Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India

Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 for COI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes, respectively. Almost all species were represented by 2–3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis, Liodrosophila nitida, Lordiphosa parantillaria, Lordiphosa ayarpathaensis, Scaptomyza himalayana, Scaptomyza tistai, Zaprionus grandis and Stegana minuta are provided to public domains through this study.     

Association of interleukin-10 (A1082G) gene polymorphism with oral squamous cell carcinoma in north Indian population

The functional polymorphism A1082G in the gene (IL10) for interleukin-10 associated with risk of oral squamous cell carcinoma (OSCC). The present case–control study was to evaluate the possible association between IL10 A1082G gene and OSCC in north Indian population. Analysis of IL10 A1082G genotype in 232 OSCC cases and 221 healthy controls of comparable age, gender, smokers, tobacco chewing and alcohol consumption. IL10 A1082G status in cases and controls were evaluated by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP). The frequencies of IL10 A1082G polymorphism AA, AG, GG genotypes were 29.74, 68.10 and 2.15% in OSCC cases and 57.46, 42.08 and 0.45% in healthy controls. The average frequency of G mutant allele was 36.20% in OSCC cases compared with 21.50% among the controls and this allele was associated with increased risk for OSCC cases. Heterozygous AG genotype was found statistically significant in OSCC cases than in controls (OR = 1.6, 95% CI = 1.1–2.2, P = 0.003), whereas homozygous mutant GG genotype was not found significant (OR = 4.7, 95% CI = 0.55–41.1, P = 0.2). Moreover, we found that G allele was significant in OSCC cases of tobacco chewing. The frequency of IL10 A1082G polymorphism G allele and AG genotype is associated with OSCC cases as compared with controls; this may be due to smoking and tobacco chewing. Our findings showed that in IL10 A1082G gene polymorphism AG genotype and G allele may participate in the progression of OSCC.     

Statistical equivalent of the classical TDT for quantitative traits and multivariate phenotypes

Clinical end-point traits are usually governed by quantitative precursors. Hence, there is active research interest in developing statistical methods for association mapping of quantitative traits. Unlike population-based tests for association, family-based tests for transmission disequilibrium are protected against population stratification. In this study, we propose a logistic regression model to test the association for quantitative traits based on a trio design. We show that the method can be viewed as a direct extension of the classical transmission diequilibrium test for binary traits to quantitative traits. We evaluate the performance of our method using extensive simulations and compare it with an existing method, family-based association test. We found that the two methods yield comparable powers if all families are considered. However, unlike FBAT, which yields an inflated rate of false positives when noninformative trios with all three individuals’ heterozygous are removed, our method maintains the correct size without compromising too much on power. We show that our method can be easily modified to incorporate multivariate phenotypes. Here, we applied this method to analyse a quantitative endophenotype associated with alcoholism.