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Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching.

Abstract Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding. In this review, we use a phenomenon referred to as patchy switching to illustrate the interplay of nonlinearities, transport phenomena, and spatial effects. Patchy switching describes a change in the state of a network when the local concentration of a diffusible molecule surpasses a critical threshold. Using patchy switching as an example, we describe conceptual tools from nonlinear dynamics and chemical engineering that make testable predictions and provide a unifying description of the myriad possible experimental observations. We describe experimental microfluidic and biochemical tools emerging to test conceptual predictions by controlling transport phenomena and spatial distribution of diffusible signals, and we highlight the unmet need for in vivo tools.
PMID
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Authors

Mayor MeshTerms

Gene Regulatory Networks

Nonlinear Dynamics

Keywords

Damköhler number

flow

mass transfer

microfluidics

signaling

state switching

Journal Title annual review of biochemistry
Publication Year Start




PMID- 28654324
OWN - NLM
STAT- MEDLINE
DA  - 20170627
DCOM- 20170704
LR  - 20170704
IS  - 1545-4509 (Electronic)
IS  - 0066-4154 (Linking)
VI  - 86
DP  - 2017 Jun 20
TI  - Conceptual and Experimental Tools to Understand Spatial Effects and Transport
      Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching.
PG  - 333-356
LID - 10.1146/annurev-biochem-060815-014207 [doi]
AB  - Many biochemical systems are spatially heterogeneous and exhibit nonlinear
      behaviors, such as state switching in response to small changes in the local
      concentration of diffusible molecules. Systems as varied as blood clotting,
      intracellular calcium signaling, and tissue inflammation are all heavily
      influenced by the balance of rates of reaction and mass transport phenomena
      including flow and diffusion. Transport of signaling molecules is also affected
      by geometry and chemoselective confinement via matrix binding. In this review, we
      use a phenomenon referred to as patchy switching to illustrate the interplay of
      nonlinearities, transport phenomena, and spatial effects. Patchy switching
      describes a change in the state of a network when the local concentration of a
      diffusible molecule surpasses a critical threshold. Using patchy switching as an 
      example, we describe conceptual tools from nonlinear dynamics and chemical
      engineering that make testable predictions and provide a unifying description of 
      the myriad possible experimental observations. We describe experimental
      microfluidic and biochemical tools emerging to test conceptual predictions by
      controlling transport phenomena and spatial distribution of diffusible signals,
      and we highlight the unmet need for in vivo tools.
FAU - Pompano, Rebecca R
AU  - Pompano RR
AD  - Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904;
      email: [email protected]
FAU - Chiang, Andrew H
AU  - Chiang AH
AD  - Department of Chemistry and Institute for Biophysical Dynamics, The University of
      Chicago, Chicago, Illinois 60637; email: [email protected]
FAU - Kastrup, Christian J
AU  - Kastrup CJ
AD  - Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, 
      University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
      email: [email protected]
FAU - Ismagilov, Rustem F
AU  - Ismagilov RF
AD  - Division of Chemistry and Chemical Engineering, California Institute of
      Technology, Pasadena, California 91125; email: [email protected]
LA  - eng
PT  - Journal Article
PT  - Review
PL  - United States
TA  - Annu Rev Biochem
JT  - Annual review of biochemistry
JID - 2985150R
RN  - Adenocarcinoma of lung
SB  - IM
MH  - Adenocarcinoma/genetics/*metabolism/pathology
MH  - Biological Transport
MH  - Diffusion
MH  - *Gene Regulatory Networks
MH  - Humans
MH  - Lab-On-A-Chip Devices
MH  - Lung Neoplasms/genetics/*metabolism/pathology
MH  - Metabolic Networks and Pathways/*genetics
MH  - Microfluidics/instrumentation/methods
MH  - Multiple Sclerosis/genetics/*metabolism/pathology
MH  - *Nonlinear Dynamics
MH  - Osteoporosis/genetics/*metabolism/pathology
MH  - Signal Transduction
OTO - NOTNLM
OT  - Damkohler number
OT  - flow
OT  - mass transfer
OT  - microfluidics
OT  - signaling
OT  - state switching
EDAT- 2017/06/28 06:00
MHDA- 2017/07/05 06:00
CRDT- 2017/06/28 06:00
AID - 10.1146/annurev-biochem-060815-014207 [doi]
PST - ppublish
SO  - Annu Rev Biochem. 2017 Jun 20;86:333-356. doi:
      10.1146/annurev-biochem-060815-014207.