Beyond analytic solution: Analysis of FRAP experiments by spatial simulation of the forward problem.
Cowan, A.E. & Loew, L.M.
Biophys J. 2023 Jun 23;S0006-3495(23)00401-0
PUBMED:37353932/
doi: 10.1016/j.bpj.2023.06.013
VCell BioModels referenced in publication
user: les
biomodel name: FRAP_Membrane_Rel
biomodel name: FRAP_Cyt
biomodel name: FRAP_Cyt_Membrane_Binding
biomodel name: FRAP Condensate Droplet
Name: “Bacillus Spore Membrane FRAP Analysis”
Saved: Mar 1, 2023
vcell identifier: biomodel-247511065
Owned by: “dfairchild”
Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes.
Schaumburger N, Pally J, Moraru II, Kositsawat J, Kuchel GA, Blinov ML.
Frontiers in Network Physiology, 2023 May 4; 3, 1079070
PUBMED:37216041
doi: 10.3389/fnetp.2023.1079070
VCell BioModels referenced in publication
user: aging_project
biomodel name: Aging_Phenotypes
2023-05-04. The interdisciplinary team consisting of CCAM modelers Drs. Blinov and Moraru and researchers from the Center on Aging Drs. Kuchel and Kositsawat, together with former undergrad students Schaumburger and Pally published a manuscript theoretically explaining the bistability of clinical outcomes: the likelihood of an individual remaining mobile over time either increases to almost 100% or decreases to almost zero. The VCell software was extensively used for parameter scans and fitting.
Schaumburger, N., Pally, J., Moraru, […]
2023-05-01. VCell 7.5 has been released. It features parameter estimation from the latest version of COPASI; model exchange via multiple standards, including, SBML, SEDML and OMEX; parameter scans in local client simulations; and hardening of unit handling including automatic unit transformations. Full specs available https://vcell.org/run-vcell-software.
Expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide.
Korza G, DePratti S, Fairchild D, Wicander J, Kanaan J, Shames H, Nichols FC, Cowan A, Brul S, Setlow P.
Journal of Applied Microbiology. 2023 Mar 1;134(3):lxad040.
PUBMED:36841229
doi:10.1093/jambio/lxad040
VCell BioModels referenced in publication
user: dfairchild
biomodel name: Bacillus Spore Membrane FRAP Analysis
2023-03-01.VCell was used to demonstrate that expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide. Find links to the paper on our published models page.
2023-02-20. The VCell team presented a poster at the Biophysical Society Annual Meeting in San Diego (https://www.biophysics.org/2023meeting#/).
Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signalling.
Khalilimeybodi, A., Fraley, S.I. & Rangamani, P.
J Physiol. 2023 Feb;601(3): 483-515.
PUBMED:36463416
doi:10.1113/JP283966
VCell BioModels referenced in the publication
user: prangamani
biomodel name: Khalilimeybodi et al. 2022 J Physiol
2023-02-16. VCell collaborator Padmini Rangamani from University of California San Diego published a manuscript where a computational model of a mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signallingin was designed in VCell. The created system of ODEs was exported into MatLab for further simulations and processing.The model predicts context-dependent Ca2+ transient, CaMKII bistable response and frequency-dependent activation of LATS1/2 upstream regulators as mechanisms governing the Ca2+ -YAP/TAZ relationship.
Khalilimeybodi, A., Fraley, S. I., & Rangamani, […]
