pp, 30.2%; Pp, 49.7%; PP, 20.1%; xx, 71.8%; Xx, 22.5%; XX, 2.7%; bb, 76.5%; Bb, 22.2%; and BB, 1.3%. Analysis of covariance adjusted for confounding variables revealed that participants with pp allele had fewer teeth remaining than did those with P allele. There were no significant differences in oral bone mass and postcranial BMD among three alleles at the PvuII site. Participants with X and bb allele had less oral bone mass and lower postcranial BMD than did those with xx and B allele, respectively. We could not clarify the positive associations between XbaI and BsmI polymorphism and number of teeth. CONCLUSIONS: PvuII polymorphism was associated with tooth loss, but not with oral bone mass and postcranial BMD. XbaI and BsmI polymorphisms may be associated with bone mass or density; however, PvuII polymorphism might contribute to another unknown pathway related to tooth loss.     

The type-2 variant of human cytomegalovirus glycoprotein N (gN-2) is not the rarest in the Chinese population of Taiwan: influence of primer design

Studies of the human cytomegalovirus (HCMV) glycoprotein N (gpUL73-gN) showed that genotypic variations exist in different geographic areas, with gN-2 unidentified in Chinese population. The purpose of this study was to determine the HCMV gN variants in the Chinese population of Taiwan. Primers were designed and a polymerase chain reaction (PCR) was carried out on the UL73 gene. The PCR products were subjected to restriction fragment length polymorphism (RFLP) analysis. The same PCR-RFLP assay was repeated using primers published previously to demonstrate the influence of primer design. Of the 48 clinical HCMV isolates, 33 were positive for PCR products by both primer sets. Fifteen were positive only by the "in-house" PCR. The distribution of gN-1, gN-2, gN-3, and gN-4 by RFLP analysis was 14:11:7:17, with one isolate positive for both gN-1 and gN-2. The published primers detected the four genotypes with the number of 14:0:2:17. The under-representation of gN-2 and gN-3 by the method published previously may be due to inappropriate primer design when re-examining the sequences. On the basis of the results of this study, gN-2 is not the rarest gN genotype in the Chinese population of Taiwan. The design of primers used for PCR-RFLP genotyping may have a great influence on the frequency distribution of HCMV genomic variants.     

Vitamin D receptor gene polymorphisms and bone mineral density in postmenopausal Indian women

OBJECTIVES: Osteoporosis is a common condition in postmenopausal women. Bone mineral density (BMD), the major determinant of osteoporotic fracture risk, has a particular genetic background. However, consensus on the association of BMD with specific gene locus has not been reached. The race and ethnicity specific divergence in association studies must be assessed to predict the susceptibility and therapeutic response of associated genes. We investigated the potential association of Vitamin D receptor (VDR) gene polymorphisms ApaI, BsmI, FokI and TaqI with BMD in 246 postmenopausal Indian women (average age 54.2+/-3.4 years). METHODS: The subjects were genotyped by PCR-RFLP and underwent BMD measurements at spine and hip by dual energy X-ray absorptiometery. RESULTS: The average BMD at spine and hip of women with genotypes aa, bb (presence of restriction sites for ApaI and BsmI), FF and TT (absence of restriction sites for FokI and TaqI) was more than 10% higher than those with genotypes AA, BB, ff and tt, respectively. The interaction between BsmI, ApaI and TaqI genotypes showed significant effect of BsmI-ApaI genotypes (p=0.052) in this combination on BMD. However, presence of T allele in combination showed positive influence on BMD. Within the group, genotypes BB, ff and tt were significantly prevalent in women with osteoporotic bone mass, tt and BB had significantly higher adjusted odd ratio (OR) for age more than 55years. CONCLUSION: Study reveals that VDR gene polymorphisms are associated with BMD in Indian women and perhaps, influence some determinant of bone metabolism. Ethnicity may attribute to frequency variation, however, allele impact remains same.