Zhang 2024 - Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont
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ABSTRACT:
SUBMITTER: 
Shan Zhang
PROVIDER: MODEL2407300002 | BioModels | 2024-11-13
REPOSITORIES: BioModels
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Project description:Mating of budding yeast cells is a model system for studying cell-cell interactions. Haploid yeast cells secrete mating pheromones that are sensed by the partner which responds by growing a mating projection toward the source. The two projections meet and fuse to form the diploid. Successful mating relies on precise coordination of dynamic extracellular signals, signaling pathways, and cell shape changes in a noisy background. It remains elusive how cells mate accurately and efficiently in a natural multi-cell environment. Here we present the first stochastic model of multiple mating cells whose morphologies are driven by pheromone gradients and intracellular signals. Our novel computational framework encompassed a moving boundary method for modeling both a-cells and ?-cells and their cell shape changes, the extracellular diffusion of mating pheromones dynamically coupled with cell polarization, and both external and internal noise. Quantification of mating efficiency was developed and tested for different model parameters. Computer simulations revealed important robustness strategies for mating in the presence of noise. These strategies included the polarized secretion of pheromone, the presence of the ?-factor protease Bar1, and the regulation of sensing sensitivity; all were consistent with data in the literature. In addition, we investigated mating discrimination, the ability of an a-cell to distinguish between ?-cells either making or not making ?-factor, and mating competition, in which multiple a-cells compete to mate with one ?-cell. Our simulations were consistent with previous experimental results. Moreover, we performed a combination of simulations and experiments to estimate the diffusion rate of the pheromone a-factor. In summary, we constructed a framework for simulating yeast mating with multiple cells in a noisy environment, and used this framework to reproduce mating behaviors and to identify strategies for robust cell-cell interactions.
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Project description:Modelo_mod3_032020.m is a Matlab code used for the simulation of the growth curve of Antarctic thraustochytrid Oblongichytrium sp. RT2316-13.
The model is based on the genome scale model adapted for the strain that is found in the Excel file ExcelAurant_28102019.xlsx.
Flux balance analysis is used to predict the specific growth rate of the biomass, specific synthesis of neutral lipids and specific consumption rate of the nutrients.
The code crea_modelo.m transform the excel file into the array model_T.mat used in by Modelo_mod3_032020.m
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