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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(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.
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(2024)Schizophrenia (SCZ) is a chronic neuropsychiatric disorder believed to arise from the intricate interplay between genetic predisposition and environmental factors. Though the aetiology of SCZ is unknown many findings support an excessive synaptic pruning hypothesis. Maternal immune activation (MIA), encompassing prenatal infection and systemic inflammation, constitutes a significant environmental risk factor implicated in SCZ onset (Patterson, 2009; Brown, 2012). MIA induces persistent alterations in the microglia of offspring termed microglial priming, characterized by heightened reactivity to inflammatory stimuli (Choudhury and Lennox, 2021). Notably, studies have reported increased sensitivity to activation, elevated expression of inflammatory markers, and an increase in the total number of microglia (Perry and Holmes, 2014; Choudhury and Lennox, 2021). Primed microglia may contribute to excessive synaptic pruning, thereby compromising neuronal connectivity and potentially leading to the onset of SCZ. This thesis investigated the impact of microglia on neurons and explored the microglial tendency for hyperactivation in the context of SCZ predisposition. It utilized induced pluripotent stem cell (iPSC) technology to create a rat astrocyte/unaffected control human iPSC-derived neuron/induced microglia-like cell (iMGL) tri-culture model. Uniquely, iMGLs were differentiated from a library of monozygotic twin lines discordant for SCZ, and unaffected controls. This allows for exploration of the differences between iMGLs from unaffected twins with a genetic predisposition for SCZ, affected twins with clinical manifestation of SCZ, and unaffected controls without a known genetic predisposition for SCZ. The tri-culture system was subjected to lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (poly(I:C)) treatments to activate iMGLs, and differences in cytokine release, synapse pruning, and neuronal activity were assessed. The principal outcomes of our investigation revealed enhanced cytokine release from SCZ-derived iMGLs when exposed to inflammatory stimuli, alongside increased network connectivity among samples containing genetically predisposed iMGLs. While most of the results did not reach significance, they suggest a potential link between SCZ pathophysiology and hyperactive microglia. Future research will focus on enlarging the study cohort, establishing tri-culture models featuring neurons and iMGLs derived from the iPSCs of the same patient, conducting CBA analysis to confirm the elevated cytokines finding, and scrutinizing iMGL morphology.
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(2020)The interactions within plankton communities are complex, and realistic modelling of these interactions create a challenge in large-scale environmental models. The objective of this thesis was to evaluate whether Bayesian networks could be a suitable method in the modelling of these communities. Besides observing the interactions between different groups within phyto- and zooplankton communities, another goal was to focus on the potential change on the ecosystem level. To achieve this, dynamic Bayesian networks with hidden variables were used to observe whether structural changes in plankton communities could reveal larger trends in the aquatic ecosystem. To compare performance and accuracy of the model, two Bayesian food webs with differing causal links between observations were built. Of the two models, the simpler construct utilizing hidden Markov model fared better, and a clear trend was detected in the hidden variable. This trend in the time series signify that the relationships between the observed variables have changed during the study period. The plankton data set was collected from the Archipelago Sea between 1991 and 2016 and the results from the model were further analyzed alongside with this observational plankton data. In the samples the total biomass of phytoplankton grew throughout the study period, whereas at the same time the total biomass of zooplankton declined. As the Bayesian network considers the observable variables while maximizing the fit of the hidden variable, the observed trend in the hidden variable indicate that some unobservable variables are affecting both phyto- and zooplankton communities. This clear trend detected by the hidden variable might be related to a trend of increasing eutrophication in the study area, but to better understand the drivers causing this change further research is needed. Besides detecting underlying trends, the dynamic Bayesian networks are a promising method to study the interactions within plankton communities.
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(2022)As the world urbanizes at a rapid rate, urban encroachment into coastal waters has the potential to reshape global carbon cycles by modifying organic matter decomposition processes. Litter decomposition is regulated by the litter quality, environmental conditions, and the decomposer community. This study aims to investigate if different coastline characteristics (urban/hardened versus natural/vegetated) have localized differences in decomposition rates and litter stabilization. To test this, the Tea Bag Index (TBI) has been applied to aquatic systems by including a “leaching factor” to initial masses. By using uniform litter in aquatic systems, the litter quality and moisture conditions are fixed so that other environmental conditions and the decomposer community can be considered for their impact on the rate of decomposition. Three pairs (urban and natural) of sites were selected around Helsinki, Finland in the brackish coastal water of the Baltic Sea in the summer of 2021. At each site, five green and rooibos tea bags were placed with a temperature logger, and on days 15, 29, 43, 60, and 84 a tea bag of each type was removed, dried, and weighed. Additionally, water quality measurements were collected using a YSI multiparameter sonde. There was no significant difference in the decomposition rate nor stabilization factor between urban and natural sites, although, the rate calculated according to the TBI-methodology differed from the rate determined by fitting a model to the observations. Despite no significant difference, the stabilization factors were higher than average in similar environments and are indicative of efficient litter decomposition in the waters around Helsinki. Water temperature was significantly higher, and turbidity was significantly lower at natural sites. Therefore, the cooler waters and inferred higher hydrodynamic forces at urban sites may have counteracted their individual effects on the rate of litter decomposition. In fact, since the decomposer community at natural sites is suggested to be more diverse, the rooibos tea at natural sites may have begun to stabilize, thus, implying that the study period was too long. Overall, this study found that coastlines currently have no clear localized effects on litter decomposition, but in the future, this may begin to change.
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(2022)Ihmisen aiheuttama ilmastonmuutos on käynnissä. Ihmisten vaikutus ja kasvihuonekaasut ilmakehässä saavat aikaan muuttuvan ilmaston. Muuttuva ilmasto aiheuttaa riskejä ihmisille ja luonnollisille järjestelmille. Ilmaston lämmetessä myös ilmastoriskit ja niiden merkitys kasvavat. Globaalin ilmastopolitiikan päätavoitteina ovat kasvihuonekaasupäästöjen vähentäminen ja ilmastonmuutoksen hillitseminen. Uusiutuvan energian lisääminen on huomattava toimenpide näiden tavoitteiden saavuttamisessa. Ilmastoriskit vaikuttavat kuitenkin myös uusiutuvaan energiaan. Ymmärrys ilmastoriskeistä luo pohjan ilmastoriskien arvioimiselle. Ilmastoriskien arviointeja voidaan käyttää sopeutumiskyvyn ja ilmastonmuutokseen varautumisen parantamiseksi. Työssä tehtiin kaksi eri analyysiä, jotka vastaavat tutkimuskysymyksiin: millaisilla viitekehyksillä ilmastoriskejä voidaan arvioida ja millainen ilmastoriskikäsitys uusiutuvan energian -sektorin yrityksillä on? Ensimmäisessä analyysissä aineistona on ilmastoriskien arviointi -viitekehyksiä, jotta saadaan tietoa erilaisista ilmastoriskien arviointi -viitekehyksistä, niiden sisällöstä ja rakenteista. Toisen analyysin tutkimusaineisto kerättiin haastatteluin uusiutuvan energian -sektorin yrityksiltä. Haastateltavien joukoksi rajattiin yrityksiä, jotka ”tuottavat energiaa yhteiskuntaan”, uusiutuvista energianlähteistä, esimerkiksi sähköä ja lämpöä. Haastattelujen analysoinnissa käytettiin apuna ensimmäisen analyysin tuloksia. Tarkoituksena oli ymmärtää, millainen ilmastoriskikäsitys uusiutuvan energian -sektorin yrityksissä on ja miten näissä yrityksissä ilmastoriskejä arvioidaan. Ilmastoriski on monimutkainen ja moninainen asia ja sen tietämys ja tunnistaminen on hyvin eri vaiheissa yrityksissä. Työssä käytetty IPCC:n malli ilmastoriskin muodostumisesta (vaaratekijä, haavoittuvuus ja altistuminen), oli melko vieras tapa ajatella ilmastoriskiä. Yrityksissä tunnistettiin ilmastonmuutoksen vaaratekijät hyvin ja altistuminen näille vaaroille oli myös tiedossa, mutta haavoittuvuus oli tuntemattomampi käsite yrityksille. Monet erityyliset ilmastoriski-termit olivat yrityksille vieraita, mutta termien merkitys oli tuttua. Yritykset tunnistivat fyysisiä, suoria ja siirtymäriskejä kohdistuvan omaan toimintaansa, ja nämä riskit koettiin myös merkittävinä yrityksen toiminnalle. Osa yrityksistä oli hyvin tietoisia ilmastoriskeistä ja näissä yrityksissä on tehty ilmastoriskien arviointia jo pitkään. Ilmastoriskien arviointiin on vasta lähiaikoina alettu kiinnittämään enemmän huomiota. Ilmastoriskien arviointi koetaan tärkeänä ja merkittävänä asiana.
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(2023)In this thesis, I studied T cell responses to SARS-CoV-2 structural proteins in subjects who had been both vaccinated and infected (n=30), who had only been infected (n=22), and as controls, in subjects who had been neither vaccinated nor infected (n=6). In addition, I compared cellular responses between groups of subjects who had been infected with either wild-type (WT) SARS-CoV-2, Alpha (B.1.1.7), or Beta (B.1.351) variants. Before analyzing the samples to be studied, I optimized the conditions for the cell stimulations. Peripheral blood mononuclear cells (PBMCs) were collected from infected subjects six months after infection. PBMCs were stimulated with SARS-CoV-2 wild-type nucleoprotein, spike-, envelope-, and membrane protein peptide pools. I quantified cytokines and effector molecules characteristic of CD4+ and CD8+ cell responses; perforin, tumor necrosis factor alpha (TNF-a), granzyme B, interferon gamma (IFN-γ), interleukin 2 (IL-2) and interleukin 4 (IL-4) secreted by PBMCs were quantified. In this study, I found that subjects with infection, or combination of infection and vaccination had higher cellular immune responses compared to uninfected controls. Infection induced higher granzyme B, IFN-y, and IL-2 secretion, and the combination of infection and vaccination induced higher granzyme B, perforin, IFN-y, IL-2 and IL-4 secretion. I found that subjects with hybrid immunity, defined as immunity acquired from combined vaccination and infection, had on average higher IL-4 responses compared to those who had been infected only. In this study, I found that nucleoprotein, spike-, and membrane proteins stimulated T cell responses whereas envelope protein did not stimulate T cell responses. I found that WT, Alpha or Beta infection produced equally good T cell responses to WT spike peptide. In conclusion, I found that COVID-19 patients have long-lasting T cell responses. I found that T cells recognize different SARS-CoV-2 variants. Mutations present in the spike proteins of the different variants do not affect T-cell ability to recognize these antigens. Immunity based on T cells is not as susceptible to antigenic changes as the humoral immunity. T cells have a vital role in protection against variants, when new SARS-CoV-2 variants evaded antibody-based immunity.
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(2020)Tämän tutkielman aiheena ovat suomalaisten nuorten ajatukset tulevaisuudesta, koskien erityisesti ilmastonmuutoksen ja muiden ympäristöongelmien aiheuttamia uhkia ja niistä selviytymistä. Tutkielmassa tarkasteltiin 16–18-vuotiaiden eteläsuomalaisten lukio-opiskelijoiden tulevaisuuskuvia, joiden ymmärrettiin heijastelevan tulevaisuutta koskevia laajempia yhteiskunnallisia diskursseja. Tavoitteena oli selvittää osallistujien tulevaisuuskuvien sisältöä sekä analysoida niiden taustalla vaikuttavia ajatusmalleja. Tutkielman aineisto koostui 50:stä oppituntien aikana tehtävänannon mukaisesti kirjoitetusta tekstistä, joiden aiheena olivat seuraavan 80 vuoden tapahtumat. Tehtävänannon muoto ymmärrettiin tarinantäydennystehtävän (story-completion task) sovellukseksi. Aineistoa analysoitiin temaattisen analyysin keinoin, minkä jälkeen muodostettiin aineistossa esiintyviä tyypillisiä kertomusrakenteita kuvaavia tyyppikertomuksia. Tutkimustulosten mukaan nuorten tulevaisuuskuvat vastasivat monella tavalla aiempien tutkimusten tuloksia. Tulevaisuuskuvat olivat sisällöltään monipuolisia, mutta samaan aikaan monilta piirteiltään kaavamaisia. Kirjoitelmien merkittävimpiä aiheita olivat tieteellis-teknologinen kehitys sekä erilaiset kriisit ja ongelmat, kuten sota ja ympäristöongelmat, jotka kuvattiin pääasiallisesti ilmastonmuutoksen kautta. Tutkielmassa todettiin nykyisyyden ongelmia heijastelevien tulevaisuuden ongelmien liittyvän kirjoitelmissa voimattomuuden tunteisiin. Aineiston tulkinnan perusteella nuorten tulevaisuuskuvissa on huolen lisäksi toivoa, mutta toivon lähteenä toimivat ilmiötkin viittasivat laajalti yksilön vaikutusmahdollisuuksien vähäisyyteen. Lisäksi todettiin tarinantäydennystehtävän soveltuvan tulevaisuuskuvia käsittelevän aineiston keräämiseen ja olevan tarvittaessa menetelmäkirjallisuudessa esitettyjä määritelmiä joustavampi työkalu tekstipohjaisen tutkimusaineiston hankintaan. Tutkimuksen tulokset viittaavat siihen, että nuoret saattaisivat hyötyä osallistamisesta päätöksentekoon ja julkiseen keskusteluun sekä erilaisia tulevaisuuteen liittyviä valmiuksia edistävästä koulutuksesta.
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