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Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells

Perrino, Giansimone; Fiore, Davide; Napolitano, Sara; Galdi, Francesca; La Regina, Antonella; di Bernardo, Mario; di Bernardo, Diego


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  <identifier identifierType="URL">https://zenodo.org/record/4835897</identifier>
  <creators>
    <creator>
      <creatorName>Perrino, Giansimone</creatorName>
      <givenName>Giansimone</givenName>
      <familyName>Perrino</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8095-9139</nameIdentifier>
      <affiliation>Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>Fiore, Davide</creatorName>
      <givenName>Davide</givenName>
      <familyName>Fiore</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4011-5836</nameIdentifier>
      <affiliation>Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>Napolitano, Sara</creatorName>
      <givenName>Sara</givenName>
      <familyName>Napolitano</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5040-3391</nameIdentifier>
      <affiliation>Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy. -Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy.</affiliation>
    </creator>
    <creator>
      <creatorName>Galdi, Francesca</creatorName>
      <givenName>Francesca</givenName>
      <familyName>Galdi</familyName>
      <affiliation>Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy. Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy.</affiliation>
    </creator>
    <creator>
      <creatorName>La Regina, Antonella</creatorName>
      <givenName>Antonella</givenName>
      <familyName>La Regina</familyName>
      <affiliation>Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy. - Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy.</affiliation>
    </creator>
    <creator>
      <creatorName>di Bernardo, Mario</creatorName>
      <givenName>Mario</givenName>
      <familyName>di Bernardo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-3329-0839</nameIdentifier>
      <affiliation>Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy - Department of Engineering Mathematics, University of Bristol, University Walk, BS8 1TR Bristol, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>di Bernardo, Diego</creatorName>
      <givenName>Diego</givenName>
      <familyName>di Bernardo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1911-7407</nameIdentifier>
      <affiliation>Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy. - Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy.</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <dates>
    <date dateType="Issued">2019-03-27</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Preprint</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4835897</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1101/590844</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/cosy-bio</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Abstract&lt;/p&gt;

&lt;p&gt;The periodic process of cell replication by division, known as cell-cycle, is a natural phenomenon occurring asynchronously in any cell population. Here, we consider the problem of synchronising cell-cycles across a population of yeast cells grown in a microfluidics device. Cells were engineered to reset their cell-cycle in response to low methionine levels. Automated syringes enable changing methionine levels (control input) in the microfluidics device. However, the control input resets only those cells that are in a specific phase of the cell-cycle (G1 phase), while the others continue to cycle unperturbed. We devised a simplified dynamical model of the cell-cycle, inferred its parameters from experimental data and then designed two control strategies: (i) an open-loop controller based on the application of periodic stimuli; (ii) a closed-loop model predictive controller (MPC) that selects the sequence of control stimuli which maximises a synchronisation index. Both the proposed control strategies were validated in-silico, together with experimental validation of the open-loop strategy.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/766840/">766840</awardNumber>
      <awardTitle>Control Engineering of Biological Systems for Reliable Synthetic Biology Applications</awardTitle>
    </fundingReference>
  </fundingReferences>
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