A5086847747- Innovative Microfluidic and Catalytic Techniques Innovation
- Mass Spectrometry Techniques and Applications
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Cell Image Analysis Techniques
- Microfluidic and Capillary Electrophoresis Applications
- Microbial Metabolic Engineering and Bioproduction
- Microbial Natural Products and Biosynthesis
- Electrowetting and Microfluidic Technologies
- Advanced Proteomics Techniques and Applications
- Gut microbiota and health
- Microfluidic and Bio-sensing Technologies
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Biochemical and Structural Characterization
- Botanical Research and Applications
- 3D Printing in Biomedical Research
- Transgenic Plants and Applications
- Metabolomics and Mass Spectrometry Studies
- Advanced Fluorescence Microscopy Techniques
- Photosynthetic Processes and Mechanisms
- Enzyme Catalysis and Immobilization
- Enhanced Oil Recovery Techniques
- Chemical synthesis and alkaloids
University of California, San Francisco
2018-2023
QB3
2022
University of California, Berkeley
2015-2018
Abstract Self-associating split fluorescent proteins (FPs) are FPs whose two fragments spontaneously associate to form a functional FP. They have been widely used for labeling proteins, scaffolding protein assembly and detecting cell-cell contacts. Recently developments expanded the palette of self-associating beyond original GFP 1-10/11 . However, these new ones suffered from suboptimal fluorescence signal after complementation. Here, by investigating complementation process, we...
Abstract Enzymes are represented across a vast space of protein sequences and structural forms have activities that far exceed the best chemical catalysts; however, engineering them to novel or enhanced activity is limited by technologies for sensing product formation. Here, we describe general scalable approach characterizing enzyme uses metabolism host cell as biosensor which infer Since different products consume molecules in their synthesis, they perturb unique ways can be measured mass...
Single cell sequencing is useful for resolving complex systems into their composite types and computationally mining them unique features that are masked in pooled sequencing. However, while commercial instruments have made single analysis widespread mammalian cells, analogous tools microbes limited. Here, we present EASi-seq (Easily Accessible microbe sequencing). By adapting the workflow of Mission Bio Tapestri instrument, this method allows efficient individual microbes' genomes....
Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet with commercial fluid-handling robotics. The incorporate common devices including generators, mergers, sorters utilize robot's native for thermal control, incubation, plate scanning. ability automate using fluid handling will speed up integration these methods into...
Patterned surfaces can enhance the sensitivity of laser desorption ionization mass spectrometry by segregating and concentrating analytes, but their fabrication be challenging. Here, a simple method to fabricate substrates patterned with micrometer-scale wells that yield more accurate sensitive measurements compared flat is described. The also concentrate localize cells beads for cell-based assays.
Abstract Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent small fraction genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach isolate and samples using microfluidic automated plasmid library enrichment. Our provides deep coverage the target cluster, facilitating reassembly. demonstrate by isolating sequencing type I polyketide synthase from Antarctic...
Single cell sequencing is useful for resolving complex systems into their composite types and computationally mining them unique features that are masked in pooled sequencing. However, while commercial instruments have made single analysis widespread mammalian cells, analogous tools microbes limited. Here, we present EASi-seq (Easily Accessible microbe sequencing). By adapting the workflow of Mission Bio Tapestri instrument, this method allows efficient individual microbes' genomes....
Currently, the identification of new genes drastically outpaces current experimental methods for determining their enzymatic function. This disparity necessitates development high-throughput techniques that operate with same scalability as modern gene synthesis and sequencing technologies. In this paper, we demonstrate versatility recently reported DNA-Linked Enzyme-Coupled Assay (DLEnCA) its ability to support data acquisition through next-generation (NGS). Utilizing methyltransferases,...
Targeting specific cells for sequencing is important applications in cancer, microbiology, and infectious disease. Nucleic acid cytometry (NAC) a powerful approach accomplishing this because it allows to be isolated based on sequence biomarkers that are otherwise impossible detect. However, existing methods require specialized microfluidic devices, limiting adoption. Here, modified workflow described uses particle-templated emulsification (PTE) flow conduct the essential steps of cell...
Traditional enzyme characterization methods are low-throughput and therefore limit engineering efforts in synthetic biology biotechnology. Here, we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor reactions high-throughput manner. Throughput is improved by removing the need for protein purification limiting liquid chromatography mass spectrometry (LCMS) product detection linking enzymatic function DNA modification. We demonstrate DLEnCA methodology using glucosyltransferases as...
Abstract Self-associating split fluorescent proteins (FPs) have been widely used for labeling proteins, scaffolding protein assembly and detecting cell-cell contacts. Newly developed self-associating FPs, however, suffered from suboptimal fluorescence signal. Here, by investigating the complementation process, we demonstrated two approaches to improve FPs: assistance through SpyTag/SpyCatcher interaction directed evolution. The latter has yielded sfCherry3 variants with substantially...
Abstract Patterned surfaces can enhance the sensitivity of laser desorption ionization mass spectrometry by segregating and concentrating analytes, but their fabrication be challenging. Here, we describe a simple method to fabricate substrates patterned with micron-scale wells that yield more accurate sensitive measurements compared flat surfaces. The also concentrate localize cells beads for cell-based assays.
Patterned Surfaces surfaces can enhance the sensitivity of laser desorption ionization mass spectrometry by segregating and concentrating analytes, but their fabrication is challenging. In article number 2108194, Adam R. Abate co-workers introduce a simple method to pattern substrates with micrometer-scale wells yielding more-sensitive measurements compared flat-surface or cylindrical wells. The also concentrate localize cells beads for cell-based assays.
Abstract Enzymes are represented across a vast space of protein sequences and structural forms have activities that far exceed the best chemical catalysts; however, engineering them to novel or enhanced activity is limited by technologies for sensing product formation. Here, we describe general scalable approach characterizing enzyme uses metabolism host cell as biosensor which infer Since different products consume molecules in their synthesis, they perturb unique ways can be measured mass...