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In this master’s thesis project, I studied the association of lipid molecules phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 3-phosphate (PI3P) with autophagy in neurons. One of the aims of the study is to determine the level of basal autophagy in primary hippocampal neurons and to come up with a protocol for autophagosome observation without forcing radical changes in cell culture conditions. Other mammalian cells have extremely weak basal autophagy, but they increase it significantly in response to starvation, for example. However, neurons are extremely sensitive to any changes in their surroundings. They change their morphology, behaviour and biochemical properties, and often they simply do not survive. Therefore, the goal is a protocol for successful autophagy observation with minimal external influence. Despite the debate around basal autophagy in neurons, I observed high levels of basal autophagy in neuronal cells incubated in media without supplements. Also, my observations revealed that the inhibition of the last step of autophagosome processing with Bafilomycin A1, was enough to cause the massive accumulation of large autophagosomes. Results demonstrated that primary hippocampal neurons exhibit high levels of basal autophagy, suggesting that on the contrary to other mammalian cells neurons might not have enough potential to increase autophagy when it is induced pharmacologically or by stressful conditions. This would explain why autophagy induction is often claimed to be ineffective for neuronal cultures. The main goal is to observe and compare PI4P presence on autophagosomes in normal conditions and when autophagosome:lysosome fusion is inhibited with Bafilomycin A1. The side goal is to observe PI3P presence on autophagosomes as well. I transfected primary hippocampal neurons with fluorescent probes for PI4P or PI3P as well as for autophagosome-related protein LC3. Localization data was collected with live-cell imaging on a confocal microscope. As expected, PI3P was not detected on autophagosomes located in soma. It is involved in the initial vesicle biogenesis in distal axons but not in later events taking place closer to the cell body. PI4P showed high degree of colocalization with LC3, indicating PI4P presence on autophagosomes, but only when the fusion was presumably inhibited by Bafilomycin A1. These results suggest that PI4P appears on autophagosomes either as a result of compensatory pathway, where autophagosomes fuse with late endosomes instead of lysosomes; or as a molecule normally involved in autophagosome:lysosome fusion. Literature supports the latter explanation, but it cannot be confirmed without further research. These results give an insight into PI4P role in neuronal autophagy and might be relevant for the future research of autophagy disruption and aggregate accumulation in neuronal diseases as a consequence of abnormal lipid signalling, lipid metabolism and transport.

This thesis investigates whether the antidepressant-like and plasticity-promoting effects of LSD depend on TrkB expression among parvalbumin-positive interneurons (PV+ INs). Given the pivotal role of PV+ INs in facilitating critical-period-like plasticity, both during development and under the influence of conventional antidepressants, we hypothesized they may be involved in mediating psychedelic-induced neuroplasticity. Our findings challenge prevailing hypotheses, suggesting that LSD's plasticity-promoting effects may not rely on PV+ INs. We found that LSD did not increase the spine density of PV+ INs among wildtype mice, nor affected the expression of parvalbumin in PV+ INs or the perineuronal nets (PNNs) that enwrap them. Unexpectedly, we found that LSD did have subtle effects on PV+ IN spine density and the expression of parvalbumin in a mouse model with reduced TrkB expression among PV+ INs, suggesting a possible kind of compensatory mechanism at play. Our results reveal the multifaceted nature of LSD's actions on plasticity, shedding light on its therapeutic potential and prompting further exploration into its underlying mechanisms.

While weeks of continuous treatment is required for conventional antidepressant drugs (e.g. fluoxetine) to bring their full therapeutic effects, a subanesthetic dose of ketamine alleviates the core symptoms of depression (anhedonia, depressed mood) and suicidal thinking within just few hours and the effects may last for days. Nitrous oxide (N2O, “laughing gas”), another NMDAR antagonist, has recently been shown to have similar rapid antidepressant effects in treatment-resistant depressed patients (Nagele et al. 2015). We previously found using naïve mice ketamine and N2O treatment to upregulate five mRNAs related to the MAPK pathway and synaptic plasticity, both implicated as being important in the action of rapid-acting antidepressants. In the current study, these shared mechanisms were further investigated in C57BL/6JHsd mice, using behavioral test batteries to study depressive-like behaviour and RT-qPCR for biochemical analyses. We first aimed to demonstrate behavioral differences between naïve mice and a chronic corticosterone-induced animal model of depression, and to use this model to investigate antidepressant-like effects of ketamine and N2O. According to the results, chronic corticosterone produced some behaviors typical of a depressive-like phenotype, namely significant worsening of coat state and decreased saccharin consumption in the saccharin preference test. Both ketamine and N2O exhibited antidepressant-like effects by reverting decreased saccharin preference. We then aimed to elucidate the effects of ketamine and N2O on five previously found shared mRNAs: Arc, Dusp1, Dusp5, Dusp6 and Nr4a1. N2O significantly upregulated all targets in the vmPFC, except Dusp5, two hours after beginning of N2O treatment. Neither ketamine nor sole chronic corticosterone produced any significant changes. The results of this study suggest that N2O is a potential candidate for rapid alleviation of depressive symptoms. We suggest that the action of rapid-acting antidepressants, more specifically N2O, is based on a homeostatic response of the brain to a presented challenge. Here this challenge would be cortical excitation previously been shown to be caused by N2O, which leads to activation of pathways such as MAPK and subsequent Arc, Dusp and Nr4a1 signaling. The level of expression of these markers would then depend on which phase this response is in and hence, the differences in time between treatment and brain sample dissection could be a reason for conflicting results to previous research. Future studies would benefit from detailed investigation of the chronic corticosterone-induced model due to its potential in controlling for behavioral variability, thus reducing the number of animals needed for preclinical research. Overall the preliminary findings of this study could be one of the first steps in the search for the mechanisms underlying the potential antidepressant effect of N2O, how these molecular markers are related to its action and how it differs from the action of ketamine.

Marine debris is a problem that also affects sea birds. Several bird species are known to utilise marine debris among their nest materials in different parts of the world. Debris in nests can cause entanglement and increase the risk of debris ingestion, and hazardous substances leaching from plastics can have negative effects on birds. There are also anecdotal observations of debris in the great cormorant (Phalacrocorax carbo sinensis) nests in the Gulf of Finland, however, systematic studies are lacking. In this Master’s thesis I examined the prevalence of debris in cormorant nests in the Gulf of Finland, focusing mainly on plastic debris. The study was carried out in four nesting islets, which were located in Kotka, Porvoo, Espoo and Kirkkonummi. The sampling took place in autumn 2021. 50 nests were randomly sampled on each nesting islet, and plastic debris in the nest was counted and classified according to their type, colour and origin. Plastic debris was further categorized in the laboratory according to their polymer type using Fourier Transform Infrared spectroscopy (FTIR). Debris from the nesting islets was also counted and classified according to their type, colour and origin. In total, 58% of the nests contained debris, but the prevalence of debris in the nests varied between the colonies; In Kirkkonummi debris was found in 92% of the nests while in Porvoo only 34% of the nests included debris. Plastics constituted great majority of nest debris (95%). Most common source for plastic debris was consumers, most common plastic type threadlike and polymer type polyethylene (PE). The number of debris in the nests was linked to the width and location of the nests: core nests contained more debris than periphery nests and the number of debris in the nest was positively correlated with the width of the nest. The amount of threadlike plastics in the nests was higher than that in the surrounding environment, indicating active selection by cormorants for threadlike debris types as nest material. Based on the results of this thesis, nest surveys could be a useful tool in evaluating the effectiveness of certain reduction measures aiming to tackle marine plastic pollution.

Gastrointestinal stromal tumours (GISTs) are rare mesenchymal neoplasms that arise from the interstitial cells of Cajal, the so-called pacemaker cells of the intestine. GISTs typically contain an oncogenic driver mutation either in the proto-oncogene KIT or platelet-derived growth factor receptor A (PDGFRA), which belong to the class III receptor tyrosine kinases. Patients with a high-risk or advanced disease are standardly treated with a tyrosine kinase inhibitor imatinib. Despite this molecularly targeted treatment, many patients experience disease relapse, after which the prognosis is poor. Personalised treatment is rarely offered to patients as a first-line treatment option, even though several targeted therapies have been approved for GIST. Increasing treatment personalisation could improve treatment outcomes, yet the lack of patient-specific research models for GIST hinders the research. Three-dimensional (3D) cell culture models are widely used in cancer research to study the molecular mechanisms underlying tumorigenesis. Their ability to mimic the tumour biology and microenvironment is superior compared to the traditional two-dimensional (2D) cell culture model. For several cancers, these cell culture models have also been researched as platforms for personalised treatment selection with promising results. This thesis project aimed to study UPM Biomedicals’ GrowDex-based 3D cell culture model as a potential platform for personalised treatment selection for GIST patients. GrowDex is a plant-derived hydrogel that resembles the extracellular matrix. Another aim of this project was to set up a Sanger sequencing protocol covering frequently mutated areas in GIST to facilitate the validation of this cell culture model through drug testing on patient samples. To assess the GrowDex microenvironment, the viability and proliferation of two GIST cell lines, GIST-T1 and GIST48 were monitored. Furthermore, the imatinib response of GIST-T1 in GrowDex was assessed and compared to the response in other cell culturing conditions. The Sanger sequencing protocol was optimised using the aforementioned cell lines and then applied to GIST patient samples. The results of this project demonstrated that GrowDex provides a suitable microenvironment for culturing GIST cells and supports their 3D growth. GIST-T1 cells were less sensitive to imatinib when cultured in GrowDex in comparison to the 2D culturing condition, which is likely explained by the 3D organisation of the cells. Finally, the Sanger sequencing protocol was used to uncover the KIT/PDGFRA mutation status of several GIST patient samples. In conclusion, these results provide important information for further development of this cell culture model with patient samples.

It has been observed that children’s interest towards natural sciences decreases as they grow up and start middle school. The decrease of interest towards natural sciences and studying them has led to a situation, where science and technology students’ relative share of higher education students has been falling in some of the OECD countries. Formal education needs support to carry out fascinating science education for children and to maintain their interest towards natural sciences. One of the opportunities to fascinate children towards sciences are science centers and their activities either combined with formal education or organized in an informal form like science camps. The aim of this research is to survey the biological knowledge, the interest towards biology and the ability to apply the biological knowledge of science campers (mainly 5th and 6th graders) and to study the connections between them. At the same time, the effect of age and gender of the science campers is studied. To survey the biological knowledge of the campers, multiple-choice test was used and the fascination with biology was investigated with Likert scale variables. The ability to apply the biological knowledge was investigated with drawings that were produced during a biology-themed science camp program. The data was analyzed using quantitative methods. The results indicated that the science campers were relatively fascinated with biology and that they master biological knowledge quite well but the ability to apply the knowledge was varying. There were no differences between different ages nor genders but there are many factors such as the economic status of campers’ families that might have affected on the results. There was found a statistically significant connection between biological knowledge and fascination with biology, which is not surprising, but it speaks in favor of the importance of supporting fascination in terms of learning.

In this master’s thesis I examine transdisciplinarity in theory and practice. Transdisciplinarity is seen as an inevitable approach when we strive to understand and solve many of the complex problems of the modern world e.g. the environmental crisis. For this reason it has also quickly increased in popularity in the research funding. With this premise and despite the diverse theory on transdisciplinarity the implementation in practice is often relatively flimsy. This gap between theory and practice has acted as a motivation to the thesis, in which I am interested in how the transdisciplinary expectations based on the theoretical ideals and set on the cross-disciplinary environmental research intersect with the realistic transdisciplinary advancements in the research programs. In addition, I am interested to know why the practice doesn’t meet the expectations. The thesis is solidly theory-oriented. First I shed light on the background, characteristics and motivations of transdisciplinarity as well as disciplines, after which I present an array of the complex challenges of transdisciplinarity. In the results section I examine the manifestations of the challenges on a practical level that is based on three environmental research programs organized over the course of 2011–2014 by HENVI, the Helsinki University Centre for Environment (now HELSUS). In addition to the qualitative analysis based on the interview data, the results section also examines theory on a more practical level of implementing transdisciplinary research programs in general. This presentation thus enables a closer dialogue between the analysis data and practical theory. The primary results of this thesis are five problematics that are the manifestations of theory not meeting the practice properly. They are organized into the themes of funding, knowledge production, administration, socio-culture and education and help to organize and ultimately face the challenges of transdisciplinary research. From a comprehensive set of perspectives the problematics display strongly the highly disciplinary nature of the modern academia. This is the most significant single reason for the difficulties to accomplish transdisciplinarity. In addition, all the five problematics reflect the temporal restrictions that also undermine the potential of an effective transdisciplinary interaction. The essential measures to create solutions and hence also the ideal implementation of transdisciplinarity are mainly beyond the focus of the thesis. However, the problematics provide a problem-based framework that strives to contribute to the further studies focused more profoundly on the actual solutions

Energy consumption of apartment buildings account for a significant part of European Union’s total greenhouse gas emissions and improving the energy efficiency of buildings is a major part of reaching Union’s climate goals. To reach these goals the EU has revised some of its legislation and one of the latest reforms is the complete revision of Energy Efficiency of Buildings directive in 2018. Directives article 14 decreed that member states need to implement energy efficiency measures on large apartment buildings and to meet these measures member states were given three options on how to implement article 14. Finland implemented the article with so called voluntary advice method. The goal of this study is to understand the conclusion of the national implementation of article 14 and explain it with implementation theory. The study tries to understand what factors led to the implementation of voluntary advice method and whether this selection can be explained with implementation theory. Study design is one case explanatory case study. Seven semi-structured interviews were conducted for this research and the material was analysed with qualitative methods. All the interviewees were either officials in charge of the implementation or experts and researchers who took part in the implementation process. The study shows that the factors leading up to the selected implementation method were earlier experiences from other implementations, the straightforward nature of implementing advice method and the cost estimates between the given implementation options. It also became clear that the method was favoured by the officials, experts and target group and this volition might have affected the result. Study helps to understand the process of implementing EU legislation in a member state, what challenges officials face during the implementation and what kind of expectations steer the process. The study found out that previous implementation methods may have a significant impact on the implementation of revised directives. Study also verified the factors affecting implementation defined by implementation theories.

Trace element analysis is a useful tool for the study of migration and migratory connectivity in birds. Trace elements are present in the environment and, through the food chain, can be incorporated into tissues such as growing feathers. Since the concentrations of elements remain stable after the feather has stopped growing, and trace element abundances can vary at very small geographical scales, the concentration of trace elements in feathers can provide information on the location where a feather was moulted. Trace element analysis is still rarely used and there are important gaps in our understanding of how trace elements can vary at different organizational levels such as within a feather, between individuals or even between species. It is also not clear if large-scale geographical patterns can be detected by the method, as trace element concentrations can vary a lot even at small scales, which could make it impossible to see larger-scale patterns. To address that, my objectives were (1) analysing the variability of trace element concentrations within feathers, between individuals and between species and (2) determining whether trace element levels differed in feathers grown in Africa compared to feathers grown in Europe. This would shed insight on the suitability of trace element analysis for the study of migration and migratory connectivity. I analysed the concentration of 18 trace elements in the rachis of feathers from willow warblers (Phylloscopus trochilus) and barn swallows (Hirundo rustica) collected in Finland. I plucked three belly feathers from willow warblers collected in spring, whose feathers had grown in Africa. These feathers were used to analyse variability of trace element concentrations within feathers and between individuals. They were also compared to feathers plucked from barn swallows collected in spring (two feathers per bird) to analyse variability between the feathers of two species that winter in the same region. Finally, African-grown feathers of willow warblers were compared to European-grown feathers of willow warblers collected in autumn (two feathers per bird) to look for differences in trace element concentrations in feathers grown on two different continents. Trace element concentrations were analysed using Laser-Ablation Inductively-Coupled-Plasma Mass-Spectrometry (LA-ICP-MS), which allowed to measure concentration at hundreds to thousands of points along the feather rachis. The concentration of each of the 18 elements was used as the response variable in linear mixed models (LMM). To model variation in concentration within the feather I used location along the feather rachis as the explanatory variable and explored how well it predicted concentration of each element. To compare variation between feathers and individuals I fit models including and excluding the feather and individual that each measurement belonged to as random effects and compared them using AIC. To compare between willow warbler and barn swallow feathers grown in Africa I included species identity as the explanatory variable and looked at how the concentration of the 18 elements differed between them. Finally, I followed the same approach to compare willow warbler feathers moulted in Africa and in Europe. For most elements there was little variation along the feather rachis, with concentration remaining stable from feather base to tip. Zn and S showed an increase in concentration starting at the feather base until the central part of the feather and then remained constant toward the tip. Feathers belonging to the same individual showed mostly similar trace element concentrations, although there were exceptions and differences between feathers of different willow warbler individuals were also little. 10 out of 18 elements showed significant differences in feathers of willow warblers and barn swallows grown in Africa. Eight of those elements were more abundant in willow warbler feathers, while only two were more abundant in barn swallow feathers.12 out of 18 elements showed significant differences between their level in African-grown feathers and European-grown feathers. Of those, 10 elements showed higher levels in African-grown feathers, while only two were higher in European-grown feathers. My results suggest that trace elements can show variation at different organizational levels. Variability within feathers was important in at least two elements, which could be caused by physiological processes. This means that when designing sample collection for trace element analysis, unless we know that an element does not vary along a feather, it is important to consider which part of feathers we are sampling. Variability between feathers and individuals was lower than within feather variability, but still significant. Future studies should account for possible within and between individual differences in their design. Differences between barn swallows and willow warblers were large, which was expected based on the literature. It is still unknown what drives these differences between species: some explanations suggested have been physiological and dietary differences or differences in their habitats. I also found clear differences between feathers of willow warblers grown in Europe and Africa. While the exact cause is still not known, this means that at least in willow warbler feathers it is possible to study large scale geographical patterns by trace element analysis. LA-ICP-MS has potential to be a powerful tool to study migration and migratory connectivity in birds. It allows to detect variation in trace elements at continental scales while also allowing to control for different levels of variability in the study design. I encourage researchers to adopt its use in their research.

Baltic Sea has undergone major changes in the last few decades and its ecological condition has changed. Paleolimnology provides methods to detect changes in the past, mostly from the times when no surveillance was conducted. This Master's thesis is about the response of a common Cladocera, Eubosmina maritima to the past environmental change in Sandöfjärden, Gulf of Finland. I studied past isotopes, δ13C and δ15N to detect past changes in the eutrophic changes from sedimented subfossil remains to detect how the E. maritima population abundance and morphology have changed due to eutrophication and increased predation pressure. I analyzed a 30 cm sediment core of which I counted E. maritima remains. I also measured the lengths of carapaces, mucros and antennules in order to detect changes in their morphology. I used carbon nitrogen ratio, total carbon, total nitrogen, and their stable status of the sea area. To indicate predation pressure on E. maritima, I used the resting egg data of a predatory cladocera Cercopagis pengoi, that was introduced to the area at the beginning of the 1990's. The sediment core is stratigraphic, meaning that the layers are connected to each other and therefore cannot be treated as independent samples. The data was first viewed graphically to reveal correlations. I applied redundancy analysis (RDA) to find out if changes in the Eubosmina-populations are explained by the environmental changes. Associated is Monte Carlo permutation test to check which explanatory variables are the most important. Finally I performed variance partitioning to separate the effects of the environment caused by time in the sediment time series. My results show that E. maritima population has increased in number since the 1950's and a positive correlation with δ15N suggests that this has a connection to increased nutrient levels. It also seems that big E. maritima individuals became more common in eutrophic conditions. Increased predation pressure affected E. maritima populations the strongest right after C. pengoi was introduced to the area when also the longest mucros were found. There also was a slight decrease in the E. maritima abundance at that time. The changes of the lengths of the appendages seem to be more connected to predation pressure, whereas the abundance and the overall body size seem to have a connection with eutrophication. Along with the eutrophication increased the number of E. maritima in the Gulf of Finland. The effect of predation pressure was the clearest right after the introduction and then later smoothened.