Joshua A. M. Kaste
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View article: The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis
The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis Open
In the future, plants may encounter increased light and elevated CO2 levels. How consequent alterations in photosynthetic rates will impact fluxes in photosynthetic carbon metabolism remains uncertain. Respiration in light (R
View article: Metabolic modeling predicts synergistic growth benefits between arbuscular mycorrhizal fungi and theoretical N<sub>2</sub>-fixing rhizobia symbiosis in maize
Metabolic modeling predicts synergistic growth benefits between arbuscular mycorrhizal fungi and theoretical N<sub>2</sub>-fixing rhizobia symbiosis in maize Open
Engineering a novel N 2 -fixing rhizobia symbiosis in cereal crops is a strategy being pursued to improve agricultural sustainability. However, if such a symbiosis were introduced, it would have to be economically viable in the context of …
View article: Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism
Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism Open
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 t…
View article: Reaction-diffusion modeling provides insights into biophysical carbon-concentrating mechanisms in land plants
Reaction-diffusion modeling provides insights into biophysical carbon-concentrating mechanisms in land plants Open
Carbon-concentrating mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO2 around the carbon-fixing enzyme rubisco, thereby increasing CO2 assimilatory flux and reducing photorespi…
View article: Modeling With Uncertainty Quantification Identifies Essential Features of a Non-Canonical Algal Carbon-Concentrating Mechanism
Modeling With Uncertainty Quantification Identifies Essential Features of a Non-Canonical Algal Carbon-Concentrating Mechanism Open
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 CO 2 is stronger…
View article: The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis
The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis Open
In the future, plants may encounter increased light and elevated CO2 levels. How consequent alterations in photosynthetic rates will impact fluxes in photosynthetic carbon metabolism remains uncertain. Respiration in light (R
View article: Biophysical carbon concentrating mechanisms in land plants: insights from reaction-diffusion modeling
Biophysical carbon concentrating mechanisms in land plants: insights from reaction-diffusion modeling Open
Carbon Concentrating Mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO 2 around the carbon-fixing enzyme rubisco, thereby increasing CO 2 assimilatory flux and reducing photores…
View article: Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants
Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants Open
Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by ch…
View article: Model validation and selection in metabolic flux analysis and flux balance analysis
Model validation and selection in metabolic flux analysis and flux balance analysis Open
13C‐Metabolic Flux Analysis (13C‐MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models…
View article: Integrative teaching of metabolic modeling and flux analysis with interactive python modules
Integrative teaching of metabolic modeling and flux analysis with interactive python modules Open
The modeling of rates of biochemical reactions—fluxes—in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and pre…
View article: Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling
Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling Open
Motivation The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for systems biology and central to efficiently identifying biotechnological interventions that can address pressing in…
View article: Model Validation and Selection in Metabolic Flux Analysis and Flux Balance Analysis
Model Validation and Selection in Metabolic Flux Analysis and Flux Balance Analysis Open
13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction netwo…
View article: Integrative Teaching of Metabolic Modeling and Flux Analysis with Interactive Python Modules
Integrative Teaching of Metabolic Modeling and Flux Analysis with Interactive Python Modules Open
The modeling of rates of biochemical reactions – fluxes – in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and…
View article: Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in <i>Shewanella oneidensis</i> MR-1
Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in <i>Shewanella oneidensis</i> MR-1 Open
Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix…
View article: The topological shape of gene expression across the evolution of flowering plants
The topological shape of gene expression across the evolution of flowering plants Open
Since they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in nume…
View article: Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling
Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling Open
Motivation The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for systems biology and central to efficiently identifying biotechnological interventions that can address pressing in…
View article: Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies
Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies Open
Significance Photosynthesis metabolites are quickly labeled when 13 CO 2 is fed to leaves, but the time course of labeling reveals additional contributing processes involved in the metabolic dynamics of photosynthesis. The existence of thr…
View article: Molecular identification and characterization of endophytes from uncultivated barley
Molecular identification and characterization of endophytes from uncultivated barley Open
Epichloë species (Clavicipitaceae, Ascomycota) are endophytic symbionts of many cool-season grasses. Many interactions between Epichloë and their host grasses contribute to plant growth promotion, protection from many pathoge…