allele

摘要： DEAR EDITOR,Understanding the different immune responses of wild and domestic caprid species is critical for addressing certain zoonotic diseases.In this study,we generated blood transcriptomes of 13 Siberian ibex and domestic goat hybrids and performed allele-specific expression and splicing analyses.Results showed that genes exhibiting significant imbalance between the ibex and goat were highly related to the Toll-like receptor(TLR),antigen recognition,and immune activation pathways.Comparative genomic analysis of the species revealed that immune function-related genes were under strong selection pressure in the domestic goat.

摘要： This study investigated distribution of HLA alleles (HLADRB1*01, *03, *04, *07, HLA-DQB1*0201, *0301/4) in 34 healthy controls and 57 rheumatoid arthritis (RA) patients in a Bangladeshi population and correlated the genotypic frequencies with clinical parameters. Frequency distribution of HLA-DRB1*04 (34%) and HLA-DRB1*01 (32%) were the highest followed by HLA-DQB1*0301/4 (29%) and HLA-DQB1*0201 (26%) in RA patients while HLA-DRB1*03 (12%) had lowest frequency. Plasma level of anti-CCP and rheumatoid factor antibodies confirmed diagnosis of RA patients that varied significantly between patients and healthy controls. Likewise, plasma levels of C-reactive protein, triglycerides, cholesterol, HDL-cholesterol and activities of AST and ALT exhibited significant variation between the two groups. In contrast, the levels of glucose, total protein, uric acid, LDL-cholesterol and plasma activity of ALP in RA patients had no significant deviations from healthy controls. Relationship between HLA genotype frequency and clinical parameters revealed that the mean levels of anti-CCP and rheumatoid factor antibodies were highest in the patients harboring HLA-DRB1*04 allele. These findings underpin the correlation between HLA genotype with clinical markers of RA which are indicative of disease severity. The positive correlation of these markers with certain HLA genes may be used to identify susceptible individuals who are likely to have RA in Bangladeshi population.

摘要： Background: Cysteine-Cysteine Chemokine Receptor 5 (CCR5), also referred to as CD195, is a component of the mammalian cell membrane and is receptor for chemokines that are activated during cell damage and inflammations. This receptor is coded by a gene located in the human chromosome 3. A Mutation on this CCR5 through deletion of 32 base pairs results into a non-destructive gene CCR5Δ32. It enables protection against HIV infection to its homozygous carriers and slows progression of the disease to heterozygous carriers. Objective: To systematically review and establish global distribution of CCR5Δ32 allele in HIV-1 infected individuals over the history of the epidemic and compare regions inhabited by Caucasians, Asians and Africans. Methodology: This meta-analysis comprised of published papers with over 10,000 individuals from whom CCR5-Delta 32 allele was successfully genotyped and recorded. The study review period was from 1984 to 2017. The search targeted online sources such as Hinari specifically PubMed Central, Google scholar, Science Direct, Research4Life, National Center for Biotechnology Information (NCBI), OVID databases, AIDS Journal and Google. The searches were not limited to a particular publication language or study design but excluded letters of correspondence and conference presentations. Search strategy using key words from a combination of Medical Subject Heading (MeSH) and free text including terms related to CCR5, CCR5Δ32 and HIV were performed in Medical Literature Analysis and Retrieval System Online (MEDLINE) through Ovid Open Access. Additional studies were identified by perusing the reference list of relevant and included articles. The review considered studies conducted among general population, both HIV positive and HIV negative individuals, exposed seronegatives (ESN), exposed seropositives (ESP) and highly exposed seronegatives (HESN) and resultant data pooled using a fixed effect model. Results: A total of 40 studies comprising 10,871 participants were reviewed. These were from three main regions: Europe, Africa and Asia. Of the studies accessed and reviewed, Caucasians were 22.5%, Africans were 12.5%, Europeans were 27% and others (not specified) were 37.5%. The distribution of CCR5Δ32 allele among different populations in comparison to its heterozygosity displayed significant association with a pooled Odds Ratio (OR) of 0.08 (95% CI, 0.03 - 0.18, P 2 = 0% and a P value of 0.50. Among the Caucasians alone the OR was at 0.04 (95% CI, 0.01 - 0.19, I2 = 96%) and a significant P value of < 0.00001 displaying a high presence of CCR5Δ32 homozygosity as compared to Europeans with OR of 0.09 (95% CI, 0.04 - 0.19, I2 = 21%, P = 0.25) and Africans with OR 0.25 (95% CI, 0.03 - 2.29, I2 = 0%, P = 0.81);an indication that race can be a factor that determines CCR5Δ32 homozygosity or heterozygosity and it highly favors the Caucasians. Out of 136 homozygous carriers found in the review Europeans had 6%, Caucasian 93%, Africans 0% and others combined 0.7%. Conclusion: The distribution of CCR5Δ32, an allele that is associated with lower acquisition of HIV/AIDS is at 93% among the Caucasians. The remaining 7% is shared amongst the rest of the populations, hence high susceptibility to the disease. Minimal availability of recorded data experienced in this study is a clear indication that there exist major gaps in studies that could further associate CCR5Δ32 allele frequency and HIV infection in different populations. The review recommends a mixture of population genetics and epidemiological studies in trying to understand the increasing rates of HIV prevalence among selected groups.

摘要： Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations;however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

摘要： Objective: Migraine, a common chronic neurological disorder involves a pathophysiology having both multiple genetic and environmental factors. 5, 10-Methylenetetrahydrofolate reductase (MTHFR) involved in folate metabolism has an important role in a cell for folate availability which is critical for DNA integrity. Methods: This case-control study conducted in Srinagar, Kashmir (North India) between 2013 and 2015 was designed to evaluate risk induced due to MTH-FR 677C>T gene polymorphisms to contribute in susceptibility for migraine in Kashmir population (North India). Using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, we tested the genotype distribution of 100 migraine patients in comparison with 120 healthy migraine-free controls from the same geographical region. Results: The genotypic frequencies of the patients and controls were not significantly associated (p > 0.05). Higher distribution of TT mutant genotype was found in controls as against the cases (5% versus 1%) but association was not significant (p > 0.05). Per copy frequency of T allele (Val) was found to be 0.14 in cases versus 0.19 in controls (p 0.05). Similar scenario was observed when migraine without aura was compared with controls where variant genotype (16% cases versus 39.0% controls: p > 0.05) as well as allele frequency was found to be less in cases (cases 0.15 versus 0.19 controls: p > 0.05). Conclusions: We conclude that MTHFR gene C677T polymorphism has no role in predisposition to the migraine in our population and cannot serve as a predictive factor for the risk of migraine.

摘要： 答：大多数真核生物拥有两套匹配的染色体组,通常称为二倍体生物。除了对应同源染色体可能存在的一些序列差异和性染色体（X染色体和Y）存在差异,二倍体生物在两套染色体中应具有相同的座位（称为等位基因,allele）。如果二倍体生物中对应的等位基因一致,那么这个生物称为纯合子（homozygous）。如果相应的等位基因不一致,这个生物称为杂合子（heterozygous）。

摘要： Color is one of the phenotypic markers mostly used to study soybean (Glycine max L. Merr.) in the study of genetic, molecular and biochemical processes, due to their easy recognizability. The genetic control of several soybean natural variants has not been studied. The standard phenotype of R gene is black hilum on black seed. The genetic type T16 is the only occurrence with brown hilum on black seed coat and its genetic control was not described until now. The aim of this study is to understand the genetic control of seed coat and hilum color in the genetic types T16 and in the natural variants of Bragg, BR6 and BR13. T16 was combinined with Bragg P and BR13P (black seed color) and BR6M (brown seed color) and T236 (r-m). It was found that the genetic control of the brown hilum trait in black seed coat of the T16 genotype was controlled by two loci segregating independently and controlling the expression of the color of the hilum and the seed coat color. The expression of the brown hilum trait in black seed coat is dependent on locus T_, which controls pubescence color;therefore it occurs only in genotypes with tawny brown pubescence (T_), which caracterizes the pleiotropic effect of this locus on the trait hilum brown trait in black seed coat. The color of the hilum and the seed coat color belong to the same allelic sequence. No maternal effect was found in the expression of hilum brown trait in black seed coat.

摘要： AIM: To investigate the role of endothelial nitric oxide synthase-786 T > C promoter polymorphism in the etiology of gastric cancer(GC). METHODS: A total of 150 GC patients and 150 control subjects were included in the study. The information on demographic features was elicited with an informed consent from all the patients and control subjects using a structured questionnaire. Helicobacter pylori(H. pylori) infectivity status was tested in antral biopsies from all the subjects by rapid urease test following the method of Vaira et al. Genomic DNA was isolated from whole blood samples following the salting out method of Lahiri et al. Genotype analysis of the rs2070744 polymorphism was carried out by allele-specific polymerase chain reaction method. The genotypes were determined based on the appearance of bands on an agarose gel stained with ethidium bromide under ultraviolet gel documentation with the help of 100 bp ladder. Odds ratios and corresponding 95%CIs were determined using java stat online software. RESULTS: There was a significant difference in the distribution of C allele(C vs T; P = 0.000, OR = 5.038) in patient group compared to the control subjects exhibiting a fivefold increased risk for GC. When the T/T and C/C genotypes were compared, there was an enhanced GC risk for individuals with C/C genotype(T/T vs C/C; P = 0.000). Among the demographic factors, smoking and alcoholism were the common risk factors in patients compared to the control subjects(P < 0.05). Patients with smoking and alcoholism developed cancer even in heterozygous T/C condition(smoking: P = 0.020 and alcoholism: P = 0.005). Individuals with H. pylori infection showed seven fold increased risk for cancer. All the patients with C/C genotype revealed a significant association between H. pylori infection and GC. Among the patients 2.4% of them revealed familial incidence of GC. No significant difference was noticed between cases and controls with regard to consanguinity(P = 0.473).CONCLUSION: The Present data suggest that eN OS-786 C/C genotype and C allele may be considered as potential risk factors in patients with GC.

摘要： Background: Since the identification of the cystic fibrosis transmembrane regulator (CFTR) gene in 1989, many polymorphisms have been identified in cystic fibrosis (CF) or CFTR-related disorders (CFTR-RDs) patients and still remain to be characterized at the molecular level. These polymorphisms are difficult to classify as pathogenic or non-disease causing because the polymorphisms are either located in the coding region, but are synonymous, or are found in the intronic regions. Here we investigated the potential impact of the c.743 + 40A > G polymorphism within CFTR intron 6 on the alternative splicing. Indeed, this variant has been observed frequently in our examined patients. Moreover, a family carrying this variant exhibited CFTR-RD phenotype. Methods: By denaturing high pressure liquid phase chromatography (DHPLC) and sequencing, thirty of 293 subjects French origin carried the c.743 + 40A > G variant. Of these, 16 patients were affected by CF or CFTR-RD. Wild-type sequences and mutant CFTR intron 6 and its boundaries were inserted into the pTBNdeI hybride minigene and expressed in three different cell lines. After RT-PCR analysis of mRNA using specific primers, sequences of the minigene transcripts were obtained. Results: No aberrant splicing was detected with minigene carrying c.743 + 40A > G variant in all transfected cell lines. However, an alternative splicing in the positive control was detected with a minigene carrying the c.1392G > T + 1G > T mutation: 5 nucleotides were deleted from mRNA sequences, indicating that used cell lines are appropriate for studying the splicing. Conclusion: Transient transfections of a minigene containing the c.743 + 40A > G polymorphism showed no splicing errors, and thus this intronic alteration was finally classified as non-pathogenic. As it is always associated with c.2562T > G and c.4389G > A, or TG12-7T poly-morphisms, further experiments are needed to determine the role of these complex alleles in disease pathogenesis.

摘要： Objective:To determine the distribution of Duffy blood group genotypes in Balouch population as a major ethnic group that living in a sub-tropical area in south East of Iran.Methods:In this study,the Duffy blood group FY phenolypes were determined using indireet anti-globulin technique and also genotype by PCR-RFLP in 160 vivax malaria patients and 160 control individuals.Results:The results showed that the most common Duffy geitolype was FYA/FYB(46.6%)followed by FYA/FYA(15.3%),FYA/FYO(14.4%),FYB/FYO(11.9%,),FYB/FYB(10%)and FYO/FYO(1.9%).In case individuals,frequency of FY A.FYB and FYO alleles were 0.471,0.431and 0.097,respectively compaired to 0.444,0.353 and 0.203,respectively in control(non-infected)group.Conclusions:This data provide evidence that individuals with the FYA/FYB genotype have higher susceptibility to malaria and there are significant associations between Duffy blood group variants and susceptibility or resistance to vivax malaria.

摘要： 本发明一种公开了DNA插入片段下调番茄YFT1allele表达及其在番茄品质改良中的应用。通过功能互补遗传转化实验为YFT1在番茄果色形成过程中功能确认提供了坚实的遗传学证据。启动子活性研究进一步确认了YFT1基因启动子驱动能力显著降低，并且仅与573bp DNA片段插入有关，并进一步从分子水平揭示，YFT1调控区域(启动子)的573bp DNA片段插入导致基因显著下调表达是由于其含有2个负调控区段(‑272bp～‑173bp,‑172～‑73bp)；同时该插入事件也导致了YFT1allele在yft1产生了可变剪接和5'UTR区域中的uORF被打破。

摘要： 本发明属于法医遗传学应用研究领域，具体涉及一种基于二代测序（Next Generation Sequencing，NGS）的用于法医学个体识别和亲缘关系鉴定的30个Multiple‑allele SNP位点的检测技术体系的研发及其检测技术方法。本发明应用NGS平台（illumina NOVASEQ）对30个Multiple‑allele SNP位点进行深度平行测序，可实现同时对多个样本的30个目标区域的测序分析，节约人力、物力和财力，提到了检测效率；PCR产物片段分布在58‑139 bp，体系适用于法医降解样本的检测；根据Multiple‑allele SNP位点非二等位基因的特点及基于序列内部碱基深度的读取判断，可提高对法医混合检材的分析能力。该检测体系在法医学领域具有较高的应用价值。