A5015131295- Microbial Metabolic Engineering and Bioproduction
- Photosynthetic Processes and Mechanisms
- Gene Regulatory Network Analysis
- Plant responses to elevated CO2
- Plant Water Relations and Carbon Dynamics
- Biofuel production and bioconversion
- Plant and fungal interactions
- Topological and Geometric Data Analysis
- Clusterin in disease pathology
- Algal biology and biofuel production
- Process Optimization and Integration
- Protein Structure and Dynamics
- Spectroscopy and Quantum Chemical Studies
- Microbial Fuel Cells and Bioremediation
- Viral Infectious Diseases and Gene Expression in Insects
- CRISPR and Genetic Engineering
- Hydrocarbon exploration and reservoir analysis
- Natural product bioactivities and synthesis
- Enzyme Catalysis and Immobilization
- Lipid metabolism and biosynthesis
- Mycotoxins in Agriculture and Food
- Advanced Control Systems Optimization
- Atmospheric and Environmental Gas Dynamics
- Electrocatalysts for Energy Conversion
- Mitochondrial Function and Pathology
Michigan State University
2022-2025
University of Illinois Urbana-Champaign
2025
Michigan United
2023
Noble Research Institute
2018
SignificancePhotosynthesis metabolites are quickly labeled when 13CO2 is fed to leaves, but the time course of labeling reveals additional contributing processes involved in metabolic dynamics photosynthesis. The existence three such demonstrated, and a flux model developed explore characterize them. consistent with slow return carbon from cytosolic vacuolar sugars into Calvin-Benson cycle through oxidative pentose phosphate pathway. Our results provide insight how assimilation integrated...
Abstract Carbon-concentrating mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO2 around carbon-fixing enzyme rubisco, thereby increasing assimilatory flux and reducing photorespiration. Biophysical CCMs, like pyrenoid-based CCM (PCCM) Chlamydomonas reinhardtii or carboxysome systems cyanobacteria, are common aquatic microbes, but land plants appear only among hornworts. To predict likely efficiency biophysical CCMs C3 plants, we...
Engineering N2-fixing rhizobia symbiosis in cereals and enhancing association with arbuscular mycorrhizal fungi (AMF) are two strategies being pursued to improve agricultural sustainability. However, the metabolic fluxes consequent costs benefits of these a cereal crop have not been examined. We developed model describing how relative growth rate Zea mays is impacted by hypothetical rhizobium Bradyrhizobium diazoefficiens AMF Rhizophagus irregularis. found that lower N content crops makes...
In the future, plants may encounter increased light and elevated CO2 levels. How consequent alterations in photosynthetic rates will impact fluxes carbon metabolism remains uncertain. Respiration (RL) is pivotal plant balance a key parameter photosynthesis models. Understanding dynamics of RL under varying environmental conditions essential for optimizing growth agricultural productivity. However, measuring high (HLHC) poses challenges using traditional gas exchange methods. this study, we...
Abstract Motivation The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for biology and central to efficiently identifying biotechnological interventions that can address pressing industrial needs. application gene expression data improve the accuracy flux predictions using mechanistic modeling methods balance analysis (FBA) has not been previously demonstrated multi-tissue systems, despite their importance. We hypothesized method...
Carbon Concentrating Mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO
Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in most inhospitable environments on earth. At their core, these adaptations been shaped by changes numerous, interconnected pathways genes that collectively give rise emergent biological phenomena. Linking gene expression morphological outcomes remains a grand challenge biology, new approaches are needed begin address this gap. Here, we implemented...
Epichloë species (Clavicipitaceae, Ascomycota) are endophytic symbionts of many cool-season grasses. Many interactions between and their host grasses contribute to plant growth promotion, protection from pathogens insect pests, tolerance drought stress. Resistance herbivores by endophytes associated with Hordeum has been previously shown vary depending on the endophyte-grass-insect combination. We explored genetic chemotypic diversity present in wild species. analyzed seeds bogdanii, H....
Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering photosynthetic organisms. Improving existing synthetic biology tools engineer model organisms fix carbon dioxide one route overcoming limitations In this work, we describe a pipeline that enabled deletion conditionally essential gene from Shewanella oneidensis MR-1 genome. S. simple bacterial host could be used for electricity-driven conversion in future with...
Abstract Since they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in most inhospitable environments on earth. At their core, these adaptations been shaped by changes numerous, interconnected pathways genes that collectively give rise emergent biological phenomena. Linking gene expression morphological outcomes remains a grand challenge biology, new approaches are needed begin address this gap. Here, we implemented topological...
Abstract In the future, plants may encounter increased light and elevated CO 2 levels. How consequent alterations in photosynthetic rates will impact fluxes carbon metabolism remains uncertain. Respiration ( R L ) is pivotal plant balance a key parameter photosynthesis models. Understanding dynamics of under varying environmental conditions essential for optimizing growth agricultural productivity. However, measuring high (HLHC) poses challenges using traditional gas exchange methods. this...
Abstract The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. ’s cellular affinity for CO 2 is stronger than rubisco . This provided further evidence operates CCM while lacking structures and functions characteristic of CCMs other organisms. To test how such could function, created mathematical compartmental model simple distinct from those previously...
Abstract The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. merolae's cellular affinity for CO2 is stronger than the of rubisco CO2. This finding provided additional evidence operates CCM while lacking structures and functions characteristic CCMs other organisms. To test how such could function, created mathematical compartmental model simple CCM,...
The modeling of rates biochemical reactions-fluxes-in metabolic networks is widely used for both basic biological research and biotechnological applications. A number different methods have been developed to estimate predict fluxes, including kinetic constraint-based (Metabolic Flux Analysis flux balance analysis) approaches. Although resources exist teaching these individually, to-date no teach approaches in an integrative way that equips learners with understanding each paradigm, how they...
13C-Metabolic Flux Analysis (13C-MFA) and Balance (FBA) are widely used to investigate the operation of biochemical networks in both biological biotechnological research. Both these methods use metabolic reaction network models metabolism operating at steady state, so that rates (fluxes) levels intermediates constrained be invariant. They provide estimated (MFA) or predicted values fluxes through vivo, which cannot measured directly. A number approaches have been taken test reliability...
Abstract Motivation The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for biology and central to efficiently identifying biotechnological interventions that can address pressing industrial needs. application gene expression data improve the accuracy flux predictions using mechanistic modeling methods Flux Balance Analysis (FBA) has not been previously demonstrated multi-tissue systems, despite their importance. We hypothesized...
Abstract The modeling of rates biochemical reactions – fluxes in metabolic networks is widely used for both basic biological research and biotechnological applications. A number different methods have been developed to estimate predict fluxes, including kinetic constraint-based (Metabolic Flux Analysis Balance Analysis) approaches. Although resources exist teaching these individually, to-date no teach approaches an integrative way that equips learners with understanding each paradigm, how...