Leveraging Biological Robustness to Improve Engineered Systems
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Leveraging Biological Robustness to Improve Engineered Systems. Michael Mayo, PhD. Research Physicist Environmental Genomics and Systems Biology Team Environmental Laboratory US Army Engineer Research & Development Center (ERDC) VCU Computer Science Department 9 October 2012.

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Leveraging biological robustness to improve engineered systems

Leveraging Biological Robustness to Improve Engineered Systems

Michael Mayo, PhD

Research Physicist

Environmental Genomics and Systems Biology Team

Environmental Laboratory

US Army Engineer Research & Development Center (ERDC)

VCU Computer Science Department

9 October 2012


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Robustness

“The behavior of a system is termed robust if that behavior is qualitatively normal in the face of substantial changes to the system components.”

J.W. Little et al., EMBO J. 18, 4299 (1999).

“…the preservation of particular characteristics despite uncertainty in system components.”

M.E. Csets and J.C. Doyle Science 295, 1664 (2002).

“…biological circuits are not fine-tuned to exercise their functions only for precise values of their biochemical parameters. Instead, they must be able to function under a rangeof different parameters.”

A. Wagner Proc. Natl. Acad. Sci. USA 102, 11775 (2005).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Example – Circadian oscillator

R = mRNA concentration (transcription)

P = protein concentration (translation)

P’ = post-translational modification

(dimerization/phosphorylation)

P = fraction of parameter space that yield

oscillating solutions.

A. Wagner Proc. Natl. Acad. Sci. USA 102, 11775 (2005).

Main Result

“Changing parameters at random in a topology with high P is more likely to yield a parameter combination leading to circadian oscillations than in a topology with low P.”

In certain topologies, oscillations robust against parameter fluctuations.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Why use mathematical modeling?

  • Translates the problem into unambiguous language of mathematics.

  • Mathematical model is a laboratory to conduct simulated experiments, where it is too expensive or otherwise unethical to acquire experimental data.

  • Hypotheses or other “scenarios” (like oscillator topology) can be tested or assessed more easily and rapidly.

Drawback: Models are only as good as what go into them.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study

Mammalian Gas-Exchange


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

Branching point at which velocity from convection = 0.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

M. Mayo et al., Phys. Rev. E 85, 011115 (2012).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

Cayley tree:

Main Idea

Leaves/canopy

Using conservation principles, solve for current entering branch, across the branching point.

Root

M. Mayo et al., Phys. Rev. E 85, 011115 (2012).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

Current into the tree

2r = diameter of branch

D = diffusion coefficient of O2 in air

C0 = concentration of O2 at entrance to acinar airways

m = number of branching at each branch point (m=2 in lungs)

n = depth of tree/orders of branching points

L = length of a branch

Λ = D/W = exploration length


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

Current into the tree

M. Mayo et al., Phys. Rev. E 85, 011115 (2012).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

Diffusional screening and current plateaus

M. Mayo et al., Phys. Rev. E 85, 011115 (2012).

J.S Andrade, Jr. et al., Europhys. Lett. 55, 573 (2001).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Mammalian gas-exchange

Experimental validation of model predictions

M. Mayo, P. Pfeifer, and C. Hou*. 2012. Reverse engineering the robustness of mammalian lung. Reverse Engineering, ed. A.C. Telea. InTech Publisher, Boston, pp.243-262


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Summary

  • Competition between the O2 transport across the alveolar membranes and its screening from surface sites generates plateaus.

  • Plateaus represent regions of maximum insensitivity (i.e. robustness) of the O2 current to “changes” in the Thiele modulus (i.e. changes to D or W, or both).

  • Plateaus emerge independent of any feedback loop.

  • Experimental values for current lie in the plateau, but next to the “no screening” (NS) regime, providing flexibility of the O2 current to moderate surface “damage.”


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study

Teleost Reproductive Axis


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Teleost Reproductive Axis

Chemical

FSH/LH

Hypothalamus-Pituitary

VTG

Liver

Ovary

Fecundity

E2/T

Population

http://www.tpwd.state.tx.us/fishboat/fish/images/inland_species/fathead1.jpg

Time

Hypothalamus-Pituitary-Gonadal (HPG) axis – synthesis and regulation of reproductive the hormones 17β-estradiol (E2) and testosterone (T).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Teleost Reproductive Axis

G.T. Ankley et al., Aquat. Toxicol. 92, 168 (2009).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

D.L. Villeneuve et al., Environ. HealthPerspect.117, 624 (2009).

Network inference reveals that Androgen Receptor regulation may lead to compensation of E2 in lower doses.

G. Ankley et al., Toxicol. Sci. 67, 121 (2002).

Control

2

10

50

Fadrozole (ng/ml)

GRANULOSA

T. Habib, M. Mayo, E.J. Perkins et al., (in preparation).

THECA


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Teleost Reproductive Axis

The conceptual and mathematical model

Built from equations of the type:

Creation flux

Elimination flux

(i.e. turnover, degradation etc)

M. Mayo et al., (in preparation)


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Teleost Reproductive Axis

M. Mayo et al., (in preparation)


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Teleost Reproductive Axis

Mathematical model: relative error to parameter variation

M. Mayo et al., (in preparation)


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Teleost Reproductive Axis

Mathematical model: predictive capability

M. Mayo et al., (in preparation)

K=19.53 nM

n=1.75


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Summary

  • Relative error analysis reveals that only a few components of HPG axis are “fragile,” but these fragilities are at critical regulation points of the network (i.e. cholesterol transport).

  • Compensation arises from feedback through androgen receptor complex, which activates key steroidogenic genes.

  • Competition between aromatase creation and sequestration results in long-term robustness of E2 profile when these effects are balanced.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study

Coupling Among Motifs in Transcriptional Networks


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Motif Coupling in Gene Networks

S. Mangan and U. Alon, Proc. Natl. Acad. Sci. USA 21, 11980 (2003).

R. Milo et al., Science 298, 824 (2002).

Feed-forward loops are one of the most common three-node motifs, but mostly only studied before in isolation.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Motif Coupling in Gene Networks

Maximally coupled

Sparse connectivity

Null model

Each link can act as either an activator or an inhibitor of transcriptional activity.

Other work in progress demonstrates that transcription factors play the role of nodes 1,2,4 and 5 justifying the study of coupling among the TFs only.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Motif Coupling in Gene Networks

Mathematical model

activation

repression

Maximum transcriptional activity

Degradation rate

Affinity of inhibitor (activator) to repress (induce) transcriptional activity

Parameter space will be searched using a log-uniform distribution with sufficient point density


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Motif Coupling in Gene Networks

Experimental design

Black line

Blue line

Timing is measured and correlated with network topology


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Case Study: Motif Coupling in Gene Networks

Experimental design

http://openwetware.org/wiki/Biomolecular_Breadboards

Feed-forward loops will be constructed experimentally to determine the primary variables that control correlations between robustness and topology.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Connection with Engineered Systems


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

http://nice.che.rpi.edu/Research/fuel_cells.htm

S. Kjelstrup, M.-O. Coppens, J. G. Phaoroah, and P. Pfeifer,Energy Fuels 24, 5097 (2010).


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

Acknowledgements

Case Study: Mammalian gas-exchange

Stefan Gheorghiu – Center for Complexity Studies, Bucharest Romania.

Peter Pfeifer – Chair and Professor of Physics, University of Missouri.

Chen Hou – Associate Professor, Missouri University of Science & Technology.

Case Study: Teleost Reproductive Axis

Ed Perkins – Senior Scientist, Environmental Laboratory ERDC.

Karen Watanabe – Associate Professor, Oregon Health & Science University (OHSU).

Natalia Garcia-Reyero – Associate Research Professor, Mississippi State University.

TanwirHabib – Staff Scientist, Badger Technical Services.

Dan Villeneuve – Research Biologist, Environmental Protection Agency (EPA)

Gary Ankley – Senior Scientist, Environmental Protection Agency (EPA)

Case Study: Coupling Among Motifs and Transcriptional Netowrks

PreetamGhosh – Assistant Professor, Department of Computer Science, VCU.

VijenderChaitankar, Ahmed Abdelzaher, BhanuKishore– Department of Computer Science, VCU.


Leveraging biological robustness to improve engineered systems

  • Leveraging Biological Robustness to Improve Engineered Systems

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