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Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. BIODESIGN RESEARCH 2022; 2022:9794510. [PMID: 37850136 PMCID: PMC10521664 DOI: 10.34133/2022/9794510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/10/2022] [Indexed: 10/19/2023] Open
Abstract
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.
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Affiliation(s)
- Samuel M. D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
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2
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Prangemeier T, Lehr FX, Schoeman RM, Koeppl H. Microfluidic platforms for the dynamic characterisation of synthetic circuitry. Curr Opin Biotechnol 2020; 63:167-176. [PMID: 32172160 DOI: 10.1016/j.copbio.2020.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/28/2023]
Abstract
Generating novel functionality from well characterised synthetic parts and modules lies at the heart of synthetic biology. Ideally, circuitry is rationally designed in silico with quantitatively predictive models to predetermined design specifications. Synthetic circuits are intrinsically stochastic, often dynamically modulated and set in a dynamic fluctuating environment within a living cell. To build more complex circuits and to gain insight into context effects, intrinsic noise and transient performance, characterisation techniques that resolve both heterogeneity and dynamics are required. Here we review recent advances in both in vitro and in vivo microfluidic technologies that are suitable for the characterisation of synthetic circuitry, modules and parts.
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Affiliation(s)
- Tim Prangemeier
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - François-Xavier Lehr
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - Rogier M Schoeman
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany.
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3
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3DμF - Interactive Design Environment for Continuous Flow Microfluidic Devices. Sci Rep 2019; 9:9166. [PMID: 31235804 PMCID: PMC6591506 DOI: 10.1038/s41598-019-45623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/07/2019] [Indexed: 01/16/2023] Open
Abstract
The design of microfluidic Lab on a Chip (LoC) systems is an onerous task requiring specialized skills in fluid dynamics, mechanical design drafting, and manufacturing. Engineers face significant challenges during the labor-intensive process of designing microfluidic devices, with very few specialized tools that help automate the process. Typical design iterations require the engineer to research the architecture, manually draft the device layout, optimize for manufacturing processes, and manually calculate and program the valve sequences that operate the microfluidic device. The problem compounds when engineers not only have to test the functionality of the chip but are also expected to optimize them for the robust execution of biological assays. In this paper, we present an interactive tool for designing continuous flow microfluidic devices. 3DμF is the first completely open source interactive microfluidic system designer that readily supports state of the art design automation algorithms. Through various case studies, we show 3DμF can be used to reproduce designs from literature, provide metrics for evaluating microfluidic design complexity and showcase how 3DμF is a platform for integrating a wide assortment of engineering techniques used in the design of microfluidic devices as a part of the standard design workflow.
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Xiang Y, Dalchau N, Wang B. Scaling up genetic circuit design for cellular computing: advances and prospects. NATURAL COMPUTING 2018; 17:833-853. [PMID: 30524216 PMCID: PMC6244767 DOI: 10.1007/s11047-018-9715-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.
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Affiliation(s)
- Yiyu Xiang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | | | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
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5
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Husser MC, Vo PQN, Sinha H, Ahmadi F, Shih SCC. An Automated Induction Microfluidics System for Synthetic Biology. ACS Synth Biol 2018. [PMID: 29516725 DOI: 10.1021/acssynbio.8b00025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The expression of a recombinant gene in a host organism through induction can be an extensively manual and labor-intensive procedure. Several methods have been developed to simplify the protocol, but none has fully replaced the traditional IPTG-based induction. To simplify this process, we describe the development of an autoinduction platform based on digital microfluidics. This system consists of a 600 nm LED and a light sensor to enable the real-time monitoring of the optical density (OD) samples coordinated with the semicontinuous mixing of a bacterial culture. A hand-held device was designed as a microbioreactor to culture cells and to measure the OD of the bacterial culture. In addition, it serves as a platform for the analysis of regulated protein expression in E. coli without the requirement of standardized well-plates or pipetting-based platforms. Here, we report for the first time, a system that offers great convenience without the user to physically monitor the culture or to manually add inducer at specific times. We characterized our system by looking at several parameters (electrode designs, gap height, and growth rates) required for an autoinducible system. As a first step, we carried out an automated induction optimization assay using a RFP reporter gene to identify conditions suitable for our system. Next, we used our system to identify active thermophilic β-glucosidase enzymes that may be suitable candidates for biomass hydrolysis. Overall, we believe that this platform may be useful for synthetic biology applications that require regulating and analyzing expression of heterologous genes for strain optimization.
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Affiliation(s)
- Mathieu C. Husser
- Department of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Philippe Q. N. Vo
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Hugo Sinha
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Fatemeh Ahmadi
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Steve C. C. Shih
- Department of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G 1M8, Canada
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Gach PC, Iwai K, Kim PW, Hillson NJ, Singh AK. Droplet microfluidics for synthetic biology. LAB ON A CHIP 2017; 17:3388-3400. [PMID: 28820204 DOI: 10.1039/c7lc00576h] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to most researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.
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Affiliation(s)
- Philip C Gach
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California 94608, USA
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Oono M, Yamaguchi K, Rasyid A, Takano A, Tanaka M, Futai N. Reconfigurable microfluidic device with discretized sidewall. BIOMICROFLUIDICS 2017; 11:034103. [PMID: 28503247 PMCID: PMC5415406 DOI: 10.1063/1.4983148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
Various microfluidic features, such as traps, have been used to manipulate flows, cells, and other particles within microfluidic systems. However, these features often become undesirable in subsequent steps requiring different fluidic configurations. To meet the changing needs of various microfluidic configurations, we developed a reconfigurable microfluidic channel with movable sidewalls using mechanically discretized sidewalls of laterally aligned rectangular pins. The user can deform the channel sidewall at any time after fabrication by sliding the pins. We confirmed that the flow resistance of the straight microchannel could be reversibly adjusted in the range of 101-105 Pa s/μl by manually displacing one of the pins comprising the microchannel sidewall. The reconfigurable microchannel also made it possible to manipulate flows and cells by creating a segmented patterned culture of COS-7 cells and a coculture of human umbilical vein endothelial cells (HUVECs) and human lung fibroblasts (hLFs) inside the microchannel. The reconfigurable microfluidic device successfully maintained a culture of COS-7 cells in a log phase throughout the entire period of 216 h. Furthermore, we performed a migration assay of cocultured HUVEC and hLF spheroids within one microchannel and observed their migration toward each other.
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Affiliation(s)
- Masahiro Oono
- Department of Mechanical Engineering, Graduate School of Engineering and Science, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Keisuke Yamaguchi
- Department of Mechanical Engineering, College of Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Amirul Rasyid
- Department of Mechanical Engineering, College of Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Atsushi Takano
- Digital Manufacturing and Design Centre, Singapore University of Technology and Design, 8 Somapah Rd, Singapore 487372
| | - Masato Tanaka
- Department of Materials and Life Sciences, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-machi, Hiki-gun, Saitama 350-0394, Japan
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8
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Yang YT, Wang CY. Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae. MICROMACHINES 2016; 7:mi7100185. [PMID: 30404358 PMCID: PMC6190437 DOI: 10.3390/mi7100185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]
Abstract
One goal of metabolic engineering and synthetic biology for cyanobacteria and microalgae is to engineer strains that can optimally produce biofuels and commodity chemicals. However, the current workflow is slow and labor intensive with respect to assembly of genetic parts and characterization of production yields because of the slow growth rates of these organisms. Here, we review recent progress in the microfluidic photobioreactors and identify opportunities and unmet needs in metabolic engineering and synthetic biology. Because of the unprecedented experimental resolution down to the single cell level, long-term real-time monitoring capability, and high throughput with low cost, microfluidic photobioreactor technology will be an indispensible tool to speed up the development process, advance fundamental knowledge, and realize the full potential of metabolic engineering and synthetic biology for cyanobacteria and microalgae.
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Affiliation(s)
- Ya-Tang Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Chun Ying Wang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
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9
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Silva R, Bhatia S, Densmore D. A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive. LAB ON A CHIP 2016; 16:2730-2741. [PMID: 27345339 DOI: 10.1039/c6lc00477f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microfluidic devices, by definition, are required to move liquids from one physical location to another. Given a finite and frequently fixed set of physical channels to route fluids, a primitive design element that allows reconfigurable routing of that fluid from any of n input ports to any n output ports will dramatically change the paradigms by which these chips are designed and applied. Furthermore, if these elements are "regular" regarding their design, the programming and fabrication of these elements becomes scalable. This paper presents such a design element called a transposer. We illustrate the design, fabrication and operation of a single transposer. We then scale this design to create a programmable fabric towards a general-purpose, reconfigurable microfluidic platform analogous to the Field Programmable Gate Array (FPGA) found in digital electronics.
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Affiliation(s)
- Ryan Silva
- Boston University Department of Electrical and Computer Engineering, 8 Saint Mary's St., Boston, USA. and Biological Design Center, 610 Commonwealth Avenue, Boston, USA
| | - Swapnil Bhatia
- Boston University Department of Electrical and Computer Engineering, 8 Saint Mary's St., Boston, USA. and Biological Design Center, 610 Commonwealth Avenue, Boston, USA
| | - Douglas Densmore
- Boston University Department of Electrical and Computer Engineering, 8 Saint Mary's St., Boston, USA. and Biological Design Center, 610 Commonwealth Avenue, Boston, USA
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10
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Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, Rettberg R. Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLoS One 2016; 11:e0150182. [PMID: 26937966 PMCID: PMC4777433 DOI: 10.1371/journal.pone.0150182] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/10/2016] [Indexed: 11/18/2022] Open
Abstract
We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, United States of America
- * E-mail:
| | | | | | - Kim de Mora
- iGEM Foundation, Cambridge, MA, United States of America
| | | | | | - Randy Rettberg
- iGEM Foundation, Cambridge, MA, United States of America
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11
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Ma KC, Perli SD, Lu TK. Foundations and Emerging Paradigms for Computing in Living Cells. J Mol Biol 2016; 428:893-915. [DOI: 10.1016/j.jmb.2016.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023]
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12
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Liu Q, Zhang Y, Jing W, Liu S, Zhang D, Sui G. First airborne pathogen direct analysis system. Analyst 2016; 141:1637-40. [DOI: 10.1039/c5an02367j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This is the first portable “sample to answer” system for the rapid detection of pathogenic bacteria in air.
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Affiliation(s)
- Qi Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3)
- Department of Environmental Science & Engineering
- Fudan University
- Shanghai
- China
| | - Yuxiao Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3)
- Department of Environmental Science & Engineering
- Fudan University
- Shanghai
- China
| | - Wenwen Jing
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3)
- Department of Environmental Science & Engineering
- Fudan University
- Shanghai
- China
| | - Sixiu Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3)
- Department of Environmental Science & Engineering
- Fudan University
- Shanghai
- China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System
- Ministry of Education and Shanghai Key Lab of Modern Optical System
- University of Shanghai for Science and Technology
- Shanghai
- China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3)
- Department of Environmental Science & Engineering
- Fudan University
- Shanghai
- China
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13
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Shih SCC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol 2015; 4:1151-64. [PMID: 26075958 DOI: 10.1021/acssynbio.5b00062] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.
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Affiliation(s)
- Steve C. C. Shih
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Garima Goyal
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Peter W. Kim
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Nicolas Koutsoubelis
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Paul D. Adams
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Nathan J. Hillson
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Anup K. Singh
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015; 5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
| | - Jacqueline M Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
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