A5085366639- Microbial Natural Products and Biosynthesis
- Fungal Biology and Applications
- Innovative Microfluidic and Catalytic Techniques Innovation
- Microfluidic and Capillary Electrophoresis Applications
- Enzyme Production and Characterization
- Genomics and Phylogenetic Studies
- Chemical Analysis and Environmental Impact
- Electrowetting and Microfluidic Technologies
- Plant Pathogens and Fungal Diseases
- Enzyme Catalysis and Immobilization
- Water Treatment and Disinfection
- Microbial Metabolic Engineering and Bioproduction
- Membrane Separation Technologies
- 14-3-3 protein interactions
- Synthetic Organic Chemistry Methods
- Biofuel production and bioconversion
- Membrane-based Ion Separation Techniques
- Phytochemical compounds biological activities
- Pluripotent Stem Cells Research
- Plant biochemistry and biosynthesis
- Gene Regulatory Network Analysis
- Biochemical Acid Research Studies
- Water Systems and Optimization
- Innovative Teaching Methods
- Muon and positron interactions and applications
University of California, Berkeley
2012-2020
System Biosciences (United States)
2020
Joint BioEnergy Institute
2011-2018
University of California, San Francisco
2017-2018
Lawrence Berkeley National Laboratory
2015
University of Illinois Urbana-Champaign
2013
We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence FLS enables design new carbon fixation pathway, consisting small number thermodynamically favorable chemical transformations that convert formate sugar in central metabolism. pathway is predicted to use more efficiently and with less backward flux than any naturally occurring assimilation...
Significance Single-cell biology requires the ability to construct experiments with single-cell precision, large numbers, and extremely small fluid volumes. To address this need, we have developed a new technology, printed droplet microfluidics, which encapsulates reagents single cells in picoliter droplets, then actively selects deposits desired droplets an arrayed format on printing substrate. This technology enables construction of number relevant single-cellular multicellular methods detection.
Polyketides have enormous structural diversity, yet polyketide synthases (PKSs) thus far been engineered to produce only drug candidates or derivatives thereof. Thousands of other molecules, including commodity and specialty chemicals, could be synthesized using PKSs if composing hybrid from well-characterized parts derived natural was more efficient. Here, modern mass spectrometry techniques as an essential part the design-build-test cycle, we a chimeric PKS enable production one most...
Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible biology-friendly operation robotic equipment is key to its successful integration in laboratories, efforts required operate a robot must be much smaller than alternative manual lab work. To achieve these goals, simple high-level programming language needed. We have developed experimentally validated language: Programming Robot (PaR-PaR)....
An enzyme that catalyzes the formose reaction, termed "formolase", was recently engineered through a combination of computational protein design and directed evolution. We have investigated kinetic role computationally designed residues further characterized enzyme's product profile. Kinetic studies illustrated mutations were synergistic in their contributions towards enhancing activity. Mass spectrometry revealed produces two products reaction-dihydroxyacetone glycolaldehyde-with profile...
To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform system. Beyond liquid-handling robotics, now supports microfluidic microscopy well translation into human languages, such English. While same set of basic commands features are available for each supported platform, underlying optimization modules vary from...
Abstract The gem ‐dimethyl groups in polyketide‐derived natural products add steric bulk and, accordingly, lend increased stability to medicinal compounds, however, our ability rationally incorporate this functional group modified is limited. In order characterize the mechanism of formation, with a goal toward engineering novel compounds containing moiety, producing polyketide synthase (PKS) modules yersiniabactin and epothilone were characterized using mass spectrometry. work demonstrated,...
Existing methods for perchlorate remediation are hampered by the common co-occurrence of nitrate, which is structurally similar and a preferred electron acceptor. In this work, potential removal using cell-free bacterial enzymes as biocatalysts was investigated crude cell lysates soluble protein fractions Azospira oryzae PS, well encapsulated in lipid polymer vesicles. The showed activities between 41 700 to 54 400 U L–1 (2.49 3.06 mg–1 total protein). Soluble had 15 29 900 (1.70 1.97 mg–1)...
The borrelidin polyketide synthase (PKS) begins with a carboxylated substrate and, unlike typical decarboxylative loading PKSs, retains the carboxy group in final product. specificity and tolerance of incorporation carboxyacyl into type I PKSs have not been explored. Here, we show that first extension module is promiscuous its ability to extend both non-carboxyacyl substrates. However, has requirement for substrates containing moiety, which are decarboxylated situ. Thus, basis observed...
Droplet microfluidics enables massively-parallel analysis of single cells, biomolecules, and chemicals, making it valuable for high-throughput screens. However, many hydrophobic analytes are soluble in carrier oils, preventing their quantitative with the method. We apply Printed Microfluidics to construct defined reactions chemicals cells incubated under air on an open array. The method interfaces most bioanalytical tools retains compounds compartmentalized reactors, allowing quantitation.
In the search for molecular machinery custom biosynthesis of valuable compounds, modular type I polyketide synthases (PKSs) offer great potential. this study, we investigate flexibility BorM5, iterative fifth module borrelidin synthase, with a panel non-native priming substrates in vitro. BorM5 differentially extends various aliphatic and substituted substrates. Depending on substrate size substitution can exceed three iterations it natively performs. To probe effect methyl branching chain...
Acyltransferases determine which extender units are incorporated into polyketide and fatty acid products. The ping-pong acyltransferase mechanism utilizes a serine in conserved GHSxG motif. However, the role of histidine this motif is poorly understood. We observed that to alanine mutation (H640A) malonyl-CoA specific yersiniabactin results an approximately seven-fold higher hydrolysis rate over wildtype enzyme, while retaining transacylation activity. propose two possibilities for reduction...
Abstract Cerebral organoids provide unparalleled access to human brain development in vitro. However, variability induced by current culture methodologies precludes using as robust disease models. To address this, we developed an automated Organoid Culture and Assay (ORCA) system support longitudinal unbiased phenotyping of at scale across multiple patient lines. We then characterized organoid novel machine learning methods found that the contribution donor, clone, batch is significant...
Abstract The gem ‐dimethyl groups in polyketide‐derived natural products add steric bulk and, accordingly, lend increased stability to medicinal compounds, however, our ability rationally incorporate this functional group modified is limited. In order characterize the mechanism of formation, with a goal toward engineering novel compounds containing moiety, producing polyketide synthase (PKS) modules yersiniabactin and epothilone were characterized using mass spectrometry. work demonstrated,...
Abstract Although the elementary unit of biology is cell, high throughput methods for microscale manipulation cells and reagents are limited. The existing options either slow, lack single cell specificity, or utilize fluid volumes out scale with those cells. Here, we present Printed Droplet Microfluidics, a technology to dispense picoliter droplets deterministic control. core fluorescence-activated droplet sorter coupled specialized substrate that together act as printer, enabling generation...
Abstract Authenticity Promotes Student Engagement and Learning in a Stand-Alone Technical Communications CourseTechnical for Chemical Engineers has recently been re-introduced to the chemicalengineering undergraduate curriculum at large public university on west coast. The goal of thecourse is students gain skills written, oral, interpersonal communications that will helpthem excel their careers senior-level capstone design laboratory courses. course runsas one-semester, stand-alone (not...
Pilot Testing of a High-Rate Disk Filter for Water Recycling Applications and Title 22 ApprovalPilot testing the Nova Ultrascreen® (a high rate disk filter) was conducted at two water reclamation facilities in Orlando, Florida area to demonstrate that can produce an effluent meets California Criteria turbidity requirements, hydraulic loading rates ranging from 6 16 gpm/ft2. The pilot water...Author(s)Keith BourgeousNicola FontaineJennifer StokkeKathy MarksSean PoustDan LoyDavid...