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Search Results: 1 - 10 of 145168 matches for " Rana K. Gupta "
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Elucidating the Interacting Domains of Chandipura Virus Nucleocapsid Protein
Kapila Kumar,Sreejith Rajasekharan,Sahil Gulati,Jyoti Rana,Reema Gabrani,Chakresh K. Jain,Amita Gupta,Vijay K. Chaudhary,Sanjay Gupta
Advances in Virology , 2013, DOI: 10.1155/2013/594319
Abstract: The nucleocapsid (N) protein of Chandipura virus (CHPV) plays a crucial role in viral life cycle, besides being an important structural component of the virion through proper organization of its interactions with other viral proteins. In a recent study, the authors had mapped the associations among CHPV proteins and shown that N protein interacts with four of the viral proteins: N, phosphoprotein (P), matrix protein (M), and glycoprotein (G). The present study aimed to distinguish the regions of CHPV N protein responsible for its interactions with other viral proteins. In this direction, we have generated the structure of CHPV N protein by homology modeling using SWISS-MODEL workspace and Accelrys Discovery Studio client 2.55 and mapped the domains of N protein using PiSQRD. The interactions of N protein fragments with other proteins were determined by ZDOCK rigid-body docking method and validated by yeast two-hybrid and ELISA. The study revealed a unique binding site, comprising of amino acids 1–30 at the N terminus of the nucleocapsid protein (N1) that is instrumental in its interactions with N, P, M, and G proteins. It was also observed that N2 associates with N and G proteins while N3 interacts with N, P, and M proteins. 1. Introduction Chandipura virus (CHPV) is a recently recognized emerging human pathogen [1–3] of the genus Vesiculovirus and family Rhabdoviridae [4]. The ~11?kb genome of CHPV [5] is encapsidated by nucleocapsid (N) protein and serves as a template for both replication and transcription. The transcription of the genome by viral encoded RNA-dependent RNA polymerase (RdRp; L protein) produces five capped and polyadenylated mRNAs which code for five proteins nucleocapsid protein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and large protein (L) in sequential order and in decreasing amounts [6]. Interactions among these proteins are essential for functioning of key processes during virus replication and pathogenesis. However, only few details of the molecular functions of these viral proteins that orchestrate the virus life cycle are known. The N protein plays a pivotal role in virus biology by virtue of its interactions with other viral proteins. The interaction of monomeric N protein with P maintains it in the encapsidation competent soluble (active) form [7, 8]. In its active form, N protein tightly wraps the RNA genome and maintains the structural integrity along with the template function of the negative strand genome RNA. Within the virion, this encapsidated RNA (N-RNA) template is associated with the
Deformation in 28Si* produced via 16O + 12C reaction
S. Kundu,C. Bhattacharya,S. Bhattacharya,T. K. Rana,K. Banerjee,S. Muhkopadhayay,D. Gupta,A. Dey,R. Saha
Physics , 2013, DOI: 10.1103/PhysRevC.87.024602
Abstract: The energy spectra of the $\alpha$ particles emitted in the reactions $^{16}$O (7-10 MeV/nucleon) + $^{12}$C have been measured in the center of mass angular range of 25$^\circ$ $\lesssim \theta_{c.m.} \lesssim$ 70$^\circ$. The experimental energy spectra have been compared with those obtained from the statistical model calculation with "deformability" parameters predicted by rotating liquid drop model (RLDM) and also fitted the same with optimized "deformability" parameters, which are quite different from the respective RLDM values. The data have also been found to be explained quite well using "frozen" deformation approximation, where the "deformability" parameters have been kept fixed at RLDM values of the parent nucleus throughout the decay process. The effective radius in the latter case is smaller compared to that obtained using the optimized parameters; however, in both cases, the deformations (effective radii) are larger than the corresponding RLDM values. So, considering the uncertainties in the estimation of actual compound nucleus deformations, it can, only qualitatively, be said that equilibrium orbiting, which is similar to particle evaporation in time scale, could also be one of the contributing factors for the observed deformation.
Evidence of large nuclear deformation of $^{32}$S$^{*}$ formed in $^{20}$Ne + $^{12}$C reaction
Aparajita Dey,S. Bhattacharya,C. Bhattacharya,K. Banerjee,T. K. Rana,S. Kundu,S. Mukhopadhyay,D. Gupta,R. Saha
Physics , 2006, DOI: 10.1103/PhysRevC.74.044605
Abstract: Deformations of hot composite $^{32}$S$^{*}$ formed in the reaction $^{20}$Ne ($\sim$ 7 -- 10 MeV/nucleon) + $^{12}$C have been estimated from the respective inclusive $\alpha$-particle evaporation spectra. The estimated deformations for $^{32}$S$^{*}$ have been found to be much larger than the `normal' deformations of hot, rotating composites at similar excitations. This further confirms the formation of highly deformed long-lived configuration of $^{20}$Ne + $^{12}$C at high excitations ($\sim$ 70 -- 100 MeV) -- which was recently indicated from the analysis of the complex fragment emission data for the same system. Exclusive $\alpha$-particle evaporation spectra from the decay of hot composite $^{32}$S$^{*}$ also show similar behaviour.
Hybrid Evolutionary Techniques to Restricted Feed Forward Neural Network with Distributed Error for Recognition of Handwritten Hindi ‘MATRAS’
Meenu Gupta,Ajay Rana
International Journal of Soft Computing & Engineering , 2012,
Abstract: This paper evaluates the performance of restricted feed forward neural network trained by hybrid evolutionary algorithm with generalized delta learning rule for distributed error to obtain the pattern classification for the given training set of Handwritten Hindi ‘MATRAS’. Generally, the feed forward neural network considers the performance index as back-propagated instantaneous unknown error for output of hidden layers. Within this proposed endeavor, we are considering the performance index of distributed instantaneous unknown errors i.e. different errors for different layers. In this case, the convergence is obtained only when the minimum of every error on different layer is determined. The simulation for the performance evaluation is conducted for hand-written ‘MATRAS’ of Hindi language scripted by five different people. These samples are stored as scanned images. The MATLAB is used to determine the densities of these scanned images after partitioning each image into 16 portions. These 16 densities for each character are used as an input pattern of training set. We consider five trials for each learning method and results are presented with their mean value.
Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium
Humira Sonah, Rupesh K. Deshmukh, Anshul Sharma, Vinay P. Singh, Deepak K. Gupta, Raju N. Gacche, Jai C. Rana, Nagendra K. Singh, Tilak R. Sharma
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021298
Abstract: Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).
Light charged particle emission from hot $^{32}$S$^{*}$ formed in $^{20}$Ne + $^{12}$C reaction
Aparajita Dey,S. Bhattacharya,C. Bhattacharya,K. Banerjee,T. K. Rana,S. Kundu,S. R. Banerjee,S. Mukhopadhyay,D. Gupta,R. Saha
Physics , 2008, DOI: 10.1140/epja/i2009-10772-y
Abstract: Inclusive energy distributions for light charged particles ($p, d, t$ and $\alpha$) have been measured in the $^{20}$Ne (158, 170, 180, 200 MeV) + $^{12}$C reactions in the angular range 10$^{o}$ -- 50$^{o}$. Exclusive light charged particle energy distribution measurements were also done for the same system at 158 MeV bombarding energy by in-plane light charged particle -- fragment coincidence. Pre-equilibrium components have been separated out from proton energy spectra using moving source model considering two sources. The data have been compared with the predictions of the statistical model code CASCADE. It has been observed that significant deformation effects were needed to be introduced in the compound nucleus in order to explain the shape of the evaporated $d, t$ energy spectra. For protons, evaporated energy spectra were rather insensitive to nuclear deformation, though angular distributions could not be explained without deformation. Decay sequence of the hot $^{32}$S nucleus has been investigated through exclusive light charged particle measurements using the $^{20}$Ne (158 MeV) + $^{12}$C reaction. Information on the sequential decay chain has been extracted through comparison of the experimental data with the predictions of the statistical model. It is observed from the present analysis that exclusive light charged particle data may be used as a powerful tool to probe the decay sequence of hot light compound systems.
Study of Dissipative Collisions of $^{20}$Ne ($\sim$7-11 MeV/nucleon) + $^{27}$Al
Aparajita Dey,C. Bhattacharya,S. Bhattacharya,T. K. Rana,S. Kundu,K. Banerjee,S. Mukhopadhyay,S. R. Banerjee,D. Gupta,R. Saha
Physics , 2006, DOI: 10.1103/PhysRevC.75.064606
Abstract: The inclusive energy distributions of complex fragments (3 $\leq$Z $\leq$ 9) emitted in the reactions $^{20}$Ne (145, 158, 200, 218 MeV) + $^{27}$Al have been measured in the angular range 10$^{o}$ - 50$^{o}$. The fusion-fission and the deep-inelastic components of the fragment yield have been extracted using multiple Gaussian functions from the experimental fragment energy spectra. The elemental yields of the fusion-fission component have been found to be fairly well exlained in the framework of standard statistical model. It is found that there is strong competition between the fusion-fission and the deep-inelastic processes at these energies. The time scale of the deep-inelastic process was estimated to be typically in the range of $\sim$ 10$^{-21}$ - 10$^{-22}$ sec., and it was found to decrease with increasing fragment mass. The angular momentum dissipations in fully energy damped deep-inelastic process have been estimated from the average energies of the deep-inelastic components of the fragment energy spectra. It has been found that, the estimated angular momentum dissipations, for lighter fragments in particular, are more than those predicted by the empirical sticking limit.
Regulation of Early Adipose Commitment by Zfp521
Sona Kang,Peter Akerblad,Riku Kiviranta,Rana K. Gupta,Shingo Kajimura,Michael J. Griffin,Jie Min,Roland Baron,Evan D. Rosen
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001433
Abstract: While there has been significant progress in determining the transcriptional cascade involved in terminal adipocyte differentiation, less is known about early events leading to lineage commitment and cell fate choice. It has been recently discovered that zinc finger protein 423 (Zfp423) is an early actor in adipose determination. Here, we show that a close paralog of Zfp423, Zfp521, acts as a key regulator of adipose commitment and differentiation in vitro and in vivo. Zfp521 exerts its actions by binding to early B cell factor 1 (Ebf1), a transcription factor required for the generation of adipocyte progenitors, and inhibiting the expression of Zfp423. Overexpression of Zfp521 in cells greatly inhibits adipogenic potential, whereas RNAi-mediated knock-down or genetic ablation of Zfp521 enhances differentiation. In addition, Zfp521?/? embryos exhibit increased mass of interscapular brown adipose tissue and subcutaneous white adipocytes, a cell autonomous effect. Finally, Ebf1 participates in a negative feedback loop to repress Zfp521 as differentiation proceeds. Because Zfp521 is known to promote bone development, our results suggest that it acts as a critical switch in the commitment decision between the adipogenic and osteogenic lineages.
Securinine, a Myeloid Differentiation Agent with Therapeutic Potential for AML
Kalpana Gupta, Amitabha Chakrabarti, Sonia Rana, Ritu Ramdeo, Bryan L. Roth, Munna L. Agarwal, William Tse, Mukesh K. Agarwal, David N. Wald
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021203
Abstract: As the defining feature of Acute Myeloid Leukemia (AML) is a maturation arrest, a highly desirable therapeutic strategy is to induce leukemic cell maturation. This therapeutic strategy has the potential of avoiding the significant side effects that occur with the traditional AML therapeutics. We identified a natural compound securinine, as a leukemia differentiation-inducing agent. Securinine is a plant-derived alkaloid that has previously been used clinically as a therapeutic for primarily neurological related diseases. Securinine induces monocytic differentiation of a wide range of myeloid leukemia cell lines as well as primary leukemic patient samples. Securinine's clinical potential for AML can be seen from its ability to induce significant growth arrest in cell lines and patient samples as well as its activity in significantly impairing the growth of AML tumors in nude mice. In addition, securinine can synergize with currently employed agents such as ATRA and decitabine to induce differentiation. This study has revealed securinine induces differentiation through the activation of DNA damage signaling. Securinine is a promising new monocytic differentiation inducing agent for AML that has seen previous clinical use for non-related disorders.
Genetic characterization of Chikungunya virus from New Delhi reveal emergence of a new molecular signature in Indian isolates
Jatin Shrinet, Shanu Jain, Anil Sharma, Shashi Shekhar Singh, Kalika Mathur, Vandita Rana, Raj K Bhatnagar, Bhupendra Gupta, Rajni Gaind, Monorama Deb, Sujatha Sunil
Virology Journal , 2012, DOI: 10.1186/1743-422x-9-100
Abstract: Clinical samples were subjected to RT-PCR to detect CHIK viral RNA. The PCR amplified products were sequenced and the resulting sequences were genetically analyzed. Phylogenetic analysis based on partial sequences of the structural proteins E1 and E2 revealed that the viruses in the latest outbreak exhibited ECSA lineage. Two novel mutations, E1 K211E and E2 V264A were observed in all Delhi isolates. In addition, CHIKV sequences from eight states in India were analyzed along with Delhi sequences to map the genetic diversity of CHIKV within the country. Estimates of average evolutionary divergence within states showed varying divergence among the sequences both within the states and between the states. We identified distinct molecular signatures of the different genotypes of CHIKV revealing emergence of a new signature in the New Delhi clade. Statistical analyses and construction of evolutionary path of the virus within the country revealed gradual spread of one specific strain all over the country.This study has identified unique mutations in the E1 and E2 genes and has revealed the presence of ancestral CHIKV population with maximum diversity circulating in Maharashtra. The study has further revealed the trend of CHIK spread in India since its first report in 1963 and its subsequent reappearance in 2005.
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