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Search Results: 1 - 10 of 431 matches for " Vijayaraj Nagarajan "
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SAMMD: Staphylococcus aureus Microarray Meta-Database
Vijayaraj Nagarajan, Mohamed O Elasri
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-351
Abstract: SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL).SAMMD is hosted and available at http://www.bioinformatics.org/sammd/ webcite. Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes.Staphylococcus aureus is an important human pathogen, causing diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is the foremost cause of nosocomial infections. S. aureus is also posing serious threats because of its ability to acquire multiple antibiotic resistances. Microarray studies enable the analysis of the pathogens response at a global level. There have been several studies carried out on the global expression profiles of S. aureus in response to different effectors like vancomycin [1], mild acid [2], stress [3] etc. There are also several transcriptional profiles of regulatory genes like sigB [4], sarA [5], mgrA [6] etc. To date there are about 30 published journal articles that contain about 67 microarray experiments in S. aureus. The use of this large amount of
GeneVenn - A web application for comparing gene lists using
Mehdi Pirooznia,Vijayaraj Nagarajan,Youping Deng
Bioinformation , 2007,
Abstract: Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a Venn diagram. Venn diagrams are graphical ways of representing interactions among sets to display information that can be read easily. Here we propose a simple but effective web application creating Venn diagrams from two or three gene lists. Each gene in the group list has link to the related information in NCBI’s Entrez Nucleotide database.
SATRAT: Staphylococcus aureus transcript regulatory network analysis tool
Tamilselvi Gopal,Vijayaraj Nagarajan,Mohamed O. Elasri
PeerJ , 2015, DOI: 10.7717/peerj.717
Abstract: Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool—SATRAT—the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems.
The Role of msa in Staphylococcus aureus Biofilm Formation
Karthik Sambanthamoorthy, Antony Schwartz, Vijayaraj Nagarajan, Mohamed O Elasri
BMC Microbiology , 2008, DOI: 10.1186/1471-2180-8-221
Abstract: We found that mutation of msa results in reduced expression of sarA in biofilm and that the msa mutant formed a weak and unstable biofilm. The msa mutant is able to adhere to surfaces and begins to form biofilm but fails to mature indicating that the defect of the msa mutant biofilm is in the accumulation stage but not in primary adhesion.The msa gene plays an important role in biofilm development which is likely due to its role in modulating the expression of sarA. This finding is significant because it identifies a new gene that plays a role in the development of biofilm.Staphylococcus aureus is a gram-positive pathogen that causes potentially life threatening nosocomial- and community-acquired infections, such as osteomyelitis and endocarditis. An important characteristic of S. aureus is its ability to form a biofilm, a characteristic associated with several diseases [1]. Bacteria in biofilms are encased in a polysaccharide glycocalyx [2], which provides them with protection against host defenses and antimicrobial drugs [2]. Staphylococcal biofilms form in two distinct stages: (1) primary adhesion to surfaces by means of adhesins or cell wall components, and (2) accumulation of multilayered clusters of cells via the production of a polysaccharide [3]. Cells are also able to detach from the biofilm and disperse to distant sites for colonization or infection.The staphylococcal accessory regulator sarA is a major global regulator that is essential for biofilm formation both in vitro and in vivo [4-6]. Additionally, O'Neill et al.[7] showed that sarA is essential for biofilm formation in both MRSA and MSSA. However the mechanism of sarA regulation of biofilm is not yet understood. Previously we identified the msa gene as a positive modulator of sarA [8]. We also showed that mutation of msa resulted in differential expression of several virulence factors [8]. These findings prompted the present study, focused on the role of msa in biofilm formation. We show here that
Blocking Probability in All-Optical WDM Network Using IMCA  [PDF]
G. Karpagarajesh, M. Vijayaraj
Circuits and Systems (CS) , 2016, DOI: 10.4236/cs.2016.76090
Abstract: The analysis of WDM (Wavelength-Division Multiplexing) optical network is essential to have the routed wavelength blocking probability with the conversion of wavelength using techniques. In this paper, an enhanced analytical model is proposed to evaluate the blocking performances in topology network and to improve the performances of reduction of blocking probability. The variation of probability is based on the wavelength and load used in the network. The conversion is carried out with the support of optical backbone of the inherent flexibility of the network using the proposed IMCA in Sparse-Partial Wavelength Conversion (SPWC) architecture. It reduces the number of converters significantly with efficient process and provides placement scheme of wavelength converters in the network. The proposed model utilizes the network with the assignment and routing of wavelength using dynamic process of assignment algorithm. The proposed model provides dynamic and static routing process with the range limit to have a minimum conversion for the same probabilities of blocking. The proposed system analysis and the simulation results show the better performances in faster coverage, minimum number of conversions, blocking probability improvement for high load.
The Fat Body Transcriptomes of the Yellow Fever Mosquito Aedes aegypti, Pre- and Post- Blood Meal
David P. Price, Vijayaraj Nagarajan, Alexander Churbanov, Peter Houde, Brook Milligan, Lisa L. Drake, John E. Gustafson, Immo A. Hansen
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022573
Abstract: Background The fat body is the main organ of intermediary metabolism in insects and the principal source of hemolymph proteins. As part of our ongoing efforts to understand mosquito fat body physiology and to identify novel targets for insect control, we have conducted a transcriptome analysis of the fat body of Aedes aegypti before and in response to blood feeding. Results We created two fat body non-normalized EST libraries, one from mosquito fat bodies non-blood fed (NBF) and another from mosquitoes 24 hrs post-blood meal (PBM). 454 pyrosequencing of the non-normalized libraries resulted in 204,578 useable reads from the NBF sample and 323,474 useable reads from the PBM sample. Alignment of reads to the existing reference Ae. aegypti transcript libraries for analysis of differential expression between NBF and PBM samples revealed 116,912 and 115,051 matches, respectively. De novo assembly of the reads from the NBF sample resulted in 15,456 contigs, and assembly of the reads from the PBM sample resulted in 15,010 contigs. Collectively, 123 novel transcripts were identified within these contigs. Prominently expressed transcripts in the NBF fat body library were represented by transcripts encoding ribosomal proteins. Thirty-five point four percent of all reads in the PBM library were represented by transcripts that encode yolk proteins. The most highly expressed were transcripts encoding members of the cathepsin b, vitellogenin, vitellogenic carboxypeptidase, and vitelline membrane protein families. Conclusion The two fat body transcriptomes were considerably different from each other in terms of transcript expression in terms of abundances of transcripts and genes expressed. They reflect the physiological shift of the pre-feeding fat body from a resting state to vitellogenic gene expression after feeding.
Development of Genetic System to Inactivate a Borrelia turicatae Surface Protein Selectively Produced within the Salivary Glands of the Arthropod Vector
Job E. Lopez ,Hannah K. Wilder,Reid Hargrove,Christopher P. Brooks,Karin E. Peterson,Paul A. Beare,Daniel E. Sturdevant,Vijayaraj Nagarajan,Sandra J. Raffel,Tom G. Schwan
PLOS Neglected Tropical Diseases , 2013, DOI: 10.1371/journal.pntd.0002514
Abstract: Background Borrelia turicatae, an agent of tick-borne relapsing fever, is an example of a pathogen that can adapt to disparate conditions found when colonizing the mammalian host and arthropod vector. However, little is known about the genetic factors necessary during the tick-mammalian infectious cycle, therefore we developed a genetic system to transform this species of spirochete. We also identified a plasmid gene that was up-regulated in vitro when B. turicatae was grown in conditions mimicking the tick environment. This 40 kilodalton protein was predicted to be surface localized and designated the Borrelia repeat protein A (brpA) due to the redundancy of the amino acid motif Gln-Gly-Asn-Val-Glu. Methodology/Principal Findings Quantitative reverse-transcriptase polymerase chain reaction using RNA from B. turicatae infected ticks and mice indicated differential regulation of brpA during the tick-mammalian infectious cycle. The surface localization was determined, and production of the protein within the salivary glands of the tick was demonstrated. We then applied a novel genetic system for B. turicatae to inactivate brpA and examined the role of the gene product for vector colonization and the ability to establish murine infection. Conclusions/Significance These results demonstrate the complexity of protein production in a population of spirochetes within the tick. Additionally, the development of a genetic system is important for future studies to evaluate the requirement of specific B. turicatae genes for vector colonization and transmission.
Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Olga Golosova,Ross Henderson,Yuriy Vaskin,Andrei Gabrielian,German Grekhov,Vijayaraj Nagarajan,Andrew J. Oler,Mariam Quiones,Darrell Hurt,Mikhail Fursov,Yentram Huyen
PeerJ , 2015, DOI: 10.7717/peerj.644
Abstract: The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines “Variant Calling with SAMtools”, “Tuxedo Pipeline for RNA-seq Data Analysis” and “Cistrome Pipeline for ChIP-seq Data Analysis” integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.
High recombination rates and hotspots in a Plasmodium falciparum genetic cross
Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-4-r33
Abstract: Here, we used a high-density tiling array to estimate the genetic recombination rate among 32 progeny of a P. falciparum genetic cross (7G8 × GB4). We detected 638 recombination events and constructed a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb per centimorgan and identified 54 candidate recombination hotspots. Similar to centromeres in other organisms, the sequences of P. falciparum centromeres are found in chromosome regions largely devoid of recombination activity. Motifs enriched in hotspots were also identified, including a 12-bp G/C-rich motif with 3-bp periodicity that may interact with a protein containing 11 predicted zinc finger arrays.These results show that the P. falciparum genome has a high recombination rate, although it also follows the overall rule of meiosis in eukaryotes with an average of approximately one crossover per chromosome per meiosis. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination rate observed. The lack of recombination activity in centromeric regions is consistent with the observations of reduced recombination near the centromeres of other organisms.The human malaria parasite Plasmodium falciparum kills approximately one million people each year, mostly children in Africa [1]. The goal of developing an effective vaccine to control infection or disease has yet to be met. Parasite resistance to multiple antimalarial drugs has also spread rapidly in recent years. Genome plasticity and genetic variation are significant challenges to vaccine development and contribute to the worldwide problem of drug resistance.The P. falciparum malaria parasite has a unique and complex life cycle involving multiple DNA replications both in the mosquito and in human hosts. Except for a brief diploid phase after mating events in the mosquito midgut, the parasite stages in both hosts are haploid. Human infection commences with t
Alterations in the transcriptome and antibiotic susceptibility of Staphylococcus aureus grown in the presence of diclofenac
James T Riordan, JoAnne M Dupre, Stephanie A Cantore-Matyi, Atul Kumar-Singh, Yang Song, Shahrear Zaman, Sonia Horan, Nada S Helal, Vijayaraj Nagarajan, Mohamed O Elasri, Brian J Wilkinson, John E Gustafson
Annals of Clinical Microbiology and Antimicrobials , 2011, DOI: 10.1186/1476-0711-10-30
Abstract: Transcriptional alterations in response to growth with diclofenac were measured using S. aureus gene expression microarrays and quantitative real-time PCR. Antimicrobial susceptibility was determined by agar diffusion MICs and gradient plate analysis. Ciprofloxacin accumulation was measured by fluorescence spectrophotometry.Growth of S. aureus strain COL with 80 μg/ml (0.2 × MIC) of diclofenac resulted in the significant alteration by ≥2-fold of 458 genes. These represented genes encoding proteins for transport and binding, protein and DNA synthesis, and the cell envelope. Notable alterations included the strong down-regulation of antimicrobial efflux pumps including mepRAB and a putative emrAB/qacA-family pump. Diclofenac up-regulated sigB (σB), encoding an alternative sigma factor which has been shown to be important for antimicrobial resistance. Staphylococcus aureus microarray metadatabase (SAMMD) analysis further revealed that 46% of genes differentially-expressed with diclofenac are also σB-regulated. Diclofenac altered S. aureus susceptibility to multiple antibiotics in a strain-dependent manner. Susceptibility increased for ciprofloxacin, ofloxacin and norfloxacin, decreased for oxacillin and vancomycin, and did not change for tetracycline or chloramphenicol. Mutation to DcRS did not affect susceptibility to the above antibiotics. Reduced ciprofloxacin MICs with diclofenac in strain BB255, were not associated with increased drug accumulation.The results of this study suggest that diclofenac influences antibiotic susceptibility in S. aureus, in part, by altering the expression of regulatory and structural genes associated with cell wall biosynthesis/turnover and transport.Staphylococcus aureus is a human pathogen associated with integumental infections and life-threatening systemic diseases, such as sepsis and endocarditis. The tendency of S. aureus to acquire antibiotic resistance has led to the global dissemination of clones expressing multiple antimicrobia
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