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Search Results: 1 - 10 of 438 matches for " Pratap Venepally "
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Monitoring the Long-Term Molecular Epidemiology of the Pneumococcus and Detection of Potential ‘Vaccine Escape’ Strains
Gagan A. Pandya,M. Catherine McEllistrem,Pratap Venepally,Michael H. Holmes,Behnam Jarrahi,Ravi Sanka,Jia Liu,Svetlana A. Karamycheva,Yun Bai,Robert D. Fleischmann,Scott N. Peterson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015950
Abstract: While the pneumococcal protein conjugate vaccines reduce the incidence in invasive pneumococcal disease (IPD), serotype replacement remains a major concern. Thus, serotype-independent protection with vaccines targeting virulence genes, such as PspA, have been pursued. PspA is comprised of diverse clades that arose through recombination. Therefore, multi-locus sequence typing (MLST)-defined clones could conceivably include strains from multiple PspA clades. As a result, a method is needed which can both monitor the long-term epidemiology of the pneumococcus among a large number of isolates, and analyze vaccine-candidate genes, such as pspA, for mutations and recombination events that could result in ‘vaccine escape’ strains.
Genetic Analysis Using an Isogenic Mating Pair of Aspergillus fumigatus Identifies Azole Resistance Genes and Lack of MAT Locus’s Role in Virulence
Liliana Losada?,Janyce A. Sugui?,Michael A. Eckhaus?,Yun C. Chang?,Stephanie Mounaud?,Abigail Figat?,Vinita Joardar?,Suman B. Pakala?,Suchitra Pakala?,Pratap Venepally
PLOS Pathogens , 2015, DOI: 10.1371/journal.ppat.1004834
Abstract: Invasive aspergillosis (IA) due to Aspergillus fumigatus is a major cause of mortality in immunocompromised patients. The discovery of highly fertile strains of A. fumigatus opened the possibility to merge classical and contemporary genetics to address key questions about this pathogen. The merger involves sexual recombination, selection of desired traits, and genomics to identify any associated loci. We constructed a highly fertile isogenic pair of A. fumigatus strains with opposite mating types and used them to investigate whether mating type is associated with virulence and to find the genetic loci involved in azole resistance. The pair was made isogenic by 9 successive backcross cycles of the foundational strain AFB62 (MAT1-1) with a highly fertile (MAT1-2) progeny. Genome sequencing showed that the F9 MAT1-2 progeny was essentially identical to the AFB62. The survival curves of animals infected with either strain in three different animal models showed no significant difference, suggesting that virulence in A. fumigatus was not associated with mating type. We then employed a relatively inexpensive, yet highly powerful strategy to identify genomic loci associated with azole resistance. We used traditional in vitro drug selection accompanied by classical sexual crosses of azole-sensitive with resistant isogenic strains. The offspring were plated under varying drug concentrations and pools of resulting colonies were analyzed by whole genome sequencing. We found that variants in 5 genes contributed to azole resistance, including mutations in erg11A (cyp51A), as well as multi-drug transporters, erg25, and in HMG-CoA reductase. The results demonstrated that with minimal investment into the sequencing of three pools from a cross of interest, the variation(s) that contribute any phenotype can be identified with nucleotide resolution. This approach can be applied to multiple areas of interest in A. fumigatus or other heterothallic pathogens, especially for virulence associated traits.
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
Charles Ansong, Nikola Toli?, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith, Scott N Peterson, Fred Heffron, Michael McClelland, Joshua N Adkins
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-433
Abstract: We experimentally annotated the bacterial pathogen Salmonella Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in Salmonella pathogenesis. We also characterized post-translational features in the Salmonella genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of Salmonella as a resource for systems analysis.Many aspects of modern biological research are dependent on accurate identification of the protein-coding genes in each genome, as well as the nature of the mature functional protein products, a process commonly referred to as genome annotation. With the exponential increase in the number of sequenced prokaryotic genomes afforded by advances in genome sequencing technologies over the last decade, present day prokaryotic genome annotation is essentially an automated high-throughput process that relies heavily on de novo gene prediction programs [1-3].While de novo gene prediction programs have significantly improved for prokaryotic genomes consider
Representation of Object-Oriented Database for the Development of Web Based Application Using Db4o  [PDF]
Vipin Saxena, Ajay Pratap
Journal of Software Engineering and Applications (JSEA) , 2012, DOI: 10.4236/jsea.2012.59082
Abstract: Impedance mismatch of data flow is the major problem in the relational database when one is using the web based application development on the computer system. It effects the development of scalable and reusable web application. Due to this, the research cost of development and maintenance increases. Therefore the present work is an attempt towards an object-oriented database system by using Db4o to overcome the impedance mismatch problem. In the current work, the development of web application for Indian Postal Services by using Db4o is demonstrated on dot NET platform. Before developing the application, the authors used a Unified Modeling Language (UML) model in the form of UML class, sequence and use-case diagrams. The Db4o is used to store the object-oriented database and the performance of Db4o is observed through several object-oriented queries and corresponding results are demonstrated.
Keeping It Simple: Comparative Analysis of TFP across Manufacturing Industries and Major States of India  [PDF]
Awadhesh Pratap Singh
Theoretical Economics Letters (TEL) , 2017, DOI: 10.4236/tel.2017.76124
Abstract: The measurement of total factor productivity in Indian economic development has been greatly debated especially after economic reforms set in. While a fair amount of research is done on this subject, however the findings were lost in the shadow of complex econometric techniques. This paper is an honest attempt to simplify the complex area of productivity for a geographically multifaceted country—India. The paper carries out a comprehensive and comparative TFP (total factor productivity) analysis across 19 major India states and their 15 Indian manufacturing industries. The intent of this paper is fourfold. First, it estimates TFP using a simple technique (growth accounting). Second, it performs the state and the industry level comparative TFP analysis. Third, it discusses the outliers and justifies their outcomes and fourth provides recommendations for policy making and states the implications.
Does Size Matter?—The Effect of Size of Production Workers, Management Staff and Proprietors on Productivity  [PDF]
Awadhesh Pratap Singh
Theoretical Economics Letters (TEL) , 2018, DOI: 10.4236/tel.2018.811149
Abstract: The importance of production workers is widely acknowledged in Industrial Economics. With respect to India where many industries are dominated by large family owned enterprises, this paper analyzes the impact of the size of production workers, management staff and proprietors on productivity for 11 manufacturing industries aggregated for 20 major states of India. The paper employs latest econometric techniques namely, panel cointegration and FMOLS that deals with widely known non-stationary and endogeneity issues in panel data. The results show that Indian manufacturing sector is highly sensitive to production workers and management staff. The externalities of production workers and management staff on TFP, output and labor productivity are consistently significant across the models. The significance to proprietors is found neither consistent nor significant.
Mapping Spatial Data on the Web Using Free and Open-Source Tools: A Prototype Implementation  [PDF]
Sunil Pratap Singh, Preetvanti Singh
Journal of Geographic Information System (JGIS) , 2014, DOI: 10.4236/jgis.2014.61004
Abstract:

There is a growing need for web-based geographic information systems for easy and fast dissemination, sharing, displaying and processing of spatial information. The tremendous growth in the use of web and open-source geospatial resources has sparked development of web-based spatial applications to address multidisciplinary issues with spatial dimensions. This paper presents the integration of open-source geospatial tools and web technology to visualize and interact with spatial data using web browser. The goal of this paper is to implement a prototype system for web-based mapping by providing step-by-step instructions in order to encourage the eager developers and interested readers to publish their maps on the web with no prior technical experience in map servers. The implementation of mapping prototype shows the utilization of open-source geospatial tools which results in a rapid implementation with minimal or no software input cost.

Ameloblastoma—A Locally Destructive and Invasive Tumour—Review of Literature  [PDF]
Mir Ruquaya, Vikram Pratap Singh
International Journal of Otolaryngology and Head & Neck Surgery (IJOHNS) , 2014, DOI: 10.4236/ijohns.2014.35040
Abstract: The ameloblastoma is the second most common odontogenic tumour [1]. It occurs exclusively in the jaws, with a strong predilection for the posterior region of the mandible. Although benign, the ameloblastoma is a destructive tumour, locally invasive and presents a high rate of recurrence despite adequate surgical removal. A thorough understanding of its clinico-pathological behaviour is essential to avoid recurrence associated with inadequately treated disease. Currently wide resection and immediate reconstruction are the treatment of choice.
Distribution, Enrichment and Ecological Risk Assessment of Six Elements in Bed Sediments of a Tropical River, Chottanagpur Plateau: A Spatial and Temporal Appraisal  [PDF]
Kumar Manoj, Pratap Kumar Padhy
Journal of Environmental Protection (JEP) , 2014, DOI: 10.4236/jep.2014.514136
Abstract: Distribution and enrichment of six elements (iron, zinc, copper, lead, cadmium and manganese) in surface bed sediments, collected from seventeen selected locations during pre-monsoon and postmonsoon periods, of the tropical Chottanagpur plateau river Subarnarekha along with the ecological risks involved were investigated. Owing to the rich occurrence of mineral resources, the Subarnarekha river basin has a large scale presence of industrial and mining units especially in the Indian State of Jharkhand. An assessment, which involved examining distribution pattern of elements, comparative studies with sediment quality guidelines (SQGs) and geochemical background values and a sequential and integrated index analyses approach (containing contamination factor (CF), pollution load index (PLI), contamination degree (CD), enrichment factor (EF), geo-accumulation index (Igeo) and potential ecological risk index (PERI)), was followed to estimate enrichment and risks of elements in the bed sediments. Sediments collected from areas having abundance of population, industrial conglomerates and mining units recorded elevated element concentrations, which exceeded SQGs, and significantly higher values of CF, CD, PLI, EF, Igeo and PERI. Cadmium demonstrated surprising regularity in its enrichment; contributed most to the ecological risks; and high toxicity risks due to cadmium exceeded 64% of the sites. Moreover, chronic exposures of other elements would also lead to similar ecological risks. In addition to revealing potential ecological risks due to cadmium and other elements our investigation markedly highlighted anthropogenic control over sediment quality deterioration and some immediate sediment quality management strategies are needed to remediate and control river bed contamination.
Novel Bianchi VII Space Times and Their Properties  [PDF]
Manavendra Mahato, Ajay Pratap Singh
Journal of Modern Physics (JMP) , 2016, DOI: 10.4236/jmp.2016.75046
Abstract: We construct and investigate non conformal anisotropic Bianchi type VII0 solutions in 5 dimensions. The solutions are asymptotically flat with a singularity. We also construct anisotropic solutions of Einstein-Maxwell gravity using a procedure similar to Majumdar-Papapetrou solutions with various profiles of charged dust and explore ways to hide the singularity behind the horizon. We further embed it in one higher dimension to get an asymptotically anti de Sitter space and approximate two point correlator of operators with higher conformal dimensions by calculating geodesic lengths. We find a peculiar power law decay of the correlator as a function of separation.
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