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AMATH 382: Computational Modeling of Cellular SystemsPowerPoint Presentation

AMATH 382: Computational Modeling of Cellular Systems

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### AMATH 382:Computational Modeling of Cellular Systems

Dynamic modelling of biochemical, genetic, and neural networks

Introductory Lecture, Jan. 6, 2014

Dynamic biological systems -- multicellular

http://megaverse.net/chipmunkvideos/

Dynamic biological systems -- cellular

Neutrophil chasing a bacterium

http://astro.temple.edu/~jbs/courses/204lectures/neutrophil-js.html

Dynamic biological systems -- intracellular

Calcium waves in astrocytes in rat cerebral cortex

http://stke.sciencemag.org/cgi/content/full/sigtrans;3/147/tr5/DC1

Our interest: intracellular dynamics

- Metabolism: chemical reaction networks, enzyme-catalysed reactions, allosteric regulation
- Signal Transduction: G protein signalling, MAPK signalling cascade, bacterial chemotaxis, calcium oscillations.
- Genetic Networks: switches(lac operon, phage lambda lysis/lysogeny switch, engineered toggle switch), oscillators (Goodwin oscillator, circadian rhythms, cell cycle, repressilator), computation
- Electrophysiology: voltage-gated ion channels, Nernst potential, Morris-Lecar model, intercellular communication (gap junctions, synaptic transmission, neuronal circuits)

Our tools: dynamic mathematical models

- Differential Equations:models from kinetic network description, describes dynamic (not usually spatial) phenomena, numerical simulations
- Sensitivity Analysis:dependence of steady-state behaviour on internal and external conditions
- Stability Analysis:phase plane analysis, characterizing long-term behaviour (bistability, oscillations)
- Bifurcation Analysis: dependence of system dynamics on internal and external conditions

- Metabolism: chemical reaction networks, enzyme-catalysed reactions, allosteric regulation
- Signal Transduction: G protein signalling, MAPK signalling cascade, bacterial chemotaxis, calcium oscillations.
- Genetic Networks: switches(lac operon, phage lambda lysis/lysogeny switch, engineered toggle switch), oscillators (Goodwin oscillator, circadian rhythms, cell cycle, repressilator), computation
- Electrophysiology:voltage-gated ion channels, Nernst potential, Morris-Lecar model, intercellular communication (gapjunctions, synaptic transmission, neuronal circuits)

Metabolic Networks

http://www.chemengr.ucsb.edu/~gadkar/images/network_ecoli.jpg

Enzyme-Catalysed Reactions

http://www.uyseg.org/catalysis/principles/images/enzyme_substrate.gif

Allosteric Regulation

http://courses.washington.edu/conj/protein/allosteric.gif

http://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpghttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

Metabolic Networkshttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

E. Coli metabolism

KEGG: Kyoto Encyclopedia of Genes and Genomes (http://www.genome.ad.jp/kegg/kegg.html)

- Metabolismhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg: chemical reaction networks, enzyme-catalysed reactions, allosteric regulation
- Signal Transduction: G protein signalling, MAPK signalling cascade, bacterial chemotaxis, calcium oscillations.
- Genetic Networks: switches(lac operon, phage lambda lysis/lysogeny switch, engineered toggle switch), oscillators (Goodwin oscillator, circadian rhythms, cell cycle, repressilator), computation
- Electrophysiology:voltage-gated ion channels, Nernst potential, Morris-Lecar model, intercellular communication (gapjunctions, synaptic transmission, neuronal circuits)

Transmembrane receptorshttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

http://fig.cox.miami.edu/~cmallery/150/memb/fig11x7.jpg

Signal Transduction pathwayhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

Bacterial Chemotaxishttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

http://www.aip.org/pt/jan00/images/berg4.jpg

http://www.life.uiuc.edu/crofts/bioph354/flag_labels.jpg

Apoptotic Signalling pathwayhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

- Metabolismhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg: chemical reaction networks, enzyme-catalysed reactions, allosteric regulation
- Electrophysiology:voltage-gated ion channels, Nernst potential, Morris-Lecar model, intercellular communication (gapjunctions, synaptic transmission, neuronal circuits)

Simple genetic networkhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg: lac operon

- www.accessexcellence.org/ AB/GG/induction.html

Phage Lambdahttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

http://de.wikipedia.org/wiki/Bild:T4-phage.jpg

http://fig.cox.miami.edu/Faculty/Dana/phage.jpg

Lysis/Lysogeny Switchhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

http://opbs.okstate.edu/~Blair/Bioch4113/LAC-OPERON/LAMBDA%20PHAGE.GIF

Circadian Rhythmhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

http://www.molbio.princeton.edu/courses/mb427/2001/projects/03/circadian%20pathway.jpg

Large Scale Genetic Networkhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

Eric Davidson's Lab at Caltech (http://sugp.caltech.edu/endomes/)

Genetic Toggle Switchhttp://www.cm.utexas.edu/academic/courses/Spring2002/CH339K/Robertus/overheads-3/ch15_reg-glycolysis.jpg

Gardner, T.S., Cantor, C.R., and Collins, J.J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342.

http://www.cellbioed.org/articles/vol4no1/i1536-7509-4-1-19-f02.jpg

http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v420/n6912/full/nature01257_r.htmlhttp://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v420/n6912/full/nature01257_r.html

Construction of computational elements (logic gates) and cell-cell communication

Genetic circuit building blocks for cellular computation, communications, and signal processing, Weiss, Basu, Hooshangi, Kalmbach, Karig, Mehreja, Netravali. Natural Computing. 2003. Vol. 2, 47-84.

http://www.molbio.princeton.edu/research_facultymember.php?id=62

- Metabolism cell-cell communication: chemical reaction networks, enzyme-catalysed reactions, allosteric regulation

Excitable Cells cell-cell communication

Resting potential

Ion Channel

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/ExcitableCells.html

http://campus.lakeforest.edu/~light/ion%20channel.jpg

Measuring Ion Channel Activity: Patch Clamp cell-cell communication

http://www.ipmc.cnrs.fr/~duprat/neurophysiology/patch.htm

Measuring Ion Channel Activity: Voltage Clamp cell-cell communication

http://soma.npa.uiuc.edu/courses/physl341/Lec3.html

Action Potentials cell-cell communication

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/ExcitableCells.html

http://content.answers.com/main/content/wp/en/thumb/0/02/300px-Action-potential.png

voltage gated ionic channels cell-cell communication

heart.med.upatras.gr/ Prezentare_adi/3.htm

www.syssim.ecs.soton.ac.uk/. ../hodhuxneu/hh2.htm

Hodgkin-Huxley Model cell-cell communication

http://www.amath.washington.edu/~qian/talks/talk5/

Neural Computation cell-cell communication

http://www.dna.caltech.edu/courses/cns187/

Our tools: dynamic mathematical models cell-cell communication

- Differential Equations:models from kinetic network description, models dynamic but not spatial phenomena, numerical simulations
- Sensitivity Analysis:dependence of steady-state behaviour on internal and external conditions
- Stability Analysis:phase plane analysis, characterizing long-term behaviour (bistability, oscillations)
- Bifurcation Analysis: dependence of system dynamics on internal and external conditions

rate of degradation cell-cell communication

rate of change of concentration

rate of production

Differential Equation ModellingFrom Chen, Tyson, Novak Mol. Biol Cell 2000. pp. 369-391

Differential Equation Modelling cell-cell communication

Differential Equation Modelling: Numerical Simulation cell-cell communication

Our tools: dynamic mathematical models cell-cell communication

- Differential Equations:models from kinetic network description, numerical simulations
- Sensitivity Analysis:dependence of steady-state behaviour on internal and external conditions
- Stability Analysis:phase plane analysis, characterizing long-term behaviour (bistability, oscillations)
- Bifurcation Analysis: dependence of system dynamics on internal and external conditions

complete sensitivity analysis: cell-cell communication

Our tools: dynamic mathematical models cell-cell communication

- Differential Equations:models from kinetic network description, numerical simulations
- Sensitivity Analysis:dependence of steady-state behaviour on internal and external conditions
- Bifurcation Analysis: dependence of system dynamics on internal and external conditions

unstable cell-cell communication

stable

Our tools: dynamic mathematical models cell-cell communication

- Differential Equations:models from kinetic network description, numerical simulations
- Sensitivity Analysis:dependence of steady-state behaviour on internal and external conditions
- Bifurcation Analysis: dependence of system dynamics on internal and external conditions

Why cell-cell communicationdynamic modelling?

allows construction of falsifiable models

in silico experiments

gain insight into dynamic behaviour of complex networks

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