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Abstract
Increased control of biological growth and form is an essential gateway to transformative medical advances. Repairing of birth defects, restoring lost or damaged organs, normalizing tumors, all depend on understanding how cells cooperate to make specific, functional large-scale structures. Despite advances in molecular genetics, significant gaps remain in our understanding of the meso-scale rules of morphogenesis. An engineering approach to this problem is the creation of novel synthetic living forms, greatly extending available model systems beyond evolved plant and animal lineages. Here, we review recent advances in the emerging field of synthetic morphogenesis, the bioengineering of novel multicellular living bodies. Emphasizing emergent self-organization, tissue-level guided self-assembly, and active functionality, this work is the essential next generation of synthetic biology. Aside from useful living machines for specific functions, the rational design and analysis of new, coherent anatomies will greatly increase our understanding of foundational questions in evolutionary developmental and cell biology.
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Affiliation(s)
- Mo R. Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, A809B Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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2
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Karkaria BD, Treloar NJ, Barnes CP, Fedorec AJH. From Microbial Communities to Distributed Computing Systems. Front Bioeng Biotechnol 2020; 8:834. [PMID: 32793576 PMCID: PMC7387671 DOI: 10.3389/fbioe.2020.00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
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Affiliation(s)
- Behzad D. Karkaria
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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3
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Erkurt M. Emergence of form in embryogenesis. J R Soc Interface 2018; 15:20180454. [PMID: 30429261 PMCID: PMC6283983 DOI: 10.1098/rsif.2018.0454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/12/2018] [Indexed: 11/23/2022] Open
Abstract
The development of form in an embryo is the result of a series of topological and informational symmetry breakings. We introduce the vector-reaction-diffusion-drift (VRDD) system where the limit cycle of spatial dynamics is morphogen concentrations with Dirac delta-type distributions. This is fundamentally different from the Turing reaction-diffusion system, as VRDD generates system-wide broken symmetry. We developed 'fundamental forms' from spherical blastula with a single organizing axis (rotational symmetry), double axis (mirror symmetry) and triple axis (no symmetry operator in three dimensions). We then introduced dynamics for cell differentiation, where genetic regulatory states are modelled as a finite-state machine (FSM). The state switching of an FSM is based on local morphogen concentrations as epigenetic information that changes dynamically. We grow complicated forms hierarchically in spatial subdomains using the FSM model coupled with the VRDD system. Using our integrated simulation model with four layers (topological, physical, chemical and regulatory), we generated life-like forms such as hydra. Genotype-phenotype mapping was investigated with continuous and jump mutations. Our study can have applications in morphogenetic engineering, soft robotics and biomimetic design.
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Affiliation(s)
- Murat Erkurt
- Department of Mathematics, Centre for Complexity Science, Imperial College London, London SW7 2AZ, UK
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Hynes WF, Chacón J, Segrè D, Marx CJ, Cady NC, Harcombe WR. Bioprinting microbial communities to examine interspecies interactions in time and space. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aad544] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Solé R, Ollé-Vila A, Vidiella B, Duran-Nebreda S, Conde-Pueyo N. The road to synthetic multicellularity. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2017.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Davies J. Using synthetic biology to explore principles of development. Development 2017; 144:1146-1158. [PMID: 28351865 DOI: 10.1242/dev.144196] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/14/2017] [Indexed: 12/31/2022]
Abstract
Developmental biology is mainly analytical: researchers study embryos, suggest hypotheses and test them through experimental perturbation. From the results of many experiments, the community distils the principles thought to underlie embryogenesis. Verifying these principles, however, is a challenge. One promising approach is to use synthetic biology techniques to engineer simple genetic or cellular systems that follow these principles and to see whether they perform as expected. As I review here, this approach has already been used to test ideas of patterning, differentiation and morphogenesis. It is also being applied to evo-devo studies to explore alternative mechanisms of development and 'roads not taken' by natural evolution.
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Affiliation(s)
- Jamie Davies
- Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XB, UK
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7
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Gutiérrez M, Gregorio-Godoy P, Pérez del Pulgar G, Muñoz LE, Sáez S, Rodríguez-Patón A. A New Improved and Extended Version of the Multicell Bacterial Simulator gro. ACS Synth Biol 2017; 6:1496-1508. [PMID: 28438021 DOI: 10.1021/acssynbio.7b00003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits and microbial consortia. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use, and provide new functionalities. The new version of gro is between 1 and 2 orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 105 cells in less than 10 min. A new library, CellEngine, accelerates the resolution of spatial physical interactions between growing and dividing cells by implementing a new shoving algorithm. A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. We also propose a more convenient language specification layer, ProSpec, based on the idea that proteins drive cell behavior. CellNutrient, another library, implements Monod-based growth and nutrient uptake functionalities. The intercellular signaling management was improved and extended in a library called CellSignals. Finally, bacterial conjugation, another local cell-cell communication process, was added to the simulator. To show the versatility and potential outreach of this version of gro, we provide studies and novel examples ranging from synthetic biology to evolutionary microbiology. We believe that the upgrades implemented for gro have made it into a powerful and fast prototyping tool capable of simulating a large variety of systems and synthetic biology designs.
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Affiliation(s)
- Martín Gutiérrez
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Escuela
de Informática y Telecomunicaciones, Universidad Diego Portales, 8370190 Santiago, Chile
| | - Paula Gregorio-Godoy
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Guillermo Pérez del Pulgar
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Luis E. Muñoz
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Sandra Sáez
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfonso Rodríguez-Patón
- Departamento
de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Naylor J, Fellermann H, Ding Y, Mohammed WK, Jakubovics NS, Mukherjee J, Biggs CA, Wright PC, Krasnogor N. Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations. ACS Synth Biol 2017; 6:1194-1210. [PMID: 28475309 DOI: 10.1021/acssynbio.6b00315] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Simbiotics is a spatially explicit multiscale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, and user-defined processes may be in a variety of forms depending on desired model abstraction. Simbiotics provides a library of modules such as cell geometries, physical force dynamics, genetic circuits, metabolic pathways, chemical diffusion and cell interactions. Model defined processes are integrated and scheduled for parallel multithread and multi-CPU execution. A virtual lab provides the modeler with analysis modules and some simulated lab equipment, enabling automation of sample interaction and data collection. An extendable and modular framework allows for the platform to be updated as novel models of bacteria are developed, coupled with an intuitive user interface to allow for model definitions with minimal programming experience. Simbiotics can integrate existing standards such as SBML, and process microscopy images to initialize the 3D spatial configuration of bacteria consortia. Two case studies, used to illustrate the platform flexibility, focus on the physical properties of the biosystems modeled. These pilot case studies demonstrate Simbiotics versatility in modeling and analysis of natural systems and as a CAD tool for synthetic biology.
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Affiliation(s)
- Jonathan Naylor
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Harold Fellermann
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Yuchun Ding
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Waleed K. Mohammed
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, U.K
| | | | - Joy Mukherjee
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, U.K
| | - Catherine A. Biggs
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, U.K
| | - Phillip C. Wright
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Natalio Krasnogor
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
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9
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Agent-based modelling in synthetic biology. Essays Biochem 2017; 60:325-336. [PMID: 27903820 PMCID: PMC5264505 DOI: 10.1042/ebc20160037] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/08/2016] [Indexed: 11/17/2022]
Abstract
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions.
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Nuñez IN, Matute TF, Del Valle ID, Kan A, Choksi A, Endy D, Haseloff J, Rudge TJ, Federici F. Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies. ACS Synth Biol 2017; 6:256-265. [PMID: 27794593 DOI: 10.1021/acssynbio.6b00149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Morphogenetic engineering is an emerging field that explores the design and implementation of self-organized patterns, morphologies, and architectures in systems composed of multiple agents such as cells and swarm robots. Synthetic biology, on the other hand, aims to develop tools and formalisms that increase reproducibility, tractability, and efficiency in the engineering of biological systems. We seek to apply synthetic biology approaches to the engineering of morphologies in multicellular systems. Here, we describe the engineering of two mechanisms, symmetry-breaking and domain-specific cell regulation, as elementary functions for the prototyping of morphogenetic instructions in bacterial colonies. The former represents an artificial patterning mechanism based on plasmid segregation while the latter plays the role of artificial cell differentiation by spatial colocalization of ubiquitous and segregated components. This separation of patterning from actuation facilitates the design-build-test-improve engineering cycle. We created computational modules for CellModeller representing these basic functions and used it to guide the design process and explore the design space in silico. We applied these tools to encode spatially structured functions such as metabolic complementation, RNAPT7 gene expression, and CRISPRi/Cas9 regulation. Finally, as a proof of concept, we used CRISPRi/Cas technology to regulate cell growth by controlling methionine synthesis. These mechanisms start from single cells enabling the study of morphogenetic principles and the engineering of novel population scale structures from the bottom up.
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Affiliation(s)
- Isaac N. Nuñez
- Escuela
de Ingeniería, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
- Fondo
de Desarrollo de Areas Prioritarias Center for Genome Regulation,
Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
| | - Tamara F. Matute
- Escuela
de Ingeniería, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
- Fondo
de Desarrollo de Areas Prioritarias Center for Genome Regulation,
Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
| | - Ilenne D. Del Valle
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
| | - Anton Kan
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Atri Choksi
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States,
| | - Drew Endy
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States,
| | - Jim Haseloff
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Timothy J. Rudge
- Escuela
de Ingeniería, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
| | - Fernan Federici
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
- Fondo
de Desarrollo de Areas Prioritarias Center for Genome Regulation,
Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 7820436, Santiago, Chile
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