Tapas Kumar Chaudhuri

Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen for complete sequencing from a collection of >800 control-region sequences sampled across India. We identified five new autochthonous haplogroups (R7, R8, R30, R31, and N5) and fully characterized the autochthonous haplogroups (R5, R6, N1d, U2a, U2b, and U2c) that were previously described only by first hypervariable segment (HVS-I) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings demonstrate that the Indian mtDNA pool, even when restricted to macrohaplogroup N, harbors at least as many deepest-branching lineages as the western Eurasian mtDNA pool. Moreover, the distribution of the earliest branches within haplogroups M, N, and R across Eurasia and Oceania provides additional evidence for a three-founder-mtDNA scenario and a single migration route out of Africa.

Zebu Cattle Are an Exclusive Legacy of the South Asia Neolithic

Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P < 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

Chicken domestication: an updated perspective based on mitochondrial genomes.

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A–I and W–Z. Common haplogroups A–G were shared by domestic chickens and red junglefowl. Rare haplogroups H–I and W–Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.

Decreased serum levels of interleukin-2 and interleukin-6 in Indian Bengalee schizophrenic patients

BACKGROUND AND PURPOSE Autoimmune process is thought to be involved in the pathophysiology in some cases of schizophrenia. Alteration in interleukin (IL) regulation is regarded as additional proof of autoimmunological background in schizophrenia. Most of the research in interleukin activity in schizophrenia has been in Caucasian and some Mongoloid patients. We have studied the serum IL-2 and IL-6 level in psychotropic medication free and antipsychotic medicating schizophrenic patients who are Indian Bengalee by ethnicity. METHOD Twenty psychotropic medication free and 30 antipsychotic medicating schizophrenic patients who fulfilled DSM-IV-TR criteria and 30 of the same age and sex matched controls were recruited. Serum level of IL-2 and IL-6 were measured by enzyme-linked immunosorbent assay (ELISA). RESULT There was a significant decrease of IL-2 and IL-6 in both antipsychotic medicating and psychotropic medication free patients. Further the medicating patients showed lower level of IL-2 and IL-6 than the psychotropic medication free patients. CONCLUSION This is the first study to describe a decrease serum level of IL-6 in schizophrenic patients. The study provides the evidence that some kind of immune dysregulation is involved in pathophysiology of schizophrenia. The study also provides the evidence for the immunosuppressive effect of antipsychotic drugs.

Multifaceted role of matrix metalloproteinases (MMPs)

Matrix metalloproteinases (MMPs), a large family of calcium-dependent zinc-containing endopeptidases, are involved in the tissue remodeling and degradation of the extracellular matrix. MMPs are widely distributed in the brain and regulate various processes including microglial activation, inflammation, dopaminergic apoptosis, blood-brain barrier disruption, and modulation of α-synuclein pathology. High expression of MMPs is well documented in various neurological disorders including Parkinsons disease (PD), Alzheimers disease (AD), Japanese encephalitis (JE), and Glaucoma. Although potentially critical, the role of MMPs in neuronal disorders is under-investigated. The present review summarizes the role of MMPs in neurodegeneration with a particular emphasis on PD, AD, JE, and Glaucoma.

Role of C-reactive protein in schizophrenia: an overview.

Over the years, schizophrenia is speculated to be associated with immune or inflammatory reactions mediated by cytokines. It is proposed that chronic inflammation might damage the micro-vascular system of brain and hamper cerebral blood flow. Scientific evidence suggests that an increase of stress hormone like norepinephrine may activate the inflammatory arm of the immune system and trigger the expression of genes that cause chronic, low-grade inflammation. Thus, studies were conducted to decipher the potentiality of CRP as a marker for inflammation in schizophrenia. This article reviews the findings of CRP in schizophrenia, and the limitations of the previous studies have been discussed. The importance of simultaneous study of CRP modulating cytokines and CRP gene polymorphism in the study of serum or plasma level of CRP has been emphasized.

Increased interleukin-4 and decreased interferon-γ levels in serum of children with asthma.

BACKGROUND AND PURPOSE Immune and inflammatory responses, mediated by cytokines, play important roles in the pathophysiology of asthma. These responses are associated with over expression of T helper (Th)-2 cytokine, particularly interleukin (IL)-4 and IL-5, and decreased expression of Th-1 cytokine, IL-2 and IFN-γ. We hypothesized that there would be an imbalance in the levels of circulating IL-4 and IFN-γ in the asthmatic subjects. METHOD We investigated serum levels of IL-4 and IFN-γ among eighty children (18 steroid-naïve, 30 steroid-treated children with asthma and 32 healthy controls) using commercially available ELISA kits. RESULTS Serum level of IL-4 was significantly higher in steroid-naïve group of asthmatic children compared to the healthy control subjects and was lower in steroid-treated group though the level was statistically not significant. In contrast, serum levels of IFN-γ were significantly lower in both steroid-naïve and steroid-treated groups of asthmatic children compared to healthy control subjects. CONCLUSION The results of our study suggest that serum level of IL-4 may be elevated in concert with decreased level of IFN-γ in asthma. Determination of serum levels of IL-4 and IFN-γ may be a useful tool for understanding the disease processes in asthma.

Genetic affinities of north and northeastern populations of India: inference from HLA-based study

India is like a microcosm of the world in terms of its diversity; religion, climate and ethnicity which leads to genetic variations in the populations. As a highly polymorphic marker, the human leukocyte antigen (HLA) system plays an important role in the genetic differentiation studies. To assess the genetic diversity of HLA class II loci, we studied a total of 1336 individuals from north India using DNA-based techniques. The study included four endogamous castes (Kayastha, Mathurs, Rastogies and Vaishyas), two inbreeding Muslim populations (Shias and Sunnis) from north India and three northeast Indian populations (Lachung, Mech and Rajbanshi). A total of 36 alleles were observed at DRB1 locus in both Hindu castes and Muslims from north, while 21 alleles were seen in northeast Indians. At the DQA1 locus, the number of alleles ranged from 11 to 17 in the studied populations. The total number of alleles at DQB1 was 19, 12 and 20 in the studied castes, Muslims and northeastern populations, respectively. The most frequent haplotypes observed in all the studied populations were DRB1*0701-DQA1*0201-DQB1*0201 and DRB1*1501-DQA1*0103-DQB1*0601. Upon comparing our results with other world populations, we observed the presence of Caucasoid element in north Indian population. However, differential admixturing among Sunnis and Shias with the other north Indians was evident. Northeastern populations showed genetic affinity with Mongoloids from southeast Asia. When genetic distances were calculated, we found the north Indians and northeastern populations to be markedly unrelated.

Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes

Himalayas was believed to be a formidably geographical barrier between South and East Asia. The observed high frequency of the East Eurasian paternal lineages in Nepal led some researchers to suggest that these lineages were introduced into Nepal from Tibet directly; however, it is also possible that the East Eurasian genetic components might trace their origins to northeast India where abundant East Eurasian maternal lineages have been detected. To trace the origin of the Nepalese maternal genetic components, especially those of East Eurasian ancestry, and then to better understand the role of the Himalayas in peopling Nepal, we have studied the matenal genetic composition extensively, especially the East Eurasian lineages, in Nepalese and its surrounding populations. Our results revealed the closer affinity between the Nepalese and the Tibetans, specifically, the Nepalese lineages of the East Eurasian ancestry generally are phylogenetically closer with the ones from Tibet, albeit a few mitochondrial DNA haplotypes, likely resulted from recent gene flow, were shared between the Nepalese and northeast Indians. It seems that Tibet was most likely to be the homeland for most of the East Eurasian in the Nepalese. Taking into account the previous observation on Y chromosome, now it is convincing that bearer of the East Eurasian genetic components had entered Nepal across the Himalayas around 6 kilo years ago (kya), a scenario in good agreement with the previous results from linguistics and archeology.

Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India

The sub-Himalayan Terai and Duars, the important outermost zones comprising the plains of East India, are known as the reservoirs of ethnic diversity. Analysis of the paternal genetic diversity of the populations inhabiting these regions and their genetic relationships with adjacent Himalayan and other Asian populations has not been addressed empirically. In the present investigation, we undertook a Y-chromosome phylogeographic study on 10 populations (n=375) representing four different linguistic groups from the sub-Himalayan Terai and Duars regions of East India. The high-resolution analysis of Y-chromosome haplogroup variations based on 76 binary markers revealed that the sub-Himalayan paternal gene pool is extremely heterogeneous. Three major haplogroups, namely H, O and R, are shared across the four linguistic groups. The Indo-European-speaking castes exhibit more haplogroup diversity than the tribal groups. The findings of the present investigation suggest that the sub-Himalayan gene pools have received predominant Southeast Asian contribution. In addition, the presence of Northeast and South Asian signatures illustrate multiple events of population migrations as well as extensive genetic admixture amongst the linguistic groups.