• Scientists create a global repository fo

    From ScienceDaily@1:317/3 to All on Wed Feb 9 21:30:36 2022
    Scientists create a global repository for cell engineering
    A cloud-based repository that creates a digital fingerprint of engineered microorganisms has been successfully trialled.

    Date:
    February 9, 2022
    Source:
    Newcastle University
    Summary:
    An international team has launched CellRepo, a species and strain
    database that uses cell barcodes to monitor and track engineered
    organisms. The database keeps track and organizes the digital data
    produced during cell engineering. It also molecularly links that
    data to the associated living samples.



    FULL STORY ==========================================================================
    A cloud-based repository that creates a digital fingerprint of engineered microorganisms has been successfully trialled.


    ==========================================================================
    An international team led by Newcastle University has launched CellRepo,
    a species and strain database that uses cell barcodes to monitor and
    track engineered organisms. Reported in a new study in the journalNature Communications, the database keeps track and organises the digital data produced during cell engineering. It also molecularly links that data
    to the associated living samples.

    Available globally, this resource supports international collaboration
    and has significant safety advantages, such as limiting the impact of deliberately or accidentally released genetically modified microorganisms
    by enabling faster tracing of organisms lab of origin and design details.

    CellRepo is built on version control, a concept from software engineering
    that records and tracks changes to software code. The scientists believe
    that version control for cell engineering will make engineering biology
    more open, reproducible, easier to trace and share, and more trustworthy.

    The research team highlights additional benefits of this community
    resource, such traceability -- providing the exact documentation for a
    strain and properly crediting laboratory work. The database also puts responsibility in focus by making it easier to track and assign ownership.

    With access to a global database, researchers will be able to reproduce
    results and collaborate more easily. The scientists also argue that the repository will improve transparency and reduce costs associated with
    data and source code losses.



    ==========================================================================
    Lead author, Natalio Krasnogor, Professor of Computer Science and
    Synthetic Biology at Newcastle University's School of Computing, said: "Engineering biology is not rocket science. It is much, much harder. And because of that it is imperative that we do it more openly and more collaboratively. CellRepo, at its core, is a collaboration platform in
    which cell engineers can document their work and share it with others
    (within their own lab or more widely). By enabling more collaboration and
    the seamlessly sharing of engineered strains we hope to accelerate and
    improve synthetic biology processes and reporting for everybody. CellRepo
    is a community resource and as such we invite engineering biologists,
    synthetic biologists, biotechnologists and life scientists more generally
    to try it and get in touch with us so we know what works and what needs
    to be improved!" Dr. Jonathan Tellechea, a synthetic biologist in the
    project says: "I have always had some misidentification issues during
    my projects.

    Fortunately I was able to find them early on and solve them but I
    can't imagine how many good projects have failed or stalled because of
    this. Some other chunk of my time as a biologist goes into retroactively building the history of the plasmids and strains I use. I may get the
    genetic material from someone, but who was the original author? Sometimes
    I am lucky and it is just one paper away, sometimes its down a rabbit hole
    that may end up in the 80s. CellRepo fixes these and other important
    problems for experimentalists. " Leanne Hobbs, the senior software
    engineer in the project reflects: "As a software engineer coming from
    industry to academia, it has been both a challenge and pleasure to work
    on a project where I can use my skills for the public good. Version
    control is a staple of software engineering and I am proud that we are
    now bringing these tools to engineering biology." Dr. Lenka Pelechova,
    a social scientist working at The Interdisciplinary Computing and Complex Biosystems (ICOS) research group, added: "As a social scientist, I believe
    the Responsible Research and Innovation framework is crucial in addressing societal expectations and in opening up public's conversations about new research and technology. In my view, these conversations should start
    early on and CellRepo supports this by making research transparent from
    its onset.'


    ========================================================================== Study co-author, Professor Vi'ctor de Lorenzo, from the Systems and
    Synthetic Biology Program at the Centro Nacional de Biotecnologi'a
    in Madrid, Spain, said: "Given the innate tendency of engineered
    constructs to mutate and overcome any type of genetic firewall, decades
    of efforts for containment of recombinant bacteria have delivered few
    practical results. Instead, CellRepo offers stable and unequivocal identification of given strains that can be rigorously tracked and
    associated to digital twins with all information available -- should
    it be required for countermeasures, ownership or liability purposes."
    Elena Vela'zquez, PhD student in Vi'ctor de Lorenzo's lab, added: "As
    a synthetic biologist who works all day with plasmids and strains from different origins, I am used to find that the plasmid or strain I was
    using in my experiments were not what I requested. This, of course, cannot
    be blamed on scientists who kindly donate their hard work altruistically
    and, moreover, since there was not an easy way to label and identify if
    the strain at stake was the intended one.

    "CellRepo is a platform that represents an incredible advance in this
    matter and that can save a ton of time and useless work to researchers
    all around the world. Moreover, the global repositories of strains
    that are to be shared through this platform can be an invaluable
    open-source of samples and a bridge for new collaborations between
    different labs. Thanks to CellRepo, scientists have the possibility to
    speed up their investigations and the reliability of their Science."
    Co-author Simon Woods, Professor of Bioethics at the Policy Ethics
    and Life Sciences Research Centre, Newcastle University, added:
    "The wide adoption of the CellRepo platform will make a major
    beneficial contribution to the culture of science by providing a
    mechanism that ensures traceability and transparency and enabling reproducibility. In addition, CellRepo is a novel instrument of
    science governance that supports responsible but innovative science." ========================================================================== Story Source: Materials provided by Newcastle_University. Note: Content
    may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Jonathan Tellechea-Luzardo, Leanne Hobbs, Elena Vela'zquez, Lenka
    Pelechova, Simon Woods, Vi'ctor de Lorenzo, Natalio
    Krasnogor. Versioning biological cells for trustworthy
    cell engineering. Nature Communications, 2022; 13 (1) DOI:
    10.1038/s41467-022-28350-4 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/02/220209093400.htm

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