Preprint Open Access

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


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://zenodo.org/record/4835897">
    <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/>
    <dct:type rdf:resource="http://purl.org/dc/dcmitype/Text"/>
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/4835897</dct:identifier>
    <foaf:page rdf:resource="https://zenodo.org/record/4835897"/>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-8095-9139">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0001-8095-9139</dct:identifier>
        <foaf:name>Perrino, Giansimone</foaf:name>
        <foaf:givenName>Giansimone</foaf:givenName>
        <foaf:familyName>Perrino</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-4011-5836">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-4011-5836</dct:identifier>
        <foaf:name>Fiore, Davide</foaf:name>
        <foaf:givenName>Davide</foaf:givenName>
        <foaf:familyName>Fiore</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-5040-3391">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0001-5040-3391</dct:identifier>
        <foaf:name>Napolitano, Sara</foaf:name>
        <foaf:givenName>Sara</foaf:givenName>
        <foaf:familyName>Napolitano</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Galdi, Francesca</foaf:name>
        <foaf:givenName>Francesca</foaf:givenName>
        <foaf:familyName>Galdi</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>La Regina, Antonella</foaf:name>
        <foaf:givenName>Antonella</foaf:givenName>
        <foaf:familyName>La Regina</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-3329-0839">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-3329-0839</dct:identifier>
        <foaf:name>di Bernardo, Mario</foaf:name>
        <foaf:givenName>Mario</foaf:givenName>
        <foaf:familyName>di Bernardo</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-1911-7407">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-1911-7407</dct:identifier>
        <foaf:name>di Bernardo, Diego</foaf:name>
        <foaf:givenName>Diego</foaf:givenName>
        <foaf:familyName>di Bernardo</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2019</dct:issued>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/766840/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-03-27</dct:issued>
    <owl:sameAs rdf:resource="https://zenodo.org/record/4835897"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/4835897</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <owl:sameAs rdf:resource="https://doi.org/10.1101/590844"/>
    <dct:isPartOf rdf:resource="https://zenodo.org/communities/cosy-bio"/>
    <dct:description>&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;</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dcat:distribution>
      <dcat:Distribution>
        <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
        <dcat:accessURL rdf:resource="https://zenodo.org/record/4835897"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.1101/590844</dcat:accessURL>
        <dcat:byteSize>1761651</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/4835897/files/Perrino et al 2019 bioRxiv .pdf">https://zenodo.org/record/4835897/files/Perrino et al 2019 bioRxiv .pdf</dcat:downloadURL>
        <dcat:mediaType>application/pdf</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/766840/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">766840</dct:identifier>
    <dct:title>Control Engineering of Biological Systems for Reliable Synthetic Biology Applications</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
</rdf:RDF>
8
5
views
downloads
Views 8
Downloads 5
Data volume 8.8 MB
Unique views 8
Unique downloads 5

Share

Cite as