Deepak Sharma

Bio: Deepak Sharma is an academic researcher from National Institute of Technology, Hamirpur. The author has contributed to research in topics: Chemistry & Medicine. The author has an hindex of 26, co-authored 222 publications receiving 2754 citations. Previous affiliations of Deepak Sharma include Translational Health Science and Technology Institute & Council of Scientific and Industrial Research.

Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation

Abstract: Motivation: Repetitive DNA sequences, besides having a variety of regulatory functions, are one of the principal causes of genomic instability. Understanding their origin and evolution is of fundamental importance for genome studies. The identification of repeats and their units helps in deducing the intra-genomic dynamics as an important feature of comparative genomics. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length. Results: The Spectral Repeat Finder program circumvents these problems by using a discrete Fourier transformation to identify significant periodicities present in a sequence. The specific regions of the sequence that contribute to a given periodicity are located through a sliding window analysis, and an exact search method is then used to find the repetitive units. Efficient and complete detection of repeats is provided together with interactive and detailed visualization of the spectral analysis of input sequence. We demonstrate the utility of our method with various examples that contain previously unannotated repeats. A Web server has been developed for convenient access to the automated program. Availability: The Web server is available at http://www.imtech.res.in/raghava/srf and http://www2.imtech.res.in/raghava/srf

Childhood obesity: prevention is better than cure.

Abstract: Obesity and its associated comorbidities have emerged as a major health problem garnering interests from both public health agencies and mainstream media consumers. With increasing awareness on its impact on health, finances, and community at large, it has come to the forefront for scientific research and development of health plans. The need for better strategies and novel interventions to manage obesity is now being recognized by the entire health care system. Obesity and overweight is now the fifth leading global risk factor for mortality. Strategic investment is thus urgently needed to implement population-based childhood obesity prevention programmes which are effective and also culturally appropriate. Population-based prevention is crucial to stem this rising tide of childhood obesity which is fast reaching epidemic proportions. Obesity has its onset very early in life; therefore, children constitute a major group of this disease. It is thus imperative to lay utmost importance on prevention of obesity in children and herald its progress, if present already. Furthermore, treatment is still in preliminary stage, so early prevention holds better than treatment at later stages. This article is an attempt to lay emphasis on childhood obesity as a problem that needs to be recognized early and measures for its prevention.

Biomarkers for diagnosis of neonatal sepsis: a literature review

Abstract: Sepsis is an important cause of mortality and morbidity in neonatal populations. There has been constant search of an ideal sepsis biomarker that have high sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), so that both the diagnosis and exclusion of neonatal sepsis can be made at the earliest possible and appropriate antibiotics can be started to neonate. Ideal sepsis biomarker will help in guiding us when not to start antibiotics in case of suspect sepsis and total duration of antibiotics course in case of proven sepsis. There are numerous sepsis biomarkers that have been evaluated for early detection of neonatal sepsis but till date there is no single ideal biomarker that fulfills all essential criteria's for being an ideal biomarker. The most commonly used biomarkers are C-reactive protein (CRP) and procalcitonin (PCT), but both have shown varied sensitivity, specificity, PPV and NPV in different studies. We conducted literature search for various neonatal sepsis biomarkers and this review article will cover briefly all the markers with current available evidence.

Intrauterine growth restriction – part 1

Abstract: Intrauterine growth restriction (IUGR) is a major and silent cause of various morbidity and mortality for the fetal and neonatal population. It is defined as a rate of fetal growth that is less than normal for the growth potential of that specific infant. The terms IUGR and small for gestational age (SGA) are often used interchangeably, although there exists subtle differences between the two. IUGR/SGA is an end result of various etiologies that includes maternal, placental and fetal factors and recently added genetic factors too, also contribute to IUGR. In this review article we will cover the antenatal aspect of IUGR and management with proven preventive intervention.

Disruption of response regulator gene, devR, leads to attenuation in virulence of Mycobacterium tuberculosis

Abstract: The devR-devS two-component system of Mycobacterium tuberculosis was identified earlier and partially characterized in our laboratory. A devR::kan mutant of M. tuberculosis was constructed by allelic exchange. The devR mutant strain showed reduced cell-to-cell adherence in comparison to the parental strain in laboratory culture media. This phenotype was reversed on complementation with a wild-type copy of devR. The devR mutant and parental strains grew at equivalent rates within human monocytes either in the absence or in the presence of lymphocytic cells. The expression of DevR was not modulated upon entry of M. tuberculosis into human monocytes. However, guinea pigs infected with the mutant strain showed a significant decrease in gross lesions in lung, liver and spleen; only mild pathological changes in liver and lung; and a nearly 3 log lower bacterial burden in spleen compared to guinea pigs infected with the parental strain. Our results suggest that DevR is required for virulence in guinea pigs but is not essential for entry, survival and multiplication of M. tuberculosis within human monocytes in vitro. The attenuation in virulence of the devR mutant in guinea pigs together with DevR-DevS being a bona fide signal transduction system indicates that DevR plays a critical and regulatory role in the adaptation and survival of M. tuberculosis within tissues.

The spectrum of latent tuberculosis: rethinking the biology and intervention strategies

Abstract: Immunological tests provide evidence of latent tuberculosis in one third of the global population, which corresponds to more than two billion individuals. Latent tuberculosis is defined by the absence of clinical symptoms but carries a risk of subsequent progression to clinical disease, particularly in the context of co-infection with HIV. In this Review we discuss the biology of latent tuberculosis as part of a broad range of responses that occur following infection with Mycobacterium tuberculosis, which result in the formation of physiologically distinct granulomatous lesions that provide microenvironments with differential ability to support or suppress the persistence of viable bacteria. We then show how this model can be used to develop a rational programme to discover effective drugs for the eradication of M. tuberculosis infection.