Apolipoprotein E gene polymorphism in cerebrovascular disease: a case-control study

The association between apolipoprotein E (apo E) polymorphism and stroke has been controversial. So far there are no studies reported on the polymorphism of apolipoprotein E in cerebrovascular diseases in the Asian Indians. A blinded case-control study was therefore undertaken and the apo E genotypes and lipid profile of a total of 120 subjects (63 stroke patients and 57 healthy controls) were done. The frequency distribution of apo E alleles and genotypes were assessed and their relation with the occurrence of stroke in Asian Indian subjects was determined. A significantly high frequency of apo epsilon4 allele (30%) was observed in the stroke patients than the controls (11%) (p < 0.005), and patients with epsilon4 allele had a fourfold higher odds to develop stroke OR (95%CI) 4.2 (1.8-10.1) (p < 0.005). On multivariate analysis, after adjusting for age, triglycerides and hypertension, the association of epsilon4 allele with stroke was found to be no longer statistically significant, OR (95%CI) 1.2 (0.4-4.5) (p = NS). On multiple logistic regression analysis age, OR (95%CI) 1.1 (1.1-1.2) (p < 0.001), and hypertension OR (95%CI) 15.1 (2.6-89.1) (p < 0.005) were found to be independent risk factors for development of stroke. This is the first report to have examined the association of apo E gene polymorphism with stroke in the Asian Indians. This study suggests that apo epsilon4 allele, triglycerides, age and hypertension are the predictors for stroke development.     

The apolipoprotein CIII T2854G variants are associated with postprandial triacylglycerol concentrations in normolipidemic Korean men

This study investigated associations between the apolipoprotein (apo) CIII polymorphism and triacylglycerol (TAG) concentrations in fasting and postprandial plasma. Polymerase chain reaction followed by a restriction fragment length genotyping was conducted to assess the allele frequency of the apo CIII T2854G variants in healthy and normolipidemic Korean men (n=262). Waist circumference, body mass index (kilograms per meter squared), fasting plasma concentrations of TAG, total cholesterol, high-density lipoprotein cholesterol (HDLC), low-density lipoprotein cholesterol (LDLC), glucose, and insulin were compared across the genotypes. Compared to TT homozygotes and TG heterozygotes, GG homozygotes had 22% higher fasting TAG concentrations, respectively (p<0.05). A subgroup of 60 subjects (TT homozygotes=20, TG heterozygotes=22, GG homozygotes= 18) were further invited to participate in a high-fat meal test to assess postprandial TAG concentrations. During the high-fat meal test, the GG homozygotes had 21% higher TAG area under the curve (AUC) than the TT homozygotes (p<0.05) and 22% higher TAG AUC than the TG heterozygotes (p<0.05). In conclusion, this is the first study to show that the apo CIII T2854G variants are associated with elevated postprandial TAG concentrations in the study population of Korean men.     

Comprehensive typing of DQB1 alleles by PCR-RFLP

Abstract: The protocols represented in this report can resolve all 22 DQB1 alleles. The second exon of DQB1 was subjected to PCR using two group-specific primers to obtain DQB1 group 1 (DQ5 and DQ6) and group 2 (DQ2, DQ3, DQ4) specific amplified products, respectively. Three endo-nucleases, Apal, BssHII and Ncil, can provide typing of DQ5 and DQ6 based on easy-to-read uncleaved, cleaved and a combination of uncleaved/cleaved patterns. Similarly, two endonucleases, FokI and BgII can define the specificities DQ2, DQ3 and DQ4. Moreover, all 13 group 1 DQB1 alleles and all but one of their 78 possible heterozygotes can be unambiguously resolved using an extended panel of 10 endonucleases. The remaining pair of heterozygotes, DQB1*05031/0603 and 05032/0608, can however be resolved by double digestion with BsmFI and SfaNI. RsaI splits the previously unresolved alleles DQB1*0602 and 0603 in the amplified products of the modified primer SDQ-01. Fnu4HI can resolve DQB1*0606 from 0605. DQB1*0603, 0607 and 0608 can be resolved by SfaNI and the new endonuclease BsmFI. The comprehensive typing of group 2 DQB1 alleles can be achieved using five endonucleases. All 9 group 2 DQB1 alleles and all but one pair (DQB1*0301/0302 from DQB1*03032/0304) of 36 possible heterozygotes can be resolved. Thus, PCR-RFLP remains a simple, inexpensive and reliable method for DQB1 typing. The PCR-RFLP can be used for comprehensive DQB1 typing either independently or to complement the PCR-SSP and PCR-SSOP methods.     

Identification of tuna species (Thunnini tribe) by PCR-RFLP analysis of mitochondrial DNA fragments

Tunas are highly priced and the Atlantic bluefin tuna is most endangered trade fish in the world. For effective fishery management and protection of consumers’ rights, it is important to develop a molecular method to identify the species of tuna products. In this study, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was developed to identify 10 tuna or tuna-like species. Primers were designed to amplify six mitochondrial DNA fragments from each specimen, and three restriction enzymes including AfaI, DdeI, and AluI were used to analyze the short length fragments produced from ATPase and control region (CR) genes. Besides these, the phylogenetic relationships among tested fish species were analyzed based on phylogenetic trees constructed using the amplified COI and CR sequences. The results indicated that the developed PCR-RFLP really provided a useful and academic technique to identify high-priced tuna species.     

Contribution of Toll like receptor polymorphisms to dengue susceptibility and clinical outcome among eastern Indian patients

Dengue infection has been one of the major public health concerns in India causing simple dengue fever (DF) to severe dengue infection. In the present study, contribution of TLR3, 7 and 8 polymorphisms towards dengue disease susceptibility and severity among Eastern Indian patients was analysed. Genomic DNA was extracted from blood of 201 dengue infected patients and 157 healthy individuals, followed by genotyping of eight polymorphisms of TLR3 (rs3775290), TLR7 (rs5741880, rs3853839, rs179008 and rs179010) and TLR8 (rs3764879, rs3764880 and rs5744080) genes by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Functional analyses of the polymorphisms were predicted. Genotypic association of polymorphisms, alone and in combination, with dengue disease susceptibility and development of WHO-defined warning signs among patients was calculated by using SPSS software. TLR7-rs179008 & TLR8-rs3764880 were implicated to be non-synonymous polymorphisms. Specific genotypes of majority of the analysed TLR polymorphisms exhibited significant positive association with disease susceptibility. CC/C and AA/A of TLR7-rs179008 (p < 0.0001) and TLR8-rs3764880 (p < 0.00001) respectively were significantly associated with development of warning signs among dengue infected patients. Particular genotypic combinations of rs3853839-rs5744080 and rs179008-rs3764880 increased the risk of dengue infectivity, whereas, presence of last combination was more prevalent among dengue patients with warning signs. Thus these polymorphic variants of TLR3, 7 and 8 might act as potential prognostic biomarkers for predicting disease severity among dengue virus infected patients.     

Association of PON1-L55M Genetic Variation and Breast Cancer Risk: A Case-Control Trial

Background: Paraoxonase 1 (PON1), a multifactorial antioxidant enzyme, has a defensive role against oxidative stress, which is believed to contribute to cancer development. This study aimed to investigate the association of PON1-L55M functional polymorphism with breast cancer risk. Material and methods: In the experimental study, blood samples were collected from 150 healthy women controls and 150 breast cancer subjects. The L55M genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism. Results: Our analysis showed that the genotypes distribution is in Hardy-Weinberg equilibrium for both case and control groups. Our data revealed that there are significant associations between PON1-L55M polymorphism and breast cancer risk in homozygote (OR= 2.13, 95%CI= 1.14-4.00, p= 0.018), dominant (OR= 1.72, 95%CI= 1.07-2.76, p= 0.024), and allelic (OR= 1.55, 95%CI= 1.12-2.15, p= 0.008) models. Conclusions: Our results suggest that the PON1-L55M genetic variation could be a genetic risk factor for breast cancer risk and it could be considered as a molecular biomarker for screening of susceptible women.     

Polymorphism of the human retinoid X receptor beta and linkage disequilibrium with HLA-DPB1

The human retinoid X receptor beta (RXRB) gene is localized in the major histocompatibility complex (MHC) region between DPB1 and RING2. The RXRB gene sequence reported by different investigators suggests that the gene may be polymorphic. In this study, we confirmed one polymorphism by sequencing genomic DNA from four Caucasian individuals. We also developed a restriction fragment length polymorphism (RFLP) analysis to detect this specific polymorphism. Linkage analysis studies between RXRB alleles and a number of HLA markers showed significant linkage disequilibrium between RXRB*T and HLA-DPB1*0401.     

STAT3 基因多态性与儿童癫痫易感性的相关性

目的探讨信号转导和转录活化因子3(STAT 3)基因两个SNP位点rs1053005和rs744166多态性与儿童癫痫易感性的关系。方法采用病例对照研究,选取462例癫痫患儿,其中包括121例难治性癫痫(RE)患儿,以493例健康儿童作为对照组。利用PCR-RFLP方法进行两个SNP位点的多态性检测,比较不同基因型及等位基因与儿童癫痫患病风险的关系。结果癫痫患儿SNP位点rs1053005的基因型(AA,AG,GG)频率与对照组比较,差异有统计学意义(χ~2=9.705,P?=0.008);癫痫患儿的等位基因G频率明显低于对照组(OR=0.734,P=0.002,95%CI:0.604~0.892);SNP位点rs744166的基因型(TT,TC,CC)频率和等位基因频率与对照组比较,差异均无统计学意义(P0.05)。在癫痫患儿中,RE患儿与非RE患儿比较,SNP位点rs1053005和rs744166的基因型频率和等位基因频率的差异均无统计学意义(P0.05)。结论 STAT3基因SNP位点rs1053005与癫痫的遗传易感性相关。     

Development of PCR based assays for detection of lethal Holstein haplotype 1, 3 and 4 in Holstein Friesian cattle

Holstein haplotype (HH) 1, 3 and 4 are lethal mutations, responsible for early embryonic losses in Holstein Friesian (HF) cattle, worldwide. Three PCR based assays – tetra Amplification Refractory Mutation System PCR, PCR primer induced restriction analysis and PCR-restriction fragment length polymorphism techniques for screening of HH1, 3 and 4, respectively were developed and validated. During screening, six among 60 HF bulls were found as carrier for either of three mutations. These PCR assays are highly accurate and reproducible and can be used for screening of the haplotypes in HF cattle.     

Species-level identification of clinical staphylococcal isolates based on polymerase chain reaction–restriction fragment length polymorphism analysis of a partial groEL gene sequence

A pair of degenerate primers that amplified, by polymerase chain reaction (PCR), a partial groEL gene sequence (550 bp) was used for the identification of the 12 most common human staphylococcal pathogens. The amplified products were digested by AluI endonuclease, and distinctive PCR restriction fragment length polymorphism (RFLP) patterns for reference strains were obtained. This protocol was validated by the identification of 89 clinical staphylococcal isolates, and the results were compared with those obtained by the reference biochemical identification, showing 100% concordant results. Two species, Staphylococcus aureus and Staphylococcus lugdunensis, showed intraspecies polymorphisms on their PCR-RFLP patterns. All strains were also identified using the API Staph ID test (bioMérieux, Durham, NC) and the MicroScan WalkAway automated system (Dade Behring, West Sacramento, CA). When 17 Staphylococcus isolates were tested in a blind experiment by the PCR-RFLP of the groEL gene method, all strains were also correctly identified. We propose the PCR-RFLP of the groEL gene with AluI as a reliable and reproducible method for identification of Staphylococcus spp.