1
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Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024; 135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.
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Affiliation(s)
- Yue Casey Chen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Louie Destouches
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alice Cook
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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2
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Marken JP, Murray RM. Addressable and adaptable intercellular communication via DNA messaging. Nat Commun 2023; 14:2358. [PMID: 37095088 PMCID: PMC10126159 DOI: 10.1038/s41467-023-37788-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains' ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages' dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it using plasmid conjugation in E. coli. Our system can bias the transfer of messages to targeted receiver strains by 100- to 1000-fold, and their recipient lists can be dynamically updated in situ to control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.
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Affiliation(s)
- John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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3
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Moškon M, Mraz M. Programmable evolution of computing circuits in cellular populations. Neural Comput Appl 2022. [DOI: 10.1007/s00521-022-07532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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4
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Barbier I, Kusumawardhani H, Schaerli Y. Engineering synthetic spatial patterns in microbial populations and communities. Curr Opin Microbiol 2022; 67:102149. [DOI: 10.1016/j.mib.2022.102149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 02/03/2023]
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5
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Müller J, Jäkel AC, Richter J, Eder M, Falgenhauer E, Simmel FC. Bacterial Growth, Communication, and Guided Chemotaxis in 3D-Bioprinted Hydrogel Environments. ACS APPLIED MATERIALS & INTERFACES 2022; 14:15871-15880. [PMID: 35349260 PMCID: PMC9012179 DOI: 10.1021/acsami.1c20836] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/14/2022] [Indexed: 06/06/2023]
Abstract
Bioprinting of engineered bacteria is of great interest for applications of synthetic biology in the context of living biomaterials, but so far, only a few viable approaches are available for the printing of gels hosting live Escherichia coli bacteria. Here, we develop a gentle extrusion-based bioprinting method based on an inexpensive alginate/agarose ink mixture that enables printing of E. coli into three-dimensional hydrogel structures up to 10 mm in height. We first characterize the rheological properties of the gel ink and then study the growth of the bacteria inside printed structures. We show that the maturation of fluorescent proteins deep within the printed structures can be facilitated by the addition of a calcium peroxide-based oxygen generation system. We then utilize the bioprinter to control different types of interactions between bacteria that depend on their spatial position. We next show quorum-sensing-based chemical communication between the engineered sender and receiver bacteria placed at different positions inside the bioprinted structure and finally demonstrate the fabrication of barrier structures defined by nonmotile bacteria that can guide the movement of chemotactic bacteria inside a gel. We anticipate that a combination of 3D bioprinting and synthetic biological approaches will lead to the development of living biomaterials containing engineered bacteria as dynamic functional units.
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6
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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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7
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Ortiz Y, Carrión J, Lahoz-Beltrá R, Gutiérrez M. A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication. Front Bioeng Biotechnol 2021; 9:660148. [PMID: 34041231 PMCID: PMC8141851 DOI: 10.3389/fbioe.2021.660148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Metaheuristics (MH) are Artificial Intelligence procedures that frequently rely on evolution. MH approximate difficult problem solutions, but are computationally costly as they explore large solution spaces. This work pursues to lay the foundations of general mappings for implementing MH using Synthetic Biology constructs in cell colonies. Two advantages of this approach are: harnessing large scale parallelism capability of cell colonies and, using existing cell processes to implement basic dynamics defined in computational versions. We propose a framework that maps MH elements to synthetic circuits in growing cell colonies to replicate MH behavior in cell colonies. Cell-cell communication mechanisms such as quorum sensing (QS), bacterial conjugation, and environmental signals map to evolution operators in MH techniques to adapt to growing colonies. As a proof-of-concept, we implemented the workflow associated to the framework: automated MH simulation generators for the gro simulator and two classes of algorithms (Simple Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits. Implementation tests show that synthetic counterparts mimicking MH are automatically produced, but also that cell colony parallelism speeds up the execution in terms of generations. Furthermore, we show an example of how our framework is extended by implementing a different computational model: The Cellular Automaton.
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Affiliation(s)
- Yerko Ortiz
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
| | - Javier Carrión
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
| | - Rafael Lahoz-Beltrá
- Department of Biodiversity, Ecology and Evolution (Biomathematics), Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - Martín Gutiérrez
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
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8
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Yang S, Pieters PA, Joesaar A, Bögels BWA, Brouwers R, Myrgorodska I, Mann S, de Greef TFA. Light-Activated Signaling in DNA-Encoded Sender-Receiver Architectures. ACS NANO 2020; 14:15992-16002. [PMID: 33078948 PMCID: PMC7690052 DOI: 10.1021/acsnano.0c07537] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/14/2020] [Indexed: 05/22/2023]
Abstract
Collective decision making by living cells is facilitated by exchange of diffusible signals where sender cells release a chemical signal that is interpreted by receiver cells. A variety of nonliving artificial cell models have been developed in recent years that mimic various aspects of diffusion-based intercellular communication. However, localized secretion of diffusive signals from individual protocells, which is critical for mimicking biological sender-receiver systems, has remained challenging to control precisely. Here, we engineer light-responsive, DNA-encoded sender-receiver architectures, where protein-polymer microcapsules act as cell mimics and molecular communication occurs through diffusive DNA signals. We prepare spatial distributions of sender and receiver protocells using a microfluidic trapping array and set up a signaling gradient from a single sender cell using light, which activates surrounding receivers through DNA strand displacement. Our systematic analysis reveals how the effective signal range of a single sender is determined by various factors including the density and permeability of receivers, extracellular signal degradation, signal consumption, and catalytic regeneration. In addition, we construct a three-population configuration where two sender cells are embedded in a dense array of receivers that implement Boolean logic and investigate spatial integration of nonidentical input cues. The results offer a means for studying diffusion-based sender-receiver topologies and present a strategy to achieve the congruence of reaction-diffusion and positional information in chemical communication systems that have the potential to reconstitute collective cellular patterns.
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Affiliation(s)
- Shuo Yang
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Pascal A. Pieters
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Alex Joesaar
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Bas W. A. Bögels
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Rens Brouwers
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Iuliia Myrgorodska
- Centre
for Protolife Research and Max Planck Bristol Centre for Minimal Biology,
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Stephen Mann
- Centre
for Protolife Research and Max Planck Bristol Centre for Minimal Biology,
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Tom F. A. de Greef
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 MB, The Netherlands
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9
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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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10
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Joesaar A, Yang S, Bögels B, van der Linden A, Pieters P, Kumar BVVSP, Dalchau N, Phillips A, Mann S, de Greef TFA. DNA-based communication in populations of synthetic protocells. NATURE NANOTECHNOLOGY 2019; 14:369-378. [PMID: 30833694 PMCID: PMC6451639 DOI: 10.1038/s41565-019-0399-9] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/22/2019] [Indexed: 05/20/2023]
Abstract
Developing molecular communication platforms based on orthogonal communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled 'biomolecular implementation of protocellular communication' (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.
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Affiliation(s)
- Alex Joesaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Shuo Yang
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bas Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Ardjan van der Linden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Pascal Pieters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - B V V S Pavan Kumar
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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11
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A Synthetic Bacterial Cell-Cell Adhesion Toolbox for Programming Multicellular Morphologies and Patterns. Cell 2018; 174:649-658.e16. [DOI: 10.1016/j.cell.2018.06.041] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/18/2018] [Accepted: 06/22/2018] [Indexed: 01/08/2023]
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12
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Dalchau N, Szép G, Hernansaiz-Ballesteros R, Barnes CP, Cardelli L, Phillips A, Csikász-Nagy A. Computing with biological switches and clocks. NATURAL COMPUTING 2018; 17:761-779. [PMID: 30524215 PMCID: PMC6244770 DOI: 10.1007/s11047-018-9686-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The complex dynamics of biological systems is primarily driven by molecular interactions that underpin the regulatory networks of cells. These networks typically contain positive and negative feedback loops, which are responsible for switch-like and oscillatory dynamics, respectively. Many computing systems rely on switches and clocks as computational modules. While the combination of such modules in biological systems leads to a variety of dynamical behaviours, it is also driving development of new computing algorithms. Here we present a historical perspective on computation by biological systems, with a focus on switches and clocks, and discuss parallels between biology and computing. We also outline our vision for the future of biological computing.
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Affiliation(s)
| | | | | | | | - Luca Cardelli
- Microsoft Research, Cambridge, UK
- University of Oxford, Oxford, UK
| | | | - Attila Csikász-Nagy
- King’s College London, London, UK
- Pázmány Péter Catholic University, Budapest, Hungary
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13
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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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14
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Yoon JY. Towards the 10-year milestone of Journal of Biological Engineering. J Biol Eng 2017; 11:3. [PMID: 28101135 PMCID: PMC5237302 DOI: 10.1186/s13036-016-0038-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 11/10/2022] Open
Abstract
October 10th, 2016 marked the 9th anniversary for the Journal of Biological Engineering (JBE), the official journal of Institute of Biological Engineering (IBE), published by BioMed Central. We are entering into the 10th year of its exciting and productive history. In this editorial, a brief history of JBE is summarized, along with a series of analyses on average number of citations, breakdown of topical subjects, geographical representations and so forth for all published articles in JBE. Future prospects and new directions of JBE are also described in this editorial.
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Affiliation(s)
- Jeong-Yeol Yoon
- Department of Biomedical Engineering and Department of Agricultural & Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
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15
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Lentini R, Yeh Martín N, Mansy SS. Communicating artificial cells. Curr Opin Chem Biol 2016; 34:53-61. [DOI: 10.1016/j.cbpa.2016.06.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
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16
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Bernheim AG, Libis VK, Lindner AB, Wintermute EH. Phage-mediated Delivery of Targeted sRNA Constructs to Knock Down Gene Expression in E. coli. J Vis Exp 2016. [PMID: 27023729 PMCID: PMC4829038 DOI: 10.3791/53618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA-mediated knockdowns are widely used to control gene expression. This versatile family of techniques makes use of short RNA (sRNA) that can be synthesized with any sequence and designed to complement any gene targeted for silencing. Because sRNA constructs can be introduced to many cell types directly or using a variety of vectors, gene expression can be repressed in living cells without laborious genetic modification. The most common RNA knockdown technology, RNA interference (RNAi), makes use of the endogenous RNA-induced silencing complex (RISC) to mediate sequence recognition and cleavage of the target mRNA. Applications of this technique are therefore limited to RISC-expressing organisms, primarily eukaryotes. Recently, a new generation of RNA biotechnologists have developed alternative mechanisms for controlling gene expression through RNA, and so made possible RNA-mediated gene knockdowns in bacteria. Here we describe a method for silencing gene expression in E. coli that functionally resembles RNAi. In this system a synthetic phagemid is designed to express sRNA, which may designed to target any sequence. The expression construct is delivered to a population of E. coli cells with non-lytic M13 phage, after which it is able to stably replicate as a plasmid. Antisense recognition and silencing of the target mRNA is mediated by the Hfq protein, endogenous to E. coli. This protocol includes methods for designing the antisense sRNA, constructing the phagemid vector, packaging the phagemid into M13 bacteriophage, preparing a live cell population for infection, and performing the infection itself. The fluorescent protein mKate2 and the antibiotic resistance gene chloramphenicol acetyltransferase (CAT) are targeted to generate representative data and to quantify knockdown effectiveness.
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Affiliation(s)
- Aude G Bernheim
- U1001, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes
| | - Vincent K Libis
- U1001, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes
| | - Ariel B Lindner
- U1001, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes
| | - Edwin H Wintermute
- U1001, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes;
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17
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Furubayashi T, Nakano T, Eckford A, Okaie Y, Yomo T. Packet Fragmentation and Reassembly in Molecular Communication. IEEE Trans Nanobioscience 2016; 15:284-8. [PMID: 26890919 DOI: 10.1109/tnb.2016.2526051] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This paper describes packet fragmentation and reassembly to achieve reliable molecular communication among bionanomachines. In the molecular communication described in this paper, a sender bionanomachine performs packet fragmentation, dividing a large molecular message into smaller pieces and embedding into smaller molecular packets, so that molecular packets have higher diffusivity to reach the receiver bionanomachine. The receiver bionanomachine then performs packet reassembly to retrieve the original molecular message from a set of molecular packets that it receives. To examine the effect of packet fragmentation and reassembly, we develop analytical models and conduct numerical experiments. Numerical results show that packet fragmentation and reassembly can improve the message delivery performance. Numerical results also indicate that packet fragmentation and reassembly may degrade the performance in the presence of drift in the environment.
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18
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Artificial cell-cell communication as an emerging tool in synthetic biology applications. J Biol Eng 2015; 9:13. [PMID: 26265937 PMCID: PMC4531478 DOI: 10.1186/s13036-015-0011-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/25/2015] [Indexed: 01/14/2023] Open
Abstract
Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.
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19
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Ball P. Forging patterns and making waves from biology to geology: a commentary on Turing (1952) 'The chemical basis of morphogenesis'. Philos Trans R Soc Lond B Biol Sci 2015; 373:rsta.2014.0218. [PMID: 25750229 DOI: 10.1098/rsta.2014.0218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 05/21/2023] Open
Abstract
Alan Turing was neither a biologist nor a chemist, and yet the paper he published in 1952, 'The chemical basis of morphogenesis', on the spontaneous formation of patterns in systems undergoing reaction and diffusion of their ingredients has had a substantial impact on both fields, as well as in other areas as disparate as geomorphology and criminology. Motivated by the question of how a spherical embryo becomes a decidedly non-spherical organism such as a human being, Turing devised a mathematical model that explained how random fluctuations can drive the emergence of pattern and structure from initial uniformity. The spontaneous appearance of pattern and form in a system far away from its equilibrium state occurs in many types of natural process, and in some artificial ones too. It is often driven by very general mechanisms, of which Turing's model supplies one of the most versatile. For that reason, these patterns show striking similarities in systems that seem superficially to share nothing in common, such as the stripes of sand ripples and of pigmentation on a zebra skin. New examples of 'Turing patterns' in biology and beyond are still being discovered today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
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Affiliation(s)
- Philip Ball
- 18 Hillcourt Road, East Dulwich, London SE22 0PE, UK
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20
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Barcena Menendez D, Senthivel VR, Isalan M. Sender-receiver systems and applying information theory for quantitative synthetic biology. Curr Opin Biotechnol 2015; 31:101-7. [PMID: 25282688 PMCID: PMC4332572 DOI: 10.1016/j.copbio.2014.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 12/31/2022]
Abstract
Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.
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Affiliation(s)
- Diego Barcena Menendez
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Vivek Raj Senthivel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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21
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DiSCUS: A Simulation Platform for Conjugation Computing. UNCONVENTIONAL COMPUTATION AND NATURAL COMPUTATION 2015. [DOI: 10.1007/978-3-319-21819-9_13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Libis VK, Bernheim AG, Basier C, Jaramillo-Riveri S, Deyell M, Aghoghogbe I, Atanaskovic I, Bencherif AC, Benony M, Koutsoubelis N, Löchner AC, Marinkovic ZS, Zahra S, Zegman Y, Lindner AB, Wintermute EH. Silencing of antibiotic resistance in E. coli with engineered phage bearing small regulatory RNAs. ACS Synth Biol 2014; 3:1003-6. [PMID: 25524110 DOI: 10.1021/sb500033d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In response to emergent antibiotic resistance, new strategies are needed to enhance the effectiveness of existing antibiotics. Here, we describe a phagemid-delivered, RNA-mediated system capable of directly knocking down antibiotic resistance phenotypes. Small regulatory RNAs (sRNAs) were designed to specifically inhibit translation of chloramphenicol acetyltransferase and kanamycin phosphotransferase. Nonlytic phagemids coding for sRNA expression were able to infect and restore chloramphenicol and kanamycin sensitivity to populations of otherwise resistant E. coli. This modular system could easily be extended to other bacteria with resistance profiles that depend on specific transcripts.
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Affiliation(s)
| | | | - Clovis Basier
- 2013 Paris Bettencourt iGEM team, 75014 Paris, France
| | | | | | | | | | | | | | | | | | | | - Sarah Zahra
- 2013 Paris Bettencourt iGEM team, 75014 Paris, France
| | | | - Ariel B. Lindner
- 2013 Paris Bettencourt iGEM team, 75014 Paris, France
- U1001 Institut National de la Santé et de la Recherche Médicale, 75654 Paris, France
| | - Edwin H. Wintermute
- 2013 Paris Bettencourt iGEM team, 75014 Paris, France
- U1001 Institut National de la Santé et de la Recherche Médicale, 75654 Paris, France
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23
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A yeast pheromone-based inter-species communication system. Appl Microbiol Biotechnol 2014; 99:1299-308. [PMID: 25331280 DOI: 10.1007/s00253-014-6133-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
We report on a pheromone-based inter-species communication system, allowing for a controlled cell-cell communication between the two species Saccharomyces cerevisiae and Schizosaccharomyces pombe as a proof of principle. It exploits the mating response pathways of the two yeast species employing the pheromones, α- or P-factor, as signaling molecules. The authentic and chimeric pheromone-encoding genes were engineered to code for the P-factor in S. cerevisiae and the α-factor in S. pombe. Upon transformation of the respective constructs, cells were enabled to express the mating pheromone of the opposite species. The supernatant of cultures of S. pombe cells expressing α-factor were able to induce a G1 arrest in the cell cycle, a change in morphology to the typical shmoo effect and expression driven by the pheromone-responsive FIG1 promoter in S. cerevisiae. The supernatant of cultures of S. cerevisiae cells expressing P-factor similarly induced cell cycle arrest in G1, an alteration in morphology typical for mating as well as the activation of the pheromone-responsive promoters of the rep1 and sxa2 genes in a pheromone-hypersensitive reporter strain of S. pombe. Apparently, both heterologous pheromones were correctly processed and secreted in an active form by the cells of the other species. Our data clearly show that the species-specific pheromone systems of yeast species can be exploited for a controlled inter-species communication.
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24
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Nakano T, Suda T, Okaie Y, Moore MJ, Vasilakos AV. Molecular Communication Among Biological Nanomachines: A Layered Architecture and Research Issues. IEEE Trans Nanobioscience 2014; 13:169-97. [DOI: 10.1109/tnb.2014.2316674] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Judd J, Ho ML, Tiwari A, Gomez EJ, Dempsey C, Van Vliet K, Igoshin OA, Silberg JJ, Agbandje-McKenna M, Suh J. Tunable protease-activatable virus nanonodes. ACS NANO 2014; 8:4740-6. [PMID: 24796495 PMCID: PMC4046807 DOI: 10.1021/nn500550q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/30/2014] [Indexed: 05/19/2023]
Abstract
We explored the unique signal integration properties of the self-assembling 60-mer protein capsid of adeno-associated virus (AAV), a clinically proven human gene therapy vector, by engineering proteolytic regulation of virus-receptor interactions such that processing of the capsid by proteases is required for infection. We find the transfer function of our engineered protease-activatable viruses (PAVs), relating the degree of proteolysis (input) to PAV activity (output), is highly nonlinear, likely due to increased polyvalency. By exploiting this dynamic polyvalency, in combination with the self-assembly properties of the virus capsid, we show that mosaic PAVs can be constructed that operate under a digital AND gate regime, where two different protease inputs are required for virus activation. These results show viruses can be engineered as signal-integrating nanoscale nodes whose functional properties are regulated by multiple proteolytic signals with easily tunable and predictable response surfaces, a promising development toward advanced control of gene delivery.
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Affiliation(s)
- Justin Judd
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Michelle L. Ho
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Abhinav Tiwari
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Eric J. Gomez
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Christopher Dempsey
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Kim Van Vliet
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32611, United States
| | - Oleg A. Igoshin
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32611, United States
| | - Junghae Suh
- Department of Bioengineering and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
- Address correspondence to
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26
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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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27
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Rogacs A, Santiago JG. Particle Tracking and Multispectral Collocation Method for Particle-to-Particle Binding Assays. Anal Chem 2014; 86:608-14. [DOI: 10.1021/ac402830q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anita Rogacs
- Department
of Mechanical
Engineering, Stanford University, Stanford, California 94305, United States
| | - Juan G. Santiago
- Department
of Mechanical
Engineering, Stanford University, Stanford, California 94305, United States
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28
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Goñi-Moreno A, Amos M, de la Cruz F. Multicellular computing using conjugation for wiring. PLoS One 2013; 8:e65986. [PMID: 23840385 PMCID: PMC3688716 DOI: 10.1371/journal.pone.0065986] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/01/2013] [Indexed: 12/24/2022] Open
Abstract
Recent efforts in synthetic biology have focussed on the implementation of logical functions within living cells. One aim is to facilitate both internal "re-programming" and external control of cells, with potential applications in a wide range of domains. However, fundamental limitations on the degree to which single cells may be re-engineered have led to a growth of interest in multicellular systems, in which a "computation" is distributed over a number of different cell types, in a manner analogous to modern computer networks. Within this model, individual cell type perform specific sub-tasks, the results of which are then communicated to other cell types for further processing. The manner in which outputs are communicated is therefore of great significance to the overall success of such a scheme. Previous experiments in distributed cellular computation have used global communication schemes, such as quorum sensing (QS), to implement the "wiring" between cell types. While useful, this method lacks specificity, and limits the amount of information that may be transferred at any one time. We propose an alternative scheme, based on specific cell-cell conjugation. This mechanism allows for the direct transfer of genetic information between bacteria, via circular DNA strands known as plasmids. We design a multi-cellular population that is able to compute, in a distributed fashion, a Boolean XOR function. Through this, we describe a general scheme for distributed logic that works by mixing different strains in a single population; this constitutes an important advantage of our novel approach. Importantly, the amount of genetic information exchanged through conjugation is significantly higher than the amount possible through QS-based communication. We provide full computational modelling and simulation results, using deterministic, stochastic and spatially-explicit methods. These simulations explore the behaviour of one possible conjugation-wired cellular computing system under different conditions, and provide baseline information for future laboratory implementations.
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Affiliation(s)
- Angel Goñi-Moreno
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain.
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29
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Weyland M, Griveau A, Bejaud J, Benoit JP, Coursaget P, Garcion E. Lipid nanocapsule functionalization by lipopeptides derived from human papillomavirus type-16 capsid for nucleic acid delivery into cancer cells. Int J Pharm 2013; 454:756-64. [PMID: 23769994 DOI: 10.1016/j.ijpharm.2013.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/06/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
Plasmid DNA (pDNA) and small interfering RNAs (siRNAs) are very useful tools for the treatment of cancer. However, pDNA and siRNAs efficacy is restricted by their negative charge and susceptibility to degradation by endonucleases that prevent them penetrating tissue and cellular barriers such as the plasma and endolysosomal membranes. Viral vectors have some advantages but their use is largely limited by their immunogenicity. On the other hand, synthetic nanoparticles have advantage of being relatively non-immunogenic but their ability to deliver nucleic acids remains less efficient than their viral counterparts. The present study is focussed on the development and evaluation of biomimetic lipid nanocapsules (LNCs) functionalized with a L1 papillomavirus type-16 capsid-derived lipopeptide on their surface, for transfection of U87MG glioma cells and Caco-2 colorectal adenocarcinoma cells with pDNA or siRNAs. Since the L1-peptide has been described as a nuclear localization signal able to complex with nucleic acids and bind to heparan sulfate on the cell surface, the structure and function of L1-peptide bound to LNCs (L1-LNCs) were investigated. Although L1-LNCs were shown to complex with both pDNA and siRNAs, the pDNA-L1-LNC complexes showed only weak transfection efficiency. In contrast, siRNA-L1-LNC complexes appeared as effective repressors of targeted messengers.
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Affiliation(s)
- M Weyland
- Inserm U1066, Micro et nanomédecines biomimétiques, F-49933 Angers, France
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30
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Kahl LJ, Endy D. A survey of enabling technologies in synthetic biology. J Biol Eng 2013; 7:13. [PMID: 23663447 PMCID: PMC3684516 DOI: 10.1186/1754-1611-7-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/30/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies. RESULTS We conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants. CONCLUSIONS The set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential.
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Affiliation(s)
- Linda J Kahl
- Bioengineering Department, Stanford University, Y2E2 Room 269C, 473 Via Ortega, Stanford, CA, 94305-4201, USA
| | - Drew Endy
- Bioengineering Department, Stanford University, Y2E2 Room 269C, 473 Via Ortega, Stanford, CA, 94305-4201, USA
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31
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Abstract
Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulates transcription rates. We realized permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic-gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.
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Affiliation(s)
- Jerome Bonnet
- Department of Bioengineering, Y2E2-269B, 473 Via Ortega, Stanford, CA 94305-4201, USA
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32
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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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33
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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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34
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Siuti P, Yazbek J, Lu TK. Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 2013; 31:448-52. [PMID: 23396014 DOI: 10.1038/nbt.2510] [Citation(s) in RCA: 333] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/17/2013] [Indexed: 01/13/2023]
Abstract
Logic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications.
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Affiliation(s)
- Piro Siuti
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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35
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Byun CK, Hwang H, Choi WS, Yaguchi T, Park J, Kim D, Mitchell RJ, Kim T, Cho YK, Takayama S. Productive Chemical Interaction between a Bacterial Microcolony Couple Is Enhanced by Periodic Relocation. J Am Chem Soc 2013; 135:2242-7. [DOI: 10.1021/ja3094923] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Chang Kyu Byun
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Hyundoo Hwang
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Woon Sun Choi
- School of Mechanical and Advanced
Materials Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Toshiyuki Yaguchi
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Jiwoon Park
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Dasol Kim
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Robert J. Mitchell
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Taesung Kim
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
- School of Mechanical and Advanced
Materials Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Yoon-Kyoung Cho
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
- School of Mechanical and Advanced
Materials Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
| | - Shuichi Takayama
- School of Nano-Bioscience and
Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Republic of Korea
- Department of Biomedical Engineering, University of Michigan, Biointerfaces Institute, 2800
Plymouth Rd, Ann Arbor, Michigan 48109-2800, United States
- Macromolecular Science and Engineering
Center, University of Michigan, 2300 Hayward
Street, Ann Arbor, Michigan 48109, United States
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