Samir Kumar Sil

Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists.

Although considerable cultural impact on social hierarchy and language in South Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of South Asia. We sought to resolve this conflict, using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially, and linguistically representative ethnic groups of South Asia. We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000-15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high-frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus Valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and with significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment for distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene-era--not Indo-European--expansions have shaped the distinctive South Asian Y-chromosome landscape.

DNA Sequence Variation and Haplotype Structure of the ICAM1 and TNF Genes in 12 Ethnic Groups of India Reveal Patterns of Importance in Designing Association Studies

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non‐synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF‐376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between‐population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case‐control association studies.

A Rare HBV Subgenotype D4 with Unique Genomic Signatures Identified in North-Eastern India –An Emerging Clinical Challenge?

Background/Aims HBV has been classified into ten genotypes (A–J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura. Methods From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes. Results HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1–D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T120 and R129 in ORF-S that may cause immune/vaccine/diagnostic escape and N128 in ORF-P, implicated as compensatory Lamivudine resistance mutation. Conclusions IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.

Nutritional Status of Rural Bengali Adolescent Boys of Tripura.

To the Editor: Assessment of nutritional status is significant in developing countries like India where the vast majority of the populations are undernourished and underprivileged. Studies describing the nutritional status of adolescents from northeastern part of India are limited. This community based cross-sectional study was conducted to determine the current nutritional status of rural adolescent Bengali boys of Tripura. A total of 550 school-going Bengali boys (aged 8–16 y) from 30 randomly selected villages, representing the state of Tripura, were included using multistage cluster sampling method. Standing height and body weight were measured; body mass index (BMI) was derived. Age specific prevalences of stunting, thinness, overweight and obesity were calculated according to the classification of World Health Organization (WHO) [1], using the new IAP growth charts [2]. Nutritional status was also assessed using the 2007 WHO growth reference data [3]. These boys had lower socio-economic status. Using the IAP growthcharts [2] as reference,the overall (agecombined) prevalence of stunting (height-for-age <3rd percentile) was found low: 9.09 %. Prevalence across age groups fluctuated from 0 to 21.31 % below the 3rd percentile. The overall prevalence of thinness (i.e., BMI-for-age <5th percentile) was 12 %, which is higher than that of stunting. Prevalence across age groups fluctuated from 6.45 to 16.67 % below the 5th percentile. The overall prevalence of overweight (i.e. ,B MIfor-age ≥23 adult equivalent) was 7.09 %. Prevalence across age groups fluctuated from 1.67 to 11.29 %. The overall age specific prevalence of obesity (i.e., BMI-for-age ≥27 adult equivalent) was very low (0.36 %). The overall prevalence of stunting and thinness (21.15 and 40.32 % respectively) was found higher and overweight (4.30 %) was found lower when WHO reference data [3] was used. The prevalence rate of undernutrition among the boys of the present study was comparatively lower than the urban Bengali boys of Kolkata [4] and rural tribal children of Tripura [5]. In general, the Bengali boys of Tripura had lower rates of undernutrition. The over diagnosis of undernutrition and under diagnosis of overnutrition may be avoided by using the new IAP growth charts. We propose that future studies should use these charts to determine the growth and nutritional status of children and adolescents from India.

Determination of Virulence Factors and Biofilm Formation Among Isolates of Vulvovaginal Candidiasis

Context: Under morphogenesis-inducing conditions, Candida spp. begins to undergo yeast-to-hypha switch. This shift from commensal to pathogenic state is dependent on several virulence factors. Aim: To find out whether the isolated Candida spp. were pathogens causing vulvovaginal candidiasis or mere bystanders. Settings and Design: Cross-sectional observational study conducted on 275 symptomatic hospital patients in Tripura between August 2012 and April 2015. Subjects and Methods: Discharge was collected from patients and identified by Grams staining and wet mount test. Culturing was done in Sabouraud dextrose agar followed by speciation. To test for virulence factors, assays for adherence, plasma coagulase, phospholipase, lipase, protease, hemolysin, and biofilm formation were carried out. Statistical Analysis Used: Significance between two groups was compared using one-way analysis of variance along with Tukey test, and Chi-square 2 × 2 contingency table at 95% confidence interval. Results: Fifty-six Candida spp. could be isolated in the study which was used for further virulence tests. One hundred percent of isolates expressed adherence. Among other virulence factors, maximum virulence 25 (45%) was shown through protease production. Hemolysin production and biofilm formation were the second most 22 (39%) expressed virulence factors. In a comparison of virulence factors between biofilm-forming isolates and planktonic cells, significant difference was seen for plasma coagulase and hemolysin production. Conclusions: All the isolates expressed one or more virulence factors. Adherence was expressed in all isolates but highest number was observed for Candida albicans. Furthermore, C. albicans strain number was highest for protease, hemolysin and coagulase expression and biofilm formation. Candida krusei isolates were the least in number for expressing any of the virulence factors. Significantly higher number of biofilm forming isolates produced hemolysin and coagulase in comparison to planktonic cells.

A study on various Neisseria gonorrhoeae phenotypes circulating in Tripura

References 1. Moisini I, Davidson A. BAFF: A local and systemic target in autoimmune diseases. Clin Exp Immunol 2009;158:155‐63. 2. Matsushita T, Hasegawa M, Matsushita Y, Echigo T, Wayaku T, Horikawa M, et al. Elevated serum BAFF levels in patients with localized scleroderma in contrast to other organ‐specific autoimmune diseases. Exp Dermatol 2007;16:87‐93. 3. Mejri K, Abida O, Kallel‐Sellami M, Haddouk S, Laadhar L, Zarraa IR, et al. Spectrum of autoantibodies other than anti‐desmoglein in pemphigus patients. J Eur Acad Dermatol Venereol 2011;25:774‐81. 4. Asashima N, Fujimoto M, Watanabe R, Nakashima H, Yazawa N, Okochi H, et al. Serum levels of BAFF are increased in bullous pemphigoid but not in pemphigus vulgaris. Br J Dermatol 2006;155:330‐6. 5. Abida O, Zitouni M, Kallel‐Sellami M, Mahfoudh N, Kammoun A, Ben Ayed M, et al. Tunisian endemic pemphigus foliaceus is associated with the HLA‐DR3 gene: Anti‐desmoglein 1 antibody‐positive healthy subjects bear protective alleles. Br J Dermatol 2009;161:522‐7. 6. Nagel A, Podstawa E, Eickmann M, Müller HH, Hertl M, Eming R. Rituximab mediates a strong elevation of B‐cell‐activating factor associated with increased pathogen‐specific IgG but not autoantibodies in pemphigus vulgaris. J Invest Dermatol 2009;129:2202‐10. 7. Malheiros D, Petzl‐Erler ML. Individual and epistatic effects of genetic polymorphisms of B‐cell co‐stimulatory molecules on susceptibility to pemphigus foliaceus. Genes Immun 2009;10:547‐58. 8. Mahieu MA, Strand V, Simon LS, Lipsky PE, Ramsey‐Goldman R. A critical review of clinical trials in systemic lupus erythematosus. Lupus 2016;25:1122‐40. How to cite this article: Mejri K, Sellami MK, Zaraa IR, Laadhar L, Lahmar H, Mokni M, et al. High B‐cell‐activating factor levels in endemic Tunisian pemphigus. Indian J Dermatol Venereol Leprol 2017;83:496‐9.

Anthropometric Assessment of Nutritional Status of Adolescents in Rural School of Unokoti District of Tripura, North-East India

Abstract A cross-sectional survey was conducted among 300 boys and girls (1:1) of 10-15 years, randomly selected, from three Govt. Secondary School of Unokoti District of Tripura State, to assess their nutritional status. The weight, height, head circumference (HC) and mid-upper-arm circumference (MUAC), body mass index (BMI) and chest circumference (CC) were taken as nutritional status indices. Nutritional status was evaluated using the age and sex-specific cut-off points of anthropometric indicators of the NHANES-I percentile values. The percent of malnourished children was found varying from 53% to 76% on the basis of different nutritional status indices, socio-economic status, and sex. There is a decreasing trend in the proportion of undernourished child with increasing socio-economic status (SES). The low values of anthropometric indices and high rate of malnourished child obtained from this study suggest that there is need for improvement in the nutritional status of adolescents.

Nutritional Status of Urban Tripuri Tribal Boys of Agartala, Tripura

Abstract A cross-sectional study of the nutritional status was made on 365 Tripuri boys (aged 8 to 15 years) in Agartala, the capital of Tripura. This study was carried out to determine the nutritional status of school going Tripuri tribal boys of Agartala. The cluster random sampling method was followed for selecting the subjects from different schools of Agartala city. Nutritional status such as stunting, thinness and overweight was analyzed by using the growth reference data of World Health Organization. Prevalence of stunting, thinness and overweight were 7.67%, 17.81% and 6.03% respectively.