A5103481322- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Microbial Metabolic Engineering and Bioproduction
- Mine drainage and remediation techniques
- Microbial Fuel Cells and Bioremediation
- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- Wastewater Treatment and Nitrogen Removal
- Probiotics and Fermented Foods
- Legume Nitrogen Fixing Symbiosis
- Bacteriophages and microbial interactions
- Aquaculture disease management and microbiota
- Porphyrin Metabolism and Disorders
- Plant-Microbe Interactions and Immunity
- Metal Extraction and Bioleaching
- Chromium effects and bioremediation
- Biochemical and biochemical processes
- Gut microbiota and health
- Photoreceptor and optogenetics research
- Plant Pathogenic Bacteria Studies
- Immune Cell Function and Interaction
- Enzyme Catalysis and Immobilization
- Light effects on plants
- Arsenic contamination and mitigation
Lawrence Berkeley National Laboratory
2012-2022
Siksha O Anusandhan University
2021
University of California, Santa Cruz
2007-2014
University of Illinois Urbana-Champaign
2007
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the was developed for two-group comparisons match independent, "control" versus "disease" experimental design. Here, we introduce an enhanced interface that enables users perform dependent (paired) comparisons, meta-analysis, multigroup with comprehensive statistical output interactive visualization tools. Newly...
Harnessing the microbiota for beneficial outcomes is limited by our poor understanding of constituent bacteria, as functions most their genes are unknown. Here, we measure growth a barcoded transposon mutant library gut commensal Bacteroides thetaiotaomicron on 48 carbon sources, in presence 56 stress-inducing compounds, and during mono-colonization gnotobiotic mice. We identify 516 with specific phenotype under only one or few conditions, enabling informed predictions gene function. For...
Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine genetic basis of energy conservation, we measured fitness thousands pooled mutants Desulfovibrio alaskensis G20 during growth 12 different combinations electron donors acceptors. We show that ion pumping by ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation not possible. The uncharacterized complex...
ABSTRACT The genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity experimental data and genetic tools. To meet this challenge, we generated an archived library 15,477 mapped transposon insertion mutants in the bacterium Desulfovibrio alaskensis G20. demonstrate utility individual mutants, profiled gene expression six regulatory genes used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays...
The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many which are contaminated with nitrate, as well uranium various metals. nitrate ranges 0.1 μM to 230 mM <0.2 nM 580 μM, respectively. Almost all examined had significantly greater median a subset that highly (≥126 nM). They included cadmium, manganese, cobalt, 1,300- 2,700-fold higher. A notable exception, however, was Mo, lower...
Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, development suitable TnSeq strategy given bacterium can be costly and time-consuming. To meet this challenge, we describe part-based constructing libraries hundreds transposon delivery vectors, which term "magic pools." Within magic pool, each vector has different combination upstream sequences (promoters ribosome binding sites) antibiotic...
Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization, especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) perform a genome-wide screen and identify key bacterial fitness of the vascular pathogen Xanthomonas campestris pv (Xcc) cauliflower plant (Brassica oleracea). This...
Summary The adaptation capability of D esulfovibrio to natural fluctuations in electron acceptor availability was evaluated by studying alaskensis strain G 20 under varying respiratory, fermentative and methanogenic coculture conditions chemostats. Transition from lactate pyruvate resulted a dramatic shift the population structure closer interspecies cell‐to‐cell interactions. Lower methane production rates than predicted input attributed redirection flow fumarate reduction. Without partner,...
Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, ketodeoxyribonate, cleaved acetyl coenzyme A (acetyl-CoA) glyceryl-CoA. have genetic evidence this pathway three genera confirmed oxidation ketodeoxyribonate vitro. In Pseudomonas simiae, expression enzymes induced by or while Paraburkholderia bryophila Burkholderia...
Summary The function of nearly half all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and assayed phenotypes across hundreds distinct conditions. From 3,903 genome-wide fitness assays, obtained 14.9 million gene phenotype measurements a for 8,487 proteins with previously unknown functions. majority hypothetical (57%) had that were either...
Synthetic microbial ecology has the potential to enhance productivity and resiliency of biotechnology processes compared approaches using single isolates. Engineering consortia is challenging; however, one approach that attracted significant attention creation synthetic obligate mutualism auxotrophic mutants depend on each other for exchange or cross-feeding metabolites. Here, we describe integration mutant library fitness profiling with mass spectrometry based exometabolomics as a method...
ABSTRACT Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report complete genome sequence and annotation of 4G11. The contains 8,421,483 bp, 7,661 predicted protein-coding genes, a total GC content 64.4%.
Abstract The genomic catalogue of the human microbiota has expanded dramatically in recent years, and insights derived from genomics vast potential to generate treatments for diseases. However, predictably harnessing beneficial outcomes is currently limited by our lack understanding physiology constituent bacteria. For instance, functions most their genes are not known. Here, we systematically measure mutant phenotypes gut commensal Bacteroides thetaiotaomicron . Using a barcoded transposon...
Sulfate-reducing bacteria such as Desulfovibrio vulgaris Hildenborough are often found in environments with limiting growth nutrients. Using lactate the electron donor and carbon source, sulfate acceptor, wild type D. shows motility on soft agar plates. We evaluated this phenotype mutants resulting from insertional inactivation of genes potentially related to motility. Our study revealed that cheA3 (DVU2072) kinase mutant was impaired ability form halos. Insertions two other cheA loci did...
Conformational changes, internal electron transfer, and CO rebinding processes in cytochrome c oxidase from Rhodobacter sphaeroides reduced to different degrees were investigated. The reactions followed using a gated optical spectrometric multichannel analyzer. Light-induced difference spectra, recorded the 350−700 nm region over 100 ns 1 s time interval, analyzed by singular value decomposition global exponential fitting. photolyzed fully enzyme showed two relaxations, ∼1 190 μs, prior 20...
Cytochrome bo3 ubiquinol oxidase from Escherichia coli catalyzes the reduction of O2 to water by ubiquinol. The reaction mechanism and role continue be a subject discussion. In this study, we report detailed kinetic scheme cytochrome with steps specific was investigated using CO flow-flash method, time-resolved optical absorption difference spectra were collected 1 μs 20 ms after photolysis. Singular value decomposition-based global exponential fitting resolved five apparent lifetimes, 22...
Cytochrome c oxidase from Rhodobacter sphaeroides is frequently used to model the more complex mitochondrial enzyme. The O(2) reduction in both enzymes generally described by a unidirectional mechanism involving sequential formation of ferrous-oxy (compound A), P(R) state, oxyferryl F form, and oxidized state. In this study we investigated reaction dioxygen with wild-type reduced R. cytochrome EQ(I-286) mutant using CO flow-flash technique. Singular value decomposition multiexponential...
The dissimilatory sulfate-reducing
The crystallization technique has been established as a cost-effective and simple approach to improve the dissolution rate oral bioavailability of poorly soluble drugs. This study was carried out effect some selected hydrophilic polymers such methyl cellulose, hydroxypropyl methylcellulose (HPMC), polyvinyl alcohol, carboxymethyl cellulose on crystal behavior properties celecoxib (CLX), common nonsteroidal anti-inflammatory drug. Structural spectral characteristics crystallized CLX have...
Abstract Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine genetic basis of energy conservation, we measured fitness thousands pooled mutants Desulfovibrio alaskensis G20 during growth 12 different combinations electron donors acceptors. We show that ion pumping by ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation not possible. The uncharacterized...
Abstract Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, development suitable TnSeq strategy given bacterium can be costly and time-consuming. To meet this challenge, we describe parts-based constructing libraries hundreds transposon delivery vectors, which term “magic pools”. Within magic pool, each vector has different combination promoters antibiotic resistance markers as well random DNA...
Abstract Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) perform a genome-wide screen and identify key bacterial fitness of the vascular pathogen Xanthomonas campestris pv. ( Xcc ) cauliflower plant Brassica...