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  • Ojalehto, Tuomas (2016)
    Proteins responsible for homologous recombination are collectively called recombinases. They also have an important role in maintaining genome integrity. Recombinases are found in all three kingdoms of life. The first identified and characterized recombinase was RecA from Escherichia coli. Recombinases exhibit ATP hydrolysis coupled DNA-binding activity and strand exchange activities during homologous recombination. Homologous recombination produces new genetic combinations for evolution and general way to describe the different steps of homologous recombination is a DSBR model. Homologous recombination occurs in eukaryotic and prokaryotic cells during meiosis crossover and horizontal gene transfer, respectively. The homologous recombination machineries are remarkably complex and synergistic and much is not known about detailed mechanisms for a majority of the species. More recently, recombinases have been used in isothermal nucleic acid amplification methods, mainly in recombinase polymerase amplification RPA and strand invasion based amplification SIBA. The aim of this study was to identify, clone, produce and analyze the functionality of novel recombinases from bacteria and viruses. The acitivity for single-stranded DNA binding and strand exchange was studied. The compatibility of the produced recombinases in strand invasion based amplification SIBA method was evaluated. Two recombinases from Enterobacteria phages T2 and RB69 were found to be functional and compatible in three SIBA assays.
  • Varis, Vera (2020)
    Protein kinases are signaling molecules that regulate vital cellular and biological processes by phosphorylating cellular proteins. Kinases are linked to variety of diseases such as cancer, immune deficiencies and degenerative diseases. This thesis work aimed to identify direct substrates for protein kinases in the CMGC family, which consists of the cyclin-depended kinases (CDK), mitogen activated protein kinases (MAPK), glycogen synthase kinase-3 (GSK3) and CDC-like kinases (CLK). CMGC kinases have been identified as cancer hubs in interactome studies, but large-scale identification of direct substrates has been difficult due to the lack of efficient methods. Here, we present a heavy-labeled 18O-ATP-based kinase assay combined with LC-MS/MS analysis for direct substrate identification. In the assay, HEK and HeLa cell lysates are treated with a pan-kinase inhibitor FSBA which irreversibly blocks endogenous kinases. After the removal of FSBA, cell lysates are incubated with the kinase of interest and a heavy-labeled ATP, which contains 18O isotope at the γ-phosphate position. Resulting phosphopeptides are enriched with Ti4+- IMAC before the LC-MS/MS analysis, which distinguishes the desired phosphorylation events based on a mass shift caused by the heavy 18O. With this pipeline of methods, we managed to quantify and identify direct substrates for 26 members of CMGC kinase family. A total of 1345 substrates and 3841 interacting kinase-substrate pairs were identified in cytosolic cell lysates, from which 165 were annotated in the PhosphoSitePlus® database. To identify substrates for kinases with nuclear localization, ten kinases were tested with nuclear HEK cell lysate. We identified 194 kinase-substrate pairs, 141 of which were unique to the nuclear fraction and 27 annotated in the PhosphoSitePlus® database. Finally, kinases with outstandingly high amounts of novel substrates were subjected to gene ontology analysis. We were able to link the gene ontology classifications of novel substrates to the biological processes regulated by the kinase of interest. These results indicate that heavy-labeled 18O-ATP-based kinase assay linked LC-MS/MS is a useful tool for large-scale direct kinase substrate identification.
  • Domènech Moreno, Eva (2017)
    In this Master’s project, I have studied a mammalian serine-threonine kinase NUAK2 implicated in human disease but whose molecular functions and interacting proteins are as of yet poorly characterized. The goal was to identify new interacting proteins to increase understanding of the molecular functions and potentially link to human physiology and disease. Recent work from the host lab shows NUAK2 loss in cultured primary cells mimics loss of the tumor suppressor LKB1 which also acts upstream of NUAK2, together suggesting NUAK2 could be involved in tumor suppression. Currently, only two protein-protein interacting proteins with NUAK2 have been identified: NUAK2 is targeted to actin stress fibers by the myosin phosphatase Rho-interacting protein (MRIP), and it is involved in regulating cell contractility by affecting indirectly the phosphorylation cycle of the myosin light chain through inactivation of the myosin phosphatase target subunit 1 (MYPT1). In this project, I utilized a novel protein-protein interaction screening method that utilizes proximity-dependent biotin labeling to identify new interacting proteins with NUAK2 in human embryonic kidney cells (HEK 293). This method is based on fusing an E.Coli promiscuous biotin ligase, BirA*(R118G), to the investigated protein. The BirA*(R118G) ligase biotinylates all the proteins in close proximity of the fusion protein creating a history of protein-protein associations over time. Afterwards, the biotinylated proteins can be isolated by affinity purification methods and identified by mass-spectrometry. The screening identified the previously known interaction partners of NUAK2 indicating it was technically successful. In addition, I also identified in total 108 novel potential protein interaction partners for NUAK2. One of the top hits was Cytospin-A, a cross-linking protein between microtubules and actin cytoskeleton, supporting a role of NUAK2 as regulator of cytoskeleton. Supporting the validity of our finding, Cytospin-A depletion in mammalian cells causes defective actin-cytoskeleton reorganization, a very similar phenotype seen with NUAK2 depletion. In future studies, I will continue to investigate the specific role of NUAK2 and Cytospin-A aiming for detailed information on the function of NUAK2 in regulation of microtubules and actin cytoskeleton. Validation of some of the other identified interactions is expected to provide novel insights to the biology and role of NUAK2 in LKB1 tumor suppressor functions.
  • Huusari, Anna (2018)
    Plants control the exchange of gases through the stomatal pores. Stomata are formed by guard cells and the closure of stomata are regulated via a complex signaling network in response to various biotic and abiotic stimuli, such as pathogens, elevated levels of CO2 and darkness. The leucine-rich repeat receptor-like kinase (LRR-RLK) GUARD CELL HYDROGEN PEROXIDE-RESISTANT1 (GHR1) is part of the network regulating stomatal closure. GHR1 is an inaktive pseudokinase that can activate SLOW ANION CHANNEL-ASSOCIATED1 (SLAC1), an anion channel that is crucial for stomatal closure, via interacting proteins. The exact role of GHR1 is still partly unknown, however, it has been suggested that GHR1 could function as a scaffold or as an allosteric regulator of additional components required for stomatal closure. The aim of this study was to identify novel interactors of GHR1. First stable plant lines expressing fusion proteins GHR1-YFP, GHR1W799*-YFP and plain YFP as a negative control were generated and from these lines fusion protein expression levels and the subcellular localization were studied. Next the plant lines were used for purifying GHR1 interacting proteins with the use of co-immunoprecipitation and identification of the proteins with mass spectrometry. The unlikely GHR1 interactor candidates were then filtered from the mass spectrometry data. The subcellular localization and the protein expression of the interacting proteins were studied with the use of internet databases. Literature of the GHR1 interacting proteins were studied in order to make possible connections with GHR1 and stomatal closure. In this study 38 GHR1 interactors were identified. Literature search revealed that many of the identified interactors had a known role in stomatal movements. These included proteins such as PLASMA MEMBRANE INTRINSIC PROTEIN2-1 (PIP2-1) and BETA CARBONIC ANHYDRASE 4 (BCA4), that are known to have a role in stomatal closure. Future work includes confirming the interactions with independent methods and studying the molecular mechanisms related to stomatal movements. The GHR1 interactome identified here for the first time reveals novel parts of the network regulating stomatal movements and thus increases our understanding of molecular mechanisms behind stomatal functions.
  • Doagu, Fatma (2013)
    Intellectual disability (ID) is a clinically diverse and genetically heterogeneous disorder characterized by central nervous system defects of varying severity resulting in substantial impairment of intellectual and adaptive functioning as expressed in conceptual (IQ<70), social and practical adaptive skills diagnosed before 18 years of age. The condition is referred to as non-syndromic when ID is the only clinical feature and syndromic when ID is accompanied by specific other features, for example, Down syndrome. Intellectual disability is one of the largest unsolved problems of health care with a prevalence of 2-3% in the population. There is a 30-40% excess of male versus female patients in ID which refers to over-representation of X chromosomal defects causing ID. In this study, exome sequencing of the X chromosome was applied in order to identify genes and their mutations in two Finnish families with intellectual disability of unknown cause. The mutations were identified using Agilent Sure select array that covers almost 93% of the coding region of the chromosome. Exome sequencing resulted in 11 variations in total. Segregation of these variants was studied using PCR, ExoSAP-IT purification protocol and BigDye® Terminator v3.1 Cycle Sequencing Kit. Eventually, two novel mutations were identified: one for each family. Both mutations reside in genes that have previously been shown to cause X-linked intellectual disability. Both of the mutations were absent in over 120 control DNA samples. In one family with three affected males, a novel splice mutation was identified in discs large homolog 3 (DLG3), which encodes synapse-associated protein 102 (SAP102). The mutation is located at the splice site in intron 1 (500+1 G>C) and its effect on protein function needs to be analyzed at the RNA-level using cDNA-sequencing. The clinical phenotype of the three affected brothers is mild to moderate intellectual disability. In the other family with three severely affected male patients, a novel mutation in exon 12 was identified on glutamate receptor, ionotropic, AMPA 3 (GRIA3) resulting in amino acid glycine (GGG) changing to arginine (CGG) at codon 630 (G630R). GRIA3 belongs to AMPA receptors implicated in the regulation of several biological processes. Our findings elucidate the power of exome sequencing in the diagnosis of rare, genetically heterogeneous disorders like intellectual disability. The results obtained will help in assessing the prognosis of the disease, in estimating the risk of the disorder to other family members, and in facilitating the development of future therapies for these devastating disorders. The results also further confirm the role of DLG3 and GRIA3 in human cognitive development.
  • Keränen, Fanny (2021)
    This study aimed to identify conservation landscapes with potential to be mutually beneficial for people and African savanna elephants (Loxodonta africana) in South Africa through spatial conservation planning analyses that integrate ecological and socioeconomic data. The research questions were: (i) what are the most ecologically suitable areas for the reintroduction of elephants, and (ii) which of these areas provide the best opportunities for also sustaining socioeconomic development of local people. The first question was answered with an ecological model that predicts habitat suitability for elephants, developed by a combination of literature review, expert opinion, and GIS-based methods. The second question was answered by combining the ecological model with socioeconomic criteria in Zonation spatial conservation planning software. The results show that the central part of South Africa holds most potential for elephant conservation as it has the largest uniform area of high-quality habitat, while the area also meets the socioeconomic criteria. The priority areas for the conservation of elephants were classified into top priority classes of 1%, 2%, 5%, 10% and 20%. The identified areas hold an unrealized opportunity in the wildlife and ecotourism sectors, and the reintroduction of elephants to those areas could provide the foundation for long-term economic activity of local communities e.g. in the form of elephant-based ecotourism, while contributing to the conservation of elephants. Conserving just the top 5% priority areas would grow South African protected area estate by approximately three million hectares and increase the current elephant range by approximately 75%. Ideally, the results of this study could be used to inform the on-going decision-making process on where to allocate resources for elephant conservation in South Africa.
  • Kavanagh, Kayleigh C (2022)
    Urban densification is resulting in the rapid loss of urban green spaces and their associated values. Moreover, the remaining urban green spaces are under increasing pressure to meet diverse resident needs and preferences. While past studies have investigated the intrinsic, instrumental, and relational values associated with such spaces, little attention has been paid to the sub-sets of relational values referred to a fundamental-relational (i.e., contributions toward enhanced social resilience) and eudemonic-relational values (i.e., actions, experiences, and habits linked to a “good life”). This study used public participation geographic information systems (PPGIS) surveys in a residential neighborhood of Helsinki, Finland to spatially explore and examine the differences between intrinsic, instrumental, fundamental-relational, and eudemonic-relational values in urban green spaces. I analyzed responses from residents and stakeholders (n = 1089) using Chi-square tests for significant associations and density-based clustering. Mapped values indicated that green spaces were primarily valued for their relational value, with an emphasis on eudemonic-relational values. Moreover, there were differences in the spatial distribution of instrumental, intrinsic, and relational values between green space types and values were spatially clustered by land use. Notably, there were few differences in how these values were assigned by different sociodemographic groups. I discuss the implications of these findings for local- and city-scale planning and the use of value typologies in PPGIS surveys. Further research in this field will benefit from the use of further value subcategories, increased geographic scale, and additional study of the influence of sociodemographic factors.
  • Kiviluoma, Tomi (2021)
    Education research has for decades acknowledged that prior knowledge is a strong predictor of academic success. This idea is largely based on constructivist theory of learning which postulates that all learning occurs by actively building on existing knowledge. When this prior knowledge conflicts with the normative scientific understanding, students are dealing with incompatible knowledge structures, or misconceptions. Misconceptions need to be revised and sometimes even replaced through a learning process called conceptual change. Research shows that the level of prior knowledge can determine students’ academic success and performance. Undergraduate biology students enrol to university with diverse levels of prior knowledge and concepts regarding topics such as photosynthesis, cellular respiration, primary production in ecosystems, and Darwinian evolution. These topics present challenges for learning because of their complexity. At the same time, a robust understanding of them is essential. These topics are at the heart of mitigating and resolving the climate crisis and other global natural threats. This study explored the level of prior knowledge and the nature of misconceptions held by undergraduate biology students at the beginning of their academic degree in fall of 2019, and further sought to describe how their conceptual understanding developed during the first academic year. Students (N = 41) completed a questionnaire consisting of eight open-ended questions that were designed to assess declarative knowledge of facts and meaning, and procedural integration and application of knowledge. This pre-test measurement was conducted in September 2019. In the post-test measurement, the same questionnaire was repeated a year later. The data were analysed with a mixed methods approach where the answers were quantitatively scored as well as qualitatively analysed for misconceptions. The qualitative content analysis of the answers relied both on existing literature and on the content of the answers themselves. Results showed that the students’ prior knowledge was relatively poor in the beginning of their studies. Most students performed well in tasks measuring knowledge of facts and meaning but struggled in tasks measuring integration and application of knowledge. During the first academic year, the students’ understanding generally improved as demonstrated by the improvement in mean scores of the tasks. Misconceptions were robust and pervasive. The most pervasive misconceptions reflected difficulties in understanding emergent properties and processes. Misconceptions related to the process of Darwinian evolution became more prominent in the post-test. Persistent misconceptions became integrated with the new conceptual frameworks that the students acquired during the first academic year. If students held no misconceptions in the post-test, they performed significantly better in both tests than those with misconceptions. During this first academic year learning seemed to be mainly additive as conceptual change turned out to be rare. The need for more encompassing biology teaching at least in the University of Helsinki became evident. Introductory courses should acknowledge the large degree of variation in students’ prior knowledge and assess the most common and serious misconceptions even over course theme disciplines to ensure more equal learning outcomes.
  • Piekkari, Ella (2021)
    Mature T-cell leukemias/lymphomas (MaTCLs) represent a rare and clinically heterogenous group of diseases that vary from indolent stages to aggressive malignancies with very limited therapy options due to the resistance development against conventional chemotherapies. T-cell prolymphocytic leukemia (T-PLL) is the most common subtype of MaTCLs and was therefore selected as a model disease to study the genetic mechanisms leading to the resistance development with eight clinically relevant cancer drugs. In this Master’s thesis genome-wide CRISPR/Cas9 knock-out screen with Brunello lentiviral library was used to study genetic aberrations that could induce resistance or sensitivity towards the selected cancer drugs. Two main pathways were enriched in multiple drug conditions including p53 regulating genes as well as epigenetic regulation, suggesting these pathways could be related to resistance development mechanisms. p53 pathway is dysregulated in most cancer types and therefore it can also be seen as a positive control of the screen. Epigenetic modulations play an important role regulating cell proliferation and genes related to this pathway are frequently altered in MaTCL patients. The screening results show enrichment of epigenetic regulation and suggest that it has a role in drug resistance development. This thesis work included results only from one genome-wide screening experiment and in the future is important to compare the findings with replicate screen results as well as with other cell lines to confirm the findings. In addition, validation of the most biologically interesting genes should be performed, most optimally in primary cells.
  • Szeto, Usko (2020)
    Sammakkoeläinten laji- ja yksilömäärät ovat voimakkaassa laskussa maailmanlaajuisesti. Lajeista yli 40 prosenttia on uhanalaisia ja sammakkoeläimet ovat siten kaikkein uhatuin selkärankaisryhmä. Syynä laji- ja yksilömäärien rajuun laskuun pidetään muun muassa elinympäristöjen tuhoutumista, tauteja ja ilmastonmuutosta. Korkeusvaihtelun tiedetään vaikuttavan sammakkoeläinten levinneisyyteen. Topografinen vaihtelu vaikuttaa lajistoon pääasiassa kahdella tapaa: korkeuden kasvaessa sademäärä yleensä nousee ja keskilämpötila laskee. Kosteus ja lämpötila ovat sammakkoeläimille tärkeitä ympäristötekijöitä, sillä ne ovat vaihtolämpöisiä eläimiä, joiden lisääntyminen on yleensä sidoksissa vesistöihin. Tarpeeksi kostea elinympäristö on tärkeää sammakkoeläimille myös sen takia, että ne hengittävät osittain kostean ihonsa avulla. Ihminen vaikuttaa sammakoiden laji- ja yksilömääriin sekä suoraan että epäsuorasti. Esimerkkejä suorista vaikutustavoista ovat muun muassa sammakkoeläinten metsästys ruoaksi ja pyydystäminen harraste-eläimeksi. Epäsuoria vaikutustapoja ovat muun muassa elinympäristöjen muuttaminen, tautien leviäminen sekä vieraslajit. Elinympäristöjen tuhoutuminen on yksi suurimmista uhista sammakkoeläimille. Taitavuoret sijaitsevat Etelä-Keniassa ja ovat osa Itäisiä Kaarivuoria. Alue tunnettaan merkittävänä monimuotoisuuskeskuksena ja sieltä on kuvattu kolme alueella endeemistä sammakkoeläinlajia. Näiden lisäksi alueella tiedetään esiintyvän ainakin 23 muuta sammakkolajia. Topografinen korkeusvaihtelu ja voimakas ihmistoiminta tekevät alueesta kiinnostavan kohteen sammakkoeläinten kohdistuvalle tutkimukselle. Ihmistoiminnan ja korkeusvaihtelun vaikutuksia sammakkoeläinten laji- ja yksilömäärät tutkittiin tutkimuslinjojen ja niille sijoitettujen tutkimuspisteiden avulla. Sammakkoeläimiä pyydystettiin 10 minuutin ajan jokaiselta tutkimuspisteeltä ja kiinni otetuista sammakoista kirjattiin ylös paino ja pituus. Lisäksi niistä otettiin tunnistamisen mahdollistavat valokuvat. Tutkimuspisteistä kirjattiin ylös topografinen korkeus (mpy) ja maankäyttötapa. Tutkimuspisteet luokiteltiin kolmeen eri habitaattityyppiin: avoimiin paikkoihin, rehevän kasvillisuuden pisteisiin ja luonnontilaisiin metsiin. Tutkimuksessa saatiin paljon lisätietoa Taitavuorten alueen sammakkoeläinlajistosta. Alueelta tunnistettiin useita lajeja, jotka suosivat tiettyä habitaattityyppiä. Myös korkeusvaihtelun todettiin vaikuttavan lajistoon. Sammakkoeläinten yksilömäärä oli pienin rehevän kasvillisuuden tutkimuspisteissä. Tähän vaikutti sekä sammakkoeläinten vaikea havainnointi tiheässä kasvillisuudessa, että tyypillisten luonnonmetsälajien puuttuminen näiden pisteiden lajistosta.
  • Oikarinen, Kaisa (2022)
    Tässä tutkimuksessa selvitettiin, millaisia kehyksiä ilmastoahdistus saa kahdeksassa, vuonna 2021 julkaistussa suomalaisessa podcast-jaksossa. Näin pyritään lisäämään ymmärrystä ilmastoahdistuksen ilmiöstä, sekä siitä, millaisia kehystyksiä aihe mediassa saa. Tutkimus on tehty laadullisella kehysanalyysilla, joka perustuu Erwin Goffmanin (1974) kehittämään kehysteoriaan ja sen myöhempiin sovellutuksiin. Lyhyesti sanottuna, tutkimus pohjaa siihen olettamukseen, jossa median tavat kehystää ja esittää jokin aihe tai asia ohjaavat sitä, millä tavalla asiat meille esitetään ja millaisina me asiat näemme. Tutkimuksen aineisto kerättiin suoratoistopalvelu Spotifysta, Yle Areenasta ja Suplasta. Kehyksien muodostamisessa hyödynnettiin Robert Entmanin (1993) median kehysanalyysin periaatetta, jossa kehyksillä on neljä tarkoitusta: Ongelmien määritteleminen, ongelman aiheuttavien tekijöiden tunnistaminen, moraalisten arvioiden tekeminen sekä ratkaisujen ehdottaminen. Tutkimuksen tuloksena syntyi kolme kehystä, jotka nimettiin luonnollisen ilmastoahdistuksen, ilmastoahdistus sukupolvikysymyksenä sekä ilmastoahdistus tarvitsee vertaistukea, käsittelyä ja toimintaa kehyksiksi. Jokainen kehys kuvaa omalla tavallaan sitä, millaisena ilmastoahdistus nähdään viime aikaisissa podcast-keskusteluissa. Luonnollisen ilmastoahdistuksen kehyksessä korostuvat näkemykset siitä, kuinka ilmastoahdistus voidaan nähdä luonnollisena ja normaalina, sekä hyvänä reaktiona motivoivan vaikutuksensa kautta. Kaiken kaikkiaan kehys kuvaa ilmasto- ja ympäristöahdistuksen ilmiön monitahoisuutta ja yksilöllisyyttä, sekä pyrkii vahvistamaan näkemyksiä siitä, mitä ilmastoahdistus on ja mitä se ei ole. Lisäksi ilmastoahdistuksen sisältämä ahdistus sana kyseenalaistetaan. Ilmastoahdistus sukupolvikysymyksenä - kehys avaa puolestaan näkemyksiä nuorten ilmastoahdistuksen syihin ja korostumiseen, sekä ottaa kantaa aikaisempaan ilmastoahdistuskeskusteluun, joka joidenkin keskustelijoiden mielestä näyttäytyi ilmiötä vähättelevänä. Kokonaisuudessaan kehyksessä kuitenkin korostuu näkemys siitä, että ilmastoahdistus ei ole vain nuoria koskettava asia, vaikka se tällä hetkellä korostuu ja ilmenee eniten nuoremmissa sukupolvissa. Kehys ilmastoahdistus tarvitsee vertaistukea, käsittelyä ja toimintaa, tuo esiin keskustelijoiden näkemyksiä ja kokemuksia liittyen ilmastoahdistuksen käsittelyyn ja lievittämiseen, sekä osallistuu keskusteluun koskien ilmastotekojen merkityksellisyyttä. Tutkimuksen tulosten perusteella voidaan sanoa, että ilmastoahdistus saa vuonna 2021 julkaistuissa, suomalaisissa podcastkeskusteluissa monia eri sävyjä ja ilmastoahdistusta käsitellään niissä laajasti. Ja vaikka keskustelijoiden näkemykset ovat pitkälti linjassa ilmastoahdistusta käsittelevien julkaisujen kanssa, muutamia kiinnostavia ja tutkimattomiakin näkökulmia ja kehystyksiä ilmenee. Osaltaan tutkimuksen tulokset täydentävät kuvaa siitä, miten valtavirtamediaa hitaammat lajityypit – kuten podcastit – mukautuvat muualla esitettyihin määritelmiin ja kehystyksiin, mutta myös täydentävät niitä. Tällöin podcast-keskustelujen voidaan nähdä tarjoavan vaihtoehtoisia kehyksiä, jotka osittain haastavat ja täydentävät julkisuudessa hallitsevia kehyksiä.
  • Blom, Heidi (2020)
    The significance of preventing the climate change in cities and urban areas is nowadays increasingly recognized. The increasing relevance of urban areas in climate policy has created new opportunities for collaboration between the private and public sector. The non-state actors have often a key role when climate policy is implemented locally in urban areas. The Ilmastokumppanit project is founded by Helsinki city and it is a part of the activities that aims for a carbon neutral Helsinki. This thesis explores the motivations, drivers and barriers to implement climate actions and to participate in the voluntary Ilmastokumppanit project among companies. The thesis was carried out using qualitative content analysis and only companies from the Ilmastokumppanit project were used as the target group to improve the comparativity. The supportive members in the project were not accepted as a part of the target group. The data for the thesis were collected as semi-structured expert interviews which were recorded, transcribed and coded. Deductive content analysis and a framework examining the reasons behind the climate actions of the UK FTSE 100 companies was used to analyse the data. The framework categorizes the reasons behind the climate actions into motivations, drivers and barriers which is subdivided into themes. The interviewees highlighted for-profit activities, networking, corporate responsibilities and remaining competitive in the future as motivators. Drivers were less identified and the interviewees highlighted factors related to climate-friendly activities as a manifestation of their time and the need for networking. Factors related to legislative issues and the low oil price were identified as barriers. The framework lacks internal factors influencing the company and creating a new theme to the motivations titled employee pressure or internal pressures should be considered. Several factors were raised which influence the willingness of companies to act in the field of climate issues and to participate in networks. The results might be interesting to those leading the Ilmastokumppanit project. It would be useful to examine the legislative barriers more comprehensively to facilitate wider climate actions.
  • Evokari, Viliina (2017)
    The impacts of climate change are going to be significant in Finland, thus the need to adapt is inevitable. Municipalities are the key to adaptation because the impacts of climate change are met locally. Several cities have developed their measures to climate impacts. However, multiple barriers may hinder the planning and implementation of adaptation measures in the cities. The purpose of this research is to identify and overcome the barriers in urban climate change adaptation in the City of Helsinki. The main data of this research was collected in a workshop and it consists of the blank form replies collected with 6-3-5 method and focus group discussions. 11 civil servants from the City of Helsinki who deal with adaptation issues in their daily work participated in the workshop. The participants identified the barriers and evaluated the most important ones in the workshop: lack of cost-benefit analyses, rivalry of the resources with other interests, lack of urgency regarding adaptation, lack of information, fragmentation of the organization and unclear roles and responsibilities. Identifying the barriers does not solely promote the resilience of the cities but it is an important step in the development of adaptation work. It is essential to seek possible solutions to overcome the identified barriers. Six solutions that can tackle simultaneously several barriers emerged from the data gathered in the workshop: costbenefit analyses, increasing training and information, concrete examples, increasing co-operation, clear modes of action and responsibilities and the support and commitment of the management. With these solutions, the City of Helsinki has the possibility to simultaneously overcome several barriers that were identified in this research. To conclude, the responsibility of climate change adaptation should be clarified in the new city organization and silos between different sectors should be addressed, if possible. It would be useful to utilise the multi-criteria decision analysis in prioritising and argumenting of the adaptation measures in the city. As additional conclusions, it seems that improved co-operation with the universities and research institutions, and legislation indicating clear roles and responsibilities in terms of adaptation might benefit the adaptation work in the City of Helsinki. As for the need for further research, the analytical framework developed and utilized in this research needs to be tested in other case studies also.
  • Haapanen, Liisa (2013)
    In this master's thesis, I examine 21st century criticism of economic growth. The aim of the study is to understand what economic growth represents to growth critics. The research question is: what are the central themes of contemporary growth critique? The research material consists of three books: Tim Jackson's Prosperity without growth – economics for a finite planet (2009), Peter Victor's Managing without growth – slower by design, not disaster (2008) and the Finnish translation of Serge Latouche's Petit traité de la décroissance sereine (2007, Finnish translation Jäähyväiset talouskasvulle published in 2010). A qualitative content analysis was conducted on the material. In this method, manifest and latent meanings of the text are condensed and categorized in order to identify the key themes of the text. The analysis reveals three central themes in the criticism of economic growth. Each offers a different perspective to economic growth, to the proposed alternatives and to the opposition between growth protagonists and antagonists. First theme is growth as a phenomenon, which focuses on concrete ecological and social impacts of economic growth. The main argument of the growth critics is that the social and ecological costs of growth exceed its benefits in the western countries. In addition, they argue that economic growth cannot be viably combined with reducing ecological impact of human activities. The second theme is growth as an institution, which focuses on the institutional dependence on growth as well as institutional structures supporting growth. The critics' opinion is that these institutions now form a vicious circle in which people serve the economic growth and not vice versa. Also the proposed institutional change for disentangling society from growth is relevant to this theme. The third theme is growth as an ideology, which focuses on economic growth as a hegemonic belief and value system as well as a political goal above other goals. Under this theme, the growth critics promote emancipation and outline an alternative ideology. One main conclusion of the study is that the growth critics are not in favour of the opposite of economic growth, i.e. they do not promote a diminishing economy as an end in itself. Instead, their critique opens up a discussion on an alternative society which does not revolve around the economy and its size. However, this alternative is not pictured very clearly in the research material. It seems that the growth antagonists are able to describe what they oppose more elaborately than what they support. Another conclusion is that there is an internal tension within current growth critique. When examining economic growth as a concrete phenomenon the critics suggest indifference towards economic growth. Yet, under the other two themes the approach is everything but nonchalant since dismantling the institutions and ideology of growth will hardly be achieved without intentional resistance. Since the three books analyzed lean on and draw from earlier and contemporary references critical to economic growth, the three themes might be utilized in analyzing and understanding growth critique in general. However, this should be verified in further studies. What is more, when applied to other texts one might discover new themes not covered in this study. Because this study concentrates on the aspects that the three books representing growth critique have in common, in the future one should examine whether there are different schools of thought within the 21st century growth critique. Another interesting subject for further studies would be to apply the three themes to analyzing degrowth visions and possible degrowth experiments.
  • Uski, Ilona (2021)
    Tumors contain variable number of different immune cells that infiltrate the tumor microenvironment, such as tumor infiltrating lymphocytes (TILs). More research is needed to understand the functional and clinical importance of various TIL subgroups in cancer. Understanding the differences between individual cancer patients will help development of new treatment methods and discovering why only some patients respond to immunological treatments. Renal cell carcinoma (RCC) is the most common kidney cancer type with good overall survival prognosis when the tumor is surgically removed before it has metastasized. However, the prognosis of RCC is significantly decreased when the cancer has spread. The aim of this master’s thesis project was to characterize the tumor infiltrating lymphocyte populations in patient derived RCC samples. Characterization was done with flow cytometry and a custom antibody panel designed to detect various lymphocyte subpopulations. We also wanted to further study the TILs by expanding the lymphocytes from the tumor samples and test their function in an impendence-based assay against matched autologous tumor cells. Based on the flow cytometry results, the different RCC subtypes in the cohort showed some variation in TILs. Still, more research is needed to investigate these differences. We were able to culture the TILs from the RCC tumor samples, and most of them were CD4+ T cells expressing memory markers CD45RO and CCR7. Some expanded TILs expressed markers related to T cell activity and terminal differentiation. In conclusion, this thesis provided material and insights for future RCC TIL experiments as well as considerations for optimization needed in further studies.
  • Gawriyski, Lisa (2018)
    Life historyresearch seeks to explain how natural selection and ecological challenges shape organisms to optimize their fitness. A strong immune defense is energetically demanding to upkeep and there may be trade-offs among other life history traits. Investing a lot of energy to upkeep a strong immune defense in conditions where there are less pathogens and parasites might have negative fitness effects. Heliconius eratois a neotropical species of butterfly found widely in South America. The immune defense, ecologicalfactors affecting its immune defense, and possible life history trade-offs of the butterfly are currently not well known. Environmental moisture conditions have been shown to affect the diversity, quality and amount of microorganisms and parasites. The aim of this thesis was to use real-time quantitative PCR (RT-qPCR) to quantify immune gene expression of individuals of the butterfly species Heliconius eratocollected from different environmental moisture conditions. Additionally, individual variation in encapsulation rates, a physiological measure of immunity, was compared across the moisture gradient. Results indicate reduced expression of the gene encoding the antimicrobial peptide attacin in dry conditions, but no difference in encapsulation rates across the moisture gradient. Additionally, differential expression of the prophenoloxidase encoding gene was found between male and female butterflies. These results indicate a possibility of differential immune threats in different environmental moisture conditions in H. erato, but requires further study.
  • Failla, Laura (2019)
    The vagus nerve is the longest nerve of the autonomic nervous system. It innervates, among other organs, the stomach, the lungs and the heart, and it reaches several areas of the brain, including the locus coeruleus and the amygdala. The invasive stimulation of this nerve (vagus nerve stimulation, or VNS) is a currently used method for the treatment of refractory epilepsy and pharmaco-resistant depression (Englot et al. 2011; O’Reardon et al., 2006), but the impact that this technique might have on the brain physiology and functions is still under investigation. Various studies (Frangos et al., 2015; Yakunina et al., 2016; Hansen, 2019) have shown that VNS increases noradrenaline production in the brain, a neurotransmitter that is involved in several cognitive processes, such as sleep and mood control. Furthermore, in a study on patients with epilepsy, by Sun et al. in 2017, VNS appeared to have a clear effect on working memory and emotion-attention interaction. Nevertheless, VNS presents all the risks and potential complications that characterize invasive procedures requiring surgery. Therefore, research is now focusing on safer, non-invasive alternatives, such as transcutaneous vagus nerve stimulation (tVNS). This technique allows to stimulate the nerve through its sensory fibres, located in the cymba and tragus of the ear. The scope of the present study was to see whether tVNS would have the same effects on cognitive and affective functions as VNS. The sample for this single blind placebo-controlled study was composed of 30 healthy subjects between 18 and 45 years old. Exclusion criteria included a history of psychiatric, neurological or cardiovascular diseases. All subjects were asked to complete a computer-based task, the Executive Reaction Times-Test. Throughout the test the subjects alternately received an active or a placebo stimulation, and their brain activity was recorded for the whole duration of the test using a 64-channel EEG cap. The Executive-Reaction Times-Test was chosen for this study because it allows to test multiple executive functions simultaneously. The subjects were presented with a series of stimuli on a screen and were asked to react as fast and accurately as possible to “Go” signals, and to refrain from responding when “NoGo” signals appeared. The test started with a triangle pointing either up- or downwards, followed by a brief pause and a traffic light image. The traffic light showed either a red or a green light and included an emotional distractor in the form of a spider or a flower. The red and green lights were alternately used as “Go” or “NoGo” signals, and the rule changed at each test block. In order to complete the task, subjects needed to keep the image of the triangle in their working memory, stay focused on the stimuli and be ready to react or be able to inhibit any responses, thus several main executive functions are being tested: inhibitory control, working memory, attention and emotion-attention interaction. Active stimulation was delivered through clip electrodes that were attached to the tragus of the left ear, whereas placebo stimulation was delivered through clip electrodes that were attached to the left ear lobe. The subjects were not aware of the difference between the two locations. Only the data of 18 subjects was used for the results analysis, because of technical difficulties with the EEG data (some recordings were too noisy, some presented flat channels). The behavioural data was divided into reaction times and errors, which were separately analysed. The EEG data was used to extract the amplitudes of the ERP peaks N2 and P3. The former is a negative peak visible at 200-350ms; the latter is a positive peak visible at 300-500ms. Previous studies have shown the peaks to be associated with response conflict and inhibition (Falkenstein et al., 1999; Donkers et al., 2004; Smith et al., 2013). The behavioural data analysis did not show any significant effect of stimulation on reaction times or error amounts. The ERP analysis, instead, returned interesting results. We observed a main effect of stimulation (p=0.04) in “NoGo” conditions. There was a significant reduction in the N2P3 amplitude and the N2 amplitude in “NoGo” conditions, with active stimulation compared to placebo. These results seem to suggest that with tVNS, fewer cognitive resources are allocated to resolve the inhibitory task, without worsening the subjects’ performance. The lack of significance in the behavioural results might have been due to a ceiling effect, with the Executive Reaction Times-test being too easy for our sample. Overall, the number of errors was too low to conduct a reliable statistical analysis. Nevertheless, the effects we observed on brain physiology would suggest that further research is needed to explore the actual impact of tVNS on cognitive and affective functions.
  • Kangas, Jonna (2022)
    Climate change is expected to cause salinity change in the Baltic Sea and therefore may affect organisms living in the Baltic such as plankton. The microbial loop is an important part of the plankton food web. It consists of heterotrophic bacteria, nanoflagellates and ciliates and is connected with the classic plankton food chain through interactions with primary producers and mesozooplankton. Therefore, salinity affects the functioning of the microbial food web not only directly, but also through salinity induced changes on primary producers and mesozooplankton. In this master’s thesis I studied the effects of salinity change on microbial loop components bacteria, nanoflagellates and ciliates in an outdoor mesocosm experiment containing four salinity treatments with salinities of 3.5, 5.5, 7.5 and 9.5, three replicas each. The experiment took place offshore at the Tvärminne Zoological Station. Bacteria were sampled from the mesocosms every other day and nanoflagellates and ciliates every 6th day. Bacteria were analysed with the flow cytometer, nanoflagellates with epifluorescent microscopy and ciliates using an inverted microscope. The effects of salinity on microbial loop components were statistically tested using linear mixed effects models. Results of the experiment show that salinity had an indirect effect on microbial loop components through changes in mesozooplankton composition. There were significant differences between high and low salinity treatments in bacteria abundance and composition, the interaction strength between HNFs and bacteria and in the mean cell size of ciliate communities. These were mainly caused by differences in mesozooplankton community structure between salinity treatments, which had cascading effects on the strength of top-down and bottom-up control on the trophic levels of the microbial loop, leading to changes in bacteria abundances and composition. Based on the results of this thesis, more studies are needed to detect the effects that changes in the composition and functioning of the microbial loop might have on the ecosystem. Further research should also focus on the significance of the structure and diversity of the communities within the microbial loop as well as the functional roles of different species in the microbial food web.
  • Backman, Torgny Richard Jr (2022)
    The intensification of agriculture is one of the main drivers of biodiversity loss worldwide. One of the intensification shifts has occurred from cattle grazing on biodiversity-rich semi-natural grasslands to ceased grazing or grazing on cultivated species-poor grasslands. While the effect of different grazing pressure on biodiversity in semi-natural grasslands has been studied extensively, little is known of how current grazing regimes on cultivated grasslands affect biodiversity and ecosystem services in different farming systems. Here, we investigated how arthropod abundance and potential ecosystem services are related to varying grazing pressure on cultivated grasslands at conventional and organic farms with meat or dairy production. We sampled aerial arthropods with sticky tape traps in four land-use types within the farms. Relative arthropod abundance was derived from the tapes using an imagery analysis, and the numbers of pollinators and predators from 4 taxonomic groups were counted. The results showed no difference in the relative arthropod abundance in relation to grazing pressure, but there was weak evidence for higher predator abundance at low and high grazing pressure. The relative arthropod abundance showed a positive trend in organic farms. However, pollinator abundance was higher in conventional farms, and predator abundance did not differ between farming systems. Land-use type was related to the occurrence of predators and pollinators: both groups had the lowest abundance in farmyards compared to cultivated pastures, silage fields, and cereal crop fields. Predator numbers were also higher in silage fields than in the other land-use types. However, there was no significant interaction between land-use types and farming systems in their effect on the arthropod groups. The results suggest that grazing pressure on cultivated grasslands has a minor or negligible impact on arthropod abundance in the two commonest farming systems. However, the effect of farming systems on relative arthropod abundance might be obscured by low sample sizes, high abundance of only a few species, and other variables not included here, such as the use of manure or pesticides. In addition, pollinators included only two taxonomic groups, potentially leading to results not applicable to all pollinators. Consequently, more large-scale studies with higher sample sizes and the inclusion of arthropod diversity and data on the key on-farm practices and landscape structure are needed to disentangle the relationship between biodiversity and grazing on cultivated grasslands in Finland.
  • Ihalainen, Vilma (2020)
    Ongoing climate warming has unprecedented impacts on glacial melt and associated fjord systems in Greenland. As the glaciers are shrinking, freshwater inflow to the sea is increasing resulting in increased nutrient supply by upwelling. In this study I examined environmental factors impacting marine primary productivity, biomass (chlorophyll a), phytoplankton abundance and species composition along a transect from the glacier front to the outer fjord in Godthåbsfjord, SW-Greenland, in August 2019. Gradients in nitrogen and phosphate concentrations were explained by glacial runoff and coastal water inflow while silicate concentration did not follow these patterns. The main variables explaining phytoplankton biomass distribution were nitrogen together with phosphate concentrations, salinity, and depth. Silicate limited waters were strongly dominated (≥ 90%) by the diatom Chaetoceros socialis, which had a strong influence on phytoplankton community response to environmental conditions. High dominance of C. socialis was also related to high species richness. Nitrogen depleted waters were usually related to relatively high abundances (9–46%) of mixotrophic Dinobryon balticum. Higher number of species and higher dominance of C. socialis was detected closer to the glacier. Phytoplankton abundance and biomass (chlorophyll a) were higher in the inner fjord region, whereas primary productivity had the opposite pattern (higher productivity in the outer fjord). This suggested that an autumn bloom was peaking in the inner fjord, whereas in the outer fjord the autumn bloom was still developing. Thus, glacial surface runoff and subglacial discharge contributed to higher phytoplankton abundance and chlorophyll a concentrations, whereas primary production was also dependent on other factors such as light availability and vertical mixing. Melting of Greenland Ice sheet is predicted to accelerate in the future. Thus, the upwelling effect might increase, leading to transitory increase in marine primary production. Increased surface runoff might increase silicate concentrations benefiting diatom species, although turbid runoff water will also decrease the primary productivity due to light limitation. Nevertheless, if marine-terminating glaciers retreat further and become land-terminating glaciers, lack of nutrient upwelling will lead to faster exhaustion of nitrogen in the upper water column and primary productivity will eventually decrease. Thus, global warming and retrieving of glaciers will change the productivity of the fjord and inevitably shape the rich and unique fjord ecosystems of the Arctic.