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  • Razumov, Vitali (2022)
    Climatic cycles lead to changes in habitat suitability, which in turn can lead to allopatry, i.e. isolation, between populations. Lack of gene flow between allopatric populations causes them to diverge through accumulation of genetic differences that can create incompatibilities between lineages upon secondary contact in the form of lowered survivability or reproduction rate in hybrids. Incompatible genes act as reproductive barriers and keep lineages isolated by selection against hybrids, while gene flow and recombination work as a counterforce to selection promoting admixture. Reproductive barriers like these are most often found inside hybrid zones and are well demonstrated in nature, but the isolating effect of individual genetic incompatibilities on genome-wide gene flow is still an open question. Here we test if selection counteracting gene flow maintains a narrow hybrid zone between two subspecies of the meadow grasshopper Pseudochorthippus parallelus. We targeted 0,01 % of the 13 GB genome, recovering a 29,1 mean coverage per locus per individual in targeted regions, when mapping against a transcriptome. We find that, for the nuclear markers, the hybrid zone is narrower than expected under a neutral scenario of no selection, suggesting that it is maintained by selection against hybrids. We also find significant isolation by distance, suggesting gene flow across the hybrid zone despite selection against hybrids. Different parts of the genome show significant excess or deficit of heterozygotes, suggesting that selection and gene flow are heterogeneous throughout the genome. Combined, our results show that reproductive isolation between recently diverged lineages can evolve quickly despite gene flow in neutral and positively selected sites.
  • Hiltunen, Antti Olavi (2022)
    Triple-negative breast cancer (TNBC) accounts for 10-15% of all breast cancer cases and has the worst clinical outcome. Characterizing features of TNBC are high recurrence and mortality rates, and the absence of three commonly targetable breast cancer biomarkers estrogen receptor, progesterone receptor, and HER2, limiting the number of targetable therapy options. Cytotoxic CD8 positive T cells play a crucial role in the anticancer immune response and act as a major component of successful cancer immunotherapies. However, cancer cells can evade T cell-mediated killing by overexpressing programmed death-ligand 1 (PD-L1) resulting in T cell exhaustion and limited immune response via the interaction with programmed death protein 1 (PD-1). Systemic anti-PD-L1/PD-1 therapies aim to prevent this immunosuppressive mechanism, but they are burdened with potentially life-threatening autoimmunity-type adverse effects. Therefore, cancer cell-specific targets to downregulate PD-L1 could offer efficacious and less harmful ways to overcome PD_L1/PD-1 mediated immunosuppression. Serine protease hepsin is commonly overexpressed in many solid tumors where it is responsible for the activation of HGF/MET signaling pathway as well as degradation of desmosomes and hemidesmosomes leading to the loss of epithelial integrity, invasion, and metastasis. Earlier studies have linked hyperactive HGF/MET pathway to the upregulation of immune checkpoint molecule PD-L1. In this thesis, I show how pharmacological inhibition of hepsin leads to decreased MET activity and downregulation of PD-L1 in a panel of TNBC cell lines. My results demonstrate the potential of hepsin-mediated regulation of PD-L1 in tumor immunosuppression, and hint at the potential of hepsin as a therapeutic avenue towards safe and efficacious immunotherapy in the future. These results are part of a larger study addressing the role of hepsin as a regulator of PD-L1 breast cancer.
  • Koskinen, Netta (2022)
    SerpinE2 is a serine protease inhibitor (serpin) family protein that inhibits several extracellular proteases, such as thrombin, urokinase-type plasminogen activator and trypsin. Proteases and their inhibitors are often involved in cancer. SerpinE2 transcripts are upregulated in several cancers and found to predict poor prognosis of cancer patients. However, such studies regarding protein levels of serpinE2 are scarce. In this study, serpinE2 protein was analysed in three urological cancers, with patient groups that address the greatest needs for clinical biomarkers. The major aim of this study was to examine the association of serpinE2 staining with patient survival and clinicopathological features in prostate, urinary bladder and kidney cancers, and to evaluate its usability as an immunohistochemical biomarker. Tissue microarray slides from cancer patient tissues were stained immunohistochemically for serpinE2. The staining intensity was scored with four-point scale from 0 (no staining) to 3 (very intensive staining). Prostate and kidney cancer patients had been treated surgically and some of the cancers had relapsed after the surgery. In bladder cancer, association of serpinE2 with treatment response to neoadjuvant chemotherapy was evaluated. SerpinE2 expression was also measured in two prostate cancer cell lines with quantitative PCR and Western blotting. The serpinE2 staining was observed both in cancer cells and epithelial structures of benign tissues. The results showed that cancer tissue serpinE2 is not associated with relapse, treatment response or survival in prostate and bladder cancer patients. However, serpinE2 staining was more pronounced in prostate cancer tissues compared with benign tissues adjacent to cancer, and, surprisingly, the staining in such benign tissues was stronger in tissues from patients who developed metastases after surgery as compared to those without detectable metastases during 10.3-year (median) follow-up (p = 0.017). In addition, higher serpinE2 staining intensity was observed in higher grade bladder cancers (p = 0.034). In kidney cancer, on the other hand, serpinE2 staining intensity was significantly lower in patients whose cancer relapsed (p = 0.048), and high intensity predicted favourable disease-specific survival (p = 0.013). To conclude, serpinE2 is worth of further investigation in urological cancers. In prostate cancer, the possible field effect of cancer on serpinE2 in adjacent benign tissues could be examined more closely. In kidney cancer, the impact of serpinE2 on patient survival was inverse compared to transcript data in the Cancer Genome Atlas/the Human Protein Atlas database, and most other cancers. Thus, further validation studies need to be performed, and if the results hold true, serpinE2 staining could be used as part of a prognostic model predicting kidney cancer-specific survival.
  • Suomalainen, Milla (2021)
    Climate change is expected to increase the frequency and intensity of heatwaves in Finland. Heatwaves increase morbidity and mortality, especially among the elderly and chronically ill. Home care services are in an important role supporting the functioning ability and quality of life among populations vulnerable to heat. This study presents a qualitative empirical case study to understand heatwave adaptation in municipal home care services in Helsinki. The purpose of this study is to explore, describe and analyse the effects of the 2018 heatwave in the context of home care services, and the services’ capacity to adapt to heat. The data was collected by conducting semi-structured interviews with home care workers both on the operational and strategical levels. Theoretical frameworks regarding extreme heat vulnerability and local adaptive practices were used to support the analysis. The results suggest that heatwaves have caused challenges for both workers and customers. While the working ability of home care staff may be reduced due to thermal stress, the customers’ reduced functioning ability may simultaneously increase the need for care. Some workers had experienced fatigue, and customers were described having typical heat exhaustion symptoms. Workers adaptive practices were mostly reactive responses aimed at reducing the vulnerability of customers to heat. Interviewees described having taken preventive measures to limit customers’ exposure to heat and prevent adverse heat-related health outcomes by monitoring customers’ hydration more carefully. No long-term preparedness measures were identified on the strategical level. The city had supported workers by offering mineral drink bottles and providing instructions for coping in hot weather. In conclusion, workers have an active role in adaptation, but it might be limited by their own thermal stress, customers’ different health conditions and resources, as well as service-level stressors such as lack of staff. Because heatwaves are expected to increase in the future, home care services’ preparedness to heatwaves might need to be improved. It would be important to consider adaptation needs of both workers and customers as they can be interrelated in the sense, that care is dependent on workers ability to function. In a wider societal framework, the adaptive capacity of home care should be secured through providing sufficient resources for these services. The latter is even more important in the light of future trends regarding the aging of population, increase in need for home-based services and decrease in workforce availability. More research is required on the effects of heatwaves on the most vulnerable populations, what adaptation needs there might be as well as how this relates to service provision.
  • Warren, Andrew (2019)
    A novel method of somatic cell reprogramming employing CRISPR/Cas mediated gene activation (CRISPRa) may lead to improvements in the quality and efficiency of induced pluripotent stem cell (iPSC) generation by directly activating the endogenous factors of the cell. However, this method is yet to be optimized and is inefficient in its current form. Thorough characterization of the molecular events that occur during CRISPRa-mediated reprogramming could permit the fine-tuning of this method to improve iPSC production. B-lymphoblastoid cell lines (LCLs) adhere to culture plates during reprogramming, offering a form of selection for reprogramming cell populations. This thesis aimed to establish a system using LCLs for the characterisation of CRISPRa-mediated pluripotent reprogramming at the single-cell transcriptomic level. In this thesis LCL reprogramming conditions were characterized using alkaline phosphatase staining, immunocytochemistry, embryoid body formation, and live cell imaging. CRISPRa-mediated reprogramming efficiency was greatly increased by the targeting of the miR-302/367 cluster, a group of microRNAs known to improve the efficiency of transgenic reprogramming. Samples were collected for single-cell RNA sequencing (scRNA-seq) at multiple stages of reprogramming, the pluripotency of the iPSC samples was assessed, and a subset of the samples was sequenced. Clustering analysis of the sequencing data showed that the samples clustered apart from one another distinctly based on gene expression. The expression of notable genetic markers of LCLs, pluripotency, and developmental stages was consistent with the loss of somatic cell identity and rise of subpopulations characteristic of reprogramming. These results show that this is a functional system for scRNA-seq sample preparation that can be used to investigate reprogramming kinetics, and the samples collected will be part of a larger study of CRISPRa reprogramming.
  • Sokka, Joonas (2019)
    Pluripotent stem cells (PSC) can exists in both primed and naïve states. The conventionally derived human PSCs represent the later primed state of pluripotency during embryo development, while the naïve state resembles the inner cell mass (ICM) of pre-implantation blastocyst. Primed human PSCs can be reverted chemically by transient histone deacetylase (HDAC) inhibition back to the naïve state in vitro. The reverted PSCs can then be characterized based on their morphology and expression of selected naïve markers using immunocytochemistry and RT-qPCR assays. Leucine twenty homeobox (LEUTX) is one of the genes expressed during the early stages of embryo development and is capable of activating the transcription of multiple genes, including pluripotency-associated genes, which are upregulated during the human embryonic genome activation (EGA). LEUTX expression could potentially improve the naïve reversion efficiency or the maintenance of naïve PSCs by driving the transcriptome of primed PSCs back towards the earlier cell stages of embryo development, potentially even to cell stages that precede the naïve state. The aim of this thesis was to setup the naïve reversion protocol and study the effects of LEUTX on the reversion by using the generated and tested H9 activator cell line for targeted activation of endogenous LEUTX expression. First, a conditionally stabilized CRISPRa activator cell line was generated for targeted activation of endogenous gene expression in H9 cells. Then sequence-specific guide RNAs (gRNA) targeting LEUTX for activation were introduced to the activator cell line. Using the generated activator cell line during the naïve reversions allows the targeted activation of specific genes, here LEUTX, and thus enables studying the effects of these genes on PSCs during the naïve reversion protocol. The induced activator cells expressing LEUTX managed to form four times as many naïve resembling colonies during the reversion compared to the controls, but most of these were lost after changing the medium conditions towards the end of the protocol. After the reversion was complete, the reverted PSCs were characterized as naïve PSCs based on their domed morphology and the high expression of naïve markers NANOG, KLF17, TFCP2L1 and DNMT3L when compared to the primed PSCs. The naïve reversion protocol was set up and optimized successfully and can now be used as a reliable way of obtaining human naïve PSCs for further experiments studying and modelling the earlier developmental stages during embryo development. Furthermore, the generated H9 activator cell line worked as intended and can be utilized for studying the effects of other targeted genes during the reversion or in the reverted naïve PSCs.
  • Malmberg, Jenny (2022)
    Many maternally inherited bacterial infections in insect species can have negative or positive effects on their hosts. One of the diverse phenotypes these bacteria can induce in their hosts is the selective death of the male offspring at early development stages. Male-killing (MK) symbiotic bacteria have been reported in diverse insect species, and these symbionts have been shown to play important roles in shaping the ecology and evolution of diverse host species. One such species is the African Monarch butterfly: Danaus chrysippus, the target species of my study. There are four subspecies of D. chrysippus, which are geographically loosely isolated in different parts of Africa. However, they do interbreed in a hybrid zone located in central Africa. The MK phenotype in D. chrysippus is caused by a Spiroplasma bacterium, which is highly prevalent in the host hybrid zone, where the MK phenotype is so strong that females can only reproduce thanks to a few males that migrate from the surrounding subspecies. Other studies have found a correlation between the size of the female (wingspan) and infection rate. In my thesis the main objective is to study parts of the internal female structures, aiming to investigate if the size of the female reproductive organs correlates with infection as well. My hypothesis is that the female reproductive organs are smaller in highly infected areas because the rare males produce small and resource-depleted spermatophores. This study considered if D. chrysippus females collected from different populations (with different infection rates and sex-ratios) showed a difference in the size of their reproductive organs (corpus bursae and signa). Some females were also dissected to count the amount of spermatophores, and to measure their size. My study includes photographs of these particular organs (corpus bursae and signum) because those have not been published before. The results showed that (A) Danaus chrysippus has two signa, one on the ventral- and one on the dorsal side of the corpus bursa, and they are covered with spike-like structures; (B) spermatophores varied in size between females, but that population, female infection status and population sex-ratio did not significantly affect spermatophore count nor spermatophore size, and (C) in Rwanda, where the sex-ratio is slightly female-biased, the signa covered a significantly smaller portion of the females’ corpus bursa than observed in females from other populations showing either no or a strong female sex-ratio bias.
  • Holla, Annele Jenni Tuulikki (2021)
    Binge eating disorder (BED) is a common eating disorder that includes eating a large amount of food in a short period of time and is often associated with obesity. Patients can suffer from stress, anxiety, and metabolic syndrome caused by the weight gain, but no effective medication for both psychological and physiological issues have been discovered. This thesis studies the potential of short-chain fatty acids (SCFA) in reducing binge-like eating behaviour in a mouse model that does not include food restriction. The model includes a 24 h bingeing period with high-fat food once a week. SCFA butyrate, propionate, and acetate were administered to mice via 1 g/kg i.p. injections or 200 mM drinking water for three days, and their effects on energy intake during the bingeing period were measured. The results show that SCFA can significantly reduce binge-like eating behaviour in mice in the short term, but long-term effects vary. I.p. butyrate, propionate, and acetate decreased energy intake by 68%, 57%, and 62% during the first hour, respectively. SCFA via drinking water did not decrease energy intake a lot, and the results were inconsistent between animals. These results suggest a potential for SCFA to attenuate bingeing episodes when administered acutely, but the mechanisms remain to be discovered.
  • Manninen, Juulia (2022)
    Immune-mediated diseases, such as various allergies and asthma, are increasing rapidly in an urbanized world where biodiversity is steadily declining. Decreased biodiversity and homogenous microbiota have been associated with weaker immune defence. Studies show that contact with the natural environment enriches the human microbiota, promotes immune response, and protects against allergies and inflammatory diseases. For this reason, in order to prevent immune-mediated diseases, solutions have been sought from nature-based approaches in which the immune system encounters environmental microbial stimuli in a natural way. The aim of this master's thesis was to study how different nature-based materials (sod and forest floor) affect the skin microbiota of kindergarten-age children and to examine how different factors such as varying weather conditions and different sampling times affect the results. The results supported the hygiene hypothesis and previous research according to which increasing biodiversity can have a positive effect on human skin microbial communities. A positive effect on children's skin was achieved with sod alone, which is important information in the development of suitable biodiverse materials for urban planning. The results also supported the surmise that different weather conditions and sampling methods can significantly affect the results.
  • Vuoristo, Mikko (2020)
    Eliölajit ovat jatkuvassa vuorovaikutuksessa niin fysikaalisen ympäristönsä, kuin muiden eliölajienkin kanssa. Nämä vuorovaikutukset voivat olla osapuolille negatiivisia, neutraaleja tai positiivisia. Fasilitaatio tarkoittaa sitä, että joku laji edesauttaa toisen lajin selviytymistä. Äärimmäinen esimerkki fasilitaatiosta on perustajalaji. Perustajalaji on laji, joka pelkällä läsnäolollaan tarjoaa muille eliöille kriittisiä resursseja, joita ilman muut lajit eivät voi selviytyä. Nämä resurssit voivat olla esimerkiksi ravintoa, suojaa tai elintilaa. Alustaansa kiinnittyvät simpukat ovat perustajalajeja, joita tavataan kaikilta maailman merialueilta. Esiintyessään tiheinä kasvustoina kalliorannoilla ne tarjoavat lukuisille selkärangattomille eläimille suojaa aallokon voimalta ja pedoilta, ravintoa ja elintilaa lisääntyneen sedimentaation myötä, sekä runsaasti sekundaarista kiinnittymispintaa. Alustaansa kiinnittyvät simpukat muodostavat perustan habitaatille, joka lopulta muotoutuu simpukoiden ja muiden lajien yhteisvaikutuksella. Vähäsuolaisessa ja -lajisessa Itämeressä sinisimpukka (Mytilus trossulus x edulis) on alustaansa kiinnittyvänä simpukkana erittäin tärkeässä roolissa. Sinisimpukkaa esiintyy pinnan läheltä aina kymmenien metrien syvyyteen asti, kunhan kiinnittymiseen sopivaa alustaa vain on tarjolla. Simpukoiden esiintymiseen Itämeressä vaikuttavat monet tekijät, joista tärkeimpinä ovat aallokko joka aiheuttaa fysikaalista stressiä, ja alhainen, itää ja pohjoista kohti pienentyvä suolapitoisuus joka aiheuttaa fysiologista stressiä. Paikoin erittäin runsaina esiintyvät sinisimpukat edesauttavat sedimentin kertymistä muodostamansa kolmiulotteisen matriisin onkaloihin mikä mahdollistaa myös pehmeän pohjan lajien esiintymisen kalliorannoilla. Sinisimpukkayhteisössä onkin piirteitä sekä pehmeistä, että kovista pohjista, mikä tekee niistä edullisia elinympäristöjä runsaalle määrälle erilaisia selkärangattomia eläimiä. Tässä tutkimuksessa tutkittiin sisäsaaristosta ulkosaaristoon voimistuvan aallokon vaikutusta sinisimpukka-rakkohauru -yhteisön rakenteeseen kolmella lähellä toisiaan sijaitsevilla merialueilla läntisellä Suomenlahdella, missä suolapitoisuus laskee läntisimmän ja itäisimmän tutkimusalueen välillä ainoastaan muutamilla promillen kymmenyksillä. Näytteitä noudettiin sukeltamalla 36:sta eri pisteestä kolmen metrin syvyydeltä rakkohauruvyöhykkeeltä, neljältä eri avoimuusvyöhykkeeltä. Näytteistä havaitut eläintaksonit tunnistettiin ja eläinten yksilömäärät laskettiin, ja sinisimpukoiden sekä rakkohaurun (Fucus vesiculosus) kuivapaino määritettiin. Tilastollisilla menetelmillä selvitettiin eliöyhteisön rakenteen eroja näillä kolmella alueella, sekä kasvavan avoimuuden vaikutusta. Lisäksi selvitettiin korreloivatko tavattujen eläinlajien yksilömäärät sinisimpukan tai rakkohaurun biomassan kanssa. Sinisimpukka oli kaikilla näytepisteillä runsain tavattu laji, ja jäljessä yksilömääristä puhuttaessa sinisimpukkayksilöitä ei huomioida. Alueet eivät eronneet toisistaan taksonien tai eläinyksilöiden kokonaismäärien osalta, mutta yksittäisillä taksoneilla eroja kuitenkin havaittiin. Avoimuudella havaittiin olevan merkittävä vaikutus eliöyhteisön rakenteeseen. Avoimuuden kasvaessa havaittujen taksonien määrä laski ja runsaimmat taksonit vaihtuivat sedimenttiä suosivista nilviäisistä vapaasti uiviin äyriäisiin, sen sijaan eläinten kokonaisyksilömäärissä merkitseviä eroja ei havaittu. Merkittävä osuus tavatuista yksittäisistä taksoneista korreloi negatiivisesti kasvavan avoimuuden kanssa, avoimuuden kanssa positiivisesti korreloivia taksoneita oli vähemmän. Sinisimpukoiden biomassan kanssa havaittiin korrelaatiota usealla taksonilla, kaikki positiivisia, sen sijaan rakkohaurun biomassan kanssa korrelaatiota havaittiin ainoastaan yhdellä taksonilla. Tämä tutkimus osoittaa, että avoimuudella on selkeä vaikutus perustajalajina toimivan sinisimpukan ympärille muotoutuneeseen eliöyhteisöön ja sen rakenteeseen. Suolapitoisuuden vähäinen lasku tutkimusalueiden välillä sen sijaan ei vielä merkitsevästi vaikuta sinisimpukkayhteisön rakenteeseen, vaikka yksittäisillä lajeilla - merkittävimpänä juuri sinisimpukka - viitteitä vaikutuksista havaittiinkin. Sinisimpukan merkitys muuhun lajistoon on merkittävä, rakkohaurun merkitys on sen sijaan varsin vähäinen.
  • Nousiainen, Inari (2020)
    Viime vuosikymmenien maaseutuympäristöjen muutokset, kuten lisääntynyt maankäytön tehostuminen ja kasvinsuojeluaineiden käyttö, ovat saaneet monet Euroopan maaseutuympäristöjen lintujen kannat taantumaan. Jotta lintukantojen muutoksia voitaisiin ymmärtää ja suojelutoimia suunnitella, on lintujen elämänkierron eri vaiheiden, kuten pesimämenestyksen ja elossasäilyvyyden, sekä selviytymiseen vaikuttavien tekijöiden tutkiminen tärkeää. Myös Suomessa maaseutuympäristöjen linnuston tutkimukselle on tarvetta: uusimmassa Suomen luonnon uhanalaisuusarvioinnissa (2019) uhanalaisia tai silmälläpidettäviä maatalousympäristöjen lintulajeja oli 18, mikä on neljä enemmän kuin neljä vuotta aiemmassa arvioinnissa. Yksi näistä on Suomen voimakkaimmin taantunut maalintulaji, peltosirkku (Emberiza hortulana), jonka kanta on kutistunut 80-luvulta alle yhteen prosenttiin. Tämän tutkielman tavoitteena on selvittää yksilöllisin tunnistein merkittyjen lintujen avulla, onko Suomen aikuisten peltosirkkukoiraiden elossasäilyvyys ollut vuosina 2013–2019 poikkeavan matala, mikä voisi selittää lajin kantojen voimakasta laskua. Tavoitteena on myös tarkastella elossasäilyvyyden vuosittaista ja alueellista vaihtelua, peltosirkkujen kannankehityslukuja, sekä selvittää vaikuttivatko muuttokäyttäytymisen tutkimista varten kiinnitetyt valopaikantimet (loggerit) elossasäilyvyyteen. Tutkielman aineisto on kerätty vuosina 2013–2019 niiltä alueilta, joilla peltosirkun on havaittu pesivän. Aineisto koostuu 210 aikuisen (+1kv; vanhempi kuin ensimmäistä kalenterivuottaan elävä lintu) peltosirkun pyynti-jälleenpyynti-aineistosta, jota käyttäen tehtiin elossasäilyvyysanalyysit, sekä peltosirkkujen reviirikartoituksesta, jota käytettiin kannankehityslukujen laskemiseen. Elossasäilyvyysanalyysit tehtiin käyttäen CJS -mallia (Cormack-Jolly-Seber) MARK -ohjelmassa. Analyysia varten aineistosta poistettiin naaraat, paikkaansa vaihtaneet peltosirkut ja Itä-Suomen vaillinaisesti seuratut yksilöt, sekä muodostettiin kaksi pääanalyysia: koko Suomen analyysi ja alueellinen analyysi. Koko Suomen analyysissa tarkasteltiin, oliko loggerilla vaikutusta linnun elossasäilyvyyteen ja vaihteliko elossasäilyvyys vuosien välillä. Alueellisessa analyysissa Suomen peltosirkut jaettiin kolmeen alueeseen: pohjoiseen, lounaiseen ja eteläiseen. Analyysissa tarkasteltiin, onko elossasäilyvyydessä eroa alueiden välillä ja vaihteleeko elossasäilyvyys vuosien välillä. Lopuksi laskettiin R-ohjelmiston Rtrim -paketilla kannankehitysluvut koko Suomelle sekä alueellisessa analyysissa käytetyille kolmelle alueelle. Analyysin tulos oli että Suomen peltosirkkukoiraiden elossasäilyvyys vuosina 2013–2019 oli 43,3 % koko tutkimusjaksolle. Loggeri vaikutti negatiivisesti elossasäilyvyyteen, mutta alueiden tai vuosien välillä ei ollut merkitsevää vaihtelua. Kannankehitysluvut olivat laskusuuntaisia ja niissä oli alueiden välillä merkitseviä eroja. Koko Suomessa kanta laski 19,4 % vuodessa. Alueista suurin lasku oli lounaassa, jossa kanta laski 26,5 % vuodessa. Suomen peltosirkkukoiraiden elossasäilyvyysanalyysin tulosta verrattiin muiden samankokoisten (10–40g) pitkän matkan muuttavien varpuslintujen julkaistuihin elossasäilyvyyslukuihin (41,9-58,0 %; 15 eri lajia). Vertailun perusteella Suomen peltosirkkukoiraiden elossasäilyvyys ei ole ollut poikkeavan matala, eikä siten vaikuta olevan ainakaan tärkein voimakasta kannanlaskua selittävä tekijä. Tämän tutkielman tulosten mukaan Suomen peltosirkkujen kannanlaskun taustalla on luultavimmin muita tekijöitä kuin aikuisten koiraiden elossasäilyvyys, kuten aikuisten naaraiden tai nuorten lintujen (ensimmäistä kalenterivuottaan elävät linnut) kestämättömän suuri kuolleisuus tai kestävälle populaatiokehitykselle liian heikko pesimätulos. Elossasäilyvyydessä ei havaittu myöskään alueellisia vaihteluita, mutta kannankehitysluvuissa näin oli, minkä perusteella ainakin jotkin populaatiokokoa säätelevät tekijät ilmenevät joillakin pesimäalueilla voimakkaammin kuin toisilla. Näin ollen eritoten pesintämenestykseen vaikuttavia tekijöitä kannattaisi kiireellisesti tutkia, jotta peltosirkun kannankehityksen suunta saataisiin tietoon perustuvan suojelusuunnitelman avulla käännettyä.
  • Kallio, Jarkko (2017)
    The spreading of non-indigenous species by human activities is a growing problem globally. Invasive species are generally assumed to have negative impacts on ecosystems, because they threaten biodiversity and the balance of ecological systems. Other simultaneous changes in the ecosystem can impact, or intensify the effects of, the invasion. The invasive rock shrimp Palaemon elegans, is an invasive species that has spread to the Baltic sea via human introduction in the early 2000's. There have also been drastic changes in the ecology of Baltic sea, particularly the increase of primary production. A common mesopredator, the three-spined stickleback Gasterosteus aculeatus, has greatly increased in number in the Baltic sea in recent years. It is presumed to influence the primary production by predation of zooplankton grazers. P. elegans is an omnivore that both grazes filamentous green algae, as well as preys upon the invertebrate grazers that live amongst the algae. If the invasion of P. elegans influences the populations of stickleback, it might also influence the accumulation of primary production. Recent studies have shown, that P. elegans can potentially influence the reproductive behavior of stickleback, but the effect on the success of reproduction has not been proven. This study was composed of two parts: field monitoring and a mesocosm experiment. In the monitoring, individuals of stickleback and P. elegans were caught, counted and measured in three shallow bays and two depths from May to August of 2015. The differences in number of caught individuals were analyzed using Kruskal-Wallis analysis of variance and differences in lengths were analyzed with Mann-Whitney U-test. The effect of P. elegans on sticklebacks was analyzed using covariance analysis. The hypothesis was, that the amount of P. elegans and stickleback or their lengths would show negative correlation, which could be a sign of interaction through predation or resource competition. In the mesocosm experiment stickleback fry were exposed to P. elegans or a non-parent stickleback in tanks with filamentous algae Cladophora glomerata and associated fauna. The resulting differences in in fry number, fry size and the amount of algae between treatments in the tanks were analyzed with Kruskal-Wallis analysis of variance. Correlations between variables were analyzed using Spearman's rank-order correlation. The hypothesis was that P. elegans would have a negative effect on the amount of fry through predation, or the size of the fry through perceived predation risk. In the field study, no significant correlations were found between P. elegans and sticklebacks, and therefore the results do not suggest a causal link between the two species. Differences between the areas were found, which were attributed to physical differences between the areas. In the mesocosm experiment not enough repetitions were accumulated to provide reliable results. The increase of P. elegans in the Baltic sea is most likely not going to affect the three-spined stickleback via direct predation. P. elegans appears in the shallow bays where sticklebacks reproduce later in the year and it consumes mainly algae and invertebrates. Even though P. elegans will feed on fish eggs if there is an opportunity, stickleback males defend their nests fiercely. The invasion of P. elegans in the Baltic sea is very recent, but it can affect the accumulation of filamentous algae due to their great number. It feeds on invertebrates, but can itself be a potential food item in the diet of ie. cod.
  • Laitinen, Paavo (2022)
    Schizophrenia (SZ) is a neurodevelopmental psychiatric disorder with high heritability. Patients with SZ commonly suffer from sleep problems of different types, some of them with potential underlying abnormalities in sleep oscillations. These changes in sleep are usually accompanied by deficits in cognitive performance. However, the relationship between sleep, cognitive performance and genetic risk factors are not well known in SZ. In this study, patients were selected from a nation-wide SUPER -cohort. Sleep and circadian rhythm of patients with SZ (n = 26) and age-matched healthy controls (n = 11) were followed for a week with actigraphy and sleep diary, combined with word-pair -memory task and polysomnography at the end of the week. The results showed that patients spend more time in lighter sleep and awake during the night than controls. As expected, patients had impaired sleep spindle density compared to controls. Additionally, patient had worse overnight memory consolidation. However, sleep spindle density was not associated with memory performance. Lastly, polygenic risk score (PRS) for long sleep, but not PRS for SZ, predicted lower spindle density in patients, which could be indirect evidence for deviated neurophysiological processes of sleep behind the observed deviations in EEG oscillations among the patients. These results show that, as compared to controls, patients with SZ demonstrate abnormalities in their sleep, which can be seen both in macro- and microstructures of sleep. Further analyses of the interplay between sleep oscillations and genetic risk factors are likely needed to link sleep problems with overnight memory consolidation.
  • Raulo, Aura (2015)
    Microbiota, the microbial communities living in the gut, skin and glands of vertebrates, is the functional link between a physiological individual and it s surrounding ecosystem. Mutualistic microbes play a role in social systems as well, since they are transmitted through social behaviors and claimed to affect host sociality and behavior. Furthermore, individual stress physiology can affect both behavior and microbiota. I took first steps to reveal the role of gut microbiota in the social dynamics of a group-living cooperative primate, the red-bellied lemur (Eulemur rubriventer). Gut microbiota was affected by seasonal change, stress hormonal profile and pregnancy, and individuals were found to have a strongly group-specific gut microbial composition, highlighting the role of social environment in determining gut microbial composition. Unlike expected, individual sociality was negatively associated with gut microbial diversity. Gut microbiota seems to be largely determined by social factors in this species, indicating that social transmission of beneficial microbiota might have played a role in the evolution of sociality.
  • Atti, Sanna (2021)
    Underwater light climate in mountain lakes is controlled by dissolved organic carbon concentrations and by lake ice regimes. Both are affected by local, regional and global variables linked to anthropogenic disturbances such as climate change and atmospheric pollution. Aim of this work was to investigate changes in underwater light climate over the past ~200 years in two oligotrophic mountain lakes and how it reflects on diatom (Bacillariophyceae) guild distribution. For these aims, diatom communities and ecological guilds were analyzed from sediment core and contemporary habitat samples along a depth gradient. In addition, sediment inferred chlorophyll a (CHLa) and lake water total organic carbon (TOC) were analyzed to detect development of primary production and lake water carbon content. Results showed that acidification of the lakes together with climate induced changes have been important drivers of the ecology of the lakes. Lake water TOC showed a decline and subsequent increase in line with the acidification and subsequent recovery of the lakes, likely affecting underwater light climate in the lakes. However, this did not reflect unambiguously into changes in diatom functionality. Warming has likely contributed to diversification of the diatom community over the study period while no distinct increases were observed in whole lake primary production. Overall, if the present study could not distinguish the exact role of underwater light in driving changes in diatom communities and functional traits, the result show that human pressures have left distinct imprints in the development of biotic communities in these remote mountain lakes.
  • Porkka, Kaija (2017)
    Chitinolytic enzymes belong to a group of pathogenesis-related proteins, which are induced in plants by a pathogenic attack. They have also been shown to function in abiotic stresses and related to signalling. Chitinases catalyze the degradation of β-1,4-N-acetyl glucosamine units of chitin. Chitin is not found in plants, but for example the shells of invertebrates, cell walls of certain fungi, algae and bacteria contain it abundantly. Lately chitinases have gathered attention because of their potential utilization possibilities in medicine, agriculture, food industry and biofuels. Strong chitinase gene expression and also chitinolytic activity has been found in a spruce (Picea abies L. Karst.) cell culture, which produces apoplastic lignin into the medium. Plant chitinases are known to be induced also in developmental processes. Chitinase-like genes have been shown to be essential in cellulose synthesis and in development of cell walls and tracheary elements and also affected the localisation of lignin in tissues. Therefore, the secretion of chitinases into the culture medium has not necessarily been caused by stress and chitinases might use also some endogenic substrate in addition to chitin. Because chitin is a structural component of plant pathogens but not present in plants and the growing circumstances of the studied aceptic spruce cell culture were stable, the research hypothesis was, that the secreted chitinases in the culture medium were not a stress reaction but related to development and besides chitin of the pathogens they utilize some own polysaccharide substrate of spruce. Additional hypothesis was connection of the strong expression of chitinases and chitinase-like genes in the culture medium and the production of apoplastic lignin by the spruce cell line. The aim of the study was to characterize the chitinases and chitinase-like enzymes of the spruce cell suspension culture medium and developing xylem by isolating, purifying and cloning them and by producing them heterologously. The aim was also to identify the putative endogenous substrates for the chitinases and chitinase-like proteins to reach better understanding about the meaning of the chitinases in the development of the spruce tissues. Two chitinases of the spruce cell suspension culture were isolated and purified by chromatographic methods. One chitinase gene in spruce cell culture and one chitinase-like gene in spruce xylem were cloned, after which the chitinases and chitinase-like proteins were produced in Pichia pastoris yeast. The total proteins of the culture medium, the purified chitinases isolated from the medium and the chitinases and chitinase-like proteins produced in P. pastoris were used to examine their substrate alternatives with the carbohydrate microarray method. The connection between apoplastic lignin and the chitinolytic enzymes in culture medium was not found and obvious candidates for the endogenous substrates were not detected. However, the mannan degradation in the presence of the chitinases was strong enough to give reason to further analyses.
  • Niemeläinen, Elina (2020)
    Extracellular vesicles (EVs) are lipid bilayer-enclosed nano-sized particles that are found in all body fluids. EVs are part of normal cell functions and they can carry for example proteins, RNA and lipids between cells. This makes them potential candidates as drug delivery vehicles. When nanoparticles are introduced to blood plasma, a plasma protein structure is formed on their surface, called the protein corona. The formation of a protein corona is a dynamic process, and the proteins are binding to the corona depending on their affinity to the nanoparticle surface. When administrating nanoparticles to cells, protein corona has a big impact on the half-life and cellular uptake of the particles. The aim of this work was to study the plasma protein corona of PC-3 derived EVs, and to investigate methods for protein corona isolation. First, EVs and lipoprotein particles were removed from fresh frozen plasma by membrane filtration. Using this filtrated plasma, we then tested plasma-EV incubation and removing of free plasma proteins by simple ultrafiltration. Removing of free plasma proteins was also examined by size-exclusion chromatography (SEC). The resulting EV-protein corona complex was visualized with SDS-PAGE. EVs were characterized with nanoparticle tracking analysis and western blotting. Of these two methods used, SEC appeared to be more convenient and efficient way to remove the free plasma proteins from the EV-protein corona complex. The method still requires further development and testing in order to perform optimally.
  • George Varghese, Mebin (2021)
    The Glanville fritillary (Melitaea cinxia) butterfly inhabiting the fragmented meadows and pastures in the Åland Islands, Finland, has a classic metapopulation structure: its long-term persistence depends on frequent re-colonization events counter-balancing the extinctions of local populations. The spatial structure and the temporal dynamics of the metapopulation are likely to influence genetic variation within and among local population networks. With high population turnover, population declines accelerate genetic drift, potentially leading to a reduction in neutral genetic diversity. This loss is likely to be counteracted with immigration bringing in new alleles especially in well-connected populations. Dispersal has indeed been shown to be a key mechanism in maintaining genetic variation and adaptive potential in fragmented landscapes. In my MSc-thesis, I am utilizing long-term monitoring and genetic data collected from semi-independent networks from the main Åland region (Saltivik) and from two isolated island networks Föglö and Sottunga. Specifically, I investigate how genetic variation varies in time and space, in relation to demographic change and whether the responses vary among well- and poorly-connected networks and/or between island and mainland networks. My results showed that the total number of nests fluctuated in all the networks across time. Heterozygosity appeared to track the changes in population abundance but this tracking varied among the networks. Although connectivity did not explain the change in heterozygosity during the decline years, allele frequencies shifted over time and the speed of change in allele frequencies differed among networks.
  • Wang, Shengyu (2021)
    Natural scientists study a wide variety of species, but whether they have identified all studied samples correctly to species is rarely evaluated. Species misidentification in empirical research can cause significant losses of money, information, and time, and contribute to false results. Thus, I study the abundance of species misidentification and ecologists’ perceptions of such mistakes through a web survey targeting researchers from scientific institutes around the globe (including universities, research societies and museums) who completed their doctoral degree in any ecology-related field of science. I received 117 responses with either work or educational background from 30 countries. I found that species misidentification widely existed in respondents’ research: almost 70% of the respondents noticed species misidentification in their own research, while the estimated proportion of existing studies with species misidentification was 34% (95% CI: 28% - 40%). Although misidentification was mainly found during specimen collection, specimen handling and data analysis, misidentifications in reporting stages (writing, revision and after publishing) could persist until publication. Moreover, according to respondents, reviewers seldom comment about species identification methods or their accuracy, which may affect respondents’ (both leading and not leading a research team) low reporting frequency about the possibility of misidentification. Expert checking, training students, and DNA barcoding are the most prevalent approaches to ensure identification accuracy among respondents. My results imply that species misidentification might be widespread in existing ecological research. Although the problem of species misidentification is widely recognized, such an issue seldom be appropriately handled by respondents. To increase the accuracy of species identification and maintain academic integrity, I suggest that researchers need to focus more on the study species (e.g., sampling process, identification method, and accuracy) when writing and reviewing papers. Furthermore, I appeal for guidelines about reporting species identification methods and their accuracy in papers, as well as research on education about identification skills in universities, as these two topics may constrain the precision of species identification.
  • Horsma-Heikkinen, Jenni (2020)
    The antibiotic resistance of pathogenic bacteria is becoming a major problem in treating bacterial infections and development of new antibiotics is very challenging. In traditional phage therapy the bacteriophages, viruses that infect bacteria, are being used as an optional treatment to eliminate infectious agents. Methicillin resistant Staphylococcus aureus (MRSA) is resistant to several currently used antibiotics and is one of the most common antibiotic resistant bacteria causing infections. Therefore, it is a potential target for the phage therapy. Some of the Staphylococcus aureus strains produce several different enzymes and toxins which can be harmful to patients. Products developed for phage therapy purposes need be free from the material originated from host bacteria. In this study, three different methods were tested for the purification of bacteriophages infecting S. aureus. The main goal was to produce phage lysates with purity and phage concentration suitable for therapeutic purposes using a fast and aseptic procedure upgradable for large volumes. The tested methods were ultrafiltration with filter tubes from two different manufacturers (Sartorius Vivaspin 6 ja Merck Millipore Amicon Ultra 4), polyethylene glycol (PEG) precipitation and ion exchange chromatography. Three different bacteriophage strains were used. One was isolated from a commercial Russian phage therapy product (vB_SauM_fRuSau02) and the other two from feces of pigs (vB_SauS_fPf-Sau02 and vB_SauS_fPfSau03). Host bacteria strains for the first bacteriophage were S. aureus strains TB4 and 13KP originally isolated from human infections. Two host strains for the latter two phages were MRSA strains isolated from healthy pigs. Purification of the phage lysates was evaluated by measurement of enterotoxins produced by S. aureus bacteria, measurement of free double stranded DNA (dsDNA), and by cytotoxicity test in cell cultures. All evaluation methods were commercially available tests. To determine how much of the bacteriophages were lost in the process, the phage concentrations of the lysates were determined before and after the purification and recovery rates were calculated for the viruses. After two separate ultrafiltrations, the recovery rates of the bacteriophages were mainly good, but there was a lot of variation in the results. The lowest recovery rate calculated was 5%, the highest 57%, and the mean of all the rates 24%. In this study the ion exchange chromatography was combined with ultrafiltration which was used in pre-cleaning of the lysates and changing the phages in a buffer suitable for the chromatography. The recovery rates from the ion exchange chromatography varied between 14-26% but the results may be affected by the ultrafiltration steps performed before and after, since a lot of variation was seen in ultrafiltration processes. PEG precipitation was performed for one phage lysate only in order to compare the laboriousness of the method and the rates of the recovery to the other methods used. The rate of recovery from the PEG precipitation was 9,5% which was fairly low. The purity of this lysate was not evaluated since the method was estimated to be too laborious compared to the other methods. Ultrafiltration turned out to be an efficient method in the removal of small protein molecules, such as enterotoxins from bacteriophage lysates. With two sequential ultrafiltrations 96-99% of the enterotoxins in the lysates were removed. The removal of the free dsDNA was also successful but there was variation between the phage lysates. Approximately 67-93% of the free dsDNA was removed but it is possible that some of the measured DNA originated from lysed bacteriophages as their genome also consists of dsDNA. Ion exchange chromatography produced extremely well purified phage products. The fractions had no enterotoxins left or the amount was below the detection limit of the test (<0,5-1 ng/g). Ion exchange chromatography was able to remove 96-99% of the free dsDNA of the lysates. It is possible that some of the DNA left in the lysates originated from the bacteriophages lysed during the process or in storage after that. When comparing how simple and fast the methods were, the ultrafiltration turned out to be superior. It can be used in fast production of bacteriophage products for the treatment of S. aureus infections. The purification achieved with the ultrafiltration should be adequate for a topical use of the product. When higher purity products are required, e.g. for administrating the product intravenously, ion exchange chromatography might be a safer option.