151
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Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK. Synthesis and patterning of tunable multiscale materials with engineered cells. NATURE MATERIALS 2014; 13:515-23. [PMID: 24658114 PMCID: PMC4063449 DOI: 10.1038/nmat3912] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 02/11/2014] [Indexed: 05/03/2023]
Abstract
Many natural biological systems--such as biofilms, shells and skeletal tissues--are able to assemble multifunctional and environmentally responsive multiscale assemblies of living and non-living components. Here, by using inducible genetic circuits and cellular communication circuits to regulate Escherichia coli curli amyloid production, we show that E. coli cells can organize self-assembling amyloid fibrils across multiple length scales, producing amyloid-based materials that are either externally controllable or undergo autonomous patterning. We also interfaced curli fibrils with inorganic materials, such as gold nanoparticles (AuNPs) and quantum dots (QDs), and used these capabilities to create an environmentally responsive biofilm-based electrical switch, produce gold nanowires and nanorods, co-localize AuNPs with CdTe/CdS QDs to modulate QD fluorescence lifetimes, and nucleate the formation of fluorescent ZnS QDs. This work lays a foundation for synthesizing, patterning, and controlling functional composite materials with engineered cells.
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Affiliation(s)
- Allen Y. Chen
- Biophysics Program, Harvard University, Cambridge, MA
02138, USA
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
- Harvard-MIT Health Sciences and Technology, Institute for
Medical Engineering and Science, 77 Massachusetts Avenue, Cambridge, MA 02139,
USA
| | - Zhengtao Deng
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Amanda N. Billings
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Urartu O.S. Seker
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Michelle Y. Lu
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Robert J. Citorik
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
- MIT Microbiology Program, 77 Massachusetts Avenue,
Cambridge MA 02139, USA
| | - Bijan Zakeri
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
| | - Timothy K. Lu
- Biophysics Program, Harvard University, Cambridge, MA
02138, USA
- Department of Electrical Engineering & Computer
Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
MA 02139, USA
- Department of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square,
Cambridge MA 02139, USA
- MIT Microbiology Program, 77 Massachusetts Avenue,
Cambridge MA 02139, USA
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152
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Hwang IY, Tan MH, Koh E, Ho CL, Poh CL, Chang MW. Reprogramming microbes to be pathogen-seeking killers. ACS Synth Biol 2014; 3:228-37. [PMID: 24020906 DOI: 10.1021/sb400077j] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent examples of new genetic circuits that enable cells to acquire biosynthetic capabilities, such as specific pathogen killing, present an attractive therapeutic application of synthetic biology. Herein, we demonstrate a novel genetic circuit that reprograms Escherichia coli to specifically recognize, migrate toward, and eradicate both dispersed and biofilm-encased pathogenic Pseudomonas aeruginosa cells. The reprogrammed E. coli degraded the mature biofilm matrix and killed the latent cells encapsulated within by expressing and secreting the antimicrobial peptide microcin S and the nuclease DNaseI upon the detection of quorum sensing molecules naturally secreted by P. aeruginosa. Furthermore, the reprogrammed E. coli exhibited directed motility toward the pathogen through regulated expression of CheZ in response to the quorum sensing molecules. By integrating the pathogen-directed motility with the dual antimicrobial activity in E. coli, we achieved signifincantly improved killing activity against planktonic and mature biofilm cells due to target localization, thus creating an active pathogen seeking killer E. coli.
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Affiliation(s)
- In Young Hwang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62
Nanyang Drive, Singapore 637459
| | - Mui Hua Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62
Nanyang Drive, Singapore 637459
| | - Elvin Koh
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62
Nanyang Drive, Singapore 637459
| | - Chun Loong Ho
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62
Nanyang Drive, Singapore 637459
| | - Chueh Loo Poh
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62
Nanyang Drive, Singapore 637459
| | - Matthew Wook Chang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62
Nanyang Drive, Singapore 637459
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153
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154
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Liu C, Fu X, Huang JD. Synthetic biology: a new approach to study biological pattern formation. QUANTITATIVE BIOLOGY 2014. [DOI: 10.1007/s40484-013-0021-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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155
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Biomedically relevant circuit-design strategies in mammalian synthetic biology. Mol Syst Biol 2014; 9:691. [PMID: 24061539 PMCID: PMC3792348 DOI: 10.1038/msb.2013.48] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 08/07/2013] [Indexed: 12/24/2022] Open
Abstract
The development and progress in synthetic biology has been remarkable. Although still in its infancy, synthetic biology has achieved much during the past decade. Improvements in genetic circuit design have increased the potential for clinical applicability of synthetic biology research. What began as simple transcriptional gene switches has rapidly developed into a variety of complex regulatory circuits based on the transcriptional, translational and post-translational regulation. Instead of compounds with potential pharmacologic side effects, the inducer molecules now used are metabolites of the human body and even members of native cell signaling pathways. In this review, we address recent progress in mammalian synthetic biology circuit design and focus on how novel designs push synthetic biology toward clinical implementation. Groundbreaking research on the implementation of optogenetics and intercellular communications is addressed, as particularly optogenetics provides unprecedented opportunities for clinical application. Along with an increase in synthetic network complexity, multicellular systems are now being used to provide a platform for next-generation circuit design.
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156
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Crowning: a novel Escherichia coli colonizing behaviour generating a self-organized corona. BMC Res Notes 2014; 7:108. [PMID: 24568619 PMCID: PMC3936827 DOI: 10.1186/1756-0500-7-108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/17/2014] [Indexed: 12/03/2022] Open
Abstract
Background Encased in a matrix of extracellular polymeric substances (EPS) composed of flagella, adhesins, amyloid fibers (curli), and exopolysaccharides (cellulose, β-1,6-N-acetyl-D-glucosamine polymer-PGA-, colanic acid), the bacteria Escherichia coli is able to attach to and colonize different types of biotic and abiotic surfaces forming biofilms and colonies of intricate morphological architectures. Many of the biological aspects that underlie the generation and development of these E. coli’s formations are largely poorly understood. Results Here, we report the characterization of a novel E. coli sessile behaviour termed "crowning" due to the bacterial generation of a new 3-D architectural pattern: a corona. This bacterial pattern is formed by joining bush-like multilayered "coronal flares or spikes" arranged in a ring, which self-organize through the growth, self-clumping and massive self-aggregation of cells tightly interacting inside semisolid agar on plastic surfaces. Remarkably, the corona’s formation is developed independently of the adhesiveness of the major components of E. coli’s EPS matrix, the function of chemotaxis sensory system, type 1 pili and the biofilm master regulator CsgD, but its formation is suppressed by flagella-driven motility and glucose. Intriguingly, this glucose effect on the corona development is not mediated by the classical catabolic repression system, the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex. Thus, corona formation departs from the canonical regulatory transcriptional core that controls biofilm formation in E. coli. Conclusions With this novel "crowning" activity, E. coli expands its repertoire of colonizing collective behaviours to explore, invade and exploit environments whose critical viscosities impede flagella driven-motility.
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157
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Youk H, Lim WA. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science 2014; 343:1242782. [PMID: 24503857 PMCID: PMC4145839 DOI: 10.1126/science.1242782] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cells that secrete and sense the same signaling molecule are ubiquitous. To uncover the functional capabilities of the core "secrete-and-sense" circuit motif shared by these cells, we engineered yeast to secrete and sense the mating pheromone. Perturbing each circuit element revealed parameters that control the degree to which the cell communicated with itself versus with its neighbors. This tunable interplay of self-communication and neighbor communication enables cells to span a diverse repertoire of cellular behaviors. These include a cell being asocial by responding only to itself and social through quorum sensing, and an isogenic population of cells splitting into social and asocial subpopulations. A mathematical model explained these behaviors. The versatility of the secrete-and-sense circuit motif may explain its recurrence across species.
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Affiliation(s)
- Hyun Youk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
- Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Wendell A. Lim
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
- Center for Systems and Synthetic Biology, 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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158
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Meyer M, Schimansky-Geier L, Romanczuk P. Active Brownian agents with concentration-dependent chemotactic sensitivity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022711. [PMID: 25353513 DOI: 10.1103/physreve.89.022711] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 06/04/2023]
Abstract
We study a biologically motivated model of overdamped, autochemotactic Brownian agents with concentration-dependent chemotactic sensitivity. The agents in our model move stochastically and produce a chemical ligand at their current position. The ligand concentration obeys a reaction-diffusion equation and acts as a chemoattractant for the agents, which bias their motion towards higher concentrations of the dynamically altered chemical field. We explore the impact of concentration-dependent response to chemoattractant gradients on large-scale pattern formation, by deriving a coarse-grained macroscopic description of the individual-based model, and compare the conditions for emergence of inhomogeneous solutions for different variants of the chemotactic sensitivity. We focus primarily on the so-called receptor-law sensitivity, which models a nonlinear decrease of chemotactic sensitivity with increasing ligand concentration. Our results reveal qualitative differences between the receptor law, the constant chemotactic response, and the so-called log law, with respect to stability of the homogeneous solution, as well as the emergence of different patterns (labyrinthine structures, clusters, and bubbles) via spinodal decomposition or nucleation. We discuss two limiting cases, where the model can be reduced to the dynamics of single species: (I) the agent density governed by a density-dependent effective diffusion coefficient and (II) the ligand field with an effective bistable, time-dependent reaction rate. In the end, we turn to single clusters of agents, studying domain growth and determining mean characteristics of the stationary inhomogeneous state. Analytical results are confirmed and extended by large-scale GPU simulations of the individual based model.
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Affiliation(s)
- Marcel Meyer
- Department of Physics, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Lutz Schimansky-Geier
- Department of Physics, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Pawel Romanczuk
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
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159
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Marquez-Lago TT, Padilla P. A selection criterion for patterns in reaction-diffusion systems. Theor Biol Med Model 2014; 11:7. [PMID: 24476200 PMCID: PMC3925790 DOI: 10.1186/1742-4682-11-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alan Turing's work in Morphogenesis has received wide attention during the past 60 years. The central idea behind his theory is that two chemically interacting diffusible substances are able to generate stable spatial patterns, provided certain conditions are met. Ever since, extensive work on several kinds of pattern-generating reaction diffusion systems has been done. Nevertheless, prediction of specific patterns is far from being straightforward, and a great deal of interest in deciphering how to generate specific patterns under controlled conditions prevails. RESULTS Techniques allowing one to predict what kind of spatial structure will emerge from reaction-diffusion systems remain unknown. In response to this need, we consider a generalized reaction diffusion system on a planar domain and provide an analytic criterion to determine whether spots or stripes will be formed. Our criterion is motivated by the existence of an associated energy function that allows bringing in the intuition provided by phase transitions phenomena. CONCLUSIONS Our criterion is proved rigorously in some situations, generalizing well-known results for the scalar equation where the pattern selection process can be understood in terms of a potential. In more complex settings it is investigated numerically. Our work constitutes a first step towards rigorous pattern prediction in arbitrary geometries/conditions. Advances in this direction are highly applicable to the efficient design of Biotechnology and Developmental Biology experiments, as well as in simplifying the analysis of morphogenetic models.
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Affiliation(s)
- Tatiana T Marquez-Lago
- Department of Mathematics and Center for the Spatiotemporal Modeling of Cell Signaling (STMC), University of New Mexico, Albuquerque, NM 87131, USA
- Integrative Systems Biology Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0412, Japan
| | - Pablo Padilla
- IIMAS, Universidad Nacional Autónoma de México, Circuito Escolar. Cd. Universitaria, 04510 México DF, Mexico
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160
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Yang X, Marenduzzo D, Marchetti MC. Spiral and never-settling patterns in active systems. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:012711. [PMID: 24580261 DOI: 10.1103/physreve.89.012711] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Indexed: 06/03/2023]
Abstract
We present a combined numerical and analytical study of pattern formation in an active system where particles align, possess a density-dependent motility, and are subject to a logistic reaction. The model can describe suspensions of reproducing bacteria, as well as polymerizing actomyosin gels in vitro or in vivo. In the disordered phase, we find that motility suppression and growth compete to yield stable or blinking patterns, which, when dense enough, acquire internal orientational ordering to give asters or spirals. We predict these may be observed within chemotactic aggregates in bacterial fluids. In the ordered phase, the reaction term leads to previously unobserved never-settling patterns which can provide a simple framework to understand the formation of motile and spiral patterns in intracellular actin systems.
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Affiliation(s)
- X Yang
- Physics Department, Syracuse University, Syracuse, New York 13244, USA
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH93JZ, United Kingdom
| | - M C Marchetti
- Physics Department and Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York 13244, USA
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161
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Abstract
Self-organization by bacterial cells often leads to the formation of a highly complex spatially-structured biofilm. In such a bacterial biofilm, cells adhere to each other and are embedded in a self-produced extracellular matrix (ECM). Bacillus substilis bacteria utilize localized cell-death patterns which focuses mechanical forces to form wrinkled sheet-like structures in three dimensions. A most intriguing feature underlying this biofilm formation is that vertical buckling and ridge location is biased to occur in region of high cell-death. Here we present a spatially extended model to investigate the role of the bacterial secreted ECM during the biofilm formation and the self-organization of cell-death. Using this reaction-diffusion model we show that the interaction between the cell's motion and the ECM concentration gives rise to a self-trapping instability, leading to variety of cell-death patterns. The resultant spot patterns generated by our model are shown to be in semi-quantitative agreement with recent experimental observation.
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Affiliation(s)
- Pushpita Ghosh
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
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162
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163
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Payne S, Li B, Cao Y, Schaeffer D, Ryser MD, You L. Temporal control of self-organized pattern formation without morphogen gradients in bacteria. Mol Syst Biol 2013; 9:697. [PMID: 24104480 PMCID: PMC3817405 DOI: 10.1038/msb.2013.55] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022] Open
Abstract
Diverse mechanisms have been proposed to explain biological pattern formation. Regardless of their specific molecular interactions, the majority of these mechanisms require morphogen gradients as the spatial cue, which are either predefined or generated as a part of the patterning process. However, using Escherichia coli programmed by a synthetic gene circuit, we demonstrate here the generation of robust, self-organized ring patterns of gene expression in the absence of an apparent morphogen gradient. Instead of being a spatial cue, the morphogen serves as a timing cue to trigger the formation and maintenance of the ring patterns. The timing mechanism enables the system to sense the domain size of the environment and generate patterns that scale accordingly. Our work defines a novel mechanism of pattern formation that has implications for understanding natural developmental processes.
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Affiliation(s)
- Stephen Payne
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Bochong Li
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yangxiaolu Cao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Marc D Ryser
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
- Duke Center for Systems Biology, Duke University, Durham, NC, USA
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164
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Archer E, Süel GM. Synthetic biological networks. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:096602. [PMID: 24006369 DOI: 10.1088/0034-4885/76/9/096602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics.
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Affiliation(s)
- Eric Archer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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165
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Liu QX, Doelman A, Rottschäfer V, de Jager M, Herman PMJ, Rietkerk M, van de Koppel J. Phase separation explains a new class of self-organized spatial patterns in ecological systems. Proc Natl Acad Sci U S A 2013; 110:11905-10. [PMID: 23818579 PMCID: PMC3718087 DOI: 10.1073/pnas.1222339110] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin of regular spatial patterns in ecological systems has long fascinated researchers. Turing's activator-inhibitor principle is considered the central paradigm to explain such patterns. According to this principle, local activation combined with long-range inhibition of growth and survival is an essential prerequisite for pattern formation. Here, we show that the physical principle of phase separation, solely based on density-dependent movement by organisms, represents an alternative class of self-organized pattern formation in ecology. Using experiments with self-organizing mussel beds, we derive an empirical relation between the speed of animal movement and local animal density. By incorporating this relation in a partial differential equation, we demonstrate that this model corresponds mathematically to the well-known Cahn-Hilliard equation for phase separation in physics. Finally, we show that the predicted patterns match those found both in field observations and in our experiments. Our results reveal a principle for ecological self-organization, where phase separation rather than activation and inhibition processes drives spatial pattern formation.
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Affiliation(s)
- Quan-Xing Liu
- Department of Spatial Ecology, Royal Netherlands Institute for Sea Research, 4400 AC Yerseke, The Netherlands.
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166
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Abstract
As the complexity of synthetic genetic circuits increases, modeling is becoming a necessary first step to inform subsequent experimental efforts. In recent years, the design automation community has developed a wealth of computational tools for assisting experimentalists in designing and analyzing new genetic circuits at several scales. However, existing software primarily caters to either the DNA- or single-cell level, with little support for the multicellular level. To address this need, the iBioSim software package has been enhanced to provide support for modeling, simulating, and visualizing dynamic cellular populations in a two-dimensional space. This capacity is fully integrated into the software, capitalizing on iBioSim's strengths in modeling, simulating, and analyzing single-celled systems.
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Affiliation(s)
- Jason T. Stevens
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Chris J. Myers
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United
States
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167
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Hellen EH, Dana SK, Zhurov B, Volkov E. Electronic implementation of a repressilator with quorum sensing feedback. PLoS One 2013; 8:e62997. [PMID: 23658793 PMCID: PMC3642084 DOI: 10.1371/journal.pone.0062997] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 04/01/2013] [Indexed: 11/18/2022] Open
Abstract
We investigate the dynamics of a synthetic genetic repressilator with quorum sensing feedback. In a basic genetic ring oscillator network in which three genes inhibit each other in unidirectional manner, an additional quorum sensing feedback loop stimulates the activity of a chosen gene providing competition between inhibitory and stimulatory activities localized in that gene. Numerical simulations show several interesting dynamics, multi-stability of limit cycle with stable steady-state, multi-stability of different stable steady-states, limit cycle with period-doubling and reverse period-doubling, and infinite period bifurcation transitions for both increasing and decreasing strength of quorum sensing feedback. We design an electronic analog of the repressilator with quorum sensing feedback and reproduce, in experiment, the numerically predicted dynamical features of the system. Noise amplification near infinite period bifurcation is also observed. An important feature of the electronic design is the accessibility and control of the important system parameters.
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Affiliation(s)
- Edward H Hellen
- Department of Physics & Astronomy, University of North Carolina Greensboro, Greensboro, North Carolina, United States of America.
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168
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Lim WA, Lee CM, Tang C. Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell 2013; 49:202-12. [PMID: 23352241 DOI: 10.1016/j.molcel.2012.12.020] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/30/2012] [Indexed: 12/28/2022]
Abstract
A challenge in biology is to understand how complex molecular networks in the cell execute sophisticated regulatory functions. Here we explore the idea that there are common and general principles that link network structures to biological functions, principles that constrain the design solutions that evolution can converge upon for accomplishing a given cellular task. We describe approaches for classifying networks based on abstract architectures and functions, rather than on the specific molecular components of the networks. For any common regulatory task, can we define the space of all possible molecular solutions? Such inverse approaches might ultimately allow the assembly of a design table of core molecular algorithms that could serve as a guide for building synthetic networks and modulating disease networks.
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Affiliation(s)
- Wendell A Lim
- Center for Systems and Synthetic Biology, University of California, San Francisco, CA 94158, USA.
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169
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Thamamongood T, Lim NZL, Ho TY, Ayukawa S, Kiga D, Chow KL. Cultivation of Synthetic Biology with the iGEM Competition. JOURNAL OF ADVANCED COMPUTATIONAL INTELLIGENCE AND INTELLIGENT INFORMATICS 2013. [DOI: 10.20965/jaciii.2013.p0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The main goal of synthetic biology is to create new biological modules that augment or modify the behavior of living organisms in performing different tasks. These modules are useful in a wide range of applications, such as medicine, agriculture, energy and environmental remediation. The concept is simple, but a paradigm shift needs to be in place among future life scientists and engineers to embrace this new direction. The international Genetically Engineered Machine (iGEM) competition fits this purpose well as a synthetic biology competition mainly for undergraduate students. Participants design and construct biological devices using standardized and customized biological parts that are then characterized and submitted to an existing and ever expanding library. Overall, iGEM is an eye-opening learning experience for undergraduate students. It has made a strong educational impact on participating students and cultivated a future cohort of synthetic biology practitioners and ambassadors.
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170
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171
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Bacchus W, Fussenegger M. Engineering of synthetic intercellular communication systems. Metab Eng 2013; 16:33-41. [DOI: 10.1016/j.ymben.2012.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 10/27/2022]
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172
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Qi H, Blanchard A, Lu T. Engineered genetic information processing circuits. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:273-87. [DOI: 10.1002/wsbm.1216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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173
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Qi X, Nellas RB, Byrn MW, Russell MH, Bible AN, Alexandre G, Shen T. Swimming motility plays a key role in the stochastic dynamics of cell clumping. Phys Biol 2013; 10:026005. [PMID: 23416991 DOI: 10.1088/1478-3975/10/2/026005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dynamic cell-to-cell interactions are a prerequisite to many biological processes, including development and biofilm formation. Flagellum induced motility has been shown to modulate the initial cell-cell or cell-surface interaction and to contribute to the emergence of macroscopic patterns. While the role of swimming motility in surface colonization has been analyzed in some detail, a quantitative physical analysis of transient interactions between motile cells is lacking. We examined the Brownian dynamics of swimming cells in a crowded environment using a model of motorized adhesive tandem particles. Focusing on the motility and geometry of an exemplary motile bacterium Azospirillum brasilense, which is capable of transient cell-cell association (clumping), we constructed a physical model with proper parameters for the computer simulation of the clumping dynamics. By modulating mechanical interaction ('stickiness') between cells and swimming speed, we investigated how equilibrium and active features affect the clumping dynamics. We found that the modulation of active motion is required for the initial aggregation of cells to occur at a realistic time scale. Slowing down the rotation of flagellar motors (and thus swimming speeds) is correlated to the degree of clumping, which is consistent with the experimental results obtained for A. brasilense.
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Affiliation(s)
- Xianghong Qi
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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174
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Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013; 4:69-102. [PMID: 23413816 DOI: 10.1146/annurev-chembioeng-061312-103351] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems.
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Affiliation(s)
- Yen-Hsiang Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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175
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Engineered cell-cell communication and its applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 146:97-121. [PMID: 24002441 DOI: 10.1007/10_2013_249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past several decades, biologists have become more appreciative of the fundamental role of intercellular communication in natural systems spanning prokaryotic biofilms to eukaryotic developmental systems and neurological networks. From an engineering perspective, the use of cell-cell communication provides an opportunity to engineer more complex and robust functions using cellular components. Indeed, this strategy has been adopted in synthetic biology in the creation of diverse gene circuits that program spatiotemporal dynamics in one or multiple populations. Gene circuits such as these may offer insights regarding basic biological questions and motifs or serve as a basis for novel applications.
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176
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Surface Growth of a Motile Bacterial Population Resembles Growth in a Chemostat. J Mol Biol 2012; 424:180-91. [DOI: 10.1016/j.jmb.2012.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 09/02/2012] [Accepted: 09/06/2012] [Indexed: 11/17/2022]
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177
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Tan C, Lo SJ, LeDuc PR, Cheng CM. Frontiers of optofluidics in synthetic biology. LAB ON A CHIP 2012; 12:3654-3665. [PMID: 22895798 DOI: 10.1039/c2lc40828g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The development of optofluidic-based technology has ushered in a new era of lab-on-a-chip functionality, including miniaturization of biomedical devices, enhanced sensitivity for molecular detection, and multiplexing of optical measurements. While having great potential, optofluidic devices have only begun to be exploited in many biotechnological applications. Here, we highlight the potential of integrating optofluidic devices with synthetic biological systems, which is a field focusing on creating novel cellular systems by engineering synthetic gene and protein networks. First, we review the development of synthetic biology at different length scales, ranging from single-molecule, single-cell, to cellular population. We emphasize light-sensitive synthetic biological systems that would be relevant for the integration with optofluidic devices. Next, we propose several areas for potential applications of optofluidics in synthetic biology. The integration of optofluidics and synthetic biology would have a broad impact on point-of-care diagnostics and biotechnology.
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Affiliation(s)
- Cheemeng Tan
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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178
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Maharbiz MM. Synthetic multicellularity. Trends Cell Biol 2012; 22:617-23. [PMID: 23041241 DOI: 10.1016/j.tcb.2012.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/23/2012] [Accepted: 09/04/2012] [Indexed: 11/19/2022]
Abstract
The ability to synthesize biological constructs on the scale of the organisms we observe unaided is probably one of the more outlandish, yet recurring, dreams humans have had since they began to modify genes. This review brings together recent developments in synthetic biology, cell and developmental biology, computation, and technological development to provide context and direction for the engineering of rudimentary, autonomous multicellular ensembles.
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Affiliation(s)
- Michel M Maharbiz
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA.
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179
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Lushi E, Goldstein RE, Shelley MJ. Collective chemotactic dynamics in the presence of self-generated fluid flows. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:040902. [PMID: 23214522 DOI: 10.1103/physreve.86.040902] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Indexed: 05/12/2023]
Abstract
In microswimmer suspensions locomotion necessarily generates fluid motion, and it is known that such flows can lead to collective behavior from unbiased swimming. We examine the complementary problem of how chemotaxis is affected by self-generated flows. A kinetic theory coupling run-and-tumble chemotaxis to the flows of collective swimming shows separate branches of chemotactic and hydrodynamic instabilities for isotropic suspensions, the first driving aggregation, the second producing increased orientational order in suspensions of "pushers" and maximal disorder in suspensions of "pullers." Nonlinear simulations show that hydrodynamic interactions can limit and modify chemotactically driven aggregation dynamics. In puller suspensions the dynamics form aggregates that are mutually repelling due to the nontrivial flows. In pusher suspensions chemotactic aggregation can lead to destabilizing flows that fragment the regions of aggregation.
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Affiliation(s)
- Enkeleida Lushi
- Courant Institute of Mathematical Sciences, New York University, New York 10012, USA.
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180
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Riccione KA, Smith RP, Lee AJ, You L. A synthetic biology approach to understanding cellular information processing. ACS Synth Biol 2012; 1:389-402. [PMID: 23411668 PMCID: PMC3568971 DOI: 10.1021/sb300044r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The survival of cells and organisms requires proper responses to environmental signals. These responses are governed by cellular networks, which serve to process diverse environmental cues. Biological networks often contain recurring network topologies called "motifs". It has been recognized that the study of such motifs allows one to predict the response of a biological network and thus cellular behavior. However, studying a single motif in complete isolation of all other network motifs in a natural setting is difficult. Synthetic biology has emerged as a powerful approach to understanding the dynamic properties of network motifs. In addition to testing existing theoretical predictions, construction and analysis of synthetic gene circuits has led to the discovery of novel motif dynamics, such as how the combination of simple motifs can lead to autonomous dynamics or how noise in transcription and translation can affect the dynamics of a motif. Here, we review developments in synthetic biology as they pertain to increasing our understanding of cellular information processing. We highlight several types of dynamic behaviors that diverse motifs can generate, including the control of input/output responses, the generation of autonomous spatial and temporal dynamics, as well as the influence of noise in motif dynamics and cellular behavior.
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Affiliation(s)
| | - Robert P Smith
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Anna J Lee
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
- Center for Systems Biology, Duke University, Durham, NC 27708, USA
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181
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Jang SS, Oishi KT, Egbert RG, Klavins E. Specification and simulation of synthetic multicelled behaviors. ACS Synth Biol 2012; 1:365-74. [PMID: 23651290 DOI: 10.1021/sb300034m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent advances in the design and construction of synthetic multicelled systems in E. coli and S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing design frameworks for synthetic biology do not account for the unique morphologies of growing microcolonies, the interaction of gene circuits with the spatial diffusion of molecular signals, or the relationship between multicelled systems and parallel algorithms. Here, we introduce a framework for the specification and simulation of multicelled behaviors that combines a simple simulation of microcolony growth and molecular signaling with a new specification language called gro. The framework allows the researcher to explore the collective behaviors induced by high level descriptions of individual cell behaviors. We describe example specifications of previously published systems and introduce two novel specifications: microcolony edge detection and programmed microcolony morphogenesis. Finally, we illustrate through example how specifications written in gro can be refined to include increasing levels of detail about their bimolecular implementations.
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Affiliation(s)
- Seunghee S. Jang
- Department
of Electrical Engineering, University of
Washington, Seattle, Washington 98195, United States
| | - Kevin T. Oishi
- Department
of Electrical Engineering, University of
Washington, Seattle, Washington 98195, United States
| | - Robert G. Egbert
- Department
of Electrical Engineering, University of
Washington, Seattle, Washington 98195, United States
| | - Eric Klavins
- Department
of Electrical Engineering, University of
Washington, Seattle, Washington 98195, United States
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182
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Wang B, Buck M. Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol 2012; 20:376-84. [DOI: 10.1016/j.tim.2012.05.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/30/2012] [Accepted: 05/03/2012] [Indexed: 11/28/2022]
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183
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Chuang JS. Engineering multicellular traits in synthetic microbial populations. Curr Opin Chem Biol 2012; 16:370-8. [DOI: 10.1016/j.cbpa.2012.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 04/03/2012] [Indexed: 01/02/2023]
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184
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Farrell FDC, Marchetti MC, Marenduzzo D, Tailleur J. Pattern formation in self-propelled particles with density-dependent motility. PHYSICAL REVIEW LETTERS 2012; 108:248101. [PMID: 23004336 DOI: 10.1103/physrevlett.108.248101] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 06/01/2023]
Abstract
We study the behavior of interacting self-propelled particles, whose self-propulsion speed decreases with their local density. By combining direct simulations of the microscopic model with an analysis of the hydrodynamic equations obtained by explicitly coarse graining the model, we show that interactions lead generically to the formation of a host of patterns, including moving clumps, active lanes, and asters. This general mechanism could explain many of the patterns seen in recent experiments and simulations.
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Affiliation(s)
- F D C Farrell
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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185
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Brune KD, Bayer TS. Engineering microbial consortia to enhance biomining and bioremediation. Front Microbiol 2012; 3:203. [PMID: 22679443 PMCID: PMC3367458 DOI: 10.3389/fmicb.2012.00203] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/17/2012] [Indexed: 01/28/2023] Open
Abstract
In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage.
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Affiliation(s)
- Karl D Brune
- Centre for Synthetic Biology and Innovation, Division of Molecular Biosciences, Imperial College London, London, UK
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186
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Potapov I, Zhurov B, Volkov E. "Quorum sensing" generated multistability and chaos in a synthetic genetic oscillator. CHAOS (WOODBURY, N.Y.) 2012; 22:023117. [PMID: 22757524 DOI: 10.1063/1.4705085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We model the dynamics of the synthetic genetic oscillator Repressilator equipped with quorum sensing. In addition to a circuit of 3 genes repressing each other in a unidirectional manner, the model includes a phase-repulsive type of the coupling module implemented as the production of a small diffusive molecule-autoinducer (AI). We show that the autoinducer (which stimulates the transcription of a target gene) is responsible for the disappearance of the limit cycle (LC) through the infinite period bifurcation and the formation of a stable steady state (SSS) for sufficiently large values of the transcription rate. We found conditions for hysteresis between the limit cycle and the stable steady state. The parameters' region of the hysteresis is determined by the mRNA to protein lifetime ratio and by the level of transcription-stimulating activity of the AI. In addition to hysteresis, increasing AI-dependent stimulation of transcription may lead to the complex dynamic behavior which is characterized by the appearance of several branches on the bifurcation continuation, containing different regular limit cycles, as well as a chaotic regime. The multistability which is manifested as the coexistence between the stable steady state, limit cycles, and chaos seems to be a novel type of the dynamics for the ring oscillator with the added quorum sensing positive feedback.
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Affiliation(s)
- I Potapov
- Biophysics Department, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russia
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187
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Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 2012; 13:406-20. [DOI: 10.1038/nrg3227] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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188
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Fu X, Tang LH, Liu C, Huang JD, Hwa T, Lenz P. Stripe formation in bacterial systems with density-suppressed motility. PHYSICAL REVIEW LETTERS 2012; 108:198102. [PMID: 23003092 DOI: 10.1103/physrevlett.108.198102] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Indexed: 06/01/2023]
Abstract
Engineered bacteria in which motility is reduced by local cell density generate periodic stripes of high and low density when spotted on agar plates. We study theoretically the origin and mechanism of this process in a kinetic model that includes growth and density-suppressed motility of the cells. The spreading of a region of immotile cells into an initially cell-free region is analyzed. From the calculated front profile we provide an analytic ansatz to determine the phase boundary between the stripe and the no-stripe phases. The influence of various parameters on the phase boundary is discussed.
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Affiliation(s)
- Xiongfei Fu
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong, China
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189
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Abstract
Tissue-scale organization emerges from the action of sophisticated multiscale developmental programs. But the design rules for composing elementary signaling and information processing modules into such functional systems and for integrating them into the noisy and convoluted living context remain incompletely addressed. The construction of a synthetic gene circuit encoding contact-dependent signal propagation demonstrates one broadly applicable approach to this problem. The circuit comprises orthogonal signaling through the Delta ligand and the Notch receptor, multicellular positive feedback, and transcriptional signal amplification. Positive feedback and contact signaling proved sufficient for bistability and signal propagation across a population of mammalian cells, but only when combined with signal amplification. Thus, construction and characterization of synthetic gene circuits have made it possible to establish mechanistic sufficiency and the minimal requirements for the phenotype of interest.
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Affiliation(s)
- Adrian L Slusarczyk
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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190
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Matsuda M, Koga M, Nishida E, Ebisuya M. Synthetic Signal Propagation Through Direct Cell-Cell Interaction. Sci Signal 2012; 5:ra31. [DOI: 10.1126/scisignal.2002764] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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191
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Sekine R, Kiga D, Yamamura M. Design strategy for an initial state-independent diversity generator. CHEM-BIO INFORMATICS JOURNAL 2012. [DOI: 10.1273/cbij.12.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ryoji Sekine
- Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology
| | - Daisuke Kiga
- Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology
| | - Masayuki Yamamura
- Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology
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