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[{"key": "dc.contributor.advisor", "value": "Laanto, Elina", "language": null, "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Sundberg, Lotta-Riina", "language": null, "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Niemi, Meeri", "language": "", "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2024-05-14T07:04:01Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2024-05-14T07:04:01Z", "language": null, "element": "date", "qualifier": "available", "schema": "dc"}, {"key": "dc.date.issued", "value": "2024", "language": null, "element": "date", "qualifier": "issued", "schema": "dc"}, {"key": "dc.identifier.uri", "value": "https://jyx.jyu.fi/handle/123456789/94810", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Bacteriophages, or phages, are viruses that infect bacteria. Recently, many megaphages with large (over 500 kilo base pairs) genomes have been discovered. Metagenomic analyses show that several phages, including some megaphages, encode a CRISPR-Cas system, an adaptive immune system commonly associated with prokaryotes. These systems consist of CRISPR repeat-spacer arrays and Cas proteins that enable the system to target foreign genetic material in a sequence-specific manner. Some phage-encoded CRISPR-Cas systems have been shown to target host bacterium genome, while others are thought to target competing phages, but empirical evidence is scarce. This research seeks to elucidate the functionality of CRISPR-Cas systems in megaphages, which often exhibit incomplete systems with unclear purpose. In this study, five megaphages (genome size over 600 kilo base pairs) isolated from Lake Jyv\u00e4sj\u00e4rvi were studied. Phage host range was determined with titration experiments, and the phages were found to primarily infect species of Flavobacterium. The life cycle of phage Elf16 was determined by measuring host optical density, calculating plaque forming units during infection, and by performing an adsorption to host test. The Elf16 life cycle was found to be lytic, with lysis occurring gradually and starting at roughly three hours post-infection. Thin section samples of the phage infection were imaged using transmission electron microscopy, and the phage particles were shown to be large and have a contractile tail. Images also depict the Elf16 life cycle, which matches the life cycle demonstrated by measuring the optical density and plaque forming units. Elf16 genome was analysed, but no match was found between the CRISPR spacers of the phage and the genome of its isolation host. It is possible that the purpose of the phage CRIPSR-system is to attack host genome, but it is not a requisite for a successful infection. To assess the functionality of the Elf16 CRISPR-Cas system, Cas9 gene expression was measured using qPCR. The findings suggested significant Cas9 expression during early stages of infection, therefore hinting at a potentially functional system.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Bakteriofagit eli faagit ovat viruksia, jotka infektoivat bakteereja. Viime aikoina on l\u00f6ydetty useita megafaageja, joilla on suuri (yli 500 kiloem\u00e4sparia) genomi. Metagenomianalyyseiss\u00e4 on l\u00f6ydetty faageja, my\u00f6s joitakin megafaageja, joilla on CRISPR-Cas j\u00e4rjestelm\u00e4, adaptiivinen immuunij\u00e4rjestelm\u00e4, joka on yleinen esitumallisilla. CRISPR-j\u00e4rjestelm\u00e4 koostuu CRISPR-sekvenssist\u00e4 ja Cas-geeneist\u00e4, joiden avulla bakteeri voi tunnistaa ja tuhota vierasta geneettist\u00e4 materiaalia sekvenssin tarkkuudella. T\u00e4m\u00e4 tutkimus pyrkii selvitt\u00e4m\u00e4\u00e4n CRISPR-j\u00e4rjestelm\u00e4n toimivuutta megafaageissa. Niiden CRISPR-j\u00e4rjestelm\u00e4 on usein vajavainen, ja sen toimintaa ei juurikaan tunneta. Joidenkin faagien CRISPR-j\u00e4rjestelmien on osoitettu tuhoavan is\u00e4nt\u00e4bakteerien genomia, ja joidenkin arvellaan tuhoavan kilpailevien faagien genomia, mutta empiirinen n\u00e4ytt\u00f6 on v\u00e4h\u00e4ist\u00e4. T\u00e4ss\u00e4 ty\u00f6ss\u00e4 tutkittiin viitt\u00e4 Jyv\u00e4sj\u00e4rvest\u00e4 eristetty\u00e4 megafaagia (genomi yli 600 kiloem\u00e4sparia). Faagien is\u00e4nt\u00e4kirjo selvitettiin tippatitrauksella. Todettiin, ett\u00e4 faagit infektoivat p\u00e4\u00e4asiassa eri Flavobacterium lajeja. Faagin Elf16 elinkierto selvitettiin mittaamalla optista tiheytt\u00e4, laskemalla plakin muodostavien yksik\u00f6iden m\u00e4\u00e4r\u00e4 infektion aikana ja suorittamalla adsorptiokoe. Faagin elinkierto osoitettiin lyyttiseksi. Hitaasti etenev\u00e4 lyysis alkaa noin kolme tuntia infektion alun j\u00e4lkeen. Infektion aikana otetuista n\u00e4ytteist\u00e4 tehtiin ohutleikkeit\u00e4, jotka kuvattiin l\u00e4p\u00e4isyelektronimikroskoopilla. Faagipartikkelit olivat suuria, ja ne omasivat kontraktiilin h\u00e4nn\u00e4n. Kuvat osoittavat my\u00f6s faagin elinkierron, joka t\u00e4sm\u00e4\u00e4 muissa mittauksissa todettuun kiertoon. Faagin Elf16 genomia analysoitiin, mutta ei havaittu vastaavuutta faagin CRISPR spacereiden ja is\u00e4nt\u00e4bakteerin genomin v\u00e4lill\u00e4. On mahdollista, ett\u00e4 faagin CRISPR-j\u00e4rjestelm\u00e4n tarkoitus on leikata is\u00e4nn\u00e4n genomia, mutta se ei kuitenkaan ole edellytys onnistuneelle infektiolle. Faagin Elf16 CRISPR-j\u00e4rjestelm\u00e4n toimivuutta testattiin mittaamalla Cas9-geenin ilmentymist\u00e4 qPCR:n avulla. Cas9:\u00e4\u00e4 ilmentyy infektion alkuvaiheessa, mik\u00e4 saattaa viitata toiminalliseen CRISPR-Cas j\u00e4rjestelm\u00e4\u00e4n.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by Paivi Vuorio (paelvuor@jyu.fi) on 2024-05-14T07:04:01Z\nNo. of bitstreams: 0", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2024-05-14T07:04:01Z (GMT). No. of bitstreams: 0\n Previous issue date: 2024", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "60", "language": "", "element": "format", "qualifier": "extent", "schema": "dc"}, {"key": "dc.language.iso", "value": "eng", "language": null, "element": "language", "qualifier": "iso", "schema": "dc"}, {"key": "dc.rights", "value": "In Copyright", "language": "en", "element": "rights", "qualifier": null, "schema": "dc"}, {"key": "dc.subject.other", "value": "flavobacteria", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "host-phage interaction", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "host range", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "megaphage", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "phage morphology", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "viral life cycle", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "First evidence of Cas9 expression during CRISPR-Cas containing megaphage infection", "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-202405143578", "language": null, "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": "Faculty of Sciences", "language": "en", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Matemaattis-luonnontieteellinen tiedekunta", "language": "fi", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Department of Biological and Environmental Science", "language": "en", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Bio- ja ymp\u00e4rist\u00f6tieteiden laitos", "language": "fi", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "University of Jyv\u00e4skyl\u00e4", "language": "en", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "Jyv\u00e4skyl\u00e4n yliopisto", "language": "fi", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Cell and molecular biology", "language": "en", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Solu- ja molekyylibiologia", "language": "fi", "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.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": null, "element": "subject", "qualifier": "oppiainekoodi", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bakteriofagit", "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": "bakteerit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "infektiot", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "is\u00e4nt\u00e4solut", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "elinkaariarviointi", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bacteriophages", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "viruses", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bacteria", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "infections", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "host cells", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "life cycle analysis", "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"}]
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