A5091130871- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Enzyme Catalysis and Immobilization
- CRISPR and Genetic Engineering
- Biofuel production and bioconversion
- Algal biology and biofuel production
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Bacteriophages and microbial interactions
- Plant biochemistry and biosynthesis
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Viral Infectious Diseases and Gene Expression in Insects
- Protein Structure and Dynamics
- Plant tissue culture and regeneration
- Marine and coastal ecosystems
- Quality and Management Systems
- Chromium effects and bioremediation
- Catalysis for Biomass Conversion
- Tuberculosis Research and Epidemiology
- Computational Drug Discovery Methods
- Wastewater Treatment and Nitrogen Removal
- Chemical Reactions and Isotopes
- Photosynthetic Processes and Mechanisms
Pacific Northwest National Laboratory
2023-2025
Joint BioEnergy Institute
2024
Washington University in St. Louis
2017-2023
Washtenaw Community College
2019
University of Michigan
2013-2019
Michigan United
2013
β-Ionone is a fragrant terpenoid that generates pleasant floral scent and used in diverse applications as cosmetic flavoring ingredient. A growing consumer desire for natural products has increased the market demand β-ionone. To date, chemical extraction from plants remains main approach commercial β-ionone production. Unfortunately, changing climate geopolitical issues can cause instability supply chain. Microbial fermentation using generally recognized safe (GRAS) yeast offers an...
Computational protein design is a reverse procedure of folding and structure prediction, where constructing structures from evolutionarily related proteins has been demonstrated to be the most reliable method for 3-dimensional prediction. Following this spirit, we developed novel new sequences based on families. For given target structure, set having similar fold are identified PDB library by structural alignments. A profile then constructed templates used guide conformational search amino...
<title>Abstract</title> Metabolic engineering is evolving rapidly as a result of new advances in synthetic biology and automation, well the irruption machine learning (ML). ML has been shown to provide predictive power lacked needed, be able effectively guide metabolic process. However, current technical limitations prevent independent application approaches without use previous biological knowledge form prioritized list desirable targets. Here, we present FluxRETAP, simple computationally...
In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13C-metabolic flux analysis (13C-MFA) revealed the core P. network after CRISPRi conserved, with moderate reduction of TCA cycle and pyruvate...
Abstract Background Fungi have been utilized for centuries in medical, agricultural, and industrial applications. Development of systems biology techniques has enabled the design metabolic engineering these fungi to produce novel fuels, chemicals, enzymes from renewable feedstocks. Many genetic tools developed manipulating genome creating mutants rapidly. However, screening confirmation transformants remain an inefficient step within design, build, test, learn cycle many because extracting...
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Significance Colwellia psychrerythraea 34H is a cold-adapted marine bacterium that represents genus and species cosmopolitan to the cold ocean. To our knowledge, metabolic flux studies of an obligate psychrophile like are not available. We characterized physiology metabolism 34H, at normal-growth temperature 4 °C upper-stress condition room (23 °C), by integrating (tracking 13 C-labeled compounds) genetic analyses (transcriptomics). Results from these system-level reveal unique features...
Targeted metabolite analysis in combination with 13C-tracing is a convenient strategy to determine pathway activity biological systems; however, limited by challenges separating and detecting intermediates current chromatographic methods. Here, hydrophilic interaction chromatography tandem mass spectrometry approach was developed for improved separation, isotopologue analysis, quantification. The physiological responses of Yarrowia lipolytica strain engineered produce ∼400 mg/L α-ionone...
CRISPR technology has revolutionized fungal genetic engineering by accelerating the pace and expanding feasible scope of experiments in this field. Among various CRISPR-Cas systems, Cas9 Cas12a are widely used metabolic engineering. In filamentous fungi, both have been utilized as nucleases. work we first compared efficacies types edits for CRISPR-Cas9 -Cas12a systems at polyketide synthase ( albA ) gene locus Aspergillus niger . By employing a tRNA-based gRNA polycistronic cassette,...
This study employs biomass growth analyses and 13C-isotope tracing to investigate lipid feedstock utilization by Yarrowia lipolytica. Compared glucose, oil-feedstock in the minimal medium increases yeast's yields cell sizes, but decreases its protein content (<20% of total biomass) enzyme abundances for product synthesis. Labeling results indicate a segregated metabolic network (the glycolysis vs. TCA cycle) during co-catabolism sugars (glucose or glycerol) with fatty acid substrates, which...
Abstract CRISPR technology has revolutionized fungal genetic engineering by accelerating the pace and expanding feasible scope of experiments in this field. Among various CRISPR-Cas systems, Cas9 Cas12a are widely used metabolic engineering. In filamentous fungi, both have been utilized as nucleases. work we first compared efficacies types edits for CRISPR-Cas9 -Cas12a systems at polyketide synthase ( albA ) gene locus Aspergillus niger . By employing a tRNA-based gRNA polycistronic...
Microalgae are recognized for their versatility in providing renewable energy, biopharmaceuticals, and nutraceuticals, attributed to sustainable, renewable, cost-effective nature. Genetic engineering has proven highly effective enhancing microalgae production. PCR-based genotyping is the primary method screening genetically transformed cells. Recently, we developed a novel PCR method, namely Squash-PCR, employed it molecular analysis of industrially important fungi yeasts. In this study,...
Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding function. 13 C Flux Analysis ( MFA) is considered to be gold standard measuring metabolic fluxes. MFA typically works by leveraging extracellular exchange fluxes as well data from labeling experiments calculate flux profile which best fit small, central carbon, model. However, nonlinear nature fitting procedure means that several profiles...
Abstract Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding function. 13 C Flux Analysis ( MFA) is considered to be gold standard measuring metabolic fluxes. MFA typically works by leveraging extracellular exchange fluxes as well data from labeling experiments calculate flux profile which best fit small, central carbon, model. However, nonlinear nature fitting procedure means that several...
Bioconversion processes require nitrogen for growth and production of intracellular enzymes to produce biofuels bioproducts. Typically, this is supplied as reduced in the form ammonia, which produced offsite from N 2 H via Haber-Bosch process. While has revolutionized industries dependent on fixed (e.g., modern agriculture), it highly energy-intensive its reliance natural gas combustion results substantial global CO emissions. Here we investigated feasibility situ biological fixation a...
Genetic and environmental perturbation experiments have been used to study microbes in a bid gain insight into transcriptional regulation, adaptive evolution, other cellular dynamics. These studies potential enabling rational strain design. Unfortunately, experimentally determined intracellular flux distribution are often inconsistent or incomparable due different experimental conditions methodologies. Computational design relies on constraint-based reconstruction analysis (COBRA) techniques...