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Search Results: 1 - 10 of 1127 matches for " Ranjan Deka "
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Folklore and Northeast Indian History  [PDF]
Meeta Deka
Sociology Mind (SM) , 2011, DOI: 10.4236/sm.2011.14022
Abstract: The article intends to highlight folklore as an alternative source for the writing of history, particularly of the northeastern region of India, which is inhabited by numerous tribal communities, and where there is a dearth of written documents, archaeological and other evidences. Folklore as a source is important to explain and understand societies in the context of preserving cultural diversity and protecting minority cultures, especially those of indigenous peoples and marginalized social groups. With the increased growth of several ethnic identity crises in the region in recent times, the roots for their respective indigenous history are often traced to folklore.
Deletion Hotspots in AMACR Promoter CpG Island Are cis-Regulatory Elements Controlling the Gene Expression in the Colon
Xiang Zhang,Irwin Leav,Monica P. Revelo,Ranjan Deka,Mario Medvedovic,Zhong Jiang,Shuk-Mei Ho
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000334
Abstract: Alpha-methylacyl-coenzyme A racemase (AMACR) regulates peroxisomal β-oxidation of phytol-derived, branched-chain fatty acids from red meat and dairy products — suspected risk factors for colon carcinoma (CCa). AMACR was first found overexpressed in prostate cancer but not in benign glands and is now an established diagnostic marker for prostate cancer. Aberrant expression of AMACR was recently reported in Cca; however, little is known about how this gene is abnormally activated in cancer. By using a panel of immunostained-laser-capture-microdissect?edclinical samples comprising the entire colon adenoma–carcinoma sequence, we show that deregulation of AMACR during colon carcinogenesis involves two nonrandom events, resulting in the mutually exclusive existence of double-deletion at CG3 and CG10 and deletion of CG12-16 in a newly identified CpG island within the core promoter of AMACR. The double-deletion at CG3 and CG10 was found to be a somatic lesion. It existed in histologically normal colonic glands and tubular adenomas with low AMACR expression and was absent in villous adenomas and all CCas expressing variable levels of AMACR. In contrast, deletion of CG12-16 was shown to be a constitutional allele with a frequency of 43% in a general population. Its prevalence reached 89% in moderately differentiated CCas strongly expressing AMACR but only existed at 14% in poorly differentiated CCas expressing little or no AMACR. The DNA sequences housing these deletions were found to be putative cis-regulatory elements for Sp1 at CG3 and CG10, and ZNF202 at CG12-16. Chromatin immunoprecipitation, siRNA knockdown, gel shift assay, ectopic expression, and promoter analyses supported the regulation by Sp1 and ZNF202 of AMACR gene expression in an opposite manner. Our findings identified key in vivo events and novel transcription factors responsible for AMACR regulation in CCas and suggested these AMACR deletions may have diagnostic/prognostic value for colon carcinogenesis.
Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChip
Jessica G Woo, Guangyun Sun, Mary Haverbusch, Subbarao Indugula, Lisa J Martin, Joseph P Broderick, Ranjan Deka, Daniel Woo
BMC Genetics , 2007, DOI: 10.1186/1471-2156-8-79
Abstract: Buccal cytobrushes stored for ~7 years at -80°C prior to extraction yielded sufficient double stranded DNA (dsDNA) to be successfully genotyped on the Affymetrix ~262 K NspI chip, with yields between 536 and 1047 ng dsDNA. Using the BRLMM algorithm, genotyping call rates for blood samples averaged 98.4%, and for buccal samples averaged 97.8%. Matched blood samples exhibited 99.2% concordance, while matched blood and buccal samples exhibited 98.8% concordance.Buccal cytobrushes stored long-term result in sufficient dsDNA concentrations to achieve high genotyping call rates and concordance with stored blood samples in the context of Affymetrix 500 K SNP genotyping. Thus, given high-quality collection and storage protocols, it is possible to use stored buccal cytobrush samples for genome-wide association studies.While blood is considered the optimal source for DNA, inclusion of a blood draw may deter study participation [1]. Buccal cytobrush collection is a simple, painless procedure that allows for effective DNA sampling from a large population, and has been used in several large epidemiologic studies [2,3]. However, concerns regarding the use of buccal brushes have included the lower quantity of genomic DNA isolated [4], lower quality of DNA [4,5], and the fidelity of results from buccal brushes compared with blood samples [5-7]. In addition, there is a concern that older buccal brush samples may not yield as high-quality results as fresh samples [8].The advent of large scale genotyping platforms has also resulted in a reduction in the amount of DNA required. The Affymetrix 500 K GeneChip requires only 250 ng of total genomic DNA per chip, 500 ng total, and this DNA quantity has not changed with the recent release of the Affymetrix 5.0 and 6.0 chips, which enable genotyping up to 1.8 million genetic markers [9-11]. Thus, the DNA requirements of the Affymetrix chips are well below the expected yield of total DNA for buccal samples. As the Affymetrix system uses restri
Common SNPs in FTO Gene Are Associated with Obesity Related Anthropometric Traits in an Island Population from the Eastern Adriatic Coast of Croatia
Ge Zhang,Rebekah Karns,Nina Smolej Narancic,Guangyun Sun,Hong Cheng,Sasa Missoni,Zijad Durakovic,Pavao Rudan,Ranajit Chakraborty,Ranjan Deka
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010375
Abstract: Multiple studies have provided compelling evidence that the FTO gene variants are associated with obesity measures. The objective of the study was to investigate whether FTO variants are associated with a broad range of obesity related anthropometric traits in an island population.
Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes
Ritesh Kaushal, Daniel Woo, Prodipto Pal, Mary Haverbusch, Huifeng Xi, Charles Moomaw, Padmini Sekar, Brett Kissela, Dawn Kleindorfer, Matthew Flaherty, Laura Sauerbeck, Ranajit Chakraborty, Joseph Broderick, Ranjan Deka
BMC Medical Genetics , 2007, DOI: 10.1186/1471-2350-8-49
Abstract: At the APOE locus, no individual SNP was associated with SAH after correction for multiple comparisons. Haplotype analysis revealed significant association of the major haplotype (Hap1) in APOE with SAH (p = 0.001). The association stemmed from both the 5' promoter and the 3' region of the APOE gene. APOE ε2 and ε 4 were not significantly associated with SAH. No association was observed for ELN at genotype, allele, or haplotype level and our study failed to confirm previous reports of ELN association with aneurysmal SAH.This study suggests a role of the APOE gene in the etiology of aneurysmal SAH.Non-traumatic, spontaneous subarachnoid hemorrhage (SAH) affects 16,000 to 17,000 individuals each year in the United States [1-3]. SAH has a 30-day mortality rate exceeding 40%, and surviving patients often demonstrate significant morbidity [2,4]. Over 80% of SAH can be attributed to intracranial aneurysm (IA) rupture. Familial aggregation studies of SAH have consistently identified an increased risk of a first-degree relative with SAH or family history of SAH independent of smoking and hypertension [5].Variants of the apolipoprotein E (APOE) gene have been associated with Alzheimer's disease, lipid disorders and cardiovascular disease [6-8]. Previous studies have demonstrated that APOE ε4 and/or APOE ε2 are associated with lobar intracerebral hemorrhage (ICH) [9,10]. We recently reported that haplotypes which include polymorphisms in the 5' untranslated region of the APOE gene are risk factors for lobar ICH [11]. Specific to SAH, Kokubo et al. [12] found significant association of APOE ε4 with SAH in a Japanese population. Niskakangas et al. [13] reported association of APOE ε4 with adverse outcome after aneurysmal SAH. No study on other polymorphisms of APOE with regard to risk of SAH has yet been reported.In addition to APOE, the elastin (ELN) gene emerged as a putative gene for IA after linkage was found on 7q11, where ELN is located [14]. However, prior association st
A tagging SNP in INSIG2 is associated with obesity-related phenotypes among Samoans
Ranjan Deka, Ling Xu, Prodipto Pal, Palanitina T Toelupe, Tuiasina S Laumoli, Huifeng Xi, Ge Zhang, Daniel E Weeks, Stephen T McGarvey
BMC Medical Genetics , 2009, DOI: 10.1186/1471-2350-10-143
Abstract: We studied 907 adult Samoan participants from a longitudinal study of adiposity and cardiovascular disease risk in two polities, American Samoa and Samoa. Four tagSNPs were identified from the Chinese HapMap database based on pairwise r2 of ≥0.8 and minor allele frequency of ≥0.05. Genotyping was performed using the TaqMan assay. Tests of association with BMI and ABDCIR were performed under the additive model.We did not find association of rs7566605 with either BMI or ABDCIR in any group of the Samoans. However, the most distally located tagSNPs in Intron 3 of the gene, rs9308762, showed significant association with both BMI (p-value 0.024) and ABDCIR (p-value 0.009) in the combined sample and with BMI (p-value 0.038) in the sample from Samoa.Although rs7566605 was not significantly associated with obesity in our study population, we can not rule out the involvement of INSIG2 in obesity related traits as we found significant association of another tagSNP in INSIG2 with both BMI and ABDCIR. This study suggests the importance of comprehensive assessment of sequence variants within a gene in association studies.Using genome-wide association analysis, Herbert et al. [1] reported a common variant, rs7566605, in the 5' region of the INSIG2 gene associated with obesity in the Framingham Heart Study population samples and also replicated this finding in four independent cohorts of European and African American ancestries. However, the association of this variant remains inconclusive with confirmation or lack thereof in several follow-up studies conducted in populations of diverse ethnicities [2-12]. Analysis of a single variant could be perceived as a limitation in assessing genetic association of a putative locus. To guard against this potential limitation we conducted a comprehensive association analysis of common tagging SNPs in the INSIG2 gene among adult Samoans, Polynesians of the Western Pacific, residing in Samoa and American Samoa.Our study sample derives from a lo
Suggestive linkage detected for blood pressure related traits on 2q and 22q in the population on the Samoan islands
Karolina ?berg, Feng Dai, Satupaitea Viali, John Tuitele, Guangyun Sun, Subba R Indugula, Ranjan Deka, Daniel E Weeks, Stephen T McGarvey
BMC Medical Genetics , 2009, DOI: 10.1186/1471-2350-10-107
Abstract: We found suggestive univariate linkage for SBP on chromosome 2q35-q37 (LOD 2.4) and for PP on chromosome 22q13 (LOD 2.2), two chromosomal regions that recently have been associated with SBP and PP, respectively.We have detected additional evidence for a recently reported locus associated with SBP on chromosome 2q and a susceptibility locus for PP on chromosome 22q. However, differences observed between the results from our three partly overlapping genetically homogenous study samples from the Samoan islands suggest that additional studies should be performed in order to verify these results.High blood pressure or hypertension is a major risk factor involved in the development of cardiovascular diseases (CVD) [1], which today are primary causes of death in most industrial countries. We have previously searched for genetic susceptibility to two other common CVD risk factors, adiposity-related phenotypes [2-4] and lipid-related phenotypes [5] in our sample from the Samoan islands. Here we continued the search for genetic susceptibility to CVD risk factors in this population by investigating blood pressure related traits. We performed genome-wide linkage investigation for a dichotomous trait for hypertension (HT) where the study subjects were divided into two categories, non-hypertensive and hypertensive as well as for three quantitative traits including systolic blood pressure (SBP), diastolic blood pressure (DBP) and pulse pressure (PP). In addition we studied the simultaneous variation of SBP and DBP (SBP-DBP) by performing a genome-wide bivariate quantitative analysis.The population on the Samoan islands, including both American Samoa and Samoa, has a common evolutionary history of approximately 3,000 years with homogeneity of allele frequencies and linkage disequilibrium (LD) structure [6]. However, during the last century, and especially since World War II, the two polities have been differently influenced by political economic development [7-9], which has caused
Distribution of genome-wide linkage disequilibrium based on microsatellite loci in the Samoan population
Hui-Ju Tsai, Guangyun Sun, Diane Smelser, Satupaitea Viali, Joseph Tufa, Li Jin, Daniel E Weeks, Stephen T McGarvey, Ranjan Deka
Human Genomics , 2004, DOI: 10.1186/1479-7364-1-5-327
Abstract:
Finding Missing Heritability in Less Significant Loci and Allelic Heterogeneity: Genetic Variation in Human Height
Ge Zhang, Rebekah Karns, Guangyun Sun, Subba Rao Indugula, Hong Cheng, Dubravka Havas-Augustin, Natalija Novokmet, Zijad Durakovic, Sasa Missoni, Ranajit Chakraborty, Pavao Rudan, Ranjan Deka
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051211
Abstract: Genome-wide association studies (GWAS) have identified many common variants associated with complex traits in human populations. Thus far, most reported variants have relatively small effects and explain only a small proportion of phenotypic variance, leading to the issues of ‘missing’ heritability and its explanation. Using height as an example, we examined two possible sources of missing heritability: first, variants with smaller effects whose associations with height failed to reach genome-wide significance and second, allelic heterogeneity due to the effects of multiple variants at a single locus. Using a novel analytical approach we examined allelic heterogeneity of height-associated loci selected from SNPs of different significance levels based on the summary data of the GIANT (stage 1) studies. In a sample of 1,304 individuals collected from an island population of the Adriatic coast of Croatia, we assessed the extent of height variance explained by incorporating the effects of less significant height loci and multiple effective SNPs at the same loci. Our results indicate that approximately half of the 118 loci that achieved stringent genome-wide significance (p-value<5×10?8) showed evidence of allelic heterogeneity. Additionally, including less significant loci (i.e., p-value<5×10?4) and accounting for effects of allelic heterogeneity substantially improved the variance explained in height.
Structure and Reverse Hydrogen Spillover in Mononuclear Au0 and AuI Complexes Bonded to Faujasite Zeolite: A Density Functional Study
Ajanta Deka
Journal of Catalysts , 2013, DOI: 10.1155/2013/467846
Abstract: We have studied the structure of mononuclear gold supported on acidic form of faujasite zeolite in two oxidation states, namely, 0 and +1, using density functional theory. The binding of the gold monomer to the zeolite support is stronger in the oxidation state +1 than in the oxidation state 0. For the oxidation state 0, the hydrogenated clusters AuH/(2H)-FAU, AuH2/H-FAU generated by stepwise reverse hydrogen spillover from bridging OH groups of zeolite are energetically preferred over the Au/(3H)-FAU structure. Reverse hydrogen spillover of all the three acidic protons from the zeolite to the Au monomer did not lead to a stable structure. The calculated reverse hydrogen spillover energy per hydrogen atom for zeolite supported AuH and AuH2 clusters are ?10.2 and ?5.1?kJ/mol, respectively, in the oxidation state 0, while in the oxidation state +1 it is 20.9?kJ/mol for zeolite supported Au+H cluster. 1. Introduction Oxide-supported transition metal clusters form an important class of system both for theoretical and experimental investigations mainly due to their very important applications as catalysts. The activity of supported metal clusters is found to be higher than bare clusters and these metal-support interfaces are believed to act as active sites for catalysis. The factors influencing the reactivity of supported clusters are the size, structure and oxidation state of the cluster, the nature of the support, and cluster support interaction. Zeolites form an important class of support material for nanoclusters because their pores and cavities facilitate the formation of size-selective clusters of nanometer and sub-nanometer dimensions. Also, the zeolite support enables the tuning of the charge state of the cluster, as it depends upon the concentration of the acidic centres on the support, which can be modified. Among the transition metals gold has been highly investigated due to its ability to catalyse a number of reactions like CO oxidation [1], water gas shift reaction [2], epoxidation of propylene, [3] vinyl chloride synthesis [4], and so forth. Spurt in research activities involving supported gold clusters began after the pioneering discoveries of Haruta et al. [5] and Hashmi and Hutchings [6] demonstrating strong catalytic activities of highly dispersed gold. The common metal oxide supports used for gold cluster catalysis are MgO, Al2O3, SiO2, TiO2, and so forth. It has been found by Vayssilov and R?sch [7] that transition metal clusters M6 with hydrogen impurity adsorbed on a zeolite support have more nearest neighbour M-O contacts than the
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