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  • Korpikoski, Jaan (2024)
    Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive degeneration of upper and lower motoneurons (MN) within the central nervous system (CNS), leading to muscle atrophy and eventual paralysis. Cause of death is in most cases due to respiratory failures 3-5 years after diagnosis. ALS can occur idiopathically without any know causes or it can be associated with certain genetic mutations. One of these known factors is a point mutation in the superoxide dismutase 1 (SOD1) gene, particularly the G93A mutation is known to affect the functionality of SOD1. SOD1 is an enzyme that metabolizes reactive oxygen species (ROS) and the SOD1-G93A mutation limits this functionality and propagates endoplasmic reticulum (ER) stress signalling cascades. Mutated SOD1 cannot be broken down by the cell, and hence it is associated with activation of protein degradation (ERAD) system with a prolonged ER stress signalling, followed by apoptotic cellular response. Although SOD1-G93A mutation has been widely studied, the basic mechanisms of the disease are not fully understood. Mesencephalic astrocyte derived neurotrophic factor (MANF) is an evolutionary conserved protein with trophic properties. MANF has been researched as novel treatment in a range of neurodegenerative diseases, such a Parkinson’s. MANF has been shown to promote cell survival but has limitation as an administered drug treatment. In this study we used transgenic SOD1-G93A mouse model with male mice to study the effects of a novel MANF variant for ALS. Disease progression and histology were used to assess the treatment efficacy.
  • Korkiakoski, Satu (2024)
    The RNA splicing process is an important part of gene expression in which the introns are removed from the pre-mRNA so that the mature mRNA only contains protein coding exons. The splicing process is executed by the spliceosome in two subsequent transesterification reactions that occur partly co-transcriptionally. In the first step an intron lariat is formed between the exons. This is followed by splicing of the intron lariat and ligating the exons together. Genetic variants that affect the splicing of a particular gene are called splicing variants and they may disrupt the normal splicing process. Splicing variants can be both exonic or intronic and have effects on splice site recognition, activate cryptic splice sites or create new splice sites. These changes can lead to for example exon skipping or intron retention in the transcript. Diagnosing splicing variants is challenging because of the unknown functional effects of the variants. Splicing prediction tools can help predict the possible effects of variants. Different sequencing methods enable the detection of aberrant splicing transcripts and thus may help in variant interpretation. The aim of this master’s thesis was to develop a detection method suitable for the diagnostic laboratory for RNA splicing variants in congenital disorders. The methods that were tested included RNA and Sanger sequencing. First, the patient selection was performed using splicing predictions and previous research on the variants. Secondly, after receiving patient samples, RNA was extracted, and its integrity measured. The laboratory work was then divided into two parts, the other leading to the RNA sequencing and the other to Sanger sequencing. Before Sanger sequencing primer design, RT-PCR, PCR and analysis of the PCR fragment sizes was performed. RNA sequencing was preceded by RNA library preparation. The studied variants in this thesis were BRCA2 c.476-3C>A, MSH2 c.2005+3A>T and CYLD c.2350+5G>A. The PCR fragment analysis and Sanger sequencing was able to detect an aberrant splicing transcript with exon skipping on two patients caused by a variant in the CYLD gene. The RNA sequencing results confirmed the aberrant splicing transcript. In addition, fragment analysis showed evidence of a possible splicing isoform with skipping of two exons caused by a variant in the BRCA2 gene that was not expressed enough to show on the Sanger sequencing results. The RNA sequencing detected a splicing transcript with exon skipping in two BRCA2 patients. However, this was not the same transcript as interpreted from the fragment analysis results and no results in the RNA sequencing indicated a transcript with skipping of two exons.
  • Deb, Aruna Rani (2024)
    Since mercury (Hg) may biomagnify in food webs and bioaccumulate in living things, it is considered a dangerous element globally. The two most toxic forms of mercury are methyl mercury (MgHg) and dimethyl mercury (DMgHg). The dietary Hg consumed by fish is mostly removed through the intestine, but some of the MeHg bioaccumulates and is delivered to various organs, such as the liver, kidney, muscle, or gonad. The perch (Perca fluviatilis), the national fish of Finland serves as both a popular food fish and a monitoring species for assessing the chemical health of lakes. Fish tissue exhibits seasonal variations in mercury levels, which are thought to be produced by growth dilution in the summer, which is related to rapid somatic growth during the growing season, and hunger in the winter, which condenses mercury in the muscle as well as during spawning since gonad development requires significant energy expenditure. There has been a considerable study on Hg concentration in fish but currently lack knowledge regarding potential seasonal variation in patterns of Hg content and bioaccumulation to understand the dynamics of Hg content and bioaccumulation. This study investigates (Q1): Does mercury content change in muscle, liver and gonad tissues of males and females of perch over the four seasons? (Q2): How does mercury bioaccumulation change seasonally in different organs between male and female perch? (Q3): How does the mercury content relationship among different organs (muscle, liver, and gonads) vary seasonally and between sexes? Materials were collected monthly from Lake Pääjärvi from April 2020 to March 2021, and categorized into four seasons: winter (January -March), spring (April-Jun), summer (July-September), and autumn (October-December). Each fish was taken of its length, weight, sex, and other tissues too. Total mercury (Hg) concentrations were determined in three organs (muscle, liver and gonad) in male and female perch separately. Using analysis of variance, the annual length-corrected THg content variation and simple linear regression analysis were used to examine the annual THg bioaccumulation variation and to test the relationships in Hg concentrations among three tissues separately in males and females. Seasonal THg levels in female perch significantly varied in muscle and gonads, not in the liver. Females had consistently higher THg in muscle and liver, while males had higher levels in gonads throughout the season. THg bioaccumulation peaked in spring and winter for both sexes in muscle, but lowest in autumn. Liver THg slope was highest in early summer for females and lowest in autumn. Gonads showed the highest slopes in summer for both sexes. The highest slopes between muscle and liver THg for females were in summer and for males in spring. Similar patterns were seen in both muscle-gonad and liver-gonad THg relationships. Female perch showed significant differences only in summer, while in males, the highest slopes were in autumn and lowest in summer. Long-term monitoring is crucial to understanding THg variation in fish.
  • Lappalainen-Imbert, Helmi (2024)
    This master's thesis examines environmental and climate racism in the Arctic regions. The work focuses particularly on the disproportionate effects of climate change on Indigenous peoples, as well as Indigenous peoples' opportunities to influence decision-making processes. In order to understand the phenomena, it is essential to recognize the effects of climate change on Indigenous peoples and their culture and traditions. In this thesis, the situation of the Sámi people in Finland will be explored in particular. The thesis also discusses the possibilities of indigenous peoples' participation and representation in decision-making processes, as well as the challenges and successes observed in these processes. In this context, the role of the Finnish state is analyzed in particular, emphasizing the need to increase genuine representation and expertise. The work also examines the efforts of indigenous peoples to influence politics, the responses of communities and the effects of international cooperation on adaptation strategies. My research questions are: 1) Does environmental racism exist and in what forms, and how does it impact Sámi communities within the decision-making processes and politics in Finland? 2) What policies and practices have perpetuated inequalities and environmental racism in Finland, and how can Sámi voices be included? 3) What has been the Indigenous communities’ response to these policies and practices? Is the representation of Indigenous perspectives acknowledged and can Indigenous values be observed within policies, practices, and communication? The research methods include data analysis, document analysis, and an interview with a member of the Ministry of Environment and the Sámi Climate Council. This multi-method approach allows for a deep understanding of the impacts of climate change on the Sámi and the roots of environmental racism. The theoretical framework of the analysis of the research is based on environmental justice, Indigenous studies, and resilience theory. The research highlights systematic violations of environmental rights that the Sámi people face, such as differences in resources or belittling attitudes towards Indigenous knowledge. The Sámi Climate Council and the inclusion of Sámi rights in Finnish climate legislation are identified as key steps to promote community-based adaptation. The study emphasizes the urgent consideration of environmental and climate racism in the Arctic regions, and highlights the consultation of Indigenous peoples, supporting fair and sustainable development in decision-making processes. The thesis also contributes to a wider discussion about environmental law and participatory governance.
  • Virtanen, Mimmi (2024)
    We have long been invited to engage in climate action in different forums, without specifying what is actually expected of us to solve the accelerating climate crisis. Traditionally, individual citizens have only been seen as consumers in climate action. Although citizen participation in climate work has also been studied more and more in recent years, there is a little research on how citizens themselves perceive their own role in climate action. Climate action at local level and small municipalities, as smaller administrative units, could also provide better opportunities to support individuals in their own climate actions. In this thesis, I examine the climate agency and participation of residents in local climate action through their perceived roles and means of participation. I am conducting a review at the level of one small Finnish municipality by carrying out a qualitative case study. The case municipality is Kokemäki in the Satakunta region, with a population of about 7000. My research questions are (1) how the municipal representatives and local residents perceive the roles of the municipality and local residents in local climate action, and (2) what means are identified by municipal representatives and local residents to strengthen the climate agency of local residents. The research material consists of thematic interviews of the municipal representatives, group discussions of the residents and a survey conducted for the residents. As a method of analysis, I have used qualitative content analysis. The results show that municipal representatives and local residents have a similar perception of the roles, even though there are differences. In total, six different roles were identified for the municipality, and communication as a cross-cutting role. A key finding is that local residents perceived their own role more active than the municipal representatives did. A total of five roles were outlined for the residents, two of which emerged mainly in the experiences of the residents: the role to support each other and the role to activate the municipality to act. The roles of the municipality and the residents are strongly linked, and instead of looking individual means to support climate agency, it might be useful for small municipalities to shift the examination more strongly to their own role in relation to the residents. The development of communication and interaction is a key means of supporting climate agency. In addition to communication based on positive tone and examples in particular, the need for encounter and discussion emerged. Discussions with local residents, also on the topic of climate change, could bring new knowledge, understanding and ideas to the municipality, and at the same time provide a forum for communicating the importance of climate action, which also supports sustainable choices in everyday life. Strengthening the experience of working together increases the potential for self-motivated action and also enables peer learning and interaction between residents. The desire to take care of one's own home region could also support local climate action, as long as the objectives and actions are set at a local scale.
  • Pasculli, Maria Samuela (2024)
    The S209F variant of the Abelson Interactor family member 3 (ABI3) gene has emerged as a risk factor for late-onset Alzheimer’s Disease (LOAD). The ABI3 protein is functionally related to the WAVE Regulatory Complex (WRC) participating in the control of cytoskeletal processes favoring either filopodia for chemotaxis or pseudopodia for phagocytosis. The S209F coding variant is thought to impair phosphorylation of the ABI3 protein leading to dysfunctional association with WRC. In the brain, the ABI3 gene is mainly expressed by microglia, macrophages representing the resident immune cells of the brain. Despite some research about the variant based on rodent models and reporting sometimes contrasting results, the role of the ABI3 S209F variant in AD remains poorly understood. Here, human-induced pluripotent stem cells (h-iPSCs) reprogrammed from fibroblasts of controls and variant carriers are sequenced to ensure retention of the original phenotype upon reprogramming. H-iPSCs are differentiated into microglia (iPSC-derived microglia, iMGL) following an established protocol. Morphological changes and microglia-specific gene expression partially show that iMGL between days 31 and 38 of differentiation in vitro can be considered mature. To assess the functional properties of microglia, cytokines/chemokines production, cathepsin gene expression, lysosomal activity, and Apolipoprotein E (ApoE) protein levels are measured. It is found that S209F microglia downregulate CCL5/RANTES and upregulate cathepsins B and L (CTSB and CTSL) upon LPS+IFNg stimulation which may lead to motility, migratory and endo-lysosomal dysfunctions. Lysosomal activity is found to positively correlate with CD163, but not with either CTSB or CTSL expression. ApoE protein levels show an upregulation trend in S209F microglia which may indicate modifications in lipid metabolism. Metabolic assessment based on mitochondrial respiration and glycolysis does not show any difference between S209F and control microglia, but ABI3 knock-out (KO) shows glycolysis dysfunctions. Overall, this study offers some hints into the mechanisms that make the ABI3 S209F variant a risk factor for AD pointing at the need to investigate microglia motility and migration focusing on pathologically relevant protein aggregates and their clearance and with particular attention to phagocytosis and endo-lysosomal pathway.
  • 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.
  • Puistosalo, Jaakko (2024)
    Datakeskukset ovat osaltaan mahdollistamassa vihreää siirtymää, sillä niiden toiminnasta aiheutuvalla hukkalämmöllä voidaan lämmittää kotitalouksia polttoon perustuvan lämmöntuotannon sijaan. Hukkalämpö sitoo kuitenkin yhteen energian tuottajat ja käyttäjät, ja voi siten myös aiheuttaa odottamattomia seurauksia, joita tässä tutkielmassa tarkastellaan Mäntsälässä sijaitsevan Yandexin datakeskuksen tapauksessa. Mäntsälä oli asettanut valtaosan kaukolämmön tuotannostaan Yandexin datakeskuksen hukkalämmön varaan, joka osoittautui kunnalle ongelmalliseksi ratkaisuksi Venäjän hyökättyä Ukrainaan. Tässä tutkielmassa on tapaustutkimuksen keinoin selvitetty, oliko Yandexin datakeskuksen saapuminen Mäntsälään polkuriippuvaisen kehityskulun seurausta. Järjestelmän polkuriippuvuus voi aiheuttaa sen, että järjestelmä päätyy historiallisten päätösten ja tapahtumien seurauksena epätoivottuun lopputilaan, josta on erittäin vaikeaa irrottautua. Näin voidaan katsoa tapahtuneen myös Mäntsälään ja Yandexin datakeskuksen tapauksessa. Aineiston perusteella luodusta aikajanasta havaittiin, että Yandexin Mäntsälään tulon taustalla oli polkuriippuvainen tapahtumaketju. Mäntsälän kaukolämpöverkon polkuriippuvuuden taustalla havaittiin kolme mekanismia: suuret kiinteät kustannukset, mukautuvat olettamukset ja oppimisvaikutukset. Aiemmasta kirjallisuudesta poiketen, tarkasteltavan energiajärjestelmän polkuriippuvuuden taustalla eivät olleet ainoastaan järjestelmän fyysiset tai sen ympärillä vallitsevien markkinoiden ominaisuudet, vaan polkuriippuvuutta oli aiheuttamassa myös energiajärjestelmää hallinnoivassa organisaatiossa opitut kokemukset tietyistä toimintamalleista.
  • Sigg, Milla (2024)
    The Baltic Sea is a sensitive brackish waterbody, which is facing several disturbances. These stressors include land-use changes, over-fishing, climate change, pollution, alien species and eutrophication. Eutrophication causes increased primary production of opportunistic macroal-gae. These macroalgal mats cover the seafloor and cause light and oxygen depletion as well as mortality of benthic plants and fauna. Aquatic macrophytes provide important ecosystem ser-vices and food and shelter for macrofauna. The depletion of the benthic community may have large consequences to ecosystem functioning. In this master’s thesis, I studied the recovery of a macrophyte-associated macrofauna community after disturbance in a vegetated aquatic habitat. The disturbance was mimicking drifting algal mats, and it was induced in 2017. My thesis was a part of a larger project conducted at Tvärminne Zoological station in Hanko, Finland, studying the recovery of macrophyte communities of different functional diversity and their associated macrofauna. The samples were taken annually from 2017 to 2021. I examined which factors affected the recovery. In my analyses, I focused on the communities of animal species. Additionally, I assessed if there was an edge-effect in recovery and if opportunistic species were the first to recover, i.e., return to the site. The recovery was studied statistically using non-metric multidimensional scaling (NMDS), similarity percentage i.e., SIMPER and analysis of similarities i.e., ANOSIM. Results of the experiment showed that the site recovered in 2020 the latest. There was not a clear edge effect in recovery. A gradual re-introduction of common species happened, not a replacement of species. Some of the most common species possessed opportunistic traits. These results show that the recovery of systems is not linear but complex, and several factors affect their resilience.
  • Sydorska, Karyna (2024)
    Anxiety disorders are the most prevalent mental disorders in the world and often show comorbidity with sleep disorders. The bidirectionality of sleep disturbances and anxiety disorders is a hot topic in research and the understanding of the underlying mechanisms is crucial for the development of successful methods of intervention. Studies on the effect of sleep disturbances on anxiety-like behaviour in rodents, however, are limited and have been so far inconclusive. One factor behind this could relate to the limitations that exist when studying behaviour, hindering the replicability of results. Recently, novel behavioural approaches based on deep learning have been introduced, aiming to automate behavioural tracking, thus minimising the subjectivity of manual scoring that is often required for the assessment of more complex behaviours. The aim of this thesis was to use one of the recently developed deep learning tools, namely DeepLabCut (DLC), as well as a DLC data analysis tool, DeepOF, to examine whether chronic (14-day) sleep fragmentation (SF) affects anxiety-like behaviour in female mice and if one week of recovery period affects this phenotype. For the assessment of behaviour, a battery of behavioural tests was conducted immediately after SF and repeated after a week of recovery. The behavioural test data was then analysed using conventional methods, as well as using DLC and DeepOF for supervised analysis of more complex behaviours. These results show that SF does not increase anxiety-like behaviour in female mice, in both conventional and deep learning measurements of behaviour, but may affect locomotor activity, results which contradict previous findings. Despite this, DLC and DeepOF were found to be reliable and valuable tools for the identification and comparison of complex behaviours in mice, overcoming the oversimplified nature of the conventional behavioural tests.
  • Turku, Teemu (2024)
    Distal myopathies are a group of rare progressive genetic muscle disorders that are extremely varied both genetically and clinically. Typical symptoms include weakness and atrophy limited to the skeletal muscles of distal extremities in hands and legs. The age of onset ranges from early childhood to late adulthood depending on the disease. Currently around 30 genes have been associated with distal myopathies, most of them causing a dominant disease. The objective of the thesis was to identify the disease-causing variant in a family affected by autosomal dominant distal myopathy with early adulthood onset. Affected family members expressed weakness and atrophy in muscles of both hands and legs. To narrow down the chromosomal location of the disease-causing variant, linkage analysis was conducted with genome-wide single nucleotide polymorphism data of family members. Because of the progressive nature of the disease and uncertain disease status of one family member, linkage analysis had to be repeated a few different times with different settings. Both disease statuses and pedigree size were altered to account for the possibility of presymptomatic carriers or incomplete penetrance. Analyses with different parameters led to discovery of multiple possible co-segregating regions. Rare co-segregating small-scale and structural variants as well as repeat expansions in these regions were examined from next-generation sequencing data with multiple bioinformatic detection tools. The segregation of possible candidate variants was validated with Sanger sequencing and PCR. Ultimately, no likely rare co-segregating variant of any type of genetic variation with a likelihood to cause a disease such as distal myopathy was identified by any detection method used. Lack of potential disease-causing variant could be due to incomplete penetrance of the variant or if it was in non-coding regions, such as a deep intronic splicing variant in a gene currently not known to be connected to muscles.
  • Lalli, Marianne (2024)
    Background: The infant gut microbiome undergoes major temporal changes in the first year of life, crucial for supporting normal development and long-term health. The immense diversity of fiber structures in breast milk and later in solid foods pose unique selection pressures on the gut microbiome maturation by providing novel substrates for the microbiota. However, the longitudinal impact of complementary food-derived fibers on the taxonomic and functional maturation of the gut microbiome during the gradual transition from breast milk to solid foods is not well understood. Objectives: My objective was to examine how breast milk, its fiber and complementary food fibers in the broader context of overall infant diet may affect the gut microbiome bacterial species composition and support age-appropriate gut bacterial maturation trajectories during first year of life. Methods: Longitudinal and cross-sectional development of 68 infant gut microbiomes and 33 metabolomes were examined with linear mixed models to determine the impact of infant nutrition on gut microbiome taxa and functional development. Nutrition assessments were based on detailed quantitative weighted 3-day food records (months 3,6,9,12) and the intakes of total dietary fiber with its food sources and fiber fractions relied on current internationally approved CODEX-compliant values. Questionnaires were utilized to monitor when various complementary foods were introduced, enabling more comprehensive nutritional analyses. Bacterial species identification was based on MetaPhlAn2 quantification of bacterial species from metagenomic data and metabolomic profiles were generated using four liquid chromatography-mass spectrometry (LC-MS) methods. Results: My examinations place the previously described sequential trajectories in infant gut microbiome maturation into detailed fiber-dependent nutritional context relying on metagenomic species identification. I discovered 176 complementary food derived fiber-bacterial species associations. The majority of the associations (147, 84%) were positive whereas breastfeeding and related variables tended to be inversely associated with the same species, showing strongest inverse correlations to later trajectory species indicative of slower maturation. Both bacterial species and metabolomic profiles displayed pronounced longitudinal shifts in response to solid food fibers. Each introduction of novel dietary source of fiber associated to diversification of the microbiome revealing fiber-species specific temporal patterns. Conclusions: The longitudinal analyses highlight that sufficient fiber intake from appropriate sources during the weaning period likely function to build capacity for the species permanence in the more diverse and stable mature gut microbiome composition and function reached in later childhood.
  • Ilona, Kortelahti (2024)
    Nuclei isolation is a method used e.g. as a part of chromatin structure research. DNA structure can be examined in its 3D form from isolated nuclei because DNA is still wrapped around the histone proteins. Examining the chromatin structure can offer information e.g. about gene expression and how it is regulated. Isolating nuclei from plant cells demand more optimization compared to animal cells because of the cell wall, chloroplasts and secondary metabolites. The presence of organellar DNA can hamper the later DNA analysis. Secondary metabolites can hinder the actual isolation process. Finding the suitable isolation protocol for species of interest may need careful optimization of different aspects. Different species can differ from each other based on the structural and biochemical characteristics and because of this the same protocol may not ensure as good results for them. Different tissue types of the same species may have also differences in their biochemical and structural characteristics. In this thesis work, three different isolation protocols were used for three plant species; Pinus sylvestris, Betula pendula and Arabidopsis thaliana. The purpose of the work was to compare the results from each nuclei isolation protocol. Optimization of isolation protocol for P. sylvestris and B. pendula would help the isolation process for later research. Thesis work was done to get guidance for this optimization. Samples handled with different protocols were different from each other based on the sample concentration (particles/mL) and the average size of isolated particles. Chloroplast contamination was tested with chloroplast specific primers with PCR. None of the samples were free from chloroplasts.
  • Sippola, Marine (2024)
    Background and objectives: Since early adolescence, the bedtimes and wake-up times begin to delay gradually until the early adulthood. This so-called shift to eveningness reaches its maximum at around the age of 20, and it usually occurs earlier in girls than boys. Eveningness has been previously associated with depression, anxiety, sleep problems, somatic symptoms, and other health-related issues in adolescents and adults. The aim of this study is to examine the associations between adolescents’ chronotype and their physical and mental well-being. Methods: This study examined how the self-reported chronotype was associated with self-reported problems related to adolescents’ physical and mental well-being. The chronotypes were divided into 5 types: Definitive Morning-types, Moderate Morning-types, Intermediate-types, Moderate Evening-types, and Definitive Evening-types. The participants were 7th, 8th and 9th graders, and the sample consisted of 6522 students from 83 schools in Finland. Some of the data was gathered at three time points, some at two time points, and some at one time point during the academic year. The associations between chronotype and well-being variables were studied cross-sectionally and some of them also longitudinally. Results: The main findings were that eveningness was associated with difficulty concentrating in lessons, susceptibility to give up easily on difficult tasks, school burnout symptoms, feelings of nervousness and anxiety, excessive worrying, difficulty relaxing, irritability, restlessness, difficulty falling asleep, waking up at night, daytime tiredness, and low mood as compared to morningness. Eveningness was also associated with neck and shoulder pain, lower back pain, and headache, as well as pain in the head and lower back due to the use of digital devices. Eveningness was associated with decreased concentration in lessons and increased susceptibility to give up on difficult tasks across time. On the other hand, feeling lonely and not being accepted as part of the group were associated with morningness. Conclusions: In conclusion, the physical and mental health problems were emphasized among Evening-type adolescents, as compared to Morning-type adolescents. Since adolescents shift toward eveningness, the need for thorough management of sleep and circadian problems should be highlighted, in order to intervene and improve the mental and physical well-being of adolescents both at school and at home.
  • Marttunen, Sofia (2024)
    Peatlands are a significant carbon and nitrogen reservoirs, making them potential sources of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) emissions. Variations in water table level change the oxygen content of peat, affecting the oxidation-reduction or redox state of the peat, which is known to influence the biochemical processes and thus greenhouse gas (GHG) emissions. The aim of this study was to assess the effect of controlled anoxic redox conditions and inorganic electron acceptors (TEAs) on redox potential (Eh), and N2O, CH4, and CO2 emissions. In this study during an anaerobic incubation experiment, the rates of formation of these GHGs and Eh values as a function of time were measured from drained (D) and undrained (UD) peat of three nutrient levels: mesotrophic (ME), oligotrophic (OL), and ombrotrophic (OM). Redox conditions were controlled to three levels by nitrate (NO3-), ferric iron (Fe3+), and sulphate (SO42-). In addition, measurements were performed on untreated (Ctrl) peat. The peat was in an anoxic state throughout the incubation (Eh < 300 mV) and the values were in the order of TEA reduction, even though they were mainly in the iron and manganese reduction zones, probably due to the naturally high iron content of the peat. As expected, N2O formation was highest in flasks with added NO3-, and N2O formation was weak and ceased without addition. CH4 formation was reduced in flasks with added NO3- or SO42-, and SO42- addition also inhibited CO2 formation on which NO3- addition had no effect. In contrast, the addition of Fe3+ increased both CO2 and CH4 formation compared to Ctrl treatment, and it is possible that methanogens were involved in the reduction of Fe3+. In Ctrl flask, the redox state did not decrease to the lowest level compared to the other treatments as expected, but the Ctrl treated UD ME peat had the highest CH4 formation at the end of incubation. For all treatments, GHG emissions were higher from nutrient-rich peat in the descending order ME > OL > OM. In general, UD peat also had higher gas formation than D peat. All GHGs were formed the most while Eh values were around 0 mV and the value was especially high for CH4 formation, probably due to the linkage between methanogens and iron. The poor ability of the Pt electrode to detect NO3- or oxygen was the most likely reason for the variable and low Eh values of the flasks with NO3- addition. For the same reason, oxygen leakage of the anaerobic chamber was most likely responsible for the varying Eh values measured from Ctrl treated OM peat. This study suggests that Eh measurement is a useful predictor of the redox state and reactions, but it must be considered together with other measurements and analyses such as microbial analysis, nutrient analysis, and GHG measurements to predict redox processes and GHG emissions in anaerobic peatland. In particular, the role of iron on CH4 emissions requires further research.
  • Rezola, Uxue (2024)
    The many symbiotic microbes associated with plants can represent the first line of defence against viral pathogens, which can have profound impacts on plant health and productivity. Unfortunately, although countless studies have investigated variations in the composition of microbial communities associated with crops, showing benefits in the plants’ nutrient acquisition, stress tolerance or growth promotion, much less is known about how viruses might affect the composition of the microbiota associated with plants, and especially non-crop plants. Furthermore, we also often lack an understanding of how plant viruses are transmitted across their environment. Addressing these knowledge gaps is bringing us closer to better describe and manage the complex relationships between plant microbiota and viral pathogens in their natural environment. The main objective of my Master’s study is to examine variations in the bacterial community associated with a plant in the agricultural landscape, and to identify potential players in microbial community changes. With this in mind, I chose to work with the ribwort plantain, Plantago lanceolata, because it has a widespread distribution, it is present around cultivars, and there is extensive knowledge of its biology and genetics. Thus, P. lanceolata, represents an excellent system for investigating the causes of variation in the plant-associated microbiota. More precisely, I worked with the P. lanceolata population evolving in the Åland Islands, in Southwestern Finland, which has been the target of long-term ecological and evolutionary metapopulation studies. The population is also known for co-evolving with several viral pathogens, and with diverse Hemiptera insects (plant sucking-insects) that have been suggested as possible vectors of the viruses between plants. I collected P. lanceolata leaves, and insects found on P. lanceolata specimens from 28 habitat patches, or meadows, from five localities across the Åland Islands (Geta, Sund, Lemland, Finström, Eckerö). I extracted DNA from a total of 10 leaves per patch, as well as 60 Hemiptera specimens (of several uncharacterized species). I screened for viral infection in all samples by amplifying the viral loci for reverse transcriptase form Plantago latent caulimovirus (cauV) and the replication associated protein gene from Plantago lanceolata latent virus (PlLV). In parallel, I characterized the bacterial communities associated with each plant and insect through metabarcoding of the highly variable V5-V6 region of the 16S rRNA bacterial gene. My MSc's project shows that bacterial species richness (alpha-diversity metric) and community composition (beta-diversity metric) vary between plant and insects. But that they do not vary between the virus-infected and uninfected plants tested, and neither between geographical locations within the Åland Islands. This is the first study investigating the effects of two virus infections on the microbiota of a common weed from the Åland Islands. It provides preliminary data for the study of how the bacterial microbiota of P. lanceolata might respond to virus infections, and how viruses might be transmitted between individual plants.
  • Hölttä, Jenna Katariina (2024)
    Climate change has caused a vital need to identify the coastal ecosystems with high carbon sequestration capacity, i.e. Blue Carbon ecosystems. The ability of these ecosystems to sequester carbon is strongly influenced by the physical environment. However, previous research on Blue Carbon potential of coastal macrophyte ecosystems has mainly focused on single seagrass species whereas research on multispecies meadows along environmental gradients, such as wave exposure has been scarce. Nonetheless, exposure and depth are known to shape the functional structure of macrophyte communities. The aim of this study was to investigate if exposure and depth affect the functional structure and biomass-bound carbon stocks of macrophyte communities along an exposure gradient in an archipelago area in the western Gulf of Finland, northern Baltic Sea. Macrophyte samples were collected at two different depths (1-2 m and 3-4 m) from 20 soft-bottom sites with different exposure levels. At each site, the functional community structure was quantified by measuring four functional traits (maximum height, root depth, root-to-shoot ratio, specific leaf area), associated with the variation in plant life history strategies and in addition, the plant biomass-bound carbon was determined. The results showed that when moving from the outer to the inner archipelago, the species composition shifted from marine to limnic species, and the community functional structure was shaped by environmental conditions (i.e. wave exposure, light availability, salinity) and depended on the depth. The plant carbon stocks did not differ significantly along the exposure gradient in the shallow areas, while at increasing depth, exposed sites had the highest plant carbon stocks, which can be likely explained with the environmental factors such as light availability. To conclude, these results highlight the need for further research that investigates the connection between environmental drivers, functional traits, and plant carbon stocks to assess the Blue Carbon potential of multispecies macrophyte communities in heterogenous environments.
  • Granat, Arttu (2024)
    Educational technology is advancing rapidly, with VR (virtual reality) emerging as a promising branch of XR (extended reality) technology for educational purposes. Utilizing head-mounted displays (HMD), immersive VR experiences immerse users in a virtual environment, limiting their awareness of the physical world. VR proves valuable in education by complementing traditional teaching methods, offering experiences impossible in the physical realm. Studies indicate enhanced affective factors, understanding, motivation, and memorization among students. In biology education, VR serves as a visual aid, helping students grasp complex biological concepts difficult to visualize from a two-dimensional textbook. It also shows potential in supplementing hands-on activities like laboratory work and anatomical dissections, experiences outside classrooms, and sustainability education. However, challenges persist in VR's educational application, including uncertainty about learning outcomes, health concerns, high costs, and a general lack of expertise in VR design and pedagogical implementation. Educational VR design has thus far lacked a foundation in pedagogy and learning theories. This thesis aims to address this gap by reflecting on the development of a pedagogically meaningful VR experience within sustainability education. Collaborating with the Global Campus project of the University of Helsinki, the thesis introduces a VR experience integrated into the immersive virtual sustainability learning experience, Serendip. The design process involved literature research, user and expert interviews, and consideration of learning theories such as constructivist learning, experiential learning, flow theory, gamification, CTML, SDL, and CLT. Specific aspects of VR design, like immersion levels and prior knowledge of users, were also considered. The thesis's significance lies in pioneering pedagogy-based design for educational VR, particularly addressing complex, abstract, and multidisciplinary subjects. It emphasizes the need for collaboration among pedagogy, content, and VR animation experts in future educational VR design. This work serves as a potential template and inspiration for further research in the field, aiming to refine the integration of pedagogical principles into VR experiences for education.
  • 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.
  • Huovinen, Minna (2024)
    Maailmanlaajuisesti kiihtyvä luonnon monimuotoisuuden vähentyminen uhkaa ekosysteemien toimin-taa, ja toimia luontokadon pysäyttämiseksi tarivitaan nyt. Elinympäristöjen häviäminen on yksi luonto-kadon pääasiallisista aiheuttajista. Suomessa niityt kuuluvat monimuotoisimpiin elinympäristöihin, mutta niiden määrä on vähentynyt ja erityisesti perinneniityt ovat uhanalaistuneet 1800-luvun lopulta nykypäivään. Niittyjen muutoshistoriaa on tarkasteltu lähinnä perinnebiotooppien näkökulmasta, vaikka niiden ohella niittylajeja esiintyy myös muunlaisilla niityillä, kuten ilman ihmisen myötävaikutusta syntyneillä alkuniityillä sekä erilaisissa uuselinympäristöissä. Tässä työssä niityt määritellään laajasti, sillä pyrkimyksenä on tarkentaa käsitystä niiden kokonaistilasta sekä niissä tapahtuneista muutoksista, ja tunnistaa uusia mahdollisuuksia niittyjen ja biodiversiteetin suojelemiseksi. Viime vuosina kaupun-geissa onkin herätty niittyjen ja biodiversiteetin suojeluun, ja myös Helsingissä on laadittu niittyjen sel-vitys ja kehittämissuunnitelma. Tässä työssä tarkastellaan pääkaupunkiseudun niittyjen muutoshistoriaa vuosien 1870–1907 ja 2022 vä-lillä paikkatiedon menetelmin. Historiallisten niittyjen määrän arvioimiseen käytettiin niin kutsuttujen Senaatin kartastojen pohjalta tuotettua paikkatietoaineistoa, kun taas nykypäivän niittyalan arvioiden perustana on Syken ja Scalgon tuottama maanpeiteaineisto. Työn tavoitteena oli selvittää niittyjen pin-ta-alan ja levinneisyyden muutoksia pinta-aloista laskettujen tilastojen sekä Overlap- ja Optimized hot spot -analyysien avulla, vertailla niitä Helsingin niittyverkoston paikkatietoaineistoon ja lopuksi pohtia, voisivatko työn tulokset tarjota uutta näkökulmaa niittyjen ja luonnon monimuotoisuuden suojeluun Helsingissä sekä laajemmin. Niittyjen tarkastelu laajemman määritelmän kautta paljasti, että vaikka niittyjen määrä on vähentynyt pääkaupunkiseudulla vuosista 1870–1907 nykypäivään, vähentyminen on ollut aikaisempiin arvioihin verrattuna maltillista ja niittyjä on edelleen runsaasti. Niittylaikkujen keskimääräinen koko oli kuitenkin pienentynyt, ja valtaosa niityistä sijaitsi nykyään eri alueilla kuin vuosina 1870–1907. Kuitenkin löydet-tiin joitain alueita, joilla niittyjä esiintyi molempina ajankohtina. Suurten ja vanhojen niittyjen säilyt-täminen olisi biodiversiteetin suojelun kannalta ensiarvoisen tärkeää, ja ne tulisi huomioida paremmin myös Helsingin niittyverkostostrategiassa. Elinympäristön pinta-alan ohella sen biodiversiteettiin vai-kuttavat keskeisesti kytkeytyneisyys ja laatu, ja lisää tutkimusta tarvittaisiin niiden muutoksista ja ny-kytilasta pääkaupunkiseudun niityillä. Huomattiin myös, että niittyjen määrittelyllä on valtava merkitys niiden tilan arvioinnissa, ja käsitteitä olisikin tarpeen yhdenmukaistaa.