RESTRICTION FRAGMENT LENGTH POLYMORPHISMS ASSOCIATED WITH FACTOR Ⅷ CARRIER DETECTION USING DNA RFLPs IN CHINESE

RFLPs for XbaI, BelI and BglI sites of human FⅧwere informative for 48%, 41% and 15% of females studied, respectively. BglI RFLP is different from that reported by Chan et al, a fact suggests Yangtze River region population of China would be at variance with the Southern Chinese population in certain RFLP distribution. TaqI allelic system Ⅰin the DXS52 region also shows the same variance among them, but heterozygous rate 0f 71% for system Ⅰ(alleles 1 to 8) and 49% for system Ⅱ(αand βalleles) were very similar. Using the Bell/XbaI RFLPs, accurate information could be obtained from this study for 56% of women who were at risk for hemophilia A (HA) carriership. The carrier of the remaining 44% could be determined by utilizing the TaqI RFLP. In addition, we report a new intergenie polymorphism (9%) at DXS115 as a marker for detection of heterozygotes in families at risk for HA. The advantage of using the XbaI/KpnI RFLP is that both the intragemie RFLP and the new intergenie RFLP can be evaluated on the same blot at the same time.

Comparing the frequencies of restriction fragment length polymorphisms for dystrophin gene in Chinese with those from Japanese and Caucasian populations

The restriction fragment length polymorphisms distribution and frequency of dystrophin gene in Chinese were studied by using 14 subclones of the entire 14kb cDNA for the dystrophin as hybridization probes. Allelic fragments were detected in hybridization patterns of PvuII/1a, Taq I/2b-3, Taq I/5b-7, and Xba I/10. Among them, the allelic fragments (26kb and 3.8kb) in PvuII/2b-3 pattern and the allelic fragments (10.0kb and 8.4kb) in Taq I/5b-7 patterns had never been reported previously. Compared with the data from Caucasians and Japanese, it indicated that there was a significant difference (P<0.01) of the allelic fragment frequency in Taq I/2b-3 and Xba I/10 patterns between Chinese and Caucasians. The frequencies of allelic fragments A2 (5.6kb) in Taq I/8 and A2 (10.7kb) in EcoR V/9 were high in Caucasians, yet had not been detected in Chinese, the differences were also highly significant. But in Chinese and Caucasians, the B1B2 allelic frequencies in Taq I/5b-7 are the same. As to the frequency of the allelic fragments A1A2 and B1B2 in Pvu II/1a, there was no significant difference between Chinese and Japanese.

Development of Fok-I based nested polymerase chain reaction-restriction fragment length polymorphism analysis for detection of hepatitis B virus X region V5M mutation

AIM: To develop a Fok-I nested polymerase chain reaction(PCR)-restriction fragment length polymorphism analysis(PRA) method for the detection of hepatitis B virus X region(HBx) V5 M mutation.METHODS: Nested PCR was applied into DNAs from 198 chronic patients at 2 different stages [121 patients with hepatocellular carcinoma(HCC) and 77 carrier patients]. To identify V5 M mutants, digestion of nested PCR amplicons by the restriction enzyme Fok-I(GGA TGN9↓) was done. For size comparison, the enzymetreated products were analyzed by electrophoresis on 2.5% agarose gels, stained with ethidium bromide, and visualized on a UV transilluminator.RESULTS: The assay enabled the identification of 69 patients(sensitivity of 34.8%; 46 HCC patients and 23 carrier patients). Our data also showed that V5 M prevalence in HCC patients was significantly higher than in carrier patients(47.8%, 22/46 patients vs 0%, 0/23 patients, P < 0.001), suggesting that HBx Ag V5 M mutation may play a pivotal role in HCC generation in chronic patients with genotype C infections.CONCLUSION: The Fok-I nested PRA developed in this study is a reliable and cost-effective method to detect HBx Ag V5 M mutation in chronic patients with genotype C2 infection.

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Although the gut microflora is thought to be an essential factor in the development of ulcerative colitis (UC), the entire gut microflora occurring in UC remains unknown. Most studies use feces to represent the microflora distribution;however, here we analyzed the bacterial diversity in colonic mucus from UC patients receiving colectomy surgery and control patients. The diversity of microflora was investigated using a combination of terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of the 16S rRNA gene sequences. In the T-RFLP analysis, the number of terminal restriction fragments (T-RFs) decreased significantly in UC patients when compared to control samples. Also in the clone library analysis, the number of operational taxonomic units (OTU) and the Shannon diversity index were reduced significantly in UC patients. These molecular analyses reveal an overall dysbiosis in UC patients. No specific pathogen was found, and a strong negative correlation in relative abundance of bacterial populations was observed between the phyla Bacteroidetes and Firmicutes in the UC patients. This is the first report showing a significant correlation between these two phyla, which may be important characteristics in the pathogenesis of UC.

Antibiotic-Resistant Bacterial Group in Field Soil Evaluated by a Newly Developed Method Based on Restriction Fragment Length Polymorphism Analysis

Spreading of antibiotic resistant bacteria into environment is becoming a major public health problem, implicating affair of the indirect transmission of antibiotic resistant bacteria to human through drinking water, or vegetables, or daily products. Until now, the risk of nosocomial infection of antibiotic resistant bacteria has mainly been evaluated using clinical isolates by phenotypic method. To evaluate a risk of community-acquired infection of antibiotic resistant bacteria, a new method has been developed based on PCR-RFLP without isolation. By comparing restriction fragment lengths of the 16S rDNA gene from bacterial mixture grown under antibiotic treatment to those simulated from the DNA sequence, bacterial taxonomies were elucidated using the method of Okuda and Watanabe [1] [2]. In this study, taxonomies of polymyxin B resistant bacteria group in field soils, paddy field with organic manure and upland field without organic manure were estimated without isolation. In the both field soils, the major bacteria grown under the antibiotic were B. cereus group, which had natural resistance to this antibiotic. In field applied with organic manure, Prevotella spp., and the other Cytophagales, which were suggested to be of feces origin and to acquire resistance to the antibiotic, were detected. When numbers of each bacterial group were roughly estimated by the most probable number method, B. cereus group was enumerated to be 3.30 × 106 MPN/g dry soil in paddy field soil and 1.32 × 106 MPN/g dry soil in upland filed. Prevotella spp. and the other Cytophagales in paddy field were enumerated to be 1.31 × 106 MPN, and 1.07 × 106 MPN·g-1 dry soil.

RESTRICTION FRAGMENT LENGTH POLYMORPHISM（RFLP） ANALYSIS OF GENOMIC DNA OF 5 STRAINS OF TRICHINELLA SPIRALIS IN CHINA

Five restriction endonucleases were used to digest genomic DNA from 5 isolates of Trichinella spiralis obtained from Changchun, Tianjin, Xian, Henan and Yunnan. All the isolates were secured from pigs except the Changchun strain which came from dog. The DNA fragments digested by endonuclease were separated by agarose gel electrophoresis. The Changchun isolate had a EcoRI band at 1. 12kb and a DraI band at 1. 97kb which were unique to this isolate. A cloned specific repetitive DNA sequence (1. 12kb) from the Changchun strain was selected to prepare a probe for the Southern blotting of EcoRI restriction DNA fragments for the 5 isolates. The 1.12kb hybridizing band did not appear except in the Changchun isolate.These results seem to indicate that there are differences between the isolates obtained from hosts in different geographical regions.

Bacterial Groups Concerned with Maturing Process in Manure Production Analyzed by a Method Based on Restriction Fragment Length Polymorphism Analysis

Composting is a biological aerobic decomposition process consisted from different phases. Although the Japanese Standards for manure recommended that it took at least 6 months to complete the maturing phase, there was no reliable ground. In order to find out shortening method of the maturing phase, the microorganisms concerned with a progress of the maturing was determined by using the most probable number method (MPN) and PCR-RFLP of the 16S rDNA, which was found effective to provide numbers and taxonomy of polymyxin B resistant bacterial groups in the former paper [1]. Compared to the numbers after thermophilic phase, those of Actinobacteria, δ-proteobacteria, and the other gram negative bacteria increased to 50 times, 20 times, and 105 times, respectively, after maturing phase, while those of Bacillus spp., and α and β-proteobacteria decreased to 1/10, and 1/105 after maturing phase. Numbers of the other Fumicutes, and γ-proteobacteria remained in the same revel. Actinobacteria, δ-proteobacteria, and the other gram negative bacteria might be concerned with a progress of the maturing phase, because these bacterial groups were detected and enumerated due to their proliferation ability. Although number of Acitinobacteria might be underestimated because of a PCR bias, the method was found effective for the purpose to monitor bacteria actively proliferated in culture medium.

Evaluation of the Method Based on Restriction Fragment Length Polymorphism Analysis as Simple Analysis Method of Lactic Acid Bacteria in Foods

Lactic acid bacteria have not only been used to produce various kinds of fermented food, but also used as probiotic products. As lactic acid bacterial group was consisted from diverse genera, a simple inspection method by which numbers and contained microorganisms could be automatically analyzed without any preliminary information was required to use them more effectively. In this manuscript, lactic acid bacterial groups in commercial products of kimuchi, komekouji-miso, and yoghurt were identified and enumerated by our newly developed method [1]-[3], to evaluate whether the method could be used as an inspection method of various food samples. In kimuchi, numerically dominant bacteria were Lactobacillus sakei, and L. casei (1.4 × 104 MPN g-1) and Leuconostoc spp. (l.4 × 104 MPN). In kouji-miso, numerically dominant bacteria was Bacillus spp. (3 × 103 MPN), which mainly included B. subtilis group and B. cereus group. Lactic acid bacteria such as Lactobacillus spp., or Lactococcus spp., included in the komekouji-miso, could be enumerated after 3 days incubation (1.24 × 104 MPN), but not detected after 7 days incubation. In yoghurt A and C, Lactococcus lactis was detected as numerically dominant lactic acid bacteria (3.0 × 105 MPN). In yoghurt B, Lactobacillus spp., or Lactococcus spp., was detected not only by a culturebased method but also by an unculture-based method, although there was a difference between the both estimated numbers. The present results suggested that the method might become useful as a simple inspection method of food microorganisms, because time and labor of the analysis could be reduced by using an unculture-based method and MCE-202 MultiNA. In this study, Bifidobacteriium spp. was not detected in B and C yoghurt, in spite of indicating their existence, and numbers of lactic acid bacteria were lower than the level of the daily product regulation, because 16S rDNA of Bifidobacteriium spp. might not be amplified by the used PCR condition. The PCR condition must be changed so as to amplify Bifidobacterium spp., before the method will be used as an inspection method for lactic acid bacteria.

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano

A total of 80 piglets (7.9 ± 1.0 kg) were used in a feeding experiment with dried oregano. The diets differed in their oregano content: 0 g, 2 g, 4 g and 8 g oregano/kg feed, corresponding to 0, 23.5, 46.9 and 93.9 mg carvacrol/kg DM. After the experimental period of 5 weeks, 20 piglets of both extreme feeding groups were slaughtered: 10 animals of the control group and 10 animals of the group that received 8 g oregano/kg. Ingesta samples of jejunum, caecum and colon were collected and analyzed by FISH and PCR RFLP to compare the diversity of microbiota. The results showed no significant changes in microbiota in response to oregano. The patterns of the PCR-RFLP showed a similarity of 61.8% - 91.8% in both feeding groups. In conclusion, an effect of oregano on the in- testinal microbiota could not be shown under the methods used.

中国人dystrophin基因RFLPs的初步研究

我们用dystrophin基因的cDNA全顺序(长14 kb)为核酸分子杂交探针,对中国人dystrophin基因内的RFLPs进行了初步研究。在结果中给出了PvuⅡ/1 a、Taq Ⅰ/2 b—3、PvuⅡ/2 b—3、TaqⅠ/5 b—7、Xba Ⅰ/10五种杂交中所见的六个RFLPs 的预期杂合频率和受检女性的实际杂合频率;其中PvuⅡ/2 b—3(A 1=26.0 kb,A 2=3.8 kb)和Taq Ⅰ/5 b—7(A 1=10.0 kb,A2=8.4 kb)的2个RFLPs为本文首次报道。PvuⅡ/1 a的2个RFLPs 的等位片段频率与日本人的同类研究结果比较,差异无显著性。但Taq Ⅰ/2 b—3、Taq Ⅰ/5 b—7、Taq Ⅰ/8、EcoR Ⅴ/9和Xba Ⅰ/10的5个RFLPs 与高加索人的数据比较,发现其中4个RFLPs 的等位片段频率的差异有极其显著性。这提示了东西方人在dystrophin 基因的分子结构上存在着较大的差别。在这些差异之中,Taq Ⅰ/2 b—3、Taq Ⅰ/8和EcoR Ⅴ/9检出的RFLPs 等位频率,中国人低于高加索人;而Xba Ⅰ/10检出的RFLPs 等位频率则显著高于高加索人;另外Taq Ⅰ/5 b—7检出的RFLPs的等位片段频率则与高加索人相近。实验结果还提示PvuⅡ/1 a、Taq Ⅰ/5 b—7和Xba Ⅰ/10这三种杂交,对于在中国人群中检测DMD/BMD 基因携带者以及产前诊断,具有很高的应用价值。

11个甲型血友病家系FⅧ基因的RFLPs连锁分析

应用Southern印迹杂交方法和PCR新技术,对东北地区11个甲型血友病家系检测FⅧ基因内的Bcl Ⅰ和Xba Ⅰ位点的RFLPs和基因外Stl4/Taq I RFLPs,分析了FⅧ基因的连锁状况,7名肯定携带者中4名能提供多态信息,4名可疑携带者之中2名可确定为缺陷FⅧ基因的携带者,1名可确定为正常FⅧ基因。为婚姻、生育指导和产前基因诊断提供依据。进一步明确了应用PCR技术联合进行多个位点的RFLPs连锁分析进行甲型血友病基因诊断的可行性及优越性。

水稻籼粳亚种间F_1抽穗期与RFLPs关系的初步研究

选用5个籼稻和6个广亲和粳稻品种,按5×6不完全双列杂交配制30个组合,计算杂种F1抽穗期杂种优势;并采用113个RFLP标记,检测11个亲本间的RFLP多态性,计算籼粳亚种间F1的基因型杂合度,分析杂种F1的抽穗期及其杂种优势与基因型杂合度的关系。试验结果表明,水稻籼粳亚种间F1的抽穗期呈负向优势,F1的抽穗期及其杂种优势与基因型的杂合度呈负相关。

中国人St14/Taq I RFLPs及其在产前诊断中的应用

血友病A是人类最常见的遗传性出血性疾病,大约10,000名出生男婴中有一人受累。病因是凝血第Ⅷ因子基因缺陷。我们用与FⅧ基因紧密连锁的一段基因外DNA克隆St14为基因探针对FⅧ基因的TaqⅠ多态性进行了研究。利用这一多态性为遗传标志,成功地进行了一例血友病A高危胎儿的产前基因诊断。

Association of TNF-α-238G/A and 308 G/A Gene Polymorphisms with Pulmonary Tuberculosis among Patients with Coal Worker’s Pneumoconiosis

Objectives Tumor necrosis factor-α （TNF-α） may play an important role in host＇s immune response to mycobacterium tuberculosis （M. tuberculosis） infection. This study was to investigate the association of TNF-α gene polymorphism with pulmonary tuberculosis （TB） among patients with coal worker＇s pneumoconiosis （CWP）. Methods A case-control study was conducted in 113 patients with confirmed CWP complicated with pulmonary TB and 113 non-TB controls with CWP. They were matched in gender, age, job, and stage of pneumoconiosis. All participants were interviewed with questionnaires and their blood specimens were collected for genetic determination with informed consent. The TNF-α gene polymorphism was determined with polymerase chain reaction of restriction fragment length polymorphism （PCR-RFLP）. Frequency of genotypes was assessed for Hardy-Weinberg equilibrium by chi-square test or Fisher＇s exact probability. Factors influencing the association of individual susceptibility with pulmonary TB were evaluated with logistic regression analysis. Gene-environment interaction was evaluated by a multiplieative model with combined OR. All data were analyzed using SAS version 8.2 software. Results No significant difference in frequency of the TNF-α-308 genotype was found between CWP complicated with pulmonary TB and non-TB controls （2,2=5.44, P=-0.07）. But difference in frequency of the TNF-α-308 A allele was identified between them （2,2-5.14, P=0.02）. No significant difference in frequencies of the TNF-α-238 genotype and allele （P=0.23 and P=0.09, respectively） was found between cases and controls either, with combined （GG and AA） OR of 3.96 （95% confidence interval of 1.30-12.09） at the -308 locus of the TNF-α gene, as compared to combination of the TNF-α-238 GG and TNF-α-308 GG genotypes. Multivariate-adjusted odds ratio of the TNF-α-238 GG and TNF-α-308 GA genotypes was 1.98 （95% CI of 1.06-3.71） for risk for pulmonary TB in patients with CWP. There was a synergic interaction between the TNF-a-308 GG genotype and body mass index （OR=4.92）, as well as an interaction between the TNF-α-308 GG genotype and history of BCG immunization or history of TB exposure. And, the interaction of the TNF-α-238 GG genotype and history of BCG immunization or TB exposure with risk for pulmonary TB in them was also indicated. Conclusions TNF-α-308 A allele is associated with an elevated risk for pulmonary TB, whereas TNF-α-238 A allele was otherwise.

POLYMORPHISMS OF THE HUMAN LIPOPROTEIN LIPASE GENE:POSSIBLE ASSOCIATION WITH LIPID LEVELS IN PATIENTS WITH CORONARY HEART DISEASE IN BEIJING AREA

The polymorphisms(Pvu Ⅱand Hind Ⅲ) on the lipoprotein lipase(LPL) gene locus was investigated in a sample of 100 patients surviving previous myocardial infarction and 100 age matched healthy individuals selected from Han Chinese of Beijing area.In patient group a strong association was found between H+allele of Hind Ⅲ polymorphism and raised TG levels(P<0.01).In control group P-P-genotype was observed to be associated with higher TG levels compared with P+P genotype of Pvu Ⅱ polymorphism(P<0.05).Combination of H+H+ genotype with P-P-genotype showed the highest TG levels among all nine kinds of genotype combinations in patient group(P<0.01).However,comparison of distribution of alleles and genotypes of these polymorphisms between patient group and control group demonstrated no significant difference. Our data suggest that the polymorphisms at the LPL gene,as the linkage markers with an aetiologic mutation at or around LPL gene,may constitute one of the genetic determinants for the population variation in plasma TG levels,as well as for the common dyslipidemia in Chinese population.

Analysis of polymorphisms in the promoter region of interleukin-1 β by restriction fragment length polymorphism-PCR

Objective: To investigate the frequencies of -1470, (-511) and -31 single nucleotide polymorphisms (SNPs) in the promoter of IL-1β and its haplotype constitution in Chongqing population. Methods: One hundred and twelve healthy Chongqing people were enrolled in this study. Polymorphisms at -1470 (G to C), (-511) (T to C) and -31 (C to T) of IL-1β were genotyped with the method of restriction fragment length polymorphism (RFLP). Haplotype frequencies were analyzed by Arlequine software.Results: Frequencies of IL-1β -1470, -511 and -31 SNPs were (41.67)%, 50% and (45.33)%, respectively. Genotype frequencies of -1470 locus were (39.81)%, (37.04)% and (23.15)% for G/G, G/C and C/C respectively. As for T-511C SNP, genotype frequencies of (T/T), T/C and C/C were (29.91)%, (40.18)% and (29.91)%, respectively. Genotyping results of C/C, C/T, and T/T of -31 locus were (35.51)%, (38.32)% and (26.71)% respectively. Haplotype analysis found that there were mainly three haplotypes constituted by three SNPs, ie., G-T-C, C-T-C and G-C-T. Conclusions: Polymorphisms exist in the promoter of IL-1β in Chongqing population. Three SNPs locate in the same haplotype block.

RESTRICTION ENDONUCLEASE ANALYSIS OF MITOCHONDRIALDNA FROM HUMAN LUNG ADENOCARCINOMA CELLLINE SPC-A-1

Objective: To understand the role of mitochondrial DNA (mtDNA) in carcinogenesis. Methods: single-step method was used to isolate the mtDNA from human lung adenocarcinoma cell line SPC-A-1. The mtDNA was analyzed by restriction fragment length polymorphism (RFLP) with 11 kinds of restriction endonuclease, which were Pvu II, Xho I, Pst I, EcoR I, BstE II, Hind III, Hpa I, Bc1 I, EcoR V, Sca I and Xba I. Restriction map of mtDNA from SPC-A-1 cell was obtained by the single and double-digestion method. Results: It was found that no variation at 32 restriction-sites could be detected in the coding region of mtDNA from SPC-A-1 cell line. But a new site was found at nucleotide 16276 (EcoR V) within the noncoding region. Conclusion: These results indicate that the primary structure of gene coding region of mtDNA isolated from SPC-A-1 cell is highly stable. While the major variation of nucleotide is probably located in the noncoding region.

RFLPs FOR HUMAN PAI-1 GENE IN CHINESE

Plasminogen activator inhibitor 1 (PAI-1) is considered as the main physiological inhibitor of plasminogen activators in plasma which plays an important regulatory role in the control of the fibrinolytic activity in blood. The human PAI-1 gene is located at q21-22 region of chromosome 7. By using human PAI-1 cDNA (a gift from Dr. D. Ginsburg) as a probe, restriction fragment length polymorphisms (RFLPs) were studied with 8 different endonucleases in 35 unrelated Chinese individuals and the results showed as follows: (1) Taq Ⅰdetected allelic 2.7 kb and 1.8 kb fragments, with the frequencies of 0.96 and 0.04 respectively, 2.7 kb homozygote and 2.7 kb/1.8 kb heterozygote appeared with frequencies of 91% and 9%. (2) Sac Ⅰidentified an invariant 4.8kb band and a two-allele polymorphism with fragments of either 23 kb or 16 kb whose frequencies were 0.96 and 0.04. 23kb homozygote and 23kb/16kb heterozygote appeared with the frequencies of 91% and 9%. (3) HindⅢrevealed a single two-allele polymorphism with bands at either 25 kb or 14 kb, with the frequencies of 0.34 and 0.66, 25 kb homozygote, 25 kb/14 kb heterozygote and 14 kb homozygote appeared with the frequencies of 23%, 46% and 31% respectively. The restriction fragment with a size of 1.6kb for TaqⅠwas first reported in the present paper. No polymorphism was observed for EcoRI, BamHI, BglⅡ, PvuⅡand Pst Ⅰ. The RFLPs for PAI-1 gene may be served as important genetic markers for study of thrombotic and other PAI-1 related disorders.

TLR4基因多态性与小儿反复呼吸道感染的关系

目的探究Toll样受体4(TLR4)基因多态性与小儿反复呼吸道感染(RRTI)的关系。方法选择107例RRTI病儿作为观察组,另选103例体检健康儿童作为对照组(近1年未出现RRTI),采用限制性片段长度多态性聚合酶链反应(PCR-RFLP)技术分析两组TLR4基因rs2737190位点多态性,比较不同病情严重程度病儿TLR4基因多态性的差异,并分析不同TLR4基因多态性病儿临床特征的差异。结果观察组TLR4基因rs2737190位点AG基因型、G等位基因频率均明显高于对照组,AA基因型频率明显低于对照组(χ^(2)=4.129~8.564,P<0.05);中重度RRTI病儿GG基因型、G等位基因频率明显高于轻度病儿,AA基因型频率显著低于轻度病儿(χ^(2)=9.233~13.357,P<0.05);AA基因型病儿年发作次数、合并呼吸困难比例,以及C反应蛋白、白细胞介素-6、γ-干扰素和丙二醛等指标均显著低于AG和GG基因型病儿,超氧化物歧化酶则显著高于AG和GG基因型病儿(χ^(2)=7.573,F=4.668~24.317,P<0.05)。结论TLR4基因rs2737190位点AG基因型、G等位基因频率会增加小儿RRTI易感性,并促进其炎症反应升高和病情进展。