Extracellular Vesicles in Triple-Negative Breast Cancer: Immune Regulation, Biomarkers, and Immunotherapeutic Potential

Triple-negative breast cancer (TNBC) is an aggressive subtype accounting for ~10-20% of all human BC and is characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) amplification. Owing to its unique molecular profile and limited targeted therapies, TNBC treatment poses significant challenges. Unlike other BC subtypes, TNBC lacks specific molecular targets, rendering endocrine therapies and HER2-targeted treatments ineffective. The chemotherapeutic regimen is the predominant systemic treatment modality for TNBC in current clinical practice. However, the efficacy of chemotherapy in TNBC is variable, with response rates varying between a wide range of patients, and the emerging resistance further adds to the difficulties. Furthermore, TNBC exhibits a higher mutational burden and is acknowledged as the most immunogenic of all BC subtypes. Consequently, the application of immune checkpoint inhibition has been investigated in TNBC, yielding promising outcomes. Recent evidence identified extracellular vesicles (EVs) as an important contributor in the context of TNBC immunotherapy. In view of the extraordinary ability of EVs to transfer bioactive molecules, such as proteins, lipids, DNA, mRNAs, and small miRNAs, between the cells, EVs are considered a promising diagnostic biomarker and novel drug delivery system among the prospects for immunotherapy. The present review provides an in-depth understanding of how EVs influence TNBC progression, its immune regulation, and their contribution as a predictive biomarker for TNBC. The final part of the review focuses on the recent key advances in immunotherapeutic strategies for better understanding the complex interplay between EVs and the immune system in TNBC and further developing EV-based targeted immunotherapies.

Abstract 823: Piperlongumine nanoformulation enhances gemcitabine therapeutic response in pancreatic cancer

Pancreatic cancer (PanCa) is characterized by lack of early diagnosis, poor response to available therapeutic modalities and chemoresistance. Gemcitabine (GEM) is currently considered most effective therapy for PanCa; however, it shows only a marginal survival benefit of 6 months. This poor drug response has been attributed to desmoplasia, causes suboptimal drug delivery, alters tumor microenvironment (TME), which includes tumor surrounding blood vessels, fibroblasts, immune cells, extracellular matrix, and other signaling molecules and induces chemo-resistance in tumors. To overcome these existing issues associated with chemotherapy, identification and development of novel therapeutic modalities are a pressing need. Piperlongumine (PL) is a natural alkaloid isolated from the long pepper, Piper longum L., and has shown substantial cancer-preventive and therapeutic efficacy against a variety of cancers. However, delivering its effective concentration in pancreatic tumors has been challenging. We have recently engineered a multi-layered Pluronic F127 and polyvinyl alcohol stabilized and poly-L-lysine coated piperlongumine loaded poly(lactic-co-glycolic acid) nanoparticle formulation (PLGA-PL), which effectively inhibits the growth of PanCa cells. In this study, we demonstrate that PLGA-PL effectively sensitize tumor cells to GEM via decreased desmoplasia, altered TME, SHH/CXCL12/CXCR4 and immune surveillance. Our finding show that PLGA-PL synergizes with GEM in inhibiting PanCa cell (HPAF-II and Panc-1) growth, migration, and invasion compared to free PL. Mechanistically, PLGA-PL targets the TME via inhibition of sonic hedgehog (SHH) pathway and oncogenic CXCR4/CXCL12 signaling axis that inhibits bidirectional tumor-stromal cells interaction. We have also found that PLGA-PL alone and in combination with GEM targets cancer stem cells by inhibiting pluripotency maintaining stemness factors (Nanog, Sox2, c-Myc, CD133, and Oct-4) as determined by qRT-PCR, Western blotting, and immunofluorescence analysis, and further confirmed by restricting tumor sphere formation. Furthermore, PLGA-PL also effectively targets tumor-associated macrophages (TAM) by repolarizing M2 into M1 phenotype via inhibiting expression of M2 markers and an increase in M1 markers in mouse macrophage cell line RAW264.7. M2 polarization of RAW264.7 cells were induced by culture with IL-4 (20 ng/mL) in presence of PLGA-PL or vehicle control. In additions, PLGA-PL effectively increases phagocytic capacity in murine macrophages as determined by phagocytosis assay (Vybrant Phagocytosis Assay Kit). In conclusion, we observed that PLGA-PL effectively targets TME, facilitates GEM uptake by inhibiting the activation of CXCR4/CXCL12/SHH signaling, and reprograming the tumor immune surveillance. This study suggests that PLGA-PL has great potential for future clinical use in management of PanCa.

Citation Format: Vivek Kumar Kashyap, Neeraj Chauhan, Mohammed Sikander, FNU Pranav, Rahul Tiwari, Bilal B. Hafeez, Murali M. Yallapu, Meena Jaggi, Subhash C. Chauhan. Piperlongumine nanoformulation enhances gemcitabine therapeutic response in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 823.

Abstract 305: Novel nanoformulation of piperlongumine for pancreatic cancer therapy

Background: Pancreatic cancer (PanCa) is expected to be the second leading cause of cancer-related death by 2030. The treatment of PanCa is highly challenging due to the extremely poor response to existing therapeutic options. Highly desmoplastic tumor microenvironment in pancreatic tumor causes suboptimal delivery of therapeutic agents in tumors that eventually resulted to chemo-resistance. Piperlongumine (PL) is a natural alkaloid isolated from the long pepper, Piper longum L., and has shown substantial cancer-preventive and therapeutic efficacy against variety of cancers. However, delivering its effective concentration in pancreatic tumors has been challenging. In this study, we have synthesized and characterized a novel nano-formulation of PL composed of a PLGA core (PLGA-PL), stabilized with polyvinyl alcohol (PVA) and coated with poly-L-lysine (PLL), and evaluated its therapeutic effects against PanCa.

Methods: The various physicochemical approaches (FT-IR, DSC, TEM, TGA, and HPLC) was used to characterize the PLGA-PL formulation for particle size, chemical composition, and drug loading efficiency. Cellular uptake of PLGA-PL was achieved in incubation with PLGA-PL in PanCa cells. Further, the therapeutic efficacy of PLGA-PL was determined by using various in vitro assays (MTS, wound healing, boyden chamber, cell cycle and apoptosis assays) using PanCa cells. The effects of PLGA-PL on various key oncogenic signaling pathways were evaluated by qRT-PCR, Western blot, confocal microscopy, immunohistochemistry (IHC) analyses.

Results: Our novel PLGA-PL formulation has an average size of 110 nm in dynamic light scattering and a zeta potential range of -6.52 to -7.68 mV with excellent PL loading efficiency. Cellular uptake and internalization studies show that PLGA-PL escapes lysosomal degradation, allowing for effective endosomal release into the cytosol. PLGA-PL showed superior anti-cancer activity in various PanCa cells (BxPC-3, HPAF-II, AsPC-1, Panc-1, and MIA PaCa-2) compared to free PL. Moreover, PLGA-PL showed a remarkable inhibition of the migration and invasion potential of PanCa cells. Furthermore, PLGA-PL more effectively inhibited the components of the Shh pathway and Gli targets as determined by qPCR and Western blot analysis. Additionally, PLGA-PL treatment targets cancer stem cells by regulating pluripotency, maintaining stemness factors (Oct-4, Sox2, Nanog and c-Myc), and limiting tumor sphere formation.

Conclusions: Taken together, our results demonstrate that PLGA-PL nanoformulation exhibits superior anti-cancer potential than free PL against and could be used as a novel therapeutic modality for the management of PanCa.

Citation Format: Vivek Kumar Kashyap, Godwin P. Darkwah, Swati Dhasmana, Neeraj Chauhan, Anupam Dhasmana, Sudhir Kotnala, Partha Laskar, Mohammed Sikander, Bilal B. Hafeez, Murali M. Yallapu, Meena Jaggi, Subhash C. Chauhan. Novel nanoformulation of piperlongumine for pancreatic cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 305.

Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin

Curcumin is an important bioactive component of turmeric and also one of the important natural products, which has been investigated extensively. The precise mode of action of curcumin and its impact on system level protein networks are still not well studied. To identify the curcumin governed regulatory action on protein interaction network (PIN), an interectome was created based on 788 key proteins, extracted from PubMed literatures, and constructed by using STRING and Cytoscape programs. The PIN rewired by curcumin was a scale-free, extremely linked biological system. MCODE plug-in was used for sub-modulization analysis, wherein we identified 25 modules; ClueGo plug-in was used for the pathway’s enrichment analysis, wherein 37 enriched signalling pathways were obtained. Most of them were associated with human diseases groups, particularly carcinogenesis, inflammation, and infectious diseases. Finally, the analysis of topological characteristic like bottleneck, degree, GO term/pathways analysis, bio-kinetics simulation, molecular docking, and dynamics studies were performed for the selection of key regulatory proteins of curcumin-rewired PIN. The current findings deduce a precise molecular mechanism that curcumin might exert in the system. This comprehensive in-silico study will help to understand how curcumin induces its anti-cancerous, anti-inflammatory, and anti-microbial effects in the human body.

Tannic acid inhibits lipid metabolism and induce ROS in prostate cancer cells

Prostate cancer (PCa) cells exploit the aberrant lipid signaling and metabolism as their survival advantage. Also, intracellular storage lipids act as fuel for the PCa proliferation. However, few studies were available that addressed the topic of targeting lipid metabolism in PCa. Here, we assessed the tannic acid (TA) lipid-targeting ability and its capability to induce endoplasmic reticulum (ER) stress by reactive oxygen species (ROS) in PCa cells. TA exhibited dual effects by inhibiting lipogenic signaling and suppression of lipid metabolic pathways. The expression of proteins responsible for lipogenesis was down regulated. The membrane permeability and functionality of PCa were severely affected and caused nuclear disorganization during drug exposure. Finally, these consolidated events shifted the cell's survival balance towards apoptosis. These results suggest that TA distinctly interferes with the lipid signaling and metabolism of PCa cells.

Cross-Linked Polyphenol-Based Drug Nano-Self-Assemblies Engineered to Blockade Prostate Cancer Senescence

Cellular senescence is one of the prevailing issues in cancer therapeutics that promotes cancer relapse, chemoresistance, and recurrence. Patients undergoing persistent chemotherapy often develop drug-induced senescence. Docetaxel, an FDA-approved treatment for prostate cancer, is known to induce cellular senescence which often limits the overall survival of patients. Strategic therapies that counter the cellular and drug-induced senescence are an unmet clinical need. Towards this an effort was made to develop a novel therapeutic strategy that targets and removes senescent cells from the tumors, we developed a nanoformulation of tannic acid-docetaxel self-assemblies (DSAs). The construction of DSAs was confirmed through particle size measurements, spectroscopy, thermal, and biocompatibility studies. This formulation exhibited enhanced in vitro therapeutic activity in various biological functional assays with respect to native docetaxel treatments. Microarray and immunoblot analysis results demonstrated that DSAs exposure selectively deregulated senescence associated TGFβR1/FOXO1/p21 signaling. Decrease in β-galactosidase staining further suggested reversion of drug-induced senescence after DSAs exposure. Additionally, DSAs induced profound cell death by activation of apoptotic signaling through bypassing senescence. Furthermore, in vivo and ex vivo imaging analysis demonstrated the tumor targeting behavior of DSAs in mice bearing PC-3 xenograft tumors. The antisenescence and anticancer activity of DSAs was further shown in vivo by inhibiting TGFβR1 proteins and regressing tumor growth through apoptotic induction in the PC-3 xenograft mouse model. Overall, DSAs exhibited such advanced features due to a natural compound in the formulation as a matrix/binder for docetaxel. Overall, DSAs showed superior tumor targeting and improved cellular internalization, promoting docetaxel efficacy. These findings may have great implications in prostate cancer therapy.

Abstract 3634: Tannic acid-docetaxel scaffold nanoparticles for improved prostate cancer therapy

Purpose: Prostate cancer (PrCa) is one of the leading causes of cancer-related deaths among men in the United States. Chemotherapy with docetaxel holds great promise and important therapeutic option for PrCa treatment. However, chemotherapy is often associated with incomplete cell death and leads to persistent senescent phenotype. Such phenotypic cancer cells survive and promotes tumor development, recurrence, and drug resistance. Altogether, targeting these cells can enhance chemotherapy outcomes. In the current study, we established a tannic acid-docetaxel scaffold nanoparticles (TDS NP) platform that allows for facile targeting and inhibition of drug induced senescence in prostate cancer.

Methods: TDS NP were prepared by solvent evaporation and extrusion process using a series of tannic acid and docetaxel weight ratios. The scaffold self-assembly formation was determined using a steady-state fluorescence quenching, FT-IR, XRD, DSC, and TGA. The surface and morphological properties of TDS NPs were determined by dynamic light scattering and transmission electron microscopy. The biocompatibility assessment was characterized by hemolysis assay. C4-2 and PC-3 cell lines were used as PrCa model systems for in vitro and in vivo studies. The cellular internalization (in vitro) and accumulation (in vivo) was examined using dye-tagged TDS NPs. The superior in vitro anti-cancer and metastatic potential of TDS NPs were evaluated using proliferation, colony formation, migration, invasion, and immunoblotting assays. The anti-senescence ability of TDS NPs was examined through β-Galactosidase Staining Kit. A PC-3 xenograft mouse model was used to examine its superior therapeutic activity over free docetaxel treatment.

Results: A series of physico-chemical analyses confirmed the integrity of TDS NP. An optimized formulation exhibited a spherical shape particle formulation with 124.13 ± 2.16 nm with a negative zeta potential of -14.0 mV. TDS NPs formulation exhibited superior internalization capacity in PrCa cells in a dose- and time-dependent manner. In vitro functional studies confirm superior therapeutic activity of TDS NPs over free docetaxel treatment. Enhanced pro-apoptotic while downregulating anti-apoptotic effects with treatment of TDS NPs in comparison to native drug. A profound inhibition of β-galactosidase activity was noticed with TDS NPs treatment. In vivobiodistribution studies confirm efficient accumulation of TDS NPs in mice. In addition, TDS NPs showed robust antitumor activity against PC-3 xenografts. Such improved activity was correlated with increased inhibition of senescence and induced apoptosis.

Conclusion: In summary, we developed a novel tannic acid-docetaxel scaffold nanoparticle formulation that is capable of inhibiting senescence, minimizing drug resistance, and inducing apoptosis in prostate cancer.

Citation Format: Prashanth Kumar Bhusetty Nagesh, Pallabita Chowdhury, Elham Hatami, Sonam Kumari, Vivek Kumar Kashyap, Bilal Hafeez, Sheema Khan, Manish Kumar Tripathi, Meena Jaggi, Subhash C. Chauhan, Murali M. Yallapu. Tannic acid-docetaxel scaffold nanoparticles for improved prostate cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3634.

Cucurbitacin D Reprograms Glucose Metabolic Network in Prostate Cancer

Prostate cancer (PrCa) metastasis is the major cause of mortality and morbidity among men. Metastatic PrCa cells are typically adopted for aberrant glucose metabolism. Thus, chemophores that reprogram altered glucose metabolic machinery in cancer cells can be useful agent for the repression of PrCa metastasis. Herein, we report that cucurbitacin D (Cuc D) effectively inhibits glucose uptake and lactate production in metastatic PrCa cells via modulating glucose metabolism. This metabolic shift by Cuc D was correlated with decreased expression of GLUT1 by its direct binding as suggested by its proficient molecular docking (binding energy −8.5 kcal/mol). Cuc D treatment also altered the expression of key oncogenic proteins and miR-132 that are known to be involved in glucose metabolism. Cuc D (0.1 to 1 µM) treatment inhibited tumorigenic and metastatic potential of human PrCa cells via inducing apoptosis and cell cycle arrest in G2/M phase. Cuc D treatment also showed inhibition of tumor growth in PrCa xenograft mouse model with concomitant decrease in the expression of GLUT1, PCNA and restoration of miR-132. These results suggest that Cuc D is a novel modulator of glucose metabolism and could be a promising therapeutic modality for the attenuation of PrCa metastasis.

Abstract 2101: Ormeloxifene suppresses the growth of prostate tumor via inhibition of β-catenin induced AR signaling

Background: Prostate cancer (PrCa) first manifests as an androgen-dependent disease and can be treated with androgen-deprivation therapy. Despite the initial success of androgen ablation therapy, resistance to anti-androgen therapy displays by progression to hormone refractory (androgen-independent) advanced stage PrCa which is primary cause of patient’s death. Main underlying cause for the onset of hormone refractory cancer is ligand independent activation of AR signaling in PrCa cells. It has been shown that β-catenin acts as a non-androgen activator of AR which enhances AR transactivation in PrCa cells. Thus, identification of agents with excellent pharmacokinetics and pharmacodynamics parameters that can inhibit ligand independent activation of AR signaling might be highly useful for the treatment of advanced stage PrCa. Herein, we identified a synthetic molecule, ormeloxifene (ORM), which efficiently represses β-catenin mediated ligand independent activation of AR signaling, thus, inhibits growth and metastatic features of PrCa cells.

Methods: Androgen-refractory but AR positive PrCa cell (C4-2) was used as an in vitro and in vivo model systems. Effect of ORM on AR and PSA protein levels was determined by Western blot analysis. Effect of ORM treatment was analyzed on AR and PSA luciferase activities by transiently transfecting the C4-2 cells by AR and PSA luciferase plasmids. Renilla construct was used as an internal control. C4-2 cells nuclear and cytoplasmic lysates were prepared using Active Motif kit. Immunoprecipitation analysis was performed to determine if ORM inhibits physical interaction of β-catenin with AR. Therapeutic efficacy of ORM was evaluated in cell lines and PrCa xenograft mouse models.

Results: ORM dose-dependently (10, 15 and 20 µM) inhibited the protein levels of AR and its downstream target protein PSA. ORM (10 and 20μM) treatment also inhibited AR transactivation as determined by decreased promoter activities of AR and its target gene PSA. ORM (10 and 20μM) treatment inhibited protein levels of nuclear β-catenin and physical interaction of β-catenin with AR in PrCa cells. ORM administration dose- dependently (intra-peritoneal; 100 and/or 500µg/mouse; thrice/week) significantly (P<0.01) inhibited growth of C4-2 cells derived xenograft tumors in athymic nude mice. ORM treatment significantly (P<0.01) inhibited the expressions of nuclear AR and β-catenin expressions in xenograft tumor tissues. These ORM treated mice did not show any apparent toxicity in our study.

Conclusion: Our study demonstrates that ORM is a potent inhibitor of β-catenin-mediated activation of AR signaling. Based on its safety profile, ORM might be an ideal candidate for repurposing to treat advanced stage PrCa alone or in combination with other therapies.

Citation Format: Aditya Ganju, Bilal Bin Hafeez, Mohammed Sikander, Vivek Kumar Kashyap, Murali Mohan Yallapu, Subhash C. Chauhan, Meena Jaggi. Ormeloxifene suppresses the growth of prostate tumor via inhibition of β-catenin induced AR signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2101. doi:10.1158/1538-7445.AM2017-2101

Disparity in rates of HPV infection and cervical cancer in underserved US populations

There is a higher rate of HPV infection and cervical cancer incidence and mortality in underserved US population who reside in Appalachian mountain region compared to Northern Plains. Social and behavioral factors such as smoking and alcohol consumption are for such a high incidence. However, by and large, the reasons for these discrepancies lie in the reluctance of the underserved population to adopt preventive measures such as prophylactic Human papilloma virus (HPV) vaccines and Pap smear screening that have significantly reduced the incidence and mortality rate of cervical cancer in Caucasian women. Thus, it is clear that drastic change in social behavior and implementation of preventive measures is required to effectively reduce the incidence and mortality from cervical cancer in this underserved population.

Antiquity, geographic contiguity and genetic affinity among Tibeto-Burman populations of India: A microsatellite study

BACKGROUND

The Tibeto-Burman (TB) populations are one of the four major linguistic population groups of India. They are considered belonging to different stocks and show wide variation in culture and language; however, their genetic relationship, antiquity and migration history among the regional populations has been little investigated. Molecular genetic studies are expected to clearly show the antiquity and genetic diversity of these populations.

AIM

This paper seeks to understand the extent and magnitude of genetic affinities and diversities among 14 TB populations (12 Indian and two global groups), investigate the findings based on classical genetic markers and verify the historical accounts of their migration and genetic history based on 12 microsatellite markers.

SUBJECTS AND METHODS

The allele frequency data for 12 STR loci of 13 Asian (Tibeto-Burman) populations were obtained from the literature and the Adi Pasi data was obtained by microsatellite typing of their blood samples. The 12 loci studied are D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, vWa, TPOX, D18S51. Three different distance measures, two phylogenetic trees and PCA plot have been employed to understand the genetic relationship of the studied populations.

RESULTS

Average heterozygosity values range from 68 to 79% and the average G(ST) value is 4.7%. The dendrogram, based on the D(A) distance, shows the clustering of populations based on their diversities and geographical contiguity; the Mizoram and Arunachal Pradesh populations especially cluster together, populations from Sikkim form a separate subcluster and Manipur populations along with the Garo of West Bengal separate out from the other clusters. The Harpending and Ward regression model shows isolated populations positioned below the regression line and others, who experience external gene flow, placed above the line. The results support folklore migration accounts of their possible antiquity with the Tibetan and southern Chinese populations.

CONCLUSIONS

Overall, geographic contiguity, punctuated by isolating barriers, is a major influencing factor of genetic affinity among the TB population; contiguous populations within a region show greater genetic relationship than with distant TB populations over a wide geographical area. The results of the microsatellite study also support the history of diverse routes of migration of these populations.

Allele frequency distribution at 15 autosomal STR loci in Panggi, Komkar and Padam sub tribes of Adi, a Tibeto-Burman speaking population of Arunachal Pradesh, India

Fifteen autosomal STR loci were analyzed in 223 healthy individuals belonging to three remote, isolated Tibeto-Burman speaking sub tribes namely, Panggi, Komkar and Padam of Adi tribe of Arunachal Pradesh, India. The analyzed markers exhibited a high degree of polymorphism in the studied populations. Statistical parameters of forensic interest; observed heterozygosity, probability of homozygosity, exact test, likelihood ratio test, power of discrimination, power of exclusion, match probability and typical paternity index were determined for all loci. The average heterozygosity values were found to be low in the three populations (Panggi: 0.7747; Komkar: 0.7742 and Padam: 0.7663). The combined power of discrimination and power of exclusion were 0.9999 in the studied populations thereby revealing the high forensic significance of the chosen markers. The study indicates the utility of the tested microsatellite markers in forensic human identification, paternity testing and human population genetic studies.

Allele Frequencies of 20 Y-Chromosomal Short Tandem Repeat Loci in a Tribal Population of Deccan Plateau, India

POPULATION

Eighty male individuals from a nomadic tribal population belonging to Dravidian and Indo-Caucasian ethnicities from Deccan Plateau, Andhra Pradesh, India, were analyzed in the present study.

Phylogeography of mitochondrial DNA and Y-chromosome haplogroups reveal asymmetric gene flow in populations of Eastern India

Polymorphisms in mitochondrial (mt) DNA and Y-chromosomes of seven socially and linguistically diverse castes and tribes of Eastern India were examined to determine their genetic relationships, their origin, and the influence of demographic factors on population structure. Samples from the Orissa Brahmin, Karan, Khandayat, Gope, Juang, Saora, and Paroja were analyzed for mtDNA hypervariable sequence (HVS) I and II, eight Y-chromosome short tandem repeats (Y-STRs), and lineage-defining mutations diagnostic for Indian- and Eurasian-specific haplogroups. Our results reveal that haplotype diversity and mean pairwise differences (MPD) was higher in caste groups of the region (>0.998, for both systems) compared to tribes (0.917-0.996 for Y-STRs, and 0.958-0.988 for mtDNA haplotypes). The majority of paternal lineages belong to the R1a1, O2a, and H haplogroups (62.7%), while 73.2% of maternal lineages comprise the Indian-specific M*, M5, M30, and R* mtDNA haplogroups, with a sporadic occurrence of West Eurasian lineages. Our study reveals that Orissa Brahmins (a higher caste population) have a genetic affinity with Indo-European speakers of Eastern Europe, although the Y-chromosome data show that the genetic distances of populations are not correlated to their position in the caste hierarchy. The high frequency of the O2a haplogroup and absence of East Asian-specific mtDNA lineages in the Juang and Saora suggest that a migration of Austro-Asiatic tribes to mainland India was exclusively male-mediated which occurred during the demographic expansion of Neolithic farmers in southern China. The phylogeographic analysis of mtDNA and Y-chromosomes revealed varied ancestral sources for the diverse genetic components of the populations of Eastern India.

Microsatellite diversity reveals the interplay of language and geography in shaping genetic differentiation of diverse Proto-Australoid populations of west-central India

Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations.

Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene

The phylogenetic status of the infra order Pecora is controversial, even though it is supported by paleontological, morphological, and molecular evidence. We analyzed two mitochondrial genes (i.e., 16S rRNA and cytochrome b) to resolve the phylogenetic position of pecoran species, i.e., the Bovidae, Cervidae, and Moschidae endemic to the Indian subcontinent. We used phylogenetic analysis based on different algorithms, including neighbor joining, maximum parsimony, Bayesian inference, maximum likelihood, minimum evolution, median joining network, along with multidimensional scaling, and DNA word analysis. Our results established the basal position of Tragulidae and the monophyly of the infra order Pecora within the Suborder Ruminantia. Our results also demonstrated that Bovidae, Cervidae, and Moschidae are allied with the placement of musk deer as more closely related to bovids than to cervids. Molecular dating based on sequence analysis shows that the radiation of Pecora occurred during the early Oligocene and that the majority of the pecoran families radiated and dispersed rapidly during the Oligocene/Miocene transition.

Allele frequency distribution based on 17 STR markers in three major Dravidian linguistic populations of Andhra Pradesh, India

Allele frequencies for 15 tetranucleotides and 2 pentanucleotides repeat loci were determined in 317 unrelated, healthy individuals of Andhra Pradesh, India, belonging to three pre-dominant endogamous populations namely, Kappu Naidu, Kamma Chaudhary and Kapu Reddy. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all loci with few exceptions, which were not significant after applying Bonferroni's correction. Statistical parameters of forensic interest; observed heterozygosity, probability of homozygosity, probability of extact test, power of discrimination, match probability, polymorphism information content, power of exclusion and mean paternity index were determined for all loci. The present study reveals that Penta E and D2S1338 are the most informative loci in all the studied populations. The combined power of discrimination was greater than 0.976, whereas the cumulative power of exclusion gave an expected value of 0.9999 for all the tested microsatellite loci. No difference was observed in the discriminatory power of 15 loci in studied populations on comparison with other populations of India. Population differentiation tests revealed significant differences between the studied and neighboring populations at several loci. Analyzed parameters indicate the utility and efficacy of the studied 17 STR systems as a powerful tool in forensic human identification, paternity testing and human population genetic studies.

Genomic variation in the mitochondrially encoded cytochrome b (MT-CYB) and 16S rRNA (MT-RNR2) genes: characterization of eight endangered Pecoran species

In an effort to develop species-specific identification markers, we examined genetic variants and molecular signatures within genes encoding mitochondrial cytochrome b and 16S rRNA in eight endangered Pecoran species endemic to the Indian peninsula. Our results revealed that the cytochrome b gene exhibited higher sequence diversity than the 16S rRNA gene, both between and within species. However, the 16S rRNA gene harboured a larger number of species-specific mutation sites compared with the cytochrome b gene, suggesting that it could be useful for species identification. Indeed, we successfully used 'forensically informative nucleotide sequencing' (FINS) analysis of the 16S rRNA gene to identify two previously unknown biological specimens.

Genetic structure of Indian populations based on fifteen autosomal microsatellite loci

Background

Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers.

Results

The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively.

Conclusion

Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.

Polymorphisms at fifteen tetrameric short tandem repeat loci in three ethnic populations of Bengal, India

The study presents allele frequency data at 15 tetrameric short tandem repeat (STR) loci (D3S1358, THO1, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433 and FGA) in three ethnic populations--Mahishya, Bauri and Namasudra of Bengal to evaluate their utility in Forensic testing and understanding population structure and dynamics. A total of 169 individuals were studied from the selected populations. On an average the combined power of discrimination and power of exclusion in these groups was found 0.97 and 0.99, respectively. The allele distribution pattern shows possible genetic admixture between these ethnic groups which could be attributed to their close geographical proximity and occupying almost similar position in the social hierarchy. This study suggests that the 13 Combined DNA Index System (CODIS) markers and two added markers named D2S1338, D19S433 are highly informative and therefore suitable in matching biological specimen in human identification and population genetic study.

Deletions in the Y-derived amelogenin gene fragment in the Indian population

Background

Rare failures in amelogenin-based gender typing of individuals have been observed globally. In this study, we report the deletion of a large fragment of the amelogenin gene in 10 individuals out of 4,257 male samples analyzed from 104 different endogamous populations of India.

Methods

Samples were analyzed using commercial genetic profiling kits. Those that exhibited failures in amelogenin-based gender identification were further analyzed with published as well as newly designed primers to ascertain the nature and extent of mutation.

Results

The failure rate among Indian males was 0.23 %. Though the exact size and nature of the deletion (single point mutations at a number of positions or a single large deletion) could not be determined in the present study, it is inferred that the deletion spans a region downstream of the reverse primer-binding site of commercially available amelogenin primer sets. Deletions were conspicuously absent among the Mongoloid tribes of Northeast India, while both caste and tribal groups harbored these mutations, which was predominantly among the Y-chromosomes belonging to J2 lineage.

Conclusion

Our study indicates that the different amelogenin primer sets currently included in genetic profiling multiplex kits may result in erroneous interpretations due to mutations undetectable during routine testing. Further there are indications that these mutations could possibly be lineage-specific, inherited deletions.

Molecular insights into the origins of the Shompen, a declining population of the Nicobar archipelago

The Shompen, one of the most isolated and poorly understood contemporary hunter-gatherer populations, inhabit Great Nicobar Island, the southernmost island of the Nicobar archipelago. Morphological imprints in the Shompen were interpreted to favour a mixed Indo-Chinese, Malay, Negrito and Dravidian origin. Analyses of the mitochondrial, Y-chromosomal and autosomal gene pool of contemporary Shompen have revealed low diversity, illustrating a founder effect in the island population. Mitochondrial sequence analyses revealed the presence of two haplogroups of R lineage: B5a, and a newly defined clade, R12. Y-chromosomal analyses demonstrated the occurrence of a single lineage found predominantly in Austro-Asiatic speakers across Asia. With the different types of genetic markers analysed, the Shompen exhibit varying levels of genetic relatedness with the Nicobarese, and Austro-Asiatic speakers of mainland India and Southeast Asia. These genetic analyses provide evidence that the Shompen, an offshoot of the Nicobarese, are descendants of Mesolithic hunter-gatherers of Southeast Asian origin, deriving from at least two source populations.

Genetic diversity at 15 microsatellite loci among the Adi Pasi population of Adi tribal cluster in Arunachal Pradesh, India

Genetic polymorphisms at 15 tetrameric short tandem repeat (STR) loci were studied in 203 healthy individuals of Adi Pasi population from Arunachal Pradesh, India. All the loci analyzed were highly polymorphic and there was no significant deviation from the Hardy-Weinberg equilibrium (HWE) excepting D8S1179 and D18S51. Other forensic useful statistical parameters were also calculated and the 15 microsatellite markers selected for this study were found to be suitable for human identification and population genetic studies.

A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios

Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations share a common late Pleistocene maternal ancestry in India, some studies of the Y-chromosome markers have suggested a recent, substantial incursion from Central or West Eurasia. To investigate the origin of paternal lineages of Indian populations, 936 Y chromosomes, representing 32 tribal and 45 caste groups from all four major linguistic groups of India, were analyzed for 38 single-nucleotide polymorphic markers. Phylogeography of the major Y-chromosomal haplogroups in India, genetic distance, and admixture analyses all indicate that the recent external contribution to Dravidian- and Hindi-speaking caste groups has been low. The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family. The dyadic Y-chromosome composition of Tibeto-Burman speakers of India, however, can be attributed to a recent demographic process, which appears to have absorbed and overlain populations who previously spoke Austro-Asiatic languages.

Genetic Polymorphism at 15 Tetrameric Short Tandem Repeat Loci in Four Aboriginal Tribal Populations of Bengal

POPULATIONS

This study reports the genetic polymorphism observed at 15 short tandem repeat loci D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, and FGA in four aboriginal populations of Bengal. The analysis was performed to decipher the suitability of CODIS as well as six other highly polymorphic and unlinked markers in Forensic Testing. Studied populations include four tribes: Karmali, Kora, Maheli, and Lodha.

Host microsatellite alleles in malaria predisposition?

BACKGROUND

Malaria is a serious, sometimes fatal, disease caused by Plasmodium infection of human red blood cells. The host-parasite co-evolutionary processes are well understood by the association of coding variations such as G6PD, Duffy blood group receptor, HLA, and beta-globin gene variants with malaria resistance. The profound genetic diversity in host is attributed to polymorphic microsatellites loci. The microsatellite alleles in bacterial species are known to have aided their survival in fatal environmental conditions. The fascinating question is whether microsatellites are genomic cushion in the human genome to combat disease stress and has cause-effect relationships with infections.

PRESENTATION OF THE HYPOTHESIS

It is hypothesized that repeat units or alleles of microsatellites TH01 and D5S818, located in close proximity to beta-globin gene and immune regulatory region in human play a role in malaria predisposition. Association of alleles at aforesaid microsatellites with malaria infection was analysed. To overrule the false association in unrecognized population stratification, structure analysis and AMOVA were performed among the sampled groups.

TESTING OF HYPOTHESIS

Associations of microsatellite alleles with malaria infection were verified using recombination rate, Chi-square, and powerful likelihood tests. Further investigation of population genetic structure, and AMOVA was done to rule out the confounding effects of population stratification in interpretation of association studies.

IMPLICATION OF THE HYPOTHESIS

Lower recombination rate (theta) between microsatellites and genes implicated in host fitness; positive association between alleles-13 (D5S818), 9 (TH01) and strong susceptibility to Plasmodium falciparum; and alleles-12 (D5S818) and 6 (TH01) rendering resistance to human host were evident. The interesting fact emerging from the study was that while predisposition to malaria was a prehistoric attribute, among TH01 alleles; evolution of resistant allele-6 was a recent phenomenon, which could conceivably be driven by infection related selective forces. The host's microsatellite allelic associations with malaria infection were valid in the light of low genetic variance between sampled groups and no population stratification.

Molecular identification of lizard by RAPD & FINS of mitochondrial 16s rRNA gene

In the present study, we identified the structure-less skeleton suspected to be of house lizard present in jaggery, consumption of which caused mass food poisoning using, RAPD (Random Amplification of Polymorphic DNA) with random primers and FINS (Forensically Informative Nucleotide Sequencing) with mitochondrial 16s rRNA gene. The NJ tree dendogram based on distance calculated from RAPD bands clearly identified the structure-less as Calotes versicolor (Garden Lizard). In FINS analysis of the mitochondrial 16s rRNA gene the NJ tree based on Kimura-2-parameter distance matrices clearly reveal that the unknown sample clustered with Agmidae family and closest to Calotes versicolor (Garden Lizard) with 100% bootstrap support, whereas all other species belong to Gekkonida family form a single distinct cluster including Hemidactylus fluviviridis (House Lizard). This is the first successful typing of mitochondrial 16s rRNA with FINS approach to identify the biological origin of a structure-less skeleton. Our analysis also sustained successful identification of unknown samples using RAPD method with optimized conditions in a laboratory setup with low resources.

Development of novel heminested PCR assays based on mitochondrial 16s rRNA gene for identification of seven pecora species

BACKGROUND

Characterization of molecular markers and the development of better assays for precise and rapid detection of wildlife species are always in demand. This study describes a set of seven novel heminested PCR assays using specific primers designed based on species-specific polymorphism at the mitochondrial 16S rRNA gene for identification of Blackbuck, Goral, Nilgai, Hog deer, Chital, Sambar and Thamin deer.

RESULTS

The designed heminested PCR assays are two consecutive amplifications of the mitochondrial 16S rRNA gene. In the first stage, approximately 550 bp region of the 16S rRNA gene was amplified by PCR using template DNA and universal primers. In the second stage, a species-specific internal region of the 16S rRNA gene was amplified by PCR using the amplicon of the first PCR along with one universal primer and another species-specific primer as the reverse or forward primer. The amplicon generated after two consecutive amplifications was highly unique to target species. These assays were successfully validated for sensitivity, specificity, and ruggedness under a wide range of conditions.

CONCLUSION

The validation experiments confirm that the designed heminested PCR assays for identification of the seven species are highly specific, sensitive, reliable and provide a reproducible method allowing analysis of low copy number DNA recovered from decomposed or highly processed tissues. The assays for identification of other species could be devised by extrapolating the principle of designed heminested PCR.

Genotypic polymorphisms at seventeen autosomal short tandem repeat loci in four tribal populations of Andhra Pradesh, India

Four tribal populations of Andhra Pradesh, South India (1), Chenchu (n=100), Lambadi (n=107), Naikpod Gond (n=104) and Yerukula (n=101) were analyzed for DNA polymorphisms at 15 tetranucleotide and 2 pentanucleotide short tandem repeat (STR) loci in the present study.

Mitochondrial DNA control region sequence polymorphism in four indigenous tribes of Chotanagpur plateau, India

The analysis of genetic variation, in the nucleotide sequences of mitochondrial DNA, provides unique information in tracing of maternal lineage, determination of population diversity, pharmacogenomics and human identification. This study characterizes the HVR-I and II sequence polymorphism in 80 tribal individuals, belonging to the Austro-Asiatic linguistic family of Chotanagpur plateau, India. A total of 115 polymorphic sites were observed in the sequenced regions and 77 unique haplotypes could be identified.

Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages

Background

Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.

Results

The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports.

Conclusion

This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.

Influence of language and ancestry on genetic structure of contiguous populations: a microsatellite based study on populations of Orissa

Background

We have examined genetic diversity at fifteen autosomal microsatellite loci in seven predominant populations of Orissa to decipher whether populations inhabiting the same geographic region can be differentiated on the basis of language or ancestry. The studied populations have diverse historical accounts of their origin, belong to two major ethnic groups and different linguistic families. Caucasoid caste populations are speakers of Indo-European language and comprise Brahmins, Khandayat, Karan and Gope, while the three Australoid tribal populations include two Austric speakers: Juang and Saora and a Dravidian speaking population, Paroja. These divergent groups provide a varied substratum for understanding variation of genetic patterns in a geographical area resulting from differential admixture between migrants groups and aboriginals, and the influence of this admixture on population stratification.

Results

The allele distribution pattern showed uniformity in the studied groups with approximately 81% genetic variability within populations. The coefficient of gene differentiation was found to be significantly higher in tribes (0.014) than caste groups (0.004). Genetic variance between the groups was 0.34% in both ethnic and linguistic clusters and statistically significant only in the ethnic apportionment. Although the populations were genetically close (F_ST = 0.010), the contemporary caste and tribal groups formed distinct clusters in both Principal-Component plot and Neighbor-Joining tree. In the phylogenetic tree, the Orissa Brahmins showed close affinity to populations of North India, while Khandayat and Gope clustered with the tribal groups, suggesting a possibility of their origin from indigenous people.

Conclusions

The extent of genetic differentiation in the contemporary caste and tribal groups of Orissa is highly significant and constitutes two distinct genetic clusters. Based on our observations, we suggest that since genetic distances and coefficient of gene differentiation were fairly small, the studied populations are indeed genetically similar and that the genetic structure of populations in a geographical region is primarily influenced by their ancestry and not by socio-cultural hierarchy or language. The scenario of genetic structure, however, might be different for other regions of the subcontinent where populations have more similar ethnic and linguistic backgrounds and there might be variations in the patterns of genomic and socio-cultural affinities in different geographical regions.

Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups

Background

A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations.

Results

Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average G_ST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. D_A distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe.

Conclusion

The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups.

Genetic structure and affinity among eight ethnic populations of Eastern India: based on 22 polymorphic DNA loci

The nature and extent of genetic variation at 22 polymorphic DNA loci, belonging to three distinct classes, especially, 12 STR loci (D3S1358, vWA, FGA, D5S818, D13S317, D7S820, D8S1179, D21S11, D18S51, HPRTB, F13B, LPL), four VNTR loci (D1S7, D4S139, D5S110, D17S79), and six coding loci (HLDQA1, LDLR, GYPA, HBGG, D7S8, GC) were investigated among eight population groups of West Bengal and Manipur regions of India. Of these, two groups from West Bengal belong to Caucasoid and six (one in WB and five in Manipur) belong to Mongoloid stock. Both STR and the expressed loci show wide diversity among the eight populations. For example, Manipur Muslims show differences in allele frequency when compared to four other regional populations. Similarly, Garo, one of the Mongoloid populations of West Bengal, differ in allele frequency from their counterparts in the Manipur region. Departure from Hardy-Weinberg expectations was observed at certain loci in a few populations (e.g., D21S1137 in Kayastha and Brahmin, HUM F13B in Meitei). Heterozygosity values were higher for Caucasoid than Mongoloid groups. The overall gene differentiation (GST) for STR loci is higher (5.3%) than for those at the expressed region (4.6%). The clustering pattern of the eight populations differs with respect to different classes of genetic markers used. The dendrograms based on six coding loci (HLDQA1, LDLR, GYPA, HBGG, D7S8, GC) differs from those based on STR and VNTR markers. Caucasoid and Mongoloid groups form different clusters and Manipur Muslims are distinct from others. The clustering pattern corresponded with the spatial and ethnic affiliations of the populations. Using different classes of DNA loci at the coding and noncoding region will help to better understand the influence of population structure variables on the genetic structure of populations.

Genetic Diversity at 15 Fluorescent-Labeled Short Tandem Repeat Loci in the Patel and Other Communities of Gujarat, India

Thirteen tetranucleotide and 2 pentanucleotide repeat units were analyzed in 120 unrelated individuals of Patel and other communities of Gujarat, India. Allele frequency data obtained from the analysis of 15 short tandem repeat markers of the population were found to be satisfying Hardy-Weinberg equilibrium, with marginal deviations. Departures from Hardy-Weinberg equilibrium were observed in Patel communities at locus vWA and for that of the other communities at locus D7S820 and at locus TPOX. The power of discrimination values on an average fall within the range of 0.718 and 0.870, with deviations at locus D3S1358 showing a value of 0.400 for Patels. The value ranged between 0.709 and 0.869, with slight variations among the studied alleles in the other group. Thus, the 15 markers selected for this study were found to be highly suitable in human identification and for providing information on genetic polymorphism of the population of Gujarat.

Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: Analysis based on 15 microsatellite markers

The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic level.

Haplotype diversity in mitochondrial DNA hypervariable regions I and II in three communities of Southern India

The sequence polymorphisms at the mtDNA hypervariable regions I and II (HVR-I and HVR-II) were analyzed in 87 individuals belonging to three religious groups, Hindu, Muslim and Christians of Karnataka (South India). A total of 122 polymorphic sites were observed in the sequenced regions, with HVR-I exhibiting higher variation than HVR-II. The populations exhibited high sequence and nucleotide diversity, alike other studied caste groups of Karnataka.

Genetic profile based upon 15 microsatellites of four caste groups of the eastern Indian state, Bihar

BACKGROUND

The formation of caste groups among the Hindu community and the practice of endogamy exert a great impact on the genetic structure and diversity of the Indian population. Allele frequency data of 15 microsatellite loci clearly portray the genetic diversity and relatedness among four socio-culturally advanced caste groups: Brahmin, Bhumihar, Rajput and Kayasth of Caucasoid ethnicity of Bihar.

AIM

The study seeks to understand the impact of the man-made caste system on the genetic profile of the four major caste groups of Bihar.

METHODS AND PROCEDURE

Computation of average heterozygosity, most frequent allele, allele diversity and coefficient of gene differentiation (Gst), along with genetic distance (DA)and principal coordinate analysis were performed to assess intra-population and inter-population diversity.

MAIN OUTCOMES AND RESULTS

The average Gst value for all the loci was 0.012 +/- 0.0033, and the level of average heterozygosity was approximately 75.5%, indicating genetic similarity and intra-population diversity. Genetic distance (DA) values and the phylogenetic tree along with other higher caste groups of India indicate the relative distance between them.

CONCLUSION

The present study clearly depicts the genetic profile of these caste groups, their inherent closeness in the past, and the impact of the imposed caste system that later restricted the gene flow. The study highlights the status of Bhumihar and Kayasth in the Hindu caste system. The former was found clustering with the Brahmin group (as expected, since Bhumihar is known to be a subclass of Brahmin), whereas the distance between the Brahmin and Kayasth caste groups was found to be large. North-eastern Indian Mongoloids form a separate cluster.

Genetic diversity in four tribal groups of western India: a survey of polymorphism in 15 STR loci and their application in human identification

Genetic diversity at 15 STR loci: 2 pentanucleotide and 13 tetranucleotide STR loci was determined in four highly endogamous tribal groups, viz. Madia-Gond, Mahadeo-Koli, Katkari and Pawara of western India. The distribution of genotypes at studied 15 loci was found in agreement with expected values according to Hardy-Weinberg equilibrium. The combined power of discrimination of 15 loci was calculated as 0.80 while combined power of exclusion was observed as 0.53 among the studied four tribal groups. The study demonstrate very low heterozygosity and low power of exclusion of the loci of Powerplex 16 among the selected groups indicating less informativeness of the studied markers in human identification testing.

Molecular phylogenetic exploration of bacterial diversity in a Bakreshwar (India) hot spring and culture of Shewanella-related thermophiles

The bacterial diversity of a hot spring in Bakreshwar, India, was investigated by a culture-independent approach. 16S ribosomal DNA clones derived from the sediment samples were found to be associated with gamma-Proteobacteria, cyanobacteria, and green nonsulfur and low-GC gram-positive bacteria. The first of the above phylotypes cobranches with Shewanella, a well-known iron reducer. This phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing microorganisms.