Towards a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly

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.

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Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2013.0389 ◽

2014 ◽

Vol 372 (2021) ◽

pp. 20130389 ◽

Cited By ~ 45

Author(s):

Xuejin Li ◽

Zhangli Peng ◽

Huan Lei ◽

Ming Dao ◽

George Em Karniadakis

Keyword(s):

Blood Cell ◽

Red Blood Cell ◽

Cell Model ◽

Microfluidic Channel ◽

Scale Model ◽

Cross Sectional ◽

Whole Cell ◽

Multi Scale ◽

Rbc Membrane ◽

Two Component

This study is partially motivated by the validation of a new two-component multi-scale cell model we developed recently that treats the lipid bilayer and the cytoskeleton as two distinct components. Here, the whole cell model is validated and compared against several available experiments that examine red blood cell (RBC) mechanics, rheology and dynamics. First, we investigated RBC deformability in a microfluidic channel with a very small cross-sectional area and quantified the mechanical properties of the RBC membrane. Second, we simulated twisting torque cytometry and compared predicted rheological properties of the RBC membrane with experimental measurements. Finally, we modelled the tank-treading (TT) motion of a RBC in a shear flow and explored the effect of channel width variation on the TT frequency. We also investigated the effects of bilayer–cytoskeletal interactions on these experiments and our simulations clearly indicated that they play key roles in the determination of cell membrane mechanical, rheological and dynamical properties. These simulations serve as validation tests and moreover reveal the capabilities and limitations of the new whole cell model.

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cAMP-activated anion conductance is associated with expression of CFTR in neonatal mouse cardiac myocytes

AJP Cell Physiology ◽

10.1152/ajpcell.2000.278.2.c436 ◽

2000 ◽

Vol 278 (2) ◽

pp. C436-C450 ◽

Cited By ~ 18

Author(s):

Alan S. Lader ◽

Yihan Wang ◽

G. Robert Jackson ◽

Steven C. Borkan ◽

Horacio F. Cantiello

Keyword(s):

Monoclonal Antibody ◽

Cardiac Myocytes ◽

Single Channel ◽

Cell Model ◽

Neonatal Mouse ◽

Intracellular Camp ◽

Mouse Heart ◽

Whole Cell ◽

Anion Conductance ◽

Camp Stimulation

In this study, patch-clamp techniques were applied to cultured neonatal mouse cardiac myocytes (NMCM) to assess the contribution of cAMP stimulation to the anion permeability in this cell model. Addition of either isoproterenol or a cocktail to raise intracellular cAMP increased the whole cell currents of NMCM. The cAMP-dependent conductance was largely anionic, as determined under asymmetrical (low intracellular) Cl− conditions and symmetrical Cl−in the presence of various counterions, including Na+, Mg2+, Cs+, and N-methyl-d-glucamine. Furthermore, the cAMP-stimulated conductance was also permeable to ATP. The cAMP-activated currents were inhibited by diphenylamine-2-carboxylate, glibenclamide, and an anti-cystic fibrosis transmembrane conductance regulator (CFTR) monoclonal antibody. The anti-CFTR monoclonal antibody failed, however, to inhibit an osmotically activated anion conductance, indicating that CFTR is not linked to osmotically stimulated currents in this cell model. Immunodetection studies of both neonatal mouse heart tissue and cultured NMCM revealed that CFTR is expressed in these preparations. The implication of CFTR in the cAMP-stimulated Cl−- and ATP-permeable conductance was further verified with NMCM of CFTR knockout mice [ cftr(−/−)] in which cAMP stimulation was without effect on the whole cell currents. In addition, stimulation with protein kinase A and ATP induced Cl−-permeable single-channel activity in excised, inside-out patches from control, but not cftr(−/−) NMCM. The data in this report indicate that cAMP stimulation of NMCM activates an anion-permeable conductance with functional properties similar to those expected for CFTR, thus suggesting that CFTR may be responsible for the cAMP-activated conductance. CFTR may thus contribute to the permeation and/or regulation of Cl−- and ATP-permeable pathways in the developing heart.

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Abstract 19749: Cardiac-specific Deletion of Caveolin-3 Delays Repolarization and Increases Susceptibility to Ventricular Arrhythmia

Circulation ◽

10.1161/circ.132.suppl_3.19749 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Yogananda S Markandeya ◽

Li Feng ◽

Vignesh Ramchandran ◽

Ravi Vaidyanathan ◽

Jabe Best ◽

...

Keyword(s):

Contractile Function ◽

Cell Model ◽

Histopathological Examination ◽

Scaffolding Protein ◽

Macromolecular Complex ◽

Cardiac Structure ◽

Qtc Interval ◽

Long Qt ◽

Whole Cell ◽

Significant Difference

Caveolin-3 (Cav-3) is an essential scaffolding protein for formation of caveolae in muscle cells. Cav-3 is part of a macromolecular complex including several ion channels. Mutations in Cav-3 have been associated with the inherited long QT syndrome as well as a variety of skeletal myopathies. To investigate the role of Cav-3 in heart and whether loss of function of Cav-3 explains the long QT phenotype, we generated cardiac-specific, inducible Cre-lox Cav-3 knockout mice. 8 week old mice were treated with tamoxifen in the chow to induce cardiac-specific recombination. Western blot analysis and transmitted electron microscopy demonstrated a graded loss of Cav-3 and caveolae in Cav-3 KO heterozygous mice (Cav-3-/+), Cav-3 KO homozygous mice (Cav-3-/-) relative to the littermate controls mice (WT). Echocardiography revealed no significant difference in %EF, %FS, LV chamber dimensions, and LV wall thickness between the different genotypes. Histopathological examination demonstrated no significant difference in HW/BW ratio, cardiac structure or fibrosis comparing Cav-3-/- and WT mice. Telemetry ECG recordings revealed a significant increase in QTc interval Cav-3-/- (68.5±7 ms) compared to WT (54.83±6 ms). Whole cell patch clamp analysis from isolated ventricular myocytes indicated a progressive increase in action potential duration (APD) with loss of Cav-3: WT (APD50: 4.7 ± 1ms; APD90: 28.0±3 ms; n=9); Cav-3-/+(APD50: 10.3±2 ms; APD90: 42.4±3 ms; n=13), Cav-3-/- (APD50: 32.4±6ms; APD90: 97.4±7ms; n=12). Whole cell voltage clamp measurements from Cav-3-/- revealed increased late INa, decrease in ICa,L, Ito,Iss current density without altering peak INa compared to WT cells, and these current changes were adequate to explain the increased APD based on computational representation using the Morotti et al. mouse ventricular cell model. Intracardiac programmed electrical stimulation (ventricular burst pacing) induced VT/Vfib in 8 out of 9 Cav3-/- but none of WT mice (0/5). Our results demonstrate that loss of Cav-3 and caveolae in adult mice does not alter cardiac structure or contractile function but leads to prolonged APD, an increased in QTc, and increased susceptibility to ventricular arrhythmias.

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Multiscale models quantifying yeast physiology: towards a whole-cell model

Trends in Biotechnology ◽

10.1016/j.tibtech.2021.06.010 ◽

2021 ◽

Author(s):

Hongzhong Lu ◽

Eduard J. Kerkhoven ◽

Jens Nielsen

Keyword(s):

Cell Model ◽

Multiscale Models ◽

Whole Cell ◽

Yeast Physiology

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Whole yeast model: what and why

10.7287/peerj.preprints.27327v1 ◽

2018 ◽

Author(s):

Pasquale Palumbo ◽

Marco Vanoni ◽

Federico Papa ◽

Stefano Busti ◽

Lilia Alberghina

Keyword(s):

Life Science ◽

Cell Model ◽

Model Organism ◽

Science Research ◽

Cellular Functions ◽

Cellular Division ◽

Whole Cell ◽

Proposed Model ◽

Cell Modeling ◽

Single Input

One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex molecular interactions within biological systems and to accelerate discoveries. Within this framework, a need exists to integrate different mathematical tools in order to develop quantitative models of entire organisms, i.e. whole-cell models. This note presents a first attempt to show the feasibility of such a task for the budding yeast Saccharomyces cerevisiae, a model organism for eukaryotic cells: the proposed model refers to the main cellular activities like metabolism, growth and cycle in a modular fashion, therefore allowing to treat them separately as single input/output modules, as well as to interconnect them in order to build the backbone of a coarse-grain whole cell model. The model modularity allows to substitute a low granularity module with one with a finer grain, whenever molecular details are required to correctly reproduce specific experiments. Furthermore, by properly setting the cellular division, simulations of cell populations are achieved, able to deal with protein distributions. Whole cell modeling will help understanding logic of cell resilience.

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Understanding metabolic behaviour in whole-cell model output

10.1101/2020.08.19.257147 ◽

2020 ◽

Author(s):

Sophie Landon ◽

Oliver Chalkley ◽

Gus Breese ◽

Claire Grierson ◽

Lucia Marucci

Keyword(s):

Drug Testing ◽

Graphical Representation ◽

Cell Model ◽

Single Gene ◽

Detailed Knowledge ◽

Metabolic Reaction ◽

Model Output ◽

Analysis Pipeline ◽

Whole Cell ◽

Gene Knockouts

SummaryWhole-cell modelling is a newly expanding field that has many applications in lab experiment design and predictive drug testing. Although whole-cell model output contains a wealth of information, it is complex and high dimensional, thus hard to interpret. Here, we present an analysis pipeline that combines machine learning, dimensionality reduction and network analysis to interpret and visualise metabolic reaction fluxes from a set of single gene knockouts simulated in the Mycoplasma genitalium whole-cell model. We found that the reaction behaviours show trends that correlate with phenotypic classes of the simulation output, highlighting particular cellular subsystems that malfunction after gene knockouts. From a graphical representation of the metabolic network, we saw that there is a set of reactions that can be used as markers of a phenotypic class, showing their importance within the network. Our analysis pipeline can support the understanding of the complexity of in silico cells without detailed knowledge of the constituent parts, which can help to understand the effects of gene knockouts, and, as whole-cell models become more widely built and used, aid genome design.

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Designing Minimal Genomes Using Whole-Cell Models

10.1101/344564 ◽

2018 ◽

Cited By ~ 4

Author(s):

Joshua Rees ◽

Oliver Chalkley ◽

Sophie Landon ◽

Oliver Purcell ◽

Lucia Marucci ◽

...

Keyword(s):

In Silico ◽

Genome Engineering ◽

Cell Model ◽

Mycoplasma Genitalium ◽

Computational Design ◽

Functional Assay ◽

Proof Of Concept ◽

Computational Tools ◽

Whole Cell ◽

Genome Design

AbstractIn the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay, the cell either replicates or not. We used the first (and currently only published) whole-cell model, for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in-silico minimal genomes smaller than JCVI-Syn3.0, a bacteria with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essentiality genes, 18 high essentiality genes, and produced evidence for at least two Mycoplasma genitalium in-silico minimal genomes. This work brings combined computational and laboratory genome engineering a step closer.

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