• Scientists build 'valves' in DNA to shap

    From ScienceDaily@1:317/3 to All on Fri Jan 21 21:30:42 2022
    Scientists build 'valves' in DNA to shape biological information flows


    Date:
    January 21, 2022
    Source:
    University of Bristol
    Summary:
    Scientists have developed new biological parts that are able to
    shape the flow of cellular processes along DNA.



    FULL STORY ========================================================================== Scientists at the University of Bristol have developed new biological
    parts that are able to shape the flow of cellular processes along DNA.


    ==========================================================================
    The work, now published in the journal Nature Communications, offers
    a fresh perspective on how information is encoded in DNA and new tools
    for building sustainable biotechnologies.

    Despite being invisible to the naked eye, microorganisms are integral
    for our survival. They operate using DNA, often referred to as the code
    of life. DNA encodes numerous tools that could be useful to us, but we currently lack a complete understanding of how to interpret DNA sequences.

    Matthew Tarnowski, first author and a PhD student in Bristol's School
    of Biological Sciences, said: "Understanding the microbial world is
    tricky. While reading a microbe's DNA with a sequencer gives us a window
    into the underlying code, you still need to read a lot of different DNA sequences to understand how it actually works. It's a bit like trying
    to learn a new language, but from only a few small fragments of text."
    To tackle this problem, the Bristol team focused on how the information
    encoded in DNA is read, and specifically, how the flow of cellular
    processes along DNA are controlled. These biological information flows orchestrate many of the core functions of a cell and an ability to shape
    them would offer a way to guide cellular behaviours.

    Taking inspiration from nature, where it is known that flows on DNA are
    often complex and interwoven, the team focused on how these flows could
    be regulated by creating "valves" to tune the flow from one region of
    DNA to another.

    Dr Thomas Gorochowski, senior author and Royal Society University Research Fellow at the University of Bristol, said: "Similar to a valve that
    controls the rate that a liquid flows through a pipe, these valves shape
    the flow of molecular processes along DNA. These flows allow cells to
    make sense of the information stored in their genomes and the ability to control them enables us to reprogram their behaviours in useful ways." Designing new biological parts can typically take a huge amount of
    time. To get around this problem, the team employed methods to enable the
    rapid assembly of many DNA parts in parallel and a sequencing technology
    based on 'nanopores' that allowed them to simultaneously measure how
    each part worked.

    Dr Gorochowski added: "Harnessing the unique features of nanopore
    sequencing was the step needed to unlock our ability to effectively design
    the biological valves. Rather than separately building and testing a
    couple at a time, we could instead assemble and test thousands in a mixed
    pool, helping us pull apart their design rules and better understand how
    they work." The authors go on to further show how valves can be used for regulating other biological components in the cell, opening avenues to the future simultaneous control of many genes and complex editing of genomes.

    Looking forward, the team are currently considering how this technology
    could be used responsibly. Dr Mario Pansera, distinguished researcher of
    the Post- Growth Innovation Lab at the University of Vigo, Spain, said:
    "Now that they have crafted these tools, a big question is how they
    can be used responsibly and equitably in the real world. Post-growth entrepreneurship offers useful approaches for imagining more deliberative
    and inclusive ways to put such technology at the service of people."
    This work was funded by the Royal Society, BBSRC/EPSRC Bristol Centre
    for Synthetic Biology (BrisSynBio) and EPSRC/BBSRC Synthetic Biology
    Centre for Doctoral Training (SynBioCDT) with support from the Bristol BioDesign Institute (BBI).

    ========================================================================== Story Source: Materials provided by University_of_Bristol. Note: Content
    may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Matthew J. Tarnowski, Thomas E. Gorochowski. Massively parallel
    characterization of engineered transcript isoforms using
    direct RNA sequencing. Nature Communications, 2022; 13 (1) DOI:
    10.1038/s41467-022- 28074-5 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/01/220121094313.htm

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