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Search Results: 1 - 10 of 392738 matches for " R. C. Shekhar "
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Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
Shubhada R. Hegde,Palanisamy Manimaran,Shekhar C. Mande
PLOS Computational Biology , 2008, DOI: 10.1371/journal.pcbi.1000237
Abstract: Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.
Morphological and pathogenic variability of Macrophomina phaseolina (Tassi.) Goid. incitant of Charcoal rot of maize in India
Indian Phytopathology , 2012,
Abstract: Seven isolates of Macrophomina phaseolina incitant of charcoal rot of maize, obtained from different agro-ecological zones of India, varied in their cultural characteristics and pathogenic behaviour. On the basis of colony colour, isolates were divided in to four groups i.e. grayish white, blackish gray, dark black in centre periphery cremish and cottony white colour. Hyderabad isolate produced highest number of sclerotia (180.3 sclerotia/9 mm disc and 52.0/ microscopic 10X field) of bigger size (95.7μm), whereas Coimbatore isolate produced minimum number of slcerotia (169 sclerotia) that too with smaller size (66.9 μm). On the basis of sclerotial morphology, two groups of isolates could be formed, the one with oblong shape having irregular edges and the other being round with regular edges. On the basis of disease expression the Hyderabad isolate was observed to be most virulent by giving maximum disease (8.8) while Coimbatore isolate was found to be least virulent as it exhibited a highest rating of 5.2 in the susceptible inbred CM 120 on a scale of 1-9. The noteworthy observation of the study was that sclerotial size and number had positive correlation with virulence.
Understanding Communication Signals during Mycobacterial Latency through Predicted Genome-Wide Protein Interactions and Boolean Modeling
Shubhada R. Hegde, Hannah Rajasingh, Chandrani Das, Sharmila S. Mande, Shekhar C. Mande
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033893
Abstract: About 90% of the people infected with Mycobacterium tuberculosis carry latent bacteria that are believed to get activated upon immune suppression. One of the fundamental challenges in the control of tuberculosis is therefore to understand molecular mechanisms involved in the onset of latency and/or reactivation. We have attempted to address this problem at the systems level by a combination of predicted functional protein:protein interactions, integration of functional interactions with large scale gene expression studies, predicted transcription regulatory network and finally simulations with a Boolean model of the network. Initially a prediction for genome-wide protein functional linkages was obtained based on genome-context methods using a Support Vector Machine. This set of protein functional linkages along with gene expression data of the available models of latency was employed to identify proteins involved in mediating switch signals during dormancy. We show that genes that are up and down regulated during dormancy are not only coordinately regulated under dormancy-like conditions but also under a variety of other experimental conditions. Their synchronized regulation indicates that they form a tightly regulated gene cluster and might form a latency-regulon. Conservation of these genes across bacterial species suggests a unique evolutionary history that might be associated with M. tuberculosis dormancy. Finally, simulations with a Boolean model based on the regulatory network with logical relationships derived from gene expression data reveals a bistable switch suggesting alternating latent and actively growing states. Our analysis based on the interaction network therefore reveals a potential model of M. tuberculosis latency.
Genetic variability in Macrophomina phaseolina (Tassi.) Goid. incitant of Charcoal rot of maize in India
Indian Phytopathology , 2012,
Abstract: Seven isolates of M. phaseolina incitant of maize charcoal rot were established from major maize growing agro-ecological zones of India. These isolates were analysed through RAPD marker for genetic diversity. The UPGMA cluster analysis for 706 loci score permitted identification of three main clusters. Similarity matrix and Jaccard’s similarity co-efficient between the isolates indicated that the maximum genetic variation was among isolates of Arabhavi and Coimbatore with 70.8% followed by Ludhiana and Coimbatore with 69.5%. The most closely related isolates were Hyderabad and Delhi with an affinity percentage of 65.5 followed by Udaipur and Bangalore isolate with a percentage of 62.9% similarity. Amplification of the ITS region with AD primers the entire ITS1 , rDNA and ITS2 region was amplified successfully for all the isolates studied. A single band of 750 bp was uniformally amplified in all the isolates and no polymorphism was visualized. Our results demonstrated genetic diversity among Indian isolates of M. phaseolina in maize.
Large nonlinear absorption and refraction coefficients of carbon nanotubes estimated from femtosecond Z-scan measurements
N. Kamaraju,Sunil Kumar,Srinivasan Krishnamurthy,Shekhar Guha,A. K. Sood,C. N. R. Rao
Physics , 2007, DOI: 10.1063/1.2825409
Abstract: Nonlinear transmission of 80 and 140 femtosecond pulsed light with $0.79 \mu m$ wavelength through single walled carbon nanotubes suspended in water containing sodium dodecyl sulphate is studied. Pulse-width independent saturation absorption and negative cubic nonlinearity are observed, respectively, in open and closed aperture Z-scan experiments. The theoretical expressions derived to analyze the z-dependent transmission in the saturable limit require two photon absorption coefficient $\beta_0\sim$ $1.4 cm/MW$ and a nonlinear index $\gamma \sim -5.5 \times10^{-11} cm^2/W$ to fit the data.
Prevalence of HIV Drug Resistance Mutations in HIV Type 1 Isolates in Antiretroviral Therapy Na?ve Population from Northern India
S. Sinha,H. Ahmad,R. C. Shekhar,N. Kumar,L. Dar,J. C. Samantaray,S. K. Sharma,A. Bhargava,R. M. Pandey,R. L. Mitsuyasu,J. L. Fahey
AIDS Research and Treatment , 2012, DOI: 10.1155/2012/905823
Abstract: Objective. The increased use of antiretroviral therapy (ART) has reduced the morbidity and mortality associated with HIV, adversely leading to the emergence of HIV drug resistance (HIVDR). In this study we aim to evaluate the prevalence of HIVDR mutations in ART-naive HIV-1 infected patients from northern India. Design. Analysis was performed using Viroseq genotyping system based on sequencing of entire protease and two-thirds of the Reverse Transcriptase (RT) region of pol gene. Results. Seventy three chronic HIV-1 infected ART na?ve patients eligible for first line ART were enrolled from April 2006 to August 2008. In 68 patients DNA was successfully amplified and sequencing was done. 97% of HIV-1 strains belonged to subtype C, and one each to subtype A1 and subtype B. The overall prevalence of primary DRMs was 2.9% [2/68, 95% confidence interval (CI), 0.3%–10.2%]. One patient had a major RT mutation M184V, known to confer resistance to lamivudine, and another had a major protease inhibitor (PI) mutation D30N that imparts resistance to nelfinavir. Conclusion. Our study shows that primary HIVDR mutations have a prevalence of 2.9% among ART-naive chronic HIV-1 infected individuals. 1. Introduction The national antiretroviral therapy (ART) program in India for treatment of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) was started by National AIDS Control Organization (NACO), Ministry of Health and Family Welfare, Government of India, in April 2004. By the end of November 2009, more than 2, 50,000 patients infected with HIV had received ART under the program [1]. As per the latest report by Joint United Nations programe on HIV/AIDS (UNAIDS), prevalence of HIV in India is estimated to be 0.31%, that translates to approximately 2.31 million persons living with HIV/AIDS [2]. The current standard first-line treatment for HIV in India consists of two nucleoside reverse transcriptase inhibitors (NRTIs), zidovudine or stavudine plus lamivudine, and one nonnucleoside reverse transcriptase inhibitor (NNRTI), nevirapine or efavirenz. Regimens with protease inhibitors (PIs) are available as second-line treatment options upon failure of the first-line ART under the national program. As per the time trends for evolution of primary HIVDR suggested by Grant et al., it can be expected that the prevalence of drug resistance mutations (DRMs) may soon increase in India [3, 4]. The widespread use of ART has resulted in an increased prevalence of drug-resistant HIV strains, ranging from 10% to 20% among drug-naive patients in other countries
Estimation of Global Solar Radiation for Four Selected Sites in Nepal Using Sunshine Hours, Temperature and Relative Humidity  [PDF]
Krishna R. Adhikari, Binod K. Bhattarai, Shekhar Gurung
Journal of Power and Energy Engineering (JPEE) , 2013, DOI: 10.4236/jpee.2013.13003
Abstract: Rational and accurate solar energy databases, essential for designing, sizing and performing the solar energy systems in any part of the world, are not easily accessible in different localities of Nepal. In this study, daily global solar radiation, sunshine hours and meteorological data for Biratnagar, Kathmandu, Pokhara and Jumla have been used to derive the regression constants. The linear regression technique has been used to develop a model for Biratnagar, Kathmandu, Pokhara and Jumla. The model has calculated the global solar radiation for these locations. The values of global solar radiation estimated by the model are found to be in close agreement with measured values of respective sites. The estimated values were compared with Angstrom-Prescott model and examined using the root mean square error (RMSE), mean bias error (MBE), mean percentage error (MPE), coefficient of regression (R), coefficient of determinant (R2) and correlation coefficient (CC) statistical techniques. Thus, the resultant correlations and linear regression relations may be then used for the locations of similar meteorological/geographical characteristics and also can be used to estimate the missing data of solar radiation for the respective site.
Evaluation and Management of Patients with Noncardiac Chest Pain
C. Shekhar,P. J. Whorwell
Gastroenterology Research and Practice , 2008, DOI: 10.1155/2008/708218
Abstract: Up to a third of patients undergoing coronary angiography for angina-like chest pain are found to have normal coronary arteries and a substantial proportion of these individuals continue to consult and even attend emergency departments. Initially, these patients are usually seen by cardiologists but with accumulating evidence that the pain might have a gastrointestinal origin, it may be more appropriate for them to be cared for by the gastroenterologist once a cardiological cause has been excluded. This review covers the assessment and management of this challenging condition, which includes a combination of education, reassurance, and pharmacotherapy. For the more refractory cases, behavioral treatments, such as cognitive behavioral therapy or hypnotherapy, may have to be considered.
Phamaceutical and Analytical study on Loha Bhasma
Rajendra Prasad,Shruti Shekhar,Subrahmanya A R
International Journal of Ayurvedic Medicine , 2010,
Abstract: Rasashastra is a subject which deals with metals and its therapeutic effect. It mentions the use of metals in a refined form as bhasma. Loha is used extensively in the Ayurvedic literature for the management of various diseases like Pandu (Anemia), Shotha (Oedema), Kamala (Jaundice) etc. It is very hard metal hence it should be made into bhasma for using it for medicinal purposes. Iron fillings are subjected to samamnya shodhana and vishesha shodha to prepare the bhasma. Pharmaceutical and analytical studies were conducted during the process of preparation of the Loha bhasma to know the changes in the chemical composition at various satges. Namburi Phased Spot Test was done to prove the fineness of the bhasma. In this study an attempt has been made to standardize the process of the preparation of the Loha bhasma and to establish chemical standards like iron content in the bhasma and the Namburi Phased Spot Test.
Theories of Hydrophobic Effects and the Description of Free Volume in Complex Liquids
Lawrence R. Pratt,Shekhar Garde,Gerhard Hummer
Physics , 1998,
Abstract: Recent progress on molecular theories of hydration of nonpolar solutes in aqueous solution has led to new ways of thinking about the old issue of free, or "available," volume in liquids. This article surveys the principal new results with particular attention to general issues of packing in liquids.
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