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  • Janutenas, Simas (2022)
    Epileptic patients experience spontaneous recurrent seizures and interictal epileptiform discharges that lead to brain injuries, triggering neuroinflammation and waste product accumulation. Due to the detrimental effect of waste products on brain homeostasis, their removal from the central nervous system is (CNS) is crucial. Meningeal lymphatic vessels (mLVs) located in dura matter contribute to CNS clearance by the drainage of metabolites, waste products, and immune cells from subarachnoid space into cervical lymph nodes. Therefore, because of its role in brain homeostasis, the study of mLVs in different neurological conditions and diseases, including TLE, has gotten increased attention in the last decade. In this study, we sought to understand mLVs role in neuroinflammation and changes in rapid eye movement (REM) sleep stage during epilepsy. For this purpose, we induced mLVs ablation followed by kainic acid (KA) epilepsy model in mice. Shortly, animals were inoculated with AAV-VEGFR3-1-4 to induce mLVs ablation and subsequently challenged with KA to induce status epilepticus. Simultaneously, a control group of animals were injected with a sham AAV and later injection of KA. Afterward, spontaneous EEG activity was registered continuously, and data analysed to compare durations of REM sleep. Also, immunohistochemistry of brain samples was performed to investigate neuroinflammatory changes between experimental groups. Ex-vivo analyses of Iba1 and GFAP expression in brain tissue did not show statistically significant changes in neuroinflammation between experimental groups. However, we observed a trend towards lower expression of inflammatory markers in mLVs ablated animals. The analysis of REM sleep duration shows a progressive reduction of this sleep stage in both groups during the first recording period with a subsequent stabilization during the second one. Our data also indicate that mLVs ablated animals present prolonged REM sleep duration compared to the control group. Although this data contradicts our initial hypothesis it is consistent with the well-established negative correlation between neuroinflammation and REM sleep duration. Future studies should consider a deeper analysis of the glial cell profile for a better understanding of the effect of mLVs dysfunction on epileptic pathology. Moreover, the impact of mLVs ablation on REM sleep duration should be characterized in healthy animals.
  • Kauppi, Kati; Kauppi, Kati (2024)
    Brown trout is classified as vulnerable species in the Baltic Sea region and endangered in Finland, and wide conservation efforts have been conducted to restore the populations. Understanding the migration patterns of the species allows e.g. more accurate assessment of the population stock sizes and needed measures for conservation. Well-known life history strategy of brown trout (Salmo trutta) includes habitat shifts such as downstream marine feeding migration and upstream spawning migration. More recently, this simplified life history has been observed to be variable among populations and individuals. Environmental and biological factors, such as water discharge, temperature and fish size are known drivers for downstream migration. For this study, data derived from a field study conducted by Natural Resources Institute Finland was analyzed together with environmental data to understand the factors influencing the timing of the out-migration in an urban brook (Longinoja brook), in Helsinki, Finland. The PIT tagging method and automatic antennas were used to track the movements of the fish in the brook. Results indicated that the fish out-migration occurs in peaks. Individuals migrating in spring seemed to favor decreasing water flow and water temperatures between 6-9 °C, and their migration peak was specific to late April and early May. During the autumn and winter seasons, increase in water flow and a relatively cold (1-4 °C) water temperature created suitable conditions for the fish to start moving downstream. Fish migrating in the spring were smaller in size compared to those migrating during winter. The study results demonstrate how brown trout can adopt multiple and complex life history strategies even in the same population. Suitable environmental conditions for downstream migrations were diverse overall, but especially during winter. Motivation and reason for out-migration might differ between the seasons, and future research should focus on understanding the behavioral differences between the individuals within the populations better.
  • Silvennoinen, Minna (2022)
    Antimony (Sb) is an element that is used widely for industrial purposes, for example, as a hardening agent in lead (Pb) ammunition. In soil, antimony typically occurs as antimonous acid Sb(OH)3 in anaerobic conditions and as antimonate Sb(OH)6- in aerobic conditions. Antimony mobility is controlled by sorption to oxide surfaces in soil and low pH favors the adsorption. Antimony contamination in shooting range soil can pose a risk for human health and ecosystems. In shooting range soil, antimony co-occurs with lead that is typically found in cationic Pb2+ form. Different adsorption behaviour of cationic Pb2+ and anionic Sb(OH)6- renders remediation of contaminated shooting range soil challenging, since amendments designed for lead stabilization can increase solubility of antimony. The aim of this study was to reveal how apatite ore mine tailings-treatment of antimony-contaminated soil affects antimony solubility in soil and if it has potential for immobilizing antimony in shooting range soil. The hypothesis of the research was that mine tailings treatment decreases the mobility of antimony in soil due to reactions of between antimony and components of the mine tailings material. In laboratory, soil samples from O horizon, B horizon, and C horizon of a former shooting range area in Svärdfelt, Sipoo were incubated for 2.5 years with and without tailings. Tailings-induced changes in the distribution of antimony between various chemical pools in soil were investigated with a sequential extraction method. Soil pH, electrical conductivity, oxalate-extractable Al, Fe and Mn concentrations, and calcium Ca2+ concentrations, as well as tailings-induced changes in the distribution of phosphorus P between chemical pools, were also determined. Contrary to the hypothesis, the increase in pH and phosphorus concentration induced by the tailings treatment can decrease the adsorption of antimony to oxide surfaces and, thus, increase its solubility. Results of the study indicate that the mine tailings treatment decreases total extractability of antimony possibly through formation of poorly soluble calcium antimonates. No significant increase in potentially bioavailable (soluble and labile) antimony fractions was observed, either. These results indicate that mine tailings material has the potential to act as an amendment in in situ remediation of shooting range soil.
  • Lassila, Marika Jenna Janina (2022)
    Colorectal cancer (CRC), which refers to the cancer of the colon and the rectum currently ranks as the second leading cause of cancer related death worldwide and as the third most common form of cancer in both males and females. The latest reports show that approximately 10% of all new cancer cases globally are diagnosed as CRC annually. Initiation of sporadic CRC is commonly caused by somatic mutations causing the loss of function of the tumor suppressor gene APC. This leads to aberrant activation of the canonical Wnt signalling pathway. The ApcMin/+ mice model the progression of CRC as they carry a constitutive heterozygous nonsense mutation in Apc allele and develop intestinal adenomas. TCF/LEF transcription factor family members are best known as the main downstream effectors of canonical Wnt signalling. In the presence of nuclear β-catenin, TCF/LEF proteins bind to it through their β-catenin-binding domain and activate the transcription of Wnt target genes. The TCF7 gene encodes several isoforms of TCF1 protein, which are traditionally divided into long and short isoforms, transcribed from different promoters. Previously, it has been shown that Tcf7 deletion (Tcf7-/-) in ApcMin/+ mice increases the formation of adenomas. The aim of my study is to better understand the role of Tcf7 and its isoforms in CRC tumorigenesis. To study the Tcf7 deletion in intestinal adenoma development, ApcMin/+; Tcf7mut/mut; Villin CreERT2 mouse strain was established. The expression of the full-length isoforms (p45) is constitutively prevented in the Tcf7mut/mut mice. Moreover, tamoxifen administration to these mice led to the deletion of all isoforms in the intestinal epithelium. The number of intestinal tumors, their sizes and the survival of the Tcf7 deleted ApcMin/+ mice were analyzed and compared to ApcMin/+ mice. Intestinal tissues of the mice were collected after euthanasia. The tissue samples were preserved in paraffin, and later cut into sections for IHC, stained and imaged. The deletion of Tcf7 was confirmed at the RNA level by qPCR, and at the protein level by immunohistochemistry (IHC). IHC and single-cell RNA sequencing was used to further analyze the effect of Tcf7 deletion in mouse intestinal adenomas. The deletion of all Tcf7 isoforms or only the p45 isoforms in ApcMin/+ mice increased robustly the numbers of intestinal tumors. IHC analysis of the intestinal adenomas showed that the deletion of p45 isoforms was sufficient to cause a dramatic decrease in total Tcf1 expression in the adenoma cells. These results were supported by the qPCR results. In summary, our results lead us to believe that the deletion of p45 isoforms causes an acceleration of tumorigenesis in the adenoma model. Without the Apc mutation, the mice did not develop intestinal adenomas. Interestingly, the expression of the Wnt-target gene Prox1 in intestinal adenomas was decreased when Tcf7 was deleted. We next aim to optimize our protocol for single cell dissociation of adenomas and re-run the single-cell RNA sequencing analysis for further analysis of the mechanisms behind the increased tumorigenesis.
  • Collins, Steven G. (2016)
    Cities of the 21st century consume massive amounts of energy, and indoor climate control within the built environment is responsible for a large fraction of the total demand. With pressures to make buildings more environmentally friendly, new energy efficient technologies and designs are continually sought after. A green roof, or a living roof, is a structural design approach that can provide a variety of ecosystem services along with the reduction of building energy demands. It has been shown that green roofs are effective tools for reducing cooling energy demands in warm and sunny climates; however, in cold climates, where heat energy demands dominate, there is a lack of research and general uncertainty about how beneficial a green roof may be. This thesis, conducted during the winter of 2013-2014, focused on the thermal performance of green roofs in cold weather (winter) conditions. The aim of the study was to quantify the reduction in energy loss that a green roof achieves and to examine the thermal behaviour of each of the green roof layers. Extensive green roofs with hot boxes underneath were constructed in Lahti (southern Finland). Heat sensors were placed vertically through the bare and green roofs to measure linear heat transfer from the interior to the exterior. Heat transfer by conduction was assessed, and a steady state analysis was used to quantify heat flux values. Furthermore, a green roof thermal conductivity model was developed to estimate the thermal conductivity of each of the layers under various environmental conditions (changing moisture contents, frost depths, and during freezing and thawing periods). Monthly comparisons of the energy lost through the two roofing structures were quantified. My results showed that green roofs reduced the amount of energy loss through the surface compared to bare roofs throughout the winter season. The overall reduction in energy loss, due to the presence of green roofs, was on average, 32.6%. Layer analysis showed that thermal conductivity of each of the layers decreased when penetrated by frost. A frost depth that extended through the whole green roof yielded the highest thermal resistance for the green roof at 3.96 m2KW-1. Comparatively, the bare roof had a thermal resistance of 0.27 m2KW-1. During times of snow coverage, the snow acted as a good thermal insulator, reducing the relative benefits achieved from green roofs. During refreezing and thawing, the green roof experienced the lowest values of thermal resistance at 1.83 m2KW-1. These results can be used for quantifying possible heat loss reductions in similar climates using a similar green roof, and the layer analysis provides information of how to best design green roof components for thermal resistance.
  • Kotilainen, Aino Kaarina (2023)
    Climate change poses an ever-increasing threat on biodiversity as the global mean temperature rises causing changes in weather patterns. Species will have to adapt to the circumstances or follow their climatic niches across space to avoid decline and extinction. Many species are already threatened by extinction due to climate change. Understanding how species are reacting to rising temperatures can help us preserve biodiversity. Genetic adaptation is a long process and takes several generations to occur. A more immediate means to cope with variation is adjusting through phenotypic plasticity, which can help species cope with environmental changes in the short-term. Plasticity can help individuals maintain fitness in different environments and with fluctuating environmental conditions. Flowering phenology is a plastic trait which can have a large impact on reproductive success. Flowering is an important part of a plant’s life cycle as it can produce offspring with new combinations of genes. In this thesis I examine how temperature affects the flowering phenology of Hypericum species and how this thermal plasticity affects fitness. Populations of Hypericum perforatum, H. maculatum and H. montanum from different parts of their distribution across Europe were studied in greenhouse experiments. The plants were grown in four different temperature treatments (16/6°C, 20/10°C, 24/14°C, 28/20°C) and the timing of first flowering was monitored. Seed mass and flower count were recorded and used as measures of fitness. In general, the plants flowered later in the colder temperature treatments. The results differed between species: in H. maculatum the leading-edge populations were less plastic while in H. perforatum differences between areas were negligible. More plastic accessions produced more flowers due to earlier flowering. There was no effect on seed mass. The possible effects of plasticity on overall fitness highlight the need for detailed information on plasticity for predicting species response to climate change.
  • Nygård, Elisa (2020)
    Global surface temperature is increasing at an alarming rate. Local populations can cope with the change, if they have adaptive potential to face the new thermal regime. Hybridization with a closely related lineage is one potential source of adaptive genetic variability. My thesis aimed to investigate thermal adaptation by looking into thermal tolerance differences between two mound-building wood ants Formica polyctena and Formica aquilonia and their hybrids. The two parental species have distinct distributions: F. aquilonia can be found in Northern Europe while F. polyctena is distributed from Central Europe to Fennoscandia. The samples for this thesis were collected from a relatively small area in southern Finland and Åland Islands. Aim of my thesis was to clarify whether the two parental species have distinct thermal tolerances, which would reflect the differences in their distributions. I also tested whether hybrid individuals have wider thermal limits since they have alleles from both northern and southern parental species and could therefore show adaptive potential. I tested thermal tolerance differences with two temperature assays: heat-knockdown resistance and chill-coma recovery. I hypothesized that F. aquilonia would express more cold-tolerant thermal limits whereas F. polyctena would express more heat-tolerant limits. My results showed that the parental species differed in their thermal tolerance and expressed thermal limits which reflected their distribution. These results support the thermal adaptation hypothesis: parental species expressed thermal limits that reflected the thermal environment in their native habitat. The results also showed that hybrids could not combine the thermal tolerance of both parental species as they did not have wider thermal tolerance than parental species. Intriguingly, dry weight had a significant role in thermal tolerance, bigger ants coping better with higher temperatures. These results contribute to building up knowledge on the outcomes of hybridization and the potential that species possess in coping with the environmental change. Wood ants are keystone species in boreal forests and the findings of my thesis shed a light on the changes in population dynamics for these species in the face of global climate change.
  • Burg, Skylar (2021)
    In this study, a greenhouse experiment was used to assess if temperature sensitivity, specifically, thermoregulatory plasticity, has a functional role in floral reflectance and pigmentation in a population of P. lanceolata grown in three different temperature treatments, reflecting past, present, and future summer temperatures. Spectrophotometry, surface temperature readings, and near-infrared (NIR) region image analysis were used to identify how the spectral absorbance properties and biochemical makeup of P. lanceolata flowers differed between treatments. Reflectance and phenolic absorbance were both found to be influenced by ambient temperature. However, surface temperature of flower spikes was not affected by growing temperature, reflectance, or phenolic absorbance. The results suggest that Plantago lanceolata may utilize thermoregulatory plasticity in reflectance and phenolic absorbance to adjust to rising temperatures. These findings have important implications in species reactions to climate change and denotes that increased selection on thermal function traits may occur under a future climate scenario of continued warming in temperate and boreal biomes.
  • Bottega, Paolo (2024)
    Vaccines have proven to be one of the most effective methods of mitigating the effects of infectious diseases. One of the most prominent hurdles facing widespread vaccine delivery is the cost and added time attributed to cold chain logistics. That is that vaccines need to be kept constantly below a certain temperature to retain their effectiveness, which in many cases is as low as -80°C. Application of specific biopolymers is one method of enhancing vaccine thermostability, diminishing the need for such cold chains by preservation at lower temperatures. This enhanced vaccine formulation is achieved through a technique known as microencapsulation, in which an active agent, in this case the vaccine, is protected through storage in a thin film of polymeric material. This preserves vaccine efficacy until later use and release from the protective film upon vaccine delivery. In the following study, a naturally derived biopolymer was investigated for its cryopreserving properties with the aim of exceeding the current benchmark of preservation at ambient temperature for 72 hours. This involved evaluation of the formulation, referred to as our designed technology (DT) across different stress parameters (4°C, 22°C and 37°C) for differing periods of time, applicability to different vaccine systems (adenovirus, envelope virus and mRNA based) and finally efficacy in both in vitro and in vivo settings. The results demonstrate that adenovirus based vaccines are able to withstand the physical, pH and temperature alterations of diverse stress tests when protected by biopolymer microencapsulation both in vitro and in vivo. This suggests that microencapsulation with the naturally derived biopolymer is a strong method of preserving adenovirus vaccine stability at temperatures up to 37°C for up to three weeks. As such, naturally derived biopolymer microencapsulation stands to drastically reduce the cost of vaccines by mitigating the need for cold chain logistics through preservation at temperatures up to 37°C.
  • Ojala, Reetta (2023)
    Beta frequency (15-25 Hz) oscillations in the extracellular field potential recorded by cortical EEG and depth electrodes have been connected to stopping. Especially short increases in beta power, so called beta bursts, occur more frequently close to stopping an ongoing movement or when cancelling a planned action. However, there are discrepancies about the causal role of these beta bursts on stopping. Although some studies indicate causality, in others the bursts occur too late for being causal or their number does not increase prior to stopping. One explanation to the disagreement may lie in the behavioral task commonly used to study the neural correlates of action inhibition, the stop signal task. In this task the movement is cancelled before it starts, and actual stopping is thus hidden from the experimenter. Instead, an estimated stop signal reaction time is mathematically modelled. It is likely that this reaction time varies trial by trial, which causes inaccuracy in the results. We were able to define an exact stopping time using head fixed rats running on a treadmill. This enabled us to align brain activity precisely with stopping. With this task, we showed that the number of transient beta bursts increases just prior to stopping. Moreover, the increase correlates with the velocity. These results indicate that beta bursts are causal to stopping. Beta bursts have been noted to be disturbed in Parkinson’s disease and our results may open new doors for early diagnoses or treatments.
  • Ahdekivi, Ellen (2022)
    Peatlands are ecosystems of global importance for biodiversity conservation. Peatlands are wetland ecosystems which provide a critical habitat for many rare and specialized species. Biodiversity maintains the provision of ecosystem services, which are the benefits people obtain from ecosystems. The loss of biodiversity and peatland degradation constitute global challenges. One of the main reasons why biodiversity loss and peatland degradation remain challenges is nested in the failure to account for the range of economic benefits of ecosystem services and biodiversity in relevant policy making. The role of peatlands in maintaining global biodiversity has often been underestimated in global, regional and local land use planning and conservation measures. This thesis undertakes a systematic literature review on the empirical economic valuation literature on peatland ecosystem services and biodiversity. The two main aims of this literature review are to synthesize the current state of knowledge on this phenomenon and analyse the role of biodiversity in the economic valuation of peatland ecosystem services by answering specific research questions. This systematic literature review employs the data of 23 peer-reviewed English language papers published between 2006 and June 2021. The studies were chosen for analysis based on a selected search strategy and screening process. The data analysis was undertaken using the qualitative data analysis software Atlas.ti which is a tool used to help organize analysed material with the help of descriptive codes. Based on the findings of this thesis, the inclusion of biodiversity in the economic valuation of peatland ecosystem services has become a standard procedure. This is showcased by the number of studies applying stated preference approaches. The sample included studies applying different valuation methods in order to value many ecosystem services. The studies including biodiversity in economic valuation often find that biodiversity conservation policies can be cost-effective, and that people are generally willing to pay for biodiversity conservation and would derive economic benefits from this. Biodiversity is included in the studies as different elements, mainly as a specific species or as a reference to wildlife. Biodiversity is also found to be closely related to cultural ecosystem services and their benefits. Many studies find that people value familiar peatland landscapes, and biodiversity plays an important part in defining that value. Some studies find that human activity plays an important role in maintaining biodiversity in semi-natural peatland landscapes. Hence, biodiversity conservation needs to be in some accordance with local interests. Biodiversity provided founding principles for policy making, but previously implemented practices, such as existing conservation measures and the extractive use of peatlands exerted much influence on final economic values. Moreover, biodiversity plays different roles in determining the objectives of the studies. Eight studies use biodiversity as the justification for conducting the economic analysis. Most studies include biodiversity as a study component among others under valuation. The portrayal of biodiversity influences the focus of the studies and how biodiversity contributes to the findings of the literature. The body of literature on the economic valuation of peatland ecosystem services remains small. The geographical distribution of the sample is skewed towards Europe and Southeast Asia. There is a notable upward trend in the number of studies which have been published in the last five years. The literature demonstrates that the economic valuation of peatland ecosystem services and the need to adopt sustainable peatland management with biodiversity conservation have become relevant and topical issues in policy making. There is a significant need to address the issue of peatland degradation and biodiversity loss by increasing awareness. Further research is needed to establish a more comprehensive understanding of the links between peatlands, ecosystem services and their values. In addition, future research could study how the provision of information and the contribution of biodiversity awareness and knowledge influence economic valuation.
  • Puustinen, Taru (2024)
    Colorectal cancer (CRC) poses a considerable global health challenge, with high mortality rates despite advancements in cancer research. Approximately one in ten CRC cases have a hereditary basis, with Lynch syndrome and Familial adenomatous polyposis standing as the two predominant cancer-predisposing syndromes. These conditions are mainly attributed to specific dominant germline mutations in CRC-related genes. However, as the role of epigenetic modifications, including DNA methylation, has become increasingly recognized in colorectal tumorigenesis, identifying these distinct signatures is paramount in gaining deeper insights into the molecular mechanisms underlying CRC. This thesis, conducted as a part of ongoing research into the DNA methylation profile of Lynch syndrome and Familial adenomatous polyposis-associated colorectal tumors, aimed to validate methylation patterns previously obtained from a genome-wide Illumina Methylation EPIC BeadChip array. The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on differential methylation observed with EPIC and literature and were limited to regions that included at least one GCGC site for the HhaI digestion enzyme for future in-house MS-MLPA probe design. The results of this study demonstrate a clear differential methylation pattern of the selected genes, with CRC cell lines generally exhibiting higher methylation levels compared to non-cancerous samples, as expected. Specifically, high concordance between EPIC results and bisulfite sequencing data was observed in the methylation status of ADHFE1, EYA4, ITGA4, FBLIM1, and SEPT9, whose connection to CRC has been also shown in the previous studies. Further investigations of the genes in this study could contribute to a better understanding of epigenetic changes underlying colorectal tumors and hold the potential for developing novel biomarkers for early diagnosis and improved patient prognosis.
  • Rahaman, Atikur (2018)
    Some flavonoids are thought to have antioxidant functions in plants, but this is still controversial because of a lack of in planta evidence. Methyl viologen (MV) sensitivity was assayed in sterile culture by growing seven day old Arabidopsis seedlings on 0.5x MS media supplemented with and without MV. Seedlings grew for 9 days after that, and then were photographed and root growth measured. We used several flavonoid deficient Arabidopsis transparent testa (tt) mutants and found they were hypersensitive to MV that produces reactive oxygen species (ROS) in chloroplasts and mitochondria. Flavonoids are transported into different compartments of the cell via a specific flavonoid transport system but no chloroplastic or mitochondrial transporters are currently known. To identify potential chloroplastic and mitochondrial transporters, knockout mutants of candidate MATE and ABC transporters have been screened for MV sensitivity. Flavonoids modulate auxin transport, which raises the possibility of passive effects through auxin during ROS sensitivity. To test whether auxin or the inhibitions of auxin transport have a role in protecting against ROS stress, MV sensitivity was assayed under exogenous treatment of artificial auxin (NAA) and an auxin transport inhibitor (NPA) during MV stress. From this study, we obtained data about the role of flavonoids and auxin in ROS signalling. The inhibition of auxin transport modulated MV sensitivity. We found that NAA had no effect or very modest effect. However, a protective effect of NPA was observed that helps against ROS formation, mimicking the effect of flavonoids. NPA induced more protection. One MATE transporter also gave the mimic of (tt) phenotype, however their role in the movement of flavonoids into or out of the chloroplast or mitochondria remains unclear, as they may be transporting some other protective agent that helps against oxidative stress. However, At1g54350 is a candidate for further testing.
  • Nieminen, Jenni (2019)
    Cities are responsible for many of the current environmental changes in the world. Even though the need for urban sustainability transitions is apparent, city governments have been, so far, uncapable of governing the change. In this thesis, the possible urban transition and its multi-level governance is examined through the case example of Eko-Viikki neighbourhood and the urban planning changes around it. The framework of multi-level perspective on socio-technical transitions (MLP) is used for the analysis. This theory on transitions is widely used, while criticized for its inadequate conceptualization of the regime (the dominant system) and its spatial application, especially in cities. Traditionally, the framework has not been used to study transitions in cities, due to which, there is a lack of case examples of urban sustainability transitions and their governance. This thesis addresses the deficiency in question and aims to find out which types of policy instruments could be essential in bringing about urban sustainability transitions and whether the dominant regime, in this case the urban planning of Helsinki, can actively influence the steering of the transition. The materials of this thesis consist of two different sources. The document analysis was used to gather the materials for the policy instrument analysis. In addition, six semi-structured expert interviews were conducted to provide supporting material for it, as well as to examine the change of the urban planning context in Finland. The materials were analysed by qualitative content analysis using the MLP framework and a commonly used environmental policy instrument classification as a frame. The results indicate that regime actors can have endogenous power to somewhat steer the urban sustainability transitions. The regime actors of urban planning of Helsinki were active in the Eko-Viikki project, and sustainability issues have become more integrated part of the everyday urban planning in Helsinki. As for the niche level of Eko-Viikki, regulation and collaboration related policy instruments were the most successful in advancing the sustainability issues. In fact, the site transfer conditions containing sustainability demands as well as the area working group method have been scaled up to the use of the regime. The city of Helsinki has, moreover, committed in advancing sustainable city development through international agreements and its own city strategies. As regards the landscape level, the land use and construction legislation changes have remarkably tightened the requirements for sustainability of urban planning, especially for the energy efficiency. On the contrary, the lack of certain types of instruments seem to remarkably hinder the urban sustainability transitions. According to the results, information related instruments need to be developed to make the most of the technical solutions available and, ultimately, to make urban planning more like continuous learning processes rather than individual projects. Also, the issue of short-term profit seeking should be addressed by economic instruments that involve long-term investments and set sustainability issues as a first priority. All in all, it can be concluded, that much has done for promoting sustainability in urban planning of Helsinki even though a profound urban sustainability transition cannot be said to have happened. Particularly, systemic and process focused policy instruments are needed to take into account the multiple different stakeholders involved, and the governance levels where urban sustainability transitions take place. The urban sustainability transitions can be enabled only together with other governmental bodies of the city, state, construction companies, maintenance companies and, ultimately, residents.
  • Chalas, Petros (2020)
    Histamine and hypocretin/orexin are neuromodulators important for regulation of alertness and wakefulness. These systems project to major areas of the brain, are highly conserved among vertebrates and they significantly innervate each other. Different studies have indicated an interaction between the histaminergic and orexin systems, however the role of histamine in this interaction is still not well-established. The goal of this study was to examine possible changes in orexin neurons development and larvae behaviour, after genetic loss of histamine decarboxylase (hdc), the histamine-synthesizing enzyme. Using whole-mount in-situ hybridization and immunofluorescence staining we observed a significant reduction in the expression of the hcrt mRNA and the orexin A peptide in 6 dpf hdcKO zebrafish larvae. However, KO of hdc had no effect on startle response, dark flash response and sleeping behaviour of 6 dpf larvae. To further investigate the regulatory role of the histaminergic system, we employed treatment of hdcWT and KO larvae with ciproxifan, a histamine H3 receptor inverse agonist. Ciproxifan treatment increased darkness habituation in 7 dpf hdcWT and KO larvae but reduced the intensity of the dark flash response only on hdcWT larvae. Furthermore, ciproxifan treatment differentially affected the expression of the orexin A peptide in 7 dpf hdcWT and KO larvae but had no effect on the expression levels of the hcrt mRNA. Collectively, these findings suggest the significance of histaminergic signaling for normal development of orexin neurons and the implication of histamine in the execution of the dark flash response. Lastly, this study indicates the complex role of the histamine H3 receptor and the requirement of further studies for better characterization of its function.
  • Pulkkinen, Lauri (2018)
    Host factors play crucial roles in virus infections. Viruses exploit various cellular processes and are counteracted by an arsenal of host antiviral defenses. Characterization of these interactions is crucial for understanding the viral life cycle and developing novel antiviral treatments. Semliki Forest virus (SFV) is a positive-strand RNA alphavirus that has been used as a model virus for multiple clinically significant diseases such as lethal encephalitis. The aim of this thesis was to identify host factors that affect SFV infection to better understand the biology of SFV, and to provide candidate targets for therapies against more serious alphavirus infections. Here I have conducted follow up studies on a previously performed genome-wide siRNA screen that hinted that a number of genes have novel functions in SFV infection. I used an automated high-throughput imaging-based approach to confirm the roles of these host factors in SFV infection. For comparison, I also used a similar strategy to test if these genes affect negative-strand RNA virus infections, using vesicular stomatitis virus (VSV). Additionally, I studied whether the host factors affecting SFV infections perform their roles in the entry and penetration, or post-penetration steps using a previously developed endocytic bypass assay. I identified the γ-aminobutyric acid (GABA) transporter, SLC6A13, as a potential receptor for SFV. I also describe other novel genes that have roles in SFV or VSV infections. In addition, I show that TNP01, RPL18, ETF1, DMN2, and GNDPA1 promote, and HDAC6 counteracts SFV infection in the entry and membrane penetration steps. Furthermore, I report that in the later stages of the infection DDX54 boosts and EIF2B3, EIF4G1, PHB2, EDF1, DDX47, and DHX57 hinder SFV.
  • Loukasmäki, Säde (2022)
    Sensory systems display a topographical organization, and in the murine somatosensory system there is oneto-one correspondence between individual whiskers and individual cortical columns called barrels. Functional connectivity in the whisker-to-barrel system is formed prenatally and refined after birth, guided by both spontaneous and whisker-evoked activity. GABAergic connectivity emerges already prenatally and includes transient circuits, but the exact role of GABAergic signalling in early development is elusive. The neuronal, major chloride extruder, potassium-chloride cotransporter (KCC2) is heavily upregulated in the cortex during the first two postnatal weeks resulting in the emergence of hyperpolarizing inhibition. However, in cortical interneurons (INs) KCC2 expression can be detected already at the time of birth. The role of this early interneuronal KCC2 expression is unclear. The aim of this thesis was to study the role of KCC2 in the network activity of cortical INs during the perinatal period. Transgenic mice with conditional inactivation of Kcc2 gene, and expression of the calcium indicator GCaMP6f in GAD2+ neurons (INs) were used to image cortical Ca2+ activity. Transcranial widefield Ca2+ imaging in awake head-fixed mice was performed at the day of birth (P0) and showed that spontaneous, but not evoked, activity was significantly reduced in the knock-out animals. Moreover, immunostaining for the activity-induced transcription factor Egr1 showed that thalamic network activity was significantly decreased in the knock-out and heterozygous animals, suggesting involvement of subcortical areas in the decreased cortical activity. Additional experiments are needed to elucidate the role of other mechanisms contributing to the observed change in activity.
  • Stoka, Enija (2022)
    Abstract Faculty: Faculty of Biological and Environmental Sciences Degree programme: Master’s programme in Neuroscience Study track: Neuroscience Author: Enija Stoka Title: The Role of Meningeal Lymphatic Vessels in the CNS clearance Level: Master’s thesis Month and year: April 2022 Number of pages: 28 Keywords: meningeal lymphatic vessels (mLVs), brain clearance, glymphatic system, perivascular spaces Supervisor or supervisors: Anaϊs Virenque, Francesco Mattia Noe Where deposited: the Helsinki University Library Additional information: - Abstract: The lymphatic system is a drainage pathway for metabolic waste products, soluble proteins and cerebro-spinal (CSF) as well as interstitial (ISF) fluids. Classically, the lymphatic system has been described all over the body, except the central nervous system (CNS) and the retina. This fact created the question of how the brain is being cleared from harmful solutes. The first system described to being responsible for the clearance of the brain was the glymphatic system, and only recently the existence of lymphatic vessels in the meninges (the meningeal lymphatic vessels, mLVs), has been recognized. However, it is still unknown how these two systems interact in removing solutes from the brain. Here, we analyse if the absence of mLVs affects diffusion and clearance of two tracers with low and high molecular weight (3 kDa and 70 kDa), which have been injected intraparenchymally in wild type (WT) and transgenic (TG) mice lacking functional mLVs. Diffusion of 3 kDa dextran tracer in the surrounding tissue was noticeably increased in WT compared to TG mice, associated with an overall decreased accumulation of the tracer in the parenchyma of the mice lacking mLVs. At the same time, we did not observe a genotype difference in the diffusion or clearance of the 70 kDa dextran tracer. Overall, these results indicate that mLVs dysfunction affects the intraparenchymal diffusion and clearance of low molecular weight molecules.
  • Lyu, Munan (2019)
    With the aggravation of global environmental problems and the reduction of finite reserved fossil fuels, seeking for alternative energy sources has become one of the priorities for the sustainable development of human society. Vascular plants save the biomass mainly as the form of xylem (also called as wood), which is now considered as an ideal environmental-friendly energy resource. Wood is now being used as renewable biofuels, Biomass composites to replace plastic and so on. The lateral meristem vascular cambium gives rise to xylem and phloem, contributes to the radial growth of plants. Dr. Mähönen’s group choose Arabidopsis root as a model to understand the growth dynamics of vascular cambium. Auxin is essential for various plant developmental processes. The transcription factor family AUXIN RESPONSE FACTOR (ARF) is an important component in auxin signaling pathway, among which AUXIN RESPONSE FACTOR5 (ARF5)/MONOPTEROS (MP) has been discovered to be essential in various plant developmental processes. The first part of my thesis work mainly focuses on analyzing the expression of ARFs during Arabidopsis root secondary development by using both histological reporter GUS and green fluorescent protein GFP. The second part is screening the secondary growth phenotype among the arf knock out mutants. As mp mutant fails to form primary root, artificial microRNA technique is applied to inhibit MP expression in transcriptional level, this construct was established in an XVE inducible system and driven by a broadly expressed promoter to specifically inhibit MP expression at the secondary development stage. I overexpressed amiMP in both wild type background and arf7,19 double mutant background. These three ARFs have strong expressions in cambium and they might function redundantly to regulate cambium activity. Our preliminary results suggest that ARFs function redundantly in regulating root secondary growth, ARF1 and ARF2 together are functional in regulating vascular pattern formation, and ARF16 can repress the root secondary growth and secondary xylem formation. MP is proved to regulate cambium activity and secondary xylem formation by controlling various auxin-response genes, ARF7 and ARF19 might also participate in this process.
  • Boiko, Elizaveta (2023)
    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.