Skip to main content
Login | Suomeksi | På svenska | In English

Browsing by Title

Sort by: Order: Results:

  • Sartamo, Laura (2017)
    Baltic Sea has undergone major changes in the last few decades and its ecological condition has changed. Paleolimnology provides methods to detect changes in the past, mostly from the times when no surveillance was conducted. This Master's thesis is about the response of a common Cladocera, Eubosmina maritima to the past environmental change in Sandöfjärden, Gulf of Finland. I studied past isotopes, δ13C and δ15N to detect past changes in the eutrophic changes from sedimented subfossil remains to detect how the E. maritima population abundance and morphology have changed due to eutrophication and increased predation pressure. I analyzed a 30 cm sediment core of which I counted E. maritima remains. I also measured the lengths of carapaces, mucros and antennules in order to detect changes in their morphology. I used carbon nitrogen ratio, total carbon, total nitrogen, and their stable status of the sea area. To indicate predation pressure on E. maritima, I used the resting egg data of a predatory cladocera Cercopagis pengoi, that was introduced to the area at the beginning of the 1990's. The sediment core is stratigraphic, meaning that the layers are connected to each other and therefore cannot be treated as independent samples. The data was first viewed graphically to reveal correlations. I applied redundancy analysis (RDA) to find out if changes in the Eubosmina-populations are explained by the environmental changes. Associated is Monte Carlo permutation test to check which explanatory variables are the most important. Finally I performed variance partitioning to separate the effects of the environment caused by time in the sediment time series. My results show that E. maritima population has increased in number since the 1950's and a positive correlation with δ15N suggests that this has a connection to increased nutrient levels. It also seems that big E. maritima individuals became more common in eutrophic conditions. Increased predation pressure affected E. maritima populations the strongest right after C. pengoi was introduced to the area when also the longest mucros were found. There also was a slight decrease in the E. maritima abundance at that time. The changes of the lengths of the appendages seem to be more connected to predation pressure, whereas the abundance and the overall body size seem to have a connection with eutrophication. Along with the eutrophication increased the number of E. maritima in the Gulf of Finland. The effect of predation pressure was the clearest right after the introduction and then later smoothened.
  • Avila Pulido, Alan (2020)
    Psychrotrophic lactic acid bacteria (LAB) play a versatile role in research, food, farming and medicinal applications, but also play a role as a source of food spoilage. The effects of temperature changes has yet to be studied in depth. In this study, to analyze in a transcriptome level, cold and heat shock stress to spoilage lactic acid bacteria, a time-dependent RNA-seq for Lactococcus piscium with a temperature of 0 °C and 28 °C was conducted. The data of protein regulation during the experiment shows that Lactococcus piscium has the essential machinery to survive against different types of environmental stress. I observed known heat shock related genes and stress related genes to be present in the regulated response of both temperature extremes. Cold shock upregulation is observed after 35 minutes, which could indicate that the metabolic response at cold temperatures is related to growth rate. With a clear downregulation of pathways of energy consumption and an adaptation in terms of RNA being more prominent that at 28 ºC. Certain surface, cell wall and transport proteins are noticeable more upregulated at 0 ºC in addition to a downregulation of energy related proteins, which in correlation with its growth curve, we can assume it is part of a mechanism of protection against cold environments, in comparison with the regulation of proteins at 28 ºC. This gives an insight of a well controlled preservation mechanism that Lactococcus piscium exhibits that can be linked to its environment. The findings of this research offer new understandings into the survival skills of Lactococcus piscium to a cold and heat shock. Future studies should focus on analyzing the regulation and function of possible new genes for the response to heat stress, as well as the specific function of proteins related to temperature stress in the events where change of temperature plays a constant role in the environment.
  • Ikonen, Ina Kristiina (2023)
    Biallelic germline mutations in ERCC6L2 cause bone marrow failure (BMF) and predisposition to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The patients often develop varying cytopenias, and underlying hypoplasia in the bone marrow is usually evident. The aim of this thesis was to characterize the transcriptome of patient -derived fibroblasts with biallelic germline ERCC6L2 mutation. Moreover, the aim was to study changes on the gene expression at the RNA level in fibroblasts in different media conditions, ROS levels in ERCC6L2 -mutated fibroblasts, and whether addition of glutamine impacts the ROS levels. Fibroblasts from 16 skin biopsies were cultured; eight samples were from healthy controls and eight samples from patients with known mutations in ERCC6L2. Fibroblasts were cultured in different media conditions, followed by RNA extraction and RNA sequencing. We observed downregulation in base excision repair, nucleotide excision repair, mismatch repair, DNA replication, homologous recombination, and cell cycle in ERCC6L2 -mutated cells. MAPK signaling pathway, p53 signaling pathway, apoptosis, AMPK signaling pathway, and TGF-beta signaling pathway were in turn upregulated in ERCC6L2 -mutated cells. The medium did not affect the gene expression significantly across samples. We suspect that the effect of medium was not detected at the RNA level, but it might affect post-translational modifications. We also detected increased ROS levels in ERCC6L2 samples compared to control and observed decreased ROS levels in ERCC6L2 and control samples with excess glutamine. This study shows that biallelic mutations in ERCC6L2 do not only affect the bone marrow but can also affect tissues outside of the hematopoietic system. The transcriptomic analysis identified important biological processes, which could be studied with more detail in the future to further explore the pathology of the ERCC6L2 disease.
  • Prajapati, Biplu (2021)
    Transfer RNA (tRNA) is one of the most extensively modified RNA molecules. The role of tRNA modifications become apparent during physiological condition such as oxidative stress, where it serves as an adaptive response to the changing environment. These modifications are upregulated mainly at the wobble position of the tRNA to enhance the translational efficiency of the stress response genes through enhanced decoding rate and tRNA–mRNA interaction. Hence, tRNA modification has a crucial role in regulating translational fidelity, and such modifications can be utilized to fine-tune the translation for improved production of heterologous protein. Therefore, this study aimed to analyze the tRNA modification changes in two laboratory-significant E. coli strains (BL21 (DE3) and K12) during oxidative stress and utilize these modifications to enhance the production of heterologous protein using a defined cell-free protein synthesis system. Ultra-performance liquid chromatography-mass spectrometry was used to detect and quantify the tRNA modification changes in the hydrogen peroxide-treated E. coli cells. The results showed unique tRNA modification patterns and intensities between the two bacterial strains in response to oxidative stress. Modifications such as ac4c and m2,2G were upregulated in E. coli BL21 (DE3) following hydrogen peroxide treatment, whereas k2C and chm5U were increased in E. coli K12. Further analysis of the dataset revealed that most of the upregulated ribonucleoside modifications were predominant at the anticodon loop of the tRNAs, indicating the potentiality of these tRNA pools to impact on translation. Likewise, I optimized an E. coli-based cell-free protein synthesis system to investigate the effect of modified tRNA pools on translation. Hence, this study serves as a stepping stone to understand the tRNA modification landscape of E. coli and provides a platform to depict the function of post-transcriptional tRNA modifications in translation with the CFPS system.
  • Pousi, Suvi Päivikki (2015)
    Neurotrophic factors are essential for the development of the central nervous system. By signalling through Trk receptors, they have multiple effects on for example the survival of neurons, growth of axons and dendrites and stability of synapses. BDNF, which signals through TrkB receptor, is a neurotrophic factor with an important role in the formation and stabilization of glutamatergic synapses. It is also known to be released in an activity dependent manner. The mechanisms by which BDNF and TrkB signalling regulate synaptic transmission depend on the type and developmental stage of the synapse, and they are not well known. The electrical activity of immature networks consists of intrinsic activity with intermittent bursts of synchronous activity, which is believed to fine tune the synaptic connectivity through Hebbian plasticity mechanisms, which are stabilized by homeostatic mechanisms. Homeostatic regulation can be especially important during the development of the neural network while the glutamatergic transmisson is very labile. Little is known of the signalling routes that participate in the homeostatic plasticity during the development of the neural network. The aim of the thesis was to investigate how the long-term inhibition of TrkB signalling affects the glutamatergic transmission and the homeostatic regulation in area CA3 of neonatal hippocampus by using gene manipulated TrkBF616A mouse strain. The TrkB receptors in the TrkBF616A strain are modified so that they can be blocked with a kinase inhibitor (1NMPP1). In part of the work C57BL/6 -mice were used as control. In addition to the acute measurements the hippocampal slices were incubated in control conditions and with inhibitory drugs (TTX and 1NMPP1) for 15 to 20 hours, after which miniature excitatory postsynaptic currents (mEPSCs) were recorded with whole-cell patch clamp from area CA3 pyramidal cells. The research shows that continuous TrkB signalling is essential for the maintenance of AMPA receptor mediated synaptic transmission in CA3 area of neonatal hippocampus in TrkBF616A mice. Long-term inhibition of TrkB signalling decreases the amplitude of mEPSCs. TrkB-signalling seems to be needed also for the homeostatic response caused by network activity deprivation. The results also indicate that the inhibition of TrkB signalling increases the frequency of mEPSCs, possibly by a homeostatic mechanism. However, the results also show that the TrkBF616A mice strain might differ from wild type mice and the kinase inhibitor 1NMPP1 might have non-specific effects that are not currently known, so more extensive research on the matter is still needed to confirm the results.
  • Kangas, Anna (2022)
    Aims and methods: Global plastic production is increasing annually and microplastics (MPs, particles of <5 mm in size) have been reported in the environment worldwide. In aquatic systems plastic pollution is present especially in coastal habitats, and MPs can concentrate within littoral zone vegetation. Numerous marine animals are known to be able to ingest MPs, and plastics can also have adverse effects on the health and behaviour of the exposed animals. This Master’s thesis examined trophic transfer of MPs in a Baltic Sea littoral food chain. Laboratory experiments with 10 µm fluorescence microspheres were conducted to study trophic transfer between food chains of different lengths. The longest food chain had three trophic levels: zooplankton, chameleon shrimp (Praunus flexuosus) and rockpool prawn (Palaemon elegans). Also, the gut passage time of rockpool prawn was experimentally studied. The digestive tracts of the studied animals were analysed for MPs under an epifluorescence microscope. Results: The results show that trophic transfer may be an important pathway of microplastic exposure for animals at higher trophic levels. The number of ingested microspheres in both chameleon shrimp and rockpool prawn was higher when the animals were exposed through pre-exposed prey in comparison to direct exposure from the water. In addition, the prawns ingested more MPs in the experiment with three trophic levels than in the two-level experiment. The results support earlier findings, that the feeding mode affects the microplastic exposure of animals. There were no clear results from the gut passage time experiment.
  • Järvi, Jani (2018)
    Riisi (Oryza sativa) on yksi maailman viljellyimmistä ravintokasveista. Siltä tunnetaan maailmanlaajuisesti 20 merkittävää tuhohyönteistä, joista monet ovat yöllä lentäviä perhosia ja jotka runsaina esiintyessään voivat aiheuttaa huomattavia satotappioita riisinviljelijöille. Tässä tutkielmassa selvitettiin, mitkä riisin tuholaisperhoslajit ovat runsaimpia Kaakkois-Madagaskarin runsastuottoisilla märillä ja pengerretyillä riisipelloilla ja mitkä ympäristömuuttujat vaikuttavat näiden runsaimpien lajien esiintymiseen. Aiemmissa maaseutuelinympäristöjen tutkimuksissa on havaittu, että maanviljelyn tehostuminen ja sen aiheuttama luontaisten elinympäristöjen häviäminen saattaa johtaa tuholaisten runsastumiseen. Kaakkois-Madagaskarin sademetsävyöhykkeellä metsien väheneminen lisääntyneen maanviljelyn takia on viime vuosikymmeninä ollut huomattavaa voimakkaan väestönkasvun seurauksena. Tutkimus suoritettiin kenttäkokeina Kaakkois-Madagaskarilla Ranomafanan kansallispuiston läheisyydessä vuoden 2015 marras- joulukuussa. Perhosia kerättiin vetisiltä riisipelloilta kolmella valopyydyksellä kolmen yön ajan kahdeksassa, maisemarakenteeltaan erilaisessa kylässä. Pyyntijaksojen aikana mitattiin ja kerättiin tietoa pyyntiöiden sääolosuhteista. Tutkimusalueelta aiemmin tehdyn maanpeiteluokituksen avulla tarkasteltiin maisemamuuttujien vaihtelua pyyntipaikkojen läheisyydessä. Pyydyksillä kerätyt hyönteiset säilöttiin ja tuotiin Suomeen lajintunnistusta varten. Suomessa peltojen runsaslukuisimpien perhosten lajit ja sukupuolet määritettiin ulkoisten tuntomerkkien, lisääntymiselinten ja DNA-viivakoodauksen avulla. Tulosten perusteella Parapoynx-suvun (Crambidae) lajit, tunnettu riisituholainen Parapoynx stagnalis ja P. fluctuosalis, jonka tuholaisstatus vaihtelee kirjallisuuslähteistä riippuen, olivat selvästi tutkimusalueen riisipeltojen runsaimpia perhosia. Kaikkein runsain oli P. fluctuosalis -lajin tumma värimuoto. Aiempien tutkimusten mukaisesti tarkasteltavien yöperhosten runsauteen vaikuttivat ympäristömuuttujista eniten säätekijät ja maisematekijöiden vaikutus oli lähinnä suuntaa antavaa. Säätekijöistä lämmin ja kuiva sää lisäsivät perhosten määriä, kun taas pyyntiyöllä loistanut täysikuu vähensi pyyntisaalista huomattavasti. Maisematekijöistä ainoastaan riisipeltojen suuri määrä pyydyspaikan läheisyydessä lisäsi merkitsevästi vain P. fluctuosalis -lajin raidallisen värimuodon runsauksia. Lajimääritysten yhteydessä tarkasteltu tutkimuslajien sukupuolijakauma oli poikkeuksellinen: naarasperhoset olivat merkitsevästi runsaampia kuin koiraat. Tulos oli vastoin aiempia tutkimuksia, joiden mukaan valopyynti houkuttelee yleensä enemmän koiras- kuin naaraperhosia. Naaraiden runsautta suosi todennäköisesti lyhyt yökohtainen pyyntiaika, joka oli vain neljä tuntia auringonlaskusta eteenpäin. Parapoynx fluctuosalis -lajin eri värimuotojen morfologinen ja geneettinen tarkastelu varmistivat todennäköisesti ensimmäistä kertaa, että värimuodot edustavatkin kahta eri lajia, eivätkä saman lajin eri värimuotoja. Tutkielman tulokset kyseenalaistavat nykykäsityksen Parapoynx-lajien taksonomiasta. Tutkielman tulokset osoittavat ensimmäistä kertaa, että Ranomafanan kansallispuiston alueella, Kaakkois-Madagaskarilla esiintyy tunnettuja riisin tuholaisperhosia. Tulokset eivät kerro tuholaisten aiheuttamista mahdollisista satovaikutuksista, mutta vaikutukset ovat oletettavia siellä missä lajeja esiintyy. Tuholaisten tunnistamisen ja niiden alueellisen kartoittamisen sanotaan kuitenkin olevan ensimmäinen askel, jotta niiden mahdollisesti aiheuttamia haittoja pystytään myös torjumaan ja ennustamaan. Riisin tuholaisperhosten kartoittaminen tutkimusalueella on myös tärkeää, jotta paikalliset riisinviljelijät ymmärtäisivät luontaisten elinympäristöjen tärkeyden niiden torjunnassa. Tutkimukset ovat nimittäin useaan otteeseen osoittaneet, että viljapeltojen ympäristöjen eliöt ovat tärkeässä roolissa tuholaisten biologisen torjunnan suhteen. Aihetta jatkotutkimalla olisi ehkä mahdollista löytää yhteys alueen metsien häviämisen ja tuhohyönteisten määrien suhteen, mikä auttaisi paikallisia maanviljelijöitä ymmärtämään luonnontilaisten elinympäristöjen tärkeyttä myös heidän elantonsa osalta. Tutkimuksen tuottama massiivinen, Luonnontieteellisen keskusmuseon Luomuksen kokoelmiin tallennettava hyönteisaineisto antaa joka tapauksessa mahdollisuuksia moniin lisäselvityksiin. Aineisto sisältää valtavan määrän hyönteisiä, joiden biologiasta, taksonomiasta ja esiintyvyydestä ei tiedetä välttämättä mitään.
  • Feodoroff, Michaela (2020)
    Within the field of cancer immunotherapy, immune checkpoint inhibitors have been a revolution since they provoke re-activation of T-cell immune responses towards cancer. Despite their success, they only work in 13% of the patients because of a poorly immunogenic tumor, mostly due to weak T-cell infiltration. Oncolytic viruses have shown the ability to work in synergy with checkpoint inhibitors because of their tumour-specific tropism, innate immunogenicity and ability to secrete immunostimulatory agents into the tumor microenvironment. Regardless of the great potential, we lack suitable pre-clinical models to test this effect. In this study we developed renal cell carcinoma-derived organoids as in vitro platforms due to their high pre-clinical predictability compared to that of murine and in vitro 2-dimensional cell culture models. To test the ability of oncolytic viruses to stimulate the immune system, we generated three cytokine-expressing (CXCL9, CXCL10 and IL-15) oncolytic adenoviruses using a novel cloning method that we developed. We have shown that these viruses successfully produce high amount of the cytokine and attract peripheral blood mononuclear cells freshly isolated from Buffy coats. Genetically modified oncolytic adenoviruses were also shown to infect and kill human renal cell carcinoma organoids. Together, our results demonstrate the potential of organoids as test platforms for oncolytic virus -based therapy and the importance of adequate cytokine expression in T-cell recruitment. The tumor organoid platform we developed will be useful for advancing patient-specific treatment strategies and serve as a base for innovative immunotherapy models.
  • Niittynen, Taru (2022)
    Domesticated horses have been used for various tasks over their thousands of years of shared history with humans. To be able to perform these tasks every horse needs to learn the needed skills, and this requires systematic training. Training of adult horses has been studied for a long time and comparisons between the efficacy of different training methods have been done. There have also been some studies comparing how much and when young foals need to be handled for them to grow into easily trainable adults. From adult horses it is known that emotional state affects cognitive processes and with that also their learning efficiency and speed. The early stages of training young horses have not been studied very well. There is no clear picture about how young horses feel during training and how that affects their learning. In my thesis I studied young horses’ emotional states while learning new tasks and how that affects their learning. I followed the early training of 19 young horses (11 one-year-olds and 8 two- and three-year-olds) by videotaping five training sessions and collecting saliva samples before and after three of those sessions to analyse cortisol and oxytocin. From the videos I analysed how fast horses responded to trainer’s asks and how unfocused they were. From the hormone samples I measure the change in cortisol and oxytocin levels during training. Salivary cortisol has been widely used to measure acute stress. Oxytocin on the other hand is a newer indicator for positive emotions. To the best of my knowledge salivary oxytocin has never been used in horses. My data showed that the horses learned the required tasks: they became quicker at their responses and focused better during the course of training. Because my data was quite small and individual variation in the hormone levels was high, the results might have been affected by these factors. Linear mixed effect models showed that higher oxytocin levels before training session predicted quicker responses during training and lower levels after training predicted lower focusedness. Bigger increase in cortisol levels during training compared to the before level explained quicker responses and better focusedness, but higher levels before training resulted to lower focusedness and slower responses. This is in line with previous studies of adult horses, that showed that horses in a better emotional state and with less stress learn faster and are more interested in working with humans. This shows that it is important to not only focus on physical wellbeing but also mental wellbeing from early on in horses’ life.
  • Lilleberg, Tuomas (2015)
    Suoturpeen energiankäyttö kattaa n. 7 prosenttia Suomen energiantuotannosta. Tätä käytetään erityisesti talojen lämmitykseen kaupungeissa. Turpeenpoltto tuottaa kuitenkin runsaasti hiilidioksidia, kattaen n. 20 % koko energiasektorin hiilipäästöistä. Tämä taas kiihdyttää ilmastonmuutosta, joka tekee turpeenpoltosta kansainvälisen asian. Suomi on osana YK:n ilmastosopimusta sitoutunut vähentämään kasvihuonekaasupäästöjään. Vain noin 1 % Suomen suoalasta on turvetuotannossa, mutta silti sen vaikutukset paikallisesti suoekosysteemiin ja vesistöihin voivat olla huomattavat. Suomella on lisäksi kansainvälinen vastuu soiden säilyttämiseksi, sillä alun perin kolmannes pinta-alastamme on ollut suota. Soiden moniulotteisuuden vuoksi maa- ja metsätalousministeriö valmisteli vuonna 2011 soiden ja turvemaiden kestävän käytön strategian. Tässä pro gradu -tutkielmassa tarkastellaan turpeen energiakäytön ympärille muodostunutta konfliktia, jota kutsutaan aineistossani turvekiistaksi. Siihen ovat vaikuttaneet soiden käytön ristiriitainen luonne ja strategian julkaisu, joka on herättänyt keskustelua intressiryhmien, erityisesti turvetuotantosektorin ja luonnonsuojelijoiden, välille. Molempien osapuolten intressit ovat törmänneet toisiinsa monella tapaa, ja seurauksena keskustelu on jämähtänyt paikalleen. Tilanteen ratkaiseminen parantaa kestävää soiden käyttöä ja auttaa kestävän energiapolitiikan suunnittelussa. Jotta turvekeskustelussa päästään kehittävässä mielessä eteenpäin, on tärkeää selvittää Suomen turvekeskustelun kenttä. Siihen pohjaavat tutkimuskysymykseni: 1. Mistä turvekiista koostuu ja 2. millaisia ratkaisuja kiistalle on löydettävissä? Aineisto koostuu 2008 2014 aikana kerätystä kirjallisessa muodossa olevasta medianäytteestä aina sanomalehdistä adresseihin ja kommenttiketjuihin. Menetelmänä käytän laadullista sisällönanalyysiä, jonka avulla turvekiistan osapuolten intressikenttä ja kiistelyn takana olevat tulkintakehykset voidaan hahmottaa. Tulkintakehykset ovat yhtenäisiä tapoja ymmärtää ilmiö mielekkäänä kokonaisuutena, minkä kautta turvetuotannon kokonaisvaikutukset nähdään joko uhkana tai mahdollisuutena, mikä jakaa kiistan osapuolet turvetuotannon puoltajiin ja vastustajiin. Analyysin mukaan turvekiistan intressikentässä on teollisuutta edustava puoli, vesistön virkistyskäyttäjät sekä luonnonsuojeluorientoitunut puoli. Kiistan keskeiset vastakkainasettelut on jaettu ekologiseen ja teknis-taloudelliseen kestävyyteen sekä hallinnon heikkouksiin. Niissä kiistellään muun muassa turvetuotannon vesistövaikutuksista, suon luontoarvoista, turpeen uusiutuvuudesta, sen energiakäytön huoltovarmuudesta, ympäristöluvasta ja sen valituksista sekä poliittisen ohjauksen nykytilasta. Vesistön virkistyskäyttäjien hahmottuminen osana kiistaa oli tärkeä havainto, koska keskustelua tulkitaan helposti pelkästään luonnonsuojelijoiden ja teollisuuden väliseksi vastakkainasetteluksi. Kiistan osapuolia hahmottavat tulkintakehykset nimesin kotimaisen tuotannon ja luonnon kestävän käytön kehyksiksi, jotka omilla tulkinnoillaan osallistuvat edellä mainittuihin vastakkainasetteluihin. Turvekiistassa esiintynyttä retoriikkaa on havaittavissa muissakin ympäristökonflikteissa. Mahdolliset ratkaisut kiistan selvittämiseen ovat jaettavissa tiedolliseen, arvo- ja intressikiistaan. Ratkaisuja ovat esimerkiksi paikallisen tason huomiointi ympäristöluvassa, turvetuotannolle ominaisiin vesistövaikutuksiin keskittyvän tutkimuksen lisääminen ja osapuolia yhdistävän kehyksen tietoinen rakentaminen, joka toimisi ns. sillanrakentajana. Kiistassa on lopulta kyse siitä, kumpi osapuoli pystyy yhdistämään oman tulkintansa paremmin sosiokulttuuriseen kestävyyteen.
  • Kontro, Hilkka (2012)
    Core-fucosylation of N-glycoproteins is associated with different cancers and other pathologies. Identification of glycoproteins and determination of their glycan structure manually by mass spectrometry (MS) is time-consuming and laborious. In this Pro gradu thesis, the use of the mass spectrum-analyzing software Glycopeptide ID for identification of core-fucosylation from a known standard, immunoglobulin G, was studied. Also, a plasma sample with unknown glycoproteins was analyzed. For the MS analysis, the proteins were digested with trypsin, and the resulting glycopeptides were enriched using lectin affinity chromatography. From IgG and plasma, also samples treated with α-Lfucosidase were prepared in order to cleave the core fucose. The presence of glycopeptides was determined by high-performanve liquid chromatographymass spectrometry (HPLC-MS) analysis, and they were fragmented using collision-induced dissociation (CID) in a tandem-MS (MS/MS) analysis. The MS/MS spectra were analyzed with the Glycopeptide ID software. The software was found to identify core-fucosylation reliably from high-quality spectra, but identification of proteins were often incomplete from spectra with poor quality. From the plasma sample with unknown proteins, a probable corefucosylation was found from IgG2, fetuin A, serotransferrin, hemopexin and ceruloplasmin. As a conclusion, the software Glycopeptide ID can be considered as an appropriate tool for identification of core-fucosylation in N-glycopeptides.
  • Ahvenainen, Terhi (2015)
    Huntington's disease (HD) is a progressive neurodegenerative disorder that causes involuntary muscle movements, deteriorates muscle coordination and cognitive decline. Typical onset age of the disease is in mid age, although a juvenile form of HD is also known. The disease is inherited in an autosomal dominant manner via a mutation in the huntingtin gene (HTT). The characteristic mutation in HTT is an expansion of the glutamine stretch at the 5 end of the gene. Excessive amounts of glutamine residues alters the conformation and chemical features of the huntingtin protein (HTT) leading to accumulation of cellular aggregates. Although to date there are several known alterations in the cell that contribute to the disease, the pathogenesis of HD is not fully understood. Ubiquitin proteasome system (UPS) dismantles proteolytically unneeded or damaged proteins, which are targeted to proteolysis when ubiquitin tags are added to them. Deubiquitinating enzymes (DUB) recycle ubiquitin molecules by releasing them from proteasome substrates. Recycling of ubiquitin is critical to a cell as it maintains the free pool of the targeting molecule. Ubiquitin-specific protease 14 (USP14) is one of the DUB family enzymes and its distinctive function is to remove ubiquitin molecules from the tip of the ubiquitin chain and thus antagonize protein degradation. Although the specific function of the protein is unclear, it seems that USP14 operates as a fine regulator of protein turnover rate and in ER stress both in catalytic and non catalytic manner. The role of USP14 is especially emphasized in the nervous system, as it regulates synaptic transmission and neuronal development. Although it is suggested that dysfunction of UPS is involved in the pathogenesis of HD, the role of USP14 in the disease remains to be unknown. IU1 is a novel inhibitor of the catalytic domain of USP14. Studies with IU1 indicate that inhibition of USP14 enhances the clearance of aggregate prone proteins. The approach of this thesis was aimed to elucidate the routes of HD pathogenesis from diverse approaches. The general aim of the thesis was to investigate the role of USP14 in the wild-type PC6.3 cell model, and in the pathogenesis of HD by expressing HTT proteins with different lengths of glutamine stretches in PC6.3 cells. The specific aim of the study was to examine by western blot and microscopy analysis the pathogenic routes of HD that involve ER stress, oxidative stress, autophagy and mutant HTT aggregate dynamics. The function of USP14 was studied with overexpression of USP14, or by inhibiting its catalytic activity by IU1. The findings of this thesis show that overexpression of USP14 enhances the clearance of mutant HTT aggregates, and this effect is obtained in catalytic activity dependent manner. I show that upregulated USP14 is connected to improved clearance of mutant HTT and inhibition of autophagy, suggesting that the degradation is mediated via UPS. The catalytic activity of USP14 might also be important in ER stress regulation, as the results indicate that IU1 activates phosphorylation of both JNK and eIF2α. I was also able to establish a connection between USP14 and GADD34, as I show that GADD34 upregulates USP14. Finally, I show that catalytic inhibition of USP14 decreases the expression of antioxidant SOD2. The data in this thesis is lacking statistical significance, and it can be considered solely as a guideline. However, together these results indicate that the deubiquitinating activity of USP14 increases survival in PC6.3 cells in both a healthy and a HD model.
  • Sandvik, Martin (2022)
    Skeletal muscle is the most abundant tissue in the body, accounting for up to 40-50% of total bodyweight. Regeneration of this tissue is dependent on skeletal muscle stem cells, which are termed satellite cells (SCs) based on their anatomical position between the basal lamina and plasma membrane of muscle fibers. SCs exist under homeostatic conditions in a reversible G0 phase of the cell cycle. Quiescent SCs are recognized by the expression of the paired box 7 (Pax7) transcription factor, in the absence of other myogenic transcription factors such as myoblast determination protein 1 (MyoD) or myogenin (MyoG). Quiescent SCs are metabolically less active with a low oxygen consumption rate. They contain less ATP and have few mitochondria with a low membrane potential in comparison to activated SCs. Activated SCs enter the cell cycle and start to proliferate, undergoing metabolic rewiring to primarily utilize glycolysis for energy production. During early activation, there is an increase in mitochondrial content and ATP production, while the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) increase later during active proliferation. Although similar population dynamics, SCs are a heterogenous population of stem cells, with differences in the expression of notch receptors, stem cell markers, ATP and mitochondrial content, which in turn affect the myogenic potential of the cells. Mitochondria are semi-autonomous, double membrane organelles with various regulation within the cell, such as calcium homeostasis, apoptosis, production of metabolic intermediates, reactive oxygen species (ROS) metabolism, and ATP generation through oxidative phosphorylation (oxphos). Differentiation of various other stem cell types is accompanied by an increase in both mitochondrial content and oxidative phosphorylation, with ultrastructural changes that favour this shift in metabolism. The aim of this thesis was to quantify the ultrastructural changes that occur within SC mitochondria during the early proliferative phase, and to implement a method of Correlative Light and Electron Microscopy (CLEM) for identifying and studying subpopulations of SCs. After isolation and during early activation, SCs contain few mitochondria with a diffuse ultrastructure. Classification of the observed mitochondrial phenotypes revealed heterogeneity both within and between timepoints. During later phases of proliferation, there was an increase in the proportion of mature mitochondria, with an increase in cristae density and a decrease in cristae width. Utilizing genetically modified R26-Snaptag-Omp25 x PAX7CreErt2 mice in which recombination with tamoxifen initiates the expression of mitochondrial outer membrane protein 25 (omp25) bound with a SNAP-tag, allowed for specific and temporal labelling of SC mitochondria by fluorescent SNAP substrates. Performing CLEM on fluorescently labelled SC mitochondria enabled their identification during transmission electron microscopy (TEM). In addition to this, temporal labelling of pre-existing (old) and newly imported (young) omp25 revealed a few cells that contained more old mitochondria, with the cristae density being higher in these. While this indicates a correlation between mitochondrial content and ultrastructure within subpopulations of SCs, further studies are needed to validate these early observations.
  • Hillgén, Oona (2022)
    Fungi play an important role, especially in boreal coniferous forests and peatlands. For example, they are responsible for the circulation of nutrients, and are an important part of forest vegetation, such as tree function and nutrient uptake. Drainage of peatlands for silvicultural purposes has increased over the years and forest management has been found to change the structure of fungal communities. In addition to clear-cutting (CC) as one of the forest management methods, the method of continuous cover forestry (CCF) has been proposed as one of the possible forest management methods, but its effects on the soil fungal community have not been extensively studied. The aims of this master's thesis were to study how the active soil fungal community and its structure vary between the different forest management methods (CC, CCF and uncut control forest) of the peatland forest in Janakkala and between the seasons (spring, summer and autumn). The active community was studied by taking RNA samples from the area in May, July, and September 2021. In addition, the goal was to examine how potential environmental factors such as soil temperature and groundwater variations affect the active fungal community. Overall, diversity was higher in the autumn in all samples. The most stable area was the control forest, where active community members varied between seasons, but where biodiversity was similar between samples in both spring and autumn. The results of the CCF site followed in many ways the uncut forest, but in the autumn, there were large differences in the biodiversity and community structure of the samples in the forest of the CCF site. The biodiversity of the CC area was high. This may be explained by the deforestation of young trees already formed at the time of sampling, which contributes to the return of for instance, mycorrhizal fungi to the area. It should also be noted that the full number of parallel samples from the CC site in the spring and the autumn were not successful. In addition, the summer samples failed completely and no results could be obtained from them. The failure of the samples may be explained by the long hot and dry period in the area in the summer of 2021.
  • Österholm, Kaisa (2021)
    Study-related burnout is a growing problem among university students. Study-related burnout is defined by exhaustion related to studying, a cynical attitude towards studying and feelings of inadequacy. Burnout can be caused by an overtaxing workload and by a lack of personal, social, or material resources. Stress is a natural part of life, but chronic stress can lead to illness and burnout. Students experience stress in their studies and interventions aiming to reduce stress and prevent burnout are therefore necessary. Psychological flexibility increases wellbeing and prevents burnout and is also related to enhanced learning. Acceptance and Commitment Therapy (ACT) is focused on improving psychological flexibility. Good study skills can also prevent burnout. The aim of this study was to examine university students’ experiences of an online ACT-based intervention that aims to increase psychological flexibility and enhance wellbeing and learning. The aim was also to compare the experiences of two groups of students based on their change in study-related burnout during the course. The participants wrote reflective diaries that were qualitatively analyzed using inductive category development and categories that describe students’ experiences of the intervention were formed. The result of this study shows that students had benefited from the course and described effects on both wellbeing and learning. Students in both study groups experienced effects on wellbeing and learning. The importance of peer-support during studying was discussed, which highlights the need for support from peers who experience similar difficulties and concerns. There were also mentions of negative experiences which the students gave as explanations to why a part of the course had not been effective in enhancing their wellbeing and learning. These categories were more often discussed by students whose risk for burnout had increased during the course. Several categories under the themes of positive experiences of effects on wellbeing and learning were more often discussed by students whose risk for burnout had decreased during the course. The result of this study shows that the ACT-based intervention can be regarded as effective in improving wellbeing and studying, and experiences of the intervention were in general positive. Integration of similar interventions in study programs would be beneficial.
  • Ryömä, Maura (2007)
    The aim of the study was to explore the impact of commuting and location of the residence on a consumer's total emission of greenhouse gases. The subject was chosen because many Finns move to a dwelling that is situated far away from their place of work. The research questions were: 1. How big a proportion of the total emission of consumers' greenhouse gases is due to the passenger traffic? 2. What would be the increase of greenhouse gas emission if an employee moved from Helsinki (Finland's capital city) to Nurmijärvi (a municipality located 37 km from Helsinki) assuming that the employee works in Helsinki and the commuting mode is switched from the metro to a private car. (There is no metro nor train connection between Helsinki and Nurmijärvi.) Passenger traffic forms with its estimated 33% the biggest source of consumption caused greenhouse gas emissions in Finland. Private car use is the main source of greenhouse gas emissions deriving from passenger traffic. If an employee moved to an electrically heated single-family house located about 40 km from the place of work the emission rate would increase by 75% assuming that the commuting mode is switched from the metro to a private car. Most of the increase would be due to the change of commuting mode. Most public transport in Helsinki takes place by rail (metro, tram, and train). Metro is the most favorable transportation mode in regard to greenhouse gas emission. Automobiles are the most damaging commuting alternative. A car with driver and no passengers on a motorway emits about 8 times more greenhouse gas (21.84 kg per 100 km or 62.5 miles) than travel by metro in Helsinki (2.87 kg per 100 km or 62.5 miles). A car moving in city streets emits about 10 times more greenhouse gas (27.3 kg per 100 km or 62.5 miles) than does metro travel. Substituting diesel for gasoline reduces emissions by very little. The use of diesel on a motorway decreases emissions by only 7% whereas diesel driving in a city increases emissions by 4%. Travel distances between home and work in Finland increased by about 80% between 1980 and 2003. In the same period the number of private cars increased by 86% and kilometers driven per year per car increased by 92%. The results are based on statistics and calculations based on these statistics concerning traffic, housing, heating, and electrical use. Also previous studies dealing with residential sprawl, traffic, energy production, and greenhouse gas emissions produced by Finnish consumers were referred to.
  • Tahvanainen, Meeri (2022)
    The ongoing growth and densification of urban areas is threatening biodiversity in cities. Previously continuous habitats are reduced and fragmented into smaller areas, which increases the edge effect and changes the qualities of the original habitat. Urban greenspaces are frequently used by people, and disturbances, such as trampling, and understorey management are increasing the similarity of habitat patches (i.e. homogenisation). In this study, I investigated the effects of small-scale homogeneity in forests produced by urbanisation on the distribution patterns and trait composition of carabid beetles. Sampling was done with pitfall traps during the summer of 2021 and altogether 21 study sites were selected in the City of Lahti, Finland. The study sites represented three different environments: 1) structurally complex (heterogenous) habitat in remnant spruce forests in the city, 2) structurally simple (homogenous) habitat in remnant spruce forests in the city, 3) structurally simple habitat under spruce trees in managed urban parks. In addition to the beetles, a set of environmental variables was collected to quantify the complexity of the three habitat types. As expected, habitat homogeneity affected carabid beetle species composition so that the proportion of generalist and open-habitat species was greater in homogenous sites, including homogenous forest remnants and highly homogenous urban parks, whereas the proportion of forest specialists was greater in heterogenous forests. Species richness was higher in the homogenous sites due to species-rich open-habitat genera in the carabid beetle family. Trait distribution at the community level showed clear differences between the three studied habitat types. As expected, the proportions of large and heavy species were higher in the forest habitats than in the parks, whereas homogenous habitats, especially highly homogenous park sites consisted of a higher proportion of flight capable species than heterogenous forests. At the species level, individual beetles were generally smaller in the parks, whereas the results between the two forest types varied and a clear difference between habitat specialists and generalists could not be detected. As cities grow, keeping the management of greenspaces moderate, selecting native vegetation, and preserving decaying woody material are ways to increase habitat heterogeneity, which according to this study, can support biodiversity and life of different organisms in urban areas.
  • Sammallahti, Heidelinde (2020)
    Since the establishment of pathologic and cytogenetic laboratories, left-over material in the form of G-banded slides and cytogenetic fixed cells, as well as formalin-fixed, paraffin-embedded (FFPE) material, tissue samples, blood and bone marrow have been stored in archives for possible later reference. This material, which potentially contains rare and special cases, has been a welcome source for retrospective studies or e.g. for trying out new methods of analysis. Molecular genetic and molecular cytogenetic techniques such as Southern hybridization, fluorescence in situ hybridization (FISH), and comparative genomic hybridization (CGH) have been successfully applied on different kinds of archival specimens. With this study we wanted to explore, both through a literature review and through a practical experiment, the history, present day and future use of such archival material in the light of molecular cytogenetics, including the challenges of DNA extraction, sample degradation, data analysis and interpretation as well as ethical issues. The experimental part had two main objectives, (1) to investigate the use of archived cytogenetic material in the form of G-banded slides and cytogenetic fixed cells for array-based CGH (aCGH), and (2) to explore abnormalities on chromosome 1q in hematologic malignancies. Extra material on the long arm of chromosome 1 is a common recurrent chromosomal abnormality that is present in many classes of hematologic cancers as either primary or secondary aberration. It is the most common structural aberration in multiple myeloma (MM), myeloproliferative disease (MPD) and myelodysplastic syndrome (MDS) and is also a frequent aberration in pediatric acute lymphoblastic leukemia (ALL). It has been associated with increased cell proliferation, disease progression and poor outcome, the mechanisms of which are not fully understood yet. To combine these two aims, we screened the patient database for relevant cases and searched the archive for corresponding samples. The idea was to find cases of hematologic malignancies with extra material on chromosome 1q that were available as cytogenetic slides, fixed cells and frozen bone marrow, find an ideal method of DNA extraction from slides (for other material ready protocols were available), analyze the samples with aCGH and compare the results. We wanted to prove the eligibility of archived cytogenetic material for aCGH analysis and at the same time study rearrangements of 1q in our samples. Starting with 38 patient cases, DNA extraction was performed with 2 different protocols, the latter of which, using a modified version of the Puregene® DNA Purification Kit Protocol for Blood Smears, turned out to be more successful. After having obtained sufficient DNA from several slide samples, we assessed DNA quality with agarose gel electrophoresis. Because slide DNA was too fragmented to be used for aCGH and whole genome amplification (WGA) was not a choice, the experiment was continued with archived fixed cells, bone marrow and archived DNA only. Using a high resolution 60-mer oligonucleotide 44K human CGH microarray platform, we analyzed 15 patient cases that were available both as fixed cell and DNA samples (2 cases), both as fixed cell and bone marrow samples (1 case), both as fixed cell and CPT™ cell samples (1 case), frozen bone marrow (7 cases) and DNA samples (4 cases). The malignancies were pediatric ALL (6 cases), adult ALL (1 case), chronic myeloid leukemia (CML, 2 cases), non-Hodgkin lymphoma (NHL, 1 case), Burkitt lymphoma (BL, 3 cases), Hodgkin's disease (HD, 1 case) and one undefined malignancy. After analysis with CGH Analytics software, we saw that aCGH results of fixed cells compared to results from bone marrow or DNA were almost identical, which confirmed that cytogenetic fixed cells were a reliable source for aCGH analysis. Challenges of working with archived material were witnessed in the form of CG-waves and centralization errors and deviations of the hybridization ratio diagram caused by partially degraded DNA. Concerning aberrations calls, 12 of the 15 cases had detectable aberrations on 1q, which included amplification of the whole 1q arm (1 pediatric ALL, 3 BL cases) and duplications or amplifications of parts of 1q (5 pediatric ALL, 2 CML and 1 undefined malignancy cases) in addition to other aberrations. Common break points were 1q21.2 (2 CML cases), 1q23.2 (1 pediatric ALL and 1 CML case) and 1q32.3 (2 pediatric ALL cases), and we detected 2 large common overlapping areas, at 1q21.2q23.2 and 1q25.3q32.2. The areas were, however, too vast for disease gene screening, spanning several Mb each. We could thus prove and confirm the value of cytogenetic archives for scientific studies. Array CGH with fixed cells was confirmed to work well, also frozen bone marrow and archived DNA were valuable sources. We would suggest further aCGH experiments with cytogenetic slides by applying WGA but would also suggest slide and fixed cell material to be used for Next Generation Sequencing, which has not been reported yet. Regarding aberrations on 1q, further studies to more accurately delimit relevant break points and common overlapping areas are recommended.
  • Elsilä, Milla (2023)
    Tools to change current consumption patterns are needed. Nudging has shown promise in relation to increasing pro-environmental behaviour and it has been studied a lot especially in physical environments. As more and more of overall consumption is shifting to online environments, it is important to understand whether digital nudging has potential when it comes to more sustainable purchase decisions. This thesis provides a systematic literature review of the existing body of experimental research studying digital nudging as a mean to increase more environmentally sustainable consumption. Based on an analysis of 13 included studies, the outcomes of using digital nudging show inconsistencies both between as well as within studies. Therefore, the results give little support for using digital nudging as a primary tool when it comes to behavioural change. While different forms of information provision and social norms are the most commonly tested digital nudging techniques, no specific technique can be seen to work better than others. Positive outcomes can be reached through multiple techniques as long as the techniques are well designed and implemented and carefully targeted. However, unlike previous research, this literature review gives no support to the use of defaults in the context of sustainable consumption as it might even result to negative outcomes. The results of this thesis show that the experimental research combining digital nudging and sustainable consumption is still very limited both in its quantity as well as quality. Future research should aim to capture consumption behaviour in real online stores, broaden the consumption context to ones without well established routines and utilize the potential of digital nudging more fully.
  • Hällfors, Maria (2010)
    Vegetation maps and bioclimatic zone classifications communicate the vegetation of an area and are used to explain how the environment regulates the occurrence of plants on large scales. Many practises and methods for dividing the world's vegetation into smaller entities have been presented. Climatic parameters, floristic characteristics, or edaphic features have been relied upon as decisive factors, and plant species have been used as indicators for vegetation types or zones. Systems depicting vegetation patterns that mainly reflect climatic variation are termed 'bioclimatic' vegetation maps. Based on these it has been judged logical to deduce that plants moved between corresponding bioclimatic areas should thrive in the target location, whereas plants moved from a different zone should languish. This principle is routinely applied in forestry and horticulture but actual tests of the validity of bioclimatic maps in this sense seem scanty. In this study I tested the Finnish bioclimatic vegetation zone system (BZS). Relying on the plant collection of Helsinki University Botanic Garden's Kumpula collection, which according to the BZS is situated at the northern limit of the hemiboreal zone, I aimed to test how the plants' survival depends on their provenance. My expectation was that plants from the hemiboreal or southern boreal zones should do best in Kumpula, whereas plants from more southern and more northern zones should show progressively lower survival probabilities. I estimated probability of survival using collection database information of plant accessions of known wild origin grown in Kumpula since the mid 1990s, and logistic regression models. The total number of accessions I included in the analyses was 494. Because of problems with some accessions I chose to separately analyse a subset of the complete data, which included 379 accessions. I also analysed different growth forms separately in order to identify differences in probability of survival due to different life strategies. In most analyses accessions of temperate and hemiarctic origin showed lower survival probability than those originating from any of the boreal subzones, which among them exhibited rather evenly high probabilities. Exceptionally mild and wet winters during the study period may have killed off hemiarctic plants. Some winters may have been too harsh for temperate accessions. Trees behaved differently: they showed an almost steadily increasing survival probability from temperate to northern boreal origins. Various factors that could not be controlled for may have affected the results, some of which were difficult to interpret. This was the case in particular with herbs, for which the reliability of the analysis suffered because of difficulties in managing their curatorial data. In all, the results gave some support to the BZS, and especially its hierarchical zonation. However, I question the validity of the formulation of the hypothesis I tested since it may not be entirely justified by the BZS, which was designed for intercontinental comparison of vegetation zones, but not specifically for transcontinental provenance trials. I conclude that botanic gardens should pay due attention to information management and curational practices to ensure the widest possible applicability of their plant collections.