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[{"key": "dc.contributor.advisor", "value": "Takala, Heikki", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Multam\u00e4ki, Elina", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Vanhatalo, Roosa", "language": "", "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2023-09-05T06:04:15Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2023-09-05T06:04:15Z", "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/123456789/88878", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Bakteerifytokromit voivat s\u00e4\u00e4dell\u00e4 is\u00e4nt\u00e4solun sis\u00e4ist\u00e4 metaboliaa valo-olosuhteista riippuen. T\u00e4m\u00e4n mahdollistaa se, ett\u00e4 fytokromit voivat toimia osana kaksikomponenttij\u00e4rjestelmi\u00e4, jotka voivat puolestaan s\u00e4\u00e4dell\u00e4 geenien ilment\u00e4mist\u00e4 soluissa. Yhdistett\u00e4ess\u00e4 fytokromien valoa aistivat ominaisuudet ja kaksikomponenttij\u00e4rjestelmien s\u00e4\u00e4telyominaisuudet on mahdollista kehitt\u00e4\u00e4 optogeneettisi\u00e4 sovelluksia l\u00e4\u00e4ketieteellisist\u00e4 hoidoista aina biomateriaalien tuotantoon. pREDusk on optogeneettinen ty\u00f6kalu, jota voidaan k\u00e4ytt\u00e4\u00e4 Escherichia coli bakteerissa punaista fluoresoivan reportteriproteiinin geenin ilment\u00e4misen s\u00e4\u00e4telyyn. pREDuskin valoa aistiva osa on kanonisen Deinococcus radiodurans bakteerifytokromin valoa aistiva moduuli, jota voidaan kontrolloida punaisen ja kaukopunaisen valon avulla. T\u00e4m\u00e4 pro gradu tutkielma keskittyy pREDusk ty\u00f6kalun toiminnallisuuden muuttamiseen. T\u00e4ll\u00e4 hetkell\u00e4 punainen valo vaimentaa geenin ilment\u00e4mist\u00e4 ja tutkimuksen tarkoituksena oli sen sijaan aktivoida geenin ilment\u00e4minen kaukopunaisen valon avulla. Muutosta yritettiin hy\u00f6dynt\u00e4m\u00e4ll\u00e4 kahden eri bathyfytokromin valoa aistivaa moduulia, sill\u00e4 n\u00e4m\u00e4 fytokromit reagoivat kaukopunaiseen valoon punaisen valon sijasta. Vaihdokset sis\u00e4lsiv\u00e4t kaksi koko valoa aistivan moduulin vaihdosta sek\u00e4 kaksi varianttia, joissa vain ARM-osa valoa aistivasta moduulista vaihdettiin. Tutkimus toteutettiin puhdistamalla muunnellut proteiinit ja tutkimalla niiden entsymaattista aktiivisuutta. Lis\u00e4ksi varianttien spektroskopisia ominaisuuksia tarkasteltiin UV-Vis ja FTIR spektroskopioiden avulla. Lopuksi pREDusk varianttien geenin ilment\u00e4mist\u00e4 tutkittiin in vivo. Ty\u00f6n tuloksena kolme nelj\u00e4st\u00e4 proteiinivariantista saatiin puhdistettua. Variantit, joiden ARM osa oli vaihdettu, olivat valosyklilt\u00e4\u00e4n kanonisia, mutta kun koko valoa aistiva osa vaihdettiin, oli fotosykli k\u00e4\u00e4nteinen ja t\u00e4ten bathyfytokromeille tyypillinen. Variantit, joissa vain ARM-osa oli vaihdettu toimivat kuten alkuper\u00e4inen ty\u00f6kalu. Puolestaan variantteja, joiden koko valoa aistiva osa oli vaihdettu, ei muutosten j\u00e4lkeen voitu en\u00e4\u00e4 s\u00e4\u00e4dell\u00e4 valolla. Huomionarvoista on, ett\u00e4 kaikki puhdistetut proteiinit vaihtuivat kahden valosta aktivoituvan tilan v\u00e4lill\u00e4, mik\u00e4 tarkoitti, ett\u00e4 vaihdokset olivat onnistuneita vaikkakaan niiden avulla ei saatu muutettua pREDuskia valolla aktivoitavaksi. Ty\u00f6n l\u00f6yd\u00f6sten perusteella voidaan pREDusk ty\u00f6kalun kehitt\u00e4miseksi tulevaisuudessa kokeilla uudenlaisia muutoksia.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Bacterial phytochromes can regulate the metabolism of species in response to light conditions. This is achieved through their involvement in two-component systems that can control gene transcription. The light controllability of phytochromes and their regulatory properties through two-component systems offer numerous applications in optogenetics, ranging from medical treatments to bio-material production. pREDusk is an optogenetic tool used in Escherichia coli to control the transcription of a red-fluorescent reporter gene. The light-sensing part of the tool is the photosensory module (PSM) of the prototypical bacteriophytochrome of Deinococcus radiodurans, and thus pREDusk can be controlled with red and far-red light. This master\u2019s thesis project is focused on tuning the functionality of pREDusk. Currently, red light attenuates gene transcription, and the aim was to achieve upregulation of gene transcription in response to far-red light instead. This was tried by modifying the photosensory part of pREDusk by using PSMs from two bathy phytochromes with an inverted photocycle. These replacements included switching the whole PSM and only switching a specific part of the PSM known as an ARM. During this master\u2019s thesis project, the modified proteins were purified, and their enzymatic activity was studied. The spectroscopic properties were observed with UV-Vis and FTIR spectroscopy, and the modified pREDusk was studied in vivo. As a result, three out of the four protein variants were purified. The purified variants, in which only the ARM part was replaced, were prototypical, and when the entire PSM was replaced, the photocycle was bathy. Regarding gene expression controlled by pREDusk, variants with ARM replacements expressed the fluorescent marker in darkness and under far-red light, indicating no change in the activation pattern. With the whole PSM replaced variants the controllability was lost. Notably, all the purified proteins converted between two states, in response to light, which meant that the replacements were successful in this sense even though pREDusk could not be turned light activatable. Based on the findings of this study, there is a solid foundation for implementing further replacements to improve pREDusk.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by Paivi Vuorio (paelvuor@jyu.fi) on 2023-09-05T06:04:15Z\nNo. of bitstreams: 0", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2023-09-05T06:04:15Z (GMT). No. of bitstreams: 0\n Previous issue date: 2023", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "55", "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": "Agp2", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "DrBphP", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "PaBphP", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "protein engineering", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "two-component system", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "The effects of photosensory module components for phytochrome activity and spectroscopy", "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-202309054909", "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": "restrictedAccess", "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": "proteiinit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "optogenetiikka", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "spektroskopia", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "proteins", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "optogenetics", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "spectroscopy", "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"}, {"key": "dc.rights.accessrights", "value": "The author has not given permission to make the work publicly available electronically. Therefore the material can be read only at the archival workstation at Jyv\u00e4skyl\u00e4 University Library (https://kirjasto.jyu.fi/collections/archival-workstation).", "language": "en", "element": "rights", "qualifier": "accessrights", "schema": "dc"}, {"key": "dc.rights.accessrights", "value": "Tekij\u00e4 ei ole antanut lupaa avoimeen julkaisuun, joten aineisto on luettavissa vain Jyv\u00e4skyl\u00e4n yliopiston kirjaston arkistoty\u00f6semalta. Ks. https://kirjasto.jyu.fi/kokoelmat/arkistotyoasema..", "language": "fi", "element": "rights", "qualifier": "accessrights", "schema": "dc"}]
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