A5087741198- Microbial Community Ecology and Physiology
- Advanced Proteomics Techniques and Applications
- Legume Nitrogen Fixing Symbiosis
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- CRISPR and Genetic Engineering
- Plant-Microbe Interactions and Immunity
- Mycorrhizal Fungi and Plant Interactions
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Microbial Natural Products and Biosynthesis
- Botanical Research and Applications
- Mass Spectrometry Techniques and Applications
- Plant biochemistry and biosynthesis
- Plant Gene Expression Analysis
- Plant nutrient uptake and metabolism
- Biochemical and biochemical processes
- Nematode management and characterization studies
- Plant Virus Research Studies
- Bioenergy crop production and management
- Plant Stress Responses and Tolerance
- Plant Water Relations and Carbon Dynamics
- Gut microbiota and health
Oak Ridge National Laboratory
2016-2025
Houston Independent School District
2025
University of Tennessee at Knoxville
2009-2024
Vels University
2024
Laboratoire CarMeN
2022
Université Claude Bernard Lyon 1
2022
Hôpital Louis Pradel
2022
Hospices Civils de Lyon
2022
Inserm
2022
Bioenergy Life Science (United States)
2021
Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for catabolism remain unclear. Improved understanding biological process would aid our collective knowledge both carbon cycling microbial strategies valorize value-added compounds. Here, we examine modifications exoproteome three...
Carbon catabolite repression refers to the preference of microbes metabolize certain growth substrates over others in response a variety regulatory mechanisms. Such preferences are important for fitness organisms their natural environments, but may hinder performance as domesticated microbial cell factories. In Pseudomonas putida KT2440 strain engineered convert lignin-derived aromatic monomers such p-coumarate and ferulate muconate, precursor bio-based nylon other chemicals, metabolic...
Abstract Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out community-driven, multi-laboratory comparison metaproteomics: critical assessment metaproteome investigation study (CAMPI). Based well-established workflows, evaluate effect sample preparation, mass spectrometry, and bioinformatic analysis using two...
The rapidly growing industry of crop biostimulants leverages the application plant growth promoting rhizobacteria (PGPR) to promote and health. However, introducing nonnative may impact other aspects ecosystem functioning have legacy effects; these potential consequences are largely unexplored. Nontarget PGPR include changes in resident microbiomes, nutrient cycling, pollinator services, herbivores, disease suppression, organic matter persistence. Importantly, we lack knowledge whether...
Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants...
Summary RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) external (environmental) stimuli, paving the way for advances biotechnology engineer crops with improved resilience, quality productivity. In general, traditional methods analysis plants require destructive, labour‐intensive time‐consuming assays. To...
ABSTRACT Implementation of uranium bioremediation requires methods for monitoring the membership and activities subsurface microbial communities that are responsible reduction soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach simultaneously documenting strain physiology dominant Geobacter community members during in situ acetate amendment U-contaminated Rifle, CO, aquifer. Three planktonic -dominated samples were obtained from two wells down-gradient addition....
Small proteins (10–200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small has been relatively overlooked. Recent advances deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ∼2.6 million expressed sequence tag (EST) reads...
The use of woody crops for Quad-level (approx. 1 × 1018 J) energy production will require marginal agricultural lands that experience recurrent periods water stress. Populus species have the capacity to increase dehydration tolerance by lowering osmotic potential via adjustment. aim this study was investigate how inherent genetic a clone respond drought interacts with nature determine degree biochemical response.A greenhouse stress conducted on deltoides 'WV94' and resulting metabolite...
Fungi produce a wealth of pharmacologically bioactive secondary metabolites (SMs) from biosynthetic gene clusters (BGCs). It is common practice for drug discovery efforts to treat species' metabolomes as being well represented by single or small number representative genomes. However, this approach misses the possibility that intraspecific population dynamics, such adaptation environmental conditions local microbiomes, may harbor novel BGCs contribute overall niche breadth species. Using 94...
The eukaryote-specific ribosomal protein of the small subunit eS6 is phosphorylated through target rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been studied for over 50 years, its biochemical physiological significance remains controversial poorly understood. Here, we report data from
The translation of mRNA into protein is tightly regulated by the light environment as well circadian clock. Although changes in translational efficiency have been documented at level mRNA-ribosome loading, underlying mechanisms are unclear. reversible phosphorylation ribosomal small subunit 6 (RPS6) has known for forty years, but biochemical significance this event remains unclear to day. Here, we confirm using a clock-deficient strain Arabidopsis thaliana that RPS6 (RPS6-P) controlled diel...
Abstract Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary secondary metabolism in land plants. Here, we used systems biology approach to investigate global metabolic responses lignin pathway perturbations model grass Brachypodium distachyon. We identified biosynthetic protein families found that ammonia-lyases (ALs) are among most abundant proteins lignifying tissues grasses. Integrated metabolomic proteomic data...
Summary Analyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies ecosystems with low species richness. In the current study we evaluated role recombination in altering fitness chemoautotrophic bacteria their natural environment. Proteomics‐inferred genome typing (PIGT) was used to genotype dominant Leptospirillum group II populations 27 biofilms sampled from six locations Richmond Mine acid mine drainage system (Iron Mountain,...
The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge been gained of the symbionts, host remained largely unstudied. Here, we generated transcriptomes proteomes O. to better understand how this annelid gains nutrition from its it adapted physiologically symbiotic lifestyle, innate immune system recognizes responds microbiota. Key adaptations include...
Geobacter sulfurreducens PCA can reduce, sorb, and methylate mercury (Hg); however, the underlying biochemical mechanisms of these processes interdependent metabolic pathways remain unknown. In this study, shotgun proteomics was used to compare global proteome profiles between wild-type G. two mutant strains: a ΔhgcAB mutant, which is deficient in genes known be essential for Hg methylation ΔomcBESTZ five outer membrane c-type cytochromes thus impaired its ability dissimilatory metal ion...
Potent antimicrobial metabolites are produced by filamentous fungi in pure culture, but their ecological functions nature often unknown. Using an antibacterial Penicillium isolate and a cheese rind microbial community, we demonstrate that fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation global regulator, LaeA, resulted loss activity isolate. Cheese communities assembled with laeA deletion strain had significantly higher abundances than wild-type...
Cyanobacteria are the oldest form of photosynthetic life on Earth and contribute to primary production in nearly every habitat, from permafrost hot springs. Despite longstanding interest acclimation these microbes, it remains poorly understood challenging rewire. This study uses a high-density, genome-wide CRISPR interference screen examine influence gene-specific transcriptional variation growth Synechococcus sp. PCC 7002 under environmental extremes. Surprisingly, many partial knockdowns...
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