Standardization of PCR conditions for an Ancient DNA Amplification

An ancient DNA provides us a powerful tool to study the miniscule amounts of DNA present in hundreds of thousands of years old archaeological remains. Since the advent of the PCR, it became possible for the population biologists to use this scarce and rare genetic material (aDNA) to understand prehistoric population histories. Working with ancient DNA is challenging in itself as it needs a manifold attention in order to maintain the archaeological sample free from contemporary DNA contamination. Apart from that, there are several other complications associated with ancient DNA work such as the preservation of DNA itself that is in degraded state and low copy number, DNA isolation and its successful PCR amplification. Despite the critical role of PCR in this field of research, till date no study has comprehensively evaluated ancient DNA amplification.  In this paper, we have reported our results to optimize PCR component as well as PCR condition to amplify HVR1 region in 600 years old biological samples

Dyslipidemia in pre- and post-menopausal women: a study of peri-urban Paundra Kshatriya women

Dyslipidemia is an important risk factor of cardiovascular disease, whereas menopause is a decrease in ovarian follicular activity at the end of reproductive age of the women, which is significantly influenced by hormonal changes brought on by menopause’s impact on serum lipids. This study was undertaken among pre- and post-menopausal Paundra Kshatriya women in Sonarpur, South 24 Parganas, West Bengal, India in order to determine the prevalence of dyslipidemia. 142 adult Paundra Kshatriya women (n pre-menopausal women = 96; n post-menopausal women = 46) were selected from a peri-urban setting of Sonarpur, South 24 Parganas, West Bengal. Anthropometry and arterial pressure data were recorded. Blood samples were collected from study participants who were on 12 hours fasting. 19.79% of pre-menopausal women and 17.39% of post-menopausal women had normal levels of lipids. Prevalence of dyslipidemia was slightly higher (82.7%) among the post-menopausal women compared to pre-menopausal women (80.2%). While high LDL cholesterol emerged as one of the prime causes for dyslipidemia among pre-menopausal women, hypercholesterolemia emerged as one of the prime causes for dyslipidemia among post-menopausal women. Regression analysis revealed a significant impact of 3 factors in pre-menopausal women and impact of 6 factors in post-menopausal women. Though Paundra Kshatriya women maintain a relatively less stressful and high physical activity lifestyle, they exhibited high levels of lipid abnormalities. The peri-urban population is undergoing lifestyle and dietary changes due to a close proximity to the urban centre, Kolkata. FundingAnthropological Survey of India, Ministry of Culture, Government of Indi

Clinical genetic aspects of cardiomyopathies

Cardiomyopathies are a major cause of heart disease. Not only the patients, but also their families are severely burdened by these illnesses. In the past decade, studies revealed the heterogeneity of these diseases in terms of clinical presentation, as well as their genetics. Studies done in the last few decades revealed a new concept of complex manifestation of cardiomyopathies with different heterogeneity level, penetration, and inheritance. The incomplete penetrance, genetic heterogeneity, and variable expression in cardiomyopathies paradoxically raise hopes that the development of novel disease modifying therapies may be achievable

Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana.

Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years

Epidemiology of cardiomyopathy - A clinical and genetic study of hypertrophic cardiomyopathy: The EPOCH-H study

Background: Hypertrophic cardiomyopathy (HCM) is a genetic disorder with the prevalence of 1 in 500 globally. HCM is clinically characterized by thickening of the wall of the heart, predominantly left ventricle (LV), and interventricular septum (IVS). Our study aims to report the demographical, clinical and genetic profile of Indian HCM patients. Methods: HCM patients were recruited on the basis of WHO criteria. The clinical phenotypes were analyzed using electrocardiography, two-dimensional electrocardiography, and hotspot region of the MYH7 gene was sequenced for all patients as well as for controls. Results: There were 59 patients with a clinical diagnosis of HCM with a preponderance of disease in males with a ratio (men, women) of 5.5:1. Average age of onset of the disease was late 30 s (39.2 ± 14.5) with familial HCM accounting for 18% (n = 9) for total HCM families (n = 50). Nonobstructive kind of HCM was more prevalent as compared to obstructive HCM (66.1% vs. 33.9%). Average posterior wall LV thickness of the HCM patients was 16 ± 4.8 mm and IVS thickness was 21 ± 8.3 mm with familial patients having greater wall thickness as compared to sporadic patients. Sequencing of hotspot region of MYH7 identified three mutations in three different patients. Two mutations were found to be segregating in familial cases. Conclusion: HCM is more prevalent in males with a predominance of hypertrophic nonobstructive cardiomyopathy form. Eighteen percent of cases were familial and showed an early onset of the disease and worse prognosis as compared to sporadic cases. Hotspot sequencing of MYH7 only explains 6% of its genetic basis. More of the candidate genes need to be screened through advanced techniques like next generation sequencing to identify the causal genes which could make us understand the mechanistic pathways

Mutations in hotspot region of MYH7 gene exon 23 associated with restrictive cardiomyopathy

Restrictive cardiomyopathy (RCM) is characterized by restrictive filling of the ventricles. The association between the variable expressivity and age at onset of disease and disease complexity with double and compound heterozygous state is associated with severity of disease phenotype in recent reports. Sharing of variants of sarcomere genes across cardiomyopathies has implication in clinical expression of different clinical phenotypes. The present study reports Sanger DNA sequencing of MYH7 gene, exon 23 from 30 unrelated RCM patients and 15 primary relatives from sporadic families with the hypothesis that RCM has common etiology with hypertrophic cardiomyopathy (HCM). Rare variant E949K and a de novo compound heterozygous mutation (p.E902K and p.D906N), in two RCM patients with early onset and no ventricular hypertrophy were found. These variants wereabsent in 50 dilated cardiomyopathy, 50 HCM patients and 15 primary relatives screened. The present report of rare and compound heterozygosity cases will further provide basis for the complexity and variable expressivity of phenotypes in patients in such complex diseases. The possible reasons for this phenotypic heterogeneity would be the presence of any other mutations in same chromosome or in different chromosome which is modifying the outcome of the causal mutation

Epidemiology of cardiomyopathy – A clinical and genetic study of restrictive cardiomyopathy: The EPOCH-R study

Introduction: Restrictive cardiomyopathy (RCM) is characterized by diastolic dysfunction, biatrial enlargement, and normal or near-normal systolic function. RCM is the rarest kind among cardiomyopathies with a severe outcome. Methods: Here, we present the clinical outcomes of thirty RCM patients recruited from a tertiary care unit of India, All India Institute of Medical Sciences, New Delhi. For clinical assessment, patients underwent electrocardiogram, echocardiography, and cardiac catheterization, and endomyocardial biopsy whenever required. Results: Out of 190 patients with cardiomyopathy, 100 had dilated cardiomyopathy, 60 had hypertrophic cardiomyopathy, and 30 had idiopathic RCM and were recruited for the study. Out of these thirty patients, 63.3% were males. A maximum number of patients were diagnosed in their second to third decade of life. Atrial fibrillation (73.3%) and ST-T abnormalities (76.6%) were common. Most of the patients showed the early age of onset with symptoms emerging in the first and second decades of life. Shortness of breath and fatigue were found to be common symptoms. No familial cases were found. Conclusion: RCM in India is a sporadic disease, rare, and occurs in the young. Prognosis of RCM is still worse than any other cardiomyopathy

Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic <i>Ramayana - Fig 2 </i>

<p><b>a)</b> The number of chunks donated at inter and intra populations level for the Bhil, Kol and Gond with respect to the Indian, Central Asian and the Pakistani populations. <b>b)</b> Plot of 25 nearest neighbors of Bhil, Kol and Gond individuals. The match population individuals are colored in grey.</p

Standardization of PCR conditions for an ancient DNA amplification

An ancient DNA provides us a powerful tool to study the miniscule amounts of DNA present in hundreds of thousands of years old archaeological remains. Since the advent of the PCR, it became possible for the population biologists to use this scarce and rare genetic material (aDNA) to understand prehistoric population histories. Working with ancient DNA is challenging in itself as it needs a manifold attention in order to maintain the archaeological sample free from contemporary DNA contamination. Apart from that, there are several other complications associated with ancient DNA work such as the preservation of DNA itself that is in degraded state and low copy number, DNA isolation and its successful PCR amplification. Despite the critical role of PCR in this field of research, till date no study has comprehensively evaluated ancient DNA amplification. In this paper, we have reported our results to optimize PCR component as well as PCR condition to amplify HVR1 region in 600 years old biological samples