A5001212028- Plant Gene Expression Analysis
- Plant Molecular Biology Research
- Biofuel production and bioconversion
- Gene Regulatory Network Analysis
- Plant nutrient uptake and metabolism
- Lignin and Wood Chemistry
- Smart Agriculture and AI
- Plant Stress Responses and Tolerance
- Spectroscopy and Chemometric Analyses
- Microbial Metabolic Engineering and Bioproduction
- Photosynthetic Processes and Mechanisms
- Light effects on plants
- Pharmaceutical and Antibiotic Environmental Impacts
- Plant Micronutrient Interactions and Effects
- Leaf Properties and Growth Measurement
- Biochemical and biochemical processes
- Control Systems and Identification
- Numerical Methods and Algorithms
- Sensor Technology and Measurement Systems
- Digital Filter Design and Implementation
- Advanced Control Systems Optimization
- Gene expression and cancer classification
- Plant Reproductive Biology
- Remote Sensing in Agriculture
- Advanced Fluorescence Microscopy Techniques
North Carolina State University
2015-2024
North Central State College
2010-2022
American Electric Power (United States)
2018
University of Denver
2017
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in formation Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to affecting properties. We perturb these genes integrate transcriptomic, proteomic, fluxomic phenomic data 221 lines...
The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity lignin, biopolymer in wood that is recalcitrant to chemical enzymatic degradation. Here, we show multiplex CRISPR editing enables precise woody feedstock design combinatorial improvement lignin composition properties. By assessing every possible combination 69,123 multigenic strategies 21 biosynthesis genes, deduced seven different genome targeting concurrent...
The quality evaluation of sweetpotatoes is utmost importance during postharvest handling as it significantly impacts consumer satisfaction, nutritional value, and market competitiveness. This study presents an innovative approach that integrates explainable artificial intelligence (AI) with hyperspectral imaging to enhance the assessment three important attributes in sweetpotatoes, i.e., dry matter content, soluble solid firmness. Sweetpotato samples different varieties, including "Bayou...
We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, comprehensive study was performed to obtain reaction inhibition parameters all based on functional recombinant proteins. A total 104 Michaelis-Menten 85 were derived from these enzymes. Through mass spectrometry, we obtained absolute quantities in This extensive experimental data...
Significance We developed a computational pipeline that uses gene expression datasets for inferring relationships among genes and predicting their importance. showed the capacity of our to integrate spatial temporal transcriptional improves performance inference algorithms. The combination this with Arabidopsis stem cell-specific data resulted in networks capture regulations cell-enriched cells throughout root development. Our combined approach molecular biology, mathematical led successful...
As a step toward predictive modeling of flux through the pathway monolignol biosynthesis in stem differentiating xylem Populus trichocarpa, we discovered that two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact vivo vitro to form heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, mass spectrometry. The tetramer composed three subunits one 4CL5. 4CL5...
Abstract Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play crucial role cell renewal, regeneration, organization. A number stem type-specific genes have known maintenance, identity, and/or division. Yet, how expressed across different types, referred to here as stem-cell-ubiquitous genes, contribute regulation is less understood. Here, we find that, Arabidopsis root, gene, TESMIN-LIKE CXC2 (TCX2),...
Abstract 4-Coumaric acid:coenzyme A ligase (4CL) is involved in monolignol biosynthesis for lignification plant cell walls. It ligates coenzyme (CoA) with hydroxycinnamic acids, such as 4-coumaric and caffeic into hydroxycinnamoyl-CoA thioesters. The ligation ensures the activated state of acid reduction monolignols. In Populus spp., it has long been thought that one monolignol-specific 4CL involved. Here, we present evidence two 4CLs, Ptr4CL3 Ptr4CL5, trichocarpa. ortholog reported many...
In this study, the distribution of steroid hormones, phytoestrogens, and estrogenic activity was thoroughly characterized within anaerobic waste lagoon a typical commercial swine sow operation. Three independent rounds sampling were conducted in June 2009, April 2010, February 2011. Thirty-seven analytes slurry sludge assessed using LC/MS-MS, yeast estrogen screen used to determine activity. Of hormone analytes, steroidal estrogens more abundant than androgens or progesterone, with estrone...
The inflow, transformation, and attenuation of natural steroid hormones phytoestrogens estrogenic activity were assessed across the lagoon/sprayfield system a prototypical commercial swine sow operation. Free conjugated (estrogens, androgens, progesterone) detected in urine feces sows reproductive stages, with progesterone being most abundant hormone. Excreta also contained indicative soy-based diet, particularly, daidzein, genistein, equol. During storage barn pits anaerobic lagoon,...
Insight into biological stress regulatory pathways can be derived from high-throughput transcriptomic data using computational algorithms. These algorithms integrated a approach to provide specific testable predictions that answer questions of interest. This review conceptually organizes wide variety developed classification system based on desired type output predictions. is then used as structure describe completed approaches in the literature, with focus project goals, overall path...
Abstract A key remit of the NSF ‐funded “Arabidopsis Research and Training for 21 st Century” ( ART ‐21) Coordination Network has been to convene a series workshops with community members explore issues concerning research training in plant biology, including role that using Arabidopsis thaliana can play addressing those issues. first workshop focused on needs bioinformatic computational approaches biology was held 2016, recommendations from have published (Friesner et al., Plant Physiology...
Abstract Plants must tightly regulate iron (Fe) sensing, acquisition, transport, mobilization, and storage to ensure sufficient levels of this essential micronutrient. POPEYE (PYE) is an responsive transcription factor that positively regulates the deficiency response, while also repressing genes for maintaining homeostasis. However, little known about how PYE plays such contradictory roles. Under iron-deficient conditions, pPYE:GFP accumulates in root pericycle pPYE:PYE–GFP localized...
Consumer preference in produce, defined by shape and size, heavily influences this market. Understanding the environmental management factors that impact these features can improve a farmer's economic margins. Since sweetpotatoes are hand-harvested tend to have varying shapes sizes, result unpredictable profit Methods for predicting aesthetic characteristics of using agronomic with machine learning not been developed. Moreover, crop size agricultural data analysis is challenging due need...
Lignin is a polymer present in the secondary cell walls of all vascular plants. It known barrier to pulping and extraction high-energy sugars from cellulosic biomass. The challenge faced with predicting outcomes transgenic plants reduced lignin due part presence unique protein-protein interactions that influence regulation metabolic flux pathway. Yet, it unclear why certain have evolved create these protein complexes. In this study, we use mathematical models investigate role complex, formed...
Accurate manipulation of metabolites in monolignol biosynthesis is a key step for controlling lignin content, structure, and other wood properties important to the bioenergy biomaterial industries. A crucial component this strategy predicting how single combinatorial knockdowns specific gene transcripts influence abundance proteins, which are driving mechanisms biosynthesis. Computational models have been developed estimate protein abundances from transcript perturbations genes. The accuracy...