A5009454293- Microbial Metabolic Engineering and Bioproduction
- CRISPR and Genetic Engineering
- Biofuel production and bioconversion
- Evolution and Genetic Dynamics
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Antibiotic Resistance in Bacteria
- Enzyme Catalysis and Immobilization
- Bacteriophages and microbial interactions
- Catalysis for Biomass Conversion
- Antimicrobial Peptides and Activities
- Enzyme-mediated dye degradation
- Enzyme Production and Characterization
- Cancer therapeutics and mechanisms
- Gene Regulatory Network Analysis
- Advanced biosensing and bioanalysis techniques
- Plant biochemistry and biosynthesis
- Amino Acid Enzymes and Metabolism
- Fractal and DNA sequence analysis
- Virus-based gene therapy research
- Evolutionary Game Theory and Cooperation
- RNA regulation and disease
- Fungal and yeast genetics research
- Signaling Pathways in Disease
- Bioenergy crop production and management
Joint BioEnergy Institute
2019-2023
Sandia National Laboratories
2019-2023
Lawrence Berkeley National Laboratory
2020-2023
Sandia National Laboratories California
2019-2023
University of Colorado Boulder
2015-2021
University of Colorado System
2018
The University of Texas at Austin
2013-2015
Microbial production of biofuels and bioproducts offers a sustainable economic alternative to petroleum-based fuels chemicals. The basidiomycete yeast Rhodosporidium toruloides is promising platform organism for generating due its ability consume broad spectrum carbon sources (including those derived from lignocellulosic biomass) naturally accumulate high levels lipids carotenoids, two biosynthetic pathways that can be leveraged produce wide range bioproducts. While R. has great potential,...
Abstract Tools for synthetically controlling gene expression are a cornerstone of genetic engineering. CRISPRi and CRISPRa technologies have been applied extensively programmable modulation transcription, but there few such tools targeted protein translation rates. Here, we employ CRISPR-Cas13 as activator translation. We develop novel variant the catalytically-deactivated Cas13d enzyme dCasRx by fusing it to initiation factor IF3. demonstrate dCasRx-IF3’s ability enhance 21.3-fold above...
In this study, organic acids were demonstrated as a promising carbon source for bisabolene production by the non-conventional yeast, Rhodosporidium toruloides, at microscale with maximum titre of 1055 ± 7 mg/L. A 125-fold scale-up optimal process, enhanced titres 2.5-fold to 2606 Implementation pH controlled acid feeding strategy scale lead further threefold improvement in 7758 mg/L, highest reported microbial titre. Finally, proof-of-concept sequential bioreactor approach was investigated....
Manipulating gene expression using different types of plasmids (centromeric, 2-micron, and autonomously replicating sequence) can expand levels enable a quick characterization combinations, both which are highly desired for metabolic engineering applications. However, the powerful industrial workhorse Yarrowia lipolytica, only low-copy CEN plasmid is available. In this study, we engineered from Y. lipolytica by fusing promoters upstream centromeric region to regulate its function range. By...
Antibiotic-resistant bacteria are an increasingly serious public health concern, as strains emerge that demonstrate resistance to almost all available treatments. One factor contributes the crisis is adaptive ability of bacteria, which exhibit remarkable phenotypic and gene expression heterogeneity in order gain a survival advantage damaging environments. This high degree variability across biological populations makes it challenging task identify key regulators bacterial adaptation. Here,...
Abstract Background In an effort to ensure future energy security, reduce greenhouse gas emissions and create domestic jobs, the US has invested in technologies develop sustainable biofuels bioproducts from renewable carbon sources such as lignocellulosic biomass. Bio-derived jet fuel is of particular interest aviation less amenable electrification compared other modes transportation synthetic biology provides ability tailor properties enhance performance. Specific density are important...
Efficient conversion of pentose sugars remains a significant barrier to the replacement petroleum-derived chemicals with plant biomass-derived bioproducts. While oleaginous yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) has relatively robust native metabolism compared other wild yeasts, faster assimilation those will be required for industrial utilization pentoses. To increase rate in R. toruloides, we leveraged previously reported high-throughput fitness data...
The evolution of antibiotic resistance has engendered an impending global health crisis that necessitates a greater understanding how emerges. impact nongenetic factors and they influence the is largely unexplored area research. Here we present novel application CRISPR-Cas9 technology for investigating gene expression governs adaptive pathways available to bacteria during resistance. We examine changes on bacterial adaptation by constructing library deactivated synthetic devices tune set...
Abstract Multidrug-resistant (MDR) bacteria pose a grave concern to global health, which is perpetuated by lack of new treatments and countermeasure platforms combat outbreaks or antibiotic resistance. To address this, we have developed Facile Accelerated Specific Therapeutic (FAST) platform that can develop effective peptide nucleic acid (PNA) therapies against MDR within week. Our FAST uses bioinformatics toolbox design sequence-specific PNAs targeting non-traditional pathways/genes...
The root cause of the antibiotic resistance crisis is ability bacteria to evolve a multitude antibiotics and other environmental toxins. regulation adaptation difficult pinpoint due extensive phenotypic heterogeneity arising during evolution. Here, we investigate mechanisms underlying general bacterial by evolving wild-type Escherichia coli populations dissimilar chemical We demonstrate presence inter- intrapopulation across adapted in multiple traits, including minimum inhibitory...
This work demonstrates the feasibility of applying dual functional solvents called alkanolamines for biomass pretreatment, deconstruction, and conversion into biofuels.
Economically-viable biofuel production is often limited by low levels of microbial tolerance to high concentrations. Here we demonstrate the first application deactivated CRISPR perturbations gene expression improve E. coli tolerance. We construct a library 31 unique inhibitions and activations in explore their impacts on growth during ten days exposure n-butanol n-hexane. show that perturbation metabolism membrane-related genes induces greatest n-butanol, as does redox-related n-hexanes....
Proliferation of multidrug-resistant (MDR) bacteria poses a threat to human health, requiring new strategies. Here we propose using fitness neutral gene expression perturbations potentiate antibiotics. We systematically explored 270 knockout-antibiotic combinations in Escherichia coli, identifying 90 synergistic interactions. Identified targets were subsequently tested for antibiotic synergy on the transcriptomic level via multiplexed CRISPR-dCas9 and showed successful sensitization E. coli...
Abstract Background Rhodosporidium toruloides is capable of co-utilization complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast therefore an attractive host for heterologous production valuable bioproducts at high titers low-cost, deconstructed biomass in economically environmentally sustainable manner. Here we demonstrate this by engineering R. to produce the polyketide triacetic acid lactone (TAL) directly unfiltered hydrolysate with minimal...
Abstract Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers detection. Developing label‐free optical technique will require nanoscale focusing light, high‐throughput and multiplexed identification method, data compression to rapidly identify sequences analyze genomic heterogeneity big datasets. Such method should characteristic vibrations using spectroscopy,...
Building a stronger bioeconomy requires production capabilities that can be generated through microbial genetic engineering. Engineered microbes paired with engineered feedstocks and compatible deconstruction methods to improve production.
The ever-increasing threat of multi-drug resistant bacteria, a shrinking antibiotic pipeline, and the innate ability microorganisms to adapt necessitates long-term strategies slow evolution resistance. Here we develop an approach, dubbed Controlled Hindrance Adaptation OrganismS or CHAOS, involving induction epistasis between gene perturbations deter adaption. We construct combinatorial library multiplexed, deactivated CRISPR-Cas9 devices systematically perturb expression in Escherichia...
We describe a nanoelectronic method for identifying single ribonucleotides and structural modifications, laying groundwork single-molecule RNA sequencing/structural mapping.
Antibacterial resistance necessitates the development of novel treatment methods for infections. Protein aggregates have recently been applied as antimicrobials to disrupt bacterial homeostasis. Past work on protein has focused genome mining aggregation-prone sequences in genomes rather than rational design aggregating antimicrobial peptides. Here, we use a synthetic biology approach an artificial gene encoding de novo peptide. This gene, opaL (overexpressed aggregator lipophilic), disrupts...
Abstract Genetic medicines, including CRISPR/Cas technologies, extend tremendous promise for addressing unmet medical need in inherited retinal disorders and other indications; however, there remain challenges the development of therapeutics. Herein, we evaluate genome editing by engineered Cas9 ribonucleoproteins (eRNP) vivo via subretinal administration using mouse pig animal models. Subretinal adenine base editor double strand break-inducing nuclease eRNPs mediate both species. Editing...