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      In situ characterisation and manipulation of biological systems with Chi.Bio

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          Abstract

          The precision and repeatability of in vivo biological studies is predicated upon methods for isolating a targeted subsystem from external sources of noise and variability. However, in many experimental frameworks, this is made challenging by nonstatic environments during host cell growth, as well as variability introduced by manual sampling and measurement protocols. To address these challenges, we developed Chi.Bio, a parallelised open-source platform that represents a new experimental paradigm in which all measurement and control actions can be applied to a bulk culture in situ. In addition to continuous-culturing capabilities, it incorporates tunable light outputs, spectrometry, and advanced automation features. We demonstrate its application to studies of cell growth and biofilm formation, automated in silico control of optogenetic systems, and readout of multiple orthogonal fluorescent proteins in situ. By integrating precise measurement and actuation hardware into a single low-cost platform, Chi.Bio facilitates novel experimental methods for synthetic, systems, and evolutionary biology and broadens access to cutting-edge research capabilities.

          Abstract

          The precision and repeatability of biological studies are predicated upon methods for isolating a targeted subsystem from external sources of noise and variability. This article presents a low-cost, open-source culture platform, Chi.Bio, which allows biologists to automate experimental protocols with unparalleled precision.

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          Most cited references29

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          Refinement and standardization of synthetic biological parts and devices.

          Barry Canton, Anna Labno, Drew Endy (2008)
          The ability to quickly and reliably engineer many-component systems from libraries of standard interchangeable parts is one hallmark of modern technologies. Whether the apparent complexity of living systems will permit biological engineers to develop similar capabilities is a pressing research question. We propose to adapt existing frameworks for describing engineered devices to biological objects in order to (i) direct the refinement and use of biological 'parts' and 'devices', (ii) support research on enabling reliable composition of standard biological parts and (iii) facilitate the development of abstraction hierarchies that simplify biological engineering. We use the resulting framework to describe one engineered biological device, a genetically encoded cell-cell communication receiver named BBa_F2620. The description of the receiver is summarized via a 'datasheet' similar to those widely used in engineering. The process of refinement and characterization leading to the BBa_F2620 datasheet may serve as a starting template for producing many standardized genetically encoded objects.
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            The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins.

            Erik Rodriguez, Robert E. Campbell, John Lin … (2017)
            Over the past 20 years, protein engineering has been extensively used to improve and modify the fundamental properties of fluorescent proteins (FPs) with the goal of adapting them for a fantastic range of applications. FPs have been modified by a combination of rational design, structure-based mutagenesis, and countless cycles of directed evolution (gene diversification followed by selection of clones with desired properties) that have collectively pushed the properties to photophysical and biochemical extremes. In this review, we provide both a summary of the progress that has been made during the past two decades, and a broad overview of the current state of FP development and applications in mammalian systems.
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              Synchronous long-term oscillations in a synthetic gene circuit

              Laurent Potvin-Trottier, Nathan D Lord, Glenn Vinnicombe … (2016)
              Synthetically engineered genetic circuits can perform a wide range of tasks but generally with lower accuracy than natural systems. Here we revisited the first synthetic genetic oscillator, the repressilator 1 , and modified it based on principles from stochastic chemistry in single cells. Specifically, we sought to reduce error propagation and information losses, not by adding control loops, but by simply removing existing features. This created highly regular and robust oscillations. Some streamlined circuits kept 14 generation periods over a range of growth conditions and kept phase for hundreds of generations in single cells, allowing cells in flasks and colonies to oscillate synchronously without any coupling between them. Our results show that even the simplest synthetic genetic networks can achieve a precision that rivals natural systems, and emphasize the importance of noise analyses for circuit design in synthetic biology.
              Article 0 comments Cited 118 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Harrison Steel: Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: Writing – original draftRole: Writing – review & editing
                Robert Habgood:
                ORCID: http://orcid.org/0000-0002-8487-4551
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Ciarán L. Kelly:
                ORCID: http://orcid.org/0000-0002-2263-5176
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Antonis Papachristodoulou:
                ORCID: http://orcid.org/0000-0002-3565-8967
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: Writing – original draftRole: Writing – review & editing
                Tom Baden: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): PLoS Biol
                Journal ID (iso-abbrev): PLoS Biol
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosbiol
                Title: PLoS Biology
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Print): 1544-9173
                ISSN (Electronic): 1545-7885
                Publication date (Electronic): 30 July 2020
                Publication date Collection: July 2020
                Publication date PMC-release: 30 July 2020
                Volume: 18
                Issue: 7
                Electronic Location Identifier: e3000794
                Affiliations
                [1 ] Department of Engineering Science, University of Oxford, Oxford, United Kingdom
                [2 ] Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
                University of Sussex, UNITED KINGDOM
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-8487-4551
                http://orcid.org/0000-0002-2263-5176
                http://orcid.org/0000-0002-3565-8967
                Article
                Publisher ID: PBIOLOGY-D-20-00109
                DOI: 10.1371/journal.pbio.3000794
                PMC ID: 7419009
                PubMed ID: 32730242
                SO-VID: f9c8eaa7-717f-4f63-aa85-5bcc40963013
                Copyright © © 2020 Steel et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 15 January 2020
                Date accepted : 8 July 2020
                Page count
                Figures: 5, Tables: 0, Pages: 12
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
                Award ID: EP/M002454/1
                Award Recipient :
                ORCID: http://orcid.org/0000-0002-3565-8967
                This study was entirely funded by Engineering and Physical Sciences Research Council (EPSRC) project EP/M002454/1 ( https://epsrc.ukri.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Methods and Resources
                Subject: Computer and Information Sciences
                Subject: Computer Architecture
                Subject: Computer Hardware
                Subject: Biology and Life Sciences
                Subject: Biochemistry
                Subject: Proteins
                Subject: Luminescent Proteins
                Subject: Green Fluorescent Protein
                Subject: Biology and Life Sciences
                Subject: Neuroscience
                Subject: Brain Mapping
                Subject: Optogenetics
                Subject: Research and Analysis Methods
                Subject: Bioassays and Physiological Analysis
                Subject: Neurophysiological Analysis
                Subject: Optogenetics
                Subject: Physical Sciences
                Subject: Physics
                Subject: Electromagnetic Radiation
                Subject: Luminescence
                Subject: Fluorescence
                Subject: Engineering and Technology
                Subject: Electronics Engineering
                Subject: Electronics
                Subject: Diodes
                Subject: Light Emitting Diodes
                Subject: Engineering and Technology
                Subject: Industrial Engineering
                Subject: Control Engineering
                Subject: Automation
                Subject: Computer and Information Sciences
                Subject: Software Engineering
                Subject: Computer Software
                Subject: Operating Systems
                Subject: Engineering and Technology
                Subject: Software Engineering
                Subject: Computer Software
                Subject: Operating Systems
                Subject: Computer and Information Sciences
                Subject: Computer Applications
                Subject: Web-Based Applications
                Custom metadata
                PLOS Publication Stage vor-update-to-uncorrected-proof
                Publication Update 2020-08-11
                Data Availability Schematics, software, and assembly manuals for the version of Chi.Bio characterised in this study are available on the Oxford University Research Archive, DOI: https://doi.org/10.5287/bodleian:2NYdM7moX. Updated versions will be made available in the future through the project website, https://chi.bio.

                ScienceOpen disciplines: Life sciences
                Data availability:
                ScienceOpen disciplines: Life sciences

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