scholarly journals Minimal Genome Design Algorithms Using Whole-Cell Models

Author(s):  
Joshua Rees-Garbutt ◽  
Oliver Chalkley ◽  
Claire Grierson ◽  
Lucia Marucci
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Joshua Rees-Garbutt ◽  
Oliver Chalkley ◽  
Sophie Landon ◽  
Oliver Purcell ◽  
Lucia Marucci ◽  
...  
Keyword(s):  

Author(s):  
GEORGE S. B. WILLIAMS ◽  
MARCO A. HUERTAS ◽  
GREGORY D. SMITH ◽  
M. SALEET JAFRI ◽  
ERIC A. SOBIE
Keyword(s):  

2015 ◽  
Vol 308 (5) ◽  
pp. H510-H523 ◽  
Author(s):  
Xiao Wang ◽  
Seth H. Weinberg ◽  
Yan Hao ◽  
Eric A. Sobie ◽  
Gregory D. Smith

Population density approaches to modeling local control of Ca2+-induced Ca2+ release in cardiac myocytes can be used to construct minimal whole cell models that accurately represent heterogeneous local Ca2+ signals. Unfortunately, the computational complexity of such “local/global” whole cell models scales with the number of Ca2+ release unit (CaRU) states, which is a rapidly increasing function of the number of ryanodine receptors (RyRs) per CaRU. Here we present an alternative approach based on a Langevin description of the collective gating of RyRs coupled by local Ca2+ concentration ([Ca2+]). The computational efficiency of this approach no longer depends on the number of RyRs per CaRU. When the RyR model is minimal, Langevin equations may be replaced by a single Fokker-Planck equation, yielding an extremely compact and efficient local/global whole cell model that reproduces and helps interpret recent experiments that investigate Ca2+ homeostasis in permeabilized ventricular myocytes. Our calculations show that elevated myoplasmic [Ca2+] promotes elevated network sarcoplasmic reticulum (SR) [Ca2+] via SR Ca2+-ATPase-mediated Ca2+ uptake. However, elevated myoplasmic [Ca2+] may also activate RyRs and promote stochastic SR Ca2+ release, which can in turn decrease SR [Ca2+]. Increasing myoplasmic [Ca2+] results in an exponential increase in spark-mediated release and a linear increase in nonspark-mediated release, consistent with recent experiments. The model exhibits two steady-state release fluxes for the same network SR [Ca2+] depending on whether myoplasmic [Ca2+] is low or high. In the later case, spontaneous release decreases SR [Ca2+] in a manner that maintains robust Ca2+ sparks.


2015 ◽  
Vol 11 (5) ◽  
pp. e1004096 ◽  
Author(s):  
Jonathan R. Karr ◽  
Alex H. Williams ◽  
Jeremy D. Zucker ◽  
Andreas Raue ◽  
Bernhard Steiert ◽  
...  

2012 ◽  
Vol 41 (D1) ◽  
pp. D787-D792 ◽  
Author(s):  
Jonathan R. Karr ◽  
Jayodita C. Sanghvi ◽  
Derek N. Macklin ◽  
Abhishek Arora ◽  
Markus W. Covert

2017 ◽  
Vol 112 (3) ◽  
pp. 573a
Author(s):  
Zhaleh Ghaemi ◽  
Zaida Luthey-Schulten

2019 ◽  
Author(s):  
Frederico Chaves Carvalho ◽  
Paulo Eduardo Ambrósio

The use of whole-cell models in research has the potential to be a powerful tool for scientific discovery, allowing researchers to test hypotheses faster than using in-vitro or in vivo methods. Such models can be considered the equivalent of Computer Aided Design for Biology. However, given their complexity, it is still difficult to employ them as an instrument in investigations. In order to solve this problem, we are developing a framework with the purpose to guide and help scientists through the process of creating whole-cell models faster, enabling them to use these tools as part of their research. This paper brings details of the early stages of the framework’s development process


2013 ◽  
Vol 14 (1) ◽  
pp. 253 ◽  
Author(s):  
Ruby Lee ◽  
Jonathan R Karr ◽  
Markus W Covert

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