A5054775079- Plant nutrient uptake and metabolism
- Plant responses to water stress
- Microbial Metabolic Engineering and Bioproduction
- Plant Molecular Biology Research
- Gene Regulatory Network Analysis
- Crop Yield and Soil Fertility
- Rice Cultivation and Yield Improvement
- Legume Nitrogen Fixing Symbiosis
- bioluminescence and chemiluminescence research
- Plant Water Relations and Carbon Dynamics
- Plant Stress Responses and Tolerance
- Potato Plant Research
- Cell Image Analysis Techniques
- Pancreatic function and diabetes
- Greenhouse Technology and Climate Control
- Plant Micronutrient Interactions and Effects
- Bioinformatics and Genomic Networks
- Soybean genetics and cultivation
- Plant Virus Research Studies
- Tree Root and Stability Studies
- Statistical and Computational Modeling
- Lipid metabolism and biosynthesis
- Advanced Proteomics Techniques and Applications
- Bacterial Genetics and Biotechnology
- Bacillus and Francisella bacterial research
Pennsylvania State University
2020-2024
University of Nottingham
2013-2022
European Bioinformatics Institute
2011-2014
Wellcome Trust
2013-2014
Loughborough University
2013
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models biological processes. A large set curated to verify both correspondence the process that model seeks represent, and reproducibility simulation results as described in corresponding peer-reviewed publication. Many submitted database are annotated, cross-referencing its components external resources such records, terms from controlled vocabularies ontologies. comprises two main branches: one composed derived...
Abstract Background Suboptimal water and nutrient availability are primary constraints in global agriculture. Root anatomy plays key roles soil resource acquisition. In this article we summarize evidence that root anatomical phenotypes present opportunities for crop breeding. Scope influence acquisition by regulating the metabolic cost of exploration, exploitation rhizosphere, penetration hard domains, axial radial transport water, interactions with biota including mycorrhizal fungi,...
Diabetes is a chronic and complex multifactorial disease caused by persistent hyperglycemia for which underlying pathogenesis still not completely understood. The mathematical modeling of glucose homeostasis, diabetic condition, its associated complications rapidly growing provides new insights into the mechanisms involved. Here, we discuss contributions to diabetes field over past five decades, highlighting areas where more focused research required.CPT: Pharmacometrics & Systems...
Significance Multiseriate cortical sclerenchyma (MCS) is a root anatomical phenotype with utility in environments mechanical impedance. The MCS characterized by small cells thick walls outer tissue. Genotypes were associated greater lignin concentration, tensile strength, and tip bending force compared to non-MCS genotypes. improved depth plant growth under impedance the greenhouse field. heritable genetically controlled. identification of phenes their genetic control may be an important...
Abstract Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing benefits for soil exploration among root architectural phenes is beneficial under suboptimal availability. An enhanced implementation functional–structural model OpenSimRoot integrated with ORYZA_v3 crop was used to evaluate utility combinations phenes, namely nodal angle, proportion smaller diameter roots, number; L‐type...
Root anatomy is an important determinant of root metabolic costs, soil exploration, and resource capture. varies substantially within among plant species. RootSlice a multicellular functional-structural model developed to facilitate the analysis understanding anatomical phenotypes. can capture phenotypically accurate in three dimensions different classes developmental zones, both monocotyledonous dicotyledonous Several case studies are presented illustrating capabilities model. For maize...
The ability to grow crops under low-water conditions is a significant advantage in relation global food security. Bambara groundnut an underutilised crop grown by subsistence farmers Africa and known survive regions of water deficit. This study focuses on the analysis transcriptomic changes two bambara landraces response dehydration stress. A cross-species hybridisation approach based Soybean Affymetrix GeneChip array has been employed. differential gene expression water-limited treatment,...
Pearl millet is a key food security grain crop in the world's drylands due to its tolerance abiotic stresses. However, yield remains low and negatively impacted by climate change. Root phenes are potential targets improve productivity resilience environmental stress. sheer number of combinations resulting from interactions multiple challenge for empirical research. In silico approaches plausible alternative assess utility different phene varying states over diverse contexts. Here, we...
The bacterial Lux system is used as a gene expression reporter. It fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for cells, it has also been adapted eukaryotic can be whole cell biosensors, or in real time with live animals without the need euthanasia. However, correct interpretation of bioluminescent data limited: bioluminescence different from because nonlinear molecular enzyme dynamics system. We have computational approach that, first...
Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding the molecular mechanisms underlying uptake by investigating transcriptional dynamics two regulators: Ubiquitin ligase PHO2 long non-coding RNA IPS1. Temporal measurements levels been...
Drought is a primary constraint to crop yields and climate change expected increase the frequency severity of drought stress in future. It has been hypothesized that crops can be made more resistant better able sequester atmospheric carbon soil by selecting appropriate root phenotypes. We introduce OpenSimRoot_v2, an upgraded version functional-structural plant/soil model OpenSimRoot, use it test utility maize phenotype with fewer steeper axial roots, reduced lateral branching density,...
SUMMARY The root is a well‐studied example of cell specialisation, yet little known about the metabolism that supports transport functions and growth different types. To address this, we used computational modelling to study in elongation zone maize lateral root. A functional‐structural model captured cell‐anatomical features modelled how they changed as elongated. From these data, derived constraints for flux balance analysis predicted metabolic fluxes 11 concentric rings cells We...
Abstract The BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published, peer-reviewed quantitative models of biological processes.In this poster we provide an overview its capabilities, as well the curation annotation process with two use cases concerning blood coagulation glucose homeostasis.
Abstract The bacterial Lux system is used as a gene expression reporter. It fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for cells, it has been adapted eukaryotic can be whole cell biosensors, or in real time with live animals without the need slaughter. However, correct interpretation of bioluminescent data limited: bioluminescence different from because nonlinear molecular enzyme dynamics system. We have modelling approach that, first...