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  • Rostedt, Fanny (2023)
    The group has identified two rare, previously uncharacterized missense variants in the YBX3 gene in a Finnish patient presenting with an unusual form of nemaline myopathy. The patient also inherited two biallelic TPM3 variants, one RYR1 variant from the father and one SRPK3 variant from the mother. TPM3 and RYR1 are known nemaline myopathy causing genes and the other variants identified in the patients, including the YBX3 variants, are thought to have a modifying effect on the phenotype. YBX3 encodes Y-box binding protein 3 (YB-3) and, YB-3 is a member of the Y-box binding (YB) protein family, that in addition to YB-3 consists of YB-1 and YB-2. The YB-proteins have mainly been studied in the context of cancer, with most studies focusing on YB-1. Studies indicate the ability of YB-proteins to compensate for the loss of one homolog suggesting functional redundancy between YB-3 and YB-1, and YB-3 and YB-2. Compared to its homologs, YB-3 is highly expressed in skeletal muscle. The aim of this thesis was to try out a new cell culturing method when investigating the role of YB-3 in the differentiation of myoblasts into myotubes. MSY-3 is the murine orthologue of YB-3. MSY3-knockdown mouse C2C12 myoblast lines were established using GIPZ lentiviral short hairpin constructs and by selection with puromycin. The success of transfection was determined using qPCR. The myoblasts were differentiated for 20 days on a gelatin hydrogel surface to support long-term culture and to provide phenotypes of higher physiological relevance with improved contractile maturity. Myoblasts cultured on coverslips were immunofluorescently stained for MSY-3. HeLa cells were transfected with a construct encoding N-terminally FLAG-tagged human YB-3 in a pcDNA-vector. YB-3-FLAG was purified using anti-FLAG magnetic beads. The eluated immunoprecipitation sample was sent to N-terminal sequencing to obtain information on post-translational modifications, to support further experiments regarding the post-translational cleavage of YB-3. N-terminal sequencing revealed an enrichment of YB-3 and YB-1 in the immunoprecipitation sample but not of YB-2, and previously undescribed post-translational modifications were identified. The MSY3-knockdown myotubes exhibited no spontaneous twitching on the hydrogel, while the control C2C12 myotubes twitched frequently. Misalignment of the MSY3-knockdown myotubes and changes in morphology was also observed in one of the MSY3-knockdown cell lines. This suggests that differentiating myoblasts on gelatin hydrogel is a potential strategy for studying the functions of YB-3 in myoblast differentiation and to elucidate its role in skeletal muscle.
  • Er, Safak (2018)
    As a genome editing tool, CRISPR-Cas9 has provided a robust way to generate mutations in the gene of interest, at a certain time point, and in selected cell populations. The impairment of dopaminergic neurons in the substantia nigra is addressed to be one of the main pathologies of Parkinson’s disease. The histopathology of Lewy Bodies, with an undetermined role, accompanies the demise of DA neurons. Development of strategies for the prevention the neurodegeneration has a potential to slow down the progression of Parkinson’s disease. In this study, a novel, neuron-specific CRISPR-Cas9 system was developed for the purpose of dissecting neuroprotective pathways in primary dopaminergic neurons. The optimization of the tool was done by targeting EGFP at TH-positive neurons obtained from transgenic animals expressing EGFP in dopaminergic neurons. Complete loss of EGFP was achieved at day 6 after the introduction of the CRISPR-Cas9 via lentiviral vectors. There were no survival or transduction efficiency differences. Two significant pathways for the survival of dopaminergic neurons, the microRNA biogenesis and GDNF/RET signaling were selected to collect the preliminary data. Dicer, Trbp, Translin, Ago-2 and Ret were targeted with single sgRNAs, which were specifically designed to create indel mutations in these genes, and specific lentivirus vectors were produced with each guide. After transduction with the lentivirus vectors, survival of the TH-positive neurons was unaffected. Data obtained from the quantitative PCR suggested that there was 50-70% decline in transcript levels of Trbp. However, the unchanged transcript levels of the other miRNA-related targets suggest the need for further optimization of the specific guides. Knockdown of Ret was validated by inhibition of pharmacological benefits of GDNF. Overall, this research has shown the further development of this CRISPR-Cas9 tool would be useful to dissect neuroprotective signaling pathways in dopaminergic neurons.
  • Piki, Emilia (2021)
    Ovarian cancers (OCs) are gynecological malignancies that cause the most gynecological cancer related deaths due to asymptomatic early-stage development and late diagnosis. The treatment of OC has not improved significantly during the last decades, and challenges are often caused by chemoresistance and the heterogeneity of cancer cell populations. Therefore, there is an urgent need to improve OC treatment outcome and implement new targeted therapies that could address the subtype specific characteristics. The most common type of OC is epithelial ovarian cancer (EOC), that can be further divided into five subtypes with distinct molecular and histological characteristics. High-grade serous subtype represents majority of cases with up to 75% of EOC patients, while other subtypes such as low-grade serous, mucinous, clear cell and endometrioid OC being less common. Considerable progress has been made in cancer treatment via precision oncology, in which individual cancer biology and tumor molecular features are investigated and used to improve treatment decisions. For this purpose, the development of patient-derived cancer cells (PDCs) offers a good opportunity to study cancer biology in vitro and to build models for preclinical molecular profiling and functional testing. PDCs can be used to establish 2D and 3D models, and most recently, wide interest has been focused on patient-derived organoids (PDOs), that offer a better model of tumor and its microenvironment, while allowing long-term culture, cryopreservation, modification and high-throughput opportunities. In this study, the aim was to establish PDO cultures using tumor cells from low-grade serous OC patients for molecular profiling and functional drug testing. PDOs were generated from both fresh and frozen tumor tissue or ascitic samples resulting to successful development of long-term PDOs from three of the five models. In order to identify optimal culturing conditions for low-grade serous OC PDOs, two previously unpublished growth mediums were tested in parallel. The more complex of the mediums showed slightly better PDO growth in general. The immunohistochemistry staining with pan-cytokeratin and PAX8 was used to confirm the epithelial and ovarian origin of PDOs. In addition, cancer panel sequencing was performed to identify mutation profiles. Importantly, the small-scale drug testing, which was performed using conventional chemotherapeutics cisplatin and paclitaxel and targeted drugs gedatolisib and trametinib, showed sample-specific responses. In conclusion, the results from this project show that PDOs are good models for ex vivo precision medicine functional studies. Importantly, we managed to establish PDOs from frozen tumor cells, suggesting that PDOs could be initiated from living biobank samples. However, the challenges related to culturing of PDOs for functional assays included slower growth rate compared to 2D cancer cell cultures and technical challenges related to Matrigel, limiting the possibilities of high-throughput drug testing. By improving these factors, PDOs will offer an efficient 3D model for preclinical use.
  • Williams, Scott (2023)
    This thesis explores the relationship between energy justice and demand response electricity pricing schemes in the residential market. As energy retailers make the transition towards demand response contracts, many opportunities arise for justice and injustice. It is vital that consumers are protected from arising injustices, and that the benefits of demand response schemes are distributed across the population. I use a popular energy justice framework to evaluate the demand response schemes of three European electricity retailers for their adherence to the principles of energy justice. The eight evaluative criteria are availability, affordability, due process, good governance, sustainability, intragenerational equity, intergenerational equity and responsibility. The three retailers are Tibber, E.ON Next, and Helen. Through this evaluation, I demonstrate that novel developments in energy systems by some energy retailers can positively inform the policies and practices of conventional retailers. There is room for growth in customer communication, stakeholder involvement, and smart home integration. My evaluation shows that retailers are yet to meet the aspirations of energy justice with their demand response schemes, but the potential for promoting justice clearly exists. I conclude with a set of recommendations Helen can take to meet the goals of energy justice in their electricity contracts.
  • Lyytikäinen, Veera (2020)
    It is widely acknowledged that previous efforts to communicate the severity and rate of climate change have failed. Science communication has for decades relied on the presumption that more information leads to more informed decisions, thus so far, the scientific consensus about human-caused climate change has not resulted in required changes in behaviour. Previous communication efforts have, for the most part, attributed inaction to the lack of information, but in doing so, have excluded many social and psychological elements of communication. Although raising the level of awareness about climate change has been successful, climate change remains to be perceived to be a distal threat. Recently, more sophisticated approaches have been developed to meaningfully communicate climate change, drawing attention to the framing of the communication. In this study, a new approach to science-based environmental communication is evaluated. The case study seeks to address how immersive Virtual Reality (VR) can be used as a tool in science-based environmental communication for policymakers in a locally relevant context. Via immersive VR, information about forests’ role in climate change is mediated to forest policymakers. In the science communication, climate change is framed as an experiential, local, and present risk, promoting a problem definition that focuses on the climate effects of forest utilisation. I evaluate the success of the science-based environmental communication by measuring participants’ personal responses. I focus on measuring enjoyment, interest, trust, and usability. The study participants are members of the Parliament of Finland and governmental officials from the Ministry of Agriculture and Forestry; and the Ministry of the Environment. The study material consists of feedback forms from participants (N=65) and interviews of the key actors (N=7). To consider the historical background and many conflicting interests in Finnish forest and climate politics, I focus on the comparison between the natural resource position and the environmental position. The results of this study offer compelling evidence for how differently policymakers representing these two positions perceive the usage of immersive VR in science-based environmental communication. The environmental position indicated significantly higher levels of success on all measured components. Considering that the science communication framed forest utilisation as an environmental issue, it is not surprising that participants holding the environmental position perceived the science communication to be more enjoyable, interesting, trustworthy, and usable. Accordingly, the study results provide additional support for the idea of Finnish forest policy as a polarised field of policy with two main positions. With the means of immersive VR, I was able to induce strong personal responses to the science communication. Participants holding the natural resource position were more likely to challenge the legitimacy of the information and the use of VR in science communication than participants holding the environmental position. The results point to the likelihood that communicating climate change via immersive VR can induce strong negative emotions in the participants, but when the communication is comparable with the policymaker's policy preferences, they respond more positively. The study results also suggest, that to communicate climate change more meaningfully, immersive VR should be further explored as a supplementary tool in science communication.
  • Lehtonen, Jussi (2006)
    The Seychelles magpie robin Copsychus sechellarum is among the most threatened of the twelve avian species endemic to Seychelles. Originally relatively abundant and widespread in Seychelles, its population has severely diminished, mainly on account of introduced predators and habitat destruction. The lowest count was recorded in 1965, when the number of birds was between eight and fifteen, all confined to just one island. In 1990 a successful recovery program was implemented, and the population has now recovered to approximately 150 birds on four islands. Translocations to new islands are a major part of the recovery program. So far Seychelles magpie robins have been translocated to three islands, and three more target islands still need to be chosen if the long-term goals of the project are to be reached. Determining habitat suitability at the translocation target area is essential before attempting a translocation. Cockroaches are a major part of the bird's diet. Cockroach abundance has been shown to be a good indicator of magpie robin habitat quality, but it is very laborious and time consuming to measure. The objective of this study is to build a model that can be used to predict cockroach abundance, and thereby Seychelles magpie robin habitat quality, with relatively simple and inexpensive measurements. The data for this project was collected on Cousin, Cousine and Aride islands in Seychelles during October and November 2004. Several potential predictors of cockroach abundance were measured using simple and low-cost methods. The measured variables were Seychelles skink Mabuya sechellensis abundance, altitude from sea level, slope gradient, rock type, canopy cover, shrub cover, litter depth, soil depth, the relative canopy cover of different tree species, and percentage of ground covered by litter, rock, grass, woody vegetation and bare ground. These variables were measured in several 25 × 25 m plots on each island. Cockroach abundance had been measured in the same plots previously. Several multiple linear regression models were built using these variables, with cockroach abundance as the dependent variable. The Akaike Information Criterion was used to rank the models and to find the most important explanatory variables. Stepwise regression was used as a secondary method in order to see if two different methods point to the same result. Both methods indicated that slope gradient and granitic rock type are the two most important predictors of those tested. These are features that are invariably associated with granitic terrain, and both are positively correlated with cockroach abundance. A simple comparison of average cockroach abundance between granitic and coralline rock types also showed a significant difference, with granitic terrain providing higher cockroach abundance. The islands in Seychelles can be divided into two main categories: granitic and coralline islands. Steep slopes and granitic rock are both features associated with granitic terrain and granitic islands only. Therefore, based on the results of this study, granitic islands are likely to provide higher cockroach abundance and thus better Seychelles magpie robin habitat quality. Hence it is recommended that Seychelles magpie robin translocation efforts are focused preferentially on granitic islands.
  • Suonpää, Pinja (2022)
    Each year many new-borns are at risk for long-term developmental deficits due to adverse perinatal events. Early gross motor abilities have been shown to link with cognitive development and studying infant motor behaviour may provide means to assess global neurodevelopment. This thesis aims to explore a potential association between early gross motor abilities recorded at infancy with a multi-sensor wearable jumpsuit MAIJU and later neurocognitive development assessed at two years of age. The study sample (N=26) consisted of healthy full-term infants and those with prematurity or perinatal asphyxia. Spontaneous motor activity was recorded at home with the jumpsuit. Machine learning methods were used to quantitate the time infants spent in different postures and estimate the maturity of their motor abilities, which were compared to cognitive development at two years of age with correlational- and regression analyses. There was a positive trend between early motor abilities and later cognitive development. Specifically, standing posture explained the association, such that infants who spent more time standing had better cognitive abilities at two years of age. Standing may support cognitive development by increasing opportunities for visual and manual exploration and learning. Shared neuronal circuitries for motor and cognitive functions and faster neuronal maturation may also underlie the association. The current study supports the creation of future studies with larger sample sizes to establish the potential for the use of postural and movement information obtained from wearable jumpsuit MAIJU to assess the variability of neurocognitive development of at risk and typical infants with potential goal to identify future cognitive deficits at early stage.
  • Seppälä, Sini (2019)
    Not much attention is paid on the conservation of invertebrates despite their importance to the ecosystems in general and their benefits and ecosystem services to us, humans. This study is part of a project aiming to start the Sampled Red List Index (SRLI) for spiders. The IUCN Red List Index (RLI) is used for measuring the overall extinction risk of groups of species and the sampled approach is a way to evaluate the trajectory towards extinction of megadiverse groups without the need to assess every species of the whole group of interest. A random sample of 200 spider species were selected from the global checklist and assessed according to IUCN Red List Categories and Criteria. Given the availability of data, I was able to calculate the extent of occurrence and area of occupancy for 80 species, of which 70 species had an EOO above 20000 km² and 75 species an AOO above 2000 km², the thresholds below which species can be considered threatened. The trends in EOO and AOO were assumed to be stable for most species (49 species) given the inexistence of monitoring data for any taxon. Evidence of decline was found for only 10 species, usually inferred from habitat loss. Habitat data was collected for 118 species. The most common habitat type was forest (73 species), followed by grasslands (24 species) and artificial habitats (22 species). For 44 species the habitat trend was inferred to be stable, only declining, according to available knowledge, for 14 species and increasing for one species. For the remaining 141 species the habitat trend could not be inferred and was thus assumed to be unknown. The most commonly mentioned threat types were agriculture (11 species), fires (7 species) and logging (6 species). For 39 species there were no known threats and for the rest of the 132 species the threats were unknown. Conservation actions in place were observed for 104 species, most commonly site and area protection (100 species) and resource and habitat protection (88 species). Conservation actions such as education and awareness (8 species), resource and habitat protection (7 species) and site and area management (6 species) were to take into consideration. All the 200 species were estimated to be in need of further basic research especially on threats (143 species and distribution (140 species), but also on life history and ecology (135 species). Due to several knowledge shortfalls, including the Wallacean (distribution of species), Prestonian (population trends) and Hutchinsonian (response to environmental change), no threat category could be reached for the vast majority of the species. The results show that an IUCN category could be reached for only 59 species, of which 55 were assessed as Least Concern and a threatened category was reached for only 4 species (t as Critically Endangered and one as Vulnerable). The baseline SRLI at this first point in time was 0.95 (in a 0-1 scale, where 0 means all species are extinct and 1 for all species are Least Concern). We hypothesize however that among the 141 Data Deficient species there should be a higher proportion of threatened species than among the 59 evaluated. This would be due to two reasons. First, the scarcity of information on many species might in part be due to their rarity. Second, widespread species were often the only for which an assessment could be reached, creating a bias in the dataset towards a large base SRLI value. The strategy currently imposed by IUCN is therefore clearly inadequate for taxa with scarce information, which represent the vast majority of species. I propose the future use of a different, non-random, approach to the selection of species in the SRLI and its adoption for other taxa which represent in fact most extant and threatened species.
  • Maran, Suveda Vignesh (2019)
    Extracellular vesicles (EVs) are a diverse set of cell-derived membranous vesicles which have exosomes or small EVs (40 -200nm) ,large EVs (>200 nm) and larger apoptotic bodies/oncosomes (>1000 nm). They are present in most biological fluids, such as blood, sweat, and urine etc. EVs are expressed by almost all cells.Recent evidence suggests that EVs are a form of cellular communication, resulting in an intensive investigation of their role in different biological processes and also due to their biomarker potential. Ultracentrifugation (UC) is the standard method used for the isolation of EVs from different biological fluids. UC has some limitations related to laborious operation and scalability issues. Hence, there is a need for new methods for the isolation of EVs.Nanocellulose(NC) is a biopolymer obtained from wood biomass and has the ability to be functionalised with various chemical groups on its surface. The chemical groups alter the surface properties of NC for usability in different applications. Currently, It finds extensive use in different biomedical applications due to its unique physicochemical properties. The aim of the thesis is to evaluate the use of functionalised nanocellulose (FNC) as a novel alternative compared to the standard method of ultracentrifugation in the isolation of EVs from conditioned cell culture media. Cancer cell lines and mesenchymal stromal cells (MSCs) were grown in EV-depleted cell culture media after expansion in cell culture media. The EV-depleted media was collected from the cells after 48 hours and further processed by filtration to obtain the necessary conditioned cell culture media for EV isolation. Extracellular vesicles were isolated from the conditioned cell culture media by using UC and FNC. The isolated EVs from both methods were characterised and evaluated based on their different parameters using Bicinchoninic Acid (BCA) assay, Transmission Electron Microscopy (TEM), Nanoparticle Tracking Analysis (NTA), and Western Blot. The EVs isolated by FNC were smaller in size with few vesicle-like structures around 20-40 nm compared to EVs isolated by UC 60-200nm. Most EVs isolated by UC had a higher particle-to-protein ratio which indicated more purity and reduced levels of non-vesicular contaminants in the EV isolations. The EVs isolated by FNC for many samples had a low particle-to-protein ratio indicating potentially higher levels of non-vesicular contaminants being present. Hsp70, a surface marker of EVs and soluble stress protein was observed in EVs obtained from a primary MSC and another cancer cell line among all the isolation methods. No contamination from Endoplasmic reticulum(ER) components was observed in any of the samples. The EVs isolated by FNC could not be analysed more thoroughly by some of the characterisation methods due to issues such as lack of standardised sample preparation protocols, possible interference from isolation components and sample variations. The isolation method will really benefit from further optimisation of sample preparation steps and the adoption of alternative characterisation methods for evaluation. A narrower research question with focus on FNC-EDA isolation of EVs from HOS-143B and AT-MSC will be an excellent starting point for more detailed investigations.The availability of different surface modifications, faster processing and more research on the isolation mechanism will make this novel method a great alternative to UC for isolation of EVs.
  • Järvinen, Riikka (2022)
    Urban greenspaces are valuable resources for humans and are an integral part of the urban landscape. They are also popular sites for various social and cultural activities, such as dog walking. Dog ownership rates are increasing globally at a rapid rate, hence increasing the dog populations within urban cities. The increasing number of dogs could potentially have negative consequences to the quality of urban parks. Furthermore, there is a lack of research on the impacts of dogs on urban environments. The aim of this study is to gain a better understanding of the impacts of dogs on path-side soils in urban greenspaces. Soil samples were collected from both Helsinki and Lahti. The impact of dog urine was studied by comparing path-side soil samples between areas with high dog activity (i.e., parks) and similar areas with low to no dog activity (i.e., cemeteries). Soil samples were collected three times during the growing season in 2021 at three different treatments: close by 1) an evergreen tree, 2) a lamppost, and 3) a lawn area. The samples were analyzed for soil pH, electrical conductivity, organic matter, soil moisture, NO3--N, and NH4+-N. Net N mineralization and net nitrification rates were also calculated. The results indicated that dog urine is a significant contributor to the input of nitrogen in urban parks. Soil NO3-N and NH4+-N concentrations were significantly higher in parks than in cemeteries and exhibited clear seasonal trends. Soil pH was generally lower and electrical conductivity higher in parks than in cemeteries. Poles and trees exhibited the greatest concentrations, suggesting that the impact of dog urine is highly localized around path-side objects. None of the treatments in cemeteries showed little to no changes throughout the growing season. Lastly, the net nitrification rates were significantly higher in parks during spring and summer. In contrast, net mineralization rates were generally higher in cemeteries than parks. These results confirm that urban planners need to take into consideration the impact of dogs to mitigate any potential negative consequences to the quality of urban parks.
  • Järvi, Vilja (2019)
    The insular cortex has been implicated in the neurocircuitry underlying alcohol addiction. The role of the insular cortex and its projections in regulating ethanol intake in AA (Alko-Alcohol) rats has been studied using chemogenetic tools. Chemogenetic activation of the anterior agranular insula (aAI) in AA rats through excitatory DREADDs expressed in the aAI has been found to decrease ethanol consumption. The aAI projects to the central nucleus of the amygdala (CeA), another brain region involved in the development of addiction, particularly in the withdrawal/negative affect stage. In the current study, we sought to further investigate the role of the aAI and the CeA in regulating voluntary ethanol consumption in AA rats. First, we characterized the efferent projections of the aAI in AA rats by chemogenetically activating the aAI with DREADDs and then measuring c-Fos expression in various regions of interest throughout the brain. Next, we investigated the role of the aAI --> CeA projection in ethanol intake by chemogenetically activating or inhibiting the aAI --> CeA projection using the dual viral Cre-dependent DREADD approach. We examined the effects of this manipulation on voluntary ethanol consumption in AA rats in a two-bottle choice paradigm. Finally, we examined the roles of CeA D1Rs (dopamine receptors) and 5-HT2ARs (serotonin receptors) in regulating ethanol intake by examining the effects of pharmacological agonism or antagonism of these receptors on voluntary ethanol consumption in AA rats. Our results from the first experiment reveal significant activation of brain regions including the posterior agranular insula, the mediodorsal nucleus of the thalamus, and the posterior piriform cortex following chemogenetic activation of the aAI. The projections from the aAI to these regions are potentially important in the aAI circuitry in AA rats and are therefore of interest in future studies on the role of aAI circuitry in ethanol intake. In the second experiment, we found no significant effects of aAI --> CeA projection activation or inhibition on ethanol consumption in AA rats, indicating that this projection may not be a key component in regulating ethanol intake in these rats. Finally, we found no significant effects of pharmacological D1R antagonism, 5-HT2AR antagonism, or 5-HT2AR agonism in the CeA on ethanol intake in AA rats, although there was a non-significant trend towards a dose-dependent decrease in ethanol consumption with increasing dose of the D1R antagonist. Our results reveal new neural projections that should be investigated in future research on the role of the aAI in regulating ethanol intake. Studies on the neurobiology underlying alcoholism may reveal new pharmacological or anatomical targets for treatments of alcoholism in humans.
  • Timonen, Martina (2024)
    Exercise-induced hyperinsulinism (EIHI) is a pathological condition characterized by aberrant insulin secretion triggered by physical exercise or pyruvate exposure. The monocarboxylate transporter protein (MCT1), encoded by SLC16A1, is ubiquitously expressed in almost all cell types except pancreatic islet cells. In patients with EIHI, mutations in the regulatory regions of the SLC16A1 gene are thought to lead to the unwanted expression of MCT1 on the beta cell membrane, allowing the influx of elevated lactate and pyruvate blood levels during exercise. These substrates feed into the Krebs cycle, increasing insulin release. This excessive insulin secretion can lead to hypoglycemia during exercise, causing weakness, syncope, and confusion. Since EIHI has never been studied using a human stem cell-derived islets, this thesis aims to establish a robust model in which to investigate the disease mechanism in detail. To achieve this, we reprogrammed EIHI patients’ fibroblasts into a stable pluripotent state and further differentiated them into functional pancreatic stem cell-derived islets (SC-islets) in vitro. These SC-islets were then matured further in vivo (in immunocompromised mice) and compared to healthy SC-islet controls. Rigorous quality control measures were implemented throughout the differentiation process to ensure its efficacy and the expression regulation of SLC16A1 was studied during SC-islet development. Extensive phenotypic characterization was conducted using immunohistochemistry, quantitative gene expression level analysis, and insulin secretion assays with glucose and pyruvate. Contrary to expectations, the results of this study demonstrated that despite the SLC16A1 promoter mutation, the expression of SLC16A1 was downregulated similarly to the control cell line during development in vitro, resulting in similar pyruvate-stimulated insulin secretion to the control cells. Interestingly, immunohistochemical analysis of in vivo implanted SC-islets showed a clear phenotype with an increased number of MCT1-positive cells only in the mutant grafts, some of which were endocrine cells. In conclusion, the phenotypic manifestations of EIHI were not visible in the setting of in vitro modeling, which was attributed to the similar expression levels of MCT1 in both the mutant and control cell lines. However, following in vivo implantation, there was a noticeable increase in MCT1 expression exclusively in the mutant cells. This finding suggests a distinct regulatory mechanism of MCT1 expression, which might be impacted by the in vivo surroundings and the maturation state of human islets.
  • Partti, Edvard (2018)
    Kaurapohjaiset elintarvikkeet ovat terveellisiä. Monet niiden terveyshyödyt johtuvat kauran liukoisen ravintokuidun suuresta β-glukaanipitoisuudesta. β-glukaanin terveysvaikutukset ovat riippuvaisia sen molekyylipainosta ja viskositeetista. Viskositeetilla on myös muuta merkitystä kaurapohjaisissa elintarvikkeissa kuten kaurajugurteissa ja kauramaidoissa. Aiemmassa Folafibre-tutkimusprojektissa oli tutkittu kaurakuidun folaattipitoisuuden (B9 vitamiini) kasvattamista fermentoimalla sitä eri mikrobeilla. Hyvin folaattia tuottaneet mikrobit myös alensivat kaurakuituvalmisteen viskositeettia, ja erittivät glykosyylihydrolaaseja ja/tai proteaasia. Oli kuitenkin jäänyt epäselväksi, olivatko entsyymit ainut syy viskositeetin alenemiseen, ja kuinka paljon kullakin niistä oli vaikutusta viskositeettiin. Lisäksi tämän alan kirjallisuudessa on pidetty epäselvänä, onko esim. tärkkelyksen ja β-glukaanin välillä jotain interaktioita jotka mm. nostavat niiden viskositeettia yli yksittäisten polymeerien viskositeetin summan. Näitä voitaisiin selvittää puhdistamalla viskositeettia alentaneista mikrobikannoista kyseiset entsyymit ja tutkimalla niiden vaikutusta kaurakuidun viskositeettiin. Yhdeksi mikrobiksi valittiin Exiguobacterium sp. RB3 kanta, koska em. syiden lisäksi tässä bakteerisuvussa esiintyy psykrofiilejä ja mikrobeja jotka voivat kasvaa korkeassa pH:ssa, jolloin sen erittämät entsyymit saattaisivat olla aktiivisia matalissa lämpötiloissa ja korkeassa pH:ssa, ja olla siten teollisesti kiinnostavia. Toiseksi mikrobiksi valittiin Bacillus sp. ABM5119, koska sitä oli käytetty monissa Folafibre-projektin tutkimuksissa. Työn tavoitteena oli puhdistaa Bacillus sp. ABM5119:n endo-β-1,4-glukanaasi, ja Exiguobacterium sp. RB3:n α-amylaasi ainakin siinä määrin, että ne ovat muista endoaktiivisista glykosyylihydrolaaseista ja proteaaseista puhtaita, ja sitten mitata puhdistettuja entsyymejä ja proteaasia käyttäen niiden vaikutus yhdessä ja erikseen keitetyn kaurakuituvalmisteen viskositeettiin. Lisäksi tavoitteena oli karakterisoida Exiguobacterium sp. RB3 amylaasin olennaisimmat biokemialliset ominaisuudet, sekvensoida sen geenin amylaasia koodaava alue, ja selittää sen ominaisuuksia myös sekvenssistä johdettavissa olevan tiedon perusteella. Keitetyn kaurakuitupreparaatin viskositeettia alentavat eniten α-amylaasi ja endo-β-1,4-glukanaasi. Proteaasi ei vaikuta kaurakuitupreparaatin viskositeettiin, kun kuitupreparaatti on keitetty. Endo-β-1,4-glukanaasi alentaa viskositeettia yhtä hyvin kuin β-1,3-1,4-glukanaasi. Synergiaa viskositeetin alentamisessa α-amylaasilla ja endo-β-1,4-glukanaasilla ei havaittu, mutta havaittiin että β-glukaani saattaa estää tärkkelyksen retrogradaatiota. Hyvin pienetkin entsyymiaktiivisuudet vaikuttavat viskositeettiin. Jos halutaan β-glukaanin viskositeetin ja siten terveysvaikutusten säilyvän, täytyy esim. kauramaidon valmistuksessa käytettävien entsyymivalmisteiden olla β-glukanaaseista hyvin puhtaita. Mikrobifermentaatioissa tapahtuvat viskositeetin alenemat johtuvat lähinnä mikrobien erittämistä glykosyylihydrolaaseista, ei niinkään esim. niiden metabolian sivutuotteista kuten happiradikaaleista. Exiguobacterium sp. RB3 α-amylaasi on rakenteeltaan Bacillus licheniformis α-amylaasin kaltainen glykosyylihydrolaasiryhmän 13 entsyymi. Se sitoo rakenteeseensa kolme kalsiumiatomia, ja kalsiumpitoisuus vaikuttaa sen aktiivisuuteen. Se on aktiivisimmillan pH alueella 5,0 – 7,5. Se sietää detergenttejä, toisin kuin eräs aiemmin karakterisoitu Exiguobacterium-α-amylaasi. RB3 α-amylaasin turnover number oli korkea, 29000 1/s. Exiguobacterium-suvun psykrofiilisessä haarassa esiintyy kahta eri α-amylaasia, joista yksi on tässä karakterisoitu, ja toinen on selvästi erilainen rakenteeltaan ja biokemiallisilta ominaisuuksiltaan.
  • Mäkelä, Meeri (2024)
    Secondary growth in plant vasculature tissues originate from meristematic tissue vascular cambium. Vascular cambium produces xylem inwards and phloem outwards in the plant root and stem. Vascular cambium regulatory mechanisms are not completely known, and while plants and especially trees are dependent on the mechanical support and transportation systems the vasculature provide, increased knowledge of the vascular cambium and especially xylem development is valuable. In this thesis, I explored Arabidopsis thaliana single-cell RNA-sequencing data from secondary growth stage via cloning transcriptional reporter lines, and later utilized the transcriptomics data to find potential xylem development regulators. By loss-of-function mutant and inducible overexpression line screening, I found two genes in a family of MYB transcription factors to be potential regulators in xylem development. Loss-of-function mutant did not show significant phenotype, but overexpression lines under constitutive 35S promoter showed extreme halt of growth, and a stain-filled vessel phenotype in a fixed and resin-embedded Arabidopsis cross-section. Under developing xylem -specific promoters, inducible overexpression lines showed the same phenotype, and while grown to the secondary growth stage, I detected some patterning defects. Thus, these results indicate, that these MYBs expressed in the xylem parenchyma in the single-cell transcriptomics data, might have a function in xylem development.
  • Neuvonen, Tapani (2024)
    Flat-footed flies (Diptera: Platypezidae) are a group of small (3-6 mm) flies classified into four subfamilies based on diagnostic morphological characteristics. There are approximately 277 species worldwide. One of the subfamilies, the cosmopolitan Microsaniinae or the smoke-flies, is of particular interest. Smoke-flies are pyrophilic i.e. they are attracted to sources of smoke, such as burning wood or forest debris where they swarm. Smoke-flies are frequently observed in the presence of smoke; however, their biology remains entirely unknown. While the adult and larval habitat is understood for most other Palaearctic flat-footed flies, this information remains elusive for smoke-flies. Three different approaches are explored to increase knowledge on the biology of smoke-flies. Controlled burns organized by Metsähallitus are visited to observe the behavior of smoke-flies in a natural setting that mimics forest fires. Molecular and morphological identification is employed to identify the phoretic mites carried by smoke-flies, which can help to deduce the ecology and habitat preferences of the mites and consequently infer the habitats of smoke-fly larvae. Additionally, shotgun metagenomic sequencing of entire smoke-fly samples is utilized to determine if it’s possible to identify a molecular signature of the fungi in the genomic reads, which could provide insights into the ecological aspects of their habitats. The results confirm that the reproduction of smoke-flies is directly linked to forest fires. The use of an emergence trap in freshly burned forest demonstrated that smoke-fly larvae likely reside within the soil. These findings are supported by the taxonomic classification of fungal reads obtained through shotgun metagenomic sequencing, which identified soil-based arbuscular mycorrhizal fungi in adult smoke-fly samples. Although the analysis of phoretic mites provided no additional information on the biology of smoke-flies, the presence of mites in nearly all smoke-flies captured by the emergence trap confirm the ecological linkage between the habitat of mites and smoke-fly larvae. Integration of the results obtained from this study provides key information on the biology of smoke-flies and the specific habitat of the unknown larvae.
  • Lukkaroinen, Teresa (2022)
    In recent years, the science community has increasingly emphasized the influence of behavior, lifestyles, and culture on greenhouse gas emissions. Finland’s emissions per capita (~10 tCO2/yr.) are amongst the highest in the world, and it has been calculated that to comply with the Paris Agreement and to limit global warming to well below 2 °C, Finnish households should reduce their carbon footprint by 70 % by 2030. This requires drastic lifestyle changes, especially regarding mobility, housing, and nutrition. However, knowing this is not enough to change behaviors. Human behavior is influenced by several different internal and external factors such as knowledge, values, and social structures. This master’s thesis is a case study conducted in the Environmental Change and Global Sustainability (ECGS) master’s program at the University of Helsinki with the aim to enrich theories about pro-environmental behavior by providing insights on the future aspirations of sustainability science students, who have both extensive knowledge and experience in the field of sustainability. The data for this study was collected through an anonymous, online questionnaire with four open-ended questions. In total, 61 out of 274 ECGS students answered the questionnaire, after which qualitative content analysis with both inductive and deductive elements was applied to analyze the results. The results confirm that ECGS students are indeed well aware of the most impactful lifestyle changes for reducing personal carbon footprint. Despite their extensive knowledge on sustainability, the students’ future aspirations still come quite close to the dominant cultural vision of a good life in Finland. The implications of these findings once again confirm the importance of facilitating sustainable ways of living through changes in societal structures, discourses, and norms.
  • Ramos, Tuuli (2024)
    This thesis aims to illuminate expert dissensus on the policy instruments for reducing the carbon footprint of household consumption. In this thesis, I focus specifically on the policy instruments for addressing Finnish households’ consumption, proposed in the policy Delphi study by Salo et al. (2023), and experts’ responses regarding the measures’ importance. Exploring expert dissensus regarding consumption policy instruments is essential since identifying the measures that elicit expert dissensus and unveiling experts’ opinions on these measures promotes transparency in policymaking, helps to identify underlying assumptions, inconsistencies, and potential blind spots within the proposed measures, and therefore, contributes to better policy formulation. Two research questions are answered in this thesis to explore expert dissensus regarding consumption policy instruments: 1) What policy instruments to reduce the carbon footprint of household consumption elicit the most dissensus among experts? and 2) On what grounds do experts agree or disagree on the instruments exhibiting expert dissensus? A quantitative analysis involving calculating the interquartile range of experts’ responses was done to reveal which policy instruments exhibited expert dissensus. As a result, 26.8% of all proposed policy instruments were identified to exhibit expert dissensus. Subsequently, experts’ open comments regarding these policy instruments were examined through a thematic analysis to understand the grounds for expert dissensus. As a result of this research, seven themes emerging from experts’ open comments were identified: 1) Effectiveness, 2) Feasibility and practicality, 3) Content of policy mix, 4) Content of policy measure, 5) Consideration of other factors guiding consumption, 6) Consideration of possible side effects of utilizing the measure, and 7) Normative claims. Of these themes, the most prevalent was effectiveness, and the least prevalent were normative claims. As previous literature points out, the evaluation of policy instruments involves a blend of normative and empirical aspects. While it is unclear to what extent experts resorted to implicit normative assumptions within their evaluation process, this thesis concludes that information and uncertainty-related aspects, especially regarding effectiveness, require further consideration in sustainable consumption policymaking and research regarding policy measures exhibiting expert dissensus.
  • Asumaa, Nea (2023)
    Diabetes mellitus (DM) is a metabolic disorder, which in 2021 alone affected approximately 537 million adults. DM is a multi-organ disease with several comorbidities, one of which is chronic kidney disease (CKD), which often leads to renal impairment and kidney damage. While current treatment strategies have improved, they fail to protect the kidneys efficiently, which is why further understanding and renoprotective strategies are required. Podocytes are terminally differentiated cells central to the proper function of the glomerular filtration barrier (GFB) in the kidneys, and their injury can lead to the leakage of protein into the primary urine, which is a hallmark of CKD. One of the potential causes of podocyte injury in DM is hyperfiltration induced increase in fluid flow shear stress (FFSS). Podocyte responses to FFSS are still, however, relatively unknown. We exposed cultured human podocytes in vitro to FFSS at 2 dyne/cm2 for 2 hours via a novel flow chamber system. From the FFSS experiments, we studied podocyte motility from live cell imaging, protein expression levels by Western blotting and finally did immunofluorescent labelling to identify protein localizations in the cells. We discovered that podocytes express different modes of motility upon FFSS exposure, notably bleb-like motility previously only described in tumor and embryonic cells. In addition, we observed that podocytes significantly increased the phosphorylation of both AMPK and Ezrin, indicating the activation of pro-survival signalling as well as formation of bleb-like protrusions in response to FFSS stimuli. However, we did not observe significant podocyte loss, indicating that podocytes are capable of withstanding increased FFSS for short exposures such as 60 minutes. We believe that upon FFSS exposure, podocytes activate pro-survival mechanisms such as increased phosphorylation of AMPK and changes in motility in order to better withstand the increased shear stress. However, increased FFSS in for example DM patients is persistent, making it potentially a key factor in the development of podocyte injury and ultimately kidney damage.  
  • Mirko, Pomatti (2023)
    Animal welfare is a multifaceted concept that encompasses the overall well-being of animals, considering their physical and psychological health, behaviour, social interactions, and ability to engage in species-specific behaviours. Though there isn't a single universally accepted definition, the World Organisation for Animal Health (OIE) provides a widely recognized definition. According to the OIE, animal welfare refers to how well an animal copes with its living conditions. An animal is considered to have good welfare if it is healthy, comfortable, well-nourished, safe, able to express innate behaviour, and not suffering from pain, fear, or distress. In my thesis, the main objective is to identify knowledge gaps in recognizing factors that influence welfare among animal caretakers and to gather essential information that can serve as a foundation for future efforts to improve animal welfare in Korkeasaari Zoo. The project was conducted in collaboration with the zoo and involved studying and assessing the welfare of four different species. The assessments were based on scientific knowledge obtained through extensive literature research. The findings were then compared and analyzed by using a general linear model (GLM) with the zookeepers' own assessments. The results revealed that, overall, zookeepers tended to assess animal welfare more positively than the knowledge-based evaluation, although the extent of this difference varied among species. Notably, the results brought to light that certain species, especially the Asiatic lion, have specific welfare requirements that might not be fully recognized by the keepers. This implies there are opportunities for enhancing animal welfare in these cases. Furthermore, assessments varied depending on the type of question posed, with a significant observation being that nutritional requirements consistently received the highest evaluation across all species, regardless of the evaluator. This underscores the heightened attention that zookeepers pay to the nutritional well-being of the animals. This likely stems from the availability of well-documented nutritional information, in contrast to other facets of welfare in the studied species that might still be less comprehensively understood. My research is practical in nature, focusing on four specific species within one zoo. It may not primarily contribute to theoretical advancements but rather offer practical insights and applications. This marks just the starting point and indicates the need for further exploration and advancement. Shedding light on the various factors that shape animal welfare is pivotal for refining the operational protocols within the zoo setting. Such insights can pave the way for constructive measures that contribute to the betterment of the animals' well-being within the zoo environment. For instance, the notable difference in the evaluation of Asiatic lions, where the zookeepers scored them higher than the literature-based assessment, emphasizes the importance of incorporating scientific knowledge into zoo management practices. By bridging this gap and aligning assessments with well-established scientific data, we can make substantial strides in improving animal welfare in Zoos.