Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Environmental Microbiology and Microbial Ecology (3)
- Microbiology (3)
- Bioinformatics (2)
- Genetics and Genomics (2)
- Genomics (2)
-
- Bacteriology (1)
- Biochemistry (1)
- Biochemistry, Biophysics, and Structural Biology (1)
- Computational Biology (1)
- Ecology and Evolutionary Biology (1)
- Evolution (1)
- Microbial Physiology (1)
- Molecular Biology (1)
- Organismal Biological Physiology (1)
- Other Biochemistry, Biophysics, and Structural Biology (1)
- Pathogenic Microbiology (1)
- Structural Biology (1)
- Keyword
-
- Mass Spectrometry (2)
- Anaeromyxobacter dehalogenans 2CP-C (1)
- Bioinformatics (1)
- C-type cytochrome (1)
- Chemoreceptor (1)
-
- Chemotaxis (1)
- Comparative Genomics (1)
- Computational Biology (1)
- Dissimilatory Metal Reducing Bacteria (1)
- Environmental proteomics (1)
- Geobacter daltonii FRC-32 (1)
- Mass Spectrometry - based Proteomics (1)
- Microbial Ecology and Evolution (1)
- Pathogenicity (1)
- Populus trichocarpa (1)
- Post-translational Modification (1)
- Post-translational modifications (1)
- Quantitative Proteomics (1)
- Shewanella oneidensis MR-1 (1)
- Supercomputing (1)
- Systems Biology (1)
Articles 1 - 4 of 4
Full-Text Articles in Systems Biology
Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood
Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood
Doctoral Dissertations
Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …
Comparative Proteomics Reveals Core Vs. Unique Molecular Signatures For Dissimilatory Metal Reducing Bacteria Grown With Various Electron Acceptors, Xiaoxin Liu
Doctoral Dissertations
Dissimilatory metal reducing bacteria (DMRB) are probably one of the most respiratory versatile microorganisms on earth. Their ability to use metals as terminal electron acceptor allows them to survive in severe environments (e.g. radionuclide contaminated soil). In addition to metals, many other organic and inorganic substrates can be utilized as electron acceptors for DMRB respiration, including fumarate, nitrate, oxygen, etc. Genome information for many DMRB species is available, which reveals large numbers of c-type cytochrome encoding genes present in their genomes. For example, the genomes of three DMRBs, Anaeromyxobacter dehalogenans strain 2CP-C, Shewanella oneidensis strain MR-1, and Geobacter daltonii …
Development Of An Experimental And Computational Platform For Enhanced Characterization Of Modified Peptides And Proteins In Environmental Proteomics, Ritin Sharma
Doctoral Dissertations
Over the last decade, mass spectrometry based proteomics has been established as the front-runner in systems-level protein expression studies. However, with the field progressing into research of more and more complex samples, novel challenges have been raised with respect to efficient protein extraction and computational matching. In this dissertation, various aspects in the proteomics workflow, including experimental and computational approaches, have been developed, optimized and systematically evaluated. In this work, some of the critical factors with respect to proteomics sample preparation, like available biomass, detergent removal methods, and intact protein fractionation to achieve deeper proteome measurements were evaluated. The presented …
Quantitative Characterization Of Proteins And Post-Translational Modifications In Complex Proteomes Using High-Resolution Mass Spectrometry-Based Proteomics, Zhou Li
Doctoral Dissertations
Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing …