| fullrecord |
[{"key": "dc.contributor.advisor", "value": "Tiirola, Marja", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Norvasuo, Krista", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Nieminen, Janita", "language": "", "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2023-12-19T05:47:25Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2023-12-19T05:47:25Z", "language": null, "element": "date", "qualifier": "available", "schema": "dc"}, {"key": "dc.date.issued", "value": "2023", "language": "", "element": "date", "qualifier": "issued", "schema": "dc"}, {"key": "dc.identifier.uri", "value": "https://jyx.jyu.fi/handle/123456789/92395", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Kiertovesiviljely (RAS) on vedenk\u00e4yt\u00f6lt\u00e4\u00e4n tehokas ja ekologinen kalanviljelymenetelm\u00e4, joka mahdollistaa vesiviljelyn my\u00f6s alueilla, joissa veden saatavuus on rajallista. Kalojen patogeenit aiheuttavat kuitenkin haasteita vesiviljelyss\u00e4, erityisesti virukset, kuten IHNV (tarttuva vertamuodostavan kudoksen kuolio -virus) ja VHSV (virusper\u00e4inen verenvuotoseptikemia -virus), joita vastaan ei ole hoitoa tai rokotetta. Kiertovesilaitokseen p\u00e4\u00e4tyess\u00e4\u00e4n virus voi levit\u00e4 nopeasti koko laitokseen, jolloin tyhjennett\u00e4v\u00e4n ja desinfioitavan laitoksen kokemat tappiot ovat merkitt\u00e4v\u00e4t. Nykyiset testimenetelm\u00e4t eiv\u00e4t aina tunnista piilev\u00e4\u00e4 infektiota, mink\u00e4 vuoksi s\u00e4\u00e4nn\u00f6llinen tuontikalojen ja -m\u00e4din testaaminen on t\u00e4rke\u00e4\u00e4 virusten levi\u00e4misen est\u00e4miseksi. T\u00e4ss\u00e4 ty\u00f6ss\u00e4 optimoitiin RT-qPCR-testimenetelm\u00e4\u00e4 (kvantitatiivinen k\u00e4\u00e4nteiskopiointipolymeraasi-ketjureaktio) IHN- ja VHS-virusten havainnointiin ja vertailtiin virusten konsentrointimenetelmi\u00e4. Ty\u00f6ss\u00e4 tarkasteltiin my\u00f6s positiivisen kontrollin lis\u00e4\u00e4mist\u00e4 RT-qPCR-reaktioon (multiplex-PCR), sill\u00e4 kliinisess\u00e4 testauksessa menetelm\u00e4\u00e4 k\u00e4ytet\u00e4\u00e4n usein varmistamaan testin toimivuus. Ty\u00f6ss\u00e4 testattiin ultrasuodatusta, polyetyleeniglykolisaostusta (PEG-saostus), kylm\u00e4kuivausta ja InnuPrep-helmi\u00e4, jotka on valmistettu vett\u00e4 sitovasta polymeerist\u00e4. Lis\u00e4ksi tarkasteltiin IHNV-infektoituneesta RAS-laitoksesta otettuja vesin\u00e4ytteit\u00e4 ja kokeiltiin kehitetyn testin toimivuutta n\u00e4ytteill\u00e4. RT-qPCR-testist\u00e4 saatiin tarkka, ja testill\u00e4 pystyttiin havaitsemaan 400 \u00b5l:n n\u00e4ytteest\u00e4 noin kolme viruspartikkelia. Konsentrointimenetelmist\u00e4 PEG-saostus ja ultrasuodatus kasvattivat n\u00e4ytteen konsentraatiota hieman, ja ultrasuodatus valittiin menetelm\u00e4n nopeuden ja yksinkertaisuuden vuoksi RAS-laitokselta saatujen n\u00e4ytteiden k\u00e4sittelyyn. Kumpikaan menetelmist\u00e4 ei kuitenkaan kasvattanut n\u00e4ytteen konsentraatiota merkitsev\u00e4sti. Kahdessa RAS-laitokselta saadussa vesin\u00e4ytteess\u00e4 havaittiin pieni\u00e4 m\u00e4\u00e4ri\u00e4 IHN-virusta, mutta testituloksen varmistamiseksi PCR-tuote olisi tullut sekvensoida. Loput seitsem\u00e4n n\u00e4ytett\u00e4 olivat negatiivisia viruksen suhteen. Ultrasuodatuksen konsentrointitehokkuutta tarkasteltiin kalan RNA:n kautta RAS-n\u00e4ytteist\u00e4, jolloin pitoisuutta onnistuttiin kasvattamaan jopa 31-kertaiseksi. Ty\u00f6n tuloksia voidaan mahdollisesti hy\u00f6dynt\u00e4\u00e4 testaamisen nopeuttamisessa kalanviljelylaitoksilla, sill\u00e4 kehitetty testi kaikkine vaiheineen vaatii vain noin kuusi tuntia. T\u00e4m\u00e4 on huomattavasti t\u00e4ll\u00e4 hetkell\u00e4 k\u00e4yt\u00f6ss\u00e4 olevaa soluviljelytesti\u00e4 nopeampi, jonka tulosten saamiseen saattaa kulua jopa 14 vuorokautta.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Recirculating aquaculture system (RAS) is an ecologically sustainable method of fish farming, and it can be used in a variety of environments, even in places that lack water. Aquatic viral pathogens, such as diseases IHNV (infectious hematopoietic necrosis virus) and VHSV (viral hemorrhagic septicemia virus), threaten fish farming, because there are no vaccines or treatments against them. Viral pathogens can spread rather fast to the whole facility, in which case the entire facility has to be sanitized. This causes major economic losses to the facility. The way to prevent the spread of fish diseases IHN and VHS is the recurrent testing of fish fry and eggs before they are transported to facilities, but the current test methods are not fast enough for this kind of testing. This work optimized the RT-qPCR (quantitative reverse-transcript polymerase chain reaction) testing method for detecting IHN and VHS viruses and investigated four different virus concentration methods. In the study, the addition of a positive control to the \nRT-qPCR reaction (multiplex-PCR) was also investigated, as in clinical testing, this method is often used to verify the functionality of the test. Ultrafiltration, polyethylene glycol (PEG) precipitation, freeze-drying, and InnuPrep beads, which are made from a water-absorbing polymer, were the concentration methods tested in this work. In addition, water samples were taken from an IHNV-infected RAS facility, and the performance of the developed test was tested on the samples. The RT-qPCR test was accurate and could detect concentrations as little as three viral particles from a 400 \u00b5l sample. Among the concentration methods, PEG precipitation and ultrafiltration slightly increased the concentration of the sample, but ultrafiltration was selected for processing samples from the RAS facility due to its speed and simplicity. Neither of these methods had a significant effect on the concentration of the sample. Small amounts of IHN virus were detected in two out of nine water samples from RAS facility, but test results were not confirmed properly with sequencing. Samples from the RAS-facility were ultrafiltrated, and the concentration of the fish RNA in the sample was increased up to 31-fold. The results of this work could be used to improve testing at fish farming facilities, as the test developed in the work can be done in six hours, which is significantly less than the currently used testing method, which can take up to 14 days.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by Miia Hakanen (mihakane@jyu.fi) on 2023-12-19T05:47:25Z\nNo. of bitstreams: 0", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2023-12-19T05:47:25Z (GMT). No. of bitstreams: 0\n Previous issue date: 2023", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "66", "language": "", "element": "format", "qualifier": "extent", "schema": "dc"}, {"key": "dc.language.iso", "value": "fin", "language": null, "element": "language", "qualifier": "iso", "schema": "dc"}, {"key": "dc.rights", "value": "In Copyright", "language": null, "element": "rights", "qualifier": null, "schema": "dc"}, {"key": "dc.subject.other", "value": "RT-qPCR", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "kiertovesiviljely", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "IHN- ja VHS-virusten RT-qPCR-testimenetelm\u00e4n k\u00e4ytt\u00f6\u00f6notto sek\u00e4 konsentrointimenetelmien vertailu", "language": "", "element": "title", "qualifier": null, "schema": "dc"}, {"key": "dc.type", "value": "master thesis", "language": null, "element": "type", "qualifier": null, "schema": "dc"}, {"key": "dc.identifier.urn", "value": "URN:NBN:fi:jyu-202312198390", "language": "", "element": "identifier", "qualifier": "urn", "schema": "dc"}, {"key": "dc.type.ontasot", "value": "Master\u2019s thesis", "language": "en", "element": "type", "qualifier": "ontasot", "schema": "dc"}, {"key": "dc.type.ontasot", "value": "Pro gradu -tutkielma", "language": "fi", "element": "type", "qualifier": "ontasot", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Matemaattis-luonnontieteellinen tiedekunta", "language": "fi", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Faculty of Sciences", "language": "en", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Bio- ja ymp\u00e4rist\u00f6tieteiden laitos", "language": "fi", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Department of Biological and Environmental Science", "language": "en", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "Jyv\u00e4skyl\u00e4n yliopisto", "language": "fi", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "University of Jyv\u00e4skyl\u00e4", "language": "en", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Solu- ja molekyylibiologia", "language": "fi", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Cell and molecular biology", "language": "en", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "yvv.contractresearch.funding", "value": "0", "language": "", "element": "contractresearch", "qualifier": "funding", "schema": "yvv"}, {"key": "dc.type.coar", "value": "http://purl.org/coar/resource_type/c_bdcc", "language": null, "element": "type", "qualifier": "coar", "schema": "dc"}, {"key": "dc.rights.copyright", "value": "\u00a9 The Author(s)", "language": null, "element": "rights", "qualifier": "copyright", "schema": "dc"}, {"key": "dc.rights.accesslevel", "value": "openAccess", "language": null, "element": "rights", "qualifier": "accesslevel", "schema": "dc"}, {"key": "dc.type.publication", "value": "masterThesis", "language": null, "element": "type", "qualifier": "publication", "schema": "dc"}, {"key": "dc.subject.oppiainekoodi", "value": "4013", "language": "", "element": "subject", "qualifier": "oppiainekoodi", "schema": "dc"}, {"key": "dc.subject.yso", "value": "vesiviljely (kalatalous)", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "kalataudit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "diagnostiikka", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "virukset", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "testaus", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bakteerit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "RNA", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "DNA", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "laboratoriotutkimus", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "virustaudit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.rights.url", "value": "https://rightsstatements.org/page/InC/1.0/", "language": null, "element": "rights", "qualifier": "url", "schema": "dc"}]
|