<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-01656970</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-06T09:53:40+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">zPACT: Tissue Clearing and Immunohistochemistry on Juvenile Zebrafish Brain</title>
            <author role="aut">
              <persName>
                <forename type="first">Pierre</forename>
                <surname>Affaticati</surname>
              </persName>
              <idno type="halauthorid">518388-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Matthieu</forename>
                <surname>Simion</surname>
              </persName>
              <email type="md5">37bbce2d35c8f8f366da47cd3251317d</email>
              <email type="domain">inrae.fr</email>
              <idno type="idhal" notation="string">matthieu-simion</idno>
              <idno type="idhal" notation="numeric">1284599</idno>
              <idno type="halauthorid" notation="string">1046741-1284599</idno>
              <idno type="ORCID">https://orcid.org/0009-0001-8235-5299</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Elodie</forename>
                <surname>de Job</surname>
              </persName>
              <idno type="halauthorid">1208726-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Laurie</forename>
                <surname>Rivière</surname>
              </persName>
              <idno type="halauthorid">1158976-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Jean-Michel</forename>
                <surname>Hermel</surname>
              </persName>
              <idno type="halauthorid">228978-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Elodie</forename>
                <surname>Machado</surname>
              </persName>
              <idno type="halauthorid">1275384-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Jean-Stéphane</forename>
                <surname>Joly</surname>
              </persName>
              <idno type="halauthorid">178843-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Armin</forename>
                <surname>Jenett</surname>
              </persName>
              <idno type="halauthorid">3051450-0</idno>
              <affiliation ref="#struct-418266"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Matthieu</forename>
                <surname>Simion</surname>
              </persName>
              <email type="md5">37bbce2d35c8f8f366da47cd3251317d</email>
              <email type="domain">inrae.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2024-09-04 09:24:03</date>
              <date type="whenModified">2024-09-06 14:31:33</date>
              <date type="whenReleased">2024-09-06 14:31:33</date>
              <date type="whenProduced">2017-12-05</date>
              <date type="whenEndEmbargoed">2024-09-06</date>
              <ref type="file" target="https://hal.science/hal-01656970v1/document">
                <date notBefore="2024-09-06"/>
              </ref>
              <ref type="file" subtype="greenPublisher" n="1" target="https://hal.science/hal-01656970v1/file/Bio-protocol2636.pdf" id="file-4686885-4077545">
                <date notBefore="2024-09-06"/>
              </ref>
              <ref type="externalLink" target="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438491"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="1452080">
                <persName>
                  <forename>Matthieu</forename>
                  <surname>Simion</surname>
                </persName>
                <email type="md5">37bbce2d35c8f8f366da47cd3251317d</email>
                <email type="domain">inrae.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-01656970</idno>
            <idno type="halUri">https://hal.science/hal-01656970</idno>
            <idno type="halBibtex">affaticati:hal-01656970</idno>
            <idno type="halRefHtml">&lt;i&gt;Bio-protocol &lt;/i&gt;, 2017, 7 (23), &lt;a target="_blank" href="https://dx.doi.org/10.21769/BioProtoc.2636"&gt;&amp;#x27E8;10.21769/BioProtoc.2636&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Bio-protocol , 2017, 7 (23), &amp;#x27E8;10.21769/BioProtoc.2636&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-4686885-4077545"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="UNIV-PSUD">Université Paris Sud - Paris XI</idno>
            <idno type="stamp" n="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="UNIV-PSUD-SACLAY" corresp="UNIV-PARIS-SACLAY">Université Paris Sud pour Paris Saclay</idno>
            <idno type="stamp" n="INRA-SACLAY" corresp="UNIV-PARIS-SACLAY">INRA-SACLAY</idno>
            <idno type="stamp" n="GS-HEALTH-DRUG-SCIENCES">Graduate School Health and Drug Sciences</idno>
            <idno type="stamp" n="NEURO-PSI">Institut des neurosciences Paris-Saclay</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">zPACT: Tissue Clearing and Immunohistochemistry on Juvenile Zebrafish Brain</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Pierre</forename>
                    <surname>Affaticati</surname>
                  </persName>
                  <idno type="halauthorid">518388-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Matthieu</forename>
                    <surname>Simion</surname>
                  </persName>
                  <email type="md5">37bbce2d35c8f8f366da47cd3251317d</email>
                  <email type="domain">inrae.fr</email>
                  <idno type="idhal" notation="string">matthieu-simion</idno>
                  <idno type="idhal" notation="numeric">1284599</idno>
                  <idno type="halauthorid" notation="string">1046741-1284599</idno>
                  <idno type="ORCID">https://orcid.org/0009-0001-8235-5299</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Elodie</forename>
                    <surname>de Job</surname>
                  </persName>
                  <idno type="halauthorid">1208726-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Laurie</forename>
                    <surname>Rivière</surname>
                  </persName>
                  <idno type="halauthorid">1158976-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Jean-Michel</forename>
                    <surname>Hermel</surname>
                  </persName>
                  <idno type="halauthorid">228978-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Elodie</forename>
                    <surname>Machado</surname>
                  </persName>
                  <idno type="halauthorid">1275384-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Jean-Stéphane</forename>
                    <surname>Joly</surname>
                  </persName>
                  <idno type="halauthorid">178843-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Armin</forename>
                    <surname>Jenett</surname>
                  </persName>
                  <idno type="halauthorid">3051450-0</idno>
                  <affiliation ref="#struct-418266"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">104401</idno>
                <idno type="issn">2331-8325</idno>
                <title level="j">Bio-protocol </title>
                <imprint>
                  <publisher>Bio-protocol LCC</publisher>
                  <biblScope unit="volume">7</biblScope>
                  <biblScope unit="issue">23</biblScope>
                  <date type="datePub">2017-12-05</date>
                </imprint>
              </monogr>
              <idno type="doi">10.21769/BioProtoc.2636</idno>
              <idno type="pubmedcentral">PMC8438491</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">PACT</term>
                <term xml:lang="en">Tissue clearing</term>
                <term xml:lang="en">Deep imaging</term>
                <term xml:lang="en">Zebrafish</term>
                <term xml:lang="en">Immunohistochemistry</term>
                <term xml:lang="en">Confocal microscopy</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv.neu.nb">Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology</classCode>
              <classCode scheme="halDomain" n="sdv.neu.pc">Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior</classCode>
              <classCode scheme="halDomain" n="sdv.neu.sc">Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>In studies of brain function, it is essential to understand the underlying neuro-architecture. Very young zebrafish larvae are widely used for neuroarchitecture studies, due to their size and natural transparency. However, this model system has several limitations, due to the immaturity, high rates of development and limited behavioral repertoire of the animals used.We describe here a modified version of the passive clearing technique (PACT) (Chung et al., 2013; Tomer et al., 2014; Yang et al., 2014; Treweek et al., 2015), which facilitates neuroanatomical studies on large specimens of aquatic species. This method was initially developed for zebrafish (Danio rerio) (Frétaud et al., 2017; Mayrhofer et al., 2017; Xavier et al., 2017), but has also been successfully tested on other fish, such as medaka (Oryzias latipes) (Dambroise et al., 2017), Mexican cave fish (Astyanax mexicaus) and African zebra mbuna (Metriaclima zebra), and on other aquatic species, such as Xenopus spp. (Xenopus laevis, Xenopus tropicalis) (Fini et al., 2017). This protocol, based on the CLARITY method developed and modified by Deisseroth’s laboratory and others (Chung et al., 2013; Tomer et al., 2014; Yang et al., 2014), was adapted for use in aquatic species, including zebrafish in particular (zPACT).This protocol is designed to render zebrafish specimens optically transparent while preserving the overall architecture of the tissue, through crosslinking in a polyacrylamide/formaldehyde mesh. Most of the lipids present in the specimen are then removed by SDS treatment, to homogenize the refractive index of the specimen by eliminating light scattering at the water/lipid interface, which causes opacity. The final clearing step, consists of the incubation of the specimen in a fructose-based mounting medium (derived from SeeDB) (Ke et al., 2013), with a refractive index matching that of the objective lens of the microscope. The combination of this technique with the use of genetically modified zebrafish in which green fluorescent protein (GFP) is expressed in specific cell populations provides opportunities to describe anatomical details not visible with other techniques.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-418266" status="OLD">
          <orgName>Institut des Neurosciences Paris-Saclay</orgName>
          <orgName type="acronym">NeuroPSI</orgName>
          <date type="start">2015-01-01</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>Centre National de la Recherche Scientifique, Unité Mixte de Recherche-9197 Université Paris-Sudbâtiment 32 Campus de Recherche de Gif-sur-Yvette1, avenue de la Terrasse91198 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://neuropsi.cnrs.fr</ref>
          </desc>
          <listRelation>
            <relation name="UMR9497" active="#struct-92966" type="direct"/>
            <relation name="UMR9197" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-92966" status="OLD">
          <idno type="ROR">https://ror.org/028rypz17</idno>
          <orgName>Université Paris-Sud - Paris 11</orgName>
          <orgName type="acronym">UP11</orgName>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>Bâtiment 300 - 91405 Orsay cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.u-psud.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>