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(2019)Kaupungistumisen myötä yhä suurempi osa ihmisistä on yhä harvemmin yhteydessä luontoon arkielämässään. Tätä ilmiötä vahvistaa yhä tiivistyvä kaupunkirakenne, jolloin viheralueet ovat jatkuvan rakentamispaineen alla ja uhkaavat vähetä ja pirstaloitua. Ihmisten vähentyneet mahdollisuudet kokea luontoa voivat johtaa luonnosta etääntymiseen. Ihmisen ja luonnon välisen kuilun kasvaessa vähenee myös luonnonsuojeluhalukkuus, mikä voi johtaa välinpitämättömiin asenteisiin luonnonsuojelua kohtaan. Yksi tämän päivän tärkeimpiä ympäristökysymyksiä on luonnon monimuotoisuuden kato. Ihmisten luontoyhteyden katoaminen sekä sen myötä vähenevä luonnonsuojeluhalukkuus uhkaa luonnon monimuotoisuuden säilymistä, sillä välinpitämätön asenne luontoa kohtaan heijastuu myös luonnonsuojelullisiin toimenpiteisiin. Julkiset viheralueet ovat tärkeimpiä paikkoja tarjoamaan kaupunkilaisille arkielämän luontokokemuksia. Tässä tutkielmassa selvitetään, voivatko rakennetut kaupunkipuistot tarjota luonnon monimuotoisuuden kokemuksia kaupunkilaisille, sekä löytyykö eroavaisuuksia väestöryhmien kokemuksissa luonnon monimuotoisuudesta puistoympäristössä. Puistot julkisina viheralueina tuottavat kaupunkilaisille luontokokemuksia, jotka taas edistävät niin psyykkistä kuin fyysistäkin hyvinvointia. Aiemman tutkimuksen perusteella koettuun hyvinvointiin liittyy vahvemmin kokemus luonnon monimuotoisuudesta kuin viheralueen todellinen luonnon monimuotoisuus. Eri väestöryhmien erot koetussa luonnon monimuotoisuudessa voivat siten antaa osviittaa siitä, että puistot voivat tuottaa erilaisia hyötyjä eri väestöryhmille. Tutkielmassa luonnon monimuotoisuutta käsitellään lajirikkauden kautta. Tavoitteena oli selvittää, miten lajirikkaiksi puistot koetaan eri lajiryhmien osalta (puut ja pensaat, putkilokasvillisuus, koristekasvillisuus, perhoset, linnut, jäkälät ja sienet), eroaako kokemus luonnon monimuotoisuudesta eri sosioekonomisten ryhmien kesken, sekä vaikuttaako puistoon liitettävät ominaisuudet, kuten puiston todellinen lajirikkaus tai puiston pinta-ala, kokemukseen. Tutkielman aineisto on kerätty EU:n rahoittaman GREEN SURGE -tutkimushankkeen puitteissa. Tutkimusryhmässämme keräsimme haastattelu- ja lajistoaineistot kahdestatoista helsinkiläisestä puistoista, joille tutkimushanke asetti tietyt kriteerit. Haastattelut toteutettiin paikan päällä ja niitä kertyi yhteensä 596. Lajistoinventoinnit tehtiin kussakin puistossa neljälle lajiryhmälle: puut ja pensaat, putkilokasvillisuus, linnut ja jäkälät. Aineistoa analysoitiin kvantitatiivisesti, pääasiallisina tilastollisina menetelminä ANOVA ja korrelaatioanalyysit. Puistot koettiin ylipäänsä melko lajirikkaiksi ympäristöiksi. Eroja löytyi kuitenkin eri lajiryhmien välillä: puut ja pensaat sekä muu kasvillisuus koettiin kaikkein lajirikkaimmiksi lajiryhmiksi, mikä voi viitata siihen, että nämä lajiryhmät ovat puistokävijöille helpommin havaittavia muihin tässä tutkielmassa mukana oleviin lajiryhmiin verrattuna. Perhosten, jäkälien ja sienten lajirikkautta vastaajien oli vaikein hahmottaa. Myös puistojen välillä oli eroja siinä, miten lajirikkaiksi ne koettiin. Puiden ja pensaiden todellisella lajirikkaudella ei näyttänyt olevan yhteyttä siihen, miten paljon eri puu- ja pensaslajeja puistoissa koettiin olevan, vaan merkittävämpää näytti olevan puiden korkeus. Sen sijaan putkilokasvien todellisen ja koetun lajirikkauden välillä löytyi yhteys, mikä viittaa siihen, että ihmiset huomaavat kasvillisuuden lajirunsauden. Lisäksi vastaajat kokivat puiston kasvien lajirikkauden sitä suuremmaksi, itä monimuotoisempi puisto oli rakenteeltaan. Eri sosioekonomisten ja -kulttuuristen ryhmien välillä ei ollut juurikaan eroja siinä, miten monimuotoisiksi puistot koettiin, joskin iäkkäät vastaajat kokivat lintulajirikkauden suuremmaksi kuin nuoremmat vastaajat. Sen sijaan koettuun monimuotoisuuden vaikutti ennemminkin puiston käyttöaste, mikä viittaisi siihen, että osa tekijöistä, jotka vaikuttavat kokemukseen puiston luonnon monimuotoisuudesta, liittyvät itse puistoon tai alla piileviin puistoon liitettyihin arvostuksiin, jotka näyttäytyvät suurempana puiston käyttöasteena. Tämän tutkielman perusteella ei voida vetää suoria johtopäätöksiä siitä, mitkä tekijät vaikuttavat luonnon monimuotoisuuden kokemukseen rakennetuissa kaupunkipuistoissa, mutta tulokset antavat viitteitä siitä, että puiston ominaisuuksilla sekä puiston käyttöasteella on jonkinlainen vaikutus kokemukseen luonnon monimuotoisuudesta. Tämä taas osoittaa sen, että puistot tulee nähdä sosio-ekologisina kokonaisuuksina, jotka yhtäältä edistävät kaupunkilaisten hyvinvointia ja luontoyhteyttä, ja samalla ylläpitävät kaupungin luonnon monimuotoisuutta ja sopeutumiskykyä ympäristömuutoksille, sekä toisaalta taas puistot itse muokkautuvat jatkuvasti yhteiskunnassa esiintyvien toiveiden ja vaatimusten mukaisesti.
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(2022)Chemoresistance is a significant contributor to the lethality of high-grade serous ovarian cancer (HGSOC). Treatment response to traditional platinum-based chemotherapy is poor, and the need for improvement is urgent, as more than 50% of the patients pass within 5-years from diagnosis. Mitochondrial metabolism has emerged as a potential target in HGSOC, and enhanced capacity in mitochondrial oxidative phosphorylation (OXPHOS) has been shown to correlate with a better chemoresponse. The vital metabolic cofactor for mitochondrial enzymatic reactions, during e.g. OXPHOS, is nicotinamide adenine dinucleotide (NAD+). It is now well-established that NAD+ precursor supplementation can boost intracellular NAD+ content and, consequently, mitochondrial function. In cancer, NAD+ boosting shows mitochondrial activation mediated anticancer and chemosensitizing effects and presents an intriguing route to modulate cancer metabolism and treatment response. In HGSOC, NAD+ metabolism and its association with tumours’ metabolic profile is poorly understood. Also, the impact of mitochondrial activation on HGSOC chemoresponse remains unexplored. This thesis aimed to evaluate patient-derived HGSOC tumour NAD metabolite content and its association with OXPHOS. Also, the aim was to explore whether in vitro NAD+ boosting promotes mitochondrial function and subsequently enhances chemosensitivity to platinum-based treatment. Thus, I measured the NAD metabolite concentrations in HGSOC tumours and two HGSOC cell lines, OVCAR-5 and COV318. The impact of NAD+ boosting on HGSOC cells OXPHOS and chemoresponse was assessed with respirometry and cell viability assays. I found that the HGSOC tumours presented alterations in NAD metabolite content, with an increase in the reduced forms and a decrease in the metabolite redox ratios. Also, the change in the NAD metabolite seemed to be impacted by the tumours’ anatomical location and OXPHOS capacity. In vitro HGSOC cells differed in their OXPHOS capacity, with the OXPHOS-high cell line exhibiting enhanced sensitivity to chemotherapy. The NAD+ boosting increased intracellular NAD+ content and mitochondrial OXPHOS without impacting the cells’ chemoresponse or growth. In conclusion, the altered NAD+ metabolism in HGSOC tumours presents potential target pathways for the disease with poor treatment response. The NAD+ boosting mediated metabolic modulation increased the OXPHOS capacity independently of the cell lines’ OXPHOS-status. In OXPHOS-low cells’ mitochondrial activation enhanced OXPHOS to the level of chemosensitive OXPHOS-high cells but did not alter the cell lines’ chemoresponse within a short-term treatment period. These observations have increased the understanding of NAD+ metabolism. Also, as a proof-of-principle, NAD+ boosting was presented as a tool for mitochondrial activation and metabolic modulation in HGSOC cells, opening an intriguing approach to explore HGSOC mitochondrial function and chemoresponse.
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(2005)Tutkielmassa tarkastellaan makrotason kehityksen ja hyvinvoinnin mittaamiseksi kehitettyjä mittareita, ja tuodaan yhteen niistä sekä 70-luvulla että nykypäivänä käytyä keskustelua. Erityisesti keskitytään neljän esimerkkimittarin avulla mittareiden ympäristömuuttujissa viimeisen neljänkymmenen vuoden aikana tapahtuneeseen muutokseen. Tarkasteltu keskustelu pohjautuu talouskasvun arvostuksen ja kansantalouden tilinpidon keskeisten indikaattoreiden kuten bruttokansantuotteen (BKT) kritiikkiin. Aate- ja tieteenhistorialle ominaisin tavoin tutkin ympäristön käsitteelle annettuja merkityksiä mittareiden historiallisessa kontekstissa. Luokittelen esimerkkimittarit kahteen ryhmään: rahamääräisiin taloudellisen hyvinvoinnin mittareihin sekä sosiaalista ja ekologista hyvinvointia monipuolisesti yhdistäviin kokonaishyvinvointi-indekseihin. Esimerkkimittarit eli James Tobinin ja William Nordhausin kehittämä Measure of Economic Welfare (MEW), Redefining Progress -kansanlaisjärjestön Genuine Progress Indicator (GPI), Jan Drewnowskin Level of Living -indeksi (LLI) ja Robert Prescott-Allenin luoma Wellbeing-indeksi (WI) käsittelevät ympäristöä eri tavoin johtuen sekä mittareiden kehittämisen ajankohdasta ja aikakauden tavasta lähestyä ympäristökysymyksiä sekä siitä, millaisia metodologisia valintoja mittareiden kohdalla tehtiin. Sekä GPI että WI edustavat nykypäivän kehityksen mittaamisesta käytyä keskustelua ja pyrkivät korostamaan ympäristön tärkeyttä inhimilliselle hyvinvoinnille nyt ja tulevaisuudessa. Ne käsittelevät monipuolisesti erilaisia ympäristötekijöitä. Toisaalta 70-luvun alussa kehitettyjen MEW:n ja LLI:n huomioima lähiympäristön viihtyisyys ei saa GPI:ssä ja WI:ssä enää merkittävää sijaa. MEW ja LLI edustavatkin yleisen ympäristökeskustelun heräämisen aikaa ja antavat ympäristölle vielä melko vähäisen merkityksen hyvinvoinnin ja kehityksen tekijänä. Yleisesti on todettava, että hyvinvoinnin ja kehityksen mittaamiseen liittyy monia ongelmia. Samoja ongelmia, joita koettiin 70-luvulla pohditaan nytkin. Toisaalta mittarit voivat kriittisesti esiteltyinä ja tarkasteltuina tarjota hyvää materiaalia sosiaalisen ja ympäristön hyvinvoinnin ja niiden kehitysvaikutuksien määrittelyyn liittyvään arvokeskusteluun.
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Modeling climate change impacts on European tree species : comparing statistical and dynamic models (2013)Climate change has been predicted to cause extinctions and range shifts in European flora. Two common methodologies assessing climate impact on vegetation are statistical bioclimatic envelope models (BEMs) and process-based dynamic vegetation models. BEMs are relatively easy to implement, but have been criticized for being unreliable, because they assume equilibrium between species' observed ranges and climate. Dynamic models can be considered biologically more sound, but require large quantities of detailed input data, which is often not available. The aim of this study is to investigate the effects of climate change on common tree species ranges in Europe and in Scandinavia, and to find out whether two commonly used modeling strategies, dynamic and statistical models, produce similar estimates of future ranges. To address these questions, I first built statistical models (bioclimatic envelope models) for five common European trees: Pedunculate Oak (Quercus robur, L.), Common Hazel (Corylus avellana L.), European Beech (Fagus sylvatica, L.), Scots Pine (Pinus sylvestris, L.) and Norway Spruce (Picea abies (L.) H. Karst.). All species are widely distributed and characteristic species in their ecosystems and thus their possible range shifts would indicate larger shifts in ecosystem structure and function. I then compare the projections produced with the statistical models to outputs of a tree speciesparameterized dynamic global vegetation model LPJ-GUESS, obtained from another study. The statistical model predictions are compared with dynamic model results for entire European distributions, while the statistical model predictions for Scandinavian area are examined in further detail. Input distribution data had great influence in future predictions of statistical models. Statistical models and the dynamic model produced very different future predictions, statistical models predicting increasing contractions on the southern edge of distribution towards the end of the century, indicating larger climatic impacts. The role of biological interactions, successional processes and modeling relationship between distribution and climate are discussed. I propose a way to assess the possible causes of differences between statistical and dynamic models to produce more robust future predictions on plant species distributions. Statistical model predictions in the Scandinavian area indicated substantial northward shift of hemiboreal vegetation zone by 2050.
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Modeling early neuronal development in Kabuki Syndrome using human induced pluripotent stem cells. (2022)Neurodevelopmental disorders (NDDs) are disabilities in which the formation and development of the central nervous system is altered. NDDs severely impact the quality of life of the individuals that are affected by them, however little is known about the causes or the molecular mechanisms that are behind their onset. For this reason, being able to model them is pivotal to our society since, by understanding the mechanisms underlying such disorders, we could develop possible treatments. Previous research has suggested that disturbances in the early neuronal development could be at the basis of NDDs onset. Therefore, in this work, I have modeled neuronal differentiation in Kabuki syndrome (KS), a known NDD, assaying the expression of key early neurodevelopmental markers at four specific timepoints, using induced pluripotent stem cell (iPSC) technology. By concurrently differentiating three KS patient-derived and three control iPSC lines to neural precursor cells (NPCs) and profiling them with immunocytochemistry (ICC) and quantitative real-time PCR (RT-qPCR), I was able to identify differences in the early developmental trajectories of NPCs between the two conditions. The ICC data suggested that differentiating KS cell lines incur in precocious differentiation when compared to control cell lines, suggesting that the disease-causing mutations could lead to accelerated neuronal maturation of early NPCs. However, RT-qPCR analysis of the expression patterns of key neurogenesis markers was unable to statistically confirm the observed trend between the two phenotypes, likely due to limitations in statistical power. Despite this, the expression of four out of seven NPC markers was higher in early KS cells than in control cell lines, supporting the hypothesis of accelerated neuronal maturation. Taken together, this work highlighted some of the challenges related to iPSC-based disease modelling studies, and the need to further confirm the inferred mechanisms of asynchronous neuronal development observed in this work.
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(2020)Computing complex phenomena into models providing information of the causalities and future scenarios is a very topical way to present scientific information. Many claim models to be the best available tool to provide decision making with information about near-future scenarios and the action needed (Meah, 2019; Schirpke et al., 2020). This thesis studies global climate models based on objective data compared to local ecosystem services models combining ecological and societal data offer an extensive overview of modern environmental modelling. In addition to modelling, the science-policy boundary is important when analyzing the societal usefulness of models. Useful and societally-relevant modelling is analyzed with an integrative literature review (Whittemore & Knafl, 2005) on the topics of climate change, ecosystem services, modelling and science-policy boundary, n=58. Literature from various disciplines and viewpoints is included in the material. Since the aim is to create a comprehensive understanding of the multidisciplinary phenomenon of modelling, the focus is not on the technical aspects of it. Based on the literature, types of uncertainty in models and strategies to manage them are identified (e.g. van der Sluijs, 2005). Characteristics of useful models and other forms of scientific information are recognized (e.g. Saltelli et al., 2020). Usefulness can be achieved when models are fit for purpose, accessible and solution-oriented, and sufficient interaction and trust is established between the model users and developers. Climate change and ecosystem services are analyzed as case studies throughout the thesis. The relationship of science and policy is an important discussion especially important when solving the sustainability crisis. Because modelling is a boundary object (Duncan et al., 2020), the role of boundary work in managing and communicating the uncertainties and ensuring the usefulness of models is at the center of the analysis.
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(2024)Fecal indicator bacteria (FIB) concentrations are used as proxies for hygienic quality of ambient waters. The most utilized FIB are Escherichia coli and intestinal Enterococci. The laboratory methods used to reliably determine these concentrations are time-consuming and do not provide immediate information on the hygienic quality of recreational waters. In this thesis I developed regression models for FIB concentrations using physicochemical in situ water quality measurements as explanatory variables. An accurate and reliable model would enable real-time and continuous determination of FIB concentrations, thereby enhancing the monitoring of water hygienic quality. Using a flow-through system, two spatially comprehensive physicochemical datasets were collected from the sea area of Helsinki Metropolitan area in September 2022 and May 2023. Alongside, total of 56 water samples were collected for analyzing concentrations of E. coli and intestinal Enterococci. For these datasets, I fitted multiple linear regression models, other generalized linear models, zero-inflated models, and hurdle models between the measured parameters and FIB concentrations. Among the measured variables, the fluorescent dissolved organic matter proved to be the superior indicator of declining hygienic quality of water. Other significant explanatory variables included concentrations of phycocyanin and CO2, as well as turbidity. Produced models for intestinal Enterococci were generally more accurate compared to those for E. coli. The preferred model for E. coli proved to be negative binomial regression model, whereas zero-inflated negative binomial model was the optimal model for intestinal Enterococci, due to the substantial proportion of zeros in the intestinal Enterococci dataset. Applying the selected models to the entire physicochemical dataset generated elevated FIB concentration estimations in areas that are subject to FIB loading, based on previous FIB monitoring results throughout the study area. However, thorough validation and further development of presented models is essential before engaging them in FIB monitoring practices.
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(2021)The science of fish stock assessment is one that is very resource and labor intensive, with stock assessment models historically being based on data that causes a model to overestimate the strength of a population, sometimes with drastic consequences. The need of cost-effective assessment models and approaches increases, which is why I looked into using Bayesian modeling and networks as an approach not often used in fisheries science. I wanted to determine if it could be used to predict both recruitment and spawning stock biomass of four fish species in the north Atlantic, cod, haddock, pollock and capelin, based on no other evidence other than the recruitment or biomass data of the other species and if these results could be used to lower the uncertanties of fish stock models. I used data available on the RAM legacy database to produce four different models with the statistical software R, based on four different Bayes algorithms found in the R-package bnlearn, two based on continuous data and two based on discrete data. What I found was that there is much potential in the Bayesian approach to stock prediction and forecasting, as our prediction error percentage ranged between 1 and 40 percent. The best predictions were made when the species used as evidence had a high correlation coefficient with the target species, which was the case with cod and haddock biomass, which had a unusually high correlation of 0.96. As such, this approach could be used to make preliminary models of interactions between a high amount of species in a specific area, where there is data abundantly available and these models could be used to lower the uncertanties of the stock assessments. However, more research into the applicability for this approach to other species and areas needs to be conducted.
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(2023)Lethal congenital contracture syndrome 1 (LCCS1) is a severe developmental disorder that is part of the Finnish disease heritage. The affected foetuses die in utero and show a lack of motor neurons accompanied by severe atrophy of the ventral spinal cord and muscles and severe contracture of joints, which result in a lack of involuntary movements. Other associated symptoms include hydrops, micrognatia (small jaw), pulmonary hypodysplasia and small size. The syndrome leads to prenatal death before 32nd gestational week, but the cause remains elusive. LCCS1 is caused by a homozygous mutation, FINmajor, in GLE1 RNA export mediator (GLE1) -gene. The mutation is a c.432- 10A > G substitution at the border of intron three and exon four, resulting in a new splice acceptor site 10 nucleotides upstream of the intron-exon junction. This results in aberrant splicing and nine extra nucleotides in the mRNA, corresponding to three extra amino acids in the GLE1 protein of the affected individuals. GLE1 is an important player in RNA biology in cells. In humans it has two isoforms, GLE1A and GLE1B, that have distinct roles. While GLE1A plays a role in cells’ stress response by mediating the formation and disassembly of stress granules in the cytoplasm, GLE1B is found at the nuclear envelope where it mediates mRNA transport from the nucleus to the cytoplasm. Earlier studies using HeLa cells and zebrafish have demonstrated that FINmajor in GLE1 knock-down background disrupts the mRNA export from nucleus to cytoplasm and leads to apoptosis in neural precursors and abnormal arborization of motor neurons, thus mimicking some of the phenotypic features observed in human patients. Kuure group has generated a mouse model with endogenous FINmajor, but it fails to morphologically phenocopy the human disorder (unpublished data). Importantly, human-origin non-cancerous models with endogenous FINmajor mutation have not yet been used in the studies of GLE1 and LCCS1. My aim in the thesis was to create a human embryonic stem (hES) cell line carrying homozygous FINmajor mutation in its genome. A relatively new tool, CRISPR/CAS -system allows for precise genetic engineering in a variety of model organisms. By optimizing the system to efficiently edit the GLE1 gene, I was able to introduce FINmajor mutation in hES cells, creating a new model system to study this disorder. While previous models had relied on temporary silencing of the gene with morpholinos or siRNAs, the hES cell line with GLE1 FINmajor mutation will for the first time give insights on how the mutation affects cellular functions, mRNA biology and cell differentiation in LCCS1. This way the hES cell line I have generated will yield new information on the development, progression and manifestation of the syndrome to better understand its mechanisms.
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(2024)In this thesis, the migration patterns of the legacy pesticide called atrazine were studied in the Laune aquifer in Lahti, Finland, using the MODFLOW groundwater modelling program connected to the MT3D tool. Three models were built for the thesis. In the first model, the migration of atrazine in the Laune aquifer was studied by simulating the steady release of 1.22 µg/L atrazine concentration from sediments in the Lahti railway area over 15 years. In the second model, the depletion of atrazine from soil deposits was studied over time in both sudden and gradual depletion scenarios for 10 and 30 years. In the third model, the effect of pumping contaminated groundwater from an extraction well and injecting remediated water back into the aquifer from another well was investigated on the atrazine concentration in groundwater in the study area for 15 years. Concentrations of atrazine in the aquifer either increased or decreased from the baseline concentrations in the first model. In certain areas in Laune, atrazine concentrations exceeded the EU safe limit values during the whole modelling period. In the second model, the dilution of atrazine was relatively slow, even in the scenario of sudden depletion. It can take decades for the groundwater concentrations to dilute to EU-safe limits once the limits have been exceeded. In the last model, the pumping and injection of remediated groundwater showed a decline in concentration of atrazine over time. However, the effects were only local. Regional effects would have required a higher number of injection wells covering a larger area. Modelling tools are an important part of ethical ecotoxicological research solving many logistical problems related to field studies. However, as the results are highly depend- ent on the parameters, the results should be critically evaluated and used as part of other research methods. In environmental restoration work, understanding and modelling the pa- rameters related to leaching risk can be used as part of risk management. Understanding the migration of stored pesticides into the environment, the development of environmental restoration methods, and preventive measures are crucial to securing clean drinking water quality and quantity in the future.
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(2020)Ecosystem modelling gives us a tool to understand the complicated processes in an ecological system. When studying the changes in an ecosystem, the system health is one of the main characteristics to define. Healthy ecosystem can endure stress and is in stable state. Ecological network analysis and different ecological indices have been used as a basis for measuring the state of an ecosystem, characterizing the dynamics of marine environments, and quantifying the impacts of fishing. The Archipelago Sea, located in Northern Baltic Sea, is characterized by large gradients in salinity and numerous islands. The area is greatly affected by human impact and climate change. However, no broad research on ecosystem changes has been carried out, hence, there is a need for holistic models both scientifically and societally to understanding the changing ecosystem thoroughly and to provide contribution in the decision-making processes of environmental management actions. The aim of this study was to find out how the state of the Archipelago Sea food web has changed from 1990 to 2014. Three steady-state trophic models of the study area for three different years (1990, 2000 and 2014) were constructed using the Ecopath modelling software and approach. The changes in the study area were measured comparing the calculated ecological indices and fishing impact indicators. The models captured changes in the system such as before and after the invasion of non-indigenous species, increase of cormorants, increase of seals, and decrease of cod. The models consist of 23 (1990), 25 (2000) and 27 (2014) different functional groups from predators to producers and detritus. The quality of the models was tested and according to three different approaches, the models can be said to adequately represent the Archipelago Sea food web and ecosystem. The ecosystem indices calculated showed that there had been system wide changes. The state of the Archipelago Sea food web had changed during the study period to a less mature but more resilient condition. This was due to the increase in number of predator species and higher primary production and flow to detritus. The fishing impact on ecosystem changed as fishery practice experienced a change into a more industrialized direction. Changes in trophic levels and ecosystem composition were observed. The invasion of non-indigenous species and the increase in top predators such as seals and the great cormorant affected the structure of the food web. In Addition, the decrease of flounder and unsuccessful recovery of cod have had an impact on the ecosystem and its maturity. Further research on the Archipelago Sea food web is needed. The ecosystem is stressed and does not show recovery; hence, management actions may become necessary. Future simulations based on these Ecopath models would facilitate the selection of the most suitable ecosystem management application. Knowledge of the whole ecosystem and its health is required, and this can be achieved with the help of ecosystem modelling.
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(2024)The taxonomy of the green macroalgal genus Monostroma is poorly known in the Baltic Sea region and worldwide.Two species of Monostroma are currently reported from the Baltic Sea: the cosmopolitan spring species Monostroma grevillei and a proposed endemic, free-floating summer species Monostroma balticum. However, previous work has highlighted the unclear taxonomic status of M. balticum, and some consider it a growth form of the cosmopolitan species M. grevillei or a monostromatic growth form of Ulva spp. No molecular data exists of M. balticum, and the morphological characteristics distinguishing this species from M. grevillei and similar species are unclear in the literature. The aim of this thesis is to explore the taxonomic status of M. balticum by firstly systematically reviewing the historical and contemporary literature, including the original description, to illuminate the current morphological circumscription of M. balticum and related species. Secondly, using DNA barcoding based on the tufA -marker, fresh collections of foliose monostromatic green algae from the Baltic Sea region are identified molecularly and put into an evolutionary context using phylogenetics. Thirdly, novel plastid genomes are produced from monostromatic green algae to explore the genomic features of these algae and to see if they aid in species delimitation or phylogenetic approaches. Based on the literature review, the morphological and ecological features used in specimen identification currently (micromorphology, free-floatingness and occurrence in summer) may not be enough for accurate identification, and especially the micromorphological features are quite vaguely described in contemporary literature making their use difficult in practise. All monostromatic specimens collected are identified using DNA barcoding as either M. grevillei, Kornmannia leptoderma or Ulva intestinalis, and those specimens mostly resembling the original description of M. balticum are recovered as U. intestinalis. Plastid genomes were produced from M. grevillei, K. leptoderma and U. intestinalis, from the latter species separate genomes were generated from a typical tubular-morphology specimen as well as a “M. balticum”-morphology specimen. M. grevillei and K. leptoderma plastids were unusual in being large, inflated by many introns and intrageneric regions and having many rearrangements. Produced U. intestinalis plastomes are similar and resemble previously published Ulva genomes. The accurate identification of M. balticum -like specimens is discussed, and for future work DNA barcoding is suggested to be the main tool for specimen identification. This thesis provides evidence towards a previous hypothesis that M. balticum is not a distinct species but a specific growth from of U. intestinalis. Investigating historical herbarium specimens, including original material, using molecular methods is proposed to verify if M. balticum should be synonymised formally with U. intestinalis. The potential drivers of the shift in growth form of U. intestinalis are discussed. Finally, the plastid genome landscape in these foliose green algae is discussed.
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(2022)Human induced pluripotent stem cells (iPSCs) are an important in vitro model of disease and development. iPSCs can be differentiated in culture into cell types which are difficult to access from patients, such as neurons. Applying iPSC-derived cellular models to disease studies requires a thorough characterization of the derived cell types, as well as assessing reproducibility across cell lines or differentiation batches. With the aim of providing such a comprehensive molecular characterization at an early stage of cortical neuronal differentiation in vitro, six iPSC lines from four donors were differentiated to cortical neural progenitors using a modification of an established protocol (Shi et al., 2012a). The protocol successfully produced neural progenitors, with over 75% of the differentiated cells aligning with a cortical identity, as confirmed via qPCR and immunocytochemistry of established markers such as PAX6, NES and SOX1. To further classify the cell types produced as well as identify potential differences between cell lines, gene expression of the obtained cells was profiled with single cell RNA sequencing of ~22,000 cells, which uncovered the heterogeneity of neural progenitors produced. Further, although two differentiation batches produced similar cell-type compositions on a whole, a fraction of the lines showed inter-individual differences in cell type composition, which correlated with expression variability of known marker genes. Additionally, the cell types produced in vitro were compared to those produced in vivo by mapping our dataset to a reference fetal brain dataset (Polioudakis et al., 2019). It was observed that the in vitro dataset represented a subset of the cell types present at mid-gestation. Overall, the single cell characterization of differentiated cells allowed greater resolution in understanding cell-type heterogeneity of cortical neurogenesis, which is of key relevance for future applications such as disease modeling.
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(2016)This body of research focuses on establishing a drug screening pipeline for discovering drugs which increase the differentiation of pluripotent stem cells into cardiac myocytes, known as cardiogenic molecules. Cardiomyocytes can be utilized in regenerative medicine by offering a platform for testing molecules or drugs which may increase cardiomyocyte proliferation and for using cardiomyocytes produced outside of the body for clinical transplant, in order to heal the damage caused by heart attacks. Building on known models and developmental pathways three assays were designed and implemented for in vitro cardiogenic molecule screening. A pipeline comprised of three primary screening systems; an embryoid body (EB) model, a cardiomyocyte directed differentiation model, and a magnetic activated cell sort (MACS) model. The MACS model uses the cell surface receptors Fetal Liver Kinase 1 (FLK1) and/or Platelet Derived Growth Factor Receptor alpha (PDGFRα) as the most practical platform for screening drugs against an enriched mesodermal population of cells. The MACS system was confirmed with flow cytometry to ensure the enrichment of Myl2-eGFP+ (ventricular cardiomyocytes) cells in the FLK1+ cells. Furthermore unique known molecules help elucidate the molecular mechanisms governing cardiomyocyte differentiation, measured by cardiomyocyte purity in in vitro models. Also demonstrated are assay controls which decrease purity and acts as negative controls for the MACS assay such as a late stage GSK-3 Inhibitor treatment used to constitutively activate the canonical Wnt/β-catenin pathway and effectively reduce the cardiomyocyte proliferation. Additionally, an early stage Wnt Inhibitor compound IWP-4 was used as a potential positive control effectively blocking late stage activation of canonical Wnt/β-catenin pathway and increase the in vitro purity of cardiomyocytes. These controls provide two important reference points for the many molecules screened over the course of these experiments for the 3i Regeneration project. Additional molecular inhibitors are used to elucidate the mechanism of action within the MACS cells; including a Sonic Hedgehog inhibitor (cyclopamine), an NKX2.5 activator (ISX-9) and a novel small molecule (C1). These models act as an effective pipeline bringing a potential drug through first an EB model, followed by a cardiomyocyte enriched model, to finally a MACS model targeting FLK1. This pipeline tests the molecules against conditions of increasing resemblance to the native microenvironment of a cardiomyocyte.
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(2023)Breast cancer is globally the leading cause of death in women. ER positive, HER2 negative breast cancer is the most common subgroup, covering two thirds of all breast cancer cases. The different isoforms of ERα, ERα66 and ERα36 are responsible of genomic and non-genomic ER signaling respectively. Tamoxifen is one of the most used drugs in ERα+ breast cancer. As a SERM tamoxifen blocks the activity of ERα66, but plays as an agonist for ERα36, which is associated with tamoxifen resistance. Tamoxifen resistance concerns more than 25% patients with ERα+ breast cancer but the molecular mechanisms that lead to development of resistant disease remain uncovered. Thus, the aim of this thesis was to reveal how two different ERα isoforms are used and regulated in tamoxifen resistance in two commonly used ERα+ breast cancer cell lines MCF7 and T47D. We studied the effect of hormones to tamoxifen sensitivity and to utilization of ERα isoforms. Additionally, we compared the transcriptomics of resistant and parental cells in both cell lines and tested how inhibition of key regulators affect the sensitivity against tamoxifen. In this thesis we report that MCF7 and T47D cell lines obtain different mechanisms of tamoxifen resistance, and that the development of tamoxifen resistance is a parallel process with the cell identity switch from luminal to basal. The EZH2 is involved in maintaining the luminal progenitor type of mammary cells, whereas c-Myc is highly expressed in the resistant cell lines. Hence, EZH2 and c-Myc are key players in development of tamoxifen resistance and could be considered as therapy targets in ERα+ breast cancers.
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(2024)Phylogenetics is the study of the evolutionary history of life on Earth, which has shifted from relying on morphological characteristics to molecular data with the advancements in sequencing technology. Understanding Earth's biodiversity is crucial, as it has important implications for conservation, ecology, and evolution. Speciation occurs when barriers restrict gene flow between previously interbreeding populations. One such barrier may be endosymbiotic bacteria, like Wolbachia, which can manipulate host reproduction and create incompatibilities between host lineages. Wolbachia is widely distributed among arthropods and is the most common endosymbiont of insects. The bacterium is known to alter its hosts' biology, serving as a master manipulator of reproduction. Wolbachia-induced phenotypes can lead to the divergence of host lineages and speciation events. The genus Cotesia (Hymenoptera: Braconidae: Microgastrinae) is a highly diverse group of parasitoid wasps, where several species parasitize Melitaeini butterflies, including two cryptic species complexes. The current phylogenies of these species are 20 years old and need an update, as they were built with few markers and contain unresolved nodes. Wolbachia has been observed in this system, but its role remains largely unexplored. In this study, I aim to reconstruct the phylogeny of Cotesia species parasitizing Melitaeini butterflies, using two mitochondrial markers and eight nuclear markers to update our understanding of the differentiation of the cryptic Cotesia species. Additionally, I screened the specimens for Wolbachia to determine its possible role in shaping the Cotesia host phylogeny. I expect different Cotesia lineages to carry divergent Wolbachia strains or have different infection statuses (infected vs. uninfected). With fresh Cotesia specimens collected from various locations in Europe, I amplified and sequenced two mitochondrial markers (16s, COI) and eight nuclear markers (18s, 28s, CfCN, CfEN, EF1A1, LwRh, SLD5, TCEB) for phylogenetic analysis. The phylogenetic analysis revealed two main clades: Clade A, where Cotesia acuminata forms a polyphyletic group, and Clade B, where Cotesia melitaearum forms a monophyletic group. Wolbachia was detected only in one species, Cotesia melitaearum Sp. G, where the strain has persisted for over 20 years. The strains infecting Cotesia belong to supergroup B and are all closely related. The close relationship and low infection rate suggest that Wolbachia is not responsible for the original divergence but may play an ongoing role in restricting gene flow between species. The updated phylogeny is in concordance with the previous works but also strengthens our understanding of the relationships within Clade B. Further work is required to resolve some relationships within Clade B and understand the cryptic species' divergence.
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(2022)Climate change and biodiversity loss are some of the most serious challenges the humanity is facing today. Current food systems are a major contributor to both global crises with massive negative impacts on climate and biodiversity, and thus, sustainable food system transition is inevitable in slowing down the further progress of climate change and biodiversity loss. One way to tackle the unsustainabilities of the food systems is through policy interventions, which can guide both food production and consumption to a more climate- and biodiversity-friendly direction. The aim of this thesis was to examine the popularity of different policy instruments in terms of reducing food’s climate and biodiversity impact among Finnish young adults. Moreover, this thesis aspired to find out which areas of food production and consumption Finnish young adults think policy interventions should target. Young adults were chosen as a target group, because they are in an important position in sustainability transitions. This research is based on survey data and the method applied was content analysis with characteristics from both qualitative and quantitative approaches. The data was analyzed in Atlas.ti program by using inductive and deductive content analysis methods. The results indicate that the most popular policy instruments for reducing food’s impact on climate and biodiversity among Finnish young adults were market-based, including taxes as the most popular and subsidies as the second most popular individual measure. This is in contrast to previous literature, where taxation and other market-based policies have been reported to be the least favored policies. Furthermore, information-based policies, of which especially raising awareness, regulatory instruments, of which particularly price regulation, as well as public procurement policies like a vegetarian day in public food services were among the most popular policy instruments. Although not directly examining acceptability, these results offer a glimpse on policy acceptability, which is found to be crucial in successful policy implementation. Further research is needed to study the acceptability of these policies comprehensively. Moreover, policy target areas related to food consumption rather than production were more popular among the respondents. Target areas such as favoring domestic food, reducing or ending animal product consumption and production, transitioning to vegetarian diets, making better (e.g. climate-friendly) choices easier, and converting meat into a luxury product were the most suggested. These results could be scaled up in future studies and then utilized in creating sustainable policies for food consumption and production, and that way reduce the climate and biodiversity impact they cause.
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(2019)Luonnon monimuotoisuus on vähentynyt viime vuosina globaalisti. Puhutaan jopa kuudennesta massasukupuutosta. Myös Suomessa erityisesti vanhojen metsien sekä niitty- ja perinneympäristöjen lajistot ovat heikentyneet. Suurin syy monimuotoisuuden vähenemiseen on elinympäristöjen katoaminen ihmistoiminnan ja maankäytönmuutosten vuoksi. Suomen uhanalaisia lajeja uhkaavat eniten metsä- ja maatalous ja niiden myötä vähenevät lahopuun ja niittyjen määrät. Luontotyypeistä erityisesti jalopuulehdot ovat katoamassa. Osansa maa-alasta vievät myös vapaa-ajan harrastukset, kuten esimerkiksi golf. Golfkenttien vaikutus monimuotoisuuteen on jakanut mielipiteitä. Golfkentän ekologiseen arvoon vaikuttaa se, millaiseen ympäristöön se on rakennettu. Urbaanissa ympäristössä golfkenttä voi merkittävästi lisätä monimuotoisuutta päinvastoin kuin metsäiseen ympäristöön rakennettuna. Golfkentät ovat kuitenkin usein laikuittaisia sisältäen useita erilaisia, pienialaisia kaistaleita alkuperäistä luontoa. Tässä työssä selvitin golfkentän rakentamisen aiheuttamia vaikutuksia metsäekosysteemin alkuperäiseen eliöyhteisöön sekä golfkentän monimuotoisuutta itsessään sekä verrattuna ympäröiviin alueisiin. Lisäksi pohdin, miten monimuotoisuutta kentällä voitaisiin parantaa. Tutkimuskohteena oli Hirsalan golfkenttä Kirkkonummella Etelä-Suomessa. Kesän 2018 aikana tein kentällä luontokartoituksen määrittämällä kentällä havaitut kasvit, nisäkkäät, linnut, matelijat ja sammakkoeläimet, perhoset sekä maakiitäjäiset (Coleoptera: Carabidae). Maakiitäjäisiä keräsin myös kentän reuna-alueelta sekä kentän ulkopuolelta. Perhosten keräämiseen käytin valorysää ja kolmea syöttirysää, keräys kesti toukokuusta elokuuhun. Maakiitäjäiset keräsin kuoppapyydyksillä (yht. 93) samalla aikataululla. Muut taksonit määritin näkö- ja kuulohavaintojen avulla. Mallinsin perhos- ja maakiitäjäisaineistoilla kentän ja vertailualueiden lajistojen runsausjakaumia. Maakiitäjäisaineistolla vertaisin kentän, kentän reuna-alueen ja kentän ulkopuolisen alueen monimuotoisuuksia Shannonin-Wienerin ja Simpsonin diversiteetti-indekseillä. Kasviaineiston avulla tein golfkentän alueesta luontotyyppikartan QGIS- paikkatieto-ohjelmalla. Muut aineistot täydensivät tilastomenetelmillä saatuja tuloksia. Golfkentän saamat diversiteetti-indeksit olivat pienempiä kuin kentän reunalla tai kentän ulkopuolella saadut arvot. Golfkentän lajistojen runsausjakauma oli epätasaisin muiden alueiden runsausjakaumiin verrattuna. Kentällä dominoi aitosysikiitäjäinen (Pterostichus melanarius, 65 % kentän lajistosta), joka on tunnettu häiriöekosysteemien generalistilaji. Perhosaineiston runsausjakauma ei kuitenkaan poikennut vertailuaineistosta. Golfkentällä havaittiin myös uhanalaisia ja suojeltuja lajeja, kuten liito-orava (Pteromys volans) sekä kartioakankaali (Ajuga pyramidalis). Kentällä ja sen läheisyydessä havaittiin myös useita metsäisiä lajeja, joista osa käytti kenttää esimerkiksi saalistamiseen tai laiduntamiseen. Kentältä löytyi luontotyyppejä niin karuista kalliometsistä tuoreisiin kankaisiin ja pähkinäpensaslehtoon. Kentältä löytyi myös joitain haitallisia vieraslajeja, kuten keltamajavankaali (Lysichiton americanus). Kentän rakentaminen on heikentänyt ja muuttanut alkuperäistä metsäekosysteemin eliöyhteisöä. Kenttää voidaan pitää häiriöekosysteeminä, jossa generalistilajit viihtyvät spesialistilajien kadotessa. Alueella voi myös olla vielä jäljellä rakentamisesta aiheutuvaa paikallista sukupuuttovelkaa esimerkiksi kasvi- ja hyönteislajien suhteen. Kenttä yhdessä ympäröivän luonnon kanssa muodostaa laikuittaisen elinympäristön, joka mahdollistaa monien lajien ravinnonhankinnan ja pesimisen kentällä ja sen läheisyydessä. Kentän monimuotoisuutta voitaisiin parantaa lisäämällä kentällä lahopuun sekä niittyjen määrää. Luonnonkasvien lisääminen ja niiden hallittu hoitamattomuus voi lisätä hyönteisten ja kasvinsyöjien määriä ja näin edelleen vaikuttaa kaskadiefektin kautta ylemmille ravintoketjun tasoille. Myös lampien ympärille olisi hyvä jättää suojavyöhykkeet. Alkuperäisiä luontokaistaleita tulisi vaalia, erityisesti kentällä sisällä olevaa pähkinäpensaslehtoa. Kentällä esiintyvät haitalliset vieraslajit ja puutarhakarkulaiset tulisi poistaa, etteivät ne vie elintilaa alkuperäislajeilta. Pöntötyksillä voidaan myös lisätä yksittäisten lajien tilaa lisäämällä niille mahdollisia pesimis- ja levähdyspaikkoja.
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(2019)Tämän työn tutkimuskohteena on ihmisten ajattelu sekä ympäristö- ja kestävyyskysymysten kompleksisuus sekä Rittelin ja Webberin määrittelemä viheliäisyys. Tavoitteeni on kehittää sellaisia ajattelun välineitä, joilla kestävyysproblematiikkaa voisi ymmärtää mahdollisimman kokonaisvaltaisesti – monilla tasoilla sekä ilman liiallista osiin pilkkomista ja näkökulman tiukkaa rajaamista. Tämänkaltaisten työkalujen kehittämisen tarvetta on tuotu esiin varsin laajasti viime aikoina, kun huoli ilmastonmuutoksen, biodiversiteettikadon ja ilmastopakolaisuuden kaltaisista kompleksisista ongelmavyyhdeistä on kasvanut. Työn tarkempi tavoite on kehittää generalistis-holistis-holarkistinen viitekehys eli GHH-kehys jo olemassa olevan, Risto Willamon aiemmin esittelemän generalistis-holistisen GH-kehyksen pohjalta. GH-kehyksessä kokonaisvaltainen lähestymistapa tiivistetään kahteen ulottuvuuteen: tarkastelun näkökulmien ja kohteiden moninaisuutta korostavaan generalismiin sekä näiden näkökulmien ja kohteiden vuorovaikutusten merkitystä painottavaan holismiin. Lisään työssäni lähestymistapaan kolmannen ulottuvuuden: holarkismin, joka korostaa tarkasteluasetelman jäsentämistä monelle systeemiselle tasolle. Tarkemmalla tasolla tutkimustehtäviä on kolme: 1) GHH-kehyksen muodostaminen lisäämällä holarkismin idea GH-kehykseen, 2) heuristisen ja kehystä konkreettisemman GHH-mallin rakentaminen sekä 3) muodostetun kehyksen ja mallin pienimuotoinen soveltaminen kahden esimerkin avulla. Näistä ensimmäinen liittyy ihmisen luontosuhdekäsityksiin ja toinen YK:n kestävän kehityksen tavoitteiden (Agenda2030) jäsentämiseen. Jälkimmäinen sisältää lisäksi opettajien täydennyskoulutuksen yhteydessä kerätyn pienen empiirisen aineiston. Tuota havainnollistavaa aineiston käsittelyä lukuun ottamatta työ on metodologialtaan käsitteellis-teoreettinen ja työn painotus on voimakkaan epistemologinen ja näkökulmarelativistinen. GHH-kehyksen tärkein merkitys liittyy siihen, että se on eksplikoitu melko tarkasti sekä käsitejärjestelmänsä taustan että ymmärryksen edistämiseen liittyvän käyttönsä osalta. Kokonaisvaltaisessa metodologiassa on toistaiseksi tarkasti sanoitettuja työkaluja aika vähän, mikä vaikeuttaa kokonaisvaltaista työskentelyä. Empiirisen osan tulosten mukaan koulutukseen osallistuvista opettajista moni sai GHH-kehyksestä ja -mallista aidosti apua Agenda2030-tavoitteiden muodostaman kompleksisen kokonaisuuden jäsentämisessä. Nämä tulokset ovat kuitenkin vasta hyvin alustavia, ja työn lopussa esitetäänkin runsaasti ajatuksia sekä GHH-käsitejärjestelmän teoreettiseen että siitä johdettujen ajattelutyökalujen käytännölliseen jatkotutkimukseen.
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