A5006567804- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Gene Regulatory Network Analysis
- Algal biology and biofuel production
- Bacterial biofilms and quorum sensing
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
- Bacterial Identification and Susceptibility Testing
- Enzyme Catalysis and Immobilization
- Mass Spectrometry Techniques and Applications
- biodegradable polymer synthesis and properties
- Photosynthetic Processes and Mechanisms
- Microbial Fuel Cells and Bioremediation
- Bioinformatics and Genomic Networks
- Viral Infectious Diseases and Gene Expression in Insects
- thermodynamics and calorimetric analyses
- Process Optimization and Integration
- Evolutionary Game Theory and Cooperation
- Fluid Dynamics and Mixing
- Genomics and Phylogenetic Studies
- Marine and coastal ecosystems
- Evolution and Genetic Dynamics
- Cooperative Studies and Economics
- Advanced Chemical Sensor Technologies
- Analytical Chemistry and Chromatography
Montana State University
2016-2025
Johns Hopkins Medicine
2019
Johns Hopkins University
2019
Sharda University
2018
Oxford Brookes University
2015
Biotechnology Institute
2002-2006
University of Minnesota
2001-2006
Molecular Sciences Institute
2001
Lawrence Berkeley National Laboratory
1960
University of California, Berkeley
1960
Surfaces coated with the naturally-occurring polysaccharide chitosan (partially deacetylated poly N-acetyl glucosamine) resisted biofilm formation by bacteria and yeast. Reductions in viable cell numbers ranging from 95% to 99.9997% were demonstrated for Staphylococcus epidermidis, aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa Candida albicans on chitosan-coated surfaces over a 54-h experiment comparison controls. For instance, reduced S. epidermidis surface-associated growth more...
Phaeodactylum tricornutum is a unicellular diatom in the class Bacillariophyceae. The full genome has been sequenced (<30 Mb), and approximately 20 to 30% triacylglyceride (TAG) accumulation on dry cell basis reported under different growth conditions. To elucidate P. gene expression profiles during nutrient-deprivation lipid-accumulation, cultures were grown with nitrate phosphate ratio of 20:1 (N:P) whole-genome transcripts monitored over time via RNA-sequence determination.
The biological reduction of dinitrogen (N2) to ammonia (NH3) by nitrogenase is an energetically demanding reaction that requires low-potential electrons and ATP; however, pathways used deliver the from central metabolism reductants nitrogenase, ferredoxin or flavodoxin, remain unknown for many diazotrophic microbes. FixABCX protein complex has been proposed reduce flavodoxin using NADH as electron donor in a process known bifurcation. Herein, Azotobacter vinelandii was purified demonstrated...
Abstract Background Three methods were developed for the application of stoichiometry-based network analysis approaches including elementary mode to study mass and energy flows in microbial communities. Each has distinct advantages disadvantages suitable analyzing systems with different degrees complexity a priori knowledge. These tested compared using data from thermophilic, phototrophic mat communities Octopus Mushroom Springs Yellowstone National Park (USA). The models based on three...
Iron bioavailability is a major limiter of bacterial growth in mammalian host tissue and thus represents an important area study. Escherichia coli K-12 metabolism was studied at four levels iron limitation chemostats using physiological proteomic analyses. The data documented E. acclimation gradient where progressively more severe scarcity resulted larger percentage substrate carbon being directed into overflow accompanied by decrease biomass yield on glucose. Acetate the primary secreted...
Phaeodactylum tricornutum is a marine diatom in the class Bacillariophyceae and important ecologically industrially with regards to ocean primary production lipid accumulation for biofuel production, respectively. Triacylglyceride (TAG) has been reported P. under different nutrient stresses, our results show that can occur nitrate or phosphate depletion. However, greater was observed when both nutrients were depleted as using Nile Red assay fatty acid methyl ester (FAME) profiles. Nitrate...
Wound bioburden in the form of colonizing biofilms is a major contributor to nonhealing wounds. Staphylococcus aureus Gram-positive, facultative anaerobe commonly found chronic wounds; however, much remains unknown about basic physiology this opportunistic pathogen, especially with regard biofilm phenotype. Transcriptomic and proteomic analysis S. have suggested that exhibit an altered metabolic state relative planktonic Herein, comparisons extracellular intracellular metabolite profiles...
Abstract Motivation: Elementary flux mode analysis (EFMA) decomposes complex metabolic network models into tractable biochemical pathways, which have been used for rational design and of regulatory networks. However, application EFMA has often limited to targeted or simplified representations due computational demands the method. Results: Division biological networks subnetworks enables complete enumeration elementary modes (EFMs) a broad range complexities, including genome-scale. Here, are...
Chronic wounds are often colonized by consortia comprised of different bacterial species growing as biofilms on a complex mixture wound exudate. Bacteria in exhibit phenotypes distinct from planktonic growth, rendering the application antibacterial compounds ineffective. Computational modeling represents complementary tool to experimentation for generating fundamental knowledge and developing more effective treatment strategies chronic biofilm consortia. We developed spatiotemporal models...
Abstract Elementary mode analysis has been used to study a metabolic pathway model of recombinant Saccharomyces cerevisiae system that was genetically engineered produce the bacterial storage compound poly‐β‐hydroxybutyrate (PHB). The includes biochemical reactions from intermediary metabolism and takes into account cellular compartmentalization as well reversibility/irreversibility reactions. reaction network connects production and/or consumption eight external metabolites including...
Abstract Cells grow by oxidizing nutrients using a complex network of biochemical reactions. During this process new biological material is produced along with energy used for maintaining cellular organization. Because the metabolic highly branched, these tasks can be accomplished wide variety unique reaction sequences. However, evolutionary pressures under carbon‐limited growth conditions likely select organisms that utilize efficient pathways. Using elementary‐mode analysis, we demonstrate...
Computational representations of metabolism are increasingly common in medical, environmental, and bioprocess applications. Cellular growth is often an important output computational biology analyses, therefore, accurate measurement biomass constituents critical for relevant model predictions. There a distinct lack detailed macromolecular protocols, including comparisons to alternative assays methodologies, as well tools convert the experimental data into biochemical reactions Herein...
Abstract We have previously shown that the metabolism for most efficient cell growth can be realized by a combination of two types elementary modes. One mode produces biomass while second generates only energy. The identity four and energy pathway pairs changes, depending on degree oxygen limitation. identification such different conditions offers pathway‐based explanation maintenance generation. For given rate, experimental aerobic glucose consumption rates used to estimate contribution...
Poly [(R)-3-hydroxybutyric acid] (PHB) is a prokaryote storage material for carbon and energy that accumulates in cells under unbalanced growth conditions. Because this class of biopolymers has plastic-like properties, it attracted considerable interest biomedical applications as biodegradable commodity plastic. Current flow cytometric techniques to quantify intracellular PHB are based on Nile red. Here, an improved technique cellular quantification utilizing BODIPY 493/503 staining was...
Escherichia coli physiological, biomass elemental composition and proteome acclimations to ammonium-limited chemostat growth were measured at four levels of nutrient scarcity controlled via dilution rate. These data compared with published iron- glucose-limited collected from the same strain rates quantify general nutrient-specific responses. Severe resulted in an overflow metabolism differing organic byproduct profiles based on limiting Ammonium-limited cultures secreted up 35 % metabolized...
Abstract Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize classic diauxie phenotype, nor it follow common systems biology assumptions including preferential consumption of glucose with an ‘overflow’ metabolism. Despite these contradictions, P. competitive disparate environments underscoring knowledge gaps...
ABSTRACT Bacteria carry many types of obligate intracellular parasites, including plasmids and bacteriophage. During infection, these parasites redirect resources away from bacterial processes toward parasite production. Because parasite-induced metabolic changes influence host traits such as growth rate, nutrient uptake, waste excretion, parasitic infection should alter how microbes contribute to important community ecosystem functions. Yet there are few empirical tests shapes...