1
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Cockx BJR, Foster T, Clegg RJ, Alden K, Arya S, Stekel DJ, Smets BF, Kreft JU. Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. PLoS Comput Biol 2024; 20:e1011303. [PMID: 38422165 PMCID: PMC10947719 DOI: 10.1371/journal.pcbi.1011303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 03/18/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the "biofilms promote altruism" study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice.
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Affiliation(s)
- Bastiaan J. R. Cockx
- Department of Environmental and Resource Engineering, Technical University of Demark, DTU Lyngby campus, Kgs. Lyngby, Denmark
| | - Tim Foster
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Robert J. Clegg
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Kieran Alden
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Sankalp Arya
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Demark, DTU Lyngby campus, Kgs. Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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2
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Bera P, Wasim A, Ghosh P. Interplay of cell motility and self-secreted extracellular polymeric substance induced depletion effects on spatial patterning in a growing microbial colony. SOFT MATTER 2023; 19:8136-8149. [PMID: 37847026 DOI: 10.1039/d3sm01144e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Reproducing bacteria self-organize to develop patterned biofilms in various conditions. Various factors contribute to the shaping of a multicellular bacterial organization. Here we investigate how motility force and self-secreted extracellular polymeric substances (EPS) influence bacterial cell aggregation, leading to phase-separated colonies using a particle-based/individual-based model. Our findings highlight the critical role of the interplay between motility force and depletion effects in regulating phase separation within a growing colony under far-from-equilibrium conditions. We observe that increased motility force hinders depletion-induced cell aggregation and phase segregation, necessitating a higher depletion effect for highly motile bacteria to undergo phase separation within a growing biofilm. We present a phase diagram illustrating the systematic variation of motility force and repulsive mechanical force, shedding light on the combined contributions of these two factors: self-propulsive motion and aggregation due to the depletion effect, resulting in the presence of small to large bacterial aggregates. Furthermore, our study reveals the dynamic nature of clustering, marked by changes in cluster size over time. Additionally, our findings suggest that differential dispersion among the components can lead to the localization of EPS at the periphery of a growing colony. Our study enhances the understanding of the collective dynamics of motile bacterial cells within a growing colony, particularly in the presence of a self-secreted polymer-driven depletion effect.
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Affiliation(s)
- Palash Bera
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Abdul Wasim
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala, 695551, India.
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3
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Caringella G, Bandiera L, Menolascina F. Recent advances, opportunities and challenges in cybergenetic identification and control of biomolecular networks. Curr Opin Biotechnol 2023; 80:102893. [PMID: 36706519 DOI: 10.1016/j.copbio.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Cybergenetics is a new area of research aimed at developing digital and biological controllers for living systems. Synthetic biologists have begun exploiting cybergenetic tools and platforms to both accelerate the development of mathematical models and develop control strategies for complex biological phenomena. Here, we review the state of the art in cybergenetic identification and control. Our aim is to lower the entry barrier to this field and foster the adoption of methods and technologies that will accelerate the pace at which Synthetic Biology progresses toward applications.
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Affiliation(s)
- Gianpio Caringella
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Lucia Bandiera
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Filippo Menolascina
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK.
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4
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Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models. Genes (Basel) 2023; 14:genes14010154. [PMID: 36672895 PMCID: PMC9859520 DOI: 10.3390/genes14010154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023] Open
Abstract
The elevation of Synthetic Biology from single cells to multicellular simulations would be a significant scale-up. The spatiotemporal behavior of cellular populations has the potential to be prototyped in silico for computer assisted design through ergonomic interfaces. Such a platform would have great practical potential across medicine, industry, research, education and accessible archiving in bioinformatics. Existing Synthetic Biology CAD systems are considered limited regarding population level behavior, and this work explored the in silico challenges posed from biological and computational perspectives. Retaining the connection to Synthetic Biology CAD, an extension of the Infobiotics Workbench Suite was considered, with potential for the integration of genetic regulatory models and/or chemical reaction networks through Next Generation Stochastic Simulator (NGSS) Gillespie algorithms. These were executed using SBML models generated by in-house SBML-Constructor over numerous topologies and benchmarked in association with multicellular simulation layers. Regarding multicellularity, two ground-up multicellular solutions were developed, including the use of Unreal Engine 4 contrasted with CPU multithreading and Blender visualization, resulting in a comparison of real-time versus batch-processed simulations. In conclusion, high-performance computing and client-server architectures could be considered for future works, along with the inclusion of numerous biologically and physically informed features, whilst still pursuing ergonomic solutions.
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Abstract
Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.
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Affiliation(s)
- Karthik Nagarajan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Congjian Ni
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, Urbana, Illinois 61801, United States
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6
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Salzano D, Fiore D, di Bernardo M. Ratiometric control of cell phenotypes in monostrain microbial consortia. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220335. [PMID: 35858050 PMCID: PMC9277296 DOI: 10.1098/rsif.2022.0335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We address the problem of regulating and keeping at a desired balance the relative numbers between cells exhibiting a different phenotype within a monostrain microbial consortium. We propose a strategy based on the use of external control inputs, assuming each cell in the community is endowed with a reversible, bistable memory mechanism. Specifically, we provide a general analytical framework to guide the design of external feedback control strategies aimed at balancing the ratio between cells whose memory is stabilized at either one of two equilibria associated with different cell phenotypes. We demonstrate the stability and robustness properties of the control laws proposed and validate them in silico, implementing the memory element via a genetic toggle-switch. The proposed control framework may be used to allow long-term coexistence of different populations, with both industrial and biotechnological applications. As a representative example, we consider the realistic agent-based implementation of our control strategy to enable cooperative bioproduction of a dimer in a monostrain microbial consortium.
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Affiliation(s)
- Davide Salzano
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
| | - Davide Fiore
- Department of Mathematics and Applications 'R. Caccioppoli', University of Naples Federico II, Via Cintia, Monte S. Angelo, 80126 Naples, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy.,Scuola Superiore Meridionale, Largo S. Marcellino 10, 80138 Naples, Italy
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7
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de Cesare I, Salzano D, di Bernardo M, Renson L, Marucci L. Control-Based Continuation: A New Approach to Prototype Synthetic Gene Networks. ACS Synth Biol 2022; 11:2300-2313. [PMID: 35729740 PMCID: PMC9295158 DOI: 10.1021/acssynbio.1c00632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
![]()
Control-Based Continuation
(CBC) is a general and systematic method
to carry out the bifurcation analysis of physical experiments. CBC
does not rely on a mathematical model and thus overcomes the uncertainty
introduced when identifying bifurcation curves indirectly through
modeling and parameter estimation. We demonstrate, in silico, CBC applicability to biochemical processes by tracking the equilibrium
curve of a toggle switch, which includes additive process noise and
exhibits bistability. We compare the results obtained when CBC uses
a model-free and model-based control strategy and show that both can
track stable and unstable solutions, revealing bistability. We then
demonstrate CBC in conditions more representative of an in
vivo experiment using an agent-based simulator describing
cell growth and division, cell-to-cell variability, spatial distribution,
and diffusion of chemicals. We further show how the identified curves
can be used for parameter estimation and discuss how CBC can significantly
accelerate the prototyping of synthetic gene regulatory networks.
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Affiliation(s)
- Irene de Cesare
- Engineering Mathematics Department, University of Bristol, Bristol BS8 1TW, U.K.,Department of Electrical Engineering and Information Technologies, University of Naples Federico II, 80125 Naples, Italy
| | - Davide Salzano
- Engineering Mathematics Department, University of Bristol, Bristol BS8 1TW, U.K.,Department of Electrical Engineering and Information Technologies, University of Naples Federico II, 80125 Naples, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technologies, University of Naples Federico II, 80125 Naples, Italy
| | - Ludovic Renson
- Department of Mechanical Engineering, Imperial College London, London SW7 2BX, U.K
| | - Lucia Marucci
- Engineering Mathematics Department, University of Bristol, Bristol BS8 1TW, U.K.,BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
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8
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Atkinson E, Tuza Z, Perrino G, Stan GB, Ledesma-Amaro R. Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation. Microb Cell Fact 2022; 21:115. [PMID: 35698129 PMCID: PMC9195437 DOI: 10.1186/s12934-022-01842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Low-cost sustainable feedstocks are essential for commercially viable biotechnologies. These feedstocks, often derived from plant or food waste, contain a multitude of different complex biomolecules which require multiple enzymes to hydrolyse and metabolise. Current standard biotechnology uses monocultures in which a single host expresses all the proteins required for the consolidated bioprocess. However, these hosts have limited capacity for expressing proteins before growth is impacted. This limitation may be overcome by utilising division of labour (DOL) in a consortium, where each member expresses a single protein of a longer degradation pathway. RESULTS Here, we model a two-strain consortium, with one strain expressing an endohydrolase and a second strain expressing an exohydrolase, for cooperative degradation of a complex substrate. Our results suggest that there is a balance between increasing expression to enhance degradation versus the burden that higher expression causes. Once a threshold of burden is reached, the consortium will consistently perform better than an equivalent single-cell monoculture. CONCLUSIONS We demonstrate that resource-aware whole-cell models can be used to predict the benefits and limitations of using consortia systems to overcome burden. Our model predicts the region of expression where DOL would be beneficial for growth on starch, which will assist in making informed design choices for this, and other, complex-substrate degradation pathways.
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Affiliation(s)
- Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Zoltan Tuza
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Giansimone Perrino
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
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9
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Rafieenia R, Atkinson E, Ledesma-Amaro R. Division of labor for substrate utilization in natural and synthetic microbial communities. Curr Opin Biotechnol 2022; 75:102706. [DOI: 10.1016/j.copbio.2022.102706] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 01/30/2023]
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10
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Breitwieser L, Hesam A, de Montigny J, Vavourakis V, Iosif A, Jennings J, Kaiser M, Manca M, Di Meglio A, Al-Ars Z, Rademakers F, Mutlu O, Bauer R. BioDynaMo: a modular platform for high-performance agent-based simulation. Bioinformatics 2022; 38:453-460. [PMID: 34529036 PMCID: PMC8723141 DOI: 10.1093/bioinformatics/btab649] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/02/2021] [Accepted: 09/13/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. RESULTS We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology and epidemiology. For each use case, we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baselines. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research. AVAILABILITY AND IMPLEMENTATION BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in the supplementary information. SUPPLEMENTARY INFORMATION Available at https://doi.org/10.5281/zenodo.5121618.
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Affiliation(s)
- Lukas Breitwieser
- CERN openlab, IT Department, CERN, Geneva 1211, Switzerland.,Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland
| | - Ahmad Hesam
- CERN openlab, IT Department, CERN, Geneva 1211, Switzerland.,Department of Quantum & Computer Engineering, Delft University of Technology, Delft 2628CD, The Netherlands
| | | | - Vasileios Vavourakis
- Department of Mechanical & Manufacturing Engineering, University of Cyprus, Nicosia 2109, Cyprus.,Department of Medical Physics & Biomedical Engineering, University College London, London WC1E 6BT, UK
| | - Alexandros Iosif
- Department of Mechanical & Manufacturing Engineering, University of Cyprus, Nicosia 2109, Cyprus
| | - Jack Jennings
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
| | - Marcus Kaiser
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK.,Department of Functional Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Precision Imaging Beacon, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Marco Manca
- SCimPulse Foundation, Geleen 6162 BC, The Netherlands
| | | | - Zaid Al-Ars
- Department of Quantum & Computer Engineering, Delft University of Technology, Delft 2628CD, The Netherlands
| | | | - Onur Mutlu
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland.,Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich 8092, Switzerland
| | - Roman Bauer
- Department of Computer Science, University of Surrey, Guildford GU2 7XH, UK
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11
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Moškon M, Komac R, Zimic N, Mraz M. Distributed biological computation: from oscillators, logic gates and switches to a multicellular processor and neural computing applications. Neural Comput Appl 2021. [DOI: 10.1007/s00521-021-05711-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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Perrino G, Hadjimitsis A, Ledesma-Amaro R, Stan GB. Control engineering and synthetic biology: working in synergy for the analysis and control of microbial systems. Curr Opin Microbiol 2021; 62:68-75. [PMID: 34062481 DOI: 10.1016/j.mib.2021.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 01/12/2023]
Abstract
The implementation of novel functionalities in living cells is a key aspect of synthetic biology. In the last decade, the field of synthetic biology has made progress working in synergy with control engineering, whose solid framework has provided concepts and tools to analyse biological systems and guide their design. In this review, we briefly highlight recent work focused on the application of control theoretical concepts and tools for the analysis and design of synthetic biology systems in microbial cells.
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Affiliation(s)
- Giansimone Perrino
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Andreas Hadjimitsis
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Guy-Bart Stan
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK.
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13
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Koshy-Chenthittayil S, Archambault L, Senthilkumar D, Laubenbacher R, Mendes P, Dongari-Bagtzoglou A. Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review. Microorganisms 2021; 9:417. [PMID: 33671308 PMCID: PMC7922883 DOI: 10.3390/microorganisms9020417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The human microbiome has been a focus of intense study in recent years. Most of the living organisms comprising the microbiome exist in the form of biofilms on mucosal surfaces lining our digestive, respiratory, and genito-urinary tracts. While health-associated microbiota contribute to digestion, provide essential nutrients, and protect us from pathogens, disturbances due to illness or medical interventions contribute to infections, some that can be fatal. Myriad biological processes influence the make-up of the microbiota, for example: growth, division, death, and production of extracellular polymers (EPS), and metabolites. Inter-species interactions include competition, inhibition, and symbiosis. Computational models are becoming widely used to better understand these interactions. Agent-based modeling is a particularly useful computational approach to implement the various complex interactions in microbial communities when appropriately combined with an experimental approach. In these models, each cell is represented as an autonomous agent with its own set of rules, with different rules for each species. In this review, we will discuss innovations in agent-based modeling of biofilms and the microbiota in the past five years from the biological and mathematical perspectives and discuss how agent-based models can be further utilized to enhance our comprehension of the complex world of polymicrobial biofilms and the microbiome.
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Affiliation(s)
- Sherli Koshy-Chenthittayil
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA; (S.K.-C.); (L.A.); (P.M.)
| | - Linda Archambault
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA; (S.K.-C.); (L.A.); (P.M.)
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | | | - Pedro Mendes
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA; (S.K.-C.); (L.A.); (P.M.)
- Center for Cell Analysis and Modeling, Department of Cell Biology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
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14
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Shannon B, Zamora-Chimal CG, Postiglione L, Salzano D, Grierson CS, Marucci L, Savery NJ, di Bernardo M. In Vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli Using Microfluidics. ACS Synth Biol 2020; 9:2617-2624. [PMID: 32966743 DOI: 10.1021/acssynbio.0c00105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study both in silico and in vivo the real-time feedback control of a molecular titration motif that has been earmarked as a fundamental component of antithetic and multicellular feedback control schemes in E. coli. We show that an external feedback control strategy can successfully regulate the average fluorescence output of a bacterial cell population to a desired constant level in real-time. We also provide in silico evidence that the same strategy can be used to track a time-varying reference signal where the set-point is switched to a different value halfway through the experiment. We use the experimental data to refine and parametrize an in silico model of the motif that can be used as an error computation module in future embedded or multicellular control experiments.
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Affiliation(s)
- Barbara Shannon
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Criseida G. Zamora-Chimal
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Lorena Postiglione
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
| | - Davide Salzano
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, 80125 Naples, Italy
| | - Claire S. Grierson
- School of Biological Sciences, University of Bristol, Bristol BS8 1UH, U.K
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Nigel J. Savery
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Mario di Bernardo
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, 80125 Naples, Italy
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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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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Ewald J, Sieber P, Garde R, Lang SN, Schuster S, Ibrahim B. Trends in mathematical modeling of host-pathogen interactions. Cell Mol Life Sci 2020; 77:467-480. [PMID: 31776589 PMCID: PMC7010650 DOI: 10.1007/s00018-019-03382-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
Pathogenic microorganisms entail enormous problems for humans, livestock, and crop plants. A better understanding of the different infection strategies of the pathogens enables us to derive optimal treatments to mitigate infectious diseases or develop vaccinations preventing the occurrence of infections altogether. In this review, we highlight the current trends in mathematical modeling approaches and related methods used for understanding host-pathogen interactions. Since these interactions can be described on vastly different temporal and spatial scales as well as abstraction levels, a variety of computational and mathematical approaches are presented. Particular emphasis is placed on dynamic optimization, game theory, and spatial modeling, as they are attracting more and more interest in systems biology. Furthermore, these approaches are often combined to illuminate the complexities of the interactions between pathogens and their host. We also discuss the phenomena of molecular mimicry and crypsis as well as the interplay between defense and counter defense. As a conclusion, we provide an overview of method characteristics to assist non-experts in their decision for modeling approaches and interdisciplinary understanding.
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Affiliation(s)
- Jan Ewald
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Patricia Sieber
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Ravindra Garde
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Stefan N Lang
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Stefan Schuster
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
| | - Bashar Ibrahim
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, 32093, Hawally, Kuwait.
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Pedone E, Marucci L. Role of β-Catenin Activation Levels and Fluctuations in Controlling Cell Fate. Genes (Basel) 2019; 10:genes10020176. [PMID: 30823613 PMCID: PMC6410200 DOI: 10.3390/genes10020176] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
Cells have developed numerous adaptation mechanisms to external cues by controlling signaling-pathway activity, both qualitatively and quantitatively. The Wnt/β-catenin pathway is a highly conserved signaling pathway involved in many biological processes, including cell proliferation, differentiation, somatic cell reprogramming, development, and cancer. The activity of the Wnt/β-catenin pathway and the temporal dynamics of its effector β-catenin are tightly controlled by complex regulations. The latter encompass feedback loops within the pathway (e.g., a negative feedback loop involving Axin2, a β-catenin transcriptional target) and crosstalk interactions with other signaling pathways. Here, we provide a review shedding light on the coupling between Wnt/β-catenin activation levels and fluctuations across processes and cellular systems; in particular, we focus on development, in vitro pluripotency maintenance, and cancer. Possible mechanisms originating Wnt/β-catenin dynamic behaviors and consequently driving different cellular responses are also reviewed, and new avenues for future research are suggested.
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Affiliation(s)
- Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- BrisSynBio, Bristol, BS8 1TQ, UK.
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18
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McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
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Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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Soheilypour M, Mofrad MRK. Agent-Based Modeling in Molecular Systems Biology. Bioessays 2018; 40:e1800020. [PMID: 29882969 DOI: 10.1002/bies.201800020] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/11/2018] [Indexed: 12/13/2022]
Abstract
Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease.
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Affiliation(s)
- Mohammad Soheilypour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA
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