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  • Olkkonen, Emmi (2021)
    Long non-coding RNAs (lncRNAs) are over 200 bp long RNA molecules that are not translated into protein. LncRNAs can regulate the expression of protein coding genes, and studies have indicated their role in stress response. Stress response has also been associated with differences in the structure of the myelin sheaths in the mouse brain cortex. Myelin is produced by mature oligodendrocytes (OLGs), and therefore, OLGs are likely to play a role in stress response. The aim of this thesis was to find lncRNAs differentially expressed in the oligodendrocytes and myelin on the medial prefrontal cortex of stressed mice in comparison to controls. Mice of strains C57/6NCrl and DBA/2NCrl, differing in stress response, were exposed to chronic social defeat stress. After the stress paradigm, the mice were assigned as stress-susceptible or stress-resilient, the susceptible mice exhibiting anxiety-like behavior. RNA from OLGs and myelin from the medial prefrontal cortex of the mice was sequenced, and I compared the lncRNA expression levels between stressed and control mice and stress-susceptible and resilient mice using bioinformatic methods. I also assessed modules formed by lncRNAs and protein coding genes correlating in expression in both datasets. I used RT-qPCR to investigate if results from two differentially expressed lncRNAs, Gm37885 and Neat1, replicate in a stress hormone-treated oligodendrocyte cell line. Three hundred and seventy lncRNAs were differentially expressed between stressed mice and controls or stress-susceptible and resilient mice in the OLG dataset and 132 in the myelin dataset. Two hundred and 87 of them overlapped with a protein coding gene in the OLG and myelin datasets, respectively. Sixty-one percent of the differentially expressed lncRNAs were specific to comparisons in the OLG dataset and 73 % in the myelin dataset, but 39 % of the differentially expressed lncRNAs in the OLG dataset and 27 % in the myelin dataset were shared between them. No module of genes with correlating expression levels was associated with stress, but the expression levels of two correlation modules from each dataset differed between strains. The results for one of the differentially expressed lncRNAs, Gm37885, replicated in stressed Oli-neu cells in RT-qPCR. The results of my thesis indicate that multiple lncRNAs are involved in the mouse stress response, as many were differentially expressed and shared between phenotype comparisons. Additionally, significant gene expression differences were observed between strains, which could contribute to the previously reported strain differences in stress susceptibility. The results also suggest a specific role of Gm37885 in GR-mediated stress response. However, the function of Gm37885 remains unknown, and further studies regarding Gm37885 and the other differentially expressed lncRNAs should be carried out to draw conclusions of their contribution to the OLG-mediated stress response.
  • Ajosenpää, Heikki (2020)
    Maatalousympäristö on muuttunut voimakkaasti ihmistoiminnan vaikutuksesta. Viime vuosikymmeninä on havahduttu monien maatalousympäristönlajien taantumiseen ja uhanalaistumiseen maailmanlaajuisesti. Monimuotoisuus on vähentynyt ja tehostunut maataloustuotanto aiheuttaa monia uhkia peltolinnustolle. Vaikka monia syitä on tunnistettu peltolintujen ahdingon aiheuttajiksi, niin yksittäisten lajien vähenemisen taustalla olevia syitä ei usein tunneta riittävän tarkasti. Elinympäristöjen laadun heikkenemisen ja katoamisen, keinolannoitteiden käytön sekä kasvinsuojeluaineiden tiedetään vähentävän peltolintujen kantoja. Torjunta-aineiden haitallisuus myös muille kuin niiden varsinaisille kohde-eliöille on ollut tiedossa pitkään. Tehoaineista on kehitetty vähemmän myrkyllisiä, mutta niiden kertyminen ja leviäminen pelloilta elinympäristöön ja muihin eliöihin aiheuttaa ongelmia. 1990-luvulla tuhohyönteisten torjuntaan kehitettiin neonikotinoideja, joiden käyttö yleistyi nopeasti maailmanlaajuisesti. Suomessa neonikotinoideja on käytetty pääasiassa siementen käsittelyyn peittaamalla, eli siemenen pinnoittamiseen torjunta-aineella. Neonikotinoidipeittausta on käytetty öljykasveilla ja sokerijuurikkaalla. Ulkomaisissa tutkimuksissa on todettu näiden torjunta-aineiden aiheuttavan haittoja muillekin eliöryhmille kuin torjuttaville tuhohyönteisille. Tuloksia on saatu myös niiden yhteydestä peltolintujen taantumiseen. Suomessa asiaa ei ole tutkittu peltolinnuilla, mutta on todisteita, että neonikotinoideja löytyy linnuista. Linnut ovat hyviä indikaattorilajeja maatalousympäristössä tapahtuville muutoksille. Yksi voimakkaimmin taantuneista lajeista on avoimessa peltomaisemassa ruokaileva ja pesivä peltosirkku Emberiza hortulana. Sen uhanalaisuusluokitus Suomessa on nostettu äärimmäisen uhanalaiseksi, ja sen kanta on pienentynyt myös muualla Euroopassa. Lähitulevaisuudessa sen on ennustettu kuolevan Pohjois-Euroopassa sukupuuttoon, ellei tunnisteta kannankehitykseen vaikuttavia syitä. Tässä tutkimuksessa selvitetään öljykasvien ja sokerijuurikkaan peittauksessa käytettyjen neonikotinoidien yhteyttä peltosirkun kannankehitykseen. Tavoitteena on lisätä tietoa peltolintujen kantoihin vaikuttavista tekijöistä. Aineisto on kerätty peltolintulaskentojen yhteydessä kattavasti peltosirkun esiintymisalueilta eri puolilta Suomea vuosina 2000-2018. Peltosirkkureviirejä havaittiin yhteensä 4430, jotka jaettiin tutkimuksessa neljään maantieteelliseen alueeseen: 1) Pohjanmaa, 2) Etelä-Häme, 3) Lounais-Suomi ja 4) Uusimaa. Paikkatietoaineistossa muodostettiin 277 kpl peltosirkulle ominaista lauluryhmää eli osapopulaatiota, ja tutkittiin lajille tärkeiden elinympäristömuuttujien mahdollisia vaikutuksia lajin reviirimääriin. Elinympäristömuuttujia olivat pienpiirteisten maisemaelementtien määrä (tien-, ojan- ja joenpientareet), viljelykasviryhmien monimuotoisuus, rakennusten määrä, maantieteellinen alue, peltoalan osuus maisematasolla, keväällä kasvipeitteettömän peltoalan osuus sekä edelliskesän lämpötila ja sademäärä. Kiinnostuksen kohteena olivat erityisesti edellisenä kesänä viljeltyjen, neonikotinoideilla peitatuksi olettujen öljykasvien ja sokerijuurikkaan määrät. Näiden tekijöiden vaikutusta peltosirkun reviireihin selvitettiin R-ohjelmiston avulla sovittamalla aineistoon yhdeksän erilaista yleistettyä lineaarista sekamallia. Malleista valittiin neljä parasta, jotka keskiarvoistettiin luonnollisen keskiarvon menetelmällä. Peltosirkun reviirien määrää selittäviksi tekijöiksi saatiin viljelyalan osuus maisemassa, maantieteellinen alue, jokien pituus, lämpötila, vuosi sekä neonikotinoideilla peitattujen kasvien osuus. Mallilla laskettiin ennusteet kolmella eri peitattujen kasvien osuuksilla (matala, keskimääräinen tai korkea) jokaiselle neljälle osa-alueelle. Peitattujen kasvien (öljykasvit ja sokerijuurikas) osuudella ja peltosirkun reviirien määrällä on heikko negatiivinen korrelaatio jokaisella maantieteellisellä osa-alueella. Alueiden reviirimäärät muuttuivat synkronisesti eri peittaustasoilla. Tämän tutkielman tulosten perusteella öljykasvien ja sokerijuurikkaan viljelyllä on heikko yhteys peltosirkun reviirimääriin. Aineiston perusteella ei voi aukottomasti todeta, että syynä olisivat yksinomaan neonikotinoidit. Tiedetään, että ne aiheuttavat peltosirkun kaltaisille lajeille oireita, jotka voisivat selittää huonoa poikastuottoa, tai että yksilöt eivät selviä muuttomatkaltaan. Tulos nostaa esiin saman tärkeän asian, joka on todettu aiemminkin peltosirkun ja monen muun taantuvan lajin kohdalla. Emme tunne lajin käyttäytymistä ja populaatiobiologiaa riittävän hyvin, jotta voisimme nopeilla toimenpiteillä maatalousympäristössä kääntää kannankehityksen suunnan. Peltosirkun pesimämenestykseen liittyviä syitä tulisi tutkia lisää. Torjunta-ainejäämien tutkiminen voisi selittää peltosirkun kohdalla huonoa pesimätulosta. Tällaiselle tutkimukselle olisi tilausta laajemminkin, sillä tietoa kasvinsuojeluaineiden yhteisvaikutuksesta maatalousympäristön eliölajeihin ei ole.
  • Juurinen, Valtteri (2022)
    Opinnäytetyössä tutkittiin olosuhteiden muutosten vaikutusta torjunta-ainepitosuuksiin pilot-mittakaavan sedimenttipylväissä ja suodatinpylväissä. Pilot-mittakaavan pylväissä verrattiin ilmastuksen ja veden virtauksen muutosten vaikutusta pitoisuuksiin. Suodatinpylväissä tarkasteltavina tekijöinä oli orgaanisen aineen ja nollaraudan vaikutus torjunta-ainepitoisuuksiin. Tutkittavina torjunta-aineina olivat atratsiini, simatsiini, heksatsinoni ja diklobeniili, sekä hajoamistuotteet DIA, DEA, DEDIA ja BAM. Kyseisiä torjunta-aineita esiintyy pohjavesissä useissa eri Euroopan maissa mukaan lukien Suomi, vaikka niiden käyttö on lopetettu ja kielletty EU:n alueella useita vuosia sitten. Pylväistä analysoidut ulostulovedet valmisteltiin kaasukromatografia-massaspektrometria (GC-MS) mittausta varten kiinteäfaasiuutolla. Suodatinpylväiden torjunta-aineiden puhdistuskapasiteetti vaihteli testikertojen välillä ja yhdisteet käyttäytyivät eri tavalla suhteessa toisiinsa. Ensimmäisen kuukauden jälkeen talousveden raja-arvo 0,10 µg/l ylittyi heksatsinonin osalta. Toisen kuukauden jälkeen heksatsinonin pitoisuus ylitti jälleen talousveden raja-arvon, niin kuin myös BAM:n. Sitten viimeisellä testikerralla kohonneita yli 0,1 µg/l pitoisuuksia oli atratsiinilla ja heksatsinonilla. BAM:n ja heksatsinonin kulkeutuminen oli odotettavissa yhdisteiden ominaisuuksien perusteella ja niiden hajoaminen on hidasta verrattuna muihin yhdisteisiin. Puolestaan atratsiinin kohonneet pitoisuudet voidaan selittää maaperän kiintoaineksen liikkumisella suodatinpylväästä torjunta-aineiden kanssa. Pelkän hiekan vaikutus suodatinpylväissä aliarvioitiin, mikä vaikutti erityisesti BAM:n ja heksatsinonin pitoisuuksiin.
  • Laakso, Senja (2011)
    In my Master's Thesis I discuss consumption from the perspective of ecological and social sustainability. The environmental space concept is the framework for this study. The environmental space concept was developed in the beginning of the 1990's. It is a space that can be defined with different indicators and within which it is possible to live a decent and socially acceptable life and at the same time consume natural resources in a sustainable way. In this research the upper limit of environmental space is defined as the sustainable level of natural resource use calculated as material footprint and the lower limit as decent minimum reference budgets that illustrate the level of consumption allowing a household to fulfil all basic needs and to participate in society. The material of the study was collected by questionnaires and interviews on the consumption and lifestyle of the participating households. The households interviewed were all single and living on disability pension or basic unemployment allowance. The natural resource consumption of the households was calculated as material footprint. The material footprint is based on the MIPS concept (Material Input per Service Unit) that considers the whole life cycle of products and activities. The participants were also asked to report their income and consumption expenditures. We were also discussing about consumption, the social pressure to consume and use of natural resources. The results show that the low-income households have an average material footprint exceeding the ecologically sustainable level (18 100 kg per year), although the material footprint is lower than average (40 500 kg per year). They also indicate that a sustainable level of resource use cannot be achieved solely by individual choices but the society must improve the changes in the supply of products, services and infrastructure, enabling households to consume in a more sustainable way. The income level of the households remains below the level of the decent minimum reference budgets. The participating households experienced poverty as lack of possibility to consume and recognized the prevailing social pressure to consume. Consuming was characterized by pursuit of status and social comparison between people. The change in prevailing consumer culture is an essential part on the way towards sustainable society, because the amount of consumption grows as long as welfare is measured through consumption. The connection between consumption and natural resource use remained unclear to many of the households and attitudes towards nature alternated between the households. Those households that had been low-income for their whole life, hadn't thought about the sufficiency of natural resources. Their more ecological way of living than average is rather compulsory than their own choice. The rise in their income level would lead to increasing consumption, as households would want to raise their standard of living by moving to a bigger house and travelling. When we notice the limits of the Planet, we should pay more attention to the upper limit of the environmental space to those, who consume the most.
  • Stenberg, Otto (2020)
    Mammalian dentitions exhibit extraordinary diversity in morphology and function. Yet,the mechanisms governing dental development are considered highly conserved across Mammalia. The inhibitory cascade (IC) model is a developmental model explaining variation in molar size proportions observed in mammals. The IC model predicts a range of dental phenotypes based on a dynamic of cumulative inhibition and activation in the sequential development of molars. Whereas most mammals fit these predictions well, bears(Ursidae) are a known exception.Here I employ dental topographic analysis to examine the developmental basis of ursine molar dentitions defying the IC model.I quantified two aspects of tooth shape:molar complexity using orientation patch count (OPC), and tooth size as the area of occlusal surface. As the complexity and size of a tooth mainly emerge based on two different developmental processes –patterning and growth, respectively –these measurements were used to decompose the two phases of tooth development producing the final phenotype. To this end, also an estimate of feature density was calculated.As in previous studies, the molar size proportions of bears were highly incongruent with the IC model. However, complexity along the molar row followed a trend more closely matching the model. Feature density was highest in the third molar. Altogether, these observations suggest an early arrest in the growth of the third molar as the principal cause for bears falling outside the predictions of the IC model –consequently supporting the idea of the inhibitory cascade as a plesiomorphy of Mammalia.As an auxiliary part of this project, I assessed the functionality of Morphoviewer, a new piece of software for measuring complexity. Morphoviewer was successfully applied to infer diet from tooth complexity in a limited sample of carnivorans; and was thus used for all further OPC analyses.
  • Kuure, Senja (2024)
    Vaatetusala on tärkeä hyvinvointia tuottava teollisuudenala. Se on myös hyvin kuormittava ympäristölle. Kiihtyvä kulutus ja vaaralliset työolot ovat osa alan haastetta. Kiertotaloudesta on kaavailtu näihin ongelmiin ratkaisua. Sen tavoitteena on korvata vaatteiden lineaarinen tuotantomalli luonnon kiertokulkuun perustuvalla mallilla sekä mahdollistaa talouskasvun ja luonnonvarojen kulutuksen irtikytkentä lisäämällä samalla hyvinvointia. Kiertotalousprojektia leimaavat heikkoa kestävyyttä peilaavat teknis-taloudelliset ratkaisut eivät yksinään mahdollista riittävää muutosta vaan kulutuskulttuurin haastaminen on välttämätöntä. Tässä tutkielmassa on selvitetty käytäntöteorian keinoin, millaisia kiertotalouteen liittyviä käytäntöjä suomalaisissa pienissä vastuullisissa vaatetusalan yrityksissä toteutetaan. Aineistosta havaittiin kahdeksan eri käytäntöä, jotka liittyivät liiketoiminnan ja tuotannon eri osiin sekä erilaisiin kiertotalouspalveluihin. Kertotalous näyttäytyi vaatetusalalla yritysten näkökulmasta sekä inspiroivana mahdollisuutena että vakavana uhkana yritystoiminnalle. Talouskasvun ja kulutuksen irtikytkennän dilemma oli osoittautunut haastavaksi ratkaista, etenkin innovatiivisen liiketoimintaosaamisen ollessa toistaiseksi yrityksissä puutteellista. Tutkimuskirjallisuuden havaintoja mukaillen kiertotalousliiketoiminta on hyvin haastavaa ja edellyttää vaatetusalalla vallitsevien normien kyseenalaistamista, joka on pienille yrityksille lähes mahdotonta yksin. Muutos voisi mahdollistua, mikäli kuluttajat nousisivat yritysten aktiivisiksi kanssatoimijoiksi, julkisen sektorin tukiessa toimintaa. Toistaiseksi vaatetusala kuitenkin noudattaa perinteistä, lineaarista tuotantomallia ja kiertotalousprojekti sekä sen tavoittelema laajamittainen yhteiskunnallinen muutos on jäämässä utopistiseksi visioksi.
  • Nevanpää, Johanna (2017)
    Different parties such as industry, tourism and research are more and more interested in arctic regions. Tourism is one of the biggest source of livelihood there and growing all the time. Arctic nature is vulnerable and there are indigenous peoples living there. Their way of life is based on natural sources of livelihood such as reindeer breeding. Tourist industry like all the other actions in the region should be socially, economically and environmentally sustainable. So it is important to do research on problems to reconcile different forms of industries and source of livelihoods. The purpose of this thesis is to study possibilities of tourist guidance to solve problems to reconcile reindeer husbandry and tourist industry in municipality of Enontekiö in Finland. It has been noticed in the research of ecotourism that it is possible to influence tourists’ behavior and attitudes by guidance if it is carried out in the right way. This is the reason why my interest is directed to the role of guidance to solve the problems. My research questions are: 1) What kind of problems there are between tourist industry and reindeer husbandry? 2) How is it possible to decrease the harm that tourist industry causes to reindeer husbandry by tourist guidance? 3) How the tourist guidance should be improved? I have done reviews on earlier studies and reports about problems between tourist industry and reindeer husbandry and also about the role of guidance in nature tourism management. Based on these reviews I have proposed a hypothesis how it could be possible to decrease the harm that tourist industry causes to reindeer husbandry by tourist guidance. To test my hypothesis I collected interviews of 15 tourism entrepreneurs and 5 representatives of Metsähallitus. I used the methods of qualitative content analysis to analyze the data. It came out that the biggest problems between tourist industry and reindeer husbandry are disturbance of the peace of pasture, decreasing pasture area, equity in land-use decision-making, and the willingness among the tourism entrepreneurs and reindeer herders to reconcile the source of livelihoods. Tourists do not know much about reindeer husbandry. It is possible to decrease some the harm that tourist industry causes by guidance when it is carried out as recommended in the studies. The role of guidance in decreasing the harms is not very remarkable, because the biggest harms caused by tourist industry are not outcomes of tourists’ thoughtlessness or behavior against rules that could be decreased by guidance. The best education and guidance is given in reindeer farm visits and in guided tours organized by program service companies. The participants of those programs are mainly foreigners even though the majority of tourists in Enontekiö are Finns. Their main source of information is the website of Metsähallitus. The most efficient way to increase tourists’ knowledge would probably be influencing the content of websites of Metsähallitus and marketing of reindeer farm visits and guided tours to Finns.
  • Herranen, Tuulianna (2020)
    Maisterin tutkielma käsittelee uupumuksen yhteyttä oppimisen lähestymistapoihin ja opintomenestykseen. Tutkimus-kohteena ovat bio- ja ympäristötieteellisen tiedekunnan ensimmäisen vuoden opiskelijat vuonna 2018. Tutkimuksen tarkoituksena on hahmottaa uupumuksen, opintomenestyksen ja oppimisen lähestymistapojen välisiä yhteyksiä, sekä muodostaa uupumusprofiileita joiden avulla havaitaan minkälaisia opiskelijoiden joukkoja tiedekunnassamme on. Aineisto on kerätty HowULearn palautejärjestelmän avulla ja tilastolliset testit on tehty SPSS ohjelmalla. Tutkimuksen tuloksena suunnitelmallisella opiskelulla on yhteys hyvään opintomenestykseen, mutta syväsuuntautuneel-la oppimisen lähestymistavalla ei ollut merkitsevää yhteyttä parempaan opintomenestykseen. Pintasuuntautunut op-pimisen lähestymistapa on yhteydessä uupuneisuuteen. Uupumusprofiilit (jotka on toteutettu ANOVA: lla) jakavat vastaajat neljään eri ryhmään. Uupumusprofiilit ovat aiemman tutkimuksen kanssa samankaltaisia, mutta uupuneisuus on bio- ja ympäristötieteellisessä tiedekunnassa yleisempää muihin oppilaitoksiin verrattuna. Uupumusprofiilit eroavat merkitsevästi toisistaan oppimisen lähestymistapojen suhteen. Oppimisympäristö liittyy uupuneisuuteen, sekä oppimisen lähestymistapoihin. Yliopistot, lukiot ja peruskoulut voivat pyrkiä lisäämään opiskelijoiden hyvinvointia suuntaamalla oppimisen lähestymistapoja kohti suunnitelmallisempaa ja syvällisempää oppimista. Pedagogista tutkimusta oppimisen lähestymistapoihin vaikuttamisesta tulisi kuitenkin ensin tehdä enemmän, jotta syy-seuraussuhteet ymmärretään paremmin.
  • Järvinen, Maija (2010)
    The growing interest for sequencing with higher throughput in the last decade has led to the development of new sequencing applications. This thesis concentrates on optimizing DNA library preparation for Illumina Genome Analyzer II sequencer. The library preparation steps that were optimized include fragmentation, PCR purification and quantification. DNA fragmentation was performed with focused sonication in different concentrations and durations. Two column based PCR purification method, gel matrix method and magnetic bead based method were compared. Quantitative PCR and gel electrophoresis in a chip were compared for DNA quantification. The magnetic bead purification was found to be the most efficient and flexible purification method. The fragmentation protocol was changed to produce longer fragments to be compatible with longer sequencing reads. Quantitative PCR correlates better with the cluster number and should thus be considered to be the default quantification method for sequencing. As a result of this study more data have been acquired from sequencing with lower costs and troubleshooting has become easier as qualification steps have been added to the protocol. New sequencing instruments and applications will create a demand for further optimizations in future.
  • Tommila, Jenni (2021)
    Bacteraemia, the presence of bacteria in the bloodstream, may lead to severe and costly health issues. Sepsis, a serious complication of bacteraemia, is one of the top causes of mortality globally. Early and specific diagnostics as well as fast acting are essential in successful treatment. However, current diagnosis relies mainly on time-consuming blood culturing and clinical symptoms, which are unspecific for the causative agent. With the advanced technology and decreasing cost, state-of-art sequencing-based (Next generation sequencing) methods provide a new way to investigate the bacteria present. Metagenomics, which means sequencing and studying all DNA extracted from a microbial community sample, is widely used, but it only describes the genetic potential of a community and does not differentiate live from dead microbes. Metatranscriptomics, in which essentially all RNA from a sample is sequenced, provides information about expression and activity together with identification of viable bacteria, However, the high amounts of host cells and host RNA complicate the detection of bacterial transcripts from complex host-microbe samples. In this thesis, I investigated solutions for the efficient isolation and enrichment of bacterial RNA from whole blood to be used in sequencing and metatranscriptomics analysis. Firstly, I tested the capability of bacterial cell lysis of two commercial blood sampling tubes with Escherichia coli and Staphylococcus epidermidis suspensions. Both tubes, Tempus and RNAgard, were able to lyse gram-negative E. coli cells and good-quality RNA was extracted in measurable quantities with their respective RNA extraction methods. With Tempus tubes the RNA yield was clearly higher. With gram-positive S. epidermidis, RNA quantities from both extractions were below the measurement limits indicating insufficient lysis and need for further optimization. Secondly, I investigated the depletion of polyadenylated (poly-A) transcripts in order to reduce the host transcripts and thus to enrich the bacterial transcripts prior to costly sequencing step. I evaluated the performance of a previously designed in-house protocol, based on the capture of poly-A -transcripts with oligo-dT -beads, and tested different parameters to see whether the depletion efficiency could be enhanced. Most significantly, the amount of oligo-dT -bead suspension was reduced to half from the original protocol. In-house protocols were also compared to a commercial solution, which they clearly outperformed. Depletion performances were tested with a RT-qPCR and dot blot assay, which I designed along this thesis work. Finally, to make the poly-A depletion better suited for blood samples infested with globin transcripts (representing up to 80% of all poly-A transcripts extracted from whole blood), I tested and successfully pipelined the leading commercial method for depleting globin transcripts with the in-house poly-A depletion protocol. The optimized sample preparation protocol provides a platform for further bloodstream infection and sepsis studies. Next steps of the process, such as sequencing and testing with clinical samples, are already ongoing with promising preliminary results. In the future, the metatranscriptomics approach can be utilized in fast and specific identification of the pathogens and their antibiotic susceptibilities. In addition, infection mechanisms and host-pathogen interactions may be studied possibly providing novel insights for sepsis diagnostics and treatment.
  • Talka, Markus (2022)
    Acute leukemia is a life-threatening disease of blood and bone marrow, which is caused by malignant transformation of immature white blood cells. These malignant white blood cells invade space in bone marrow decreasing its ability to produce normal blood cells, eventually leading to death within weeks after the diagnosis without treatment. The acute leukemia can be broadly divided into its lymphoblastic and myeloid form, based on the affected cell lineage. Furthermore, acute leukemias can be classified based on different genomic features, such as gene fusions. Fusion genes are strong drivers in various cancers such as acute leukemias, and they are formed when two or more original genes join together forming a novel hybrid gene. If the novel hybrid gene is transcribed, it can lead to a translation of an abnormal fusion protein with altered function. The detection of the gene fusions is very important, since it affects to diagnosis and treatment of the patient. Various techniques can be used for fusion gene detection, of which the RNA sequencing is the method of choice, due to its ability to provide an unbiased identification of all known and novel gene fusions from the sample in a single experiment. In this thesis, the overarching aim was to develop an optimal sampling protocol for fusion gene detection using RNA sequencing for acute leukemia diagnostics. First, the whole blood samples in EDTA-tubes were collected from acute leukemia patients based on the findings from routine diagnostics. Next, the RNA was extracted at three different timepoints (0h, 8h, and 32h). The samples were stored at 4°C between the extractions. Finally, the RNA sequencing libraries were constructed, and the RNA sequencing was performed. After the sequencing, the data was analyzed using the FusionCatcher algorithm for fusion gene detection and the EdgeR-package for differential expression analysis. The FusionCatcher detected the same gene fusion in all the four fusion gene positive patients compared to routine diagnostics. However, the FusionCatcher failed to recognize the gene fusion in some of the samples with very low number of fusion breakpoint-spanning reads. These reads were visualized with IGV, suggesting that the detection failure resulted from the very low number of break-point-spanning reads. Furthermore, the sample storage did not affect on gene fusion detection. In addition, FusionCatcher detected PIK3AP::BLNK gene fusion from one of the fusion gene negative patients, suggesting a possibility that the patient truly was fusion gene positive. The differential expression analysis revealed changes in gene expression between the different timepoints. The results showed changes in various pathways related for example to cell death and protein biosynthesis, but also to pathways related to cancer. The results showed that prolonged sample storage alters the gene expression profile thus affecting the results of a gene expression study.
  • Kalyanaraman, Shringaa (2024)
    Schizophrenia, a mental disorder affecting over 1% of the world’s population, has a 41-65% chance of being acquired in monozygotic twins, and shows a complex heritable pattern. Research has shown the involvement of various neuronal and glial cell types in the disorder’s progression. Recent studies are focusing on cortical interneurons, as clinical features of schizophrenia such as working memory deficits emerge due to the abnormal activity of these cells . The advent of induced pluripotent stem cell (iPSC) technology has made it easier to study schizophrenia disease mechanisms, with studies revealing differences in morphological and physiological properties of cortical interneurons in patients with schizophrenia. In this thesis , the aim was to optimize iPSC-interneuron differentiation protocol and live-cell imaging method suitable for disease modelling. Interneurons were differentiated from iPSCs with overexpression of inducible transcription factor, Achaete-scute homolog 1 (ASCL1). The iPSCs were derived from twin pairs discordant for schizophrenia and from healthy controls. Expression of interneuron-specific markers was verified using RT-qPCR and validated at the protein level by an immunocytochemistry (ICC) assay in the control cell lines first. Additionally, to estimate the formation of neurites and differences in neurite length and branching, the differentiated interneurons from the controls were subjected to live-cell imaging by IncuCyte S3 live-cell imaging system. Imaging parameters such as cell body cluster filter was optimized to visualize the neurites. To study interneuron involvement in schizophrenia, iPSCs from one twin pair discordant for schizophrenia were successfully differentiated. Interneurons strongly expressed Gamma-aminobutyric acid (GABA) neurotransmitter related neuronal markers: glutamate decarboxylase 67 (GAD67) and GABA at protein level. The neurons were identified as somatostatin (SST) subtype GABAergic neurons by their mRNA and protein expression. While it was possible to observe differences in gene expression, there were no clear differences in the morphology of the differentiated cells as well as the localization of markers in comparison to the healthy controls. Further studies should focus on having a protracted time for differentiation where more mature interneurons can be produced by establishing co-cultures with excitatory neurons. This will help replicate the in vivo cortical machinery which in turn will aid in better understanding of disease mechanisms.
  • Iloglu, Zeynep (2024)
    Alzheimer's disease (AD) is a degenerative brain disorder that exhibits deterioration as one gets older. Although much remains to be learned about the pathophysiology of AD, there is strong evidence links amyloid beta (Aβ) plaques, which are responsible for cognitive impairment, to GABAergic interneurons. Model systems are of prime importance for adequately studying the pathophysiology of this disorder; however, existing in vitro models have limitations in producing patient-specific cells. The development of induced pluripotent stem cell (iPSC) technology has provided a novel opportunity for the effective production of disease-relevant cell types while preserving the molecular traits of the patient. In this thesis, the differentiation protocol established by Nicholas et al. (2013) was used to promote the development of interneurons derived from iPSCs. To enhance the efficiency of differentiation, the protocol was modified with the use of small molecules combined in different ways. The end result of the differentiation was characterized using immunocytochemistry (ICC) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The combination of molecules that produced greater efficiency in differentiation was selected, and the optimized protocol was carried out with iPSCs derived from an AD patient harbouring the APP Swedish mutation. The differentiation of cortical interneurons, demonstrated by the expression of pan-neuronal and specific GABAergic neuronal markers, signifies the successful generation of differentiated interneurons in the context of AD. AD iPSCs upregulated several markers related to AD pathology, such as APP and BACE1. However, the cell lines tolerated the small molecules differently, and thus, the protocol needs more optimization in the future. In summary, iPSC-based differentiation protocols are capable of producing disease-specific cell types that would be helpful in developing accurate AD models for revealing the mechanisms of Aβ pathology.
  • Alitalo, Olga-Sofia (2017)
    Ympäristöön päätyvät orgaaniset yhdisteet ovat maailmanlaajuinen ongelma. Tällaisiin yhdisteisiin kuuluvat muun muassa lääkeaineet, kuluttajakemikaalit sekä muoviteollisuuden raaka-aineet. Nämä yhdisteet päätyvät vesistöihin pääasiallisesti jätevedenpuhdistamoiden epätäydellisten puhdistus prosessien seurauksena ja voivat aiheuttaa vesieliöille haittavaikutuksia jo pieninäkin pitoisuuksina. Lisäksi vesilaitokset käyttävät pintavesiä raakavesilähteinään, joten mahdolliset riskit koskevat myös ihmisiä. Näistä syistä on alettu kiinnittää yhä enemmän huomiota erilaisten haitta-aineiden esiintymiseen vesiympäristössä ja niiden puhdistusmenetelmiin. Yhtenä potentiaalisena menetelmänä pidetään UV-käsittelyä, joka on tehokas desinfiointimenetelmä ja käytössä paitsi juomavedenvalmistuksessa, myös jätevedenpuhdistamoilla, joissa sen avulla saadaan tehokkaasti poistettua koliformiset bakteerit. Kyseisen menetelmän on aiemmissa tutkimuksissa havaittu hajottavan myös orgaanisia yhdisteitä. Tämän pro gradu -työn tavoitteena oli tutkia valittujen orgaanisten yhdisteiden esiintymistä Lahden Ali-Juhakkalan jätevedenpuhdistamon puhdistetussa jätevedessä, niiden vuodenaikaisvaihtelua, sekä kyseisellä puhdistamolla käytössä olevan UV-käsittelylaitoksen tehokkuutta näiden yhdisteiden hajottamisessa. Tutkittavia yhdisteitä olivat lääkeaineista diklofenaakki, ibuprofeeni, naprokseeni ja karbamatsepiini, sekä muoviteollisuuden raaka-aine bisfenoli A ja synteettinen hajuste HHCB. Lisäksi suoritettiin laboratoriokokeita sekä puhdistetulla jätevedellä, että ultrapuhtaalla vedellä kotitalouskäyttöön tarkoitetulla UV-laitteistolla. Työ suoritettiin yhteistyössä MOTREM-projektin kanssa. Näytteitä kerättiin viitenä ajankohtana syksyn 2016 ja kesän 2017 välisenä aikana. Näytteet esikäsiteltiin kiinteäfaasiuuttomenetelmällä ja analysoitiin GC-MS:lla, jolle kehitettiin tässä työssä tutkittaville yhdisteille soveltuva analyysimenetelmä. Lisäksi pyrittiin löytämään diklofenaakin mahdollisia hajoamistuotteita ja nämä näytteet analysoitiin GC-TOF-MS:lla. Puhdistamolta mitatuissa näytteissä yhdisteiden pitoisuudet vaihtelivat välillä 27–1820 ng/l, korkein pitoisuus oli diklofenaakilla, ja korkeimmat pitoisuudet mitattiin helmikuussa. UV-käsittely laski diklofenaakin ja karbamatsepiinin pitoisuuksia kaikkina ajanhetkinä hieman, muiden yhdisteiden kohdalla vastaavaa ei havaittu. Laboratoriokokeista saatujen tulosten perusteella voitiin todeta, että diklofenaakki ja naprokseeni olivat herkkiä UV-säteilytykselle, puhtaassa vedessä diklofenaakista saatiin hajotettua jopa 97 %. UV-lamppukokeilla saatiin myös tietoa diklofenaakin hajoamisesta. Tästä työstä saatujen tulosten perusteella voidaan todeta, että puhdistettu jätevesi sisältää orgaanisia yhdisteitä pieninä pitoisuuksina ja UV-käsittely voisi olla potentiaalinen hajotusmenetelmä joillekin orgaanisille yhdisteille, kuten lääkeaineille. Veden uudelleenkäyttömahdollisuuksia on tulevaisuudessa pohdittava entistä tarkemmin ja tällaisten puhdistusmenetelmien kehittäminen on tärkeää.
  • Elolahti, Auli (2020)
    Previous studies have shown that involving citizens, especially young people, in environmental decision making, increases the ability to participate in environmental action (e.g. Riemer et al. 2014, Paloniemi and Koskinen 2005). There have been various school and after school projects to promote the engagement of young people in societal environmental action. Many youth engagement projects in the third sector have succeeded in achieving positive results in promoting environmental citizenship. This thesis evaluates the involvement of young people and young adults in environmental action at WWF Finland. The theoretical framework of this thesis is based on the model by Paloniemi and Koskinen (2005) of environmental policy action as a social learning process. According to the model, positive experiences of involvement can strengthen environmental action competence and encourage participants to take environmentally responsible action. In the spiral model, the context is taken into account in the results. The data for this thesis is from a survey of 30 young people at WWF, who took part in the project. The survey mapped the effects of the project on the participants' self-empowerment, social empowerment, and environmental citizenship. It also examined skills in environmental action, and the effects of the context on the results. These results were processed using a mix of qualitative content analysis and statistical analysis methods. In the content analysis, the open-question-answers were themed. The differences between numerical answers of those who suspended the project, and those who were involved until the end were compared, for example using a T-test. In addition, narrative inquiry was developed based on the answers to describe comprehensive profile of respondents. There were no statistically significant differences between those who discontinued the project and those who participated until the end. However, the content analysis of the study provided evidence that the activities succeeded to empower participants and strengthen their environmental citizenship and environmental action competence. According to the results, 26 out of 30 respondents received more information about environmental problems, and 24 received information about their own opportunities on environmentally responsible action. Almost everyone also learned other skills that support environmental citizenship. The project had a positive effect on self-empowerment and social empowerment for 21 respondents. More than half of the respondents also reported an increase in societal engagement, or encouragement to work in the field of environmental or sustainable development. The results of this thesis conclude that the context of WWF’s project was overall successful, as the desired results were achieved. Motivating and engaging factors that contributed to the goals of the operation were also identified. The results of the thesis are in line with previous research, which indicates that environmental participation in the third sector plays an important role in promoting environmental citizenship. However, more long-term research on the topic is needed, as well as research with different control groups.
  • Nyroos, Erik (2020)
    Participatory budgeting is one of the major democratic innovations of the recent decades. This participatory method from Brazil has been started to actively utilize in Finnish municipalities during 2010s. The basic idea of this methodology is that citizens can together decide how to use public assets. The goal of this thesis is to understand how participatory budgeting can have an impact on ecological sustainability in Finland. I’m focusing on the proposals of participatory budgeting which the citizens have voted for to be implemented. Research material has been collected from public online sources on all the Finnish participatory budgeting projects. Some of these projects have been excluded as they do not fulfill the characteristics of participatory budgeting. The material is analyzed using content analysis, building categories, themes and types. There are three key findings in this thesis. First, participatory budgeting has created ecologically sustainable solutions, but sustainability has been an unintended by-product. Proposals concerning environment focus primarily on people’s living environment. Second, the changes are minor, and individuals are the ones carrying the responsibility for the sustainability. Third, the means how proposals are carried out influences ecological sustainability. Here, municipal authorities have a significant role. Finnish participatory budgeting projects therefore have the chance to create ecologically sustainable proposals. However, the capability is limited by both small, project specific budgets and processes that do not acknowledge ecological sustainability. In the long run, the changes might be more significant as participatory budgeting still is relatively new method in Finnish society.
  • Shah, Saundarya (2019)
    Tiivistelmä – Referat – Abstract OCRL1 is a phosphatase that cleaves phosphatidylinositol 4,5-bisphosphate (PI4,5P) to phosphatidylinositol-4-phosphate (PI4P). ORP4 is a lipid binding/transport protein implicated in G-protein coupled signaling, cellular calcium homeostasis, proliferation and viability. OCRL1 and ORP4 are found in the endoplasmic reticulum and membrane contact sites throughout the endosomal system and the Golgi complex. OCRL1 is also present in the plasma membrane and vesicular structures. ORP4 has high affinity for binding sterols through the OSBP related domain (ORD). ORP4 also interacts with vimentin intermediate filaments via the ORD and influences the localization and organization of vimentin. The membrane lipid phosphatidylinositol (PI) can be phosphorylated either singly or in combination at three different positions on its inositol ring (D-3, D-4, and D-5)—yielding 8 possible phosphoinositides; the interconversion between the species is regulated by kinases and phosphatases that either add or remove phosphate groups from the various positions on the ring. Phosphoinositide metabolism is heavily involved in signal transduction pathways and cytoskeletal organization. Interestingly, it has also been found to be spatially regulated with distinct phosphoinositides being enriched in particular membrane compartments. BiFC assays can provide an important tool for visualizing protein-protein interactions. Not only is BiFC able to determine protein-protein proximity but it is also able to localize the interaction with regard to compartment membranes and structures. This study examined the interaction of ORP4 with OCRL1 by using BiFC analysis. We were able to determine that the protein pair seems to be in close proximity in the endoplasmic reticulum near the Golgi. Interaction only took place when the OCRL1 was tagged with VB at the C-terminal.
  • Hietamies, Tanja (2005)
    Otsoni (O3) on ilmakehässä sekä elintärkeä että haitallinen ihmisille, eläimille ja kasvillisuudelle. Yläilmakehässä eli stratosfäärissä (15-50 km korkeudessa) otsoni estää vahingollisen UV-säteilyn pääsyä maanpinnalle. Alailmakehässä eli troposfäärissä (alle 15 km korkeudessa) otsoni on puolestaan kasvihuonekaasu sekä aiheuttaa ihmisille ja eläimille mm. hengitysteiden ärsytystä ja kasvillisuudelle vaurioita. Otsonin on todettu koeolosuhteissa aiheuttavan kasveille lehti- ja neulasvaurioita sekä vähentävän niiden fotosynteesiä ja kasvua. Myös luonnonkasveista on löydetty otsonivaurioita mm. Puolassa, Ukrainassa ja Sveitsissä. Erityisesti lämpimät ja aurinkoiset ajanjaksot lisäävät otsonivaurioita. Alailmakehän otsonipitoisuus on ihmistoiminnan vaikutuksesta noussut viimeisen sadan vuoden aikana kaksinkertaiseksi. Pohjoisella pallonpuoliskolla vuosittainen otsonipitoisuuden kasvu on viimeisen 30 vuoden aikana ollut noin 0.5-2.0 %. Otsonia ei sellaisenaan pääse ilmakehään, vaan se muodostuu ilmakehässä fotokemiallisissa reaktioissa hapesta, typen oksideista ja hiilivedyistä auringon säteilyenergian avulla. Typen oksideja ja hiilivetyjä pääsee ilmakehään lähinnä liikenteestä ja petrokemian teollisuudesta. Tässä Pro gradu -tutkielmassa tutkittiin kesällä 2002 sveitsiläisiltä LESS-aloilta (light exposed sampling site) kerättyjä pyökin (Fagus sylvatica), saarnen (Fraxinus excelsior), villaheisin (Viburnum lantana) ja kuusaman (Lonicera xylosteum) lehtinäytteitä. Alat kuuluvat kansainväliseen metsien kuntoa kartoittavaan yhteistyöhankkeeseen (IPC-forest). Aloilta oli käytettävissä otsonipitoisuus ja sademäärätiedot. Lehdistä mitattiin näkyvien vaurioiden määrä, ilmarakotiheys, huulisolupituus, lehden paksuus sekä lehden poikkileikkauksen soluja soluvälimäärät. Tutkimuksen lajeista ilman näkyviä otsonivaurioita oli säästynyt vain pyökki. Osassa saarnen ja villaheisin lehtiä oli erittäin paljon näkyviä vaurioita (51-100%). Otsonipitoisuus korreloi tilastollisesti merkittävästi (p < 0.05) vain saarnen ilmarakotiheys/huulisolupituus-suhteen kanssa, tämä oli negatiivinen korrelaatio. Suuntaa-antavia korrelaatioita otsonipitoisuudella oli useiden lehtiparametrien kanssa. Sademäärän korreloi tilastollisesti merkittävästi negatiivisesti saarnen pylväs-/hohkatylppysuhteen kanssa ja positiivisesti pyökin pylvästylpyn osuuden kanssa. Suuntaa-antavia korrelaatioita oli myös sademäärän ja lehtiparametrien välillä useita. Näkyvät vauriot korreloivat villaheisillä negatiivisesti ilmarakotiheyden kanssa. Otsonin haitallisuus ehkä vähenee sen levittyessä lehteen tasaisemmin. Tämä tutkimus vahvistaa aiempia tutkimustuloksia siitä, että Sveitsissä puusto kärsii luonnossa vallitsevista alailmakehän otsonipitoisuuksista. Koska merkit kasvillisuuden otsonivaurioista ovat selvät, täytyisi otsonipitoisuudet saada laskemaan. Kasvien vaurioitumiseen vaikuttavat monet ympäristötekijät ja eri lajien (myös yksilöiden) otsoniherkkyys vaihtelee. Tämä tulisi huomioida otsonipitoisuuden raja-arvoja tarkennettaessa. Otsonin vaikutusten tutkimus on painottunut ihmisille taloudellisesti arvokkaisiin lajeihin. Myös muita lajeja ja luontotyyppejä tulisi tutkia enemmän
  • Leinonen, Saija (2023)
    The sense of hearing is dependent on the sensory cells of the cochlea: inner and outer hair cells. The critical functional structure of these cells is the stereocilia bundle, the mechanotransduction (MET) organelle. The outer hair cells (OHCs) are highly vulnerable to environmental assaults, the effects of aging, and gene mutations. This vulnerability is thought to be mediated by challenges in maintaining intracellular calcium homeostasis. Endoplasmic reticulum (ER) stress is a form of cellular stress that was previously shown to cause hair cell impairment. A possibility is that this impairment is mediated by perturbations in calcium homeostasis. In this thesis, the aim was to find out how the OHC calcium homeostasis is affected by specific ER stress-inducing mutations and age in mouse models exhibiting progressive hearing loss. I studied OHC calcium homeostasis in Manf conditional knock-out (cKO) mice under C57BL/6 (B6) strain in which ER homeostasis-promoting protein MANF (Mesencephalic Astrocyte-derived Neurotrophic Factor) is depleted in cochlear hair cells. Previous studies have shown that these mice develop progressive hearing loss that includes OHC loss and prominent stereocilia pathology, stereocilia fusion. By itself, the B6 mouse strain is a model of age-related hearing loss due to a Cdh23 missense mutation that is known to cause progressive hearing loss and, according to earlier evidence, may be a source of ER stress. I studied B6 mice at 6–9 months of age and Manf cKO mice at 2 months of age to comparatively examine changes to OHC calcium homeostasis that may correlate with the changes in the stereocilia bundle morphology and with hearing loss. I studied hearing function by auditory brainstem recordings in vivo. I estimated the functionality of MET channels in OHCs by FM1-43 uptake. I used immunofluorescence microscopy to study subcellular expression of key calcium-buffering and calcium-extrusion proteins in OHCs. I used a novel super-resolution imaging technique, expansion microscopy (ExM), to study stereocilia bundle morphology. OHCs of Manf cKO mice showed changes in calcium homeostasis in all the studied aspects: (1) FM1-43 uptake through MET channels was reduced, (2) the expression of the calcium extrusion pump PMCA2 and its obligate partner, the cell adhesion protein neuroplastin, was decreased, (3) and the expression of calcium-buffering protein oncomodulin was increased. All this data indicated OHC calcium dyshomeostasis. These molecular changes were consistent with the hair bundle pathology—stereocilia fusion—revealed by phalloidin staining of the actin-rich core of the stereocilia followed by ExM imaging. OHCs of 6–9-month-old B6 mice exhibited reduced FM1-43 uptake, yet not to the extent seen in cKO mice, and there were no changes in PMCA2 and neuroplastin expression and no prominent stereocilia fusion. Together, I show in this study that OHC hair bundle dysmorphology is linked with changes in calcium homeostasis in the mouse model of ER stress-induced hearing loss. This is consistent with the fact that calcium dyshomeostasis is an integral part of cellular ER stress. An intriguing, yet unanswered question is whether these changes in stereocilia bundle physiology could actually be the trigger for the death of these sensory cells.
  • Joukainen, Nella (2022)
    Continuous development of urban areas poses challenges for sustainable use of resources and the management of complex waste streams. Recycling is seen as a solution for promoting sustainability, especially at the individual-level where waste sorting creates preconditions for successful material recovery operations. Behavior change strategies aim to encourage individuals to implement recycling practices in their daily lives. The effectiveness of behavior change strategies is achieved by broadly influencing capability, opportunity, and motivation to recycle, however, studies claim that many existing strategies are unable to do so. This study aims to gain an understanding in how extensively a municipal recycling service provider’s online communication on social media platforms (Instagram, Facebook, YouTube) enhances capability, opportunity, and motivation to recycle by communicating about means to overcome recycling barriers. Specifically, the study is interested in examining what types of recycling barriers are addressed in online communication and through which means it aims to deliver assistance for overcoming these barriers. Lastly, this study aims to explore the role of social media platform-based online communication as a channel to promote individual recycling behavior. This study focuses on social media materials published by a municipal service provider in the European Green Capital of 2021. The empirical material builds on a set of data collected from public and locatable online sources. The analysis includes 96 different types (pictural, textual, video) of recycling-themed online content. The data was analyzed by conducting qualitative content analysis. The results indicated that online communication addresses a broad range of recycling barriers. The most common means to overcome these was information provision through which the company aimed to increase knowledge and understanding of recycling practices. Although information provision alone is claimed to be insufficient to profoundly change behavior, results showed that it could serve as a means to generate a broad influence on areas behind behavior formation. The result of this study suggests that social media platforms as channels for online communication have the potential to create preconditions for overcoming recycling barriers especially through the means of information provision. The development of more profound recycling behavior, however, needs to include a broader range of collaborative information, motivation, and engagement elements that could engage and encourage people to implement more profound recycling behavior. This calls for future research that discovers means to stimulate behavior formation widely to support overcoming recycling barriers and the implementation of profound recycling behavior in everyday lives.