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[{"key": "dc.contributor.advisor", "value": "M\u00e4kel\u00e4, Kati", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Laanto, Elina", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Sundberg, Lotta-Riina", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Kreuze, Kim", "language": "", "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2023-07-07T09:37:39Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2023-07-07T09:37:39Z", "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/123456789/88301", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Faagit, jotka sis\u00e4lt\u00e4v\u00e4t lipidikalvon sek\u00e4 yksijuosteista DNA:ta (ssDNA) ovat v\u00e4hemm\u00e4n tutkittuja verrattuna h\u00e4nn\u00e4llisiin kaksijuosteisiin DNA- (dsDNA) faageihin, vaikka uusia ssDNA isolaatteja sek\u00e4 geneettisi\u00e4 signaaleja on alettu l\u00f6yt\u00e4\u00e4 ymp\u00e4ri maailmaa. FLiP oli ensimm\u00e4inen karakterisoitu faagi, jolla on n\u00e4m\u00e4 ominaisuudet, ja toistaiseksi ainoa Finnlakeviridae -virusperheen edustaja. Tutkielman tavoite oli karakterisoida kahta vuonna 2021 eristetty\u00e4 faagi-isolaattia (ss- ja dsDNA sis\u00e4lt\u00e4vi\u00e4) jotka infektoivat samoja Flavobakteeri- is\u00e4nti\u00e4 kuin FLiP. Lis\u00e4ksi haluttiin verrata FLiP -faagin ja uusien faagien is\u00e4nt\u00e4vuorovaikutusdynamiikkoja. Molempien bakteriofagien genomit koottiin, annotoitiin sek\u00e4 analysoitiin useita eri bioinformaattisia ohjelmia k\u00e4ytt\u00e4en. My\u00f6s faagien is\u00e4nt\u00e4kirjoja, adsorptiok\u00e4yri\u00e4, kasvuk\u00e4yri\u00e4 ja zymogrammeja verrattiin. Bakteriofagien morfologiaa tarkasteltiin l\u00e4p\u00e4isyelektronimikroskoopilla. FLiP -faagin ja uuden ssDNA -faagin geneettinen vertailu osoitti, ett\u00e4 niiden genomisekvenssien samankaltaisuus oli 96.64%, ja faagin nimeksi annettiin FLiP-2 t\u00e4ss\u00e4 tutkielmassa. Nuklelotidierot kohdistuivat muun muassa viruksen koodittamaan hypoteettiseen piikkiproteiiniin ja proteiineihin, joilla on peptidoglykaanin pilkkomis- kyky. Lis\u00e4ksi eroja l\u00f6ytyi faagien plakkikoossa, is\u00e4nt\u00e4kirjossa ja mahdollisesti peptidoglykaanin pilkkomiskyvyss\u00e4. DsDNA -faagin osoitettiin olevan h\u00e4nn\u00e4llinen myofaagi, ja sen nimeksi tuli B330-P19. T\u00e4m\u00e4n faagin plakkimorfologia ja is\u00e4nt\u00e4kirjo poikkesi suuresti molemmista FLiP -faageista. Lis\u00e4ksi B330-P19 faagin kasvuk\u00e4yr\u00e4 osoitti, ett\u00e4 se tuotti keskim\u00e4\u00e4rin 27,73 uutta partikkelia infektoitua solua kohden, kun taas FLiP ja FLiP-2 faagien kohdalla vastaavat arvot olivat 4,58 ja 2,63. Tulokset laajentavat tunnettua Finnlakeviridae -perheen monimuotoisuutta ja osoittavat, ett\u00e4 Finnlakeviridae faagit lis\u00e4\u00e4ntyv\u00e4t joko Jyv\u00e4sj\u00e4rvess\u00e4 tai sen ymp\u00e4rist\u00f6ss\u00e4. Lis\u00e4ksi FLiP -faagin erikoisen elinkaaren kaltaisia elinkaarta ei esiinny h\u00e4nn\u00e4llisell\u00e4 faagilla, joka kuitenkin infektoi samoja is\u00e4nti\u00e4.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Bacteriophages containing both a lipid membrane and single-stranded DNA are a novel and highly understudied group despite new isolates and genetic signatures being discovered around the world. FLiP, the sole phage isolate in the family Finnlakeviridae, was the first phage characterized with such properties and has an unusual life cycle. The aim of this thesis was to describe two newly isolated bacteriophages (one being similar to FLiP) from lake Jyv\u00e4sj\u00e4rvi and compare their host interactions with FLiPs to understand the diversity of Finnlakeviridae phages and confirm FLiPs unusual life cycle. To explore the phylogeny and genomic characteristics of both bacteriophages, their genomes were assembled, annotated, and analysed using a variety of bioinformatic software. In addition, phage-host interactions were studied by adsorption assay, one step growth curve, host range assay and zymography. Morphology of the bacteriophages was determined using transmission electron microscopy. Genome assembly of one of the phages revealed it to have a 96.64% nucleotide identity to FLiP and was named FLiP-2. Non-synonymous codon differences between FLiP and FLiP-2 in ORFs with functions related to peptidoglycan degradation and putative receptor binding were found. Additionally, FLiP and FLiP-2 were shown to have slightly different host ranges, plaque morphologies and potential differences in lytic enzyme activity. The second phage was determined to be a tailed bacteriophage with a myophage morphology and was named B330-P19. It was shown to have a highly different host range and plaque morphology compared to both FLiP phages. Finally, the one step growth curve revealed that the three phages differed by their calculated average burst size which was 4.58, 2.63 and 27.73 for FLiP, FLiP-2 and B330-P19 respectively. The results expand the known diversity of Finnlakevirus FLiP, the species encompassing FLiP and FLiP-2, and shows that the species is established either in lake Jyv\u00e4sj\u00e4rvi, the surrounding environment or both. Additionally, the unusual lifestyle of FLiP seems to be a trait of at least the species and can be different from some tailed phages infecting the same host.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by Miia Hakanen (mihakane@jyu.fi) on 2023-07-07T09:37:39Z\nNo. of bitstreams: 0", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2023-07-07T09:37:39Z (GMT). No. of bitstreams: 0\n Previous issue date: 2023", "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": null, "element": "rights", "qualifier": null, "schema": "dc"}, {"key": "dc.subject.other", "value": "Finnlakevirus FLiP", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "holin-endolysin", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "plaque morphology", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "myophage", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "single-stranded DNA", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "transient", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "Comparison of genomes and host interactions of Finnlakeviridae phages", "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-202307074428", "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": "j\u00e4rvet", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "ymp\u00e4rist\u00f6", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "monimuotoisuus", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bakteriofagit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "morfologia", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "perim\u00e4", "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": "bakteerit", "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": "lakes", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "environment", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "diversity", "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": "morphology (biology)", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "genome", "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": "bacteria", "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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