A5015833932- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Bacterial Genetics and Biotechnology
- Plant biochemistry and biosynthesis
- Genomics and Phylogenetic Studies
- Enzyme Structure and Function
- Enzyme Catalysis and Immobilization
- Gene Regulatory Network Analysis
- Machine Learning in Bioinformatics
- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Essential Oils and Antimicrobial Activity
- Catalysis for Biomass Conversion
- Microbial Natural Products and Biosynthesis
- Enzyme Production and Characterization
- Viral Infectious Diseases and Gene Expression in Insects
- Photosynthetic Processes and Mechanisms
- Antibiotic Resistance in Bacteria
- Algal biology and biofuel production
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
National Renewable Energy Laboratory
2018-2023
Lawrence Berkeley National Laboratory
2022
Washington University in St. Louis
2013-2017
Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of genes (resistome), yet prior studies indicate that the true diversity gut-associated resistomes has been underestimated. To deeply characterize pediatric resistome, we created metagenomic recombinant libraries in Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent exposure), performed functional selections for to 18 antibiotics eight...
Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how regulated fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism bioproduction. We performed independent component analysis of compendium 321 high-quality profiles, which were previously...
The intrinsic structural properties of branched long-chain fatty alcohols (BLFLs) in the range C12 to C18 make them more suitable as diesel fuel replacements and for other industrial applications than their straight-chain counterparts. While microbial production straight has been achieved, biosynthesis BLFLs never reported. In this work, we engineered four different biosynthetic pathways Escherichia coli produce BLFLs. We then employed a modular engineering approach optimize supply α-keto...
Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both engineering hosts to produce acid-derived molecules and development new antibiotics. However, gaps in our understanding initiation remain. Here, we demonstrate that industrially relevant microbe Pseudomonas putida KT2440 contains three distinct pathways initiate biosynthesis. The first two routes employ conventional β-ketoacyl-ACP synthase III enzymes, FabH1 FabH2, accept short- medium-chain-length acyl-CoAs,...
Terpenoids constitute a class of compounds with remarkable potential for pharmaceutical, fragrance, specialty chemical, and biofuel applications. However, their industrial production is limited by rarity within native plant hosts, creating considerable interest in microbial hosts capable manufacturing terpenoids. To reduce costs, nondestructive product recovery from these preferred, achievable using hydrophobic organic overlay. Our prior research has indicated that oxidized fatty acyl...
Branched-chain fatty acids (BCFAs) are important precursors for the production of advanced biofuels with improved cold-flow properties. Previous efforts in engineering type II acid synthase (FAS) BCFA suffered from low titers and/or co-production a large amount straight-chain (SCFAs), making it nearly impossible further conversion BCFAs to branched biofuels. Synthesis both SCFAs and requires FabH, only β-ketoacyl-(acyl-carrier-protein) Escherichia coli that catalyzes initial condensation...
Targeted proteomics is a mass spectrometry-based protein quantification technique with high sensitivity, accuracy, and reproducibility. As key component in the multi-omics toolbox of systems biology, targeted liquid chromatography-selected reaction monitoring (LC-SRM) measurements are critical for enzyme pathway identification design metabolic engineering. To fulfill increasing need analyzing large sample sets faster turnaround time high-throughput LC-SRM greatly needed. Even though nanoflow...