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  • Stendahl, Annie (2022)
    Abstract Faculty: Faculty of Biological and Environmental Sciences Degree programme: Genetics and Molecular Biosciences Study track: Molecular and Analytical Health Biosciences Author: Annie Stendahl Title: Measurement repeatability of flow cytometry and nanoparticle tracking analysis for optimization of extracellular vesicle measurements Level: Master’s thesis Month and year: 11/2022 Number of pages: 92 Keywords: extracellular vesicles, repeatability measurements, metrology, traceability, flow cytometry, nanoparticle tracking analysis, reference material, METVES Supervisor or supervisors: Virpi Korpelainen, Katariina Maaninka and Pia Siljander Collaborative partner: VTT Technical Research Centre of Finland Ltd. Where deposited: E-thesis Extracellular vesicles (EVs) are lipid bilayer-enclosed vesicles secreted by all cells, containing variable cargo from nucleic acids and proteins to carbohydrates, metabolites, and lipids. EVs are considered to be involved in many physiological and pathological cell functions. Due to their presence in biofluids hence enabling semi-invasive liquid biopsies, EVs have indicated great promise for utilization as biomarkers in clinical settings. The innate properties of EVs and their cargo could also be harnessed into therapeutic use. However, the current methods and reference materials for determining EV concentration and size have not yet achieved the metrological level of repeatability and traceability, which is needed for EV measurements to be utilized in clinical settings. The aim of this thesis project was to evaluate repeatability of the methods typically used for EV quantification and size determination, flow cytometry (FCM) and nanoparticle tracking analysis (NTA). The repeatability was analyzed with reference material made of hollow organosilica beads and biological EV test samples, both developed in an ongoing EU metrology-project METVES II for EVs. A similar biological EV test sample was also prepared as part of the thesis project. Finally, the repeatability measurements were conducted with calibration beads recommended by the instrument manufacturers. The calibration beads gave repeatable results with FCM and one of the two NTA instruments tested, but neither the reference beads nor the biological EV test samples produced repeatable results to enable determination of repeatability. However, valuable understanding was gained on what can be optimized during the measurements and operation of the instruments to generate more repeatable results with FCM and NTA in EV analysis. Prior knowledge of both the sample type and method used for measuring would enable optimization of the measurement and instrument operation. Whether the aim is EV quantification or size determination, instrument errors and bias could then be minimized by adjusting the settings according to sample type. Furthermore, EV quantification and size determination would benefit from combining different methods to ensure more reliable and repeatable results. It is clear that more research needs to be done, for i.e., the tested reference beads need to be further developed to be established as EV reference material and enabling standardization of EV measurements. Standardizing EV quantification and size determination is required to achieve metrological repeatability and ultimately, traceability, and thus for EVs to be utilized in clinical settings as biomarkers or therapeutic use.
  • Jakkli, Meera (2020)
    Neural Oscillations at large-scale local and global neural synchrony levels can be detected at the scalp using electroencephalography. This neural activity presents itself in a varied range of frequencies referred to as ‘Brain Waves’. These frequency bands have cognitive significance and have been implicated in several neural functions due to its important role in communicating with functionally-similar but spatially-distinct brain regions. Frontal Asymmetry is the difference in activity between the right and left hemispheres in frontal areas of the brain recorded via EEG and is seen to be a strong indicator of emotional states. Specifically, approach and withdrawal motivation which have been associated with positive and negative emotions respectively. Using a combination of behavioural and physiological methods in measuring preference and responses gives us an accurate representation of the participant responses. In this study, three tests were conducted during a continuous EEG recording. Test 1: The implication of inducing a positive mood before the onset of stimulus line-up and the extent of its effect on emotions and alpha asymmetry is not extensively studied. In this test, we employed the use of an instrumental soundscape for one experimental group before beginning the stimulus presentation to test this effect against a ‘silent’ control group. Test 2: This test aims to compare the participants’ physiological measures (EEG) and behavioural self-reports to audio advertisement stimuli consisting of different categories of music: ‘Brand music’ vs. ‘Campaign’ music or ‘No music’ Controls. Test 3: There is ambiguity in research regarding how frontal alpha asymmetry as measured by EEG and self-report preferences might change with changing the format of the advertisement to: only Audio, Audiovisual and Silent videos. There has been contradictory evidence regarding the impact of music on an individual’s emotions and consequent memory and decision-making. This thesis delves into these questions through the post-study behavioural test and simple binary choice paradigm that measure the above-mentioned in relation with the stimuli presented to participants. Our results did not show a significant difference in frontal asymmetry in the stimulus presentation across the three tests conducted during EEG recording. The behavioural data however indicated significant preference in behavioural self-report ratings for Brand Music- associated stimuli in Test 2 and for Audiovisual advertisement stimuli in Test 3. Results also revealed a significant correlation between ratings given to a stimulus and post-study memorability. The final binary choice paradigm test indicated higher preference to products related to stimulus presentation (‘advertised’ brand) vs similar products not related to the presented stimulus (‘non-advertised’ brand). We anticipate that these results will further help us understand and predict general preferences that can help companies, government policy-makers and the general public be more aware and better equipped to manage their valuable resources of money, time, attention and memory.
  • Raza, Shaffaq (2020)
    Growth differentiation factor 15 (GDF15), a member of TGF-β super family is a soluble cytokine that is associated with different pathological conditions including cancer, cardiac and renal failure and obesity. Its high serum levels are linked with symptoms like cachexia/anorexia in cancer patients and can be used as a marker for these diseases. Its crucial role in weight regulation and energy homeostasis has been demonstrated by treating obese mice with GDF15, which results in weight lose along with improved glucose metabolism and increased insulin tolerance. It is now known that GDF15 exerts its metabolic effect by binding to a GDNF receptor -α-Like (GFRAL) receptor along with co-receptor RET. Interestingly, these two receptors co-localize only in the brain stem area of mice and humans indicating involvement of a neuronal circuit in GDF15 mediated effects. Despite its implications in major health disorders, little is known about the interaction of GDF15 with its receptors and how this interaction in turn modulates different cellular signalling and functions. The aim of the thesis was to study the mechanism and factors involved in endocytosis of GDF15. I employed high content imaging and flow cytometry techniques to visualize and analyse the internalization of ligand-receptor complex and investigate the role of actin, dynamin and phosphoinositide 3 kinase in the process. The results suggest that similar to the internalization of other cellular growth factors, the uptake of GDF15 is affected by disruption of the actin cytoskeleton. The role of dynamin is still unclear. I also discovered that the internalization of GDF15 was inefficient even in cells that expressed the receptor GFRAL, with large cell-to-cell variation. By following the intracellular localization of the receptor GFRAL, my results revealed that the receptor GFRAL is not efficiently exported to the plasma membrane and most of the protein is retained in the Golgi compartment of cells. This phenomenon was stronger in murine fibroblast cells, where the receptor was almost exclusively trapped in the secretory compartment, explaining why the uptake of the ligand GDF15 is so inefficient in these cells. The system developed during this project will now be used to analyse different factors involved in the uptake of GDF15 and eventually uncover the possible endocytic pathway. Moreover, the Golgi retention of the receptor opens up new questions to investigate like whether the physiological function of GDF15 is regulated by receptor export signals. This will help deciphering the complex and mysterious interaction of GDF15 with its receptor GFRAL.
  • Nurmi, Aino (2023)
    The 2022 energy crisis heightened concerns about energy sufficiency. In response, Finland launched a nationwide energy-saving campaign, Astetta alemmas, to encourage Finns to take concrete and effortless energy-saving actions in their daily lives. The aim of this thesis was to analyze which energy-saving behaviors the media emphasize in the campaign and how the campaign messages are framed in the media. The analysis of media response was chosen because there is a lack of this type of study related to energy-saving campaigns. The data consisted of 94 news articles collected from the five national online news media from October 1st to December 31st, 2022. The data was analyzed using frame and content analysis. The analysis was based on a pre-determined theoretical framework consisting of nine energy-saving and general news frames: economic, social, environmental, personal, moral, health, conflict, responsibility, and human-interest frames. In addition, two new frames were recognized from the data. The energy-saving behaviors found were classified as curtailment and efficiency behaviors. The campaign was portrayed as an opportunity to save money through effortless energy-saving measures such as lowering the room temperature. Most of these actions were categorized as curtailment behaviors. The media showed the importance of individuals’ efforts to save energy in a society by emphasizing that saving energy has paid off and that new saving habits have become a routine part of daily life. On the other hand, energy-saving actions led to compromises in living standards, resulting in suffering and high electricity bills. The media portrayed the negative consequences by emphasizing conflicts and showing how far people are willing to go to save energy while risking their health. The impact on the environment was seen as a secondary principle. The crisis was a suitable moment for the media to highlight the importance of energy conservation. The campaign was well justified as a campaign of the whole nation, highlighted by solidarity and shared responsibility to save energy. Nevertheless, some of the tips given were targeted at specific households. The media raised a dichotomy by highlighting individuals as heroes or sufferers through their experiences. This is a novel contribution to previous studies. This dichotomy provides room for further studies that could focus on the people behind the news stories and the long-term effects of post-campaign energy-saving measures. This thesis provides initial insights into the media response to the Astetta alemmas campaign during the first three months and in specific news media, but the results cannot be generalized to the response of all news media during the campaign.
  • Uotila, Iiro (2021)
    Evolving societies force universities to transform from the producers of new information sat in their ivory towers towards the role of entrepreneurial universities. The theme of entrepreneurial universities is widely studied internationally, but studies concerning the University of Helsinki (UH) are scarce. The aim of this thesis is to map the current UH bioentrepreneurship ecosystem and the services it provides. The services were mapped and assessed based on how they match the needs of academic bioentrepreneurs. Measures are also suggested on how to develop the ecosystem. This thesis links strongly to the previous literature on entrepreneurial universities and academic entrepreneurship. Entrepreneurial university as a term encompasses an organisation, which strongly supports and encompasses entrepreneurial action in its different functions. Strong technology transfer and commercialization of research via licensing and spinout company formation, is usually linked to entrepreneurial universities. University spinouts are strongly linked to academic entrepreneurship. In spinouts research results and academic tacit knowledge are transformed into enterprises to produce value. The thesis was conducted as a qualitative case study. For the study UH affiliated entities offering entrepreneurship services and bioentrepreneurs originating from within the university were interviewed. The data was analysed with content analysis methods. The results show that UH bioentrepreneurship ecosystem is just in the beginning with multiple useful services but also with some significant flaws. The most significant obstacles preventing the growth of the ecosystem are the university’s negative culture towards entrepreneurship, non-existent communication about the subject and the absence of relevant supportive networks for academic entrepreneurs. Via changing these the critical mass to enable sustainable ecosystem can be achieved.
  • Katajisto, Heikki-Pekka (2019)
    Työssä on tutkittu Päijät-Hämeen Jätehuolto Oy:n (PHJ) syksyllä 2016 valmistuneen mekaanisen jätteenkäsittelylaitoksen (LATE lajittelulaitos) seula-alitteiden koostumusta ja ominaisuuksia, sekä niiden vaihtelua, joiden perusteella niille voidaan valita sopivin jatkokäsittelymenetelmä. Laitos käsittelee noin 66 0000 tonnia jätettä vuosittain (yhdyskuntasekajätettä 33 000 t, rakennusjätettä, sekä muuta vastaavaa jätettä 33 000 t). Syntyvien seula-alitteiden koostumus ja ominaisuudet vaihtelevat riippuen siitä, mitä jätelajia milloinkin käsitellään. Laitoksen tuotantoprosessi koostuu monivaiheisesta erottelusta, jossa erilaiset laitekomponentit erottelevat esimurskatusta jätevirrasta materiaaleja eri ominaisuuksien perusteella. Työssä tutkittavat neljä fraktiota ovat yhdyskuntasekajätteestä ja rakennusjätteestä erotellut 0-20 mm ja 20 -80 mm seula-alitteet. Kummankin kokoluokan fraktioita syntyy noin 30 % syötemassasta. Alitefraktioiden perusmäärittelyä varten kunkin neljän fraktion kolmesta rinnakkaisesta kokoomanäytteestä tehtiin Vna 331/2013 mukainen tavanomaisen jätteen kaatopaikkakelpoisuustestaus, soveltaen lisäksi pysyvän jätteen kriteeristöä, sekä eräiden jätteiden hyötykäytöstä maarakentamisessa (527/2014). testaus sisälsi kokonaispitoisuudet TOC, pH, ANC ja liukoisuudet 2-vaiheisesta ravistelutestistä: As, Ba, Cd, Cr, Cu, Mo, Ni, Pb, Sb, Se, Zn, Hg, Cl, F, SO4, DOC, pH, sähkönjohtokyky, TDS. Lisänä BTEX, mineraaliöljyt C10-C40, PAH, ja PCB ja Fenoli-indeksin. Lisäksi tutkittiin alitteiden metaanintuottoa 21 päivän panoskokeella, sekä alitteiden polttoaineominaisuuksia, kuten näytteen kosteus- ja tuhkapitoisuus, alkuaineet C, H, N, O, S ja kloori, sekä tehollinen ja kalorimetrinen lämpöarvo. Lisäksi näytteille tehtiin myös lajittelukokeet, jossa määriteltiin näytteiden materiaalikoostumus. Lajiteltavia materiaaleja olivat biojäte, lasi, metalli, muovi, paperi/kartonki, puu, tekstiili, kiviaines, muu aines, sekä hienoaines. Hienoaineksesta määritettiin lisäksi orgaanisen hiilen kokonaismäärä. Työssä saatujen tulosten perusteella yksikään laitoksella muodostuvista alitefraktioista ei täyttänyt tavanomaisen jätteen kaatopaikkakelpoisuutta täysin, vaan esimerkiksi alitteiden orgaanisen hiilen kokonaismäärä rajoittaa alitteiden kaatopaikkasijoitusta. Yhdyskuntasekajätteen käsittelyn alitteiden sisältämä orgaaninen aines (24 – 34 %) vastasi kaasuntuotoltaan erilliskerättyä biojätettä 403 ja 336 ml CH4 /g /VS. Rakennus- ja lavajätteiden käsittelyn 20-80 mm alitteen tehollinen lämpöarvo saapumistilassa oli 9,4 MJ/kg, kun taas yhdyskuntasekajätteen käsittelyn 20-80 mm alitteen tehollinen lämpöarvo oli saapumistilassa 7,8 MJ/kg. Yhdyskuntasekajätteiden lämpöarvoa laski alitteisiin sitoutunut kosteus, jota oli 48 – 52 % alitteiden massasta.
  • Järvilehto, Laura (2006)
    The objective of this study is twofold: Firstly, to investigate how men and women living in Tanala villages in the Ranomafana National Park buffer zone differ in their natural resource use and livelihood. Secondly, based on this information, the intention is to find out how the establishment of the park has influenced people living in the buffer zone from the gender point of view. The data have been gathered mainly by using semi-structured interviews. Group interviews and individual interviews were carried out in three buffer zone villages. In addition, members of the park personnel were interviewed, observations were made during the visits to the villages and documents related to the planning and the administration of the park were investigated. The data were analysed using qualitative content analysis. It seems that Tanala women and men relate to their environment in a rather similar way and that they have quite equal rights considering the use and the control of natural resources. Probably this is the reason why the management of the Ranomafana National Park has practically not taken gender issues into account in the planning of the park or in administering activities related to it. Both Tanala men and women can own and inherit land, and in most cases they also exert full control over it. Similarly, women and men seem to control their own labour as well as the produce of their work. There is a strong gendered division of labour in Tanala villages, based on the conception of men doing the hard and difficult work and women s tasks being easy. This idea does not appear to correspond with reality, but it rather seems to be a social construction highlighting the importance of men s work at the expense of women s tasks. At the household level, men and women have equal say considering environmental resources management as well as other kinds of issues, but at the community level women are significantly less active than men in decision making. Since the park management has not paid any special attention to this, women s voices and their interests have not been heard as much as those of men in park related meetings. In consequence, there have been no development projects focused on women s cultivation activities, for example. The establishment of the park has also had another important gendered impact. Since the creation of the park local people have been forbidden to enter the park forest. In practise this ban has mostly affected women, and the forest has become a men s space considering both the access to it and it s resources as well as the feeling of authority. As a conclusion it can be stated that for achieving socially just nature conservation, it is important to take gender issues into consideration even if gender relations seem to be quite equal. In Ranomafana area the situation could be improved, for example, by listening more carefully to women s interests and needs.
  • Rooney, Erin Jane (2022)
    Meningeal lymphatic vessels (mLVs), a recent functionally characterized structure in the meninges, contribute to the clearance of macromolecules, immune cells and metabolic waste from the central nervous system to peripheral lymph nodes. Having been identified as a route of clearance, there is a focus on understanding their role in neurological disease pathology. Here we consider their function in the pathology of traumatic brain injury (TBI) particularly in blood solute clearance, lesion progression and neuroinflammatory response. We use a transgenic model of mLV developmental dysfunction, K14-VEGFR3-Ig, to analyze the progression and severity of a controlled cortical impact (CCI) injury. We show that in mice lacking mLVs there are a higher percentage of microglia cells in an activated state in the hippocampus whereas the progression of hematoma and lesion size does not differ from wild type. Our results suggest that at two months post injury, meningeal lymphatics could be functionally important in modulating microglia activation, which is associated with chronic inflammation.
  • Granroth, Janne (2019)
    The Great Cormorant (Phalacrocorax carbo) is among the most recent additions to the Finnish avifauna: the current breeding population dates back to 1996. Historical and archeological data clearly demonstrate that the 20th century breeding range expansion of the species in the Baltic region is a re-colonisation event. The two subspecies of Cormorant in Europe are the nominate subspecies P. carbo carbo and the continental subspecies P. c. sinensis. The Cormorants currently breeding in Finland belong to the subspecies sinensis. P. c. carbo lives on the coasts of the North Sea and North Atlantic and visit Finland only during migration. However, osteological evidence suggests that carbo was prevalent subspecies in the Baltic area during prehistoric times, only to disappear in the Late Middle Age (by circa 1500 AD). The subspecies of the Cormorant differ in average size and weight, the details of the plumage and the angle of the gular pouch. P. c. carbo is on average larger than sinensis. However, males are larger than females in both subspecies. The subspecies differ in their ecological characteristics, e.g. preferred prey, breeding sites and migratory behaviour. However, only bones remain from the prehistoric Baltic Cormorants and therefore, soft tissues or behavioural characteristics cannot be used for their identification. The known osteological measurements of the subspecies overlap, and it has previously been possible to distinguish only the two extremes, large P. c. carbo males and small P. c. sinensis females. Here, I looked into features that would enable distinguishing of the skeletons of all the specimens of both subspecies. The primary material of my Master’s thesis consists of 65 specimens representing birds of both subspecies and sexes. The material has been collected from the Baltic basin and the western Gulf of Bothnia in Sweden and the Åland islands in Finland. In addition, I examined 11 specimens of the subspecies carbo from the collections of the Swedish Museum of Natural History (Naturhistoriska riksmuseet). I focused on the most diagnostic elements of the skeleton: skull, sternum and the large bones of the limbs. Moreover, I examined bones that may be associated with ecological differences between the subspecies, such as the sclerotic ring, the os nuchale, and the length of the distalmost phalanx bone of the opposable hallux toe. I wanted to find out if there are osteological differences between the males and females or the two subspecies. The statistical method used for testing the hypotheses and examining subspecific averages was the analysis of variance (ANOVA). The measurements were also analysed with Principal Component Analysis to investigate the proportional differences. The bones of the two subspecies differed in particular in the length of the forearm bones. Reliable discriminating features also included the depth of the bill and the measurements of leg bones. These are subspecific adaptations to their preferred habitats, prey, nesting sites and migratory behaviour. The relatively short wings of P. c. carbo make it an excellent diver, but a less efficient flyer. This subspecies migrates shorter distances, and is able to overwinter relatively far up in the north. In contrast, P. c. sinensis is able to fly with greater speed and efficiency during migration to avoid adverse conditions. The depth of the bill is an important factor determining the snapping power of the bill, which makes P. c. carbo better suited for handling big or powerful prey. The contemporary Baltic Sea is warmer and less marine than during earlier periods. The current brackish environment seems to favor the subspecies sinensis over carbo, although human persecution may also have had an effect on the previous demise of subspecies carbo. My results support the view that the subspecies of the Great Cormorant are clearly distinct morphologically. My result also suggest that skeletal research is an underutilised method in bird taxonomy, and studying the proportions of bones helps to perceive ecological and biological differences between bird subspecies.
  • Saari, Sanna (2007)
    Kovakuoriaiset (Coleoptera) ovat sopeutuneet hyvin erilaisiin elinympäristöihin. Kuitenkin vain pieni osa kovakuoriaislajeista elää vedessä. Lehtikuoriaisista (Chrysomelidae) parhaiten vesielämään sopeutunut ryhmä on ruokokuoriaiset (Donaciinae), joista Macroplea-suvun lajit ovat sopeutuneet täysin akvaattiseen elämään. Meriuposkuoriainen (Macroplea pubipennis) elää murtovedessä ja voi esiintyä yhdessä rantauposkuoriaisen (M. mutica) kanssa. Meriuposkuoriainen tunnetaan vain Suomen rannikolta ja Kiinasta, kun taas rantauposkuoriainen on yleinen esim. Euroopassa. Meriuposkuoriainen on uhanalainen ja kuuluu EU:n luontodirektiivin liitteen II lajeihin. Uhanalaisten lajien suojelun suunnittelua varten tarvitaan tietoa lajin biologiasta, levinneisyydestä ja ekologisista vaatimuksista elinympäristönsä suhteen. Tässä työssä halusin selvittää meriuposkuoriaisen ja rantauposkuoriaisen esiintymistä ja suhteellista runsautta Espoonlahdella sekä muodostaa käsityksen meriuposkuoriaisen tyypillisestä elinympäristöstä. Lisäksi halusin selvittää lajin sukupuolijakaumaa ja parien osuutta populaatiossa sekä kehittää ja testata uutta menetelmää lajin esiintymisen tutkimiseen. Tein uposkuoriaisten esiintymisen ja vesikasvilajiston tutkimuksen linjalaskentana pintasukeltamalla 16 näytealalla. Veden fysikaalis-kemiallisten ominaisuuksista mittasin lämpötilaa, happi- ja suolapitoisuutta sekä laskin näytealojen avoimuuden aallokolle. Kenttätyöt tein Espoonlahdella kesäkaudella 2003. Tilastollisilla testeillä selvitin miten näytealat erosivat toisistaan tutkittujen elinympäristömuuttujien suhteen ja mitkä muuttujista vaikuttivat meriuposkuoriaisen esiintymiseen ja tiheyteen. Havaitsin meriuposkuoriaisia kahdeksalla näytealalla (yhteensä 134 yksilöä) ja rantauposkuoriaisia viidellä (yhteensä 17 yksilöä). Neljällä näytealalla lajit esiintyivät yhdessä. Suurin osa (85 %) heinäkuussa havaitsemistani meriuposkuoriaisyksilöistä oli pareittain, elokuussa enää pieni osa yksilöistä oli pareittain (15 %). Yksittäin löydetyissä kuoriaisissa koiraita oli paljon naaraita enemmän. Ilmeisesti aikuiset yksilöt kuolevat syksyllä ja naaraat saattavat kuolla koiraita aikaisemmin. Espoonlahden mittakaavassa veden lämpötila, happi- ja suolapitoisuudet eivät vaikuta meriuposkuoriaisen levinneisyyteen. Meriuposkuoriaisen ravintokasveja Espoonlahdella ovat hapsivita sekä tähkä- ja kalvasärviä, joista hapsivita on suosituin. Ahvenvitaa laji ei hyödynnä. Ravintokasvin suhteellinen osuus oli tärkein meriuposkuoriaisen esiintymistä määräävä tekijä ja selittää 57,6 % lajin esiintymistiheyden vaihtelusta. Alueen liiallinen suojaisuus saattaa vaikuttaa negatiivisesti meriuposkuoriaisen esiintymiseen. Pintasukeltaminen menetelmänä soveltuu hyvin meriuposkuoriaisten kartoitukseen, jos näkyvyys vedessä on tarpeeksi hyvä suhteessa kartoitettavan alueen syvyyteen. Meriuposkuoriaistutkimusten kenttätyöt kannattaa tehdä kesä-heinäkuun aikana. Tällä hetkellä meriuposkuoriaisen esiintymistä on tutkittu kattavasti ainoastaan Espoolahdella sekä osista Paimionlahtea. Ainoat lajin suojelemiseksi rajatut alueet ovat sen neljä tärkeintä esiintymispaikkaa Espoonlahdella. Tämä tutkimus on osaltaan vaikuttanut rajauspäätöksiin. Meriuposkuoriaisesiintymät tulevat yhä eristäytyneemmiksi, kun elinympäristöt pirstoutuvat mm. vesirakentamisen vuoksi. Jos lajia suojellaan Espoonlahdella ainoastaan sille rajatuilla pienillä alueilla ja rakennetaan tai muuten muokataan väliin jääviä alueita, on lajin säilyminen vaarassa. Meriuposkuoriaisen suojelun tehostamiseksi tarvitaan ajantasaista paikkatietoa lajin levinneisyydestä Suomessa ja jo tunnettujen esiintymien tilan seurantaa. Meriuposkuoriaisen populaatiodynamiikan ja leviämiskyvyn tutkimus olisi tärkeää, jotta lajin suojelemiseksi osataan valita sopivia alueita.
  • Suvitie, Aurelia (2020)
    Insects (Insecta) are the most species-rich class of organisms on earth. Due to their vast biodiversity, insects are found in almost every environment. However, approximately 90 % of the over 1 000 000 insect species described are terrestrial. The ocean covers over 70 % of the earths surface, but less than 2 000 marine insect species are known. The purpose of this thesis is to give the reader a comprehensive understanding of marine insect biodiversity and what has caused its sparceness in the seas. Such a multi-faceted review of the topic has not previously been written. The first aim of this review is to catalogue all insect taxons containing marine species, and to examine the habitat choices and ecology of these species. For this purpose, marine insect species have been researched using the World Register of Marine Species (WoRMS) and reference literature, as well as reviews and other articles. Based mostly on WoRMS, the number of marine insect species is determined to be 1 318, divided between 10 insect orders. In addition, seven insect orders are noted to include an unknown number of marine species. As well as examining marine insect biodiversity order-by-order, this work considers the littoral and pelagic habitats in which marine insects live, and the adaptations that are required of insects living in these environments. The second aim of this review is to investigate the lack of insects in marine environments as a phenomenon. The groundwork is laid at the beginning of the review with an examination of why and how insects have diversified so successfully. Later on, possible factors to prevent a similarily successful diversification in marine environments are presented, such as issues with osmoregulation and breathing systems, the typical features of insect reproduction and life cycles, and the fact that transitions between physically contrasting habitats are rare. Pertaining to this the evolutionary history of insects, which has produced the aforementioned features impeding radiation to the seas is also explored. Ultimately insect species in the oceans are few, because insects are a terrestrial evolutionary branch of Pancrustacea. Even though marine habits are uncommon among insects, they are not unheard of. Marine species have emerged in several insect clades and these species have adapted to their environment in numerous ways. For the purposes of further analyses and research on the radiation and biodiversity of marine insects, further surveying of the species and their habits and adaptations is recommended. This work will hopefully offer a point of reference for more detailed future studies and reviews of marine insect biodiversity and the factors that have led to the near-exclusion of insects from the seas.
  • Lindholm, Viivi (2022)
    Environmental factors are important tools in constructing methane flux models and estimations. Among the abiotic factors, plants and their functional groups have been noted to have significant effect on methane fluxes for three reasons. First, the vegetation community compositions express their abiotic environmental factors that affect not only the plants, but also local methanogen and methanotroph communities. Second, the vegetation itself might produce methane emissions and have a direct effect on methane balance. Third, the plant functional groups and species have differences in their chemical and physical properties that support different methanogen communities and therefore have an indirect impact on methane fluxes. In this study, methane fluxes of different plant communities were observed during one growing season in northern boreal catchment area in Muonio. Study focuses to determine the link between methane fluxes and abiotic and biotic environmental factors in different vegetation types. Closed chamber technique was used to measure methane and carbon dioxide fluxes from 23 plots every two weeks in period of June-August. Environmental data, such as moisture, temperature species composition etc. were collected from the plots. Vegetation types for each plot were determined via ordination analysis. Linear mixed-effects regression model and generalized additive model were applied and compared to observe the relationships of methane and environmental factors in different vegetation types. Dataset was divided into four vegetation types in clustering analysis: wet fen, pine bog, spruce swamp and forest. The greatest amount (average 5959 µg/m²/h) and biggest range (standard deviation 5285 µg/m²/h) of methane emissions were observed on wettest fen-like study sites. Peatland types in general acted as net methane sources. The driest, forest-like vegetation type acted as a net methane sink. The amount (average -107 µg/m²/h) and range (standard deviation 117 µg/m²/h) of methane fluxes were very moderate in comparison to peatland types. These effects intensified towards the climax of growing season. The most significant environmental factors were mostly abiotic on driest study sites and the whole plant biomass was more significant biotic methane flux regulating factor than plant functional groups. On wetter study sites, the role of abiotic factors decreased, and plant functional group increased. Graminoids were linked to bigger methane emissions especially on wetter study sites. Forest mosses and different shrub types seemed to have a link with lower methane emissions or methane absorption. The effect of other plant functional groups on methane fluxes varied more, and their role remains unclear. None of the environmental factors could estimate the methane flux alone, and the methane budget seems to be a sum of multiple variables in each vegetation type. The role of plant functional groups varied in different vegetation types and was dependent on surrounding vegetation. More research is needed to get better tools to estimate methane balance and to understand the underlying mechanisms in climate and environmental change.
  • Savelius, Mariel (2020)
    Breast cancer remains as the leading cause of cancer deaths among women. Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes and lacks targetable receptors, consequently, cannot be treated with current hormone of anti-HER2 targeting therapies. Thus, there is a need for discovering novel and well-tolerated therapies. MYC is a proto-oncogene and a transcription factor, that is frequently amplified and overexpressed in breast cancers. MYC is involved in many cellular processes promoting cell proliferation, however, overexpression of MYC can also sensitize cells to replicative stress and apoptotic cell death. In our previous studies we have shown that pharmacological activation of AMPK, a cellular energy sensor, synergises with Bcl-2 family inhibitors, such as navitoclax and venetoclax, and activates MYC-dependent apoptosis in breast cancer cell lines, transgenic mouse models of MYC-dependent mammary tumorigenesis and in MYC-high patient-derived explant cultures (PDECs). In subsequent study we observed, that indirect AMPK activator metformin alone inhibited tumor growth in vivo, but did not induce apoptosis in mouse tumors or in PDECs. Metformin, a type II diabetes mellitus drug, has shown anti-cancer effects in some population studies and is under investigation for a cancer therapies, however the whole mechanism of action in cancer is still not well-known. To elucidate metformin’s effects on MYC overexpressing triple-negative breast cancer cells, I will present, that metformin has anti-proliferative effects and show that long term metformin treatment induces senescence biomarkers in MYC-high TNBC breast cancer cell lines. To study metformin's short and long-term anti-proliferative activity, cell proliferation during and after drug treatment was investigated, which showed, that metformin’s effects do not seem to persist long after drug withdrawal. In conclusion, the key observation of this thesis was, that metformin does inhibit the proliferation of MYC overexpressing cancer cells and presents a senescence phenotype that possibly can be exploited to find new targeted therapies for triple-negative breast cancer patients.
  • Horten, Hannah (2021)
    Methane (CH4) is a powerful greenhouse gas that has been increasing in total atmospheric concentration since the late 1980s. While more of this gas is being produced through anthropogenic sources, a significant part is still produced by microbial methanogenesis. This process, in combination with atmospheric CH4, provides methane oxidizing bacteria, methanotrophs, with consumable CH4. In this way, methanotrophs are an important part of the CH4 cycle. Most models estimating changes to CH4 concentrations as a result of increasing anthropogenic byproducts often fail to consider the importance of these bacteria as a sink. Methanotrophs have been long studied, but more still needs to be discovered about their functionality in varying ecosystem types. These microbes are cosmopolitan, found in diverse environments across the globe. In this study, soil samples collected from a boreal forest in Pallas, FI were used to measure how well soil properties can be used to approximate potential CH4 oxidation rate. The abundance of methanotrophs was analyzed in soils ranging from upland to peatland using qPCR targeting the methanotrophic bacteria specific pmoA alpha-subunit of the methane monooxygenase gene. Soil samples were also analyzed for microbial biomass, percent carbon, and percent nitrogen. Sample pH and bulk density were also measured. Significant correlations were observed for bulk density and soil layer type (pearsons r = 0.659, p-value = 0.027), pH and percent carbon (pearsons r = -0.582, p-value = 0.014), pH and bulk density (pearsons r = 0.778, p-value = 0.002), and low affinity potential CH4 oxidation rate and microbial biomass in upland and peat-forest ecosystem types (pearsons r = -0.569, p-value = 0.043). Methanotroph abundance was significantly correlated with potential oxidation rates at low and high affinity conditions when analyzed across all sampling locations (pearsons r = 0.854 p-value = 1.27e-05; pearsons r = 0.602, p-value = 0.011). Methanotroph abundance and potential CH4 oxidation under both low and high affinity conditions were not found to be significantly correlated in upland and peat-forest soils alone when peatland samples were omitted. Soil properties show a moderate accuracy to predict high affinity potential oxidation uptake in upland and peat-forest soils when trained using all sample data. The soil properties used in this analysis do not show any ability to predict potential CH4 oxidation under low affinity conditions. All model findings are exploratory and further testing and development would be necessary to strengthen the findings.
  • Dreilinger, Olivia (2023)
    Animal coloration is as striking as it is diverse; however, the transcriptional basis of coloration is not deeply understood. Cichlid fishes are a tractable system for studying coloration as they exhibit a wide range of phenotypic diversity while remaining genetically similar. This facilitates the study of genotype-phenotype correlations and the identification of causative genes. RNA sequencing is a powerful approach to investigate the genes which characterize chromatophores. However, RNA-seq results can be plagued by the high abundance of rRNA in cells. This thesis aims to investigate differential gene expression between differently pigmented regions as well as explore the effects of tissue treatments and rRNA depletion on gene expression. Gene sets acquired with polyA selection, riboPOOL probes optimized for zebrafish, and zebrafish probes complemented with newly designed riboPOOL cichlid probes were compared to assess the functionality of these different rRNA depletion strategies. The use of zebrafish probes complemented with newly designed cichlid probes captured the greatest diversity of genes, many transcripts of which were missing from the other gene sets. Furthermore, as experiments such as scRNA-seq rely on a dissociation step, the effect of dissociation on gene expression was examined and found to promote the expression of stress response genes. The results of this upstream optimization were applied in the analysis of differential gene expression between the vertical stripes of the cichlid Pseudotropheus demasoni to better understand the molecular basis of vertical striping in fish. The dark stripes exhibited upregulation of melanic marker genes and the light, iridescent stripes showed an increase in iridophore marker gene expression. These findings were corroborated with cell count data from FACS to link transcriptional profiles and cell type quantifications. Overall, the study provides insight into the transcriptional basis of coloration in cichlid fishes and underscores the importance of optimizing methods drawing meaningful conclusions.
  • Sulo, Päivi (2019)
    Retrotransposons are genetic elements with the ability to make a copy of themselves and insert the copy into a new location in a genome. Most of the retrotransposons in the human genome are not transposition competent and the remaining copies are prevented from moving by epigenetics. However, some tumors experience abnormal retrotransposon activity resulting in many copies of retrotransposons inserted into new locations. Retrotransposons can be detected from sequenced genome data by bioinformatic tools. One of them is TraFiC, a tool designed to detect somatic retrotransposon insertions from tumor samples. In this Master’s thesis, I test TraFiC with 201 colorectal cancer tumors and one colorectal adenoma and develop tools to further analyze retrotransposon insertions. These tools are TraID, a pipeline to detect transductions, insertions with flanking sequence from source elements, and InSeqR, a pipeline to recreate the inserted sequence from known insertion sites. TraFiC detected 4744 somatic insertions and TraID detected 346 somatic transductions from the tumor samples. 80 % of the detected insertions were identified as true somatic insertions based on visual examination of a subset of the calls. 87 % of insertions detected by TraFiC and 82 % of the insertions detected by TraID had their insertion breakpoints and the sequence flanking them recreated by InSeqR. The detected insertions with their sequence form a reliable and comprehensive call set that can be used to create new knowledge of somatic retrotransposon insertions in colorectal cancer.
  • Siivonen, Salla (2020)
    Finnish forests have a major impact on climate change at a national level, as approximately 86 % of Finland's surface area is forest and forests are a significant carbon sink. Continuous cover forestry is better from the point of view of carbon sequestration than even-age forestry. The Finnish Forest Act was reformed in 2014. Forest professionals and forest owners have had time to adapt to the new Act, to consider the use of alternative methods or, possibly, to take these methods into practice. Forest professionals have a clear position of power through information and communication to forest owners and the creation of a prevailing atmosphere of attitudes. Examination of the attitudes and the values of forest professionals are important as their attitudes and values have an impact on the recommendation of forest management methods. The purpose of this study was to examine how familiar continuous cover forestry was to forest professionals and forest owners as well as their perceptions of it. In addition, the values of forest professionals and how different factors influence their perceptions of continuous cover forestry were examined. The data used in this research was from a survey conducted in 2017. According to the results, forest professionals and forest owners are quite familiar with continuous cover forestry. The forest professionals’ perceptions of it were more negative compared to the forest owners’ perceptions. Gender and educational background were factors that were found to impact the attitudes of the forest professionals. Their perceptions of continuous cover forestry also affected the percentage of continuous cover forestry recommended by them. Forest professionals valued the sales proceeds of wood the most and the carbon sequestration of forests the least.
  • Takala, Terhi (2007)
    The biodiversity in Finland is dependant on the vast forest areas in Russia and Karelian Isthmus acts as an important ecological corridor which connects these forests together. However, Karelian Isthmus is also important for the forest industry and increasing forest use has caused concerns of the effects forest cuts have on the biodiversity of the area. The purpose of this study was to examine how the forests in the Karelian Isthmus have changed in the past 20 years. Special attention was given to the changes of the landscape structure and regional differences. The study was based on the data from a field survey and Landsat satellite images. After image registration the satellite images were normalized using linear regression method. This was done in order to calibrate the radiometric differences in the images. The interpretation of the images was done using supervised classification. The training areas used in classification were based on the ground truthing data collected during the field work. Two classifications were done to each image and four forest types were used: spruce, pine, mixed and deciduous forest. In the more detailed classification the forest types were further divided into young and old forests. The accuracy of the classification was assessed using reference data and contingency tables. The detailed classification was clearly less accurate and only the simple classification without the age classes was used in the following analyses. For estimating the changes in the forest structure at the landscape level, landscape metrics were calculated from the classified images. Five landscape indices were used in this study: class area (forest type area), number of patches, mean patch size, edge density and mean nearest neighbour. According to the interpretation of the satellite images the total forest area in the Karelian Isthmus has increased 4 %. Forest area of the mixed forest and especially deciduous forest had increased. Spruce forests had decreased 34 % and pine forests 25 % but these meant only 4 % change in proportion to the total land area. Regional variation also existed. In some areas changes in the forest structure were significant, particularly concerning spruce forests. The most notable changes occurred in the central areas of the Karelian Isthmus. In these areas the fragmentation of the spruce forests was significant. The number of patches had increased and the mean patch size decreased in the same areas where the total spruce forest cover had decreased. Also the edge density and the mean distance to the nearest neighbour had increased. In the case of pine forests the changes varied within different areas and although the total area had diminished, fragmentation was not clearly observed. Deciduous forests had increased in all places whereas mixed forests had increased especially in the areas where spruce forests had decreased. The increase of the deciduous and mixed forests was probably a result of regeration in harvested areas. Forest cuttings in the coniferous forests and natural regeneration after clear cuts have changed the forest type composition and the landscape structure in the Karelian Isthmus. However, changes have been fairly moderate in proportion to the total forest area. In number and also in connectivity, all of the forest types classified in this study existed broadly. Based on the results of this study it can be estimated that the ecological consequences of changes occurred in the past 20 years have not been exceptionally substantial and Karelian Isthmus is able to keep supporting forests species rich in biodiversity.
  • Lautala, Katri (2016)
    Liito-oravaa (Pteromys volans) esiintyy EU:n alueella ainoastaan Virossa ja Suomessa. Lajin kanta heikkenee jatkuvasti metsätaloustoimien vuoksi. Liito-orava kuuluu EU:n luontodirektiivin suojaamiin lajeihin ja sen lisääntymis- ja levähdyspaikkojen hävittäminen on kielletty luonnonsuojelulailla. Liito-oravaa on suojeltu vuosina 2004 2016 Elinkeino-, liikenne- ja ympäristökeskuksen (ELY) toteuttamin rajausmenettelyin, jotka vuonna 2016 poistettiin käytöstä. Metsätoimijoiden vastuu liito-oravan suojelusta on kasvanut. Tässä työssä tutkin metsänomistajien asenteita liito-oravaa, sen suojelua sekä suojeluviranomaisia kohtaan. Olin kiinnostunut lainsäädännöllisen velvoittavan suojelun vaikutuksesta metsänomistajien asenteisiin suojeltavaa lajia kohtaan. Lisäksi halusin selvittää, millaiset taustatekijät voivat vaikuttaa asenteisiin. Taustateorioina käytin sosiaalipsykologian asenneteorioita, joiden pohjalta uskoin vastaajien asenteissa näkyvän joko kielteistä tai myönteistä suhtautumista liito-oravan suojeluun. Kielteinen suhtautuminen osoittaisi reaktanssia eli psykologista ilmiötä, jossa käskeminen aiheuttaa halun rikkoa annettua käskyä, jotta oma valinnanvapaus säilytetään. Myönteinen suhtautuminen kertoisi dissonanssi-ilmiöstä eli psykologisesta ilmiöstä, jossa käyttäytymistä ei voi lainsäädännön takia muuttaa ja siksi muutetaan asenne lakia myötäileväksi. Aiempien sääntöjen noudattamista käsitelleiden asennetutkimusten perusteella molempia ilmiöitä tulisi esiintyä vastaajien joukossa. Toteutin tutkimuksen puhelimitse tapahtuvan haastattelun avulla. Metsänomistajat oli jaettu kolmeen ryhmään heidän liito-oravakokemuksensa perusteella. Kontrolliryhmällä ei ollut ollenkaan omakohtaisia liito-oravakokemuksia. Kahdella muulla ryhmällä oli joko ELY-keskuksen antama liito-oravapäätös ilman hakkuurajoituksia, tai ELY-keskuksen määrittämä liito-oravapäätös hakkuurajoituksineen. Kokemuksen merkitystä analysoin mm. lineaarisen regressioanalyysin avulla. Tulokset osoittivat, että noin puolet metsänomistajista suhtautuivat liito-oravaan ja sen suojeluun kielteisesti ja heidän vastauksissaan oli havaittavissa selkeää reaktanssia. Taustatekijöistä asenteisiin vaikutti eniten vastaajan omistaman metsän pinta-ala. Kielteiset metsänomistajat vastustivat heidän metsätaloustoimiaan rajoittavaa lainsäädäntöä, eivätkä uskoneet liito-oravan olevan kovin uhanalainen. Metsänomistajat, joille oli määrätty rajauksia, suhtautuivat kaikista kielteisemmin liito-oravaan liittyviin väittämiin. Ryhmittelyanalyysin perusteella kuitenkin noin puolet vastaajista suhtautuivat melko myönteisesti liito-oravaan ja 70 % metsänomistajista olivat tyytyväisiä saamiinsa liito-oravapäätöksiin. Vuoden 2016 muutokset tulevat varmasti heikentämään entisestään liito-oravan suojelua, kun muutokset antavat käsityksen, ettei lajinsuojelu ole tärkeää. Liito-oravan suojelun jatkosuunnitteluun kannattaisi tämän tutkimuksen tulosten perusteella ottaa metsänomistajat mukaan. Iso lajinsuojelullinen ongelma on se, ettei suuri osa metsänomistajista usko liito-oravan olevan uhanalainen. Tätä epäkohtaa voitaisiin korjata esimerkiksi osallistamalla metsänomistajia liito-oravakannan koon arviointiin.
  • Kumela, Hanna-Mari (2005)
    Tutkimuksen tavoitteena on selvittää metsänomistajien suhtautumista luonnonarvokauppaan ja sitä, millä perusteilla he osallistuvat tai eivät osallistu luonnonarvokauppaan. Samalla selvitetään myös millainen on metsänomistajien näkökulmasta hyväksyttävä ja omistajien intressit huomioiva suojelusopimus. Tutkimuskohteena ovat satakuntalaiset ja mikkeliläiset metsänomistajat. Tutkimus kuuluu yhteiskuntatieteelliseen ympäristötutkimukseen. Luonnonarvokauppa on taloudellinen ohjauskeino, jolla pyritään edistämään luonnon monimuotoisuuden säilymistä ja parantumista talouskäytössä olevilla alueilla. Luonnonarvokaupassa maanomistaja ylläpitää tiettyjä luontoarvoja rajatulla kohteella korvausta vastaan. Sopimukset perustuvat vapaaehtoisuuteen ja ne solmitaan määräajaksi. Sopimuksen päätyttyä alueen käyttö jatkuu maanomistajan haluamalla tavalla. Luonnonarvokaupan kokeiluhanke alkoi Satakunnassa kesäkuussa 2003. Tässä tutkimuksessa luonnonarvokauppaa lähestytään ympäristötietoisuuden näkökulmasta. Ympäristötietoisuudella tarkoitetaan ympäristöä koskevien arvojen, asenteiden ja toiminnan muodostamaa kokonaisuutta, jolle tieto ympäristöstä ja siinä ilmenevistä ongelmista muodostaa perustan. Osallistuminen luonnonarvokauppaan vaatii metsänomistajalta tietoa luontoarvoista ja kiinnostusta sitoutua luonnonsuojeluun. Myös muun muassa omistajan elämäntilanne, perhesuhteet sekä taloudelliset resurssit vaikuttavat osallistutaanko luonnonarvokauppaan vai ei. Luonnonarvokauppa pitää sisällään kaikki ympäristötietoisuuden osat, tiedollisen, affektiivisen sekä toiminnallisen osan. Tutkimuksessa hahmotettiin viisi metsänomistajatyyppiä, joiden avulla esitettiin metsänomistajien näkemyksiä luonnonarvokaupasta ja siihen osallistumisesta. Metsänomistajatyypit jaettiin kahteen luokkaan, hyötyryhmään ja kulttuuriryhmään, sen mukaan miten vahvasti metsän taloudellinen hyötykäyttö oli luonnonarvokauppaan suhtautumisen taustalla. Hyötyryhmään kuuluivat metsä tulonlähteenä, erikoisuuksien suojelu ja lisähyödyn tavoittelu -tyypit sekä kulttuuriryhmään luonnon seuraaminen ja koskemattoman luonnon suojelu -tyypit. Hyötyryhmän metsänomistajatyypit näkevät metsän taloudellisen hyödyntämisen ensisijaisena metsän käyttömuotona. Metsä tulonlähteenä -tyypin metsänomistaja ei ole innokas osallistumaan luonnonarvokauppaan. Erikoisuuksien suojelu -tyypin metsänomistaja haluaa suojella vain talousmetsästä poikkeavia alueita, joita voi käyttää virkistäytymiseen. Lisähyödyn tavoittelu -tyypin metsänomistaja osallistuu luonnonarvokauppaan vain, jos siitä on mahdollista hyötyä taloudellisesti tai muuten esim. säilyttämään kesämökin rauhan. Kulttuuriryhmässä taloudellinen intressi ei yksin johda toimintaa vaan myös muut intressit kuten virkistyskäyttö ja aineettomat arvot vaikuttavat metsänomistajien käyttäytymiseen. Molemmat kulttuuriryhmän tyypit ovat potentiaalisia luonnonarvokauppaan osallistujia. Luonnon seuraaminen -tyypin metsänomistaja haluaa suojella pieniä maisemallisesti kiinnostavia alueita. Koskemattoman luonnon suojelu -tyypin metsänomistaja voisi suojella luontoa ilman sopimustakin mutta korvauksen avulla alueiden määrä ja koko voivat olla suurempia. Kaikille metsänomistajille vapaaehtoisuus oli elinehto sopimuksen solmimiselle ja korvauksen suuruus vaikutti mukaan lähtemiseen ja tyytyväisyyteen. Hyvin tärkeää oli sopimuksen kokonaisuus ja metsänomistajien metsänkäytön intressien huomioiminen. Tutkimuksessa selvisi, että luonnonarvokauppaan osallistumista ei herättänyt niinkään metsänomistajien halu suojella luontoa vaan pikemmin jonkinasteinen hyödyn tavoittelu. Luonnonarvokaupasta saadun hyödyn laatu vaihteli metsänomistajatyypeittäin. Luonnonarvokauppa nähtiin enemmän metsäviranomaisten kuin ympäristö- tai luonnonsuojeluviranomaisten työkaluna. Luonnonarvokaupalla suojellaan talousmetsien luonnonarvoja metsätaloudessa tunnetuilla keinoilla. Kokonaisuudessaan suhtautuminen luonnonarvojen säilyttämiseen on kuitenkin muuttunut luonnonarvokaupan myötä myönteisemmäksi. Muutos toiminnan tasolla kertoo myös näiden metsänomistajien ympäristötietoisuuden muutoksesta.