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  • 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.
  • Ihalainen, Vilma (2020)
    Ongoing climate warming has unprecedented impacts on glacial melt and associated fjord systems in Greenland. As the glaciers are shrinking, freshwater inflow to the sea is increasing resulting in increased nutrient supply by upwelling. In this study I examined environmental factors impacting marine primary productivity, biomass (chlorophyll a), phytoplankton abundance and species composition along a transect from the glacier front to the outer fjord in Godthåbsfjord, SW-Greenland, in August 2019. Gradients in nitrogen and phosphate concentrations were explained by glacial runoff and coastal water inflow while silicate concentration did not follow these patterns. The main variables explaining phytoplankton biomass distribution were nitrogen together with phosphate concentrations, salinity, and depth. Silicate limited waters were strongly dominated (≥ 90%) by the diatom Chaetoceros socialis, which had a strong influence on phytoplankton community response to environmental conditions. High dominance of C. socialis was also related to high species richness. Nitrogen depleted waters were usually related to relatively high abundances (9–46%) of mixotrophic Dinobryon balticum. Higher number of species and higher dominance of C. socialis was detected closer to the glacier. Phytoplankton abundance and biomass (chlorophyll a) were higher in the inner fjord region, whereas primary productivity had the opposite pattern (higher productivity in the outer fjord). This suggested that an autumn bloom was peaking in the inner fjord, whereas in the outer fjord the autumn bloom was still developing. Thus, glacial surface runoff and subglacial discharge contributed to higher phytoplankton abundance and chlorophyll a concentrations, whereas primary production was also dependent on other factors such as light availability and vertical mixing. Melting of Greenland Ice sheet is predicted to accelerate in the future. Thus, the upwelling effect might increase, leading to transitory increase in marine primary production. Increased surface runoff might increase silicate concentrations benefiting diatom species, although turbid runoff water will also decrease the primary productivity due to light limitation. Nevertheless, if marine-terminating glaciers retreat further and become land-terminating glaciers, lack of nutrient upwelling will lead to faster exhaustion of nitrogen in the upper water column and primary productivity will eventually decrease. Thus, global warming and retrieving of glaciers will change the productivity of the fjord and inevitably shape the rich and unique fjord ecosystems of the Arctic.
  • Keinänen, Milka (2020)
    High Nature Value (HNV) farming systems hold significant natural values but have decreased drastically during the process of agricultural modernization. Biodiversity in Europe is dependent on these extensively farmed areas because they maintain habitats for many endangered species; e.g. 30% of Europe's butterfly species have declining populations and most live in natural and semi-natural habitats. European common agricultural policy (CAP) favour conventional agriculture, leading HNV agriculture in a foul position. HNV areas are often abandoned or replaced with intensive farming practices. Participatory agricultural innovation processes offer solutions to the distress of HNV farmlands. In these processes different actors – such as farmers, entrepreneurs, advisors, NGO and municipality representatives – are brought together to find localized solutions to the challenges of the area. HNV-Link project was active during years 2016-2019 identifying, developing and improving innovations in ten European HNV farming areas. In this thesis I examine the success of innovations in seven Learning Areas (LA) in terms of socio-economic viability, environmental conservation and cultural region. The data in this thesis is both quantitative and qualitative. I use mixed methods- approach where the statistical analysis and qualitative content analysis support each other. I carried out a survey for the LA coordinators where they responded how was the impact of the innovations to social, economic and environmental wellbeing. I complement the survey with data gathered by the project in 2016-2017. I conduct a qualitative content analysis to innovation fiches using Atlas.ti programme and a statistical analysis with IMB SPSS statistics programme with non-parametric tests. I compare the relation of socio-economic and environmental impact of the innovations, explicit aim of HNV conservation, recognition of environmental topics in the fiches and cultural region. Innovations were successful both socio-economically and environmentally. There was a possible synergy between economic and environmental impacts, which indicates economic viability of the LA’s improving HNV conservation. Innovations with explicit HNV conservation objective had more positive environmental impact than the ones without. Innovations with high recognition of environmental themes in fiches had slightly more positive environmental impact, but the difference was so weak that they fail to express the environmental outcomes reported in the survey. Congruent patterns didn’t occur inside cultural regions which might be due to the similarities of the areas or small sample size. The results display the inherent unpredictability of innovation processes, and the importance of holistic understanding and long-term monitoring of them.
  • Winquist, Emelie (2021)
    The heath vegetation in the Jauristunturit study area is highly affected by the reindeer fence that was built in the mid-1950s between Finland and Norway, to prevent summer grazing in the Norwegian side. In the study area, the Finnish and Norwegian pastures are used during different seasons, causing differences in reindeer grazing history, and with time differences in vegetation. Additionally, local topography also impacts the vegetation composition and structure creating variation in local vegetation patterns. My research questions are: How vegetation patterns differ between summer- and winter- grazed areas, and which plant functional groups have the most significant difference? How local topography affects vegetation patterns, and does the effect of topography differ between summer and winter pastures? The data was collected from five 400 m long transects that crossed the fence and had vegetation plots with 10-m intervals. The %-cover and height of each vascular plant, bryophyte, and lichen species were estimated from 0.25 m2 plots. Later, species data was grouped into functional groups and general linear models were used to analyze differences in cover, height, species number, biomass, and leaf-area indices between countries. Topography indices were calculated in GIS for each plot and analyzed with random forest models to find out the most important topography indices explaining vegetation patterns. The vegetation data was collected by four teams, and therefore, the comparability in the collected data between teams was analyzed. Significant vegetation differences were found in the ground layer, with higher cover and biomass of bryophytes on the Finnish side (mean biomass 168.2 vs. 65.2 g m-2). Reindeer lichens were more abundant on the Norwegian side (mean biomass 197.0 vs. 2.9 g m-2) which is visible in aerial and satellite images and in the field. Among vascular plants, evergreen dwarf shrubs had higher biomass and leaf area index on the Finnish side and dwarf birch had higher cover and height on the Norwegian side. Topography indices had a higher level of variance explained on the Norwegian side, and higher at the ground layer compared to vascular plants. Elevation had the greatest impact on vegetation, and after that, topography protection index for 50 m and depth to water stream network for 2 and 10 ha. The differences between data collectors were not considered to have a major impact on the results. The results indicate that there are significant differences in vegetation between summer- and winter-grazed areas, mainly in the ground layer, and most differences are caused by differences in reindeer grazing history, but also local topography has an impact.
  • Fagerholm, Freja (2021)
    In the process of decomposition soil carbon is transformed into CO2 by microbial respiration, which makes decomposition a key process for understanding carbon cycling an releases of CO2. Since the northern permafrost regions contain half of all belowground carbon and the tundra regions are expected to be markedly affected by climate warming, it is of particular interest to understand how warming will affect decomposition in the tundra. Decomposition is however influenced by many factors, from climatic factors such as temperature and precipitation to the belowground organisms inhabiting the soils and the aboveground system dictating the litter that falls to the ground and is decomposed. Further, grazing has been shown to oppose some of the effects of warming on tundra. In this thesis I analyzed data collected from two long-term field experiments, one in Kilpisjärvi (NW Finland) and the other close to Kangerlussuaq Fjord (SW Greenland), both using fencing for manipulation of grazing regime and open-top chambers for artificial warming. My aim was to not only investigate how warming and grazing affect decomposition, but also to understand whether the magnitude of changes in decomposition can be explained by changes in plant community traits and soil characteristics. I found that in contrast to my hypothesis, warming decreased decomposition in Kangerlussuaq, where the soil was drier and contained less carbon than in Kilpisjärvi. I found no effects of grazing on decomposition, plant community traits nor soil characteristics in neither of the study locations. Neither did I find any consistent associations between changes in decomposition and changes in plant community traits, indicating that the effect of litter quality on decomposition is minor in these areas likely rather limited by climate. I found an association for increased decomposition when plant community C:N ratio and C:P ratio increased as a response to warming, but only in Kilpisjärvi, and since increased plant community C:N and C:P ratios are linked to resistant litter this positive effect is unlikely driven by enhanced litter quality. However, I did find a positive relationship between increased root biomass and increased decomposition as a response to warming that was consistent across areas and grazing regimes, indicating that warming can boost decomposition in different tundra habitats by promoting root growth.
  • Finne, Hanna (2020)
    Boreal mires are natural sources of methane and contribute considerably to the global methane budget. Therefore, in order to comprehend the overall impact that these ecosystems have on climate change, it is essential to understand the factors that influence processes involved in methane production and consumption. Factors affecting methane flux vary between different mires, but there is also great spatial and temporal variation in flux within mires. In previous studies, temperature and water table position have been shown to influence methane flux, but vegetation could aid in explaining the small-scale variation. Vegetation can indicate spatial variation in water table position, but also affect methane flux directly by the transportation of methane through plant tissues, and by providing substrate for microorganisms through primary production. Furthermore, redox potential is a poorly studied factor that can reflect if chemical conditions in peat are suitable for methane production or consumption, making it a useful tool in predicting methane flux. In this thesis, I seek to identify if small-scale spatial variation in the methane flux occurs within the studied mire area. In addition, I strive to identify important controllers of the observed spatiotemporal variation in methane flux, with a specific focus on the effect of vegetation properties and redox potential. Methane and carbon dioxide fluxes were measured with the closed chamber technique at a boreal fen in Sodankylä (67°22'06.6"N 26°39'16.0"E) during the growing season in 2019. Flux measurements were carried out at nine measurement plots belonging to three different vegetation types: flark, lawn and string. Coverage and height of plant functional groups were followed during the summer and continuous redox potential was measured for each plot. CH4 fluxes of different plots and vegetation types were compared to study the spatial variation in methane flux. Generalized additive models (GAM) were used to determine which variables are best to explain spatiotemporal variation in methane flux over the growing season. Mean methane flux during the summer was 0.94 ug CH4 m-2 s-1 which is in the same magnitude as observed in a previous study at the fen. Some small-scale spatial variation in the methane fluxes was observed at the study site, with strings having lower flux than flaks and lawns. However, overall the spatial variation was small, while temporal variation in methane flux over the growing season was considerable. The best model, that was a combination of vegetation, redox potential and environmental variables, and it explained 72 % of the observed variation in methane flux. Vascular plant variables were the most important variables in the model, whereas moss functional groups were of lesser importance. Redox potential in deeper peat layers was also important in the model, but redox potential closer to the surface was not found to be significant. Vegetation is an important controller of methane flux, and this information could potentially be used when predicting methane flux over larger areas by using remote sensing to map vegetation characteristics. Redox potential, on the other hand, is relatively easy to measure, and the result suggests that it could provide a useful tool for improving the predictions of methane flux.
  • Soppa, Inkeri (2020)
    The Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated protein (Cas9) (CRISPR-Cas9) system is a widely used gene editing technology due to its potential to alter the genome precisely in desired locations. Due to the potential of the CRISPR-Cas9 system, the objective of the thesis is to improve the precise editing of genes by modifying the CRISPR-Cas9 platform. Ultimately, the aim is to develop a platform that can edit any mutation and repair it to a normal, functional gene in patient cells. In general, CRISPR-Cas9 provides opportunities in treating monogenic diseases, for example by modifying long-term hematopoietic stem cells in immunodeficiencies. CRISPR-Cas9 can target disease-causing mutation sites and introduce double-strand breaks. Afterwards, the native DNA repair machinery of a cell repairs the cut site either by more efficient, error-prone non-homologous end joining (NHEJ) or precise homology-directed recombination (HDR). In most clinically oriented genome editing studies, the desired repair outcome is the latter because it allows precise repair of the mutation according to the exogenous repair template. Despite all its positive features, the optimization of CRISPR-based editing system is crucial before medical use; CRISPR-Cas9 induces a p53-mediated DNA damage response, which leads to a transient G1 cell cycle arrest and hampers HDR-based precision genome editing. Other problems include the repair pathway depending on the cell cycle phase, repair template proximity, and off-target activity. This thesis demonstrates that Cas9 fusions allow addressing the problems mentioned above. Cas9 fusions with DNA repair proteins ensure improved editing efficiency at the close proximity to the target site in HEK293T, BJ5-ta and RPE reporter cell lines. In addition, Cas9 coupled with the engineered cell cycle timer, AcrⅡA2-cdt1, favors the editing at the S/G2 cell cycle phases avoiding the p53-mediated response. AcrⅡA2-cdt1 is a reversible, phage-derived CRISPR inhibitor that selectively inhibit CRISPR-Cas9 at the G1 cell cycle phase and releasing it at the S phase. This thesis provides extensive look on the CRISPR-Cas9 editing and its challenges in immortalized cell lines and primary cells. In the thesis, the generation of reporter cell lines is prior to the validation of the novel Cas9-fusions. Furthermore, the optimization of primary T cell and CD34+ hematopoietic stem cell electroporation with different electroporation systems brings the study closer to clinical applications. The thesis provides insights about the effect of the target site and the cell type for genome editing outcomes. The editing efficiencies depend on the Cas9 fusion protein, cell type and its proliferation rate. The editing efficiency in primary T cells and CD34+ hematopoietic stem cells can significantly improve by optimizing transfection and culturing conditions, such as concentration of the CRISPR-Cas9 complex, cell culturing time and electroporation program. Cas9 fusions improve the safety and efficiency of the CRISPR-Cas9 system depending the cell type and the proliferation rate of the cell. Timing the induction of double-strand breaks also improves the editing efficiency. Overall, the methods used in the thesis give useful tools for eventual translational applications.
  • Aro, Niilo (2022)
    With the growth and concentration of urban areas, methods for minimizing the impacts of fragmentation and habitat loss on biodiversity are needed. Spatial Conservation Prioritization (SCP) methods, which holistically assess the connectivity of urban areas, provide an effective tool for prioritizing conservation efforts, but producing these analyses require large amounts of high-quality data on e.g., the spatial distribution of biodiversity features in the area. An index-based approach is a simpler way to evaluate the ecological quality of single corridors, and could be a cheaper alternative to SCP methods, especially in cases where prior environmental data is limited or there is a frequent need for new analyses. In this study, I created an index-based method to evaluate the ecological quality and functionality of wildlife corridors. The three-step approach included a literature review on factors affecting the functionality of wildlife corridors as well as the building and testing of the index. The main objective in creating the index was to provide a tool that is easy to use and interpret, and that could be used in decision-making to minimize human impact on nature. The index is based on scientific literature and provides information on the ecological functionality of wildlife corridors in facilitating the dispersal of organisms. From the literature review I identified certain key elements of functionality for wildlife corridors. These elements included sufficient width of the corridor to form an undisturbed core habitat, the absence of barriers and disturbance within the corridor and the connectivity of the corridor habitat itself. When tested on fictitious example corridors, the index was able to differentiate wildlife corridors according to their ecological quality. To further test the index, it was applied on a real-world wildlife corridor located in Uusimaa as a case study. The index was found to be effective on evaluating the ecological functionality of wildlife corridors, but further development needs were also discovered. The most important next steps are to fine-tune the parameter values given to factors hindering dispersal (resistance values) based on an extended literature review, and systematic testing on real-world corridors to spot irregularities and possible mistakes. At its current state the index can be used to identify features that impede or promote the ecological functionality of the corridor, even without extensive prior inventories on the areas’ biodiversity features.
  • Goldsmith, Felicity (2024)
    Cameroon’s forests and forest lands are home to diverse indigenous peoples and local communities. Cameroon has endured many colonial administrations and missionary influences throughout its history with British, French, and German rule having all left their mark on the nation’s land, plantation, and forestry sectors while realising their interests. In particular, the representation of indigeneity remains tainted within and beyond today’s land use sector and forest policy arena, and its related businesses and financial services. This thesis analyses the British colonial business media landscape to examine the dominant discourses surrounding the indigenous within the context of Cameroon’s land, forests, and plantations. Through understanding the narratives that have historically been broadcast to society and the public via business media, a greater understanding of the current status quo within the forestry sector, and therefore the workings of ‘inequality machines’ and neocolonialism, can be investigated. Furthermore, business media such as newspapers and magazines historically played a central role in the colonial enterprise, informing and shaping entrepreneurial activities but also legitimising the colonial project and providing narratives to enable the realisation of interests and profits. This research examines local and indigenous narratives and considers how these representations link to the colonial enterprise. Qualitative research methods are adopted, using a systematic literature search to identify articles from four prominent British business media sources (The Economist, The Guardian, The Observer and The Times). Search criteria, in the form of two key word search strings, selected 303 relevant articles and constructed the archival landscape of Cameroon in British colonial business media from the 1850s through to the early 2010s. Newspaper articles were inductively coded using Atlas TI software with the aim to explore the main research questions: • How does British business media represent and legitimise the treatment of indigenous peoples in the context of Cameroon’s land, forests, and plantations? • How has this evolved over time? Results from coding demonstrate the emergence of 4 main code groups that aid the legitimisation and justification of indigenous exploitation in the context of indigenous representation: Comparing, Centring, Controlling and Fearing. Power dynamics, temporality, and the linkages between these core themes, also play a predominant role. What emerges as most influential is the way in which British business media shifts its representation and legitimisation of the treatment of indigenous peoples through time, whilst continuing to reinforce power inequalities. Ultimately, indigenous representation and narratives within the British business media ‘seem’ to improve, but this is largely from the colonisers’ perspective, or to be received by the colonial gaze.
  • Müller, Linda Helena (2022)
    Puberty initiation is a crucial physiological process in human development. A group of hypothalamic neurons secreting the gonadotropin-releasing hormone (GnRH) and expressing the kisspeptin receptor (KISS1R) plays a key role in launching puberty. Furthermore, cellular KISS1R signaling has been shown to regulate GnRH expression and secretion. Although the in vitro differentiation of human pluripotent stem cells into GnRH-secreting neurons has been successful, it is of high interest to generate KISS1R expressing GnRH neurons. By utilizing the CRISPR activation technology, this study aimed to establish a conditional KISS1R-activation cell line using H9 human embryonic stem cells. Through controlling dCas9VP192 abundance using the Tet-On system combined with the dihydrofolate reductase destabilizing domain, the transcriptional activation of KISS1R was temporally regulated by the addition of two antibiotic drugs - doxycycline and trimethoprim. KISS1R expression was primarily assessed by qPCR and verified by immunocytochemistry and the use of a KISS1R-GFP reporter cell line. The main finding of this study is the achievement of a 6217 ± 2286 fold change in KISS1R transcription by introducing two guide RNAs (N = 3). Nevertheless, leaky gene activation was observed without drug treatment (fold change of 63 ± 51). Concludingly, this study successfully led to the generation of a KISS1R-activation cell line. After further characterization and refinement of the activation protocol, the established cell line will enable to investigate whether KISS1R upregulation modulates in vitro GnRH neuron differentiation, electrophysiology, hormone expression, and secretion in the future. Respective outcomes may lead to advances in understanding and treating pubertal disorders.
  • Kontio, Salla (2022)
    Spontaneous and voluntary movements of infants effectively reflect the developmental integrity of brain networks. When it comes to the research of motor development, the use of intelligent technology has shown to provide objective, automated, and scalable methods for movement assessment. In addition to intelligent technology, research on the usage of surveys – in this case parental surveys – has looked at the untapped potential that parental viewpoint. Guardians have a unique and holistic image of the child’s development, thus data from parental surveys could be used to further help us to assess infant’s development. For this study, I studied how the parents’ time estimate on the positions their child spends time in holds up against the machine-learning based data obtained with the smart jumpsuit. Using the data acquired from the smart jumpsuit during the recordings, we can see the amount of time the child spends in each position. Aim was to study the relationship between these variables and gain further understanding on the utilization of parental perspective in the assessment of motor development. Data was collected from 19 video recordings and videos were annotated with Anvil video annotation software for child’s posture and movements, and the annotations were used for training a machine learning-based classifier of the smart jumpsuit. Only data regarding postures was extracted for further analysis. Parental surveys were carried alongside of recordings. In the survey of parental estimate, we asked the parent to assess how much time the child spends in a specific posture. Positions which the survey focused on were prone, supine, side, sitting, crawling, and standing. Data from the recordings as well as data from parental surveys were visualized with radar plots. In addition, correlation was visualized in a linear regression. Positions which had both correlation of higher than 0.5 and a significant p-value were sitting (p < .001**), crawl posture (p < .05*), standing (p < .001**), and supine (p < .05*). Results suggested that parents were successfully assess the time spent in following postures: sitting, crawling, standing, and supine. This indicates that parents have a holistic understanding of their child’s motor development, and the knowledge could be useful in the overall assessment of development, especially when it comes to children with developmental delay. The parent’s ability to accurately assess a child’s motor development helps the parent support the child’s development.
  • Guillon, Melina (2023)
    Faculty: Faculty of Biological and Environmental Sciences Degree programme: Master’s Programme in Neuroscience Study track: Cell and Systems Physiology Author: Mélina GUILLON Title: Inflammatory activation of Macrophages by Triglyceride-Rich Lipoproteins in Atherosclerosis Level: Master’s thesis Month and year: August 2023 Number of pages: 38 Keywords: Atherosclerosis, Inflammation, Triglycerides-Rich Lipoproteins, Emulsion Particles Supervisor or supervisors: Dr. Katariina Öörni Where deposited: Helsinki University Library Additional information: Background: Inflammation is a key factor in atherosclerotic cardiovascular disease (ASCVD) and is present at all phases. It has been shown that reducing inflammation by blocking cytokine pathways diminishes the risk of stroke and myocardial infarction. Despite the well-established linked between lipoproteins and atherosclerosis, little is known on the specific effect of lipids on inflammation. In this study, we investigated the impact of triglycerides-rich lipoproteins’ (TRLs) lipids on inflammation in the context of atherosclerosis. Methods: TRLs were isolated and purified from pooled plasma of healthy volunteers, and emulsion particles (EPs) generated by sonication using lipids extracted from TRLs. TRLs and EPs were characterized in size, triglycerides, and cholesterol content. THP-1 cells were treated with EPs, TRLs, and modified EPs (oxidation, vortexed, and lipolysis with PLA2), and the release of pro-inflammatory cytokines (IL-1β and TNF-α) was detected with ELISA. Results: EPs were successfully synthesized by sonication using an ultrasonic probe. EPs induced cytokine secretion from THP-1 cells (N=4). Modified EPs (Oxidized EPs, vortexed EPs, and PLA2-treated EPs) did not increase cytokine secretion (N=4). Conclusion: Our findings suggest that TRLs’ lipids contribute to inflammation and that TRLs may play a crucial role in the pathogenesis and pathophysiology of ASCVD. Inflammatory properties of TRLs should be extensively investigated in the future for the development of preventive and curative strategies.
  • Wei, Xiaodong (2022)
    The composition and dynamics of the early life gut microbiota plays a major role in establishing neonatal immunity and is suggested to have multiple impacts on the child’s long-term health. Meanwhile, the composition of the infant gut microbiome has been shown to be affected by the birth mode, infant health and diet. However, the characterization of the infant gut microbiome and its impact on the host’s health is still challenging as the contribution and importance of multiple co-factors on the early microbiome during infant growth is still poorly understood and characterized. The Health and Early-life microbiota (HELMi) is a cohort of more than 1000 healthy Finnish infants currently followed from birth to 4-5 years old. By now, the HELMi dataset comprises more than 400 whole genome shotgun metagenomes obtained from stool samples from 80 infants and parents, but also an in-depth characterization of the families’ lifestyle, environment, health and nutrition, allowing for a precise and cutting-edge characterization of the early gut microbiota. Based on the datasets from the HELMi, this project used Metaphlan3, Kraken and Braken to determine the best computational approach for the taxonomic profiling of the metagenomic reads. Then a PERMANOVA test was performed to evaluate and determine the factors significantly associated with the compositional microbiota variation within the infant gut metagenomes. This study first identified technical factors introducing bias in taxonomic profiling (e.g., DNA extraction batch), which served as confounders in the analysis of environmental and host variables. The investigation of these biological factors indicates that pre-natal and peri-natal variables such as the mode of delivery significantly impact the infant gut microbiota, while we did not identify any significant impact of breastfeeding habits and medication exposures in this study.
  • Abbas, Salma Magdy Hussein Jr (2024)
    Elevated low-density lipoprotein cholesterol (LDL-C), hypercholesterolemia, is characterized by complex and poorly understood genetic contributions. Cellular LDL uptake mediated by the LDL receptor is pivotal to disease progression. After LDL internalization LDLR is recycled to the plasma membrane. Genetic mutations are known to exist in factors driving LDLR recycling but their contribution to hypercholesterolemia is not known. SNX17 has been postulated to be important for LDLR recycling. The goal of this study was to investigate the effect of SNX17 on cellular LDL uptake and to evaluate whether functional characterization of SNX17 gene variants can be performed. At the same time, adjusting an existing semi-automated analysis pipeline to generate expression constructs for SNX17 genetic variants. In this study, using an SNX17 knock-out cell line and an SNX17 rescue cell line (SNX17 knock-out cells transfected with GFP-SNX17 construct), it was shown that SNX17 might have a role in LDL uptake. The semi-automated workflow for generating genetic variants was successfully adopted to SNX17, warranting further experiments to define the optimal conditions for the functional characterization of SNX17 gene variants. This thesis sets the foundation for a deeper understanding of SNX17 in LDLR recycling and provides first insights into the potential regulation of this pathway, while also initiating the way for the later characterization of SNX17 variants. Hence, functional genomic studies together with the functional characterization of genetic variants in LDLR recycling factors can improve our understanding of how genetic variation contributes to disease progression and develop better risk assessment tools.
  • Jaakola, Suvi (2020)
    Plastics are important materials in construction due to their longevity, durability and lightness. However, the use of plastics should be reduced as they are made mainly from fossil fuels and unnecessarily end up in the environment where they cause damage to various organisms. The purpose of this Master's thesis was to investigate whether the plastics currently used in infrastructure construction can be replaced by better choices in terms of recyclability and carbon footprint. The subject of the thesis was two infrastructure construction sites in the city of Helsinki, where it was studied how much and what types of plastics were purchased for the site, excluding packaging plastics. Thereafter, circular economy experts and waste management companies as well as pipe manufacturers were interviewed to clarify how well polyvinylchloride (PVC) and high density polyethylene (HDPE) plastic materials can currently be recycled. In addition, it was investigated whether nowadays used cable protection pipes could be replaced by recycled plastic pipes or biobased plastic pipes. Plastics that were used at the construction sites were PVC, HDPE, polystyrene (XPS), polypropylene (PP), cross-linked polyethylene (XLPE) and ethylene-propylene rubber (EPDM). There is no further processing of recycled PVC into the recycled plastic granulates in Finland, which is why PVC plastic is sold abroad. In addition, due to the chlorine content of PVC, incineration is not recommended for PVC products. For this reason, it would be good to replace PVC plastic in cable protection pipes with HDPE plastic. HDPE plastic can be recycled in Finland, and further processed into recycled plastic granulates, which can be used for pipe production instead of virgin material. There are no bio-based pipes yet in Finland, which is why waste management companies do not have experience in recycling bio-based pipes. Based on the literature review, no clear differences were found in the carbon dioxide emissions of HDPE and PVC plastic manufacturing. However, HDPE and PVC pipes made from recycled plastics were clearly lower in emissions than similar virgin plastic pipes. At the moment, within the framework of for recyclability and carbon footprint, the best option would be an HDPE cable protection pipes made of recycled plastic, as the use of recycled plastic itself reduces the carbon footprint of the pipe.
  • Amin, Al (2021)
    Wood development is a significant process with both financial as well as natural perspectives. Trees and wood are of highly significance in Finland where a huge part of the gross national income devises from the forestry area. Ecologically and commercially the Norway spruce (Picea abies) is one of the most common tree species in Europe. It covers about 30% of Finland's forest area. Norway spruce is frequently used in research to study many phenomena related specifically to the wood formation and lignification. The principal objective of my thesis work was to reveal an unknown step in the lignification process in developing xylem of Norway spruce, i.e. the initiation site(s) for lignification. To achieve this goal, the aim was to investigate the chemical identity of possible lignification initiation sites in the middle lamellae and cell corners of developing Norway spruce xylem, and to answer the question where in the cell wall soluble monolignols first emerge and lead to the start of lignin formation (polymerization). I was approaching this goal with immunolabeling technique for confocal microscopy and Raman spectroscopy to unravel this initiation site of lignification by using specific monoclonal antibodies for cell wall compounds and comparing the results with the initial lignin deposition sites. To detect the location/distribution of some important polysaccharides and lignin substructure for lignification initiation, monoclonal antibodies i.e. LM10, LM11, LM15, LM24 and antibody Dibenzodioxocin or DBD were applied for confocal microscopy and some monolignol specific spectra were applied for Raman microscopy. The xylan was detected by LM10 in secondary cell wall abundantly and few are in primary cell wall of Norway spruce. The LM11 against arabinoxylan was determined more in primary cell walls but less in secondary cell wall. The location of xyloglucan was identified in the middle lamellae, primary and secondary cell wall of Norway spruce by LM15. The LM24 against glycosylated xyloglucan was found in secondary cell walls, abundantly in cell corners but few in primary cell wall. The primary antibody Dibenzodioxocin or DBD for the lignin substructure revealed that these were present in the mature cells of secondary cell walls (S2 and S3 layers). The lignin substructures DBD were not found in youngest cells where secondary cell walls are absent. The developing xylem of Norway spruce was subjected Raman microscopy and which revealed the locations of cinnamyl alcohol, coniferyl alcohol and coniferyl aldehyde. The cinnamyl alcohol was abundantly found at cell corner and middle lamellae in most developing part of xylem. The coniferyl alcohol was determined only in developing xylem cell corners. The coniferyl aldehyde was observed at cell corners, middle lamella and primary cell walls of developing xylem. The coniferyl aldehyde was located more in mature cells than younger cells. So, the Confocal and Raman microscopy images revealed the possible bindings of monolignols to polysaccharide in young cell corners, cell wall layers and middle lamellae.
  • Scheinin, Ilari (2011)
    Ewing sarcoma is an aggressive and poorly differentiated malignancy of bone and soft tissue. It primarily affects children, adolescents, and young adults, with a slight male predominance. It is characterized by a translocation between chromosomes 11 and 22 resulting in the EWSR1-FLI1fusion transcription factor. The aim of this study is to identify putative Ewing sarcoma target genes through an integrative analysis of three microarray data sets. Array comparative genomic hybridization is used to measure changes in DNA copy number, and analyzed to detect common chromosomal aberrations. mRNA and miRNA microarrays are used to measure expression of protein-coding and miRNA genes, and these results integrated with the copy number data. Chromosomal aberrations typically contain also bystanders in addition to the driving tumor suppressor and oncogenes, and integration with expression helps to identify the true targets. Correlation between expression of miRNAs and their predicted target mRNAs is also evaluated to assess the results of post-transcriptional miRNA regulation on mRNA levels. The highest frequencies of copy number gains were identified in chromosome 8, 1q, and X. Losses were most frequent in 9p21.3, which also showed an enrichment of copy number breakpoints relative to the rest of the genome. Copy number losses in 9p21.3 were found have a statistically significant effect on the expression of MTAP, but not on CDKN2A, which is a known tumor-suppressor in the same locus. MTAP was also down-regulated in the Ewing sarcoma cell lines compared to mesenchymal stem cells. Genes exhibiting elevated expression in association with copy number gains and up-regulation compared to the reference samples included DCAF7, ENO2, MTCP1, andSTK40. Differentially expressed miRNAs were detected by comparing Ewing sarcoma cell lines against mesenchymal stem cells. 21 up-regulated and 32 down-regulated miRNAs were identified, includingmiR-145, which has been previously linked to Ewing sarcoma. The EWSR1-FLI1 fusion gene represses miR-145, which in turn targets FLI1 forming a mutually repressive feedback loop. In addition higher expression linked to copy number gains and compared to mesenchymal stem cells, STK40 was also found to be a target of four different miRNAs that were all down-regulated in Ewing sarcoma cell lines compared to the reference samples. SLCO5A1 was identified as the only up-regulated gene within a frequently gained region in chromosome 8. This region was gained in over 90 % of the cell lines, and also with a higher frequency than the neighboring regions. In addition, SLCO5A1 was found to be a target of three miRNAs that were down-regulated compared to the mesenchymal stem cells.
  • Castellazzi, Eugenia (2023)
    Tiivistelmä - Referat - Abstract To aim for a just and sustainable society, it is essential to consider how we manage cities and to reflect on the role of young people as agents for successful future generations. The school system must take on the responsibility of developing a sense of social justice amongst young people. However, few learning activities are established to promote learning about environmental and intergenerational justice issues, and are usually limited to a top-down approach based on STEM disciplines (Science, Technology, Engineering and Mathematics). In this work, I argue that education in sustainability needs to be opened to a relational approach that introduces new justice perspectives, becoming a driver for active citizenship and public participation. The thesis is based on ten workshops conducted in Kumpula, Helsinki, involving 197 students from two upper secondary schools. The novelty of this work consists in addressing a specific range of upper secondary school students (16 to 19) and combining cognitive and relational learning activities to elicit reflections on environmental justice. I used a learning activity based on a Role-play method to actively involve students in working with justice perceptions and nature-based solutions. The analysis is based on a mixed methods- approach where the statistical analysis (pretest-posttest) and qualitative content analysis support each other. The innovative integration of cognitive and relational learning contributed to a deeper knowledge of urban green space management. This approach elicited new recognition justice perspectives by enhancing the participants’ awareness of community values and needs, comprehending both humans and non-humans. After the learning activity, students were generally more willing to make their voice heard by policy makers and to participate in public discussions. Based on the findings, more resources and time would be needed to build a long-term project in order to assess the permanence of relational and cognitive learning and more widely the efficacy of this approach for transformative learning.
  • Salciute, Martyna (2024)
    Lynch syndrome is the most common hereditary colorectal cancer (CRC) syndrome caused by inherited mutations in DNA mismatch repair genes. Of those, MLH1 is the most mutated predisposition gene and is best known for its involvement in the DNA mismatch repair (MMR) pathway. In addition to the MMR, MLH1 has proved to have a multifunctional role in assisting in the maintenance of genomic stability. Emerging evidence suggests, that reduced levels of MLH1 directly contribute to an increased number of DNA double-strand breaks (DSBs), leading to chromosomal instability (CIN) through impaired mitochondrial function and homologous recombination directed DSB repair. This study aimed to test this hypothesis by evaluating the DNA damage status and mitochondrial functionality in MLH1 knock-down (KD) fibroblast cell lines with varying expression levels of MLH1. DNA damage levels and repair kinetics were inspected by implementing the Comet assay. Moreover, mitochondrial homeostasis examination was done by utilizing functional mitochondrial staining and analysing mitochondrial DNA copy number. Although there was variability in the results, two KD cell lines exhibiting 30% (line 3A3) and 40% (line 2B7) MLH1 expression levels showed similar outcomes: decreased mitochondrial membrane potential, increased cellular reactive oxygen species (ROS) and stalled DNA damage repair as compared to control cell lines, suggesting the involvement of MLH1 deficiency. It is known, that MLH1 depletion predisposes to DNA damage due to impaired MMR. The findings of this thesis contribute to the growing body of evidence, suggesting that MLH1 deficiency may increase the propensity for DNA DSBs, possibly due to impaired mitochondrial function and subsequent elevation in cellular ROS. Furthermore, this increase in DNA breaks may result in CIN. However, given the limited sample size, the results warrant future studies with larger datasets.
  • Uriona Egia, Garazi (2023)
    The ends of eukaryotic chromosomes are formed by a special heterochromatic structure, the telomere, which is essential to guarantee chromosome stability. Telomeres protect chromosomic ends from DNA degradation, repair, and recombination events. However, they are difficult to replicate due to their repetitive and heterochromatic nature, which hinder DNA replication fork progression. In yeast, Mph1 helicase promotes replication fork regression, cross-over suppression during homologous recombination (HR), and telomere maintenance. Moreover, Mte1 is a D-loop binding protein involved in response to DNA damage and maintenance of telomere length, which interacts with Mph1, thereby stimulating its regression capacity as a helicase and fork. Thus, the Mte1-Mph1 complex is recruited to stressed telomeres. Mte1 also shares a domain of unknown function, DUF2439, with Rad51 and Rdh54. Additionally, Esc2 protein is involved in the regulation of DNA damage through template switch (TS) recombination, preventing HR events caused by Mph1. This thesis aimed to uncover the potential roles and interactions of proteins involved in telomere maintenance, such as Mph1, Mte1, Esc2 and Rdh54, for which two main assays were conducted: (1) Telomere Stability assay, consisting of Tus/Ter barrier based on the high-affinity binding of the E. coli protein, Tus, to specific DNA sequence called Ter; (2) Template Switching assay, focused on the capability of the proteins in reconstructing a functional LYS2 gene by TS. The obtained results demonstrated that (1) the absence of Rdh54 enhances replication fork regression, (2) Mte1 and Esc2 show opposite roles in telomere maintenance, (3) the interaction between Mte1 and Rad51 plays a crucial role in ensuring telomere stability and nuclear foci formation, (4) Mph1 and Mte1 promote cell survival through the break-induced replication (BIR) pathway. Further studies should assess the plausible interaction between Mph1 and Rdh54 proteins and characterize the function and interplay of the proteins involved in TS.