101
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McKay R, Hauk P, Wu HC, Pottash AE, Shang W, Terrell J, Payne GF, Bentley WE. Controlling localization of Escherichia coli populations using a two-part synthetic motility circuit: An accelerator and brake. Biotechnol Bioeng 2017; 114:2883-2895. [PMID: 28755474 DOI: 10.1002/bit.26391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/21/2017] [Accepted: 07/23/2017] [Indexed: 12/30/2022]
Abstract
Probiotics, whether taken as capsules or consumed in foods, have been regarded as safe for human use by regulatory agencies. Being living cells, they serve as "tunable" factories for the synthesis of a vast array of beneficial molecules. The idea of reprogramming probiotics to act as controllable factories, producing potential therapeutic molecules under user-specified conditions, represents a new and powerful concept in drug synthesis and delivery. Probiotics that serve as drug delivery vehicles pose several challenges, one being targeting (as seen with nanoparticle approaches). Here, we employ synthetic biology to control swimming directionality in a process referred to as "pseudotaxis." Escherichia coli, absent the motility regulator cheZ, swim sporadically, missing the traditional "run" in the run:tumble swimming paradigm. Upon introduction of cheZ in trans and its signal-generated upregulation, engineered bacteria can be "programmed" to swim toward the source of the chemical cue. Here, engineered cells that encounter sufficient levels of the small signal molecule pyocyanin, produce an engineered CheZ and swim with programmed directionality. By incorporating a degradation tag at the C-terminus of CheZ, the cells stop running when they exit spaces containing pyocyanin. That is, the engineered CheZ modified with a C-terminal extension derived from the putative DNA-binding transcriptional regulator YbaQ (RREERAAKKVA) is consumed by the ClpXP protease machine at a rate sufficient to "brake" the cells when pyocyanin levels are too low. Through this process, we demonstrate that over time, these engineered E. coli accumulate in pyocyanin-rich locales. We suggest that such approaches may find utility in engineering probiotics so that their beneficial functions can be focused in areas of principal benefit.
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Affiliation(s)
- Ryan McKay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Alex Eli Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Wu Shang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | | | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
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102
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Transcriptional control of motility enables directional movement of Escherichia coli in a signal gradient. Sci Rep 2017; 7:8959. [PMID: 28827562 PMCID: PMC5566481 DOI: 10.1038/s41598-017-08870-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/18/2017] [Indexed: 11/08/2022] Open
Abstract
Manipulation of cellular motility using a target signal can facilitate the development of biosensors or microbe-powered biorobots. Here, we engineered signal-dependent motility in Escherichia coli via the transcriptional control of a key motility gene. Without manipulating chemotaxis, signal-dependent switching of motility, either on or off, led to population-level directional movement of cells up or down a signal gradient. We developed a mathematical model that captures the behaviour of the cells, enables identification of key parameters controlling system behaviour, and facilitates predictive-design of motility-based pattern formation. We demonstrated that motility of the receiver strains could be controlled by a sender strain generating a signal gradient. The modular quorum sensing-dependent architecture for interfacing different senders with receivers enabled a broad range of systems-level behaviours. The directional control of motility, especially combined with the potential to incorporate tuneable sensors and more complex sensing-logic, may lead to tools for novel biosensing and targeted-delivery applications.
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103
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Abstract
Classical tissue engineering is aimed mainly at producing anatomically and physiologically realistic replacements for normal human tissues. It is done either by encouraging cellular colonization of manufactured matrices or cellular recolonization of decellularized natural extracellular matrices from donor organs, or by allowing cells to self-organize into organs as they do during fetal life. For repair of normal bodies, this will be adequate but there are reasons for making unusual, non-evolved tissues (repair of unusual bodies, interface to electromechanical prostheses, incorporating living cells into life-support machines). Synthetic biology is aimed mainly at engineering cells so that they can perform custom functions: applying synthetic biological approaches to tissue engineering may be one way of engineering custom structures. In this article, we outline the ‘embryological cycle’ of patterning, differentiation and morphogenesis and review progress that has been made in constructing synthetic biological systems to reproduce these processes in new ways. The state-of-the-art remains a long way from making truly synthetic tissues, but there are now at least foundations for future work.
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104
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Shao X, Mugler A, Kim J, Jeong HJ, Levin BR, Nemenman I. Growth of bacteria in 3-d colonies. PLoS Comput Biol 2017; 13:e1005679. [PMID: 28749935 PMCID: PMC5549765 DOI: 10.1371/journal.pcbi.1005679] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/08/2017] [Accepted: 07/12/2017] [Indexed: 02/03/2023] Open
Abstract
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in physically structured habitats as colonies, within which individual cells vary in their access to nutrients. The dynamics of bacterial growth in such conditions is poorly understood, and, unlike that for liquid culture, there is not a standard broadly used mathematical model for bacterial populations growing in colonies in three dimensions (3-d). By extending the classic Monod model of resource-limited population growth to allow for spatial heterogeneity in the bacterial access to nutrients, we develop a 3-d model of colonies, in which bacteria consume diffusing nutrients in their vicinity. By following the changes in density of E. coli in liquid and embedded in glucose-limited soft agar, we evaluate the fit of this model to experimental data. The model accounts for the experimentally observed presence of a sub-exponential, diffusion-limited growth regime in colonies, which is absent in liquid cultures. The model predicts and our experiments confirm that, as a consequence of inter-colony competition for the diffusing nutrients and of cell death, there is a non-monotonic relationship between total number of colonies within the habitat and the total number of individual cells in all of these colonies. This combined theoretical-experimental study reveals that, within 3-d colonies, E. coli cells are loosely packed, and colonies produce about 2.5 times as many cells as the liquid culture from the same amount of nutrients. We verify that this is because cells in liquid culture are larger than in colonies. Our model provides a baseline description of bacterial growth in 3-d, deviations from which can be used to identify phenotypic heterogeneities and inter-cellular interactions that further contribute to the structure of bacterial communities. The vast majority of theoretical and experimental studies assume that bacteria exist as planktonic cells in well-mixed liquid cultures, all with equal access to nutrients, wastes, toxins, antibiotics, bacterial viruses, and each other. However, in the real world, bacteria are more often found in physically structured, spatially heterogeneous habitats as colonies and micro-colonies. While one can experimentally explore the population and evolutionary dynamics of bacteria in such physically structured habitats, there is dearth of mathematical models to generate hypotheses for and to interpret results of these experiments. As a step towards the construction of a theory of the population dynamics of bacteria in physically structured habitats, we develop and experientially explore the simplest such model of the dynamics of bacterial growth in 3-d structured colonies.
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Affiliation(s)
- Xinxian Shao
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | - Andrew Mugler
- Department of Physics, Emory University, Atlanta, GA 30322, USA
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Justin Kim
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Ha Jun Jeong
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Bruce R. Levin
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Ilya Nemenman
- Department of Physics, Emory University, Atlanta, GA 30322, USA
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Initiative in Theory and Modeling of Living Systems, Emory University, Atlanta, GA 30322, USA
- * E-mail:
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105
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de Paoli H, van der Heide T, van den Berg A, Silliman BR, Herman PMJ, van de Koppel J. Behavioral self-organization underlies the resilience of a coastal ecosystem. Proc Natl Acad Sci U S A 2017; 114:8035-8040. [PMID: 28696313 PMCID: PMC5544259 DOI: 10.1073/pnas.1619203114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Self-organized spatial patterns occur in many terrestrial, aquatic, and marine ecosystems. Theoretical models and observational studies suggest self-organization, the formation of patterns due to ecological interactions, is critical for enhanced ecosystem resilience. However, experimental tests of this cross-ecosystem theory are lacking. In this study, we experimentally test the hypothesis that self-organized pattern formation improves the persistence of mussel beds (Mytilus edulis) on intertidal flats. In natural beds, mussels generate self-organized patterns at two different spatial scales: regularly spaced clusters of mussels at centimeter scale driven by behavioral aggregation and large-scale, regularly spaced bands at meter scale driven by ecological feedback mechanisms. To test for the relative importance of these two spatial scales of self-organization on mussel bed persistence, we conducted field manipulations in which we factorially constructed small-scale and/or large-scale patterns. Our results revealed that both forms of self-organization enhanced the persistence of the constructed mussel beds in comparison to nonorganized beds. Small-scale, behaviorally driven cluster patterns were found to be crucial for persistence, and thus resistance to wave disturbance, whereas large-scale, self-organized patterns facilitated reformation of small-scale patterns if mussels were dislodged. This study provides experimental evidence that self-organization can be paramount to enhancing ecosystem persistence. We conclude that ecosystems with self-organized spatial patterns are likely to benefit greatly from conservation and restoration actions that use the emergent effects of self-organization to increase ecosystem resistance to disturbance.
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Affiliation(s)
- Hélène de Paoli
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research and Utrecht University, 4401 NT Yerseke, The Netherlands
| | - Tjisse van der Heide
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands;
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Aniek van den Berg
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research and Utrecht University, 4401 NT Yerseke, The Netherlands
| | - Brian R Silliman
- Division of Marine Sciences and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC 28516;
| | - Peter M J Herman
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research and Utrecht University, 4401 NT Yerseke, The Netherlands;
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
- Unit for Marine and Coastal Systems, Deltares, 2629 HV Delft, The Netherlands
| | - Johan van de Koppel
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research and Utrecht University, 4401 NT Yerseke, The Netherlands;
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
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106
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Silva KP, Chellamuthu P, Boedicker JQ. Signal Destruction Tunes the Zone of Activation in Spatially Distributed Signaling Networks. Biophys J 2017; 112:1037-1044. [PMID: 28297640 DOI: 10.1016/j.bpj.2017.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
Diverse microbial communities coordinate group behaviors through signal exchange, such as the exchange of acyl-homoserine lactones (AHLs) by Gram-negative bacteria. Cellular communication is prone to interference by neighboring microbes. One mechanism of interference is signal destruction through the production of an enzyme that cleaves the signaling molecule. Here we examine the ability of one such interference enzyme, AiiA, to modulate signal propagation in a spatially distributed system of bacteria. We have developed an experimental assay to measure signal transduction and implement a theoretical model of signaling dynamics to predict how the system responds to interference. We show that titration of an interfering strain into a signaling network tunes the spatial range of activation over the centimeter length scale, quantifying the robustness of the signaling network to signal destruction and demonstrating the ability to program systems-level responses of spatially heterogeneous cellular networks.
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Affiliation(s)
- Kalinga Pavan Silva
- Department of Physics, University of Southern California, Los Angeles, California
| | - Prithiviraj Chellamuthu
- Department of Physics, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - James Q Boedicker
- Department of Physics, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California.
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107
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108
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Active depinning of bacterial droplets: The collective surfing of Bacillus subtilis. Proc Natl Acad Sci U S A 2017; 114:5958-5963. [PMID: 28536199 DOI: 10.1073/pnas.1703997114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How systems are endowed with migration capacity is a fascinating question with implications ranging from the design of novel active systems to the control of microbial populations. Bacteria, which can be found in a variety of environments, have developed among the richest set of locomotion mechanisms both at the microscopic and collective levels. Here, we uncover, experimentally, a mode of collective bacterial motility in humid environment through the depinning of bacterial droplets. Although capillary forces are notoriously enormous at the bacterial scale, even capable of pinning water droplets of millimetric size on inclined surfaces, we show that bacteria are able to harness a variety of mechanisms to unpin contact lines, hence inducing a collective slipping of the colony across the surface. Contrary to flagella-dependent migration modes like swarming, we show that this much faster "colony surfing" still occurs in mutant strains of Bacillus subtilis lacking flagella. The active unpinning seen in our experiments relies on a variety of microscopic mechanisms, which could each play an important role in the migration of microorganisms in humid environment.
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109
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Chen Y, Tong D, Wu CI. A New Formulation of Random Genetic Drift and Its Application to the Evolution of Cell Populations. Mol Biol Evol 2017; 34:2057-2064. [DOI: 10.1093/molbev/msx161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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110
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Elements of biological oscillations in time and space. Nat Struct Mol Biol 2017; 23:1030-1034. [PMID: 27922613 DOI: 10.1038/nsmb.3320] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/13/2016] [Indexed: 12/16/2022]
Abstract
Oscillations in time and space are ubiquitous in nature and play critical roles in dynamic cellular processes. Although the molecular mechanisms underlying the generation of the dynamics are diverse, several distinct regulatory elements have been recognized as being critical in producing and modulating oscillatory dynamics. These include negative and positive feedback, time delay, nonlinearity in regulation, and random fluctuations ('noise'). Here we discuss the specific roles of these five elements in promoting or attenuating oscillatory dynamics, by drawing on insights from quantitative analyses of natural or synthetic biological networks.
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111
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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112
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Hwang W, Hyeon C. Quantifying the Heat Dissipation from a Molecular Motor's Transport Properties in Nonequilibrium Steady States. J Phys Chem Lett 2017; 8:250-256. [PMID: 27983853 DOI: 10.1021/acs.jpclett.6b02657] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Theoretical analysis, which maps single-molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and diffusivity. Unlike passive Brownian particles in equilibrium, the velocity and diffusion constant of molecular motors are closely inter-related. In particular, our study makes it clear that the increase of diffusivity with the heat production is a natural outcome of active particles, which is reminiscent of the recent experimental premise that the diffusion of an exothermic enzyme is enhanced by the heat released from its own catalytic turnover. Compared with freely diffusing exothermic enzymes, kinesin-1, whose dynamics is confined on one-dimensional tracks, is highly efficient in transforming conformational fluctuations into a locally directed motion, thus displaying a significantly higher enhancement in diffusivity with its turnover rate. Putting molecular motors and freely diffusing enzymes on an equal footing, our study offers a thermodynamic basis to understand the heat-enhanced self-diffusion of exothermic enzymes.
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Affiliation(s)
- Wonseok Hwang
- Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
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113
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Abstract
Recently developed DNA assembly methods have enabled the rapid and simultaneous assembly of multiple parts to create complex synthetic gene circuits. A number of groups have proposed the use of computationally designed orthogonal spacer sequences to guide the ordered assembly of parts using overlap-directed or homologous recombination-based methods. This approach is particularly useful for assembling multiple parts with repetitive elements. Orthogonal spacer sequences (sometimes called UNSs-unique nucleotide sequences) also have a number of other potential uses including in the design of synthetic promoters regulated by novel regulatory elements.
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Affiliation(s)
- James T MacDonald
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK. .,Department of Medicine, Imperial College, South Kensington Campus, London, SW7 2AZ, UK.
| | - Velia Siciliano
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK.,Department of Medicine, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
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114
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Cao Y, Ryser MD, Payne S, Li B, Rao CV, You L. Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria. Cell 2016; 165:620-30. [PMID: 27104979 DOI: 10.1016/j.cell.2016.03.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/11/2015] [Accepted: 03/01/2016] [Indexed: 01/12/2023]
Abstract
Scale invariance refers to the maintenance of a constant ratio of developing organ size to body size. Although common, its underlying mechanisms remain poorly understood. Here, we examined scaling in engineered Escherichia coli that can form self-organized core-ring patterns in colonies. We found that the ring width exhibits perfect scale invariance to the colony size. Our analysis revealed a collective space-sensing mechanism, which entails sequential actions of an integral feedback loop and an incoherent feedforward loop. The integral feedback is implemented by the accumulation of a diffusive chemical produced by a colony. This accumulation, combined with nutrient consumption, sets the timing for ring initiation. The incoherent feedforward is implemented by the opposing effects of the domain size on the rate and duration of ring maturation. This mechanism emphasizes a role of timing control in achieving robust pattern scaling and provides a new perspective in examining the phenomenon in natural systems.
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Affiliation(s)
- Yangxiaolu Cao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Marc D Ryser
- Department of Mathematics, Duke University, Durham, NC 27708, USA
| | - Stephen Payne
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Bochong Li
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana Champaign, IL 61801, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.
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115
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Interrogating the Escherichia coli cell cycle by cell dimension perturbations. Proc Natl Acad Sci U S A 2016; 113:15000-15005. [PMID: 27956612 DOI: 10.1073/pnas.1617932114] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed "adder-per-origin" model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.
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116
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Kong W, Blanchard AE, Liao C, Lu T. Engineering robust and tunable spatial structures with synthetic gene circuits. Nucleic Acids Res 2016; 45:1005-1014. [PMID: 27899571 PMCID: PMC5314756 DOI: 10.1093/nar/gkw1045] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/30/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Controllable spatial patterning is a major goal for the engineering of biological systems. Recently, synthetic gene circuits have become promising tools to achieve the goal; however, they need to possess both functional robustness and tunability in order to facilitate future applications. Here we show that, by harnessing the dual signaling and antibiotic features of nisin, simple synthetic circuits can direct Lactococcus lactis populations to form programmed spatial band-pass structures that do not require fine-tuning and are robust against environmental and cellular context perturbations. Although robust, the patterns are highly tunable, with their band widths specified by the external nisin gradient and cellular nisin immunity. Additionally, the circuits can direct cells to consistently generate designed patterns, even when the gradient is driven by structured nisin-producing bacteria and the patterning cells are composed of multiple species. A mathematical model successfully reproduces all of the observed patterns. Furthermore, the circuits allow us to establish predictable structures of synthetic communities and controllable arrays of cellular stripes and spots in space. This study offers new synthetic biology tools to program spatial structures. It also demonstrates that a deep mining of natural functionalities of living systems is a valuable route to build circuit robustness and tunability.
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Affiliation(s)
- Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew E Blanchard
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chen Liao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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117
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Gelimson A, Zhao K, Lee CK, Kranz WT, Wong GCL, Golestanian R. Multicellular Self-Organization of P. aeruginosa due to Interactions with Secreted Trails. PHYSICAL REVIEW LETTERS 2016; 117:178102. [PMID: 27824438 DOI: 10.1103/physrevlett.117.178102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 06/06/2023]
Abstract
Guided movement in response to slowly diffusing polymeric trails provides a unique mechanism for self-organization of some microorganisms. To elucidate how this signaling route leads to microcolony formation, we experimentally probe the trajectory and orientation of Pseudomonas aeruginosa that propel themselves on a surface using type IV pili motility appendages, which preferentially attach to deposited exopolysaccharides. We construct a stochastic model by analyzing single-bacterium trajectories and show that the resulting theoretical prediction for the many-body behavior of the bacteria is in quantitative agreement with our experimental characterization of how cells explore the surface via a power-law strategy.
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Affiliation(s)
- Anatolij Gelimson
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, United Kingdom
| | - Kun Zhao
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Bioengineering Department, Chemistry and Biochemistry Department, California Nano Systems Institute, UCLA, Los Angeles, California 90095-1600, USA
| | - Calvin K Lee
- Bioengineering Department, Chemistry and Biochemistry Department, California Nano Systems Institute, UCLA, Los Angeles, California 90095-1600, USA
| | - W Till Kranz
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, United Kingdom
| | - Gerard C L Wong
- Bioengineering Department, Chemistry and Biochemistry Department, California Nano Systems Institute, UCLA, Los Angeles, California 90095-1600, USA
| | - Ramin Golestanian
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, United Kingdom
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118
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Pascalie J, Potier M, Kowaliw T, Giavitto JL, Michel O, Spicher A, Doursat R. Developmental Design of Synthetic Bacterial Architectures by Morphogenetic Engineering. ACS Synth Biol 2016; 5:842-61. [PMID: 27244532 DOI: 10.1021/acssynbio.5b00246] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic biology is an emerging scientific field that promotes the standardized manufacturing of biological components without natural equivalents. Its goal is to create artificial living systems that can meet various needs in health care or energy domains. While most works are focused on the individual bacterium as a chemical reactor, our project, SynBioTIC, addresses a novel and more complex challenge: shape engineering; that is, the redesign of natural morphogenesis toward a new kind of developmental 3D printing. Potential applications include organ growth, natural computing in biocircuits, or future vegetal houses. To create in silico multicellular organisms that exhibit specific shapes, we construe their development as an iterative process combining fundamental collective phenomena such as homeostasis, patterning, segmentation, and limb growth. Our numerical experiments rely on the existing Escherichia coli simulator Gro, a physicochemical computation platform offering reaction-diffusion and collision dynamics solvers. The synthetic bioware of our model executes a set of rules, or genome, in each cell. Cells can differentiate into several predefined types associated with specific actions (divide, emit signal, detect signal, die). Transitions between types are triggered by conditions involving internal and external sensors that detect various protein levels inside and around the cell. Indirect communication between bacteria is relayed by morphogen diffusion and the mechanical constraints of 2D packing. Starting from a single bacterium, the overall architecture emerges in a purely endogenous fashion through a series of developmental stages, inlcuding proliferation, differentiation, morphogen diffusion, and synchronization. The genome can be parametrized to control the growth and features of appendages individually. As exemplified by the L and T shapes that we obtain, certain precursor cells can be inhibited while others can create limbs of varying size (divergence of the homology). Such morphogenetic phenotypes open the way to more complex shapes made of a recursive array of core bodies and limbs and, most importantly, to an evolutionary developmental exploration of unplanned functional forms.
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Affiliation(s)
- Jonathan Pascalie
- Complex Systems
Institute, Paris Ile-de-France (ISC-PIF), CNRS UPS3611, Paris, France
- Algorithmic,
Complexity and Logic Laboratory (LACL), Université Paris-Est Créteil, Créteil, France
- Computer
Science Research Institute (IRIT), CNRS UMR5505, Université de Toulouse, Toulouse, France
| | - Martin Potier
- Algorithmic,
Complexity and Logic Laboratory (LACL), Université Paris-Est Créteil, Créteil, France
| | - Taras Kowaliw
- Complex Systems
Institute, Paris Ile-de-France (ISC-PIF), CNRS UPS3611, Paris, France
| | - Jean-Louis Giavitto
- Institute for Research
and Coordination Acoustic/Music (IRCAM), CNRS UMR9912, Paris, France
| | - Olivier Michel
- Algorithmic,
Complexity and Logic Laboratory (LACL), Université Paris-Est Créteil, Créteil, France
| | - Antoine Spicher
- Algorithmic,
Complexity and Logic Laboratory (LACL), Université Paris-Est Créteil, Créteil, France
| | - René Doursat
- Complex Systems
Institute, Paris Ile-de-France (ISC-PIF), CNRS UPS3611, Paris, France
- Informatics
Research Centre (IRC), Manchester Metropolitan University, Manchester M1 5GD, U.K
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119
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Spontaneous formation of spiral-like patterns with distinct periodic physical properties by confined electrodeposition of Co-In disks. Sci Rep 2016; 6:30398. [PMID: 27462025 PMCID: PMC4961954 DOI: 10.1038/srep30398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/27/2016] [Indexed: 11/09/2022] Open
Abstract
Spatio-temporal patterns are ubiquitous in different areas of materials science and biological systems. However, typically the motifs in these types of systems present a random distribution with many possible different structures. Herein, we demonstrate that controlled spatio-temporal patterns, with reproducible spiral-like shapes, can be obtained by electrodeposition of Co-In alloys inside a confined circular geometry (i.e., in disks that are commensurate with the typical size of the spatio-temporal features). These patterns are mainly of compositional nature, i.e., with virtually no topographic features. Interestingly, the local changes in composition lead to a periodic modulation of the physical (electric, magnetic and mechanical) properties. Namely, the Co-rich areas show higher saturation magnetization and electrical conductivity and are mechanically harder than the In-rich ones. Thus, this work reveals that confined electrodeposition of this binary system constitutes an effective procedure to attain template-free magnetic, electric and mechanical surface patterning with specific and reproducible shapes.
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120
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Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns. Phys Life Rev 2016; 19:107-121. [PMID: 27478087 DOI: 10.1016/j.plrev.2016.07.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/30/2016] [Accepted: 07/08/2016] [Indexed: 11/21/2022]
Abstract
Many ecosystems develop strikingly regular spatial patterns because of small-scale interactions between organisms, a process generally referred to as spatial self-organization. Self-organized spatial patterns are important determinants of the functioning of ecosystems, promoting the growth and survival of the involved organisms, and affecting the capacity of the organisms to cope with changing environmental conditions. The predominant explanation for self-organized pattern formation is spatial heterogeneity in establishment, growth and mortality, resulting from the self-organization processes. A number of recent studies, however, have revealed that movement of organisms can be an important driving process creating extensive spatial patterning in many ecosystems. Here, we review studies that detail movement-based pattern formation in contrasting ecological settings. Our review highlights that a common principle, where movement of organisms is density-dependent, explains observed spatial regular patterns in all of these studies. This principle, well known to physics as the Cahn-Hilliard principle of phase separation, has so-far remained unrecognized as a general mechanism for self-organized complexity in ecology. Using the examples presented in this paper, we explain how this movement principle can be discerned in ecological settings, and clarify how to test this mechanism experimentally. Our study highlights that animal movement, both in isolation and in unison with other processes, is an important mechanism for regular pattern formation in ecosystems.
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121
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Weber M, Buceta J. The cellular Ising model: a framework for phase transitions in multicellular environments. J R Soc Interface 2016; 13:20151092. [PMID: 27307510 PMCID: PMC4938077 DOI: 10.1098/rsif.2015.1092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Inspired by the Ising model, we introduce a gene regulatory network that induces a phase transition that coordinates robustly the behaviour of cell ensembles. The building blocks of the design are the so-called toggle switch interfaced with two quorum sensing modules, Las and Lux. We show that as a function of the transport rate of signalling molecules across the cell membrane the population undergoes a spontaneous symmetry breaking from cells individually switching their phenotypes to a global collective phenotypic organization. By characterizing the critical behaviour, we reveal some properties, such as phenotypic memory and hypersensitivity, with relevance in the field of synthetic biology. We argue that our results can be extrapolated to other multicellular systems and be a generic framework for collective decision-making processes.
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Affiliation(s)
- Marc Weber
- Parc Científic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Javier Buceta
- Department of Chemical and Biomolecular Engineering, Bioengineering Program, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA
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122
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Borek B, Hasty J, Tsimring L. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS One 2016; 11:e0153679. [PMID: 27148743 PMCID: PMC4858293 DOI: 10.1371/journal.pone.0153679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/01/2016] [Indexed: 01/30/2023] Open
Abstract
The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems.
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Affiliation(s)
- Bartłomiej Borek
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
| | - Jeff Hasty
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0412, United States of America
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0116, United States of America
| | - Lev Tsimring
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
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123
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Jia X, Liu C, Song H, Ding M, Du J, Ma Q, Yuan Y. Design, analysis and application of synthetic microbial consortia. Synth Syst Biotechnol 2016; 1:109-117. [PMID: 29062933 PMCID: PMC5640696 DOI: 10.1016/j.synbio.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 12/17/2022] Open
Abstract
The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.
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Affiliation(s)
- Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Chang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Qian Ma
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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124
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Wang LZ, Wu F, Flores K, Lai YC, Wang X. Build to understand: synthetic approaches to biology. Integr Biol (Camb) 2016; 8:394-408. [PMID: 26686885 PMCID: PMC4837018 DOI: 10.1039/c5ib00252d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this review we discuss how synthetic biology facilitates the task of investigating genetic circuits that are observed in naturally occurring biological systems. Specifically, we give examples where experimentation with synthetic gene circuits has been used to understand four fundamental mechanisms intrinsic to development and disease: multistability, stochastic gene expression, oscillations, and cell-cell communication. Within each area, we also discuss how mathematical modeling has been employed as an essential tool to guide the design of novel gene circuits and as a theoretical basis for exploring circuit topologies exhibiting robust behaviors in the presence of noise.
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Affiliation(s)
- Le-Zhi Wang
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Fuqing Wu
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, USA.
| | - Kevin Flores
- Department of Mathematics, Center for Quantitative Sciences in Biomedicine, Center for Research in Scientific Computation, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Ying-Cheng Lai
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
- Institute for Complex Systems and Mathematical Biology, King’s College, University of Aberdeen, Aberdeen AB24 3UE, UK
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, USA.
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125
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Ollé-Vila A, Duran-Nebreda S, Conde-Pueyo N, Montañez R, Solé R. A morphospace for synthetic organs and organoids: the possible and the actual. Integr Biol (Camb) 2016; 8:485-503. [PMID: 27032985 DOI: 10.1039/c5ib00324e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.
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Affiliation(s)
- Aina Ollé-Vila
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
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126
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Woloszynek S, Pastor S, Mell JC, Nandi N, Sokhansanj B, Rosen GL. Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:67-124. [PMID: 27017007 DOI: 10.1016/bs.ircmb.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.
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Affiliation(s)
- S Woloszynek
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America
| | - S Pastor
- Department of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - J C Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - N Nandi
- Division of Gastroenterology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - B Sokhansanj
- McKool Smith Hennigan, P. C., Redwood Shores, CA, United States of America
| | - G L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.
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127
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Cachat E, Liu W, Martin KC, Yuan X, Yin H, Hohenstein P, Davies JA. 2- and 3-dimensional synthetic large-scale de novo patterning by mammalian cells through phase separation. Sci Rep 2016; 6:20664. [PMID: 26857385 PMCID: PMC4746622 DOI: 10.1038/srep20664] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/11/2016] [Indexed: 01/09/2023] Open
Abstract
Synthetic biology provides an opportunity for the construction and exploration of alternative solutions to biological problems - solutions different from those chosen by natural life. To this end, synthetic biologists have built new sensory systems, cellular memories, and alternative genetic codes. There is a growing interest in applying synthetic approaches to multicellular systems, especially in relation to multicellular self-organization. Here we describe a synthetic biological system that confers large-scale de novo patterning activity on 2-D and 3-D populations of mammalian cells. Instead of using the reaction-diffusion mechanisms common in real embryos, our system uses cadherin-mediated phase separation, inspired by the known phenomenon of cadherin-based sorting. An engineered self-organizing, large-scale patterning system requiring no prior spatial cue may be a significant step towards the construction of self-assembling synthetic tissues.
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Affiliation(s)
- Elise Cachat
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK
| | - Weijia Liu
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK
| | - Kim C. Martin
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK
| | - Xiaofei Yuan
- School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
| | - Huabing Yin
- School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
| | - Peter Hohenstein
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jamie A. Davies
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK,
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128
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Ciechonska M, Grob A, Isalan M. From noise to synthetic nucleoli: can synthetic biology achieve new insights? Integr Biol (Camb) 2016; 8:383-93. [PMID: 26751735 DOI: 10.1039/c5ib00271k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."
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Affiliation(s)
- Marta Ciechonska
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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129
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Branduardi P. Synthetic Biology for Cellular Remodelling to Elicit Industrially Relevant Microbial Phenotypes. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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130
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131
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Zhang H, Lin M, Shi H, Ji W, Huang L, Zhang X, Shen S, Gao R, Wu S, Tian C, Yang Z, Zhang G, He S, Wang H, Saw T, Chen Y, Ouyang Q. Programming a Pavlovian-like conditioning circuit in Escherichia coli. Nat Commun 2015; 5:3102. [PMID: 24434523 DOI: 10.1038/ncomms4102] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 12/13/2013] [Indexed: 11/09/2022] Open
Abstract
Synthetic genetic circuits are programmed in living cells to perform predetermined cellular functions. However, designing higher-order genetic circuits for sophisticated cellular activities remains a substantial challenge. Here we program a genetic circuit that executes Pavlovian-like conditioning, an archetypical sequential-logic function, in Escherichia coli. The circuit design is first specified by the subfunctions that are necessary for the single simultaneous conditioning, and is further genetically implemented using four function modules. During this process, quantitative analysis is applied to the optimization of the modules and fine-tuning of the interconnections. Analogous to classical Pavlovian conditioning, the resultant circuit enables the cells to respond to a certain stimulus only after a conditioning process. We show that, although the conditioning is digital in single cells, a dynamically progressive conditioning process emerges at the population level. This circuit, together with its rational design strategy, is a key step towards the implementation of more sophisticated cellular computing.
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Affiliation(s)
- Haoqian Zhang
- 1] Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China [2] Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China [3] Centre for Quantitative Biology, Peking University, Beijing 100871, China [4]
| | - Min Lin
- 1] Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China [2]
| | - Handuo Shi
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Weiyue Ji
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Longwen Huang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Xiaomeng Zhang
- 1] Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China [2] Centre for Quantitative Biology, Peking University, Beijing 100871, China
| | - Shan Shen
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Rencheng Gao
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Shuke Wu
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Chengzhe Tian
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Zhenglin Yang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Guosheng Zhang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Siheng He
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Hao Wang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Tiffany Saw
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Yiwei Chen
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijing 100871, China
| | - Qi Ouyang
- 1] Peking-Tsinghua Joint Centre for Life Sciences, Peking University, Beijing 100871, China [2] Centre for Quantitative Biology, Peking University, Beijing 100871, China [3] The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
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132
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Blanchard AE, Lu T. Bacterial social interactions drive the emergence of differential spatial colony structures. BMC SYSTEMS BIOLOGY 2015; 9:59. [PMID: 26377684 PMCID: PMC4573487 DOI: 10.1186/s12918-015-0188-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/08/2015] [Indexed: 12/25/2022]
Abstract
Background Social interactions have been increasingly recognized as one of the major factors that contribute to the dynamics and function of bacterial communities. To understand their functional roles and enable the design of robust synthetic consortia, one fundamental step is to determine the relationship between the social interactions of individuals and the spatiotemporal structures of communities. Results We present a systematic computational survey on this relationship for two-species communities by developing and utilizing a hybrid computational framework that combines discrete element techniques with reaction-diffusion equations. We found that deleterious interactions cause an increased variance in relative abundance, a drastic decrease in surviving lineages, and a rough expanding front. In contrast, beneficial interactions contribute to a reduced variance in relative abundance, an enhancement in lineage number, and a smooth expanding front. We also found that mutualism promotes spatial homogeneity and population robustness while competition increases spatial segregation and population fluctuations. To examine the generality of these findings, a large set of initial conditions with varying density and species abundance was tested and analyzed. In addition, a simplified mathematical model was developed to provide an analytical interpretation of the findings. Conclusions This work advances our fundamental understanding of bacterial social interactions and population structures and, simultaneously, benefits synthetic biology for facilitated engineering of artificial microbial consortia. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0188-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew E Blanchard
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, 61801, USA.
| | - Ting Lu
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, 61801, USA. .,Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 West Springfield Avenue, Urbana, 61801, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, 61801, USA.
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133
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Drees B, Reiger M, Jung K, Bischofs IB. A modular view of the diversity of cell-density-encoding schemes in bacterial quorum-sensing systems. Biophys J 2015; 107:266-77. [PMID: 24988360 PMCID: PMC4119280 DOI: 10.1016/j.bpj.2014.05.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 11/29/2022] Open
Abstract
Certain environmental parameters are accessible to cells only indirectly and require an encoding step for cells to retrieve the relevant information. A prominent example is the phenomenon of quorum sensing by microorganisms, where information about cell density is encoded by means of secreted signaling molecules. The mapping of cell density to signal molecule concentration and the corresponding network modules involved have been at least partially characterized in many bacteria, and vary markedly between different systems. In this study, we investigate theoretically how differences in signal transport, signal modification, and site of signal detection shape the encoding function and affect the sensitivity and the noise characteristics of the cell-density-encoding process. We find that different modules are capable of implementing both fairly basic as well as more complex encoding schemes, whose qualitative characteristics vary with cell density and are linked to network architecture, providing the basis for a hierarchical classification scheme. We exploit the tight relationship between encoding behavior and network architecture to constrain the network topology of partially characterized natural systems, and verify one such prediction by showing experimentally that Vibrio harveyi is capable of importing Autoinducer 2. The framework developed in this research can serve not only to guide reverse engineering of natural systems but also to stimulate the design of synthetic systems and generally facilitate a better understanding of the complexities arising in the quorum-sensing process because of variations in the physical organization of the encoder network module.
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Affiliation(s)
- Bastian Drees
- Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; BioQuant, University of Heidelberg, Germany
| | - Matthias Reiger
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians-Universität München, Germany.
| | - Ilka B Bischofs
- Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; BioQuant, University of Heidelberg, Germany.
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134
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Artificial cell-cell communication as an emerging tool in synthetic biology applications. J Biol Eng 2015; 9:13. [PMID: 26265937 PMCID: PMC4531478 DOI: 10.1186/s13036-015-0011-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/25/2015] [Indexed: 01/14/2023] Open
Abstract
Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.
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135
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Love AC. Collaborative explanation, explanatory roles, and scientific explaining in practice. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2015; 52:88-94. [PMID: 26193791 DOI: 10.1016/j.shpsa.2015.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
Scientific explanation is a perennial topic in philosophy of science, but the literature has fragmented into specialized discussions in different scientific disciplines. An increasing attention to scientific practice by philosophers is (in part) responsible for this fragmentation and has put pressure on criteria of adequacy for philosophical accounts of explanation, usually demanding some form of pluralism. This commentary examines the arguments offered by Fagan and Woody with respect to explanation and understanding in scientific practice. I begin by scrutinizing Fagan's concept of collaborative explanation, highlighting its distinctive advantages and expressing concern about several of its assumptions. Then I analyze Woody's attempt to reorient discussions of scientific explanation around functional considerations, elaborating on the wider implications of this methodological recommendation. I conclude with reflections on synergies and tensions that emerge when the two papers are juxtaposed and how these draw attention to critical issues that confront ongoing philosophical analyses of scientific explanation.
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Affiliation(s)
- Alan C Love
- University of Minnesota - Twin Cities, Department of Philosophy, Minnesota Center for Philosophy of Science, 831 Heller Hall, 271 19th Ave S, Minneapolis, MN 55455-0310, United States.
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136
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Mechanically-driven phase separation in a growing bacterial colony. Proc Natl Acad Sci U S A 2015; 112:E2166-73. [PMID: 25870260 DOI: 10.1073/pnas.1504948112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Secretion of extracellular polymeric substances (EPSs) by growing bacteria is an integral part of forming biofilm-like structures. In such dense systems, mechanical interactions among the structural components can be expected to significantly contribute to morphological properties. Here, we use a particle-based modeling approach to study the self-organization of nonmotile rod-shaped bacterial cells growing on a solid substrate in the presence of self-produced EPSs. In our simulation, all of the components interact mechanically via repulsive forces, occurring as the bacterial cells grow and divide (via consuming diffusing nutrient) and produce EPSs. Based on our simulation, we show that mechanical interactions control the collective behavior of the system. In particular, we find that the presence of nonadsorbing EPSs can lead to spontaneous aggregation of bacterial cells by a depletion attraction and thereby generates phase separated patterns in the nonequilibrium growing colony. Both repulsive interactions between cell and EPSs and the overall concentration of EPSs are important factors in the self-organization in a nonequilibrium growing colony. Furthermore, we investigate the interplay of mechanics with the nutrient diffusion and consumption by bacterial cells and observe that suppression of branch formation occurs due to EPSs compared with the case where no EPS is produced.
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137
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Davis RM, Muller RY, Haynes KA. Can the natural diversity of quorum-sensing advance synthetic biology? Front Bioeng Biotechnol 2015; 3:30. [PMID: 25806368 PMCID: PMC4354409 DOI: 10.3389/fbioe.2015.00030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/21/2015] [Indexed: 12/12/2022] Open
Abstract
Quorum-sensing networks enable bacteria to sense and respond to chemical signals produced by neighboring bacteria. They are widespread: over 100 morphologically and genetically distinct species of eubacteria are known to use quorum sensing to control gene expression. This diversity suggests the potential to use natural protein variants to engineer parallel, input-specific, cell-cell communication pathways. However, only three distinct signaling pathways, Lux, Las, and Rhl, have been adapted for and broadly used in engineered systems. The paucity of unique quorum-sensing systems and their propensity for crosstalk limits the usefulness of our current quorum-sensing toolkit. This review discusses the need for more signaling pathways, roadblocks to using multiple pathways in parallel, and strategies for expanding the quorum-sensing toolbox for synthetic biology.
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Affiliation(s)
- René Michele Davis
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA ; Biological Design Graduate Program, Arizona State University , Tempe, AZ , USA
| | - Ryan Yue Muller
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, AZ , USA ; School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Karmella Ann Haynes
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA
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138
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Li Y, Jiang Y, Chen H, Liao W, Li Z, Weiss R, Xie Z. Modular construction of mammalian gene circuits using TALE transcriptional repressors. Nat Chem Biol 2015; 11:207-213. [PMID: 25643171 PMCID: PMC4333066 DOI: 10.1038/nchembio.1736] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 11/25/2014] [Indexed: 01/14/2023]
Abstract
An important goal of synthetic biology is the rational design and predictable implementation of synthetic gene circuits using standardized and interchangeable parts. However, engineering of complex circuits in mammalian cells is currently limited by the availability of well-characterized and orthogonal transcriptional repressors. Here, we introduce a library of 26 reversible transcription activator-like effector repressors (TALERs) that bind newly designed hybrid promoters and exert transcriptional repression through steric hindrance of key transcriptional initiation elements. We demonstrate that using the input-output transfer curves of our TALERs enables accurate prediction of the behavior of modularly assembled TALER cascade and switch circuits. We also show that TALER switches employing feedback regulation exhibit improved accuracy for microRNA-based HeLa cancer cell classification versus HEK293 cells. Our TALER library is a valuable toolkit for modular engineering of synthetic circuits, enabling programmable manipulation of mammalian cells and helping elucidate design principles of coupled transcriptional and microRNA-mediated post-transcriptional regulation.
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Affiliation(s)
- Yinqing Li
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames St, Cambridge MA 02142, USA
| | - Yun Jiang
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - He Chen
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Weixi Liao
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zhihua Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118
| | - Ron Weiss
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames St, Cambridge MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames St, Cambridge MA 02142, USA
| | - Zhen Xie
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics; Department of Automation, Tsinghua University, Beijing 100084, China
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139
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Hiscock TW, Megason SG. Mathematically guided approaches to distinguish models of periodic patterning. Development 2015; 142:409-19. [PMID: 25605777 PMCID: PMC4302999 DOI: 10.1242/dev.107441] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
How periodic patterns are generated is an open question. A number of mechanisms have been proposed--most famously, Turing's reaction-diffusion model. However, many theoretical and experimental studies focus on the Turing mechanism while ignoring other possible mechanisms. Here, we use a general model of periodic patterning to show that different types of mechanism (molecular, cellular, mechanical) can generate qualitatively similar final patterns. Observation of final patterns is therefore not sufficient to favour one mechanism over others. However, we propose that a mathematical approach can help to guide the design of experiments that can distinguish between different mechanisms, and illustrate the potential value of this approach with specific biological examples.
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Affiliation(s)
- Tom W Hiscock
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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140
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Barcena Menendez D, Senthivel VR, Isalan M. Sender-receiver systems and applying information theory for quantitative synthetic biology. Curr Opin Biotechnol 2015; 31:101-7. [PMID: 25282688 PMCID: PMC4332572 DOI: 10.1016/j.copbio.2014.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 12/31/2022]
Abstract
Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.
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Affiliation(s)
- Diego Barcena Menendez
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Vivek Raj Senthivel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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141
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Hinz DF, Panchenko A, Kim TY, Fried E. Motility versus fluctuations in mixtures of self-motile and passive agents. SOFT MATTER 2014; 10:9082-9089. [PMID: 25300877 DOI: 10.1039/c4sm01562b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many biological systems consist of self-motile and passive agents both of which contribute to overall functionality. However, little is known about the properties of such mixtures. Here we formulate a model for mixtures of self-motile and passive agents and show that the model gives rise to three different dynamical phases: a disordered mesoturbulent phase, a polar flocking phase, and a vortical phase characterized by large-scale counter rotating vortices. We use numerical simulations to construct a phase diagram and compare the statistical properties of the different phases with observed features of self-motile bacterial suspensions. Our findings afford specific insights regarding the interaction of microorganisms and passive particles and provide novel strategic guidance for efficient technological realizations of artificial active matter.
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Affiliation(s)
- Denis F Hinz
- Kamstrup A/S, Industrivej 28, Stilling, 8660 Skanderborg, Denmark
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142
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Kong W, Celik V, Liao C, Hua Q, Lu T. Programming the group behaviors of bacterial communities with synthetic cellular communication. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0024-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Synthetic biology is a newly emerged research discipline that focuses on the engineering of novel cellular behaviors and functionalities through the creation of artificial gene circuits. One important class of synthetic circuits currently under active development concerns the programming of bacterial cellular communication and collective population-scale behaviors. Because of the ubiquity of cell-cell interactions within bacterial communities, having an ability of engineering these circuits is vital to programming robust cellular behaviors. Here, we highlight recent advances in communication-based synthetic gene circuits by first discussing natural communication systems and then surveying various functional engineered circuits, including those for population density control, temporal synchronization, spatial organization, and ecosystem formation. We conclude by summarizing recent advances, outlining existing challenges, and discussing potential applications and future opportunities.
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143
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Schaerli Y, Munteanu A, Gili M, Cotterell J, Sharpe J, Isalan M. A unified design space of synthetic stripe-forming networks. Nat Commun 2014; 5:4905. [PMID: 25247316 PMCID: PMC4172969 DOI: 10.1038/ncomms5905] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/02/2014] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
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Affiliation(s)
- Yolanda Schaerli
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andreea Munteanu
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Magüi Gili
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Cotterell
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mark Isalan
- 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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144
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Oishi K, Klavins E. Framework for engineering finite state machines in gene regulatory networks. ACS Synth Biol 2014; 3:652-65. [PMID: 24932713 DOI: 10.1021/sb4001799] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Finite state machines are fundamental computing devices at the core of many models of computation. In biology, finite state machines are commonly used as models of development in multicellular organisms. However, it remains unclear to what extent cells can remember state, how they can transition from one state to another reliably, and whether the existing parts available to the synthetic biologist are sufficient to implement specified finite state machines in living cells. Furthermore, how complex multicellular behaviors can be realized by multiple cells coordinating their states with signaling, growth, and division is not well understood. Here, we describe a method by which any finite state machine can be built using nothing more than a suitably engineered network of readily available repressing transcription factors. In particular, we show the mathematical equivalence of finite state machines with a Boolean model of gene regulatory networks. We describe how such networks can be realized with a small class of promoters and transcription factors. To demonstrate the effectiveness of our approach, we show that the behavior of the coarse grained ideal Boolean network model approximates a fine grained delay differential equation model of gene expression. Finally, we explore a framework for the design of more complex systems via an example, synthetic bacterial microcolony edge detection, that illustrates how finite state machines could be used together with cell signaling to construct novel multicellular behaviors.
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Affiliation(s)
- Kevin Oishi
- Department of Electrical
Engineering, University of Washington, Seattle 98195, United States
| | - Eric Klavins
- Department of Electrical
Engineering, University of Washington, Seattle 98195, United States
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145
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Matas-Navarro R, Golestanian R, Liverpool TB, Fielding SM. Hydrodynamic suppression of phase separation in active suspensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:032304. [PMID: 25314443 DOI: 10.1103/physreve.90.032304] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 05/15/2023]
Abstract
We simulate with hydrodynamics a suspension of active disks squirming through a Newtonian fluid. We explore numerically the full range of squirmer area fractions from dilute to close packed and show that "motility induced phase separation," which was recently proposed to arise generically in active matter, and which has been seen in simulations of active Brownian disks, is strongly suppressed by hydrodynamic interactions. We give an argument for why this should be the case and support it with counterpart simulations of active Brownian disks in a parameter regime that provides a closer counterpart to hydrodynamic suspensions than in previous studies.
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Affiliation(s)
- Ricard Matas-Navarro
- Department of Physics, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK
| | - Ramin Golestanian
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3NP, UK
| | | | - Suzanne M Fielding
- Department of Physics, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK
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146
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Abstract
Cells often receive signals to proliferate, but how population density is controlled is unclear. Hart et al. now show that a single secreted molecule that instructs both proliferation and death in T cells establishes a bistable response: the population is driven to either extinction or to a homeostatically defined density.
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Affiliation(s)
- Hyun Youk
- Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wendell A Lim
- Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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147
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Olson EJ, Tabor JJ. Optogenetic characterization methods overcome key challenges in synthetic and systems biology. Nat Chem Biol 2014; 10:502-11. [PMID: 24937068 DOI: 10.1038/nchembio.1559] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/21/2014] [Indexed: 12/28/2022]
Abstract
Systems biologists aim to understand how organism-level processes, such as differentiation and multicellular development, are encoded in DNA. Conversely, synthetic biologists aim to program systems-level biological processes, such as engineered tissue growth, by writing artificial DNA sequences. To achieve their goals, these groups have adapted a hierarchical electrical engineering framework that can be applied in the forward direction to design complex biological systems or in the reverse direction to analyze evolved networks. Despite much progress, this framework has been limited by an inability to directly and dynamically characterize biological components in the varied contexts of living cells. Recently, two optogenetic methods for programming custom gene expression and protein localization signals have been developed and used to reveal fundamentally new information about biological components that respond to those signals. This basic dynamic characterization approach will be a major enabling technology in synthetic and systems biology.
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Affiliation(s)
- Evan J Olson
- Graduate Program in Applied Physics, Rice University, Houston, Texas, USA
| | - Jeffrey J Tabor
- 1] Department of Bioengineering, Rice University, Houston, Texas, USA. [2] Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA
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148
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Song H, Ding MZ, Jia XQ, Ma Q, Yuan YJ. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev 2014; 43:6954-81. [PMID: 25017039 DOI: 10.1039/c4cs00114a] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.
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Affiliation(s)
- Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, and Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China.
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149
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Wittkowski R, Tiribocchi A, Stenhammar J, Allen RJ, Marenduzzo D, Cates ME. Scalar φ4 field theory for active-particle phase separation. Nat Commun 2014; 5:4351. [DOI: 10.1038/ncomms5351] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 06/09/2014] [Indexed: 11/09/2022] Open
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150
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Fu X, Huang W. Quantitative measurement and analysis in a synthetic pattern formation multicellular system. Methods Mol Biol 2014; 1151:137-49. [PMID: 24838884 DOI: 10.1007/978-1-4939-0554-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Pattern formation has been studied for more than a century in biology. In recent years there are increasing interests in studying it using bacteria and synthetic biology tools to program intercellular communication and cellular response to environment. Quantitative measurement is critical to dissect the interplay between the synthetic gene circuits with underline cellular processes and verify the mechanism determining the pattern formation. Here, we describe simple optical setups for quantitative measurements of the cell density and growth and spatial-temporal dynamic characterization of E. coli pattern formation in soft agar plates.
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Affiliation(s)
- Xiongfei Fu
- Department of Physics, The University of Hong Kong, Room 518, Chong Yuet Ming Physics Building, Pokfulam, Hong Kong, China
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