Genetic polymorphism and relationship of 24 Y-STR loci among three ethnic minorities from GuizhouCSCD

Objective: To study the distribution of haplotypes of Y-chromosomal short tandem repeats (Y-STR) loci among three ethnic minorities from Guizhou, China. Methods: Twenty four Y-STR loci of 174 unrelated males were amplified with a Microreader™ 24Y Direct ID System kit. Capillary electrophoresis was carried out on an ABI 3100 Genetic Analyzer, and the data was analyzed with GeneMapper software. Results Seventy six haplotypes were identified for the 24 Y-STR loci among the three ethnic minorities, including 13 from the Qiangs, 35 from the Manchurians, and 28 from the Shes, with the corresponding Haplotype Diversity (HD) being 0. 7327, 0. 9578, and 0. 9344. Genetic distance between the Shes and Qiangs was relatively close, whilst that for Manchurians was relatively far. Conclusion: Analysis of the genetic characteristics and relationship of the three ethnic minorities from Guizhou can provide a reference for the study of their origin, evolution and patrilineal fusion. © 2018 MeDitorial Ltd. All rights reserved.     

中国汉族群体中PDCD1基因多态性与结直肠癌的相关性CSCD

目的探讨程序性细胞死亡受体1（ programmed cell death 1,PDCD1）基因多态性与结直肠癌的发生发展的关联性。方法应用聚合酶链反应-限制性片段长度多态性（PCR-restriction fragment length polymorphism, PCR-RFLP）方法对426例结直肠癌患者及500名正常个体的rs36084323、rs11568821、rs2227981、rs2227982和rs10204525位点进行多态性分析。结果rs36084323位点G等位基因在显性遗传模型下与TNM分期进展期结直肠癌的发生正关联（OR＝1.59,95%CI：1.02～2.48）。rs36084323、rs11568821、rs2227981、rs2227982和rs10204525位点组成的单倍型G-G-C-T-A和A-G-C-C-G与结直肠癌的发生负关联。结论PDCD1基因rs36084323位点AG和GG基因型与TNM分期进展期的结直肠癌存在正关联。而G-G-C-T-A和A-G-C-C-G单倍型与结直肠癌的发生负关联。     

Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients

AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic sequences of the NR3C1 gene in 181 IBD patients, determined the single nucleotide polymorphisms, and predicted the NR3C1 haplotypes. Furthermore, we investigated whether certain NR3C1 haplotypes are significantly associated with steroid therapy outcomes. RESULTS: We detected 13 NR3C1 variants, whi...     

云南地区恒河猴线粒体DNA控制区遗传多态性研究

目的 从分子水平探讨云南地区恒河猴遗传多样性,为今后开展恒河猴遗传资源的保护及合理利用提供借鉴和背景资料.方法 采用PCR直接测序法测定云南地区恒河猴96份样品的线粒体DNA控制区全序列,用Mege 4.0和DNA SP软件对变异位点数、简约信息位点数、单倍型、单倍型多样度、核苷酸多样度等遗传信息进行分析,基于邻接法(neighbor-joining,NJ)和最小进化法(minimum-evolution,ME)构建系统发生树.结果 在96份样品中,共检测出了149个多态性位点,定义了46种单倍型,单倍型多样度(Hd)为0.968±0.007,核苷酸多样度(Pi)为0.020.结论 云南地区恒河猴存在着较丰富的遗传多态性.     

Tryptophan hydroxylase 2 gene is associated with major depressive disorder in a female Chinese population

Background

Previous candidate gene studies of major depressive disorder (MDD) have provided inconclusive evidence of association for genes with strong biological rationale for MDD. In this study, we aimed to investigate the association of tryptophan hydroxylase 2 gene with MDD and its treatment response in the Chinese Han population.

Methods

Three hundred and sixty eight depressed patients who met DSM-IV criteria for major depressive disorder were recruited for the study. 371 normal controls were recruited from local community. Patients and normal controls were genotyped for TPH2 (rs4290270 and rs7305115) variants by polymerase chain reaction. Male and female subjects were analyzed separately.

Results

No differences were found in the frequencies of the single alleles and genotypes of the tested polymorphisms between MDD patients and normal group. The frequency of the A-A haplotype was significantly higher in female MDD compared to healthy female controls (P < 0.05). No significant association with treatment response was discovered in haplotype and single-marker analysis.

Limitations

This study lacks a placebo control and we cannot definitively exclude the possibility that some patients in the responder group responded to the placebo effect alone.

Conclusion

The result suggests that TPH2 gene may have a gender dependent effect on susceptibility to MDD but not with its treatment response in Chinese Han population. Further studies are needed to replicate the association that we observed.     

APOBEC3H haplotypes and HIV-1 pro-viral vif DNA sequence diversity in early untreated human immunodeficiency virus-1 infection

We examined single nucleotide polymorphisms (SNP) in the APOBEC3 locus on chromosome 22, paired with population sequences of pro-viral human immunodeficiency virus-1 (HIV-1) vif from peripheral blood mononuclear cells, from 96 recently HIV-1-infected treatment-naive adults. We found evidence for the existence of an APOBEC3H linkage disequilibrium (LD) block associated with variation in GA → AA, or APOBEC3F/H signature, sequence changes in pro-viral HIV-1 vif sequence (top 10 significant SNPs with a significant p = 4.8 × 10(-3)). We identified a common five position risk haplotype distal to APOBEC3H (A3Hrh). These markers were in high LD (D' = 1; r(2) = 0.98) to a previously described A3H "RED" haplotype containing a variant (E121) with enhanced susceptibility to HIV-1 Vif. This association was confirmed by a haplotype analysis. Homozygote carriers of the A3Hrh had lower GA->AA (A3F/H) sequence editing upon pro-viral HIV-1 vif sequence (p = 0.01), and lower HIV-1 RNA levels over time during early, untreated HIV-1 infection, (p = 0.015 mixed effects model). This effect may be due to enhanced susceptibility of A3H forms to HIV-1 Vif mediated viral suppression of sequence editing activity, slowing viral diversification and escape from immune responses.     

The distribution of human leukocyte antigen-A, -B,and -DRB1 alleles and haplotypes based on high-resolution genotyping of 167 families from Jiangsu Province,China

We investigated the human leukocyte antigen (HLA)-A, -B, and -DRB1 allele frequencies, the A–B–DRB1, A–B, B–DRB1, and A–DRB1 haplotype frequencies, and the characteristics of linkage disequilibrium between 2 loci in high resolution based on 167 unrelated families from Jiangsu Province, China. A total of 26 alleles at the A locus, 55 alleles at the B locus, and 34 alleles at the DRB1 locus were reported in this study. The top 5 most frequent HLA alleles at the HLA-A, -B, and -DRB1 loci, respectively, were A*11:01, A*24:02, A*02:01, A*33:03, A*30:01; B*13:02, B*40:01 B*46:01, B*58:01, B*54:01; DRB1*09:01, DRB1*07:01, DRB1*12:02, DRB1*15:01, and DRB1*08:03. Several haplotypes with high frequencies were deduced in this study. The top 3 most common A–B–DRB1 haplotypes observed were A*30:01–B*13:02–DRB1*07:01, A*33:03–B*58:01–DRB1*03:01, and A*02:07–B*46:01–DRB1*09:01. The top 3 most common A–B haplotypes were A*30:01–B*13:02, A*33:03–B*58:01, and A*02:07–B*46:01. The top 4 most common A–DRB1 haplotypes were A*30:01–DRB1*07:01, A*33:03–DRB1*13:02, A*24:02–DRB1*09:01, and A*33:03–DRB1*03:01. Finally, the top 3 most common B–DRB1 haplotypes were B*13:02–DRB1*07:01, B*46:01–DRB1*09:01, and B*58:01–DRB1*03:01. From the linkage disequilibrium calculation, the most prominent associations were A*30:01–B*13:02, B*13:02–DRB1*07:01, and A*01:03–DRB1*01:02. These allele and haplotype frequencies could be useful for finding the best matched donors for patients in the China Marrow Donor Program Jiangsu Branch.     

Tumor necrosis factor-alpha gene promoter -308G/A and -238G/A polymorphisms in Mexican patients with type 2 diabetes mellitus

The association between some Tumor necrosis factor-alpha (TNF-α) promoter polymorphisms and Type 2 diabetes mellitus (T2DM) remains controversial. Ethnic differences may play a role in these conflicting results. The aim of this study was to investigate the association between -308G/A and -238G/A polymorphisms located in the promoter region of the TNF-α gene and T2DM in Mexican mestizo patients. Nine hundred four individuals (259 patients with T2DM and 645~controls) were genotyped for the -308G/A and -238G/A polymorphisms by PCR--RFLP. We found that the -238A allele increased the risk of developing T2DM in Mexican patients (OR=1.57, 95% CI: 1.07-2.29; p=0.018). Moreover, we found that the frequency of the GA haplotype (created by the -308G and -238A alleles) was significantly increased in patients with T2DM when compared with controls (OR =1.56, 95% CI: 1.05-2.31; p=0.026). Our results suggest that the -238G/A polymorphism and a specific haplotype (GA) are genetic risk factors for the development of T2DM in Mexican population.     

Association of IL8 -251A/T, IL12B -1188A/C and TNF-α -238A/G polymorphisms with Tourette syndrome in a family-based association study in a Chinese Han population

An earlier study indicated a possible relationship between Tourette syndrome (TS) and the cytokines. To explore this further, we analyzed the association of the polymorphisms, IL8 -251A/T, IL12B -1188A/C and TNF-α -238A/G, in the IL8, IL12B and TNF-α cytokine genes with TS in a Chinese Han population. A total of 108 patients diagnosed with TS and their parents were recruited for the study. The genetic contributions of the IL8 -251A/T, IL12B -1188A/C, and TNF-α -238A/G polymorphisms were evaluated using polymerase chain reaction and restriction enzyme digestion (PCR-RFLP) and haplotype relative risk (HRR) and transmission disequilibrium test (TDT) statistics. Our results revealed no significant associations between the IL8 -251A/T, IL12B -1188A/C and TNF-α -238A/G polymorphisms and TS (for IL8 -251A/T, TDT=0.418, df=1, P=0.518; HRR=2.17, X(2)=3.000, P=0.083, 95%CI: 0.900-5.230; for IL12B -1188A/C, TDT=1.131, df=1, P=0.288; HRR=1.27, X(2)=0.35, P=0.549, 95%CI: 0.580-2.790; for TNF-α -238A/G, TDT=2.793, df=1, P=0.095; HRR=0.27, X(2)=2.90, P=0.089, 95%CI: 0.061-1.217). This result was confirmed using haplotype-based haplotype relative risk (HHRR) which allows the two alleles in each genotype to be considered separately. Our data suggests that the IL-8 -251A/T, IL-12B -1188A/C and TNF-α -238A/G polymorphisms may not be associated with susceptibility to TS in the Chinese Han population studied. However, these results need to be replicated using larger datasets collected from different populations.     

Tetrahymena thermophila, a unicellular eukaryote with separate germline and somatic genomes

Tetrahymena thermophila is a ciliate - a unicellular eukaryote. Remarkably, every cell maintains differentiated germline and somatic genomes: one silent, the other expressed. Moreover, the two genomes undergo diverse processes, some as extreme as life and death, simultaneously in the same cytoplasm. Conserved eukaryotic mechanisms have been modified in ciliates to selectively deal with the two genomes. We describe research in several areas of Tetrahymena biology, including meiosis, amitosis, genetic assortment, selective nuclear pore transport, somatic RNAi-guided heterochromatin formation, DNA excision and programmed nuclear death by autophagy, which has enriched and broadened knowledge of those mechanisms.