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1.
Chandana Basu Mallick Florin Mircea Iliescu M?rt M?ls Sarah Hill Rakesh Tamang Gyaneshwer Chaubey Rie Goto Simon Y. W. Ho Irene Gallego Romero Federica Crivellaro Georgi Hudjashov Niraj Rai Mait Metspalu C. G. Nicholas Mascie-Taylor Ramasamy Pitchappan Lalji Singh Marta Mirazon-Lahr Kumarasamy Thangaraj Richard Villems Toomas Kivisild 《PLoS genetics》2013,9(11)
Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. 相似文献
2.
S. Justin Carlus Saumya Sarkar Sandeep Kumar Bansal Vertika Singh Kiran Singh Rajesh Kumar Jha Nirmala Sadasivam Sri Revathy Sadasivam P. S. Gireesha Kumarasamy Thangaraj Singh Rajender 《PloS one》2016,11(3)
Background
Optimum efficiency of the folate pathway is considered essential for adequate ovarian function. 677 C>T substitution in the 5, 10-methylene tertrahydrofolatereductase (MTHFR) gene compromises activity of the MTHFR enzyme by about 50%. The significance of correlation between 677C>T substitution and PCOS remains dubious due to the low power of published studies.Methods and Results
We analyzed MTHFR 677 C>T site in ethnically two different PCOS case-control groups (total 261 cases and 256 controls) from India. The data analysis revealed a lack of association between this polymorphism and PCOS [OR = 1.11 (95%CI = 0.71–1.72), P = 0.66]. Group-wise analysis on the basis of ethnicity also revealed no association in any of the ethnic groups [Indo-Europeans, P = 1; Dravidians, P = 0.70]. Homocysteine levels did not differ significantly between cases (15.51 μmol/L, SD = 2.89) and controls (15.89 μmol/L, SD = 2.23). We also undertook a meta-analysis on 960 cases and 1028 controls, which suggested a significant association of the substitution with PCOS in the dominant model of analysis (OR = 1.47 (95%CI = 1.04–2.09), P = 0.032]. Trial sequential analysis corroborated findings of the traditional meta-analysis. However, we found that the conclusions of meta-analysis were strongly influenced by studies that deviated from the Hardy Weinberg equilibrium. A careful investigation of each study and a trial sequential analysis suggested that 677 C>T substitution holds no clinical significance in PCOS in most of the populations.Conclusion
In conclusion, MTHFR 677 C>T polymorphism does not affect PCOS risk in India. The association seen in the meta-analysis is due to an outlier study and studies showing deviation from the Hardy Weinberg equilibrium. 相似文献3.
Deepa Selvi Rani Perundurai S. Dhandapany Pratibha Nallari Periyasamy Govindaraj Lalji Singh Kumarasamy Thangaraj 《Mitochondrion》2010,10(2):166-173
Mutations in PTPN11 gene was responsible for ~50% of the Noonan syndrome (NS), however, we did not find any mutation in PTPN11 in any of seven NS patients analysed. Whereas, the complete mtDNA sequencing revealed 146 mutations, of which five, including one heteroplasmic (A11144R; Thr → Ala) non-synonymous mutation, were novel and exclusively observed in NS patients. Interestingly all the seven probands and their maternal relatives were clustered under a major haplogroup R and its novel sub-haplogroups (R7b1b, R30a1, R30c, T2b7, U9a1) exclusive in NS, therefore we strongly suggest that these haplogroups may influence NS in South Indian populations. 相似文献
4.
Rajagopal Subramanyam Craig Jolley Balakumar Thangaraj Sreedhar Nellaepalli Andrew N. Webber Petra Fromme 《Planta》2010,231(4):913-922
The effect of high salt concentration (100 mM NaCl) on the organization of photosystem I-light harvesting complex I supercomplexes
(PSI-LHCI) of Chlamydomonas reinhardtii was studied. The electron transfer activity was reduced by 39% in isolated PSI-LHCI supercomplexes. The visible circular
dichroism (CD) spectra associated with strongly coupled chlorophyll (Chl) dimers were reduced in intensity, indicating that
pigment–pigment interactions were disrupted. This data is consistent with results from fluorescence streak camera spectroscopy,
which suggest that red-shifted pigments in the PSI-LHCI antenna had been lost. Denaturing gel electrophoresis and immunoblot
analysis reveals that levels of the PSI reaction center proteins PsaD, PsaE and PsaF were reduced due to salt stress. PsaE
is almost completely absent under high salt conditions. It is known that the membrane-extrinsic subunits PsaD and E form the
ferredoxin-docking site. Our results indicate that the PSI-LHCI supercomplex is damaged by reactive oxygen species at high
salt concentration, with particular impact on the ferredoxin-docking site and the PSI-LHCI interface. 相似文献
5.
Zerjal T Pandya A Thangaraj K Ling EY Kearley J Bertoneri S Paracchini S Singh L Tyler-Smith C 《Human genetics》2007,121(1):137-144
The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at
birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed
male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86
from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male
substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance
of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper
castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger
effective population sizes, or less strict isolation, or both.
Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.
Tatiana Zerjal and Arpita Pandya contributed equally to this work. 相似文献
6.
Mahesh R Devadoss T Pandey DK Bhatt S 《Bioorganic & medicinal chemistry letters》2011,21(4):1253-1256
A novel series of 3-ethoxyquinoxalin-2-carboxamides were designed as per the pharmacophoric requirements of 5-HT3 receptor antagonist using ligand-based approach. The desired carboxamides were synthesized from the key intermediate, 3-ethoxyquinoxalin-2-carboxylic acid by coupling with appropriate amines in the presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC·HCl) and 1-hydroxybenzotriazole (HOBt). The 5-HT3 receptor antagonism was evaluated in longitudinal muscle myenteric plexus preparation from guinea pig ileum against 5-HT3 agonist, 2-methy-5-HT, which was expressed in the form of pA2 values. Compound 6h (3-ethoxyquinoxalin-2-yl)(4-methylpiperazin-1-yl)methanone was found to be the most active compound, which expressed a pA2 value of 7.7. In forced swim test, the compounds with higher pA2 value exhibited good anti-depressant-like activity and compounds with lower pA2 value failed to show activity as compared to the vehicle-treated group. 相似文献
7.
Annadurai T Vigneshwari S Thirukumaran R Thomas PA Geraldine P 《Journal of physiology and biochemistry》2011,67(4):519-530
Acetyl-l-carnitine (ALCAR) has been shown to prevent experimental selenite cataractogenesis, a manifestation of oxidative stress,
but little is known about its potential in other settings of oxidative stress. The present study was based on the hypothesis
that ALCAR prevents carbon tetrachloride (CCl4)-induced oxidative stress in vital tissues. Male albino Wistar rats were divided into three groups, each of six rats. Group
I (control) rats received only vehicle (1 ml/kg b.w.) for 4 days; Group II (CCl4-exposed, untreated) rats received CCl4 (2 ml/kg b.w.) on the second and third days and vehicle on the first and fourth days; Group III (CCl4-exposed, ALCAR-treated) rats received ALCAR (200 mg/kg b.w.) for 4 days and CCl4 on the second and third days. All administrations were made intraperitoneally. After the experimental period, significantly
(P < 0.05) elevated mean serum levels of aspartate transaminase, alanine transaminase, alkaline phosphatase, and lactate dehydrogenase
were observed in Group II rats when compared to Group I and Group III rats. The mean levels of vitamin C, vitamin E, and reduced
glutathione and the mean activities of superoxide dismutase, catalase, and glutathione peroxidase were significantly (P < 0.05) lower in samples of hemolysate and of liver, kidney, and brain tissues of Group II rats than those in Group I and
Group III rats. The mean level of lipid peroxidation was significantly (P < 0.05) higher in Group II rats than that in Group I and Group III rats. Moreover, the CCl4-induced upregulation of inducible nitric oxide synthase expression was prevented by ALCAR in the liver and brain tissues.
These results suggest that ALCAR is able to prevent the CCl4-induced oxidative stress. 相似文献
8.
Thangaraj K Sridhar V Kivisild T Reddy AG Chaubey G Singh VK Kaur S Agarawal P Rai A Gupta J Mallick CB Kumar N Velavan TP Suganthan R Udaykumar D Kumar R Mishra R Khan A Annapurna C Singh L 《Human genetics》2005,116(6):507-517
Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNAlys) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences. 相似文献
9.
Global patterns in human mitochondrial DNA and Y-chromosome variation caused by spatial instability of the local cultural processes 下载免费PDF全文
Kumar V Langstieh BT Madhavi KV Naidu VM Singh HP Biswas S Thangaraj K Singh L Reddy BM 《PLoS genetics》2006,2(4):e53
Because of the widespread phenomenon of patrilocality, it is hypothesized that Y-chromosome variants tend to be more localized geographically than those of mitochondrial DNA (mtDNA). Empirical evidence confirmatory to this hypothesis was subsequently provided among certain patrilocal and matrilocal groups of Thailand, which conforms to the isolation by distance mode of gene diffusion. However, we expect intuitively that the patterns of genetic variability may not be consistent with the above hypothesis among populations with different social norms governing the institution of marriage, particularly among those that adhere to strict endogamy rules. We test the universality of this hypothesis by analyzing Y-chromosome and mtDNA data in three different sets of Indian populations that follow endogamy rules to varying degrees. Our analysis of the Indian patrilocal and the matrilocal groups is not confirmatory to the sex-specific variation observed among the tribes of Thailand. Our results indicate spatial instability of the impact of different cultural processes on the genetic variability, resulting in the lack of universality of the hypothesized pattern of greater Y-chromosome variation when compared to that of mtDNA among the patrilocal populations. 相似文献
10.
Ismail Thanseem Kumarasamy Thangaraj Gyaneshwer Chaubey Vijay Kumar Singh Lakkakula VKS Bhaskar B Mohan Reddy Alla G Reddy Lalji Singh 《BMC genetics》2006,7(1):1-11