A5044176533- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Electrochemical sensors and biosensors
- Microbial Fuel Cells and Bioremediation
- Geochemistry and Elemental Analysis
- Genomics and Phylogenetic Studies
- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- Electrochemical Analysis and Applications
- Radioactive element chemistry and processing
- Advanced biosensing and bioanalysis techniques
- Analytical chemistry methods development
- Microbial metabolism and enzyme function
- Virus-based gene therapy research
- Metal Extraction and Bioleaching
- Chromium effects and bioremediation
- Amino Acid Enzymes and Metabolism
- CAR-T cell therapy research
- Plant Molecular Biology Research
- Plant nutrient uptake and metabolism
- Viral gastroenteritis research and epidemiology
- Soil Carbon and Nitrogen Dynamics
- Insect symbiosis and bacterial influences
- Mercury impact and mitigation studies
- RNA regulation and disease
Emery Oleochemicals (Malaysia)
2021
Oregon Health & Science University
2012-2018
University of California, Berkeley
2016-2018
Planetary Science Institute
2016-2018
Oak Ridge National Laboratory
2016
Walker (United States)
2012
Salk Institute for Biological Studies
2011
Plant (United States)
2008
The tree of life is one the most important organizing principles in biology(1). Gene surveys suggest existence an enormous number branches(2), but even approximation full scale has remained elusive. Recent depictions have focused either on nature deep evolutionary relationships(3-5) or known, well-classified diversity with emphasis eukaryotes(6). These approaches overlook dramatic change our understanding life's resulting from genomic sampling previously unexamined environments. New methods...
Multiple small molecule hormones contribute to growth promotion or restriction in plants. Brassinosteroids (BRs), acting specifically the epidermis, can both drive and restrict shoot growth. However, our knowledge of how BRs affect meristem size is scant. Here, we study root show that are required maintain normal cell cycle activity expansion. These two processes ensure coherent gradient progression, from apical basal meristem. In addition, BR not accompanied by changes expression level...
Abstract Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a nuclease (747 amino acids in length) multiple functional states, revealing stepwise process DNA targeting involving conformational switch REC2 domain insertion. Our provide insights into intricately folded guide RNA which acts as structural...
Reactive Mn(IV) oxide minerals are ubiquitous in the environment and control bioavailability distribution of many toxic essential elements organic compounds. Their formation is thought to be dependent on microbial enzymes, because spontaneous Mn(II) oxidation slow. Several species marine Bacillus spores oxidize their exosporium, outermost layer spore, encrusting them with oxides. Molecular studies have identified mnx (Mn oxidation) genes, including mnxG, encoding a putative multicopper...
Annually, half of all plant-derived carbon is added to soil where it microbially respired CO2. However, understanding the microbiology this process limited because most culture-independent methods cannot link metabolic processes organisms present, and causative agents necessary predict results perturbations on system. We collected samples at two sub-root depths (10-20 cm 30-40 cm) before after a rainfall-driven nutrient perturbation event in Northern California grassland that experiences...
Plant growth depends on the integration of environmental cues and phytohormone-signaling pathways. During seedling emergence, elongation embryonic stem (hypocotyl) serves as a readout for light hormone-dependent responses. We screened 10,000 chemicals provided exogenously to light-grown seedlings identified 100 compounds that promote hypocotyl elongation. Notably, one subset these shares structural characteristics with synthetic auxins, 2,4-dichlorophenoxyacetic acid (2,4-D),...
CRISPR-associated (Cas) transposases (CAST) are RNA-guided systems capable of programmable integration large segments DNA without creating double-strand breaks. Engineered Cascade CAST function in human cells but challenging to deploy due the complexity targeting components. Unlike Cascade, which require three Cas proteins, type V-K a single Cas12k effector for targeting. Here, we show that compact from uncultivated microbes repurposable into genome cells. Engineering nuclear localization...
Abstract Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. However, to further expand the therapeutic application of these tools there is a need targetable systems small enough be delivered efficiently. Here, we mined an extensive genome-resolved metagenomics database and identified families uncharacterized RNA-guided, compact (between 450 1,050 aa). We report Cas9d, new CRISPR type II subtype, contains Zinc-finger motifs high...
In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome recovered from soil metagenome and found be astonishingly similar that of Delftia acidovorans SPH-1, which isolated in Germany decade ago. It suspected organism not native the sample because it lacked diversity is characteristic other organisms; suspicion confirmed when PCR testing failed detect bacterium original samples. D. also identified 16 previously published metagenomes multiple...
The dynamics of manganese solid formation (as MnOx) by the multicopper oxidase (MCO)-containing Mnx protein complex were examined electron paramagnetic resonance (EPR) spectroscopy. Continuous-wave (CW) EPR spectra samples Mnx, prepared in atmosphere and then reacted with Mn(II) for times ranging from 7 to 600 s, indicate rapid oxidation substrate (with two-phase pseudo-first-order kinetics modeled using rate coefficients of: k(1obs) = 0.205 ± 0.001 s(-1) k(2obs) 0.019 s(-1)). This process...
Manganese(ii) oxidation in the environment is thought to be driven by bacteria because enzymatic catalysis many orders of magnitude faster than abiotic processes. The heterologously purified Mn oxidase (Mnx) from marine Bacillus sp. PL-12 made up multicopper (MCO) MnxG and two small Cu heme-binding proteins unknown function, MnxE MnxF. Mnx binds oxidizes both Mn(ii) Mn(iii), generating Mn(iv) oxide minerals that resemble those found on spore surface. Spectroscopic techniques have illuminated...
Development of medicines using gene editing has been hampered by enzymological and immunological impediments. We described previously the discovery characterization improved, novel gene-editing systems from metagenomic data. In this study, we substantially advance work with three such systems, demonstrating their utility for cell therapy development. All are capable reproducible, high-frequency in primary immune cells. human T cells, disruption receptor (TCR) alpha-chain was induced >95%...
Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 nucleases have been extensively used in biotechnology and therapeutics. However, many applications are not possible owing to the size, targetability, potential off-target effects associated with currently known systems. In this study, we identified thousands of CRISPR type effectors by mining an extensive, genome-resolved metagenomics database encompassing hundreds microbial genomes. We developed a...
In a natural geochemical cycle, manganese-oxide minerals (MnOx ) are principally formed through microbial process, where putative multicopper oxidase MnxG plays an essential role. Recent success in isolating the approximately 230 kDa, enzymatically active MnxEFG protein complex, has advanced our understanding of biogenic MnOx mineralization. Here, kinetics formation catalyzed by examined using quartz crystal microbalance (QCM), and first electrochemical characterization complex is reported...
Annually, half of all plant-derived carbon is added to soil where it microbially respired CO 2 . However, understanding the microbiology this process limited because most culture-independent methods cannot link metabolic processes organisms present, and causative agents necessary predict results perturbations on system. We collected samples at two sub-root depths (10 – 20 cm 30 40 cm) before after a rainfall-driven nutrient perturbation event in Northern California grassland that experiences...
Cas12a enzymes are quickly being adopted for use in a variety of genome-editing applications. These programmable nucleases part adaptive microbial immune systems, the natural diversity which has been largely unexplored. Here, we identified novel families Type V-A CRISPR through large-scale analysis metagenomes collected from complex environments, and developed representatives these systems into gene-editing platforms. The display extensive protein variation can be programmed by single-guide...
MnxG, a multicopper oxidase, is an enzyme from the marine Bacillus species, which produces manganese oxide minerals through aerobic oxidation of dissolved Mn2+ − key process in global geochemical cycling. When isolated active form as part MnxEFG protein complex, enzymatic activity MnxG substantially enhanced by mild oxidative priming. Herein, mechanism for this effect probed using direct current (dc) and Fourier transformed alternating (ac) voltammetric analysis complex catalytically...
Abstract The type II-A CRISPR effector SpCas9 has gained widespread popularity as an efficient and programmable genome editing tool. However, much remains to be known about novel compact variants that may overcome some limitations of current systems 1,2 . Recently, alternative CRISPR-Cas with highly nucleases capable in mammalian cells have been discovered through metagenomic analysis uncultivated microbes, including Cas9d (a II-D effector) 3 Here, we report the cryo-EM structures a nuclease...