Soumen Bhattacharjee

Study of the KIR gene profiles and analysis of the phylogenetic relationships of Rajbanshi population of West Bengal, India

The natural killer (NK) cells have distinct receptors called killer cell immunoglobulin-like receptors (KIR) which are responsible for regulating NK cell responses to infections and malignancy. The extensive variations in the number and type of KIR genes can be used as a tool to understand the differentiation of populations and also for tracing genetic background. In this study, we have aimed to analyze the KIR gene polymorphism in the Rajbanshi population of West Bengal, India. To our knowledge this is the first report on the KIR gene polymorphism in the Rajbanshis, a population widely distributed in the Terai and Dooars region of West Bengal, India. Herein, we have studied the gene distribution of 14 KIR genes (KIR3DL1-3DL3, KIR 2DL1-2DL5, 2DS1-2DS5 and 3DS1) and two pseudogenes (KIR3DP1 and 2DP1). The gene frequencies and genotypic frequencies were calculated, based on which statistical analyses were performed. The presence of a considerable number of genotypic profiles suggests substantial diversity in the KIR gene pool of the Rajbanshis in the region studied. Apart from the framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1) present in all the individuals, the gene frequencies of other KIR genes varied between 0.84 and 0.15. Moreover the KIR polymorphisms of the Rajbanshis were also compared with that of available published data of the populations of other ethnicities. Though the Rajbanshi population showed a tendency to cluster with other Indian population based on KIR gene frequencies, the influence of Tibeto-Burman Lineage on their KIR genotypic profiles cannot be overlooked. Furthermore, evidences from previously published data on Y chromosome haplogroup diversity study on Rajbanshis support the view. Our results will not only help to understand the genetic background of the Rajbanshi population, but also in tracing the population migration events in the North-Eastern part of India and in illustrating the extensive genetic admixture amongst the different linguistic groups of the country and also in KIR-related disease researches.

Human migration, diversity and disease association: a convergent role of established and emerging DNA markers

With the gradual development of intelligence, human got curious to know his origin and evolutionary background. Historical statements and anthropological findings were his primary tool for solving the puzzles of his own origin, until came the golden era of molecular markers which took no time to prove it’s excellence in unveiling answers to the questions regarding the migration pattern of human across different geographical regions. As a bonus these markers proved very much beneficial in solving criminal offenses and in understanding the etiology of many dreaded diseases and to design their prevention. In this review, we have aimed to throw light on some of the promising molecular markers which are very much in application now-a-days for not only understanding the evolutionary background and ancient migratory routes of humans but also in the field of forensics and human health.

Entry, infection, replication and egress of human Polyomaviruses: an update.

Polyomaviruses (PyVs), belonging to the family Polyomaviridae, are a group of small, nonenveloped, double-stranded, circular DNA viruses widely distributed in the vertebrates. PyVs cause no apparent disease in adult laboratory mice but cause a wide variety of tumors when artificially inoculated into neonates or semipermissive animals. A few human PyVs, such as BK, JC, and Merkel cell PyVs, have been unequivocally linked to pathogenesis under conditions of immunosuppression. Infection is thought to occur early in life and persists for the lifespan of the host. Over evolutionary time scales, it appears that PyVs have slowly co-evolved with specific host animal lineages. Host cell surface glycoproteins and glycolipids seem to play a decisive role in the entry stage of viral infection and in channeling the virions to specific intracellular membrane-bound compartments and ultimately to the nucleus, where the genomes are replicated and packaged for release. Therefore the transport of the infecting virion or viral genome to this site of multiplication is an essential process in productive viral infection as well as in latent infection and transformation. This review summarizes the major findings related to the characterization of the nature of the interactions between PyV and host protein and their impact in host cell invasion.

Standardization of Genomic DNA Isolation from Minute Quantities of Fish Scales and Fins Amenable to RAPD-PCR

The main focus of this study was to standardize a non-destructive procedure for extraction of genomic DNA (gDNA) from minute quantities of scales and fins of two commonly available fishes Labeo bata and Heteropneustes fossilis and also to compare the gDNA yields from live and as well from frozen samples. The spectrophotometric and electrophoretic analyses revealed a significant difference in the DNA yields from live and frozen samples. The isolated gDNAs were used as templates for RAPD-PCR. The quality and consistency of banding pattern showed that gDNA templates from live tissues performed better than that from frozen tissue samples. It was also found that the minute quantities of fresh scales or fin tissues from live fish provided satisfactory quantity and quality of gDNAs that could support several rounds of RAPD-PCR. This non-destructive sampling has a great implication in gDNA based population genetic studies in endangered and vulnerable species of fishes, where killing or sacrificing is an ethical issue.

Study of the Genetic Diversity of the Ornamental Fish Badis badis (Hamilton-Buchanan, 1822) in the Terai Region of Sub-Himalayan West Bengal, India

Dwarf chameleon fish or Badis badis, a lesser known ornamental freshwater fish, has recently been included in the Indian threatened category of fish list. There are insufficient studies with regard to the assessment of genetic background of this ichthyofauna, especially in the western sub-Himalayan region of West Bengal, India, popularly known as the Terai. The present study is the first attempt to investigate the present status of the genetic background of this species in the Mahananda and Balason rivers, major streams of this region. Twenty-one selective RAPD primers generated 53 and 60 polymorphic fragments in the Mahananda and Balason populations, respectively. The proportion of polymorphic loci, Nei’s genetic diversity (H), and Shannon’s index were 0.4416, , and , respectively, in Mahananda river population and were 0.5041, , and , respectively, in Balason river population. Inbreeding coefficient and degree of gene differentiation were also calculated. The H and were found to be and , respectively, in overall Mahananda-Balason river system. Our study revealed considerable lack of genetic variation among the individuals of Badis badis. The genetic data obtained from the present study lend support to the view that there is a scope of stock improvement for this ichthyofauna.

Analyses of Human and Rat Clinical Parameters in Rheumatoid Arthritis Raise the Possibility of Use of Crude Aloe vera Gel in Disease Amelioration

Rheumatoid Arthritis (RA) is a chronic inflammatory condition affecting the joints causing swelling, stiffness and pain which finally leads to substantial loss of functioning and mobility in its advanced stages. In the present study we have monitored important serological parameters of fifty RA patients and also have discussed the justification of using rat as a model for human RA researches by comparing their respective serological parameters. We have also evaluated the anti-arthritic roles of raw Aloe vera gel and its effects in rat model where arthritis was induced by using Freund’s Complete Adjuvant (FCA). Three essential conclusive statements were derived from the study. Firstly, the six clinical parameters that we have selected for the study namely, RA factor, CRP, ASO, ESR, ceruloplasmin and serum creatinine were all essential for the differential diagnosis of Rheumatoid Arthritis during its early and later stages, RA factor being the most sensitive of all parameters (92% sensitivity). Secondly, this study has supported the use of the rat as a model for designing therapeutic strategies against RA. Lastly, as evident from our study, Aloe vera extracts can be beneficial for the reduction of inflammatory edema and also for the reduction of ceruloplasmin in RA condition in rat model. However, further investigations are necessary for more refined therapeutic usage of Aloe vera for the treatment of RA in human.

Recent advances in host–virus interactomics during entry and infection

Viral infections and pandemics result in millions of deaths worldwide each year. Viruses exploit host cellular processes, not only to gain entry and to deliver their genetic cargo, but also to counteract and use host immune defenses. To this end, a variety of ingenious strategies have evolved in viruses that involve fusion between virus and host membranes, channel formation through the host plasma membranes, disruption of the membrane vesicles, or a combination of these events. The entry and infection pathways of virus are thus largely defined by the inter - actions between virus particles and their cell surface and cytoplasmic receptors. A thorough analysis of virus-host interactomes may reveal novel mechanisms in virus entry, virus infection, and pathogenic strategies to modulate host metabolic pathways. The study of viral entry, infec- tion, and pathogenesis has evolved over a long period. A host of next-generation technological advancements in this field has been discussed in this review.

Quantification of human polyomavirus JC virus load in urine and blood samples of healthy tribal populations of North-Eastern part of West Bengal, India.

Background: Human polyomavirus JC (JCV) is a widespread human virus with profound pathogenic potential. A study was undertaken to quantify JCV load in urine and peripheral blood samples of immunocompetent, apparently healthy tribal individuals of North-Eastern part of West Bengal, India for the first time. Materials and Methods: One hundred and thirteen samples of urine or blood were collected from different tribal groups of this region. For the quantitative estimation of the viral load in each sample, real-time polymerase chain reaction method using the SYBR Green dye was employed. Results: The viral load estimated was found in the range between 3.5 × 102 and 2.12 × 106 copies/ml of samples having a mean and median viral copy numbers of 8.67 × 105 and 9.19 × 105 copies/ml of sample respectively. Conclusion: The mean viral DNA load in urine samples of the studied immunocompetent population was found to be higher than that found in a study conducted in the USA, but lower than similar groups of Italy and healthy adult women in the USA. However when compared with median values of viral DNA loads in urine samples of immunocompetent human subjects of Kuwait, Portugal, and Switzerland the observed viral DNA load was found to be substantially higher.

Study of genetic diversity of KIR and TLR in the Rabhas, an endogamous primitive tribe of India.

The Rabha tribe is a little known small endogamous population belonging to Indo-mongoloid group of north-eastern India. We have analyzed 16 KIR and 5 TLR gene polymorphisms in the Rabha population of northern West Bengal, India for the first time. The observed frequencies of the KIR genes (except framework and pseudogene loci) ranged between 0.26 (KIR2DS3) and 0.96 (KIR2DL1). Comparisons based on KIR polymorphism have revealed that although the Rabhas are of Indian origin the presence of mongoloid component in their gene pool cannot be denied. The frequencies of the 5 TLR genes ranged between 0.90 (TLR4) and 0.46 (TLR5). TLR variations found in the Rabhas may play a synergistic role in fighting against the bacterial invasions. Our results may contribute to the understanding of (1) genetic background and extent of genetic admixture in the Rabhas, (2) population migration events and (3) KIR-disease-TLR interactions.

Diversity of Killer Cell Immunoglobulin-Like Receptor Genes in the Bengali Population of Northern West Bengal, India

The Indian Subcontinent exhibits extensive diversity in its culture, religion, ethnicity and linguistic heritage, which symbolizes extensive genetic variations within the populations. The highly polymorphic Killer cell Immunoglobulin‐like Receptor (KIR) family plays an important role in tracing genetic differentiation in human population. In this study, we aimed to analyse the KIR gene polymorphism in the Bengali population of northern West Bengal, India. To our knowledge, this is the first report on the KIR gene polymorphism in the Bengalis of West Bengal, India. Herein, we have studied the distribution of 14 KIR genes (KIR3DL1‐3DL3, KIR2DL1‐2DL5, KIR2DS1‐2DS5 AND KIR3DS1) and two pseudogenes (KIR3DP1 and 2DP1) in the Bengalis. Apart from the framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1), which are present in all the individuals, the gene frequencies of other KIR genes varied between 0.34 and 0.88. Moreover, upon comparing the KIR polymorphism of the Bengalis with the available published data of other world populations, it has been found that the Indo‐European‐speaking Bengalis from the region share both Dravidian and Indo‐Aryan gene pool with considerable influences of mongoloid and European descents. Furthermore, evidences from previously published data on human leucocyte antigen and Y‐chromosome haplogroup diversity support the view. Our results will help to understand the genetic background of the Bengali population, in illustrating the population migration events in the eastern and north‐eastern part of India, in explaining the extensive genetic admixture amongst the different linguistic groups of the region and also in KIR‐related disease researches.