Browsing by Author "Mazumder, Raja"

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    Substrate Regulated Microaerophily and Chemotaxis by Pseudomonas jessenii strain VT10
    Mazumder, Raja (Virginia Tech, 2000-03-06)
    Low substrate regulated microaerophilic behavior (LSRMB), as measured by changes in microaerophilic band formation in semi-solid medium, was observed in several aerobic bacteria isolated from subsurface soils, Antarctic dry valley soils, an eutrophic pond, a mesophilic pond, an oligotrophic lake and activated sludge. Similar behavior was also exhibited by five Pseudomonas and two Bacillus type strains from culture collection. Isolates identified with LSRMB formed a typical band of growth below the surface of low substrate (10 mg/l of peptone, tryptone, yeast extract and glucose) semi-solid medium. Surface growth was obtained when the substrate concentration was increased (1000 mg/l of each of the above mentioned substrates). LSRMB was observed in phylogenetically disparate groups, with all the Pseudomonas and two Bacillus species testing positive for the trait. One of the Gram-negative isolates, strain VT10, was identified by phylogenetic analysis based on its 16S rDNA sequence. High 16S rDNA sequence similarity (99%) was observed with the recently discovered Pseudomonas jessenii (CIP 105274T) type strain. Strain VT10 was used as a model to examine this LSRMB, and show the relationship between oxygen stress and low-substrate growth media. The concentration of 17:0 cyclopropane fatty acid, a common stress indicator, increased 5-fold, and four additional proteins were produced when P. jessenii strain VT10 was grown at low-substrate levels and when the dissolved oxygen concentration was increased from 26 microM to 241 microM. The stress responses by P. jessenii could be due its LSRMB. This study shows that low-substrate regulated microaerophilic behavior helps some microorganisms to track the oxygen minima in their habitat and thus effectively move to an environment, which allows them to thrive. In addition to the above mentioned taxis in response to oxygen concentration, organisms may use chemotaxis to a chemical compound. Quantification of chemotaxis can be extremely difficult. To quantify chemotaxis in an easier fashion, a simplified capillary chemotaxis assay, utilizing a hypodermic needle, syringe and disposable pipette tip was developed. The method was applied to two strains of subsurface microaerophilic bacteria. Strain VT10 was chemotactically attracted toward dextrose, glycerol, and phenol, which could be used as sole carbon sources, and toward maltose, which could not be used. The deep subsurface isolate MR100 (phylogenetically related to P. mendocina) showed no tactic response to these compounds although it could use dextrose, maltose, and glycerol as carbon sources. The chemotaxis results obtained by the new method were verified by using the swarm plate assay technique. The simplified technique may be useful for routine chemotactic testing.
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    Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets
    McGarvey, Peter B.; Huang, Hongzhan; Mazumder, Raja; Zhang, Jian; Chen, Yongxing; Zhang, Chengdong; Cammer, Stephen; Will, Rebecca; Odle, Margie; Sobral, Bruno; Moore, Margaret; Wu, Cathy H. (Public Library of Science, 2009-09-25)
    The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification.