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  • Englund, Mikael (2022)
    I present a case study demonstrating how an integrative approach can be applied in systematics to describe a new lepidopteran species and genus. I apply several imaging techniques to provide unambiguous illustrations of diagnostic morphological characters with an emphasis in experimenting non-destructive imaging methods, especially the Micro CT scanning. We establish the taxonomic position and molecular phylogeny of the study species using a multigenetic dataset comprising the study species and 272 other terminal taxa from the superfamily Geometroidea. My study taxon is a largish and conspicuous geometrid moth from South Africa, which we classify to the looper moth family Geometridae, the subfamily Larentiinae of the tribe Xanthorhoini sensu lato. Based on the inspection of the study specimens and all other available information, we conclude that the study specimens belong to a yet undescribed genus and species. During the study, we found out that the species has been present in collections for at least 128 years but has not been formally described. Micro CT scanning was found to be a useful imaging method, particularly when the target structure is flat such as arthropod wing venation, and I recommend it to be applied when dealing with rare specimens. We provide images and description of the known distribution, habitat, host plant, adult and immature stages, and parasitoids of a new species, Chloecolora vergetaria sp. n. Englund & Staude. We intend to publish the formal description of the new genus and species in a separate forthcoming article. Tutkielmassani selitän tieteelle uuden perhossuvun ja -lajin soveltaen useita kuvantamis- ja muita menetelmiä, joiden avulla esitän uudelle lajille tunnusomaiset ulkoiset tuntomerkit. Erityisesti tutkin Micro CT skannauksen ja muiden näytteitä rikkomattomien kuvantamismenetelmien soveltamista integratiivisessa taksonomisessa tutkimuksessa. Selvitämme uuden lajin sukulaisuussuhteet ja taksonomisen paikan käyttäen uuden lajin ja 272 muun mittarimaisten perhosten (Geometroidea) yläheimoon kuuluvan lajin useista geenisekvensseistä koostettua tietokantaa. Tutkimuslajini on suurehko Etelä-Afrikkalainen yöperhonen, jonka luokittelemme kuuluvaksi heimoon mittarit (Geometridae), alaheimoon Larentiinae ja sukukuntaan Xanthorhoini sensu lato. Näyteyksilöiden tutkimuksiin ja kaikkeen muuhun käytössämme olleeseen aineistoon perustuen päättelemme, että näyteyksilöt kuuluvat aiemmin kuvaamattomaan sukuun ja lajiin. Tutkimuksen aikana selvisi, että lajin yksilöitä on ollut tieteellisissä kokoelmissa jo ainakin 128 vuoden ajan, mutta laji on jäänyt vaille muodollista kuvausta. Micro CT skannaus osoittautui käyttökelpoiseksi kuvantamismenetelmäksi erityisesti, kun kuvattava kohde on tasomainen, kuten esimerkiksi niveljalkaisen siipisuonitus - suosittelen sen käyttöä, kun kuvauksen kohteena on harvinainen näyteyksilö. Esitämme uuden lajin, Chloecolora vergetaria sp. n. Englund & Staude, aikuisten sekä sen tunnetun levinneisyyden, elinympäristön, ravintokasvin, kehitysasteiden sekä tunnettujen loisten kuvaukset. Aiomme julkaista uuden suvun ja lajin muodolliset kuvaukset erillisessä artikkelissa.
  • Borgman, Vesa Petteri (2023)
    Intestinal stem cells maintain the regenerative potential of intestinal epithelium, which needs to be renewed constantly. Dysregulation of intestinal stem cell proliferation is associated with aging and intestinal diseases. The midgut of Drosophila melanogaster is a valuable model for studying intestinal stem cell driven tissue regeneration. It is similar in function to the mammalian small intestine but has a simpler cellular structure. Drosophila midgut is divided into five major regions with specialized physiological functions, characteristic morphological features and distinctive gene expression profiles. The midgut consists of a monolayer of absorptive enterocytes, small secreting enteroendocrine cells, intestinal stem cells and enteroblasts. Intestinal stem cells differentiate into enterocytes through a transient enteroblast phase. 5-hydroxytryptamine has been shown to activate proliferation of intestinal epithelium in mammals, but its mechanism of action is still unknown. Also, sex-specific differences in 5-hydroxytryptamine signalling have been recorded in mammals. 5-hydroxytryptamine signalling pathway has several downstream targets that have diverse downstream effect. Thus, 5-hydroxytryptamine signalling creates a complex and versatile regulatory network. The aim of my thesis is to study the effects of 5-hydroxytryptamine signalling on intestinal stem cell proliferation and cellular turnover in Drosophila midgut in both sexes. The effects of excessive amounts of 5-hydroxytryptamine are first studied by feeding Drosophila with 5-hydroxytryptophan, a product of the rate-limiting step in the 5-hydroxytryptamine synthesis pathway. The effects of 5-hydroxytryptamine signalling are further studied by knocking down and overexpressing a component of the 5-hydroxytryptamine signalling pathway in intestinal stem cells and enteroblasts. Dissected midguts are immunofluorescently stained, imaged and analysed both visually and with bioinformatics tools. The results indicate that 5-hydroxytryptamine signalling has both regional and sex-specific functions that affect intestinal stem cell proliferation and cellular turnover in Drosophila midgut. The most dramatic effects are seen in cellular turnover, which indicates that 5-hydroxytryptamine signalling plays a role in enteroblast differentiation. Furthermore, the results suggest that bidirectional signalling between enteroblasts and dying enterocytes facilitates cellular turnover in the midgut. As 5-hydroxytryptamine signalling is indicated in inflammatory bowel diseases such as Crohn’s disease, my results might help in the development of treatments for such conditions.
  • Hyvönen, Hanna (2015)
    Northern aapa mires are important carbon sinks. Their CO2 exchange with the atmosphere is based on plant photosynthesis and respiration, and the decomposition of peat and other dead organic matter by microbial activity. The photosynthetic efficiency of plants depends on environmental factors and the amount and development of plant leaf area and biomass. There is not much research on the leaf area index and biomass of plants on aapa mires which makes them an interesting and important subject of research. This study investigated plant community composition, development and their effect on CO2 exchange at a northern aapa mire in Finland. The purpose of this study was to survey the biomass and leaf area index of plants within mire types and determine how they, together with water level and microbial activity, and explain the CO2 exchange between the mire and atmosphere. Another aim of this study was to construct regression models for predicting biomass and leaf area index using the plants height and coverage data. The study was conducted in summer 2014 at Halssiaapa, an aapa mire in Sodankylä. The mire was divided into oligotrophic, mesotrophic and eutrophic hummocks, lawns and hollows. The plant community species, their height and coverage were determined in early June, mid-July and mid-August. Moreover, the growth of plant groups was monitored weekly at 16 inventory squares between 6th June and 18th August. Biomass and leaf area samples were collected from different mire types in mid-July, and by the use of regression analysis, two equations were modelled for each plant group, one for predicting biomass and another for predicting leaf area index. The equations were used for predicting biomass and leaf area index for plant groups and mire types based on early June and mid-August data, and the weekly inventory squares. CO2 exchange, and factors controlling it, were measured via an eddy covariance method (measures exchange at ecosystem scale), and a closed chamber method (measures exchange from 1m2). Biomass, leaf area index, species composition, water level and soil factors (indicators of decomposer activity) were used to explain CO2 fluxes. The activity of decomposers in peat was measured via a decomposition test where litter bags containing tea or straw were placed at sampling sites on the mire. The regression models based on plant sample data explained well the biomass and leaf area indices of plant groups. The mire s overall and maximum biomass and leaf area indices were 147 g m-2 and 0,73 m2 m-2 respectively for vascular plants, and 351 g m-2 and 5,5 m2 m-2 respectively for mosses. Hollows displayed the lowest leaf area index and biomass values, whilst hummocks showed the highest values. Mesotrophic hummocks had the highest values for vascular plants and eutrophic lawns showed the highest values for mosses. Despite having a considerably higher level of biomass and leaf area index than vascular plants, Sphagnum mosses had a much lower gross photosynthetic capacity. Plant communities on lawns and hummocks with an abundancy of sedges (Cyperaceae) had a higher gross photosynthetic capacity and respiration level than plant communities in hollows. Factors leading to increased respiration were increasing vascular leaf area index, release of carbon from straw (indicating decomposer activity), decreasing water level (drier peat) and carbon content in surface peat. Factors leading to increased gross photosynthetic capacity were increasing vascular leaf area index, decreasing water level and decreased straw mass in surface peat (indicating decomposer activity). Temperature and PAR (Photosynthetically Active Radiation) explained 25 % of the variation in gross primary production and 39 % in respiration. The other environmental factors explained 55 % of the residual variation in gross primary production and 78 % in respiration. The mire s gross primary production showed highest increase rate in June and reached its maximum level in early August. Mean plant biomass and leaf area index had the same growth pattern as gross primary production, reaching peak levels at the end of July. The plants Menyanthes trifoliata , Potentilla palustris, Andromeda polifolia and the functional group containing sedges and Scheuchzeria palustris, had a similar growth pattern, but no change in biomass and leaf area index of Betula nana and Vaccinium oxycoccos was detected during the growing season. The models constructed in this study for predicting biomass and leaf area index can be used at Halssiaapa and other nearby aapa mires. Plant surveying and CO2 exchange measurements will be continued at the site in future. Longterm changes in plant community species and CO2 exchange can be researched by comparing results from year 2014 with in coming summers.
  • Tolvanen, Oula (2015)
    Tutkielman tavoitteena oli laatia todennäköisyyspohjainen kanta-arviomalli merivaelteisen taimenen (Salmo trutta L.) juveniili vaiheen populaatiodynamiikan kuvaamiseksi. Mallin tarkoituksena on kuvata taimenen jokipoikasvaihe kuoriutumisesta merivaellukselle lähtöön tai sukukypsyyteen saakka, tiivistämällä saatavilla oleva tieto taimenen ekologiasta populaatioparametreiksi. Näitä parametreja olivat ikäryhmäkohtainen selviytymisen todennäköisyys ja ikäryhmäkohtainen syönnösvaellukselle lähdön todennäköisyys. Epävarmuuden huomioimiseksi mallin parametrien kuvaamiseen käytettiin todennäköisyysjakaumia. Ikäryhmäkohtainen syönnösvaellukselle lähdön todennäköisyys kuvattiin käyttämällä käyräfunktiota, jonka parametrit liitettiin aikaisemmin julkaistuihin aineistoihin taimenen keskimääräisen vaellusiän vaihtelusta leveyspiirin mukaan. Mallin muiden parametrien odotusarvojen asettaminen ja mallin rakenteen laatiminen perustui asiantuntija-arvioihin ja aikaisemmin julkaistuun taimenta tai sen sukulaislajeja koskevaan tutkimustietoon. Mallissa käytettyjen parametrien posteriorijakaumat ratkaistiin käyttämällä Markov chain Monte Carlo (MCMC) -simulointia. MCMC-simuloinnin toimivuus tarkastettiin käyttämällä keinotekoisesti tuotettua havaintoaineistoa. Mallin yhteensopivuutta todellisiin havaintoaineistoihin tutkittiin sovittamalla malli kahdesta Suomenlahteen laskevasta joesta kerättyyn sähkökoekalastus ja vaelluspoikaspyyntiaineistoon. Viron puoleisen Pirita joen aineisto koostui vuosien 2005 - 2013 sähkökoekalastusaineistosta ja vuosien 2006 - 2014 vaelluspoikaspyyntiaineistosta. Suomen puoleisen Ingarskilan joen aineisto koostui vuosien 2009 - 2013 sähkökoekalastusaineistosta ja vuosien 2012 ja 2013 vaelluspoikaspyyntiaineistosta. Molempien jokien aineistojen, sekä kirjallisuudesta kerätyn 41 muun joen vaelluspoikasten keskimääräisistä i'istä koostuva aineiston analysointi toteutettiin samanaikaisesti hierarkkisena meta-analyysina. Mallin sovituksen yhteydessä havaittiin, että malli systemaattisesti yliarvioi keväisin tutkimusjoista alasvaeltavien taimenen poikasten määrän. Mallin havaittiin kuitenkin ennustavan onnistuneesti analyysistä poisjätetyn Piritajoen vuoden 2014 vaelluspoikaspyyntiaineiston ikäjakauman. Kirjallisuudesta kerätyn aineiston pohjalta taimenten syönnösvaellukselle lähtemisen todennäköisyyttä kuvaavan käyrän µ parametrin havaittiin korreloivan positiivisesti leveyspiirin kanssa. Kirjallisuuskatsauksen perusteella tämä työ on ensimmäinen yritys laatia todennäköisyyspohjainen populaatiodynamiikkaan perustuva kanta-arviomalli, joka pystyy huomioimaan myös taimen populaatioiden vaelluskäyttäytymisen. Mallin laajamittainen käyttö kalastuksen säätelyn tukemisessa vaatii vielä parannuksia mallin rakenteisiin.
  • Väisänen, Enni (2010)
    Ligniini on maakasveille hyvin tärkeä makromolekyyli. Se on olennainen osa esimerkiksi vettä ja ravinteita kuljettavien puusolukon solujen soluseinää. Ligniini on myös osallisena kasvien puolustuksessa muita organismeja vastaan. Lisäksi se on tärkeä osa metsien ekologiassa ja ihmisen hyödykkeenä. Prosessia, jossa kasvisolun seinään muodostuu ligniiniä, sanotaan puutumiseksi, eli lignifikaatioksi. Tällöin lignifikoituvan solun sisällä syntetoidut ligniinin monomeerit – monolignolit - kuljetetaan solukalvon yli soluseinään, jossa ne polymeroituvat ligniiniksi. Vähitellen kasvisolun soluseinän selluloosan, hemiselluloosien, pektiinien ja rakenne-proteiinien muodostama verkosto tukkiutuu ligniinistä. Lignifikoituessaan solu käy samalla läpi ohjelmoidun solukuoleman. Monolignolien synteesistä tiedetään suhteellisen paljon, samoin kuin ligniinin polymerisaatiosta. Monolignolien kuljetuksesta sen sijaan ei ole tietoa. Eri hypoteesien mukaan monolignolit voivat kulkeutua solukalvon yli joko diffuusion, golgin laitteen rakkuloiden tai kuljettajaproteiinien eli transportterien avulla. Teoria golgin laitteesta on osoitettu epätodennäköiseksi ja diffusiostakaan ei ole todisteita aidoilla solukalvoilla. Siksi pro gradu –tutkielmani tarkoituksena onkin testata hypoteesia transportterivälitteisestä kuljetuksesta. Tutkittavina ovat kasveissa hyvin yleiset ABC-transportterit, joiden tiedetään kuljettavan sekundaarisen aineenvaihdunnan tuotteita. Tutkielmassani testasin ABC-transportterihypoteesia kuusen (Picea abies) ligniiniä tuottavilla A3/85-liuosviljelmäsoluilla sekä bioninformatiikan keinoin. A3/85-soluille syötettiin radioaktiivista fenyylialaniinia – monolignolisynteesin raaka-ainetta – yhdessä ABC-transportteri-inhibiittoreiden (Reversin 121 ja vanadaatti) kanssa. Inhibiittoreilla ei kuitenkaan ollut vaikutusta solujen erittämien fenyylialaniinin fenolituotteiden tai näiden sokerijohdannaisten määrään. Bioinformatiikan keinoin taas yritettiin löytää kuusen (Picea spp.) ja männyn (Pinus spp.) EST-kirjastoista hyviä ABC-transportteriehdokkaita monolignolien kuljetukseen. Erityisesti lignifikoituvassa solukossa esiintyvää, ominaisuuksiltaan sopivaa ABC-transportteria ei kuitenkaan löytynyt. Tämän perusteella kuljetuksesta vastaa todennäköisesti jokin muu transportteri tai kuljetus ei tapahdu lainkaan transportterin välityksellä. Tutkielmassani oli testattavana myös usein esitetty ajatus monolignolien myrkyllisyydestä, josta ei kuitenkaan ole tehty asiaan kuuluvaa selvitystä. Monolignolien odotetulla myrkyllisyydellä saatetaan kasvitieteessä perustella erinäisiä väittämiä, joten ajatuksen paikkansapitävyys on syytä varmistaa. Hypoteesia monolignolien myrkyllisyydestä testasin lisäämällä ligniiniä tuottamattomien tupakan (Nicotiana tabacum) liuosviljelmäsolujen (BY-2) kasvatusalustaan monolignoli koniferyylialkoholia. Koniferyylialkoholi aiheutti solujen lignifikaation sekä tappoi solut korkeissa pitoisuuksissa. Näiden kokeiden perusteella voidaan myrkyllisyys-hypoteesin sanoa olevan mahdollinen, joskin koniferyylialkoholin mahdollinen osallisuus lignifikoituvassa solussa tapahtuvaan ohjelmoituun solukuolemaan täytyy ottaa huomioon.
  • Kallo, Henna (2021)
    During the brain development, GABAergic neurons, also referred as interneurons, migrate tangentially from the subpallium to the pallium. After intracortical dispersion, the interneurons start radial migration towards their final location in the cortex. Although the radial migration of interneurons is extensively studied, mechanisms guiding the migration remain relatively unknown. Here we studied how manipulation of cortical activity affects the radial migration and allocation of the cortical GABAergic neurons in the developing mouse brain. For this purpose, we utilized whisker trimming induced sensory deprivation in GAD67-GFP mice at postnatal days 2-5 (P2-P5) followed by cell counting in brain slices derived from P5 and P10-aged mice. In addition, we performed live-imaging of migrating neurons in organotypic cultures derived from P2 SST-TdTomato and 5HT3aR-GFP mice and cultured for 1 day in vitro. These two mouse lines roughly represent early- and late-born subpopulations of the GABAergic neurons. Live-imaging was accompanied by activity manipulations using different drugs and the Designer Receptors Exclusively Activated by Designer Drugs (DREADD) technology. Analysis of the interneurons’ allocation on the barrel cortex after the unilateral sensory deprivation revealed misallocation of GAD67+ neurons on deep cortical layers of the contralateral hemisphere of the ablation group at P5. Analysis of the tracks from the live-imaged migrating interneurons revealed altered saltatory movement behaviour of 5HT3aR+ interneurons when clozapine-N-oxide (CNO) was used to activate the electroporated GFP-GCaMP3-mCherry-hM3Dq neurons located on L2/3 of the cortex. Moreover, we observed reduced motility of migrating interneurons in the organotypic cultures treated with a KCC2 inhibitor that alters GABAA-receptor mediated transmission. Altogether, our results suggest that activity is important in promoting the radial migration of late-born interneurons during the first days of the postnatal development.
  • Aho, Niina (2022)
    Breast cancer is the most prevalent cancer in women worldwide and in 2020 it was the fifth deadliest. In Finland 2019 more than 5000 breast cancer cases were diagnosed, 94% in women and 6% in men. Until now, the high-risk breast cancer susceptibility genes have been identified including BRCA1, BRCA2 and TP53 as well as many of the moderate risk genes. Still, together all the identified genes explain only approximately half of the familial breast cancer cases. Furthermore, all the known breast cancer susceptibility genes are linked to the DNA repair mechanism. Serpina3 stands out as a non-DNA repair gene but as a gene that encodes a protease inhibitor which belongs to the serpin superfamily. Serpina3 has been associated with various diseases before and especially changes in its expression levels are linked to the tumor prognosis in many cancers including breast cancer. However, a previous study proposed that Serpina3 c.918-1G>C is a susceptibility variant for breast cancer in the Northern Finland population. This thesis a case-control study to investigate whether Serpina3 c.918-1G>C variant is associated with breast cancer in the Southern Finland population. In addition, the tumor histology and cellular markers of Serpina3 c.918-1G>C carriers were examined. This study utilized DNA collected from breast cancer patients as well as DNA from blood donors and healthy biobank controls. Breast cancer patients included both familial and unselected cases. The prevalence of Serpina3 c.918- 1G<C variant was studied by genotyping the cases and controls. Genotyping was done by TaqMan real-time PCR and carriers were further confirmed by Sanger sequencing. Moreover, statistical tests were used in the data analyses. The studied Serpina3 c.918-1G>C variant was not found to be significantly (p>0.05) enriched in the breast cancer cases. The variant was found in 0.23 % of familial and 0.36 % of unselected cases, altogether in 0.28 % of all studied breast cancer cases, the frequency in controls was 0.27 %. The tumor histology was found to be ductal in 73 % of the Serpina3 c.918- 1G>C variant carriers and only 9 % had lobular tumor. In other words, the tumor histology followed the usual distribution. All the carriers had a HER2 negative tumor and all except one case were both ER and PR positive. About half of the carriers expressed the cellular proliferation marker Ki67. As a conclusion, the results from this study do not suggest Serpina3 c.918-1G>C as a breast cancer risk variant at least in the Southern Finland population.
  • Korkman, Nadia (2023)
    Previous research has shown that beef have higher environmental impacts of land use (LU) and global warming potential (GWP) than the legumes, though the production type of beef makes a difference in its environmental impacts. Beef as a protein source produced within High Nature Value (HNV) farming systems has not yet been compared to other protein sources in terms of nutritional and environmental impact. HNV farmland is defined as farmland areas in Europe “where agriculture is a major land use and where that agriculture supports or is associated with, either a high species and habitat diversity or the presence of species of European conservation concern or both” (Andersen et al. 2003). Though beef has higher environmental impacts, it can provide an important nutrient source, especially if the bioavailability (BA) of protein is taken into account. It is known that legumes have lower BA for protein than beef, which means that the beef protein and some nutrients are made more available for the human body. It remains unknown to what degree this could affect the required mass of foods consumed to meet nutrition requirements, which could in turn effect the environmental impacts of food consumption. The aim is to assess if HNV beef and plant-based protein-rich alternatives differ in environmental impacts when BA of proteins is considered. The objectives are i) to compare HNV beef in relation to its nutritional content and environmental impact to three alternative protein sources (red kidney beans, chickpeas, and fava beans) and ii) to assess the difference in environmental impacts when BA of these protein sources is and is not considered. The results showed that taking into account protein BA affects the available nutritional value of the protein and the environmental impacts of HNV beef and the other protein sources. The impacts of GWP and LU are highest for HNV and conventional beef even when the impacts were corrected for BA. This means that the inclusion of beef produced on HNV farmland in a sustainable diet is more environmentally impactful than protein intake from legumes when considering the chosen environmental categories. Future studies should include environmental impacts such as water use, carbon sequestration, biodiversity and also different socio-cultural metrics in order to justly assess HNV farming system and HNV products.
  • Azam, Gausul (2020)
    Dog activities (urination and defecation) can be a source of nitrogen accumulation in the snowpack of urban parks. Urban parks are commonly visited by urban residents and excessive buildup of nitrogen in snowpack can be a health concern. This accumulation of nitrogen in snowpack may wash away during spring with the runoff of melting snow, which can cause the eutrophication and deterioration of lake ecosystems. In this study, I investigated the concentration of some nitrogen-related compounds along with a few physical parameters in the snowpack of urban parks and compared these between areas with high dog activities and areas with no dog activities. I hypothesized that, nitrogen concentrations will be higher in areas with high dog activities, like snowpack beside paths than in areas with no dog activities. The study was performed in 10 parks of two cities in Finland; Helsinki and Lahti. In these parks, samples were collected from snowpack immediately next to walking paths (path edge), and in control areas 8 m away from these paths, where dogs were unlikely to visit. Samples were collected from February to April of 2019. The concentration nitrogen from snow samples of both parts of parks were compared. The study showed that, the concentration of most nitrogen species, e.g. Total Nitrogen (TN), ammonium (NH4+), Total Organic Nitrogen (TON), and electrical conductivity followed a similar pattern of having higher values in snow from path edges where dog activities were the highest. However, the concentration of NO3 – and pH values were both slightly lower in the path edge samples compared to control areas undisturbed by dogs, but differences were not statistically significant. Information from this study can be useful for understanding the connection between dog activities and nitrogen build up in snowpack of urban parks, and can also be helpful for designing urban parks by considering environmental and health effects of nitrogen accumulation in the snow from dog activities. My findings can also be useful to urban waterbody related studies, e.g. eutrophication, and the accumulation of nutrients in lakes.
  • Kuan Kiat, Chew (2019)
    Proteostasis is used by cells to maintain proteome health and understanding the biological mechanisms underpinning proteostasis is important. Despite many studies on small molecule-mediated inhibition of Sec61-dependent protein translocation, a knowledge gap exists in the quality control pathway(s) of pharmacologically-displaced secretory polypeptides. Genetic screens can be used to discover proteostasis regulators of pharmacologically-displaced secretory polypeptides. Near-haploid human HAP1 cells with an inducible Tet-on GFP reporter (reporter HAP1 cells) can be used as a cellular tool to screen for human host factors pertinent to proteostasis of secretory polypeptides. The isolation of haploid-enriched reporter HAP1 cells ensures that the inability to efficiently recover bi-allelic gene trap mutants is avoided. The use of haploid-enriched cells is a prerequisite to gene trap mutagenesis screens. Here, I present data on the isolation of haploid-enriched reporter HAP1 cells that could be used as a cellular tool in gene trap mutagenesis screens. A workflow for the isolation of haploid-enriched reporter HAP1 cells was optimised using a diploid reporter HAP1 cell line as a control. Both DNA content analysis and karyotyping showed that the isolated HAP1 reporter cell lines were haploid. In the haploid-enriched HAP1 reporter cells, the GFP-reporter compartmentalised in the ER, and a Sec61-translocon inhibitor CT8 could inhibit the GFP-mediated fluorescence. The haploid reporter HAP1 cell lines produced in this study are suitable for future gene-trap mutagenesis experiments.
  • Linna, Susanna (2022)
    While there is no current consensus on what characterizes a heathy gut microbiome, there are evidence supporting the association of high microbial diversity with health stability in the host species. A growing literature suggests that microbial communities can withstand short-term anthropogenic changes with resilience, however enduring long-term changes might have a negative impact on the natural composition of host microbiome. Parasitism and anthropogenic disturbances resulting in habitat degradation might represent two of such long-term challenges to the invisible diversity of microbial communities, with consequences for the fitness of their host species. In this study, I tested whether parasitism by a specialist parasitoid and ecological changes due to anthropogenic habitat degradation affected the microbial community associated with the diapausing larvae of the Glanville Fritillary butterfly (Melitaea cinxia). The larval samples were collected in September 2012 from seven different communes across the Åland islands, from two extreme types of habitat patches (i.e., highly human-impacted habitats versus natural meadows). The parasitoid wasp Hyposoter horticola naturally parasitize approximately a third of the M. cinxia larvae in Åland, giving an opportunity to further investigate how parasitism might affect the larvae-associated bacterial community in this system. The DNA from the gut of each larva was extracted, and the bacterial V5-V6 region of the 16S gene was amplified and sequenced at the Finnish Institute for Molecular Medicine. The sequencing data was prepared for analysis by processing it through Mothur and QIIME2 data cleaning protocols. According to alpha- and beta-diversity metrics analyses, anthropogenic degradation of the habitat did not cause significant changes in the bacterial composition of the microbiota associated with diapausing larvae of M. cinxia, however, parasitism with the parasitoid wasp has a significant negative effect on the beta diversity of the microbial communities associated with the diapausing larvae.
  • Kuncheva, Ema (2022)
    Mutations in the KCNQ1 gene have been implicated in the onset of hypopituitarism. Regulating KCNQ1 expression would therefore enable future clinical research on the mechanism of the disease. CRISPR offers a flexible toolset for controlling genetic expression via knockout, knock-in, knockdown, and gene activation. Of these approaches, CRISPR activation (CRISPRa) is distinguished by its ability to induce gene overexpression in a cell’s native context, making it a valuable tool in the interrogation of genetic disorder pathogenesis. This thesis therefore tested the efficacy of a CRISPRa subsystem in increasing KCNQ1 expression. The CRISPRa subsystem, VPR, was chosen because of its high activation efficiency and the ease of controlling the activation system of its doxycycline-inducible mode of action. The cell line used for the experiment, HEK293, was similarly chosen because of its ease of culture and transfection. To validate the proper functioning of the activation system, expression rates of the related genes ASCL1 and GHRH were measured as positive controls. The activation system successfully upregulated the expression rates of the two genes. As the dCas9-VPR system is dependent on the Tet-ON operator for inducing activation in a controllable manner, a test for dCas9 leakage was conducted. RT-qPCR analysis showed the upregulation of ASCL1 expression in the uninduced state of the system, confirming the presence of dCas9-VPR leakage. The dCas9-VPR system finally aimed to test the expression rate of KCNQ1. Although one novel guide RNA successfully upregulated KCNQ1 expression, it did so inefficiently and its success was not shared by any of the other tested guide RNAs. Altogether, the dCas9-VPR system was successfully established in HEK293 cells, and the leakage of the inducible system was confirmed, however, KCNQ1 activation by CRISPRa requires further optimization.
  • Ryöppy, Selja (2022)
    A systemic change in the current modes of production and consumption, a so-called sustainability transition, is required to overcome large-scale society-transforming phenomena such as the climate change. This in turn demands changes in socio-technical systems, i.e., the networks of actors, institutions, technologies, material artefacts, and knowledge creation. In this thesis, the Finnish construction and housing sector is used as a case study, and an example of one socio-technical system. By focusing on the socio aspect of the socio-technical, I analyse how actors who are involved in the current system may inhibit or enable a sustainability transition. I seek to answer the following questions: what the relevant definitions of and foci for climate-wise action are among stakeholders in the sector in Finland; how actor-related barriers manifest themselves; and which actors could enable or speed up the transition. This thesis builds on sustainability transition theories, especially multi-level perspective and strategic niche management, to better understand actor roles and relationships. Based on a literature review, I define three actor-related barriers to transition (misaligned vision and focus, small network, and pro-regime actor resistance) and one potential enabler (intermediaries). These are then applied to the Finnish context. In this thesis, I employed stakeholder analysis as the methodology, interviewing a pre-defined set of 21 stakeholders. The results were analysed using content and social network analyses. The results suggest that although the understanding of climate-wise construction and housing is gaining a more holistic perspective, the three barriers all still manifest in the sector in Finland: all the stakeholders are engaged in energy-related topics, but hold differing foci on household choices, low-carbon materials and circularity; the network amongst actors seems relatively dense and inclusive, but improvement points emerge with closer examination; although results suggest that development has happened in the recent years, industries and incumbents are still considered too slow-moving. The importance of intermediation is also recognised by many but defining and picking potential intermediaries out of the crowd is a complex task. Overall, the sector may be moving forward in the transition, but the stakeholders create and uphold both barriers and opportunities in the process.
  • Aula, Onerva (2022)
    This study aims to understand how cities adapt to environmentally induced hazards, like floods. Extreme floods are interesting firstly, because climate change is predicted to increase flooding in several places globally in the future, and secondly, because even a small risk could be realised in the right conditions. The methods are a case study of flood adaptation in Helsinki, qualitative content analysis, interviews, and a scenario. Land use planning is chosen as the context of the case study, because densification challenges flood preparedness. The material consists of the zoning plan of Helsinki, its flood risk management related appendixes and interviews with city experts. The qualitative content analysis aims to answer the first research question: How does land use planning consider extreme floods in Helsinki? The scenario, in turn, aims to answer the second research question: In what ways might an extreme flood challenge the current land use planning in Helsinki? The interviews are mainly used to support the other methods. The results lead to one main argument, for which I present several justifications. The argument is that the flood risk management and land use planning in Helsinki, the urban structure of which is densifying, do not sufficiently consider the risk related to extreme floods, even though climate change is increasing the likelihood of such. In the end, I present some policy recommendations to change this.
  • Hynynen, Outi (2022)
    A common understanding of partnership goals is widely acknowledged to be one of the most crucial factors of a partnership project’s success. This thesis examines a partnership between the city of Espoo and five company partners and looks for processes and conditions that support a common understanding of the project goals. The aim is to support future sustainability-partnerships by giving managers concrete tools for facilitating goal-alignment by answering the research question “how did the partners accept and adapt to a common sustainability goal?” The data consists of interviews conducted with the project employees from both the city and the private entities, the project contract and web communications published by the partners. The data was analyzed using theme categories derived from the literature, seeking to first find the answer of whether the official partnership goal was adopted an accepted by the partners, and then comparing those observations to the experiences that partners had had working in the collaboration. It seems that the project goal was adopted and accepted in this case, and based on the findings five key mechanisms for how that was achieved and what future managers can therefore consider were recognized: 1) the organizational goals of the partner organizations were sufficiently compatible with the partnership goal, 2) the partnership goal was broad enough to leave room for later adjustments, 3) the partners were further divided into smaller sub-tasks with supporting sub-goals, 4) there was a lot of mandatory group-work and 5) all of the above-mentioned features were taken into account already in the design-phase of the partnership, and programmed into the day-to-day activities of the collaboration.
  • Palonen, Aura (2020)
    Early life conditions have long-term effects on the fitness and survival of individuals. Foetal development is an especially crucial period and even small changes may have large impacts on the development of individuals. Mammal foetuses may be exposed to additional testosterone either from their male littermates or their mother. This additional prenatal androgen exposure leads to masculinization of female features and behavior. In males the effects of additional prenatal androgen exposure are less drastic due to their own testosterone production. The anogenital distance, defined as the distance between the anus and genitalia, has been used to determine the sex of young mammals since males have longer anogenital distances than females. An elongated anogenital distance is an indicator of additional prenatal androgen exposure in females, and in some species also in males. It correlates with for example increased aggressiveness in both females and males. In females a longer anogenital distance has also been connected to delayed puberty and decreased fertility. I studied the effects of additional prenatal androgen exposure on weight and important life-history traits in banded mongooses (Mungos mungo) with data from a long-term study. Banded mongooses are small co-operatively breeding mammals living in family groups of 10-30 individuals across sub-Saharan Africa. Breeding is extremely synchronized within groups and in most cases all pregnant females give birth on the same day. The resulting communal litter is cared for by most adults in the group regardless of relatedness. Adults escort the pups until three months of age, providing the pup with food, grooming and protection. This early life care has long-term fitness benefits for the pups. Pregnant females may change the phenotype of their offspring via maternal effects. When the competition faced by breeding females is more intense, they compensate by investing more resources to their foetuses, making them bigger. Using the anogenital distance as a proxy for additional prenatal androgen exposure, I measured its effects on weight at early life and maturity, the amount of care received as pups and whether the individual reproduced in its lifetime or not. I hypothesized that a longer anogenital distance may be an indicator of increased competitiveness in the banded mongoose. It could lead to a cumulative advantage since more aggressive individuals may be able to access more food and care, which leads to higher maturity weight and lifetime reproductive success. I also measured the effects of resource abundance and intensity of competition during gestation on the anogenital distance of the pups. I hypothesized that mothers may prepare their offspring for future competitive environment by exposing them to androgens during gestation. In males a longer anogenital distance predicted higher weight both at early life and maturity. Higher weight at the beginning of the escorting increased the amount of care received, which in turn increased weight at maturity. A longer anogenital distance therefore has both direct and indirect fitness benefits in male banded mongooses. In females, a longer anogenital distance predicted lighter weight at maturity, suggesting that it may have negative effects on female growth and development. This study offers evidence that additional prenatal androgen exposure has long-term fitness consequences on banded mongooses and that these consequences are sex specific. Future research should focus on confirming the connection between additional prenatal androgen exposure and longer anogenital distance in this species, as well as assessing the effects of prenatal androgen exposure on survival, puberty and growth of especially female individuals.
  • Juntunen, Valtteri (2021)
    Adeno-Associated Viruses (AAVs) are quickly becoming one of the most applied vectors for gene therapy applications. In the recent years three new AAV-based gene therapies have been approved by U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA). The regulatory bodies require accurate and reliable characterisation of the clinical grade viral vectors during and after production. Analytic methods measuring the purity, potency and safety of the product support the up-stream and down-stream processes during the production and are used for final-drug substance characterisation. Median Tissue Culture Infectious Dose (TCID50) is a well-established method for measuring the infectious titer of a virus. Here, an assay for determining the infectious titer of AAVs, which has previously been used to characterise the existing AAV2 Reference Standard Material (AAV2RSM) was set up and optimised for research use at Kuopio Center for Gene and Cell Therapy (KCT). The assay utilizes the HeRC32-cell line, a HeLa clone, that stably expresses AAV Rep and Cap -proteins and in presence of adenovirus, enables the replication of recombinant AAV-vectors. The cells were grown in 96-well plates and infected with 10-fold dilution series of AAV vectors (AAV2 and AAV6) using human adenovirus type 5 as the co-infector. 72 hours post infection the vector genome replication of AAV was detected with quantitative PCR (qPCR). Thresholds for qPCR determined copy number and cycle threshold (Ct) were set and used for the determination of infection-positive wells. The 50-percent endpoint was observed and used to calculate the infectious titer according to the Spearman-Kärber method. The assay was set up and optimised with the AAV2 Reference standard material (AAV2RSM) using two different primer-probe sets (targeted sequences were; SV40 polyadenylation signal and AAV inverted terminal repeats (ITRs)). Plates infected with AAV2RSM were analysed separately with both primers resulting in mean infectious titers of 8.07 ± 3.13 x 108 TCID50 Infectious Units (IU) / mL (n = 9) and 1.27 ± 0.464 x 109 TCID50 IU/mL (n = 9) for SV40 and ITR, respectively. After the assay was set up with the AAV2RSM, an in-house AAV6 product was analysed with the ITR primers yielding 6.09 ± 3.94 x 109 TCID50 (IU) / mL (n = 5). The assay protocol was successfully set up for research use at the KCT laboratory. Improvements were added to the original protocol to increase assay robustness, accuracy and precision as well as to minimize the possibility of over-estimation of the infectious titer. The assay can be further optimised for a particular therapeutic AAV product in the research laboratory or technology transferred to a production facility for optimisation and validation for the analytics needs of a production pipeline.
  • Nykänen, Roope (2023)
    Diets of wild owls have been studied by pellets, when the nutritional value of owl prey remains unclear. Fatty acids are an essential part of animal nutrition, acting as energy reserve, building blocks of membranes and precursors for signaling molecules. I studied whether Finnish owl species have species-specific characteristics in the fatty acid profiles of adipose tissue due to different diets and feeding habits. I also compared fatty acid profiles between wild and captive owls to elucidate if the diet of captive owls resembles the diet in the wild. Fatty acids from visceral adipose tissue and a liver were transesterified to fatty acid methyl esters, which were identified and quantified by gas-chromatographs linked to either a mass spectrometry or flame ionisation detector. The fatty acid compositions were compared with Principal Component Analysis and statistical significance of the separations between species, origins and tissues were studied by Soft Independent Modelling of Class Analogies. Differences in the relative concentrations of individual fatty acids and their structural category sums were evaluated by the Kruskal-Wallis test followed by the Wilcoxon rank-sum test. Compared to wild owls, captive owl (snowy owl Bubo scandiacus and Eurasian eagle-owl Bubo bubo) adipose tissues had lower relative concentrations of many long-chain polyunsaturated fatty acids (PUFAs), such as arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid. The captive owls also had lower n-3 PUFA/n-6 PUFA ratio than the wild owls. I suggest that these differences arise from anthropogenic food given to the prey of the captive owls. In the future, the feeding and breeding of captive owls could be improved and potential health hazards prevented by giving the owls a diet rich in long-chain PUFAs, either by giving the prey more versatile diet or adding supplements to the owl’s diet. The adipose tissues of wild Eurasian eagle-owls contained higher total relative concentrations of monounsaturated fatty acids than the species belonging to the Strix genus. On the other hand, long-chain PUFAs were more prominent in the Strix owls. I suggest that these differences in the fatty acid composition are due to the disparities in feeding behaviour: the Eurasian eagle-owls eat carrions and large prey that cannot be swallowed whole, which may lead to consuming more the body outer parts of the prey. The fatty acid composition of the eagle-owls can also be affected by urban prey that have consumed anthropogenic food. In the future, the fatty acid composition of wild prey should be examined to be able to evaluate the prey composition of owls and its effect on the owl fatty acid profile with physiological consequences, the knowledge that could be used in the future decision-making that supports the conservation of owls.
  • Korhonen, Henni (2021)
    The focus of this thesis is on environmental agency in two different video games, The Sims 4 Eco Lifestyle and Final Fantasy VII Remake. The research questions aim to answer how the player can act as an environmental agent in these two games and what are the key differences between these games. The study is executed in a form of qualitative two-case case study with the help of close reading. With close reading eight different types of agencies that form the typology of this study, will be analysed in order to answer the research questions. The data for this thesis was collected by playing both games and taking notes by following close reading. The notes were then analysed with the different types of agencies. The results showed clear overlapping of the types of agencies, and it could be said that environmental agency can be used better in the game when the overlapping is happening. The agencies complemented each other and made the possible learning process in the game more fulfilling. The main difference between the game seems to be that The Sims 4 Eco Lifestyle as a life simulation game offers more diverse possibilities for environmental player agency. The studies about environmental games are mainly focused on serious games and not so much on commercial games. Video games hold great potential to engage people in environmental things especially with the help of player agency. It offers the player the ability to make meaningful choices and if they are structure well, the player can see the consequences of their agency which serves as an effective feedback which could lead to positive learning. In this case, the environmental agency in the game could be transformed into real-life environmental agency. As video games have become more immersive and their environments more realistic, it could be worth considering that separating virtual environment from the real-life one might not be necessary anymore. Therefore, games like The Sims 4 Eco Lifestyle and Final Fantasy VII Remake could serve as an example of how environmental agency within them could be harnessed into wider use.
  • Gustafson, Karl (2024)
    Although scientific knowledge is centered around academic institutions of the Global North, publications claiming to be “global” have surged recently. This thesis used a rigorous systematic literature review to identify articles with “global” in the title or author keywords, then analyzed the exact locations from where their dataset originates. Furthermore, it examined circulation metrics of each assessed article, as determined by their journal’s impact factor, to investigate if there are any discrepancies among an article’s impact factor and its global representativeness. Finally, it compared the impact factor of these “global” papers to similar non-global articles to get an idea if “global” papers are published in more reputable journals than their non-global counterparts. The results of this thesis show there is an overrepresentation of “global” environmental science data from Eastern Asia, Northern America, Western Europe, Southern Europe and Northern Europe, and an underrepresentation of environmental science data from Southern America, Eastern Europe and Northern Asia, Eastern Africa, Western Africa, Northern Africa, Middle Africa, and Central Asia. Moreover, all journals, regardless of their prestige, publish articles with these globally unrepresentative results. Yet, articles with “global” in the title or keywords circulate in journals with higher impact factors than non-global papers. My results signal that data from only a few regions dilute “global” environmental studies, while marginalizing many parts of the world. Therefore, “global” environmental science research needs a stricter threshold of globality.