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  • 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.
  • 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.
  • 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.
  • 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.
  • Kõbin, Mihkel (2020)
    Intersectins (ITSNs) are important scaffold and adaptor proteins that play an important role in various cellular processes such as endocytosis. Although we know a lot about their function, there is little information on the regulation of these proteins. On the other hand, microRNAs have been shown to have an extensive function in regulating numerous genes in animals and their dysfunction is credited for down regulation of many proteins. In this study, I demonstrate that microRNAs are potential regulators of ITSNs in HEK293 cells and human neuronal cell cultures. In this study, I cloned 3’UTRs of different isoforms of intersectins (ITSNs) and microRNAs to the expression vectors to express them in cells. I then transfected HEK293T or neuronal stem cell line (HEL47.2) with the constructed vectors and used various methods to analyse the effect of microRNAs on the expression of ITSNs. The main methods I used were dual-luciferase assay, reverse transcription quantitative PCR and western blotting, human neuronal stem cell culturing and lentiviral transduction. My results demonstrate that there were two microRNAs that stood out from other and had a significant downregulation of ITSNs mRNA levels in HEK293T cells. Those were miR-124 and miR-19. However, in the human neuronal cell line I did not observe a significant alteration of the ITSNs transcript level. Additionally, I suggest that the given microRNAs regulate protein levels by promoting the decay of the ITSN transcripts. However, more studies are needed to show a stronger causative effect of microRNAs on ITSNs. Subsequent studies should also look at how multiple microRNAs can influence gene expression cooperatively.
  • Lammensalo, Linda Sofia (2021)
    The intersections of climate change and sexual and reproductive health and rights (SRHR) have increasingly received attention from international organisations but also from academia. For some, establishing these intersections is about reducing human pressure on the Earth systems, while for others it is about the human rights of vulnerable individuals and communities. Many have lauded these connections for providing a win-win solution for both. While these benefits are championed, there has been little reflection on the underlying motives and justifications for establishing these connections in the first place. Given the problematic past of population control policies, understanding these justifications is necessary to break away from the neo-colonial practices of the past. This thesis investigates the motives and justifications for establishing such intersections between SRHR and climate change. Specifically, the thesis addresses two questions, namely: 1) In what ways are the interconnections between SRHR and climate change justified in academic literature? 2) What are the implications of the ways in which these interconnections are justified? By drawing on a postcolonial feminist theoretical framework rooted in understanding this nexus critically, and carefully reflecting on the implications of these discourses, the thesis answers these questions by systematically drawing on a sustained body of research. The data consist of 88 academic publications that are systematised through discourse analysis. The findings identify six distinctive intersectional discourses which reflect the ways in which SRHR, and climate change are justified, namely: public health, population dynamics, reproductive rights, critical, sustainable development and environment discourses. Largely reflecting adherence to liberal feminist and populationist frameworks, these findings imply that the discourses, justifications, and motives do not sufficiently address the neo-colonial practices and structural inequalities that shape intersections between SRHR and climate change. Analytically, therefore, this thesis suggests that postcolonial feminism offers a more effective way for understanding intersectional discourses because it recognises how power inequalities manifest in the discourses, while contributing towards more justice-based approaches to sustainability.
  • Donner, Jalmar (2020)
    Climate warming is expected to cause changes in winter conditions in northern regions. These changes include reduced depth and duration of the snow cover, and strong fluctuations in winter temperatures. A mesocosm experiment was planned to study the short term effects of contrasting winter conditions, and an introduced species (garden lupin; Lupinus polyphyllus), on chlorophyll fluorescence and pigment concentrations of native meadow species in southern Finland. Twelve different meadow species, representing different overwintering strategies were planted in each mesocosm at the beginning of summer in 2016 in Viikki, Helsinki. One year later, a lupin was planted in half of the mesocosms. Over the winter 2017-18, one half of the mesocosms was moved to Nåtö on the Åland islands, and the other half was moved to Lammi, Hämeenlinna. To each site, both lupin-containing mesocosms and lupin free controls were moved. In the inland site in Lammi, the mesocosms spent the winter covered by a thick snow cover that isolated them from harsh air temperatures from beginning of December to end of March. In coastal Nåtö, a thin snow cover formed in January and melted by mid-March. In the experiment, the maritime winter climate on Nåtö represented such winter conditions that are expected to be common on the mainland in the future, when climate warming progresses. Leaf chlorophyll fluorescence as well as concentrations of leaf chlorophyll and flavonoids were repeatedly measured nondestructively for all species using optical apparatus. Growth and flowering of the lupin was monitored during spring and summer 2018. No marked differences were observed in the meadow species chlorophyll fluorescence and content between sites, indicating that these are well adapted to variable winter conditions. The flavonoid composition of the meadow species seemed to be regulated by seasonal changes in light intensity and temperature. Small reductions in chlorophyll content for some species indicated that these were disadvantaged by the lupins presence. This was attributed to the lupins shadowing effect. In contrast, two evergreen species seemed to take advantage of the nitrogen input from the lupin in terms of higher chlorophyll content in summer 2018. The lupin overwintered successfully in mainland Lammi, but seemed to suffer from the maritime and snow poor winter conditions in Nåtö, which led to reduced production of leaves and inflorescences during the growing season 2018. The results indicate that native meadow species in Finland are relatively tolerant of the expected changes in mainland winter conditions, whereas these changes will be disadvantageous for the lupin.
  • Levo, Martti (2023)
    Climate change is applying pressures to plant populations, which must adapt or move to retain fitness. A changing climate highlights the need for us to understand the potential that species possess to evolve in addition to any plastic responses. Approaches that allow the study of contemporary evolution, such as resurrection studies, have the capacity to provide insights into the responses of populations to these changes. In this resurrection experiment, seeds from seven populations of Hypericum perforatum collected from the UK and France, and their historic counterparts, were grown and subjected to four temperature treatments. Three traits were measured and compared between historic and contemporary populations: date of flowering, average seed weight and flower abundance. I found that temperature influenced date of flowering and flower abundance, leading to an overall earlier flowering time and an overall decrease in flower abundance with increase in temperature. The only significant difference between historic and contemporary populations was found in flower abundance - where, whilst flower abundance declined with increasing temperature, contemporary populations produced proportionally more flowers than historic populations per degree of temperature increase. These results suggest that plasticity allows this species to adjust its flowering phenology to retain fitness in warmer conditions but that evolution during the past decades may have selected for a decreased flower abundance at higher temperatures. These findings contribute to our overall understanding of how species have and will react under climate change, as we try to disentangle the roles that plasticity and evolution play in enabling populations to retain fitness under changing conditions.
  • Turunen, Ossi Artturi (2022)
    Life-history decisions, and trade-offs, are affected by resource acquisition, which can vary among individuals, and during the life cycle of an individual. In Atlantic salmon (Salmo salar) many life-history decisions, such as age-of-maturity, are strongly associated with two genomic regions, vgll3 and six6. Previously, these genomic regions have been associated with food acquisition in adult sea-run Atlantic salmon; however, this has not yet been studied in juvenile salmon. Furthermore, population density strongly affects the food availability of juvenile salmon through resource competition. Here, using controlled crosses reared in semi-natural stream conditions, I investigated the effect and relationship of life-history genetics and population density on juvenile Atlantic salmon food acquisition. Stomach contents from 148 juvenile Atlantic salmon were quantified for their prey item composition, total number of prey items and dry weight, and environmental and genetic basis of food acquisition were analysed using mixed effects models. Late maturing six6 genotype fish had higher stomach-content dry weights and fuller stomachs than early maturing individuals, in low densities. Furthermore, low density fish were of better condition and had higher growth rates than high density fish. There was no association between six6 and vgll3 genotypes and food acquisition in high densities. The results support the existing knowledge of the negative effect of increasing population density on juvenile Atlantic salmon growth and condition. Furthermore, the density dependent association of six6 and food acquisition suggest a trade-off between early maturation and maximised food acquisition.
  • Fischbach, Lea (2022)
    Establishing and maintaining cell polarity is critical to all multicellular organisms. Apicobasal polarity is a type of cell polarity specific to epithelial cells, which is established and maintained by three distinct protein complexes. Among them, the Scribble (Scrib) complex plays a role as a basolateral determinant. Scrib is a scaffold protein with multiple functions, including maintenance of the basolateral polarity of epithelial cells and a tumor suppressor, acting as a regulator of the Hippo signalling, an evolutionarily conserved pathway which controls organ size through regulation of cell proliferation and apoptosis by inhibiting the transcriptional co-activator protein Yorkie (Yki). A recent experiment proposed that Scrib is involved in maintaining tissue homeostasis through relaying apicobasal polarity regulation across the tissue. This mechanism can be used both by normal cells to rescue hypomorphic scrib cells and by loss of scrib cells to spread loss of polarity. The signal is likely related by cell-cell contact and the junctions present in epithelial cells may be involved in this communication. This project aims to identify the genes involved in tissue homeostasis through intercellular alignment of apicobasal polarity together with Scrib. First, a screening protocol was established by studying genetic interactions and tissue structure. Second, a systematic screening was carried out by using deficiency lines of left arm of the third chromosome in Drosophila. Fly stock expressing spatially and temporally controlled scrib RNAi was established and crossed with deficiency lines to identify genes that have synergy with Scrib. The wing discs of the offspring were dissected, imaged, and the phenotypes were sorted into categories according to the degree of overgrowth. Five strong candidates and four candidates with milder phenotype were identified. The results show the screening method is robust and suitable to carry out a finer, single gene level screen of the candidates, as well as screening for additional candidates in the rest of the Drosophila genome. The identified candidates provide new leads to develop the theorical model of intercellular alignment of apicobasal polarity. Understanding how apicobasal polarity is maintained in the dynamic environment of a living organism is important for physiological and pathological conditions. This study provides an important insight into further understanding tissue development and homeostasis.
  • Ruuska, Janika (2022)
    Individuals suffering from anorexia nervosa (AN) have one of the highest mortality rates of all psychiatric disorders, as a consequence of health complications that follows severe malnutrition. The impairments in cognitive flexibility, including an extreme focus on restricting food despite a rapid decline in body weight in AN, also plays an important role in the development of the disorder and has been suggested as a hallmark of AN. This cognitive inflexibility, common among many psychiatric disorders such as depression and obsessive-compulsive disorder, is linked to alterations in serotonin (5-HT) signaling in the medial prefrontal cortex (mPFC). Reduced 5-HT2A receptor activity and potentially increased 5-HT1A receptor activity are evident in the mPFC in individuals with AN and may be linked to impaired cognitive flexibility, however, the mechanisms through which 5-HT and inflexibility interact in AN are not fully understood. A better understanding of this link could pave the way toward more effective pharmacological treatments for AN. Psilocybin, a psychedelic compound produced by so-called “magic” mushrooms, has a high affinity for several 5-HT receptor subtypes including 5-HT1A and 5-HT2A receptors, and has now been empirically demonstrated to increase cognitive flexibility in individuals with major depressive disorder (MDD). In this study, we sought to understand how the development of pathological weight loss and/or psilocybin administration influenced the expression of RNA molecules of 5-HT2A and 5-HT1A receptors expression in the mPFC of rats. To this end, we used the activity-based anorexia (ABA) model, the only experimental model known to elicit voluntary reductions in food intake and voluntary hyperactivity that leads to rapid body weight loss in the majority of animals exposed to ABA conditions. Outcomes were compared against an age-matched control group that were not exposed to the ABA paradigm. Animals were administered psilocybin (1.5 mg/kg) or saline (control) and 4-10 days later brain tissue was collected for processing. Receptor expression was detected using a novel multiplex RNA fluorescent in situ hybridization (FISH) technology, RNAscope®. The main aim of this study was to examine changes in the expression of RNA molecules of 5-HT2A and 5-HT1A receptors in the mPFC elicited by ABA conditions and determine whether these were ameliorated by the administration of psilocybin. We found that animals exposed to ABA demonstrated a significant reduction of 5-HT2A receptors’ RNA levels in the mPFC, and that this was not influenced by psilocybin treatment. There have been reports from clinical trials that individuals with AN experience “less than expected” subjective effects from psilocybin, which may be explained by reduced expression of RNA molecules of 5-HT2A receptors in the mPFC, and is supported by our results in rats. Taken together, these results highlight a specific serotonergic mechanism that could underly the development of pathological weight loss and offers insight into possible issues with the therapeutic application of psilocybin for AN. Future studies will need to examine the effects of psilocybin during a more acute period following treatment to define these effects. Moreover, whether or not the reduced 5- HT2A receptors’ RNA level expression induced by ABA is restored with body weight recovery should be determined.
  • Ranki, Jukka-Pekka (2020)
    Loisten vaikutus isäntäpopulaatioihin ja isäntäyksilöiden elinkiertoon vaihtelee isäntä–lois-suhteittain. Loisten leviämistä ja vaikutuksia isäntäpopulaatioissa on kuvattu erilaisilla matemaattisilla malleilla, joissa on keskitytty joihinkin loisen yleistymisen kannalta olennaisiksi arvioituihin tekijöihin, kuten loisen transmissioon ja isäntien kuolleisuuteen, syntyvyyteen ja vastustuskykyyn. Mallien taustaoletukset ja painotukset vaihtelevat. Isäntä–lois-suhteiden muodostumisen taustalla onkin monia vaihtoehtoja tai syitä, joita on hyvä selvittää. Isäntä–lois-suhteiden muodostumista ja loisen leviämistä voidaan tarkastella myös ohjelmallisesti esimerkiksi simulaatioilla, joilla voidaan selvittää eri tekijöiden tai parametrien arvojen vaikutusta loisintaan. Simulaatio voi mallintaa loisintaa isäntäpopulaation tasolla ja kuvata tartunnan leviämistä isäntäpopulaatiossa eri hetkinä. Se voi mallintaa loisintaa myös yksilötasolla, jolloin siinä voidaan huomioida eri tavoin yksilöön liittyviä ominaisuuksia, kuten yksilön liikkumista tai parinvalintaa. Tällaisten isäntäpopulaation ja loispopulaation yksilöiden suhteita, sijainteja ja tilanteita eri hetkillä mallintavien ohjelmien suunnittelun tueksi on hyödyllistä luoda käsitteellinen malli, joka kuvaa loisintaa yksilötasolta lähtien samalla selventäen isäntien ja loisten ominaisuuksia ja loisintaan liittyviä vuorovaikutussuhteita. Tutkimuksen tavoitteena olikin luoda loisintasuhteita yleisesti kuvaava käsitteellinen malli. Tutkimuksen aineisto muodostui loisinnan biologiasta ja siihen kytkeytyvistä ilmiöistä. UML-mallinnuskieltä (Unified Modeling Language) käytetään yleisesti oliopohjaisten ohjelmistojen suunnittelussa ja järjestelmien kuvauksessa. Loisintaakin voi tarkastella isäntien ja loisten välisenä järjestelmänä, jossa loisinnan osapuolet ovat olioita. Menetelmänä käytinkin UML-luokkakaavioita. Tutkimus selvittää isäntä–lois-suhteiden olennaisia piirteitä ja muodostaa niiden pohjalta loisintaa yksilötasolla yleisesti kuvaavan UML-luokkakaavion. Osoittautui, että ’tavanomaisen’ loisinnan, jossa loinen elää kiinni isännässään hyödyntäen sitä ravintolähteenään, sekä kleptoparasitismin tai sosiaalisen loisinnan yhdistäminen samaan UML-luokkakaaviomalliin saattaa johtaa tulkinnallisiin epäselvyyksiin. Osoittautui myös, että isäntä–lois-suhteisiin liittyy erilaisia vuorovaikutuksia ja ilmiöitä esimerkiksi loishyökkäysten torjunnan osalta. UML-luokkakaaviomallista jäi pois muun muassa isännän loisintaa ehkäisevä käyttäytyminen, jotta mallin rakenne säilyi selkeänä. Isäntä–lois-suhteisiin liittyvät myös eliöiden liikkuminen ja lisääntyminen, jotka vaihtelevat lajeittain ja kehitysvaiheittain. Niitä voi tarkastella omina malleinaan, jotka kytkeytyvät loisinnan osapuoliin tai niiden kehitysvaiheisiin. Loisinnan osapuolten suhteisiin liittyy koevoluutiokin. Nopeasti ja runsaasti lisääntyvillä ja muuntuvilla mikroloisilla evoluutio voi olla nopeaa. Kuitenkin evoluutiota tarkasteltaessa pitäisi tietää, mitä mallinnetaan ja mitä rajoituksia evoluution mallinnukseen sisältyy. UML-luokkakaaviossa ei mallinnettukaan evoluutiota, vaan se vaatisi tarkempaa analyysia.