1
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Asensio‐Calavia A, Ceballos‐Munuera Á, Méndez‐Pérez A, Álvarez B, Fernández LÁ. A tuneable genetic switch for tight control of tac promoters in Escherichia coli boosts expression of synthetic injectisomes. Microb Biotechnol 2024; 17:e14328. [PMID: 37608576 PMCID: PMC10832536 DOI: 10.1111/1751-7915.14328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Biosafety of engineered bacteria as living therapeutics requires a tight regulation to control the specific delivery of protein effectors, maintaining minimum leakiness in the uninduced (OFF) state and efficient expression in the induced (ON) state. Here, we report a three repressors (3R) genetic circuit that tightly regulates the expression of multiple tac promoters (Ptac) integrated in the chromosome of E. coli and drives the expression of a complex type III secretion system injectisome for therapeutic protein delivery. The 3R genetic switch is based on the tetracycline repressor (TetR), the non-inducible lambda repressor cI (ind-) and a mutant lac repressor (LacIW220F ) with higher activity. The 3R switch was optimized with different protein translation and degradation signals that control the levels of LacIW220F . We demonstrate the ability of an optimized switch to fully repress the strong leakiness of the Ptac promoters in the OFF state while triggering their efficient activation in the ON state with anhydrotetracycline (aTc), an inducer suitable for in vivo use. The implementation of the optimized 3R switch in the engineered synthetic injector E. coli (SIEC) strain boosts expression of injectisomes upon aTc induction, while maintaining a silent OFF state that preserves normal growth in the absence of the inducer. Since Ptac is a commonly used promoter, the 3R switch may have multiple applications for tight control of protein expression in E. coli. In addition, the modularity of the 3R switch may enable its tuning for the control of Ptac promoters with different inducers.
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Affiliation(s)
- Alejandro Asensio‐Calavia
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Álvaro Ceballos‐Munuera
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Almudena Méndez‐Pérez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
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2
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Nava A, Fear AL, Lee N, Mellinger P, Lan G, McCauley J, Tan S, Kaplan N, Goyal G, Coates RC, Roberts J, Johnson Z, Hu R, Wu B, Ahn J, Kim WE, Wan Y, Yin K, Hillson N, Haushalter RW, Keasling JD. Automated Platform for the Plasmid Construction Process. ACS Synth Biol 2023; 12:3506-3513. [PMID: 37948662 PMCID: PMC10729297 DOI: 10.1021/acssynbio.3c00292] [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: 05/07/2023] [Indexed: 11/12/2023]
Abstract
There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Anna Lisa Fear
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Peter Mellinger
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Guangxu Lan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joshua McCauley
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Stephen Tan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Nurgul Kaplan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Garima Goyal
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - R. Cameron Coates
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Zahmiria Johnson
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Romina Hu
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Bryan Wu
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jared Ahn
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Woojoo E. Kim
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yao Wan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin Yin
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Nathan Hillson
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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3
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Meng X, Wu TG, Lou QY, Niu KY, Jiang L, Xiao QZ, Xu T, Zhang L. Optimization of CRISPR-Cas system for clinical cancer therapy. Bioeng Transl Med 2023; 8:e10474. [PMID: 36925702 PMCID: PMC10013785 DOI: 10.1002/btm2.10474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/25/2022] Open
Abstract
Cancer is a genetic disease caused by alterations in genome and epigenome and is one of the leading causes for death worldwide. The exploration of disease development and therapeutic strategies at the genetic level have become the key to the treatment of cancer and other genetic diseases. The functional analysis of genes and mutations has been slow and laborious. Therefore, there is an urgent need for alternative approaches to improve the current status of cancer research. Gene editing technologies provide technical support for efficient gene disruption and modification in vivo and in vitro, in particular the use of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Currently, the applications of CRISPR-Cas systems in cancer rely on different Cas effector proteins and the design of guide RNAs. Furthermore, effective vector delivery must be met for the CRISPR-Cas systems to enter human clinical trials. In this review article, we describe the mechanism of the CRISPR-Cas systems and highlight the applications of class II Cas effector proteins. We also propose a synthetic biology approach to modify the CRISPR-Cas systems, and summarize various delivery approaches facilitating the clinical application of the CRISPR-Cas systems. By modifying the CRISPR-Cas system and optimizing its in vivo delivery, promising and effective treatments for cancers using the CRISPR-Cas system are emerging.
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Affiliation(s)
- Xiang Meng
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Tian-Gang Wu
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qiu-Yue Lou
- Anhui Provincial Center for Disease Control and Prevention Hefei People's Republic of China
| | - Kai-Yuan Niu
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK.,Department of Otolaryngology The Third Affiliated Hospital of Anhui Medical University Hefei China
| | - Lei Jiang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qing-Zhong Xiao
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products Anhui Medical University Hefei China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province Hefei China
| | - Lei Zhang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China.,Department of Periodontology Anhui Stomatology Hospital Affiliated to Anhui Medical University Hefei China
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4
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Buecherl L, Myers CJ. Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology. Curr Opin Microbiol 2022; 68:102155. [PMID: 35588683 DOI: 10.1016/j.mib.2022.102155] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 01/23/2023]
Abstract
Synthetic biology (SynBio) is a field at the intersection of biology and engineering. Inspired by engineering principles, researchers use defined parts to build functionally defined biological circuits. Genetic design automation (GDA) allows scientists to design, model, and analyze their genetic circuits in silico before building them in the lab, saving time, and resources in the process. Establishing SynBio's future is dependent on GDA, since the computational approach opens the field to a broad, interdisciplinary community. However, challenges with part libraries, standards, and software tools are currently stalling progress in the field. This review first covers recent advancements in GDA, followed by an assessment of the challenges ahead, and a proposed automated genetic design workflow for the future.
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Affiliation(s)
- Lukas Buecherl
- Biomedical Engineering Program, University of Colorado Boulder, 1111 Engineering Drive, Boulder, 80309 CO, United States
| | - Chris J Myers
- Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, 425 UCB, Boulder, 80309 CO, United States.
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5
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Bartley BA. Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing. ACS Synth Biol 2022; 11:1373-1376. [PMID: 35226470 DOI: 10.1021/acssynbio.1c00450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As synthetic biology becomes increasingly automated and data-driven, tools that help researchers implement FAIR (findable-accessible-interoperable-reusable) data management practices are needed. Crucially, in order to support machine processing and reusability of data, it is important that data artifacts are appropriately annotated with metadata drawn from controlled vocabularies. Unfortunately, adopting standardized annotation practices is difficult for many research groups to adopt, given the set of specialized database science skills usually required to interface with ontologies. In response to this need, Take Your Terms from Ontologies (Tyto) is a lightweight Python tool that supports the use of controlled vocabularies in everyday scripting practice. While Tyto has been developed for synthetic biology applications, its utility may extend to users working in other areas of bioinformatics research as well. Tyto is available as a Python package distribution or available as source at https://github.com/SynBioDex/tyto.
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Affiliation(s)
- Bryan A. Bartley
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
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6
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Luo Y, James JS, Jones S, Martella A, Cai Y. EMMA-CAD: Design Automation for Synthetic Mammalian Constructs. ACS Synth Biol 2022; 11:579-586. [PMID: 35050610 DOI: 10.1021/acssynbio.1c00433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational design tools are the cornerstone of synthetic biology and have underpinned its rapid development over the past two decades. As the field has matured, the scale of biological investigation has expanded dramatically, and researchers often must rely on computational tools to operate in the high-throughput investigational space. This is especially apparent in the modular design of DNA expression circuits, where complexity is accumulated rapidly. Alongside our automated pipeline for the high-throughput construction of Extensible Modular Mammalian Assembly (EMMA) expression vectors, we recognized the need for an integrated software solution for EMMA vector design. Here we present EMMA-CAD (https://emma.cailab.org), a powerful web-based computer-aided design tool for the rapid design of bespoke mammalian expression vectors. EMMA-CAD features a variety of functionalities, including a user-friendly design interface, automated connector selection underpinned by rigorous computer optimization algorithms, customization of part libraries, and personalized design spaces. Capable of translating vector assembly designs into human- and machine-readable protocols for vector construction, EMMA-CAD integrates seamlessly into our automated EMMA pipeline, hence completing an end-to-end design to production workflow.
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Affiliation(s)
- Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Joshua S. James
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Sally Jones
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, U.K
| | - Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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7
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Buecherl L, Roberts R, Fontanarrosa P, Thomas PJ, Mante J, Zhang Z, Myers CJ. Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA. ACS Synth Biol 2021; 10:2532-2540. [PMID: 34606710 DOI: 10.1021/acssynbio.1c00159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In synthetic biology, combinational circuits are used to program cells for various new applications like biosensors, drug delivery systems, and biofuels. Similar to asynchronous electronic circuits, some combinational genetic circuits may show unwanted switching variations (glitches) caused by multiple input changes. Depending on the biological circuit, glitches can cause irreversible effects and jeopardize the circuit's functionality. This paper presents a stochastic analysis to predict glitch propensities for three implementations of a genetic circuit with known glitching behavior. The analysis uses STochastic Approximate Model-checker for INfinite-state Analysis (STAMINA), a tool for stochastic verification. The STAMINA results were validated by comparison to stochastic simulation in iBioSim resulting in further improvements of STAMINA. This paper demonstrates that stochastic verification can be utilized by genetic designers to evaluate design choices and input restrictions to achieve a desired reliability of operation.
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Affiliation(s)
- Lukas Buecherl
- Department of Biomedical Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Riley Roberts
- Department of Electrical and Computer Engineering, Utah State University, Logan, Utah 84322, United States
| | - Pedro Fontanarrosa
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Payton J. Thomas
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jeanet Mante
- Department of Biomedical Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Zhen Zhang
- Department of Electrical and Computer Engineering, Utah State University, Logan, Utah 84322, United States
| | - Chris J. Myers
- Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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8
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Plahar HA, Rich TN, Lane SD, Morrell WC, Springthorpe L, Nnadi O, Aravina E, Dai T, Fero MJ, Hillson NJ, Petzold CJ. BioParts-A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform. ACS Synth Biol 2021; 10:2649-2660. [PMID: 34449214 DOI: 10.1021/acssynbio.1c00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Capturing, storing, and sharing biological DNA parts data are integral parts of synthetic biology research. Here, we detail updates to the ICE biological parts registry software platform that enable these processes, describe our implementation of the Web of Registries concept using ICE, and establish Bioparts, a search portal for biological parts available in the public domain. The Web of Registries enables standalone ICE installations to securely connect and form a distributed parts database. This distributed database allows users from one registry to query and access plasmid, strain, (DNA) part, plant seed, and protein entry types in other connected registries. Users can also transfer entries from one ICE registry to another or make them publicly accessible. Bioparts, the new search portal, combines the ease and convenience of modern web search engines with the capabilities of bioinformatics search tools such as BLAST. This portal, available at bioparts.org, allows anyone to search for publicly accessible biological part information (e.g., NCBI, iGEM, SynBioHub, Addgene), including parts publicly accessible through ICE Registries. Additionally, the portal offers a REST API that enables third-party applications and tools to access the portal's functionality programmatically.
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Affiliation(s)
- Hector A. Plahar
- DOE Agile BioFoundry, Emeryville, California 94608 ,United States
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Thomas N. Rich
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- TeselaGen Biotechnology Inc., San Francisco, California 94107, United States
| | - Stephen D. Lane
- DOE Agile BioFoundry, Emeryville, California 94608 ,United States
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia National Laboratories, Livermore, California 94550, United States
| | - William C. Morrell
- DOE Agile BioFoundry, Emeryville, California 94608 ,United States
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia National Laboratories, Livermore, California 94550, United States
| | - Leanne Springthorpe
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oge Nnadi
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Elena Aravina
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tiffany Dai
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- TeselaGen Biotechnology Inc., San Francisco, California 94107, United States
| | - Michael J. Fero
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- TeselaGen Biotechnology Inc., San Francisco, California 94107, United States
| | - Nathan J. Hillson
- DOE Agile BioFoundry, Emeryville, California 94608 ,United States
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- DOE Agile BioFoundry, Emeryville, California 94608 ,United States
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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9
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Peccoud J. Data sharing policies: share well and you shall be rewarded. Synth Biol (Oxf) 2021; 6:ysab028. [PMID: 34604538 PMCID: PMC8482415 DOI: 10.1093/synbio/ysab028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Sharing research data is an integral part of the scientific publishing process. By sharing data, authors enable their readers to use their results in a way that the textual description of the results does not allow by itself. In order to achieve this objective, data should be shared in a way that makes it as easy as possible for readers to import them in computer software where they can be viewed, manipulated and analyzed. Many authors and reviewers seem to misunderstand the purpose of the data sharing policies developed by journals. Rather than being an administrative burden that authors should comply with to get published, the objective of these policies is to help authors maximize the impact of their work by allowing other members of the scientific community to build upon it. Authors and reviewers need to understand the purpose of data sharing policies to assist editors and publishers in their efforts to ensure that every article published complies with them.
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Affiliation(s)
- Jean Peccoud
- Department of Chemical & Biological Engineering, Colorado State University, Fort Collins, CO, USA
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10
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Gupta D, Sharma G, Saraswat P, Ranjan R. Synthetic Biology in Plants, a Boon for Coming Decades. Mol Biotechnol 2021; 63:1138-1154. [PMID: 34420149 DOI: 10.1007/s12033-021-00386-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/16/2021] [Indexed: 02/01/2023]
Abstract
Recently an enormous expansion of knowledge is seen in various disciplines of science. This surge of information has given rise to concept of interdisciplinary fields, which has resulted in emergence of newer research domains, one of them is 'Synthetic Biology' (SynBio). It captures basics from core biology and integrates it with concepts from the other areas of study such as chemical, electrical, and computational sciences. The essence of synthetic biology is to rewire, re-program, and re-create natural biological pathways, which are carried through genetic circuits. A genetic circuit is a functional assembly of basic biological entities (DNA, RNA, proteins), created using typical design, built, and test cycles. These circuits allow scientists to engineer nearly all biological systems for various useful purposes. The development of sophisticated molecular tools, techniques, genomic programs, and ease of nucleic acid synthesis have further fueled several innovative application of synthetic biology in areas like molecular medicines, pharmaceuticals, biofuels, drug discovery, metabolomics, developing plant biosensors, utilization of prokaryotic systems for metabolite production, and CRISPR/Cas9 in the crop improvement. These applications have largely been dominated by utilization of prokaryotic systems. However, newer researches have indicated positive growth of SynBio for the eukaryotic systems as well. This paper explores advances of synthetic biology in the plant field by elaborating on its core components and potential applications. Here, we have given a comprehensive idea of designing, development, and utilization of synthetic biology in the improvement of the present research state of plant system.
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Affiliation(s)
- Dipinte Gupta
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Gauri Sharma
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Pooja Saraswat
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Rajiv Ranjan
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India.
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11
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Hatch B, Meng L, Mante J, McLaughlin JA, Scott-Brown J, Myers CJ. VisBOL2-Improving Web-Based Visualization for Synthetic Biology Designs. ACS Synth Biol 2021; 10:2111-2115. [PMID: 34324811 DOI: 10.1021/acssynbio.1c00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
VisBOL is a web-based visualization tool used to depict genetic circuit designs. This tool depicts simple DNA circuits adequately, but it has become increasingly outdated as new versions of SBOL Visual were released. This paper introduces VisBOL2, a heavily redesigned version of VisBOL that makes a number of improvements to the original VisBOL, including proper functional interaction rendering, dynamic viewing, a more maintainable code base, and modularity that facilitates compatibility with other software tools. This modularity is demonstrated by incorporating VisBOL2 into a sequence visualization plugin for SynBioHub.
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Affiliation(s)
- Benjamin Hatch
- University of Utah, Salt Lake City, Utah 84112, United States
| | - Linhao Meng
- Eindhoven University of Technology, Eindhoven, 5612 AZ, Netherlands
| | - Jeanet Mante
- University of Colorado Boulder, Boulder, Colorado 80309, United States
| | | | | | - Chris J. Myers
- University of Colorado Boulder, Boulder, Colorado 80309, United States
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12
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McCarthy J. Engineering and standardization of posttranscriptional biocircuitry in Saccharomyces cerevisiae. Integr Biol (Camb) 2021; 13:210-220. [PMID: 34270725 DOI: 10.1093/intbio/zyab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022]
Abstract
This short review considers to what extent posttranscriptional steps of gene expression can provide the basis for novel control mechanisms and procedures in synthetic biology and biotechnology. The term biocircuitry is used here to refer to functionally connected components comprising DNA, RNA or proteins. The review begins with an overview of the diversity of devices being developed and then considers the challenges presented by trying to engineer more scaled-up systems. While the engineering of RNA-based and protein-based circuitry poses new challenges, the resulting 'toolsets' of components and novel mechanisms of operation will open up multiple new opportunities for synthetic biology. However, agreed procedures for standardization will need to be placed at the heart of this expanding field if the full potential benefits are to be realized.
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Affiliation(s)
- John McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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13
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Terry L, Earl J, Thayer S, Bridge S, Myers CJ. SBOLCanvas: A Visual Editor for Genetic Designs. ACS Synth Biol 2021; 10:1792-1796. [PMID: 34152132 DOI: 10.1021/acssynbio.1c00096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SBOLCanvas is a web-based application that can create and edit genetic constructs using the SBOL data and visual standards. SBOLCanvas allows a user to create a genetic design visually and structurally from start to finish. It also allows users to incorporate existing SBOL data from a SynBioHub repository. By the nature of being a web-based application, SBOLCanvas is readily accessible and easy to use. A live version of the latest release can be found at https://sbolcanvas.org.
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Affiliation(s)
- Logan Terry
- University of Utah, Salt Lake City, 84132 Utah, United States
| | - Jared Earl
- University of Utah, Salt Lake City, 84132 Utah, United States
| | - Sam Thayer
- University of Utah, Salt Lake City, 84132 Utah, United States
| | - Samuel Bridge
- University of Utah, Salt Lake City, 84132 Utah, United States
| | - Chris J. Myers
- University of Colorado Boulder, Boulder, 80309 Colorado, United States
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14
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Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs. PLoS One 2021; 16:e0252263. [PMID: 34097703 PMCID: PMC8183995 DOI: 10.1371/journal.pone.0252263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Reproducibility is a key challenge of synthetic biology, but the foundation of reproducibility is only as solid as the reference materials it is built upon. Here we focus on the reproducibility of fluorescence measurements from bacteria transformed with engineered genetic constructs. This comparative analysis comprises three large interlaboratory studies using flow cytometry and plate readers, identical genetic constructs, and compatible unit calibration protocols. Across all three studies, we find similarly high precision in the calibrants used for plate readers. We also find that fluorescence measurements agree closely across the flow cytometry results and two years of plate reader results, with an average standard deviation of 1.52-fold, while the third year of plate reader results are consistently shifted by more than an order of magnitude, with an average shift of 28.9-fold. Analyzing possible sources of error indicates this shift is due to incorrect preparation of the fluorescein calibrant. These findings suggest that measuring fluorescence from engineered constructs is highly reproducible, but also that there is a critical need for access to quality controlled fluorescent calibrants for plate readers.
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15
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Oberortner E, Evans R, Meng X, Nath S, Plahar H, Simirenko L, Tarver A, Deutsch S, Hillson NJ, Cheng JF. An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology. Methods Mol Biol 2021; 2205:3-18. [PMID: 32809190 DOI: 10.1007/978-1-0716-0908-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bioCAD/CAM tools developed and used at the US Department of Energy (DOE) Joint Genome Institute (JGI), Joint BioEnergy Institute (JBEI), and Agile BioFoundry (ABF). We demonstrate the use of these bioCAD/CAM tools on a common workflow for designing and building a multigene pathway in a hierarchical fashion. Each tool presented in this book chapter is specifically tailored to support one or more specific steps in a workflow, can be integrated with the others into design and build workflows, and can be deployed at academic, government, or commercial entities.
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Affiliation(s)
- Ernst Oberortner
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA. .,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Robert Evans
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xianwei Meng
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sangeeta Nath
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hector Plahar
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Technology Division, DOE Joint BioEnergy Institute (JBEI), Emeryville, CA, USA
| | - Lisa Simirenko
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Angela Tarver
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Deutsch
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nathan J Hillson
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Technology Division, DOE Joint BioEnergy Institute (JBEI), Emeryville, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA.,TeselaGen Biotechnology, Inc., San Francisco, CA, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute (JGI), Berkeley, CA, USA.,Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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16
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Yeoh JW, Swainston N, Vegh P, Zulkower V, Carbonell P, Holowko MB, Peddinti G, Poh CL. SynBiopython: an open-source software library for Synthetic Biology. Synth Biol (Oxf) 2021. [PMCID: PMC8063678 DOI: 10.1093/synbio/ysab001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.
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Affiliation(s)
- Jing Wui Yeoh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Neil Swainston
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Edinburgh, UK
| | | | - Pablo Carbonell
- Instituto Universitario de Automática e Informática Industrial, Universitat Politècnica de València, Valencia, Spain
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Maciej B Holowko
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Gopal Peddinti
- VTT Technical Research Center of Finland, Espoo, Finland
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
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17
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Rampadarath A, Nickerson DP. Automated Execution of Simulation Studies in Systems Medicine Using SED-ML and COMBINE Archive. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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18
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Choi K, Karr JR, Sauro HM. Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11525-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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19
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McLaughlin JA, Beal J, Mısırlı G, Grünberg R, Bartley BA, Scott-Brown J, Vaidyanathan P, Fontanarrosa P, Oberortner E, Wipat A, Gorochowski TE, Myers CJ. The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Front Bioeng Biotechnol 2020; 8:1009. [PMID: 33015004 PMCID: PMC7516281 DOI: 10.3389/fbioe.2020.01009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use.
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Affiliation(s)
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, United States
| | - Göksel Mısırlı
- School of Mathematics and Computing, Keele University, Keele, United Kingdom
| | - Raik Grünberg
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - James Scott-Brown
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | | | - Pedro Fontanarrosa
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
| | - Ernst Oberortner
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | | | - Chris J Myers
- Department of Electrical, Computer, and Energy Engineering, University of Colorado, Boulder, CO, United States
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20
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Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5. Methods Mol Biol 2020. [PMID: 32809191 DOI: 10.1007/978-1-0716-0908-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Modern DNA assembly techniques are known for their potential to link multiple large DNA fragments together into even larger constructs in single pot reactions that are easier to automate and work more reliably than traditional cloning methods. The simplicity of the chemistry is in contrast to the increased work needed to design optimal reactions that maximize DNA fragment reuse, minimize cost, and organize thousands of potential chemical reactions. Here we examine available DNA assembly methods and describe through example, the construction of a complex but not atypical combinatorial and hierarchical library using protocols that are generated automatically with the assistance of modern synthetic biology software.
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21
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Patron NJ. Beyond natural: synthetic expansions of botanical form and function. THE NEW PHYTOLOGIST 2020; 227:295-310. [PMID: 32239523 PMCID: PMC7383487 DOI: 10.1111/nph.16562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 05/05/2023]
Abstract
Powered by developments that enabled genome-scale investigations, systems biology emerged as a field aiming to understand how phenotypes emerge from network functions. These advances fuelled a new engineering discipline focussed on synthetic reconstructions of complex biological systems with the goal of predictable rational design and control. Initially, progress in the nascent field of synthetic biology was slow due to the ad hoc nature of molecular biology methods such as cloning. The application of engineering principles such as standardisation, together with several key technical advances, enabled a revolution in the speed and accuracy of genetic manipulation. Combined with mathematical and statistical modelling, this has improved the predictability of engineering biological systems of which nonlinearity and stochasticity are intrinsic features leading to remarkable achievements in biotechnology as well as novel insights into biological function. In the past decade, there has been slow but steady progress in establishing foundations for synthetic biology in plant systems. Recently, this has enabled model-informed rational design to be successfully applied to the engineering of plant gene regulation and metabolism. Synthetic biology is now poised to transform the potential of plant biotechnology. However, reaching full potential will require conscious adjustments to the skillsets and mind sets of plant scientists.
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Affiliation(s)
- Nicola J. Patron
- Engineering BiologyEarlham InstituteNorwich Research Park, NorwichNorfolkNR4 7UZUK
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22
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Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J Integr Bioinform 2020; 17:jib-2020-0005. [PMID: 32598315 PMCID: PMC7756615 DOI: 10.1515/jib-2020-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 01/23/2023] Open
Abstract
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.
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Affiliation(s)
- Dagmar Waltemath
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Esther Thea Inau
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Olga Krebs
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Ernst Oberortner
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Labs, Berkeley, CA, USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Falk Schreiber
- Department of Computer and Information Science, University ofKonstanz, Germany.,Faculty of IT, Monash University, Melbourne, VIC, Australia
| | - Lucian Smith
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Melanie I Stefan
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.,ZJU-UoE Institute, Zhejiang University, Haining, China.,University of Utah, Salt Lake City, UT, USA
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Chris J Myers
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
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23
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Abstract
Standardizing the visual representation of genetic parts and circuits is essential for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts and their relationships. However, the implementation and maintenance of the relationships between biological elements or concepts and their associated glyphs has up to now been left up to tool developers. We address this need with the SBOL Visual 2 Ontology, a machine-accessible resource that provides rules for mapping from genetic parts, molecules, and interactions between them, to agreed SBOL Visual glyphs. This resource, together with a web service, can be used as a library to simplify the development of visualization tools, as a stand-alone resource to computationally search for suitable glyphs, and to help facilitate integration with existing biological ontologies and standards in synthetic biology.
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Affiliation(s)
- Göksel Mısırlı
- School of Computing and Mathematics, Keele University, Keele, Staffordshire ST5 5BG, U.K
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | | | | | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Chris J. Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
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24
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Calles B, Goñi‐Moreno Á, de Lorenzo V. Digitalizing heterologous gene expression in Gram-negative bacteria with a portable ON/OFF module. Mol Syst Biol 2019; 15:e8777. [PMID: 31885200 PMCID: PMC6920698 DOI: 10.15252/msb.20188777] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 01/24/2023] Open
Abstract
While prokaryotic promoters controlled by signal-responding regulators typically display a range of input/output ratios when exposed to cognate inducers, virtually no naturally occurring cases are known to have an OFF state of zero transcription-as ideally needed for synthetic circuits. To overcome this problem, we have modelled and implemented a simple digitalizer module that completely suppresses the basal level of otherwise strong promoters in such a way that expression in the absence of induction is entirely impeded. The circuit involves the interplay of a translation-inhibitory sRNA with the translational coupling of the gene of interest to a repressor such as LacI. The digitalizer module was validated with the strong inducible promoters Pm (induced by XylS in the presence of benzoate) and PalkB (induced by AlkS/dicyclopropyl ketone) and shown to perform effectively in both Escherichia coli and the soil bacterium Pseudomonas putida. The distinct expression architecture allowed cloning and conditional expression of, e.g. colicin E3, one molecule of which per cell suffices to kill the host bacterium. Revertants that escaped ColE3 killing were not found in hosts devoid of insertion sequences, suggesting that mobile elements are a major source of circuit inactivation in vivo.
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Affiliation(s)
- Belén Calles
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSICMadridSpain
| | - Ángel Goñi‐Moreno
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSICMadridSpain
- Present address:
School of ComputingNewcastle UniversityNewcastle upon TyneUK
| | - Víctor de Lorenzo
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSICMadridSpain
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25
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HamediRad M, Chao R, Weisberg S, Lian J, Sinha S, Zhao H. Towards a fully automated algorithm driven platform for biosystems design. Nat Commun 2019; 10:5150. [PMID: 31723141 PMCID: PMC6853954 DOI: 10.1038/s41467-019-13189-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Large-scale data acquisition and analysis are often required in the successful implementation of the design, build, test, and learn (DBTL) cycle in biosystems design. However, it has long been hindered by experimental cost, variability, biases, and missed insights from traditional analysis methods. Here, we report the application of an integrated robotic system coupled with machine learning algorithms to fully automate the DBTL process for biosystems design. As proof of concept, we have demonstrated its capacity by optimizing the lycopene biosynthetic pathway. This fully-automated robotic platform, BioAutomata, evaluates less than 1% of possible variants while outperforming random screening by 77%. A paired predictive model and Bayesian algorithm select experiments which are performed by Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB). BioAutomata excels with black-box optimization problems, where experiments are expensive and noisy and the success of the experiment is not dependent on extensive prior knowledge of biological mechanisms. Existing efforts have been focused on one of the elements in the automation of the design, build, test, and learn (DBTL) cycle for biosystems design. Here, the authors integrate a robotic system with machine learning algorithms to fully automate the DBTL cycle and apply it in optimizing the lycopene biosynthetic pathway.
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Affiliation(s)
- Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,LifeFoundry Inc., 60 Hazelwood Dr., Champaign, IL, 61820, USA
| | - Ran Chao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,LifeFoundry Inc., 60 Hazelwood Dr., Champaign, IL, 61820, USA
| | - Scott Weisberg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Departments of Chemistry and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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26
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Kent R, Dixon N. Contemporary Tools for Regulating Gene Expression in Bacteria. Trends Biotechnol 2019; 38:316-333. [PMID: 31679824 DOI: 10.1016/j.tibtech.2019.09.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Insights from novel mechanistic paradigms in gene expression control have led to the development of new gene expression systems for bioproduction, control, and sensing applications. Coupled with a greater understanding of synthetic burden and modern creative biodesign approaches, contemporary bacterial gene expression tools and systems are emerging that permit fine-tuning of expression, enabling greater predictability and maximisation of specific productivity, while minimising deleterious effects upon cell viability. These advances have been achieved by using a plethora of regulatory tools, operating at all levels of the so-called 'central dogma' of molecular biology. In this review, we discuss these gene regulation tools in the context of their design, prototyping, integration into expression systems, and biotechnological application.
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Affiliation(s)
- Ross Kent
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, UK.
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27
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Rennig M, Mundhada H, Wordofa GG, Gerngross D, Wulff T, Worberg A, Nielsen AT, Nørholm MHH. Industrializing a Bacterial Strain for l-Serine Production through Translation Initiation Optimization. ACS Synth Biol 2019; 8:2347-2358. [PMID: 31550142 DOI: 10.1021/acssynbio.9b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Turning a proof-of-concept synthetic biology design into a robust, high performing cell factory is a major time and money consuming task, which severely limits the growth of the white biotechnology sector. Here, we extend the use of tunable antibiotic resistance markers for synthetic evolution (TARSyn), a workflow for screening translation initiation region (TIR) libraries with antibiotic selection, to generic pathway engineering, and transform a proof-of-concept synbio design into a process that performs at industrially relevant levels. Using a combination of rational design and adaptive evolution, we recently engineered a high-performing bacterial strain for production of the important building block biochemical l-serine, based on two high-copy pET vectors facilitating expression of the serine biosynthetic genes serA, serC, and serB from three independent transcriptional units. Here, we prepare the bacterial strain for industrial scale up by transferring and reconfiguring the three genes into an operon encoded on a single low-copy plasmid. Not surprisingly, this initially reduces production titers considerably. We use TARSyn to screen both experimental and computational optimization designs resulting in high-performing synthetic serine operons and reach industrially relevant production levels of 50 g/L in fed-batch fermentations, the highest reported so far for serine production.
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Affiliation(s)
- Maja Rennig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Hemanshu Mundhada
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Gossa G. Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Daniel Gerngross
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Worberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
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28
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Zhang M, Zundel Z, Myers CJ. SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories. ACS Synth Biol 2019; 8:2287-2294. [PMID: 31532640 DOI: 10.1021/acssynbio.9b00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper describes SBOLExplorer, a system that is used to provide intuitive searching within the SynBioHub genetic design repository. SynBioHub stores genetic constructs encoded in the SBOL data format. These constructs can represent genetic parts, circuits, and sequences. These constructs are often numerous, exist in various states of completeness and documentation, and do not lend themselves to simple searching and discovery. In particular, this paper focuses on improving the search capabilities of SynBioHub. Inspiration is drawn from the techniques used to organize and search over the World Wide Web, a linked data set with many of the same properties of the SBOL data in SynBioHub. SBOLExplorer integrates these methods into SynBioHub's data representation and search, providing significant improvement over the previous search implementation based on pattern-matching.
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Affiliation(s)
- Michael Zhang
- School of Computing, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zach Zundel
- School of Computing, University of Utah, Salt Lake City, Utah 84112, United States
| | - Chris J. Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
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Beal J, Nguyen T, Gorochowski TE, Goñi-Moreno A, Scott-Brown J, McLaughlin JA, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo Hair S, Clancy K, Luna A, Le Novère N, Palchick Z, Pocock M, Sauro H, Sexton JT, Tabor JJ, Voigt CA, Zundel Z, Myers C, Wipat A. Communicating Structure and Function in Synthetic Biology Diagrams. ACS Synth Biol 2019; 8:1818-1825. [PMID: 31348656 PMCID: PMC8023477 DOI: 10.1021/acssynbio.9b00139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.
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Affiliation(s)
- Jacob Beal
- BioCoder Consulting , Carlsbad 92008 , California , United States
- Raytheon BBN Technologies , Arlington , Virginia 22209 , United States
| | - Tramy Nguyen
- University of Utah , Salt Lake City , Utah 84112 , United States
| | | | | | | | | | - Curtis Madsen
- Boston University , Boston , Massachusetts 02215 , United States
| | | | - Bryan Bartley
- Raytheon BBN Technologies , Arlington , Virginia 22209 , United States
| | - Shyam Bhakta
- Rice University , Houston , Texas 77005 , United States
| | - Mike Bissell
- Amyris, Inc. , Emeryville , California 94608 , United States
| | | | - Kevin Clancy
- BioCoder Consulting , Carlsbad 92008 , California , United States
| | - Augustin Luna
- Harvard Medical School , Boston , Massachusetts 02115 , United States
| | | | - Zach Palchick
- Zymergen , Emeryville , California 94608 , United States
| | - Matthew Pocock
- Turing Ate My Hamster, Ltd. , Tyne And Wear NE27 0RT , U.K
| | - Herbert Sauro
- University of Washington , Seattle , Washington 98195 , United States
| | - John T Sexton
- Rice University , Houston , Texas 77005 , United States
| | | | | | - Zach Zundel
- University of Utah , Salt Lake City , Utah 84112 , United States
| | - Chris Myers
- University of Utah , Salt Lake City , Utah 84112 , United States
| | - Anil Wipat
- Newcastle University , Newcastle upon Tyne NE1 7RU , U.K
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30
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Misirli G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones TS, Densmore D, Myers C, Wipat A. A Computational Workflow for the Automated Generation of Models of Genetic Designs. ACS Synth Biol 2019; 8:1548-1559. [PMID: 29782151 DOI: 10.1021/acssynbio.7b00459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.
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Affiliation(s)
- Göksel Misirli
- School of Computing and Mathematics, Keele University, Staffordshire, U.K
| | - Tramy Nguyen
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | | | - Prashant Vaidyanathan
- Department of Electrical and Computer Engineering Boston University, Boston, Massachusetts 02215, United States
| | - Timothy S. Jones
- Department of Electrical and Computer Engineering Boston University, Boston, Massachusetts 02215, United States
| | - Douglas Densmore
- Department of Electrical and Computer Engineering Boston University, Boston, Massachusetts 02215, United States
| | - Chris Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Anil Wipat
- ICOS, School of Computing, Newcastle University, Newcastle upon Tyne, U.K
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Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A. SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information. ACS Synth Biol 2019; 8:1498-1514. [PMID: 31059645 DOI: 10.1021/acssynbio.8b00532] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on capturing data using graphs. The language provides the syntax using a free text document that is accessible to humans only. This paper describes SBOL-OWL, an ontology for a machine understandable definition of SBOL. This ontology acts as a semantic layer for genetic circuit designs. As a result, computational tools can understand the meaning of design entities in addition to parsing structured SBOL data. SBOL-OWL not only describes how genetic circuits can be constructed computationally, it also facilitates the use of several existing Semantic Web tools for synthetic biology. This paper demonstrates some of these features, for example, to validate designs and check for inconsistencies. Through the use of SBOL-OWL, queries can be simplified and become more intuitive. Moreover, existing reasoners can be used to infer information about genetic circuit designs that cannot be directly retrieved using existing querying mechanisms. This ontological representation of the SBOL standard provides a new perspective to the verification, representation, and querying of information about genetic circuits and is important to incorporate complex design information via the integration of biological ontologies.
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Affiliation(s)
- Göksel Mısırlı
- School of Computing and Mathematics, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Renee Taylor
- School of Computing and Mathematics, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Angel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
| | | | - Chris Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - John H. Gennari
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington 98195, United States
| | - Phillip Lord
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
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32
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Haines MC, Storch M, Oyarzún DA, Stan GB, Baldwin GS. Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). Synth Biol (Oxf) 2019; 4:ysz019. [PMID: 32995542 PMCID: PMC7445825 DOI: 10.1093/synbio/ysz019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro selection of ligand-responsive ribozymes can identify rare, functional sequences from large libraries. While powerful, key caveats of this approach include lengthy and demanding experimental workflows; unpredictable experimental outcomes and unknown functionality of enriched sequences in vivo. To address the first of these limitations, we developed Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). LigASERR is scalable, amenable to automation and requires less time to implement compared to alternative methods. To improve the predictability of experiments, we modeled the underlying selection process, predicting experimental outcomes based on sequence and population parameters. We applied this new methodology and model to the enrichment of a known, in vitro-selected sequence from a bespoke library. Prior to implementing selection, conditions were optimized and target sequence dynamics accurately predicted for the majority of the experiment. In addition to enriching the target sequence, we identified two new, theophylline-activated ribozymes. Notably, all three sequences yielded riboswitches functional in Escherichia coli, suggesting LigASERR and similar in vitro selection methods can be utilized for generating functional riboswitches in this organism.
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Affiliation(s)
- Matthew C Haines
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Marko Storch
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,London BioFoundry, Imperial College Translation & Innovation Hub, London, UK
| | - Diego A Oyarzún
- School of Informatics, University of Edinburgh, Edinburgh, UK.,School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR. Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning. ACS Synth Biol 2019; 8:1337-1351. [PMID: 31072100 DOI: 10.1021/acssynbio.9b00020] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.
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Affiliation(s)
- Paul Opgenorth
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Takuya Okada
- Research Institute for Bioscience Product & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8680, Japan
| | - Garima Goyal
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Yan Chen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Gin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Veronica Benites
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Trent R. Northen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Kai Deng
- Sandia National Laboratories, Livermore, California 94550, United States
| | - Samuel Deutsch
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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35
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Andrews LB, Nielsen AAK, Voigt CA. Cellular checkpoint control using programmable sequential logic. Science 2018; 361:361/6408/eaap8987. [PMID: 30237327 DOI: 10.1126/science.aap8987] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 08/03/2018] [Indexed: 12/15/2022]
Abstract
Biological processes that require orderly progression, such as growth and differentiation, proceed via regulatory checkpoints where the cell waits for signals before continuing to the next state. Implementing such control would allow genetic engineers to divide complex tasks into stages. We present genetic circuits that encode sequential logic to instruct Escherichia coli to proceed through a linear or cyclical sequence of states. These are built with 11 set-reset latches, designed with repressor-based NOR gates, which can connect to each other and sensors. The performance of circuits with up to three latches and four sensors, including a gated D latch, closely match predictions made by using nonlinear dynamics. Checkpoint control is demonstrated by switching cells between multiple circuit states in response to external signals over days.
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Affiliation(s)
- Lauren B Andrews
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Voigt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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36
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Vazquez-Vilar M, Orzaez D, Patron N. DNA assembly standards: Setting the low-level programming code for plant biotechnology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:33-41. [PMID: 29907307 DOI: 10.1016/j.plantsci.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes. These advances and technologies are now being applied to plants, for which there are a growing number of software and wetware tools for the design, construction and delivery of DNA molecules and for the engineering of endogenous genes. Here we review the efforts of the past decade that have established synthetic biology workflows and tools for plants and discuss the constraints and bottlenecks of this emerging field.
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Affiliation(s)
- Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Spain.
| | - Nicola Patron
- Department of Engineering Biology, The Earlham Institute, Norwich Research Park, Norfolk, NR1 7UZ, UK.
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37
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Beal J, Haddock-Angelli T, Baldwin G, Gershater M, Dwijayanti A, Storch M, de Mora K, Lizarazo M, Rettberg R. Quantification of bacterial fluorescence using independent calibrants. PLoS One 2018; 13:e0199432. [PMID: 29928012 PMCID: PMC6013168 DOI: 10.1371/journal.pone.0199432] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/07/2018] [Indexed: 11/25/2022] Open
Abstract
Fluorescent reporters are commonly used to quantify activities or properties of both natural and engineered cells. Fluorescence is still typically reported only in arbitrary or normalized units, however, rather than in units defined using an independent calibrant, which is problematic for scientific reproducibility and even more so when it comes to effective engineering. In this paper, we report an interlaboratory study showing that simple, low-cost unit calibration protocols can remedy this situation, producing comparable units and dramatic improvements in precision over both arbitrary and normalized units. Participants at 92 institutions around the world measured fluorescence from E. coli transformed with three engineered test plasmids, plus positive and negative controls, using simple, low-cost unit calibration protocols designed for use with a plate reader and/or flow cytometer. In addition to providing comparable units, use of an independent calibrant allows quantitative use of positive and negative controls to identify likely instances of protocol failure. The use of independent calibrants thus allows order of magnitude improvements in precision, narrowing the 95% confidence interval of measurements in our study up to 600-fold compared to normalized units.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, United States of America
- * E-mail: (JB); (TH-A); (GB)
| | - Traci Haddock-Angelli
- iGEM Foundation, Cambridge, MA, United States of America
- * E-mail: (JB); (TH-A); (GB)
| | - Geoff Baldwin
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (JB); (TH-A); (GB)
| | | | - Ari Dwijayanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Marko Storch
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - 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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38
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Swainston N, Dunstan M, Jervis AJ, Robinson CJ, Carbonell P, Williams AR, Faulon JL, Scrutton NS, Kell DB. PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. Bioinformatics 2018; 34:2327-2329. [DOI: 10.1093/bioinformatics/bty105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/22/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Neil Swainston
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Mark Dunstan
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Adrian J Jervis
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Pablo Carbonell
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Alan R Williams
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Jean-Loup Faulon
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- MICALIS, INRA-AgroParisTech, Domaine de Vilvert, Jouy en Josas Cedex, France
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Douglas B Kell
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- School of Chemistry, The University of Manchester, Manchester, UK
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39
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McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A. SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synth Biol 2018; 7:682-688. [PMID: 29316788 DOI: 10.1021/acssynbio.7b00403] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The SynBioHub repository ( https://synbiohub.org ) is an open-source software project that facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g., the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation. SynBioHub also provides a central reference point for other resources to link to, delivering design information in a standardized format using the Synthetic Biology Open Language (SBOL). The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs.
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Affiliation(s)
| | - Chris J. Myers
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Zach Zundel
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Göksel Mısırlı
- School
of Computing and Mathematics, Keele University, Newcastle, ST5 5BG, U.K
| | - Michael Zhang
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Irina Dana Ofiteru
- School
of Engineering, Newcastle University, Newcastle upon Tyne, NE1
7RU, U.K
| | - Angel Goñi-Moreno
- School
of Computing, Newcastle University, Newcastle upon Tyne, NE1
7RU, U.K
| | - Anil Wipat
- School
of Computing, Newcastle University, Newcastle upon Tyne, NE1
7RU, U.K
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40
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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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41
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Abstract
Visualization of complex genetic systems can help efficiently communicate important design features and clearly illustrate overall structures. To aid in the creation of such diagrams, standards such as the Synthetic Biology Open Language Visual (SBOLv) have been established to ensure that specific symbols and shapes convey the same meaning for genetic parts across the field. Here, we describe several ways that the computational tool DNAplotlib can be used to automate the generation of SBOLv standard-compliant diagrams covering simple genetic designs to large libraries of genetic constructs.
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Affiliation(s)
- Vittorio Bartoli
- BrisSynBio, University of Bristol, Bristol, UK
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
| | - Daniel O R Dixon
- BrisSynBio, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Thomas E Gorochowski
- BrisSynBio, University of Bristol, Bristol, UK.
- School of Biological Sciences, University of Bristol, Bristol, UK.
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42
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Bates M, Lachoff J, Meech D, Zulkower V, Moisy A, Luo Y, Tekotte H, Franziska Scheitz CJ, Khilari R, Mazzoldi F, Chandran D, Groban E. Genetic Constructor: An Online DNA Design Platform. ACS Synth Biol 2017; 6:2362-2365. [PMID: 29020772 DOI: 10.1021/acssynbio.7b00236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.
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Affiliation(s)
- Maxwell Bates
- Autodesk Life Sciences , San Francisco, California 94111, United States
| | - Joe Lachoff
- Autodesk Life Sciences , San Francisco, California 94111, United States
| | - Duncan Meech
- Autodesk Life Sciences , San Francisco, California 94111, United States
| | - Valentin Zulkower
- Edinburgh Genome Foundry, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Anaïs Moisy
- Edinburgh Genome Foundry, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Yisha Luo
- Edinburgh Genome Foundry, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Hille Tekotte
- Edinburgh Genome Foundry, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | | | - Rupal Khilari
- Autodesk Life Sciences , San Francisco, California 94111, United States
| | | | - Deepak Chandran
- Radiant Genomics , Emeryville, California 94608, United States
| | - Eli Groban
- Autodesk Life Sciences , San Francisco, California 94111, United States
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43
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Vazquez-Vilar M, Quijano-Rubio A, Fernandez-Del-Carmen A, Sarrion-Perdigones A, Ochoa-Fernandez R, Ziarsolo P, Blanca J, Granell A, Orzaez D. GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucleic Acids Res 2017; 45:2196-2209. [PMID: 28053117 PMCID: PMC5389719 DOI: 10.1093/nar/gkw1326] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022] Open
Abstract
Modular DNA assembly simplifies multigene engineering in Plant Synthetic Biology. Furthermore, the recent adoption of a common syntax to facilitate the exchange of plant DNA parts (phytobricks) is a promising strategy to speed up genetic engineering. Following this lead, here, we present a platform for plant biodesign that incorporates functional descriptions of phytobricks obtained under pre-defined experimental conditions, and systematically registers the resulting information as metadata for documentation. To facilitate the handling of functional descriptions, we developed a new version (v3.0) of the GoldenBraid (GB) webtool that integrates the experimental data and displays it in the form of datasheets. We report the use of the Luciferase/Renilla (Luc/Ren) transient agroinfiltration assay in Nicotiana benthamiana as a standard to estimate relative transcriptional activities conferred by regulatory phytobricks, and show the consistency and reproducibility of this method in the characterization of a synthetic phytobrick based on the CaMV35S promoter. Furthermore, we illustrate the potential for combinatorial optimization and incremental innovation of the GB3.0 platform in two separate examples, (i) the development of a collection of orthogonal transcriptional regulators based on phiC31 integrase and (ii) the design of a small genetic circuit that connects a glucocorticoid switch to a MYB/bHLH transcriptional activation module.
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Affiliation(s)
- Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alfredo Quijano-Rubio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Asun Fernandez-Del-Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alejandro Sarrion-Perdigones
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rocio Ochoa-Fernandez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Peio Ziarsolo
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - José Blanca
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
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44
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A standard-enabled workflow for synthetic biology. Biochem Soc Trans 2017; 45:793-803. [PMID: 28620041 DOI: 10.1042/bst20160347] [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] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 11/17/2022]
Abstract
A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.
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45
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Abstract
GeneMill officially launched on 4th February 2016 and is an open access academic facility located at The University of Liverpool that has been established for the high-throughput construction and testing of synthetic DNA constructs. GeneMill provides end-to-end design, construction and phenotypic characterization of small to large gene constructs or genetic circuits/pathways for academic and industrial applications. Thus, GeneMill is equipping the scientific community with easy access to the validated tools required to explore the possibilities of Synthetic Biology.
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46
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Cox RS, McLaughlin JA, Grünberg R, Beal J, Wipat A, Sauro HM. A Visual Language for Protein Design. ACS Synth Biol 2017; 6:1120-1123. [PMID: 28173698 DOI: 10.1021/acssynbio.6b00286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to-draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in a "drag and drop" interface for visualization and computer-aided-design of engineered proteins, as well as conversion of annotated protein sequences to Protein Language diagrams and figure export. Protein Designer can be accessed at http://biocad.ncl.ac.uk/protein-designer/ .
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Affiliation(s)
- Robert Sidney Cox
- Material
Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | | | - Raik Grünberg
- Computational
Bioscience Research Center, King Abdullah University for Science and Technology, Thuwal 23955, Saudi Arabia
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Anil Wipat
- School
of Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Herbert M. Sauro
- Department
of Bioengineering, University of Washington, Seattle, Washington 98105, United States
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47
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Zundel Z, Samineni M, Zhang Z, Myers CJ. A Validator and Converter for the Synthetic Biology Open Language. ACS Synth Biol 2017; 6:1161-1168. [PMID: 28033703 DOI: 10.1021/acssynbio.6b00277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This paper presents a new validation and conversion utility for the Synthetic Biology Open Language (SBOL). This utility can be accessed directly in software using the libSBOLj library, through a web interface, or using a web service via RESTful API calls. The validator checks all required and best practice rules set forth in the SBOL specification document, and it reports back to the user the location within the document of any errors found. The converter is capable of translating from/to SBOL 1, GenBank, and FASTA formats to/from SBOL 2. The SBOL Validator/Converter utility is released freely and open source under the Apache 2.0 license. The online version of the validator/converter utility can be found here: http://www.async.ece.utah.edu/sbol-validator/ . The source code for the validator/converter can be found here: http://github.com/SynBioDex/SBOL-Validator/ .
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Affiliation(s)
- Zach Zundel
- Department of Bioengineering, University of Utah, 36 S. Wasatch Drive, SMBB Room 3100, Salt
Lake City, Utah 84112, United States
| | - Meher Samineni
- Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, MEB Room 2110, Salt Lake City, Utah 84112, United States
| | - Zhen Zhang
- Department of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Avenue, ENB 118, Tampa, Florida 33620, United States
| | - Chris J. Myers
- Department of Electrical and Computer Engineering, University of Utah, 50 S. Central Campus Drive, MEB Room 2110, Salt Lake City, Utah 84112, United States
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48
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Der BS, Glassey E, Bartley BA, Enghuus C, Goodman DB, Gordon DB, Voigt CA, Gorochowski TE. DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data. ACS Synth Biol 2017; 6:1115-1119. [PMID: 27744689 DOI: 10.1021/acssynbio.6b00252] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNAplotlib ( www.dnaplotlib.org ) is a computational toolkit for the programmable visualization of highly customizable, standards-compliant genetic designs. Functions are provided to aid with both visualization tasks and to extract and overlay associated experimental data. High-quality output is produced in the form of vector-based PDFs, rasterized images, and animated movies. All aspects of the rendering process can be easily customized or extended by the user to cover new forms of genetic part or regulation. DNAplotlib supports improved communication of genetic design information and offers new avenues for static, interactive and dynamic visualizations that map and explore the links between the structure and function of genetic parts, devices and systems; including metabolic pathways and genetic circuits. DNAplotlib is cross-platform software developed using Python.
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Affiliation(s)
- Bryan S. Der
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emerson Glassey
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bryan A. Bartley
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Casper Enghuus
- MIT Microbiology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel B. Goodman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired
Engineering, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - D. Benjamin Gordon
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas E. Gorochowski
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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49
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Zhang M, McLaughlin JA, Wipat A, Myers CJ. SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design. ACS Synth Biol 2017; 6:1150-1160. [PMID: 28441476 DOI: 10.1021/acssynbio.6b00275] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As the Synthetic Biology Open Language (SBOL) data and visual standards gain acceptance for describing genetic designs in a detailed and reproducible way, there is an increasing need for an intuitive sequence editor tool that biologists can use that supports these standards. This paper describes SBOLDesigner 2, a genetic design automation (GDA) tool that natively supports both the SBOL data model (Version 2) and SBOL Visual (Version 1). This software is enabled to fetch and store parts and designs from SBOL repositories, such as SynBioHub. It can also import and export data about parts and designs in FASTA, GenBank, and SBOL 1 data format. Finally, it possesses a simple and intuitive user interface. This paper describes the design process using SBOLDesigner 2, highlighting new features over the earlier prototype versions. SBOLDesigner 2 is released freely and open source under the Apache 2.0 license.
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Affiliation(s)
- Michael Zhang
- Department of Electrical
and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | | | - Anil Wipat
- School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Chris J. Myers
- Department of Electrical
and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
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50
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Bartley BA, Kim K, Medley JK, Sauro HM. Synthetic Biology: Engineering Living Systems from Biophysical Principles. Biophys J 2017; 112:1050-1058. [PMID: 28355534 DOI: 10.1016/j.bpj.2017.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 01/02/2023] Open
Abstract
Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties.
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Affiliation(s)
- Bryan A Bartley
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Kyung Kim
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - J Kyle Medley
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington.
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