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Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JTS, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 2016; 538:201-206. [PMID: 27654912 PMCID: PMC5161557 DOI: 10.1038/nature18964] [Citation(s) in RCA: 796] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
Abstract
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
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Velavan TP, Van Hoang T, Ojurongbe O, Thangaraj K, Toan NL, Song LH, Messias-Reason IJ, Meyer CG. Lectin complement proteins in infectious diseases. Immunobiology 2016. [DOI: 10.1016/j.imbio.2016.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Vandana VP, Bindu PS, Sonam K, Govindaraj P, Chiplunkar S, Gayathri N, Govindaraj C, Arvinda HR, Nagappa M, Sinha S, Thangaraj K, Taly AB. Reply to Letter to the Editor: Hearing impairment in m.3243A>G carriers requires comprehensive work- and follow-up. Clin Neurol Neurosurg 2016; 150:198-199. [PMID: 27600858 DOI: 10.1016/j.clineuro.2016.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 11/26/2022]
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Tabasum W, Ara S, Rai N, Thangaraj K, Gaur A. Complete mitochondrial genome sequence of Asiatic lion ( Panthera leo persica). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:619-620. [PMID: 33473572 PMCID: PMC7800587 DOI: 10.1080/23802359.2016.1214541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complete mitochondrial genome sequence 17,059 bp of Asiatic lion (Panthera leo persica) has been sequenced with the use of next generation sequencing technology using Ion Torrent PGM platform. The complete mitochondrial genome sequence of Asiatic lion consists of 13 protein-coding, 22 tRNA, and two rRNA genes, and 1 control region (CR). The mitochondrial genome is relatively similar to other felid mitochondrial genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases to be typical of those reported for other mammals. The nucleotide composition of Asiatic lion mitogenome shows that there is more A-T% than G-C% on the positive strand as revealed by positive AT and CG skews. The overall base composition is 31.9% of A, 27.2% of C, 14.5% of G, and 26.2% of T. Most of the genes have ATA start codons, except ND1, COX2, ATP8, ATP6, ND4, and ND5 have ATG start codons.
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Phanindranath R, Sudhakar DV, Sharma AK, Thangaraj K, Sharma Y. Optimization of purification method and characterization of recombinant human Centrin-1. Protein Expr Purif 2016; 124:48-54. [DOI: 10.1016/j.pep.2016.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/06/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
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Clark EL, Macdonald SE, Thenmozhi V, Kundu K, Garg R, Kumar S, Ayoade S, Fornace KM, Jatau ID, Moftah A, Nolan MJ, Sudhakar NR, Adebambo AO, Lawal IA, Álvarez Zapata R, Awuni JA, Chapman HD, Karimuribo E, Mugasa CM, Namangala B, Rushton J, Suo X, Thangaraj K, Srinivasa Rao ASR, Tewari AK, Banerjee PS, Dhinakar Raj G, Raman M, Tomley FM, Blake DP. Cryptic Eimeria genotypes are common across the southern but not northern hemisphere. Int J Parasitol 2016; 46:537-44. [PMID: 27368611 PMCID: PMC4978698 DOI: 10.1016/j.ijpara.2016.05.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/20/2016] [Accepted: 05/24/2016] [Indexed: 01/09/2023]
Abstract
The seven Eimeria spp. recognised to infect chickens are present globally. Cryptic Eimeria operational taxonomic units (OTUs) are common in the southern but not northern hemisphere. Parasite population structure appears to vary between Eimeria spp.
The phylum Apicomplexa includes parasites of medical, zoonotic and veterinary significance. Understanding the global distribution and genetic diversity of these protozoa is of fundamental importance for efficient, robust and long-lasting methods of control. Eimeria spp. cause intestinal coccidiosis in all major livestock animals and are the most important parasites of domestic chickens in terms of both economic impact and animal welfare. Despite having significant negative impacts on the efficiency of food production, many fundamental questions relating to the global distribution and genetic variation of Eimeria spp. remain largely unanswered. Here, we provide the broadest map yet of Eimeria occurrence for domestic chickens, confirming that all the known species (Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox, Eimeria tenella) are present in all six continents where chickens are found (including 21 countries). Analysis of 248 internal transcribed spacer sequences derived from 17 countries provided evidence of possible allopatric diversity for species such as E. tenella (FST values ⩽0.34) but not E. acervulina and E. mitis, and highlighted a trend towards widespread genetic variance. We found that three genetic variants described previously only in Australia and southern Africa (operational taxonomic units x, y and z) have a wide distribution across the southern, but not the northern hemisphere. While the drivers for such a polarised distribution of these operational taxonomic unit genotypes remains unclear, the occurrence of genetically variant Eimeria may pose a risk to food security and animal welfare in Europe and North America should these parasites spread to the northern hemisphere.
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Carlus SJ, Sarkar S, Bansal SK, Singh V, Singh K, Jha RK, Sadasivam N, Sadasivam SR, Gireesha PS, Thangaraj K, Rajender S. Is MTHFR 677 C>T Polymorphism Clinically Important in Polycystic Ovarian Syndrome (PCOS)? A Case-Control Study, Meta-Analysis and Trial Sequential Analysis. PLoS One 2016; 11:e0151510. [PMID: 26983014 PMCID: PMC4794143 DOI: 10.1371/journal.pone.0151510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
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.
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Nizamuddin S, Govindaraj P, Saxena S, Kashyap M, Mishra A, Singh S, Rotti H, Raval R, Nayak J, Bhat BK, Prasanna BV, Dhumal VR, Bhale S, Joshi KS, Dedge AP, Bharadwaj R, Gangadharan GG, Nair S, Gopinath PM, Patwardhan B, Kondaiah P, Satyamoorthy K, Valiathan MS, Thangaraj K. Reply to 'Lack of replication of association of THSD7A with obesity'. Int J Obes (Lond) 2016; 40:727-8. [PMID: 26902698 DOI: 10.1038/ijo.2016.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 2016; 6:19157. [PMID: 26754573 PMCID: PMC4709632 DOI: 10.1038/srep19157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022] Open
Abstract
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
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Khan NA, Govindaraj P, Meena AK, Thangaraj K. Mitochondrial disorders: challenges in diagnosis & treatment. Indian J Med Res 2016; 141:13-26. [PMID: 25857492 PMCID: PMC4405934 DOI: 10.4103/0971-5916.154489] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial dysfunctions are known to be responsible for a number of heterogenous clinical presentations with multi-systemic involvement. Impaired oxidative phosphorylation leading to a decrease in cellular energy (ATP) production is the most important cause underlying these disorders. Despite significant progress made in the field of mitochondrial medicine during the last two decades, the molecular mechanisms underlying these disorders are not fully understood. Since the identification of first mitochondrial DNA (mtDNA) mutation in 1988, there has been an exponential rise in the identification of mtDNA and nuclear DNA mutations that are responsible for mitochondrial dysfunction and disease. Genetic complexity together with ever widening clinical spectrum associated with mitochondrial dysfunction poses a major challenge in diagnosis and treatment. Effective therapy has remained elusive till date and is mostly efficient in relieving symptoms. In this review, we discuss the important clinical and genetic features of mitochondrials disorders with special emphasis on diagnosis and treatment.
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Ali A, Qureshi SF, Medikare V, Venkateshwari A, Calambur N, Rao H, Jayakrishnan MP, Shenthar J, Thangaraj K, Nallari P. Heat shock protein 70 gene polymorphisms’ influence on the electrophysiology of long QT syndrome. J Interv Card Electrophysiol 2015; 45:119-30. [DOI: 10.1007/s10840-015-0082-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
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Paramasivam A, Meena AK, Pedaparthi L, Jyothi V, Uppin MS, Jabeen SA, Sundaram C, Thangaraj K. Novel mutation in C10orf2 associated with multiple mtDNA deletions, chronic progressive external ophthalmoplegia and premature aging. Mitochondrion 2015; 26:81-5. [PMID: 26689116 DOI: 10.1016/j.mito.2015.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/11/2015] [Accepted: 12/11/2015] [Indexed: 11/15/2022]
Abstract
Chronic progressive external ophthalmoplegia (CPEO) is caused by defects in both mitochondrial and nuclear genes, however, the causal genetic factors in large number of patients remains undetermined. Therefore, our aim was to screen 12 unrelated patients with CPEO for mutation/multiple deletions in mtDNA and mutations in the coding regions of C10orf2, which is essential for mtDNA replication. Histopathological study of muscle biopsy revealed cytochrome c oxidase-deficient fibers and ragged blue fibers in all the patients. Long-range PCR of DNA from skeletal muscle revealed multiple mtDNA deletions in all the 12 patients. Further, sequencing coding regions of C10orf2 revealed three variants in three different patients, of which two were novel (c.1964G>A/p.G655D; c.204G>A/p.G68G) variants and one was reported (c.1052A>G/p. N351S). Sequencing of other nuclear genes that are associated with CPEO and multiple mtDNA deletions, such as; POLG1, POLG2, TK2, ANT1, DGUOK, MPV17 and RRM2B did not reveal any pathogenic mutation in patients with C10orf2 mutation. Since in silico analyses revealed p.G655D could be a potentially pathogenic and it was absent in 200 healthy controls, p.G655D could be the causative factor for CPEO. Therefore, we suggest that C10orf2 gene should be screened in CPEO individuals with multiple mtDNA deletions, which might help in prognosis of this disease and appropriate genetic counseling.
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Choubey VK, Sankhwar SN, Carlus SJ, Singh AN, Dalela D, Thangaraj K, Rajender S. SRD5A2 gene polymorphisms and the risk of benign prostatic hyperplasia but not prostate cancer. Asian Pac J Cancer Prev 2015; 16:1033-6. [PMID: 25735326 DOI: 10.7314/apjcp.2015.16.3.1033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Testosterone, a primary androgen in males, is converted into its most active form, dihydrotestosterone (DHT), by 5α-reductase type 2 (encoded by the SRD5A2 gene) in the prostate. DHT is necessary for prostatic growth and has five times higher binding affinity than testosterone for androgen receptors. We hypothesized that polymorphic variations in the SRD5A2 gene may affect the risk of benign prostatic hyperplasia and prostate cancer. MATERIALS AND METHODS We analyzed SRD5A2 gene polymorphisms in 217 BPH patients, 192 PCa cases, and 171 controls. Genotyping was undertaken using direct DNA sequencing. Genotype data were compared between cases and controls using a Chi square statistical tool. RESULTS We found that the A49T locus was monomorphic with 'AA' genotype in all subjects. At V89L locus, the presence of 'VV' showed a marginally significant correlation with increased BPH risk (p=0.047). At the (TA)n locus, longer TA repeats were found to be protective against BPH (p=0.003). However, neither of these polymoprhisms correlated with the risk of PCa. CONCLUSIONS We conclude that A49T is monomorphic in the study population, VV marginally correlates with BPH risk, and longer (TA)n repeats are protective against BPH. None of these polymorphisms affect the risk of PCa.
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Qureshi SF, Ali A, Venkateshwari A, Rao H, Jayakrishnan M, Narasimhan C, Shenthar J, Thangaraj K, Nallari P. Genotype-phenotype correlation in long QT syndrome families. Indian Pacing Electrophysiol J 2015; 15:269-85. [PMID: 27479201 PMCID: PMC4867973 DOI: 10.1016/j.ipej.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Heterogeneity in clinical manifestations is a well-known feature in Long QT Syndrome (LQTS). The extent of this phenomenon became evident in families wherein both symptomatic and asymptomatic family members are reported. The study hence warrants genetic testing and/or screening of family members of LQTS probands for risk stratification and prediction. Of the 46 families screened, 18 probands revealed novel variations/compound heterozygosity in the gene/s screened. Families 1-4 revealed probands carrying novel variations in KCNQ1 gene along with compound heterozygosity of risk genotypes of the SCN5A, KCNE1 and NPPA gene/s polymorphisms screened. It was also observed that families- 5, 6 and 7 were typical cases of "anticipation" in which both mother and child were diagnosed with congenital LQTS (cLQTS). Families- 16 and 17 represented aLQTS probands with variations in IKs and INa encoding genes. First degree relatives (FDRs) carrying the same haplotype as the proband were also identified which may help in predictive testing and management of LQTS. Most of the probands exhibiting a family history were found to be genetic compounds which clearly points to the role of cardiac genes and their modifiers in a recessive fashion in LQTS manifestation.
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Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
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Narayanappa G, Govindraju C, Bindu P, Kothari S, Taly A, Nahid K, Thangaraj K. Mitochondrial disorders with novel mutations – a study from a tertiary referral center in South India. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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92
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Qureshi SF, Ali A, John P, Jadhav AP, Venkateshwari A, Rao H, Jayakrishnan MP, Narasimhan C, Shenthar J, Thangaraj K, Nallari P. Mutational analysis of SCN5A gene in long QT syndrome. Meta Gene 2015; 6:26-35. [PMID: 26401487 PMCID: PMC4561237 DOI: 10.1016/j.mgene.2015.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 07/05/2015] [Accepted: 07/31/2015] [Indexed: 12/20/2022] Open
Abstract
The SCN5A gene encodes for the INa channel implicated in long QT syndrome type-3 (LQTS-type-3). Clinical symptoms of this type are lethal as most patients had a sudden death during sleep. Screening of SCN5A in South Indian cohort by PCR-SSCP analyses revealed five polymorphisms — A29A (exon-2), H558R (exon-12), E1061E and S1074R (exon-17) and IVS25 + 65G > A (exon-25) respectively. In-silico and statistical analyses were performed on all the polymorphisms. Exon-2 of SCN5A gene revealed A282G polymorphism (rs6599230), resulting in alanine for alanine (A29A) silent substitution in the N-terminus of SCN5A protein. Exon-12 showed A1868G polymorphism (H558R — rs1805124) and its ‘AA’ genotype and ‘A’ allele frequency were found to be higher in LQTS patients pointing towards its role in LQTS etiology. Two polymorphisms A3378G (E1061E) and the novel C3417A (S1074R) were identified as compound heterozygotes/genetic compounds in exon-17 of SCN5A located in the DIIS6–DIIIS1 domain of the SCN5A transmembrane protein. IVS25 + 65G > A was identified in intron-25 of SCN5A. The ‘G’ allele was identified as the risk allele. Variations were identified in in-silico analyses which revealed that these genetic compounds may lead to downstream signaling variations causing aberrations in sodium channel functions leading to prolonged QTc. The compound heterozygotes of SCN5A gene polymorphisms revealed a significant association which may be deleterious/lethal leading to an aberrant sodium ion channel causing prolonged QTc. Screening of SCN5A in South Indian cohort showed 4 reported and 1 novel polymorphism. Compound heterozygotes found to have a significant association with LQTS Genetic compounds maybe deleterious leading to an aberrant sodium ion channel
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Kabekkodu SP, Chakrabarty S, Shukla V, Varghese VK, Singh KK, Thangaraj K, Satyamoorthy K. Mitochondrial biology: From molecules to diseases. Mitochondrion 2015. [PMID: 26210788 DOI: 10.1016/j.mito.2015.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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94
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Bindu PS, Arvinda H, Taly AB, Govindaraju C, Sonam K, Chiplunkar S, Kumar R, Gayathri N, Bharath Mm S, Nagappa M, Sinha S, Khan NA, Govindaraj P, Nunia V, Paramasivam A, Thangaraj K. Magnetic resonance imaging correlates of genetically characterized patients with mitochondrial disorders: A study from south India. Mitochondrion 2015; 25:6-16. [PMID: 26341968 DOI: 10.1016/j.mito.2015.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/16/2015] [Accepted: 08/21/2015] [Indexed: 01/31/2023]
Abstract
BACKGROUND Large studies analyzing magnetic resonance imaging correlates in different genotypes of mitochondrial disorders are far and few. This study sought to analyze the pattern of magnetic resonance imaging findings in a cohort of genetically characterized patients with mitochondrial disorders. METHODS The study cohort included 33 patients (age range 18 months-50 years, M:F - 0.9:1) with definite mitochondrial disorders seen over a period of 8 yrs. (2006-2013). Their MR imaging findings were analyzed retrospectively. RESULTS The patients were classified into three groups according to the genotype, Mitochondrial point mutations and deletions (n=21), SURF1 mutations (n=7) and POLG1 (n=5). The major findings included cerebellar atrophy (51.4%), cerebral atrophy (24.2%), signal changes in basal ganglia (45.7%), brainstem (34.2%) & white matter (18.1%) and stroke like lesions (25.7%). Spinal cord imaging showed signal changes in 4/6 patients. Analysis of the special sequences revealed, basal ganglia mineralization (7/22), lactate peak on magnetic resonance spectrometry (10/15), and diffusion restriction (6/22). Follow-up images in six patients showed that the findings are dynamic. Comparison of the magnetic resonance imaging findings in the three groups showed that cerebral atrophy and cerebellar atrophy, cortical signal changes and basal ganglia mineralization were seen mostly in patients with mitochondrial mutation. Brainstem signal changes with or without striatal lesions were characteristically noted in SURF1 group. There was no consistent imaging pattern in POLG1 group. CONCLUSION Magnetic resonance imaging findings in mitochondrial disorders are heterogeneous. Definite differences were noted in the frequency of anatomical involvement in the three groups. Familiarity with the imaging findings in different genotypes of mitochondrial disorders along with careful analysis of the family history, clinical presentation, biochemical findings, histochemical and structural analysis will help the physician for targeted metabolic and genetic testing.
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Nagappa M, Bindu PS, Taly AB, Sonam K, Shwetha C, Kumar R, Gayathri N, Srinivas‐Bharath M, Arvinda HR, Sinha S, Paramasivam A, Thangaraj K. Palatal Tremor in POLG-Associated Ataxia. Mov Disord Clin Pract 2015; 2:318-320. [PMID: 30363534 PMCID: PMC6178733 DOI: 10.1002/mdc3.12195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 11/08/2022] Open
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Mishra A, Antony JS, Gai P, Sundaravadivel P, Van TH, Jha AN, Singh L, Velavan TP, Thangaraj K. Mannose-binding Lectin (MBL) as a susceptible host factor influencing Indian Visceral Leishmaniasis. Parasitol Int 2015; 64:591-6. [PMID: 26297290 DOI: 10.1016/j.parint.2015.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
Visceral Leishmaniasis (VL), caused by Leishmania donovani is endemic in the Indian sub-continent. Mannose-binding Lectin (MBL) is a complement lectin protein that binds to the surface of Leishmania promastigotes and results in activation of the complement lectin cascade. We utilized samples of 218 VL patients and 215 healthy controls from an Indian population. MBL2 functional variants were genotyped and the circulating MBL serum levels were measured. MBL serum levels were elevated in patients compared to the healthy controls (adjusted P=0.007). The MBL2 promoter variants -78C/T and +4P/Q were significantly associated with relative protection to VL (-78C/T, OR=0.7, 95% CI=0.5-0.96, adjusted P=0.026 and +4P/Q, OR=0.66, 95% CI=0.48-0.9, adjusted P=0.012). MBL2*LYQA haplotypes occurred frequently among controls (OR=0.69, 95% CI=0.5-0.97, adjusted P=0.034). MBL recognizes Leishmania and plays a relative role in establishing L. donovani infection and subsequent disease progression. In conclusion, MBL2 functional variants were associated with VL.
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97
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Sonam K, Bindu PS, Taly AB, Govindaraju C, Gayathri N, Arvinda HR, Nagappa M, Sinha S, Khan NA, Govindaraj P, Thangaraj K. Clinical and Neuroimaging Features in Two Children with Mutations in the Mitochondrial ND5 Gene. Neuropediatrics 2015; 46:277-81. [PMID: 25974876 DOI: 10.1055/s-0035-1550149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mutations in the mitochondrial-encoded nicotinamide adenine dinucleotide dehydrogenase 5 gene (MT-ND5) has been implicated as an important genetic cause of childhood mitochondrial encephalomyopathies. This study reports the clinical and magnetic resonance imaging findings in two pediatric patients with mutations in the ND5 gene of mitochondrial DNA. The 8-month-old boy with m.13513 G>A mutation presented with infantile basal ganglia stroke syndrome secondary to mineralizing angiopathy. The 7-year-old girl with the m.13514A>G mutation had episodic regression, progressive ataxia, optic atrophy, and hyperactivity. Magnetic resonance imaging of the brain showed bilateral symmetrical signal intensity changes in the thalamus, tectal plate, and inferior olivary nucleus, which subsided on follow-up image. Both the patients had a stable course. Familiarity with the various phenotypic and magnetic resonance imaging findings and the clinical course in childhood mitochondrial encephalomyopathies may help the physician in targeted metabolic-genetic testing and prognostication.
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98
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Mathews S, Lakshmi Rao K, Suma Prasad K, Kanakavalli MK, Govardhana Reddy A, Avinash Raj T, Thangaraj K, Pande G. Propagation of pure fetal and maternal mesenchymal stromal cells from terminal chorionic villi of human term placenta. Sci Rep 2015; 5:10054. [PMID: 25975441 PMCID: PMC4432313 DOI: 10.1038/srep10054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/20/2015] [Indexed: 12/14/2022] Open
Abstract
Long term propagation of human fetal mesenchymal stromal cells (MSC) in vitro has proven elusive due to limited availability of fetal tissue sources and lack of appropriate methodologies. Here, we have demonstrated the presence of fetal and maternal cells within the tips of terminal chorionic villi (TCV) of normal human term placenta, and we have exploited inherent differences in the adhesive and migratory properties of maternal vs. fetal cells, to establish pure MSC cultures of both cell types. The origin and purity of each culture was confirmed by X-Y chromosome-specific fluorescence in situ hybridization (FISH) and short tandem repeat (STR) genotyping. This is the first demonstration of fetal and maternal cells in the TCV of human term placenta and also of deriving pure fetal MSC cultures from them. The concomitant availability of pure cultures of adult and fetal MSC from one tissue provides a good system to compare genetic and epigenetic differences between adult and fetal MSCs; and also to generate new models of cell based therapies in regenerative medicine.
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99
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Antony JS, Ojurongbe O, Meyer CG, Thangaraj K, Mishra A, Kremsner PG, Velavan TP. Correlation of Interleukin-6 levels and lectins during Schistosoma haematobium infection. Cytokine 2015; 76:152-155. [PMID: 25982844 DOI: 10.1016/j.cyto.2015.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 12/23/2022]
Abstract
Urogenital schistosomiasis caused by Schistosoma haematobium induces a Th2 immune response, including expression of Interleukin-6. IL-6 confers protection from experimental Schistosoma-induced pulmonary hypertension and modulates production of mannose-binding lectin (MBL) and other lectins. We studied IL-6 levels in schistosomiasis and its effect on lectins production. Elevated IL-6 levels occurred in cases, compared to controls. IL-6 correlated with the lectins MBL, ficolin-2 and Collectin Kidney-1 (CL-K1) in cases, but correlated inversely in controls. The study shows that IL-6 levels are elevated in individuals infected with urogenital schistosomiasis. IL-6 was also found to be correlated with the production of lectins in S. haematobium infection. A similar correlation between IL-6 and MBL was observed during visceral leishmaniasis.
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100
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Mishra A, Antony JS, Sundaravadivel P, Tong HV, Meyer CG, Jalli RD, Velavan TP, Thangaraj K. Association of Ficolin-2 Serum Levels and FCN2 Genetic Variants with Indian Visceral Leishmaniasis. PLoS One 2015; 10:e0125940. [PMID: 25965808 PMCID: PMC4428791 DOI: 10.1371/journal.pone.0125940] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/26/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Visceral leishmaniasis (VL), one of the neglected tropical diseases, is endemic in the Indian subcontinent. Ficolins are circulating serum proteins of the lectin complement system and involved in innate immunity. METHODS We have estimated ficolin-2 serum levels and analyzed the functional variants of the encoding gene FCN2 in 218 cases of VL and in 225 controls from an endemic region of India. RESULTS Elevated levels of serum ficolin-2 were observed in VL cases compared to the controls (adjusted P<0.0001). The genetic analysis revealed that the FCN2 structural variant +6359 C>T (p.T236M) was associated with VL (OR=2.2, 95% CI=1.23-7.25, P=0.008) and with high ficolin-2 serum levels. We also found that the FCN2*AAAC haplotype occurred more frequently among healthy controls when compared to cases (OR=0.59, 95%CI=0.37-0.94, P=0.023). CONCLUSIONS Our findings indicate that the FCN2 variant +6359C>T is associated with the occurrence of VL and that ficolin-2 serum levels are elevated in Leishmania infections.
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