A5013704427- Microbial Metabolic Engineering and Bioproduction
- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
- Protein Structure and Dynamics
- Plant-Microbe Interactions and Immunity
- Model Reduction and Neural Networks
- Cell Image Analysis Techniques
- Transgenic Plants and Applications
- Insect symbiosis and bacterial influences
- Biofuel production and bioconversion
- Machine Learning in Bioinformatics
- Gaussian Processes and Bayesian Inference
- Bioinformatics and Genomic Networks
- Cancer Research and Treatments
- Viral Infectious Diseases and Gene Expression in Insects
- Genetics, Aging, and Longevity in Model Organisms
- Neonatal and Maternal Infections
- Biochemical and biochemical processes
- Plant and Biological Electrophysiology Studies
Pacific Northwest National Laboratory
2019-2025
Lawrence Berkeley National Laboratory
2015-2019
University of Washington
2006-2016
Efficient genome engineering is critical to understand and use microbial functions. Despite recent development of tools such as CRISPR-Cas gene editing, efficient integration exogenous DNA with well-characterized functions remains limited model bacteria. Here, we describe serine recombinase-assisted engineering, or SAGE, an easy-to-use, highly efficient, extensible technology that enables selection marker-free, site-specific up 10 constructs, often efficiency on par superior replicating...
The fast-growing nonmodel marine bacterium Vibrio natriegens has recently garnered attention as a host for molecular biology and biotechnology applications. In order to further its capabilities synthetic chassis, we have characterized wide range of genetic parts tools use in V. natriegens. These include many commonly used resistance markers, promoters, ribosomal binding sites, reporters, terminators, degradation tags, origin replication sequences, plasmid backbones. We the behavior these...
ABSTRACT Rhodopseudomonas are a group of phototrophic microbes with marked metabolic versatility and flexibility that underpins their potential use in the production value-added products, bioremediation, plant growth promotion. Members this have an average genome size about 5.5 Mb, but two closely related strains sizes 4.0 Mb. To identify types genes missing reduced strain, we compared strain DSM127 other isolates at genomic phenotypic levels. We found can grow as well members genus retains...
The parameters in a complex synthetic gene network must be extensively tuned before the functions as designed. Here, we introduce simple and general approach to rapidly tune networks Escherichia coli using hypermutable sequence repeats embedded spacer region of ribosome binding site. By varying repeat length, generated expression libraries that incrementally predictably sample levels over 1,000-fold range. We demonstrate utility by creating bistable switch library programmatically samples...
Recent advances in the design and construction of synthetic multicelled systems E. coli S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing frameworks for biology do not account unique morphologies growing microcolonies, interaction gene circuits spatial diffusion molecular signals, or relationship between parallel algorithms. Here, we introduce a framework specification simulation behaviors...
Microbially produced alkanes are a new class of biofuels that closely match the chemical composition petroleum-based fuels. Alkanes can be generated from fatty acid biosynthetic pathway by reduction acyl-ACPs followed decarbonylation resulting aldehydes. A current limitation this is restricted product profile, which consists n-alkanes 13, 15, and 17 carbons in length. To expand we incorporated part, FabH2 Bacillus subtilis, an enzyme known to have broader specificity profile for initiation...
Graphical abstractAbstractMicrobial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of predicting microbial interactions currently lacking. Here we propose supervised deep learning as a new tool network inference. An agent-based model was used to simulate spatiotemporal evolution two interacting organisms under diverse growth and interaction...
Recent proteomic advancements have revealed widespread Nε-lysine acetylation in pathways governing pathogenicity, metabolism, and antibiotic resistance bacteria. The spontaneous, non-specific nature of this modification prokaryotes obscures its biological role, necessitating prokaryotic specific vivo interrogation systems. Genetic Code Expansion (GCE) offers a powerful method to investigate the roles regulation dynamics acetyl-lysine with precise incorporation suite non-canonical amino...
Abstract Genetic screens are essential for uncovering novel molecular mechanisms and identifying the functions of hypothetical proteins. CRISPR interference (CRISPRi) is a powerful, programmable, sequence-specific gene repression technology that can be used high-throughput screening targeted repression. Despite its ease use, initial development CRISPRi systems labor-intensive in many non-model organisms. Our goal to simplify this by establishing host-agnostic platform utilizes serine...
Advances in whole genome sequencing have led to a rapid and ongoing increase the amount of sequence data available, but 40-50% known genes no functional annotation only 25-30% specific annotations. Current approaches typically rely on computationally expensive pairwise or multiple alignments, preventing development models for novel protein functions sometimes limiting methods one ontology. Representation short segments (kmers) has been used many applications nucleotide sequence, more...
Precision genome editing accelerates the discovery of genetic determinants phenotype and engineering novel behaviors in organisms. Advances DNA synthesis recombineering have enabled high-throughput circuits biosynthetic pathways via directed mutagenesis bacterial chromosomes. However, highest recombination efficiencies to date been reported persistent mutator strains, which suffer from reduced genomic fidelity. The absence inducible transcriptional regulators these strains also prevents...
Abstract Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins growth promotion by microbes. Sorghum bicolor is a cereal crop that feeds animals humans used for bioethanol production. Its root tips exude large amounts of lipophilic benzoquinone called sorgoleone. Sorgoleone an allelochemical suppresses the competing seedlings mineralized microbes in soil. As avenue to understand how sorghum its microbiome may be connected through exudates, we...
Abstract Sustainable enhancements to crop productivity and increased resilience adverse conditions are critical for modern agriculture, application of plant growth promoting rhizobacteria (PGPR) is a promising method achieve these goals. However, many desirable PGPR traits highly regulated in their native microbe, limited certain rhizospheres, or insufficiently active agricultural purposes. Synthetic biology can address limitations, but its by availability appropriate tools sophisticated,...
Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster more sensitive methods to assess evolutionary functional relationships between proteins. Representing proteins as sets short peptide sequences (kmers) been used rapid, accurate classification into categories; however, this approach employs an exact-match methodology thus may be limited in terms sensitivity coverage. We have previously similarity...
Abstract Cooperation through division of labor underpins biological complexity for organisms and communities. In microbes, stochastic differentiation coupled to programmed cell death drives diverse altruistic behaviors that promote cooperation. Utilizing developmental multicellular programs requires control over rate balance proliferation against the utility sacrifice. However, these are often controlled by complex regulatory networks have yet be demonstrated from first principles. Here we...
A selective activity-based probe for C5a peptidase profiles pathogenic streptococci .
Abstract Sorghum ( bicolor ) is a major food and bioenergy grass species cultivated worldwide. To promote more robust sustainable growth of this important crop, we need deeper understanding the plant-microbe interactions between sorghum soil microbial communities that benefit plant host resiliency enhance nutrient acquisition. The release specific metabolites from roots, or root exudation, drives these interactions, but molecular pathways by which exudates shape rhizosphere microbiome...
ABSTRACT The rhizosphere represents a dynamic and complex interface between plant hosts the microbial community found in surrounding soil. While it is recognized that manipulating has potential to improve fitness health, engineering microbiome through inoculation often proved challenging. This large part due competitive ecosystem which added microbes must survive, lack of adaptation these specific metabolic environmental pressures rhizosphere. Here, we constructed an formula using defined...
In this paper, we consider the problem of learning a predictive model for population cell growth dynamics as function media conditions. We first introduce generic data-driven framework training operator-theoretic models to predict rate. then experimental design and data generated in study, namely curves Pseudomonas putida casein glucose concentrations. use driven approach identification, specifically nonlinear autoregressive (NAR) represent dynamics. show theoretically that Hankel DMD can be...
Abstract Agriculture is the largest source of greenhouse gases (GHG) production. Conversion nitrogen fertilizers into more reduced forms by microbes through a process known as biological nitrification drives GHG production, enhances proliferation toxic algal blooms, and increases cost crop Some plants reduce in soils exuding diverse array inhibitors (BNIs) that inhibit ammonium oxidizing responsible for nitrification. Applying synthetic biology to enhance transfer BNI production food...