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Pompano RR, Chiang AH, Kastrup CJ, Ismagilov RF. Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching. Annu Rev Biochem 2017; 86:333-356. [PMID: 28654324 PMCID: PMC10852032 DOI: 10.1146/annurev-biochem-060815-014207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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.
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Affiliation(s)
- Rebecca R Pompano
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904;
| | - Andrew H Chiang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637;
| | - Christian J Kastrup
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125;
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2
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Jahed Z, Shahsavan H, Verma MS, Rogowski JL, Seo BB, Zhao B, Tsui TY, Gu FX, Mofrad MRK. Bacterial Networks on Hydrophobic Micropillars. ACS NANO 2017; 11:675-683. [PMID: 28045495 DOI: 10.1021/acsnano.6b06985] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bacteria have evolved as intelligent microorganisms that can colonize and form highly structured and cooperative multicellular communities with sophisticated singular and collective behaviors. The initial stages of colony formation and intercellular communication are particularly important to understand and depend highly on the spatial organization of cells. Controlling the distribution and growth of bacterial cells at the nanoscale is, therefore, of great interest in understanding the mechanisms of cell-cell communication at the initial stages of colony formation. Staphyloccocus aureus, a ubiquitous human pathogen, is of specific clinical importance due to the rise of antibiotic resistant strains of this species, which can cause life-threatening infections. Although several methods have attempted to pattern bacterial cells onto solid surfaces at single cell resolution, no study has truly controlled the 3D architectures of growing colonies. Herein, we present a simple, low-cost method to pattern S. aureus bacterial colonies and control the architecture of their growth. Using the wetting properties of micropatterened poly(dimethyl siloxane) platforms, with help from the physiological activities of the S. aureus cells, we fabricated connected networks of bacterial microcolonies of various sizes. Unlike conventional heterogeneous growth of biofilms on surfaces, the patterned S. aureus microcolonies in this work grow radially from nanostrings of a few bacterial cells, to form micrometer-thick rods when provided with a nutrient rich environment. This simple, efficient, and low-cost method can be used as a platform for studies of cell-cell communication phenomena, such as quorum sensing, horizontal gene transfer, and metabolic cross-feeding especially during initial stages of colony formation.
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Affiliation(s)
- Zeinab Jahed
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley , 208A Stanley Hall, Berkeley, California 94720-1762, United States
| | - Hamed Shahsavan
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Mohit S Verma
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jacob L Rogowski
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Brandon B Seo
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Boxin Zhao
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ting Y Tsui
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Frank X Gu
- Department of Chemical Engineering, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley , 208A Stanley Hall, Berkeley, California 94720-1762, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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3
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Rana K, Neeves KB. Blood flow and mass transfer regulation of coagulation. Blood Rev 2016; 30:357-68. [PMID: 27133256 DOI: 10.1016/j.blre.2016.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/17/2016] [Accepted: 04/12/2016] [Indexed: 12/12/2022]
Abstract
Blood flow regulates coagulation and fibrin formation by controlling the transport, or mass transfer, of zymogens, co-factors, enzymes, and inhibitors to, from, and within a growing thrombus. The rate of mass transfer of these solutes relative to their consumption or production by coagulation reactions determines, in part, the rate of thrombin generation, fibrin deposition, and thrombi growth. Experimental studies on the influence of blood flow on specific coagulation reactions are reviewed here, along with a theoretical framework that predicts how flow influences surface-bound coagulation binding and enzymatic reactions. These flow-mediated transport mechanisms are also used to interpret the role of binding site densities and injury size on initiating coagulation and fibrin deposition. The importance of transport of coagulation proteins within the interstitial spaces of thrombi is shown to influence thrombi architecture, growth, and arrest.
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Affiliation(s)
- Kuldeepsinh Rana
- Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
| | - Keith B Neeves
- Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA; Pediatrics, University of Colorado-Denver, Aurora, CO, USA.
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4
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McCarty OJT, Ku D, Sugimoto M, King MR, Cosemans JMEM, Neeves KB. Dimensional analysis and scaling relevant to flow models of thrombus formation: communication from the SSC of the ISTH. J Thromb Haemost 2016; 14:619-22. [PMID: 26933837 PMCID: PMC4829115 DOI: 10.1111/jth.13241] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/08/2015] [Indexed: 01/31/2023]
Affiliation(s)
- O J T McCarty
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR
| | - D Ku
- GW Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - M Sugimoto
- Department of Regulatory Medicine for Thrombosis, Nara Medical University, Nara, Japan
| | - M R King
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - J M E M Cosemans
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - K B Neeves
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
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5
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Panteleev MA, Dashkevich NM, Ataullakhanov FI. Hemostasis and thrombosis beyond biochemistry: roles of geometry, flow and diffusion. Thromb Res 2015; 136:699-711. [DOI: 10.1016/j.thromres.2015.07.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/22/2015] [Accepted: 07/26/2015] [Indexed: 11/16/2022]
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6
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Weth D, Benetti C, Rauch C, Gstraunthaler G, Schmidt H, Geisslinger G, Sabbadini R, Proia RL, Kress M. Activated platelets release sphingosine 1-phosphate and induce hypersensitivity to noxious heat stimuli in vivo. Front Neurosci 2015; 9:140. [PMID: 25954148 PMCID: PMC4406086 DOI: 10.3389/fnins.2015.00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/04/2015] [Indexed: 11/19/2022] Open
Abstract
At the site of injury activated platelets release various mediators, one of which is sphingosine 1-phosphate (S1P). It was the aim of this study to explore whether activated human platelets had a pronociceptive effect in an in vivo mouse model and whether this effect was based on the release of S1P and subsequent activation of neuronal S1P receptors 1 or 3. Human platelets were prepared in different concentrations (10(5)/μl, 10(6)/μl, 10(7)/μl) and assessed in mice with different genetic backgrounds (WT, S1P1 (fl/fl), SNS-S1P1 (-/-), S1P3 (-/-)). Intracutaneous injections of activated human platelets induced a significant, dose-dependent hypersensitivity to noxious thermal stimulation. The degree of heat hypersensitivity correlated with the platelet concentration as well as the platelet S1P content and the amount of S1P released upon platelet activation as measured with LC MS/MS. Despite the significant correlations between S1P and platelet count, no difference in paw withdrawal latency (PWL) was observed in mice with a global null mutation of the S1P3 receptor or a conditional deletion of the S1P1 receptor in nociceptive primary afferents. Furthermore, neutralization of S1P with a selective anti-S1P antibody did not abolish platelet induced heat hypersensitivity. Our results suggest that activated platelets release S1P and induce heat hypersensitivity in vivo. However, the platelet induced heat hypersensitivity was caused by mediators other than S1P.
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Affiliation(s)
- Daniela Weth
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of InnsbruckInnsbruck, Austria
| | - Camilla Benetti
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of InnsbruckInnsbruck, Austria
| | - Caroline Rauch
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of InnsbruckInnsbruck, Austria
| | - Gerhard Gstraunthaler
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of InnsbruckInnsbruck, Austria
| | - Helmut Schmidt
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical PharmacologyFrankfurt, Germany
| | - Gerd Geisslinger
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical PharmacologyFrankfurt, Germany
| | | | - Richard L. Proia
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney DiseasesBethesda, MD, USA
| | - Michaela Kress
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of InnsbruckInnsbruck, Austria
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7
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Hozumi T, Ohta S, Ito T. Analysis of the Calcium Alginate Gelation Process Using a Kenics Static Mixer. Ind Eng Chem Res 2015. [DOI: 10.1021/ie5044693] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takuro Hozumi
- Department
of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Seiichi Ohta
- Center
for Disease Biology and Integrative Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taichi Ito
- Department
of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Center
for Disease Biology and Integrative Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Spatial aspects of blood coagulation: two decades of research on the self-sustained traveling wave of thrombin. Thromb Res 2014; 135:423-33. [PMID: 25550187 DOI: 10.1016/j.thromres.2014.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/10/2014] [Accepted: 12/13/2014] [Indexed: 01/27/2023]
Abstract
In a number of experimental studies, it has been demonstrated that the forefront of blood coagulation can propagate in the manner of a signal relay. These data strongly support the concept that the formation of a blood clot is governed by a self-sustained traveling wave of thrombin. The present review critically appraises the experimental data obtained in recent decades concerning the self-sustained spatial propagation of thrombin. Open questions regarding the experimental detection of the self-sustained propagation of thrombin are discussed.
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9
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Collier CP, Simpson ML. Micro/nanofabricated environments for synthetic biology. Curr Opin Biotechnol 2011; 22:516-26. [PMID: 21636262 DOI: 10.1016/j.copbio.2011.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/06/2011] [Indexed: 11/17/2022]
Abstract
A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints.
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Affiliation(s)
- C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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10
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Kuo JS, Chiu DT. Controlling mass transport in microfluidic devices. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:275-96. [PMID: 21456968 PMCID: PMC5724977 DOI: 10.1146/annurev-anchem-061010-113926] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Microfluidic platforms offer exquisite capabilities in controlling mass transport for biological studies. In this review, we focus on recent developments in manipulating chemical concentrations at the microscale. Some techniques prevent or accelerate mixing, whereas others shape the concentration gradients of chemical and biological molecules. We also highlight several in vitro biological studies in the areas of organ engineering, cancer, and blood coagulation that have benefited from accurate control of mass transfer.
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Affiliation(s)
- Jason S Kuo
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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11
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Das T, Maiti TK, Chakraborty S. Augmented stress-responsive characteristics of cell lines in narrow confinements. Integr Biol (Camb) 2011; 3:684-95. [DOI: 10.1039/c1ib00001b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Hochbaum AI, Aizenberg J. Bacteria pattern spontaneously on periodic nanostructure arrays. NANO LETTERS 2010; 10:3717-3721. [PMID: 20687595 DOI: 10.1021/nl102290k] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Surface-associated bacteria typically form self-organizing communities called biofilms. Spatial segregation is important for various bacterial processes associated with cellular and community development. Here, we demonstrate bacterial ordering and oriented attachment on the single-cell level induced by nanometer-scale periodic surface features. These surfaces cause spontaneous and distinct patterning phases, depending on their periodicity, which is observed for several strains, both gram positive and negative. This patterning is a general phenomenon that can control natural biofilm organization on the cellular level.
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Affiliation(s)
- Allon I Hochbaum
- The Department of Chemistry and Chemical Biology, The Wyss Institute for Biologically Inspired Engineering, The School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, MA 02138, USA
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13
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Vincent ME, Liu W, Haney EB, Ismagilov RF. Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals. Chem Soc Rev 2010; 39:974-84. [PMID: 20179819 PMCID: PMC2829723 DOI: 10.1039/b917851a] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Rare cells can be difficult to analyze because they either occur in low numbers or coexist with a more abundant cell type, yet their detection is crucial for diagnosing disease and maintaining human health. In this tutorial review, we introduce the concept of microfluidic stochastic confinement for use in detection and analysis of rare cells. Stochastic confinement provides two advantages: (1) it separates rare single cells from the bulk mixture and (2) it allows signals to locally accumulate to a higher concentration around a single cell than in the bulk mixture. Microfluidics is an attractive method for implementing stochastic confinement because it provides simple handling of small volumes. We present technologies for microfluidic stochastic confinement that utilize both wells and droplets for the detection and analysis of single cells. We address how these microfluidic technologies have been used to observe new behavior, increase speed of detection, and enhance cultivation of rare cells. We discuss potential applications of microfluidic stochastic confinement to fields such as human diagnostics and environmental testing.
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Affiliation(s)
- Meghan E Vincent
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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