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  • Jakobsson, Emma (2023)
    The lymphatic system is a network of vessels that permeate a substantial part of the whole body. It plays an essential role in fluid homeostasis by the drainage of interstitial fluid from the blood capillaries, after which the fluid, now called lymph, is transported through the vessel network and back to the blood circulation. The lymphatic system also plays an important role in the transportation of immune cells and in activation and maintenance of the immune system. Due to these crucial functions, there is a growing interest in exploiting the lymphatic system in the treatment of many immunological and inflammatory diseases. In many cases, an ideal treatment method would be to induce lymphatic growth (lymphangiogenesis) to boost immunological functions, facilitate resolution of inflammation and reduce the harm from lymphatic vascular abnormalities. However, there is a gap in knowledge in how to induce lymphangiogenesis in a controlled manner, with the major lymphangiogenic growth factor, vascular endothelial factor C (VEGF-C), tending to create disorganized lymphatic networks. The purpose of this thesis is to investigate factors influencing lymphangiogenesis, in an attempt to find ways to control it. Vaahtomeri research group has preliminary results showing a role of planar cell polarity (PCP) in control of dermal lymphatic vessel sprouting (the initial step for the formation of new lymphatic branches) and lymphatic network expansion. The focus of Vaahtomeri research group has been the core PCP protein Van Gogh-like protein 2 (VANGL2), which together with the other core PCP proteins is known to play an important role in the collective cell polarization and morphogenesis in many tissue types. The role of VANGL2 has previously been studied in the lymphatic system, and so far, VANGL2 has been implicated in both lymphatic valve morphogenesis and in flow-induced control of lymphatic endothelial cell (LEC) polarization. However, there still remains a gap in knowledge in what role VANGL2 plays in lymphangiogenesis and the lymphatic network as a whole. In this thesis, I investigated the role of VANGL2 in lymphangiogenesis, firstly by the use of an in vivo lymph node experiment, which offered a robust model to investigate the role of VANGL2 in the mature lymph node lymphatic network. In the experiment, I induced growth of the lymph node lymphatic network by means of an immunization reaction, and then I compared the lymphatic networks of Vangl2-deleted and control mice. Despite some minor differences between the Vangl2-deleted and control lymphatic networks, this experiment did not show a role for VANGL2 in the mature lymph node lymphatic network. Secondly, I investigated the potential mechanistic role of VANGL2 in control of dermal lymphatic vessel sprouting in growth conditions. This experiment showed a specific role for VANGL2 in sprouting of the lymphatic network, thus providing valuable research in understanding how lymphangiogenesis is regulated. Altogether, the results presented in this thesis work as a steppingstone for finding new treatments relating to the safe induction of lymphangiogenesis.
  • Gelman, Valeria (2014)
    The increased rates of population growth and urbanization worldwide raises the question of food security and self-reliance in cities. In view of this situation, in recent years there has been a re-emergence of urban agriculture in its traditional form and in new variations, such as on urban rooftops. A number of rooftop urban farms exist in the world; however, very few studies have been done to establish the quality of crops they produce, specifically concerning the concentrations of contaminants. The main purpose of this study was to investigate levels of contamination in edible plants grown on urban rooftops. I determined concentrations of polycyclic aromatic hydrocarbons (PAH) and trace metals in the biomass of three types of horticultural crops grown in the city of Helsinki, Finland. Lettuce, radish and peas were planted on five rooftops in various areas of Helsinki and control samples were acquired from local food stores and markets. Both groups of crops were analyzed for concentrations of 11 trace elements using the Elan 6000 ICP-MS and 16 PAHs using Shimadzu GC-MS-QP2010 Ultra system with the AOC-20i /AOC-20s autosampler. Additionally, lettuce and pea samples from the roofs were analyzed washed and unwashed to establish levels of particulate contamination on the surface of plants that can be mechanically removed through washing. Results obtained suggest that concentrations of PAHs and trace metals in rooftop vegetables in Helsinki are very low and the differences in their concentrations compared to control (store) samples are insignificant. This demonstrates that the consumption of vegetables produced in uncontaminated soil on urban roofs in Helsinki is safe. All samples showed concentrations well below the safety limits for heavy metals and PAHs established in the European Union (EC, 2006). Finally, there was a difference in concentration of PAHs and trace metals between washed and unwashed samples, however most of the results did not show statistical significance.
  • Hämäläinen, Lotta (2023)
    Norway rats are common commensal species across the world. Despite their long history with humans, the ecology of urban rats is still relatively unknown. Which is why in my thesis, I model the population dynamics of wild urban rats of Helsinki using trap data from a professional pest management company. To protect the privacy of the company’s customers, the data are on the scale of postal code areas. Using a generalized linear mixed model, I investigate several different factors that might affect rat populations. As the data come from a pest management company, trapping factors need to be considered. Other factors include environmental, such as the proportion of parks or the type of sewer present in the postal code area. But as urban rats live in cities, anthropogenic factors such as human density and income matter too. In the span on seven and half years, 8 415 rats were trapped all across Helsinki, in some places more than others. Of all the factors only the trapping factors along with household median income were significant. Median income was negatively associated with trapped rats, so more rats were trapped in areas with lower income. Future studies should try to uncover for what unknown factor income acts as a proxy for.
  • Tornikoski, Taru (2023)
    Social behaviour can be divided into neutral, positive, and negative, depending on the social context. Positive social behaviour involves affiliative prosocial interactions that encourage social and emotional cohesion. Rat (Rattus norvegicus) is a globally distributed common rodent species adapted to living near humans. Rats are intelligent and social animals with reciprocal prosocial behaviour. However, research on the social behaviour of rats is concentrated in laboratory settings and very little is known about the social behaviour of free-living rats. Rats arouse strong prejudice in humans and are considered aggressive. Despite a long history of coexistence, there are still strong conflicts between humans and rats. In this study, I used camera trap data to investigate the types of social behaviour in free-living rats and the time allocation of different behaviours. I investigated how the rats' behaviour is divided into socially neutral or positive and negative behaviour in relation to the total time spent on the behaviour. I also investigated the types of social behaviour that occur when rats approach each other and the frequencies of these different behavioural models. For the behavioural analyses, I used data-driven ethograms that I made and the behavioural analysis software BORIS. I found that the majority (over 96.2 %) of the social behaviour of the free-living rats in my study population was neutral or positive behaviour as measured by the duration of the behaviour categories. I also found that the most significant proportion of social behavioural models in rats was socially neutral or positive. Agonistic behavioural models were rare and occurred mostly between adults. In contrast, rats exhibited a moderate amount of prosocial behaviour, particularly in the form of food sharing and muzzle touching. My study brings new information to the limited previous research on the behaviour of free-living rats. The results suggest that most of the social behaviour in free-living rats would be neutral or positive behaviour, and agonistic behaviour in rats would be relatively rare. To the best of my knowledge, this work is the first study to analyse the social behaviour of free-living rats from camera trap data. Objective research data on the social behaviour of rats may mitigate prejudice against rats and attitudes towards rats may become more positive. This can mitigate conflict between humans and rats and promote peaceful coexistence. This work can be used as a pilot for future studies. The information this work provides can also be used, for example, to educate people about their attitudes towards rats.
  • Jäntti, Tuomas (2023)
    The external nutrient load of the Archipelago Sea weakens the state of the sea. Gypsum is applied to fields in the catchment area because it has been found to reduce phosphorus leaching from fields. Gypsum treatment of fields is organised by the the Centre for Economic Development, Transport and the Environment (ELY) of Southwest Finland through "KIPSI-hanke" (GYPSUM Project). Participation in gypsum treatment is free of charge for farmers. To achieve water protection objectives, more farmers in the area should participate in gypsum treatment. I study what factors that influence the participation of farmers in the catchment area in gypsum treatment of their fields. The underlying motivation for this study was to promote gypsum treatment of fields and improve the state of the Archipelago Sea. My research is a qualitative interview study. My interview data consists of nine farmer interviews. In my analysis, I also use scientific and social research literature and other sources. I compare the interviewees' perceptions of the effects of gypsum with the information presented in the natural science literature. On the other hand, I will unpack social phenomena and events that affect farmers' perception of gypsum treatment and their activities. According to my observations, farmers' participation is influenced by knowledge about gypsum treatment, or the lack of thereof. Also, farmers' perceptions of the effects of gypsum treatment affect their participation decisions. Yield and yield impacts are at the heart when a farmer decides on participation in gypsum treatment, even though gypsum treatment is free of charge for the farmer. Based on my results, farmers' participation in gypsum treatment of their fields is promoted by available solid, experience based, research data on effects of gypsum, especially on the effects on yields. Agricultural advice also proved to be a factor influencing participation in gypsum treatment. At least some farmers would receive information on gypsum treatment of fields as part of other agricultural advice. According to my research, agricultural advisors' knowledge of the effects of gypsum was variable and partly incomplete. According to my research, expert and active gypsum advice would promote participation in gypsum treatment. The historical tensions between rural and urban areas, as well as tension between the implementors and targets of environmental projects, have an impact on farmers' attitudes towards the KIPSI-hanke. From the point of view of the rural population, unjust and top-down environmental projects will also hamper future projects if the design of projects does not consider the involvement of the rural population as participants of the projects, not only as targets of measures.
  • Kiviluoma, Juha (2003)
    Työn tavoitteena oli muodostaa kokonaiskuva sähköjärjestelmän sisäisistä ja ulkoisista vuorovaikutussuhteista. Sähköntuotantoa tarkasteltiin ympäristöönsä kytkeytyvänä systeeminä tieteidenvälisestä näkökulmasta. Tätä tarkoitusta varten rakennettiin menetelmä laajan kokonaisuuden hahmottamiseksi ja sovellettiin sitä sähköntuotannon alalle. Menetelmäperustuu grounded theoryyn ja systeemiajatteluun: Aineisto kerättiin ja luokiteltiin grounded theorya soveltaen. Systeemiajattelua käytettiin aineiston analyysissä ja aihealuetta kuvaavien mallien luomisessa. Aineisto kerättiin haastattelemalla sähköntuotannon ja -kulutuksen asiantuntijoita. Sen pohjalta rakennettiin useita alamalleja kuvaamaan sähköntuotantokompleksin osajärjestelmiä sekä näitä yhdistävä päämalli. Alamallien aihealueiksi muodostuivat tekninen sähköjärjestelmä, sähköjärjestelmän talous, sähkönsäästö, yhteiskunnallinen vaikuttaminen, ympäristö sekä tuotantorakenteen uusiminen. Lisäksi työssä esitettiin aineistosta nousseita kriteerejä hyvälle sähköjärjestelmälle ja sähköjärjestelmään liittyviä toimijoita. Mallien yhteydessä käsiteltiin myöseri tuotantomuotojen ominaisuuksia. Työn tuloksia tarkasteltiin kriittisesti kirjallisuuden valossa ja arvioitiin luotujen mallien sovellettavuutta. Malleja on mahdollista hyödyntää tieteenalarajoja ylittävän energiatutkimuksen jäsentäjänä sekä arvioitaessa kestävämmän energiapolitiikan edellytyksiä järjestelmätasolla.
  • Mäkilouko, Miia (2019)
    Antibioottien ylenmääräinen käyttö ja uusien antibioottien puute ovat johtaneet antibiooteille vastustuskykyisten bakteerien aiheuttamien sairauksien yleistymiseen. Lisääntynyt antibioottiresistenssi on maailmanlaajuinen ongelma, joka uhkaa globaalia terveyttä ja ruoan turvallisuutta. Staphylococcus aureus ja Pseudomonas aeruginosa ovat sairaaloissa yleisiä infektioita aiheuttavia mikrobeja. Metisilliiniresistentti S. aureus eli MRSA pystyy aiheuttamaan infektioita lähes missä tahansa kudoksessa. P. aeruginosa on akvaattisissa ympäristöissä yleinen mikrobi, joka on usein luonnollisesti vastustuskykyinen useille antibiooteille. Lisäksi molemmat bakteerit kykenevät biofilmin muodostamiseen, joka heikentää entisestään antibioottien tehoa. Jätevesien puhdistamoilla on yleisesti havaittu esiintyvän S. aureus- ja P. aeruginosa -bakteereita, mutta suurin osa tutkimuksista on keskittynyt tulevan ja käsitellyn jäteveden mikrobimääriiin ja/tai aktiivilietteeseen. Jätevesillä on ehdotettu olevan merkittävä rooli antibioottiresistenssin kehittymisessä ja leviämisesessä. Jätevesien puhdistamot keräävät yhteen kotitalouksien, teollisuuden ja sairaaloiden jätevesiä ja luovat niiden mukana tulleille mikrobeille tilaisuuden sekoittua ja vaihtaa geneettistä materiaalia, kuten antibioottiresistenssigeenejä. Toisaalta ne ovat myös paikkoja, joissa antibioottiresistenssejä bakteereita vastaan voi kehittyä uusia antimikrobiaalisia aineita tuottavia mikrobeja. Pro Gradu tutkielmani on osa TWIN-A konsortion hanketta ”uusia antibiootteja jätteistä”, jonka päämääränä on uusien antimikrobiaalisten aineiden löytäminen jätevesistä ja teollisista komposteista. Pro Gradu tutkielmassani kartoitan S. aureus ja P. aeruginosa bakteerien esiintymistä jätevedenpuhdistamoiden eri prosesseissa reaaliaika-PCR:n perusteella. Tutkimukseni tuloksia voidaan käyttää hankkeen jatkotutkimuksissa sekä jätevedenpuhdistamoiden riskinarvioinnissa. S. aureus -bakteeria kartoitettiin metisilliiniresistenttiä koodaavan mecA-geenin avulla ja S. aureus -bakteerille spesifistä nukleaasia koodaavan nucA-geenien avulla. P. aeruginosa -bakteeria kartoitettiin gyrB- ja ecfX-geenien avulla. Lisäksi näiden geenien kartoituksessa oli apuna koettimet.GyrB- ja ecfX-geeneissä olevilla muutoksilla on havaittu olevan vaikutusta bakteerin virulenssikykyyn. Kartoitettuja geenejä havaittiin esiintyvän yleisesti jätevedenpuhdistamojen prosesseissa, mutta pitoisuudet olivat alle määritysrajan. MecA-geenin esiintymisfrekvenssi oli nucA-geeniä suurempi, joka voi johtua siitä, että mecA-geeniä esiintyy myös muilla stafylokokki-lajeilla, kun nucA-geeni on spesifinen S. aureus-lajille. Myös gyrB-geenin esiintymisfrekvenssi oli korkeampi kuin ecfX-geenin, joka selittynee gyrB-geenin heikommalla lajispesifisyydellä. Kaikkien kartoitettujen geenien esiintyminen oli painottunut välppeeseen, aktiivilietteisiin, raakalietteeseen, palautuslietteeseen ja tiivistämölietteisiin. Välppeen läheinen kontakti ihmisen kanssa ja suuri orgaanisen aineen määrä selittävät korkeita esiintymisfrekvenssejä tässä prosessissa. Mikrobeille otolliset olot ja mikrobien sorptio aktiivilietteeseen selittävät kartoitettujen bakteerien yleisyyden aktiivilietteissä ja sen jälkeisissä prosesseissa mädättämölle asti. Mädättämöllä anaerobinen mädätys johtaa kartoitettujen geenien vähenemiseen. Mädättämöliete käsitellään Suomessa pääosin kompostoimalla, jossa lämpötilan nousu tappaa suurimman osan patogeeneistä. Kartoitettujen geenien poistuminen jätevedenpuhdistusprosesseista aktiivilietteen mukana, selittää myös geenien matalamman esiintymisfrekvenssin käsitellyssä jätevedessä verrattuna tulevaan jäteveteen. Tulosten perusteella kartoitetut bakteerit ja niiden antibioottiresistenssigeenit eivät aiheuta riskiä ympäristölle. Vaikka havaitut pitoisuudet olivat alle määritysrajan on kuitenkin hyvä pitää mielessä, että ympäristötekijöistä riippuen antibioottiresistenssigeenit ja bakteerit voivat kertyä ympäristöön ja sopivissa olosuhteissa lisääntyä ekspotentiaalisesti. Multiresistenssien bakteerien on myös havaittu selviävän paremmin jätevedenpuhdistusprosesseista, jonka vuoksi tilannetta olisi hyvä seurata tulevaisuudessa.
  • Kiuru, Jukka (2020)
    Tiivistelmä – Referat – Abstract Ikääntymiseen liittyvien biologisten ilmiöiden, kuten rappeutumisen ja sairauksien tutkiminen on ensiarvoisen tärkeää, koska näistä ilmiöistä on haittaa niin yksilölle kuin koko yhteiskunnalle. Erityisen kiinnostavaa on, jos sairaudet ja rappeutuminen pystytäisiin parantamaan tai niiden haitallisia vaikutuksia voitaisiin vähentää. Ikääntymiseen voidaan yhdistää monia vakavia sairauksia kuten hermostorappeumasairaudet, syöpä ja diabetes. Hermostorappeumasairauksille on tunnusomaista proteiiniaggregaattien muodostuminen. SBC003-yhdiste on luonnon yrtistä eristetty molekyyli, joka on potentiaalinen lääke hermostorappeumasairauksiin. Aikaisemmin tehdyt tutkimukset hermostorappeuma sairausmalleilla osoittavat yhdisteellä olevan voimakas konsentraatiosta riippuvainen hermosoluja suojaava vaikutus. Malliorganismit ovat tärkeitä, koska niillä pystytään testaamaan potentiaalisten molekyylien vaikutusta vahingoittamatta kuitenkaan ihmistä. Hiivasta on tullut mielenkiintoinen malliorganismi ikääntymisen ja ikääntymiseen liittyvien sairauksien tutkimuksessa. Monet biologiset prosessit ja aineenvaihduntareitit ovat konservoituneet hiivasta aina ihmiseen asti. Lisäksi geneettiset muutokset on helppo jäljittää. Ikääntymisen tutkimisessa leivinhiiva (Saccharomyces cerevisiae) on osoittautunut erinomaiseksi malliorganismiksi. Hiivan kronologinen ikääntyminen on osoittautunut myös hyväksi menetelmäksi tutkittaessa solujen post-mitoottista ikääntymistä. Hiivasoluissa pystytään havaitsemaan nopeasti, edullisesti ja helposti proteiiniaggregaattien aiheuttamat haitalliset vaikutukset. Käytettäessä hiivaa malliorganismina tutkimuksessa pystytään luomaan suora linkki geenien ja kemiallisten yhdisteiden välille. Hiivalla tehdyt solujen sairausmekanismien tutkimukset ovat vertailukelpoisia ihmisten sairauksien kanssa. Nämä seikat tekevät hiivasta kiinnostavan malliorganismin myös hermostorappeumasairauksien lääkeainetutkimuksessa. Työn tavoitteena oli selvittää, voidaanko hiivasairausmalleja käyttää SBC003-yhdisteen vaikutuksien arvioimiseen hermostorappeumasairauksissa, ja onko tutkittavalla yhdisteellä pelastava vaikutus haitallisia aggregaatteja muodostavia proteiineja vastaan hiivasairausmalleissa. Lisäksi tarkoitus oli tutkia, onko SBC003-yhdisteellä vaikutusta ikääntymisestä aiheutuvaan elinvoimaisuuden heikkenemiseen hiivasoluissa. Tutkimuksissa käytettiin seuraavia menetelmiä ja koejärjestelyjä 1. spottitestejä ja 2. elinkiertotestejä ravistelukasvatuksina, joiden elinvoimaisuutta mitattiin näytteillä, joita puolestaan analysoitiin edelleen Bioscreen-kasvatuksia apuna käyttäen. Spottitestien ja elinkiertotestien tuloksien mukaan SBC003-yhdisteellä saattaa olla pelastava vaikutus haitallisia FUS-aggregaatteja vastaan hiivan ihmisen sairausmallin soluissa. Tutkimustulosten mukaan SBC003-yhdisteellä on solun elinvoimaisuutta parantava vaikutus soluihin, jotka rappeutuvat ikääntymisen seurauksena. Saatujen tulosten varmentamiseksi pitäisi elinkierotestit ja spottitestit toistaa ja lisäksi tehdä sekä geneettisiä että epigeneettisiä tutkimuksia.
  • Coles, Eric Anthony (2019)
    Tiivistelmä–Referat–Abstract Background: Cancer is one of the leading causes of death around the world and in Finland. Ambitious research projects have been carried out for decades investigating cancer and how it spreads. Over 35 years ago, the systems that regulate vascular formation were discovered; the vascular endothelial growth factor (VEGF)-VEGF receptor VEGFR system and the more recent Angiopoietin-TIE system. These are the main endothelial growth factor receptor pathways involved in regulation of vessel quiescence and angiogenesis. The VEGF-VEGFR system is the first discovered endothelial cell (EC) specific receptor tyrosine kinase (RTK) signaling system. VEGF is a major growth factor involved in proangiogenic activity and vascular permeability when bound to its receptor, VEGFR2. Tumor cells take advantage of the VEGF-VEGFR2 system by secreting VEGF to stimulate angiogenesis in surrounding tissue to create new blood vessels allowing for greater access to nutrients and oxygen for tumor growth. The Angiopoietin-TIE system is the second EC specific RTK signaling system that was discovered. Angiopoietin-1 (ANG1) is the ligand for the TIE2 RTK. ANG1 is an obligatory TIE2 agonist and its effects on intracellular signaling, cell cytoskeleton, and junction-related molecules allows ANG1 to restrict the amount and size of gaps that are formed at EC junctions in inflamed vessels, increasing barrier function and decreasing vascular permeability. Angiopoietin-2 (ANG2) is an autocrine context-dependent TIE2 agonist/antagonist which is implicated in stimulating pathological angiogenesis, inflammation and vascular permeability. Integrins are important cell surface receptors that all cells use to communicate with their environment. Recently, it has been discovered that ANG2 is capable of inducing pathological angiogenesis, and can destabilize ECs when bound to integrin, specifically β1-integrin, via ANG2 N-terminal region. Objectives: The general aim of this study was to discover which part of angiopoiten-2’s N-terminus region was responsible for integrin activation. Materials and Methods: Fibronectin fragment containing type III 7-10 domains was produced and fluorescently labeled with Alexa 647. Integrin activation was measured using the fluorescently labeled Fibronectin III 7-10 and angiopoietins. Fluorescence activated cell sorting (FACS) was used to collect the results, which were analyzed using excel. Chimeric angiopoietins were produced using retroviral vectors and used for FACS experiments. A cell internalization assay was performed in Hela cells using CellTracker™ Orange CMRA and angiopoietin proteins, stained with secondary antibody anti-human Alexa 488 and Texas Red Phallodin. Results: Optimization of the FACS assay defined the minimum number of cells required to reliably measure integrin activation and showed that BD Accuri FACS machine was better suited than Guarva FACS machine for the assay and that the amount of integrin varied between cell passages used for the assay. In addition, it was essential to ensure a homogenous mix of cells and recombinant proteins during the assay and the quality of the produced FN III 7-10 was critical for the success of the assay. Results from the FACS assay confirmed that ANG2 is capable of activating integrin. In addition, chimeric angiopoietins that were expressed and secreted from CHO cells, were capable of activating integrins to a variable degree. The results confirmed the importance of ANG2 N-terminus in integrin activation. Cell internalization assay visually demonstrated angiopoietin binding to Hela cells. ANG2 was internalized by the cell and resistant to the acid wash, while the majority of ANG1 bound to the cell surface was washed away by acid wash. Conclusions: In this thesis work, integrin activation assays were optimized and carried out, along with cell internalization assays, to determine which specific part of ANG2 is responsible for inducing integrin activation. The findings from this work confirmed that ANG2 is capable of activating integrin. Several chimeric constructs were successfully expressed in CHO cells, and the cell supernatants were used to activate integrins. However, more studies are needed to determine which specific region of ANG2 is responsible for integrin activation. Investigating angiopoietin induced integrin activation would allow for a better understanding of the angiopoietin signaling pathway with potential translational significance.
  • Rajala, Salla (2022)
    Tiivistelmä * Referat * Abstract Brownification is a serious environmental problem, which means a substantial increase in water color. Suggested reasons for brownification are soil recovery from acidification, land-use change, especially ditching, climate change. Brownification changes the light conditions in the lakes, increases thermal stratification, and sedimentation. Despite the considerable effects of brownification on lake ecosystem, currently in the EU Water Framework Directive, there is no sufficient biological indicator for lake browning. Biological indicators of the Water Framework Directive are mainly targeted to eutrophication, and thus are not sufficient for measuring the effects of brownification. Macrophyte chlorophyll a:b ratio has been shown to decrease with decreasing light conditions, thus making it a potential indicator for browning. The seasonal variation of macrophyte chlorophyll content is not well studied. This master’s thesis aims to find out, how the chlorophyll content of yellow water lily (Nuphar lutea) changes during the growing season in lakes with variable water quality. N. lutea was chosen as a study species, as it is very common in different lakes in Finland. It is important to study the seasonal variation of the macrophyte chlorophyll content, because if the chlorophyll content reacts rapidly for example changes in the weather, it might be too sensitive to be used as a long-term indicator for lake browning. It is also needed to study, if the seasonal variation is different in lakes with variable water quality, so that in the future, the possible sampling can be timed right in different lakes. The study lakes were clear water lakes, humic and eutrophic lake, and their water quality and the chlorophyll content of N. lutea were examined with two weeks intervals from June to September. The concentration of chlorophyll a and chlorophyll b were measured from the floating leaf and from the petiole at 10 cm intervals. Based on these, the total chlorophyll concentration (CHL a+b) and CHL a:b ratio was calculated. In addition to macrophyte samples, water samples were taken from each lake from both epilimnion and hypolimnion. From the water samples, dissolved organic carbon, water color, iron concentration and specific ultraviolet absorbance at 254 nm were measured. In addition, water temperature, light intensity, oxygen concentration and water turbidity were measured at each sampling time. The results of this thesis showed, that the CHL a:b ratio, and total CHL concentration (a+b) were significantly lower in the humic than in the clear water lake. In the eutrophic lake, CHL a:b ratio and CHL a+b concentration was higher than in the humic lake but lower than in the clear water lake. In each lake, the CHL a:b ratio increased during the growing season, together with the increasing water clarity. The change in the CHL a:b ratio was detected best in the 10-30 cm petiole depth. In the floating leaf, CHL a:b ratio and CHL a+b concentration varied a lot, meaning that the floating leaf is not a sufficient indicator for brownification. The change in CHL a:b ratio took approximately 5 to 7 weeks, and the seasonal variation was similar in each lake. Based on the results of this thesis, the CHL a:b ratio of the N. lutea petiole seems to be a very promising long-term indicator for lake browning. In the future, it would be, however, important to study, how the carbon sequestration changes as a result of brownification, if the macrophyte chlorophyll concentration decreases, since this might have considerable effects on lake carbon sequestration. Also, the eutrophic study lake of this thesis had a water color over 100 mg Pt l-1, so it would be important to study, what is the macrophyte chlorophyll content in clear, but eutrophic lakes.
  • Rossinyol Fernàndez, Aina (2023)
    Driven by the growing world population and increased food demand, the conversion of natural habitats into agricultural lands is occurring at an unprecedented rate. This is in turn the leading driver of the current biodiversity crisis, particularly in tropical forest areas characterised by prominent species diversity. Due to an accelerating cash-crop expansion, the once forest-savannah landscape of Northern Guinea-Bissau is now notably occupied by cashew orchards, in addition to scattered forest patches and floodable rice paddies. So far, it remains unknown how these kinds of human-modified landscapes can sustain mammal species over contrasting seasons, and how the habitat use varies across feeding guilds. To address this gap, this study aimed to understand how medium-sized mammals make use of mosaic-like landscapes in Northern Guinea-Bissau by considering the interactive effects of (1) habitat type: forest patch, cashew orchard and rice paddy and (2) season: before (June-July 2022) and after (October-November 2022) the peak of the rainy season. To do so, in each of the two seasons we conducted a 30-day consecutive camera-trap survey across seven landscapes, each of which comprised the three habitat types, amounting to 21 sampling sites. I evaluated mammal species richness, abundance (number of records) and composition across habitat types and seasons at the assemblage-level and discussed the species-specific habitat dependency. I further analysed species abundance across four feeding guilds: carnivores, insectivores, herbivores and omnivores. Based on a sampling effort of 1200 camera-trap days and 940 records, I identified 21 mammal species from 10 families and five orders. At the assemblage-level, species richness and abundance were similar between habitat types, but higher after the peak of the rainy season, except for rice paddies. Forest and cashew habitats shared similar species composition, which differed from rice paddies. Habitat-dependent species were found in each of the habitat types. At the feeding guild-level, in both seasonally periods carnivores and insectivores were less abundant in cashew orchards, while omnivores were more abundant. The results demonstrate that habitat conversion is likely to disrupt the functional structure of mammal assemblages. Maintaining heterogeneous landscapes, including both forested and open-area habitats, is crucial to maximize the integrity of mammal assemblages in Northern Guinea-Bissau. These findings can be used as baseline information in effective conservation measures in Guinea-Bissau and other tropical regions undergoing rapid conversion for cashew cultivation.
  • Liao, Wenfei (2017)
    Urbanisation has caused many environmental problems, such as air pollution and the loss of biodiversity. One way to mitigate these problems is to expand green spaces. Roofs, as the last frontier, could be made full use of. Green roofs have become a hot topic in recent years. In this study, I investigated the ability of green roofs to support urban biodiversity by conducting a literature review, and then I sought the criteria for biodiversity roofs under Finnish conditions by interviewing ecologists. My research questions in this study were 1) What kinds of habitats could be 'ideal ecosystems' to be mimicked on biodiversity roofs in Finland; 2) which plant species could exist on roofs and whether they contribute to biodiversity; 3) what kinds of substrates support the biodiversity on roofs; 4) whether green roofs support faunal diversity and what faunal taxa could exist on roofs; 5) if and how roof structural characteristics influence roof biodiversity; 6) what kinds of management are practiced on biodiversity roofs; 7) what are people s attitudes towards or perceptions of biodiversity roofs in general. In this study, I conduct that 1) Sunny dry habitats, such as meadows and tundra, can be regarded as 'model ecosystems' for biodiversity roofs in the Finnish context. 2) Substrate heterogeneity is a key to biodiversity on green roofs. Different materials and different combinations of materials could be applied on the same roof to mimic diverse types of soil types in the most biodiverse Finnish ecosystems. 3) Native species from the model ecosystems are ideal plants for biodiversity roofs. Combining multiple greening methods on the same roof can be a solution to achieve 'instant greening effects' with only native species. 4) An ideal biodiversity roof in the Finnish context could support birds, bats, and invertebrates, such as spiders. To attract and support fauna, a roof needs a diverse plant community, as well as extra elements, such as deadwood. 5) Roof structural characteristics (i.e. roof height, size, slope, direction, location, and age) impact biodiversity by determining the accessibility to and the dispersal of flora and fauna, as well as microclimates on roofs. 6) Management, such as irrigation, might help biodiversity at least for newly established biodiversity roofs, but biodiversity roofs aim at being self-sustaining eventually. 7) People have generally positive attitudes towards green roofs, but their willingness to actually install a biodiversity roof is influenced by other issues, such as the financial cost and roof safety.
  • 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.
  • Salmelin, Natasha Emmie Astrid (2023)
    Triple Negative Breast Cancer (TNBC) has the worst prognosis among all breast cancer subtypes. The lack of hormonal receptors and Her2 expression makes targeting with hormone-based treatments or anti-Her2 antibodies ineffective. Furthermore, TNBCs exhibit the highest expression of the oncogene MYC which negatively affects immune cell function. Natural Killer (NK) cells target transformed cells like cancer cells and have demonstrated promising clinical efficacy as treatments for hematological malignancies. However, NK cells have not yet been as successful in treating solid cancers, like breast cancer. The mechanism behind the lack of efficacy is not well understood, and therefore studies elucidating the mechanism are critical for improving the efficacy of NK cell therapies. In this study, we show that MYC-overexpression by itself does not affect the NK cell cytotoxicity of TNBC cell lines, however, if the NK cell response is initiated through antibody-dependent cellular cytotoxicity (ADCC) then MYC expression inhibits NK cell-mediated killing. Many TNBC cell lines are resistant to classical NK cell cytotoxicity, which we show can be overcome with ADCC-inducing antibodies. MYC overexpression has an inhibitory effect in two out of three NK cell donors, when overexpressed in the presence of ADCC-enabling antibodies. This indicates some degree of heterogeneity in MYC regulation of ADCC-dependent cytotoxicity. Our results also demonstrate that when MYC is overexpressed in TNBC cell lines, NK cell activating ligands are downregulated on the tumor cell surface, which could explain the MYC-mediated inhibition of NK cells. This is consistent with other studies where MYC overexpression downregulates NK cell activating ligands in cancer cell lines and inhibits NK cell killing. Altogether, we demonstrate a functional role of MYC in the inhibition of ADCC-dependent NK cell cytotoxicity in TNBC. These findings could explain the inhibitory function of tumor cells on NK cells and provide the rationale for exploring MYC-overexpression as a biomarker for predicting a response of breast cancer patients to NK cell-based immunotherapies.
  • 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.