Skip to main content
Login | Suomeksi | På svenska | In English

Browsing by Title

Sort by: Order: Results:

  • Kuussalo, Lauri (2024)
    Neurodegenerative disorders are globally the most common cause of disability leading up to 10 million deaths every year, but the mechanisms underlying neurodegeneration are not understood well. Methylation of messenger RNAs (mRNA) at adenosine base position N6 (m6A) by a methyltransferase-complex is a modification that regulates gene expression by influencing mRNA stability, transport, translation and degradation. The mRNA m6A levels are decreased in many neurodegenerative diseases. Our group has shown that dopamine neurons can be rescued, by unknown mechanisms, by activating the methyltransferase-like 3 (Mettl3) enzyme, which increases mRNA m6A levels. The aim of this study was to understand the mechanisms underlying mRNA m6A-induced neuronal survival. We investigated with reverse transcription quantitative polymerase chain reaction (RT-qPCR) how the changes in mRNA m6A modifications affect gene expression. We validated with female rat striatum samples that Mettl3 activation upregulates Neurexophilin-3 (Nxhp3), an important protein for neurotransmitter release and motor functions. Pellino 1 (Peli1), a E3 ubiquiting ligase, was upregulated in nucleus accumbens region of the same rats. Finally, we found with in vitro mouse cortical neurons that Mettl3 inhibition induces endoplasmic reticulum (ER) stress and an unfolded protein response. We saw the activation of inositol-requiring enzyme-1 (Ire1-alpha) and PKR-like ER kinase (Perk) signalling pathways. ER stress is a hallmark of neurodegenerative diseases. This is the first study to show a connection between Mettl3 inhibition and ER stress but the mechanism is still unknow. Further studies need to be performed in order to see if Mettl3 inhibition regulates Ire1-alpha and Perk activity directly, or does Mettl3 inhibition induce ER stress indirectly. Our results highlight how crucial mRNA m6A modification is for neuronal survival.
  • Boiko, Elizaveta (2023)
    In this master’s thesis project, I studied the association of lipid molecules phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 3-phosphate (PI3P) with autophagy in neurons. One of the aims of the study is to determine the level of basal autophagy in primary hippocampal neurons and to come up with a protocol for autophagosome observation without forcing radical changes in cell culture conditions. Other mammalian cells have extremely weak basal autophagy, but they increase it significantly in response to starvation, for example. However, neurons are extremely sensitive to any changes in their surroundings. They change their morphology, behaviour and biochemical properties, and often they simply do not survive. Therefore, the goal is a protocol for successful autophagy observation with minimal external influence. Despite the debate around basal autophagy in neurons, I observed high levels of basal autophagy in neuronal cells incubated in media without supplements. Also, my observations revealed that the inhibition of the last step of autophagosome processing with Bafilomycin A1, was enough to cause the massive accumulation of large autophagosomes. Results demonstrated that primary hippocampal neurons exhibit high levels of basal autophagy, suggesting that on the contrary to other mammalian cells neurons might not have enough potential to increase autophagy when it is induced pharmacologically or by stressful conditions. This would explain why autophagy induction is often claimed to be ineffective for neuronal cultures. The main goal is to observe and compare PI4P presence on autophagosomes in normal conditions and when autophagosome:lysosome fusion is inhibited with Bafilomycin A1. The side goal is to observe PI3P presence on autophagosomes as well. I transfected primary hippocampal neurons with fluorescent probes for PI4P or PI3P as well as for autophagosome-related protein LC3. Localization data was collected with live-cell imaging on a confocal microscope. As expected, PI3P was not detected on autophagosomes located in soma. It is involved in the initial vesicle biogenesis in distal axons but not in later events taking place closer to the cell body. PI4P showed high degree of colocalization with LC3, indicating PI4P presence on autophagosomes, but only when the fusion was presumably inhibited by Bafilomycin A1. These results suggest that PI4P appears on autophagosomes either as a result of compensatory pathway, where autophagosomes fuse with late endosomes instead of lysosomes; or as a molecule normally involved in autophagosome:lysosome fusion. Literature supports the latter explanation, but it cannot be confirmed without further research. These results give an insight into PI4P role in neuronal autophagy and might be relevant for the future research of autophagy disruption and aggregate accumulation in neuronal diseases as a consequence of abnormal lipid signalling, lipid metabolism and transport.
  • Michalowski, Piotr (2019)
    The TrkB signaling pathway plays an important role in synaptic transmission and plasticity. Synaptic plasticity is disrupted in many neurological disorders, such as major depression and dementia. A number of studies indicate that TrkB (tropomyosin-related kinase B) signaling is required for the therapeutic effects of antidepressants. Both conventional and rapid-acting antidepressants encompass the TrkB pathway but the underlying mechanism of this remains unknown. Recent studies have, however, revealed an intriguing link between emergence of slow wave EEG activity (SWA) or sedation and the TrkB pathway. Notably, various anesthetics and sedatives (e.g. isoflurane and medetomidine) that increase SWA concomitantly induce TrkB signalling, and this seems to happen independently of BDNF (brain-derived neurotrophic factor), the primary ligand of TrkB. Given the ability of Src kinase to transactivate TrkB in vitro, we have examined the acute effects of medetomidine and isoflurane on SrcY416 and TrkBY816 phosphorylation in the adult rodent cortex and hippocampus by using Western blotting. Pyrazolopyrimidine 2 (PP2), a Src kinase inhibitor, was implemented in order to inhibit TrkB signalling pathway induced by medetomidine. The study was further extended to sleep deprivation experiments to investigate the effects of deep sleep on the Src and TrkB protein phosphorylation. Phosphorylation of GSK3βS9, another important molecular event coupled with antidepressant effects, was also investigated. The results indicate that both isoflurane and medetomidine activate Src kinase and TrkB signalling pathway. Such an effect was not, however, seen in the PP2 study and thus we failed to confirm the mechanistic connection between Src and TrkB. A trend in the phosphorylation of TrkB, Src and GSK3β was found in the brain samples collected after 15 minutes of recovery sleep, suggesting that TrkB signalling is also facilitated during physiological SWA. In conclusion, these results reinforce the hypothesis that SWA occurs simultaneously with TrkB signaling. Future studies are required to test the involvement of Src kinase in this phenomenon.
  • Rastogi, Neetika (2024)
    This thesis investigates whether the antidepressant-like and plasticity-promoting effects of LSD depend on TrkB expression among parvalbumin-positive interneurons (PV+ INs). Given the pivotal role of PV+ INs in facilitating critical-period-like plasticity, both during development and under the influence of conventional antidepressants, we hypothesized they may be involved in mediating psychedelic-induced neuroplasticity. Our findings challenge prevailing hypotheses, suggesting that LSD's plasticity-promoting effects may not rely on PV+ INs. We found that LSD did not increase the spine density of PV+ INs among wildtype mice, nor affected the expression of parvalbumin in PV+ INs or the perineuronal nets (PNNs) that enwrap them. Unexpectedly, we found that LSD did have subtle effects on PV+ IN spine density and the expression of parvalbumin in a mouse model with reduced TrkB expression among PV+ INs, suggesting a possible kind of compensatory mechanism at play. Our results reveal the multifaceted nature of LSD's actions on plasticity, shedding light on its therapeutic potential and prompting further exploration into its underlying mechanisms.
  • Ryhänen, Emma (2023)
    Rare mutations in the primate specific ZNF808 gene are a novel cause of pancreatic agenesis, a congenital developmental disorder that leads to neonatal diabetes. ZNF808 loss-of-function has been shown to lead to aberrant activation of regulatory MER11 elements, followed by upregulation of genes in proximity to these elements and increased expression of hepatic lineage markers. These findings suggest ZNF808 to play a key role in balancing the differentiation of endoderm progenitor cells between pancreatic and liver lineages during early human development. This thesis work aimed to study the gene regulatory mechanisms of ZNF808 in the differentiating endoderm progenitor cells to understand its function in controlling pancreatic lineage specification. This was achieved by comparing the lineage specification processes in wild-type (H1) and ZNF808 knockout (H1-ZNF808-KO) human embryonic stem cells (hESCs) during pancreatic differentiation. Further characterization of cellular heterogeneity and gene expression profiles upon ZNF808 loss was done using single-cell RNA sequencing (scRNA-seq). To validate the role of ZNF808 as the mediator of the observed lineage specification bias, the phenotype rescue was examined in a ZNF808 knockout overexpression cell line (H1-ZNF808-KO-OX). The results of this study demonstrate a clear lineage specification bias in the ZNF808 knockout, seen as divergence of the multipotent endoderm progenitors towards alternate hepatic and biliary fates at the posterior foregut stage. By modifying the pancreatic differentiation protocol, we were able to observe phenotype manifestation and cellular heterogeneity suppressed in the standard differentiation conditions. The scRNA-seq data analysis revealed the emergence of a biliary cell population showing upregulation of several hepatic markers, suggesting an alternative lineage specification process governed by ZNF808. Additionally, preliminary results from ZNF808 overexpression showed rescue of the ZNF808 knockout phenotype, further supporting its critical role in the normal pancreatic lineage development. In conclusion, these findings demonstrate the important role of ZNF808 in early human pancreatic development and warrant further studies on the detailed gene regulatory network guiding pancreatic lineage specification.
  • Saarreharju, Roosa (2020)
    While weeks of continuous treatment is required for conventional antidepressant drugs (e.g. fluoxetine) to bring their full therapeutic effects, a subanesthetic dose of ketamine alleviates the core symptoms of depression (anhedonia, depressed mood) and suicidal thinking within just few hours and the effects may last for days. Nitrous oxide (N2O, “laughing gas”), another NMDAR antagonist, has recently been shown to have similar rapid antidepressant effects in treatment-resistant depressed patients (Nagele et al. 2015). We previously found using naïve mice ketamine and N2O treatment to upregulate five mRNAs related to the MAPK pathway and synaptic plasticity, both implicated as being important in the action of rapid-acting antidepressants. In the current study, these shared mechanisms were further investigated in C57BL/6JHsd mice, using behavioral test batteries to study depressive-like behaviour and RT-qPCR for biochemical analyses. We first aimed to demonstrate behavioral differences between naïve mice and a chronic corticosterone-induced animal model of depression, and to use this model to investigate antidepressant-like effects of ketamine and N2O. According to the results, chronic corticosterone produced some behaviors typical of a depressive-like phenotype, namely significant worsening of coat state and decreased saccharin consumption in the saccharin preference test. Both ketamine and N2O exhibited antidepressant-like effects by reverting decreased saccharin preference. We then aimed to elucidate the effects of ketamine and N2O on five previously found shared mRNAs: Arc, Dusp1, Dusp5, Dusp6 and Nr4a1. N2O significantly upregulated all targets in the vmPFC, except Dusp5, two hours after beginning of N2O treatment. Neither ketamine nor sole chronic corticosterone produced any significant changes. The results of this study suggest that N2O is a potential candidate for rapid alleviation of depressive symptoms. We suggest that the action of rapid-acting antidepressants, more specifically N2O, is based on a homeostatic response of the brain to a presented challenge. Here this challenge would be cortical excitation previously been shown to be caused by N2O, which leads to activation of pathways such as MAPK and subsequent Arc, Dusp and Nr4a1 signaling. The level of expression of these markers would then depend on which phase this response is in and hence, the differences in time between treatment and brain sample dissection could be a reason for conflicting results to previous research. Future studies would benefit from detailed investigation of the chronic corticosterone-induced model due to its potential in controlling for behavioral variability, thus reducing the number of animals needed for preclinical research. Overall the preliminary findings of this study could be one of the first steps in the search for the mechanisms underlying the potential antidepressant effect of N2O, how these molecular markers are related to its action and how it differs from the action of ketamine.
  • Nousiainen, Susanna (2018)
    Endometriosis is a common complex disease that affects the quality of life of millions of women worldwide. It is characterized as an inflammatory condition where endometrium-like tissue is found at ectopic sites. The main symptoms are pain and infertility. There is no cure for the disease yet. Diagnosis requires surgery in most cases, the invasiveness is a problem. The costs for societies due to endometriosis are immense. Endometriosis, despite being a benign disease, shares characteristics with malignancies: invasion, proliferation, and angiogenesis. These enigmatic aspects make this disease an interesting subject for research. Endometriosis is shown to have a heritability of 50%. Research on the molecular genetic background is needed for the development of low-invasive diagnostic methods and better treatments for the disease. Genetic research has recently focused on genome-wide association studies of large patient and control cohorts. By design, these studies can only explain a portion of the low-risk genetic variants of common diseases. No causal high-risk gene defects behind endometriosis are found yet. In this study whole exome analysis is utilized for searching a heritable gene defect from a family of four closely related Finnish endometriosis patients in two generations. Two of the patients have a combined phenotype of endometriosis and ovarian or tubal carcinoma. Endometriosis is known to increase the risk for certain types of malignancies, endometriosis-associated ovarian cancers. Four candidate susceptibility genes for endometriosis were identified in this study FGFR4, NALCN, ZNFX1, and NAV2. The findings still need to be validated in patients not related to the study family. The variants found in this study lay a basis for screening additional endometriosis patients and functional analysis of the variants. Subsequent research on these found candidate susceptibility genes may elucidate the pathogenic pathways behind endometriosis or endometriosis-associated ovarian cancer in the future.
  • Jylhä-Vuorio, Anni (2023)
    Marine debris is a problem that also affects sea birds. Several bird species are known to utilise marine debris among their nest materials in different parts of the world. Debris in nests can cause entanglement and increase the risk of debris ingestion, and hazardous substances leaching from plastics can have negative effects on birds. There are also anecdotal observations of debris in the great cormorant (Phalacrocorax carbo sinensis) nests in the Gulf of Finland, however, systematic studies are lacking. In this Master’s thesis I examined the prevalence of debris in cormorant nests in the Gulf of Finland, focusing mainly on plastic debris. The study was carried out in four nesting islets, which were located in Kotka, Porvoo, Espoo and Kirkkonummi. The sampling took place in autumn 2021. 50 nests were randomly sampled on each nesting islet, and plastic debris in the nest was counted and classified according to their type, colour and origin. Plastic debris was further categorized in the laboratory according to their polymer type using Fourier Transform Infrared spectroscopy (FTIR). Debris from the nesting islets was also counted and classified according to their type, colour and origin. In total, 58% of the nests contained debris, but the prevalence of debris in the nests varied between the colonies; In Kirkkonummi debris was found in 92% of the nests while in Porvoo only 34% of the nests included debris. Plastics constituted great majority of nest debris (95%). Most common source for plastic debris was consumers, most common plastic type threadlike and polymer type polyethylene (PE). The number of debris in the nests was linked to the width and location of the nests: core nests contained more debris than periphery nests and the number of debris in the nest was positively correlated with the width of the nest. The amount of threadlike plastics in the nests was higher than that in the surrounding environment, indicating active selection by cormorants for threadlike debris types as nest material. Based on the results of this thesis, nest surveys could be a useful tool in evaluating the effectiveness of certain reduction measures aiming to tackle marine plastic pollution.
  • Doraisamy, Sri Suhashini (2024)
    Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an evolutionarily conserved, secreted protein. Structurally, MANF has a saposin-like and SAP-like domain that is commonly found in proteins in the lysosome and nucleus, respectively. In addition to it, it has a RTDL motif which is a KDEL-like sequence representing the ER retention signal. Previous studies have revealed that MANF has cytoprotective effects in several disease models, making it a putative therapeutic molecule. However, its exact function and molecular mechanism are yet to be elucidated. Therefore, knowing the exact function of MANF is crucial for its effective use as a therapeutic. Subcellular localisation is an effective way to determine a protein’s exact function as it provides an enclosed environment and surface for possible chemical interaction in which a protein can execute its specialised function(s). Due to the lack of studies on the subcellular localisation of endogenous MANF at a basal state and preliminary unpublished results from the group on MANF’s ability to regulate catalase mRNA expression, the aim of this study was to investigate MANF’s subcellular localisation through the development and validation of biochemical methods. Methods such as immunofluorescence, immunoelectron microscopy and biochemical fractionation were explored and validated for studying subcellular localisation. Here, the limitations of immunoelectron microscopy and biochemical fractionation are described, as the protocols used need further optimisation. Using immunofluorescence microscopy, MANF was detected particularly in the perinuclear region and ER. The findings are suggestive of MANF localisation but not conclusive due to the inadequate physiological condition of the cells; indicating the need for further optimisation of the methodology to study MANF’s localisation.
  • Lindfors, Iida (2024)
    Gastrointestinal stromal tumours (GISTs) are rare mesenchymal neoplasms that arise from the interstitial cells of Cajal, the so-called pacemaker cells of the intestine. GISTs typically contain an oncogenic driver mutation either in the proto-oncogene KIT or platelet-derived growth factor receptor A (PDGFRA), which belong to the class III receptor tyrosine kinases. Patients with a high-risk or advanced disease are standardly treated with a tyrosine kinase inhibitor imatinib. Despite this molecularly targeted treatment, many patients experience disease relapse, after which the prognosis is poor. Personalised treatment is rarely offered to patients as a first-line treatment option, even though several targeted therapies have been approved for GIST. Increasing treatment personalisation could improve treatment outcomes, yet the lack of patient-specific research models for GIST hinders the research. Three-dimensional (3D) cell culture models are widely used in cancer research to study the molecular mechanisms underlying tumorigenesis. Their ability to mimic the tumour biology and microenvironment is superior compared to the traditional two-dimensional (2D) cell culture model. For several cancers, these cell culture models have also been researched as platforms for personalised treatment selection with promising results. This thesis project aimed to study UPM Biomedicals’ GrowDex-based 3D cell culture model as a potential platform for personalised treatment selection for GIST patients. GrowDex is a plant-derived hydrogel that resembles the extracellular matrix. Another aim of this project was to set up a Sanger sequencing protocol covering frequently mutated areas in GIST to facilitate the validation of this cell culture model through drug testing on patient samples. To assess the GrowDex microenvironment, the viability and proliferation of two GIST cell lines, GIST-T1 and GIST48 were monitored. Furthermore, the imatinib response of GIST-T1 in GrowDex was assessed and compared to the response in other cell culturing conditions. The Sanger sequencing protocol was optimised using the aforementioned cell lines and then applied to GIST patient samples. The results of this project demonstrated that GrowDex provides a suitable microenvironment for culturing GIST cells and supports their 3D growth. GIST-T1 cells were less sensitive to imatinib when cultured in GrowDex in comparison to the 2D culturing condition, which is likely explained by the 3D organisation of the cells. Finally, the Sanger sequencing protocol was used to uncover the KIT/PDGFRA mutation status of several GIST patient samples. In conclusion, these results provide important information for further development of this cell culture model with patient samples.
  • Merenheimo, Salla (2018)
    Nuorten kiinnostus luonnontieteiden opiskelua kohtaan on heikentynyt sekä Suomessa että kansainvälisesti ja nuoria hakeutuu luonnontieteellisille aloille yhä vähemmän. Samaan aikaan Eurooppaan tarvitaan yli 700 000 uutta tutkijaa. Eräänä syynä nuorten kiinnostuksen puutteeseen luonnontieteiden opiskelua kohtaan pidetään nuorten stereotyyppistä tutkijakuvaa. Tutkijakuvalla tarkoitetaan henkilön mielikuvia ja käsityksiä tutkijoista. Stereotyyppiseen tutkijakuvaan kuuluvat käsitykset laboratoriotakkiin ja silmälaseihin pukeutuneista miehistä, jotka työskentelevät laboratoriossa tehden kokeita ympärillään monenlaisia tutkimusvälineitä. Stereotyyppisen tutkijakuvan väitetään vaikuttavan negatiivisesti nuorten asenteisiin ja kiinnostukseen luonnontieteiden opiskelua kohtaan ja jopa heidän halukkuuteensa hakeutua opiskelemaan luonnontieteellisille aloille. Suomalaisten lasten ja nuorten tutkijakuvaa ei ole aiemmin kartoitettu. Tämän tutkimuksen tavoitteena oli selvittää suomalaisten lasten ja nuorten käsityksiä tutkijoista. Tutkimuskohteena olivat Helsingin yliopiston LumA-tiedekasvatuskeskuksen kesän 2017 tiedeleireille osallistuneet lapset ja nuoret (N=455). Tutkimuksessa selvitettiin sukupuolen, iän sekä tiedeleirin teeman yhteyttä leiriläisten tutkijakuvaan. Tutkimusmenetelmänä käytettiin kyselylomaketutkimusta, jossa vastaajat piirsivät omiin mielikuviinsa pohjautuvan kuvan tutkijasta. Piirroksia käsiteltiin määrällisenä aineistona. Jokainen piirustus analysoitiin tarkistuslistan avulla, johon listattiin kirjallisuudesta ja aineistosta nostettuja stereotyyppiseen tutkijakuvaan liittyviä piirteitä. Tulokset analysoitiin deskriptiivisellä analyysillä. Sukupuolten välisiä eroja tarkasteltiin khiin neliö -testien ja Mann-Whitneyn U-testin avulla. Iän yhteyttä tutkijakuvaan selvitettiin Kruskal-Wallis -testillä. Tutkimuksen luotettavuutta tarkasteltiin validiteetin ja reliabiliteetin avulla. Tutkimuksessa selvisi, että suomalaisilla lapsilla ja nuorilla on stereotyyppisinä pidettyjä käsityksiä tutkijoista, vaikkakin stereotyyppisiä piirteitä esiintyi piirroksissa vähemmän aiempiin tutkimuksiin verrattuna. Tyypillisimmät piirroksissa esiintyneet stereotyyppiset piirteet olivat työskentely sisällä, miestutkija sekä erilaiset tutkimuksen symbolit ja teknologiavälineet. Sukupuolella oli yhteys tutkijakuvaan tyttöjen piirtäessä merkitsevästi enemmän naistutkijoita ja hymyileviä tutkijoita kuin pojat. Vastaajan ikä ei ollut yhteydessä stereotyyppisten piirteiden määrään, toisin kuin aiemmissa tutkimuksissa. Leirin teema oli vahvasti yhteydessä niihin tarvikkeisiin, joita tutkijan ympärille piirrettiin. Tutkimuksessa havaittiin piirrosten tulkinnan olevan subjektiivista ja vaikuttavan tutkimuksen tuloksiin. Siten nuorten tutkijakuvaa tulisi jatkossa kartoittaa useiden metodien avulla. Tämä tutkimus antaa viitteitä tiedeleirien potentiaalista lasten ja nuorten tutkijakuvan muovaamisessa. Tutkimuksen tuloksia voidaan hyödyntää luonnontieteiden opetuksen kehittämisessä sekä formaalissa että nonformaalissa tiedekasvatuksessa: tiedostamalla nuoren oman tutkijakuvan muodostuminen voidaan opetuksessa tarjota oppijalle mahdollisuuksia muodostaa realistisempaa ja monipuolisempaa tutkijakuvaa esimerkiksi tutkijavierailujen ja toiminnallisten aktiviteettien kautta. Tämä voi lisätä nuorten kiinnostusta ja minäpystyvyyttä tutkijan uraa kohtaan.
  • Tiihonen, Eeva (2023)
    It has been observed that children’s interest towards natural sciences decreases as they grow up and start middle school. The decrease of interest towards natural sciences and studying them has led to a situation, where science and technology students’ relative share of higher education students has been falling in some of the OECD countries. Formal education needs support to carry out fascinating science education for children and to maintain their interest towards natural sciences. One of the opportunities to fascinate children towards sciences are science centers and their activities either combined with formal education or organized in an informal form like science camps. The aim of this research is to survey the biological knowledge, the interest towards biology and the ability to apply the biological knowledge of science campers (mainly 5th and 6th graders) and to study the connections between them. At the same time, the effect of age and gender of the science campers is studied. To survey the biological knowledge of the campers, multiple-choice test was used and the fascination with biology was investigated with Likert scale variables. The ability to apply the biological knowledge was investigated with drawings that were produced during a biology-themed science camp program. The data was analyzed using quantitative methods. The results indicated that the science campers were relatively fascinated with biology and that they master biological knowledge quite well but the ability to apply the knowledge was varying. There were no differences between different ages nor genders but there are many factors such as the economic status of campers’ families that might have affected on the results. There was found a statistically significant connection between biological knowledge and fascination with biology, which is not surprising, but it speaks in favor of the importance of supporting fascination in terms of learning.
  • Kalliokoski, Laura (2021)
    During the Covid-19 pandemic in Finland, there was a debate about the usefulness of face masks in suppressing the epidemic. Lack of scientific knowledge was emphasised in the debate, and the participants sought to define the role of science in decision-making. In this thesis, the ways in which ignorance and uncertainty were discussed and used to define the boundaries of science in the Finnish face mask debate are studied. In the theoretical part of the thesis, the meanings of ignorance and uncertainty are clarified and the boundary-work of science as well as uncertainty as a boundary-ordering device are discussed. The politicisation of non-knowledge and the characteristics of policy-relevant science are also examined. In the empirical part, the knowledge/non-knowledge claims of the Finnish experts and decision-makers who participated in the face mask debate are analysed. The data consists of 99 quotations collected from news articles published from March 1 to October 31, 2020. Qualitative frame analysis is employed to examine the forms of knowledge and ignorance along with the boundary-ordering devices used in the debate. The results show that experts working at the science-policy boundary highlighted uncertainty and ignorance most often. They also used uncertainty as a boundary-ordering device the most, although overall, this came up very rarely in the debate. The main discrepancy was between the assessments of different expert bodies, as research scientists did not usually mention the underlying uncertainties of scientific findings. Different actors had different approaches towards knowledge and ignorance, reflecting differences in epistemic cultures. Regulatory science and academic science have different criteria for assessing the credibility of knowledge. Moreover, not all ignorance and uncertainty in decision-making can be reduced with scientific methods. Therefore, more resilient decision-making processes should be developed, in which ignorance and limitations of scientific knowledge are identified and embedded in the decisions.
  • Sainio, Aki (2018)
    In this master’s thesis I examine transdisciplinarity in theory and practice. Transdisciplinarity is seen as an inevitable approach when we strive to understand and solve many of the complex problems of the modern world e.g. the environmental crisis. For this reason it has also quickly increased in popularity in the research funding. With this premise and despite the diverse theory on transdisciplinarity the implementation in practice is often relatively flimsy. This gap between theory and practice has acted as a motivation to the thesis, in which I am interested in how the transdisciplinary expectations based on the theoretical ideals and set on the cross-disciplinary environmental research intersect with the realistic transdisciplinary advancements in the research programs. In addition, I am interested to know why the practice doesn’t meet the expectations. The thesis is solidly theory-oriented. First I shed light on the background, characteristics and motivations of transdisciplinarity as well as disciplines, after which I present an array of the complex challenges of transdisciplinarity. In the results section I examine the manifestations of the challenges on a practical level that is based on three environmental research programs organized over the course of 2011–2014 by HENVI, the Helsinki University Centre for Environment (now HELSUS). In addition to the qualitative analysis based on the interview data, the results section also examines theory on a more practical level of implementing transdisciplinary research programs in general. This presentation thus enables a closer dialogue between the analysis data and practical theory. The primary results of this thesis are five problematics that are the manifestations of theory not meeting the practice properly. They are organized into the themes of funding, knowledge production, administration, socio-culture and education and help to organize and ultimately face the challenges of transdisciplinary research. From a comprehensive set of perspectives the problematics display strongly the highly disciplinary nature of the modern academia. This is the most significant single reason for the difficulties to accomplish transdisciplinarity. In addition, all the five problematics reflect the temporal restrictions that also undermine the potential of an effective transdisciplinary interaction. The essential measures to create solutions and hence also the ideal implementation of transdisciplinarity are mainly beyond the focus of the thesis. However, the problematics provide a problem-based framework that strives to contribute to the further studies focused more profoundly on the actual solutions
  • Sjöblom, Robin (2020)
    In winter plants are exposed to harsh winter conditions with low temperatures being one of the major challenging factors. Traditionally winter has been considered a period unfavourable for plant growth and activity, but newer findings reveal higher levels of activity than previously assumed possible. Adaptations to different winter conditions are observed between species but also within species between populations which can be expressed in differing phenology between populations. Dormancy is a widespread phenomenon in the plant kingdom with major importance in plant evolution. Dormancy is considered to be present in seeds and buds of a wide spectre of plant groups, but asexual reproductive units like bulbils have been thought to lack the ability to undergo the phenomenon of dormancy. Findings suggest that a dormancy-like phenomenon can also be present in bulbils. Allium oleraceum is a bulb forming geophyte with a widespread distribution in Europe that grows on many differing habitats. The predominate form of reproduction in the species is the vegetative formation of bulbils. The wide distribution has led to adaptation to different environmental conditions, furthermore the species displays six levels of polyploidi partially differing in traits like ecology. The differences between cytotypes are regional and there are large intracytotytpic variations. In Finland tetra- and pentaploid populations have been reported, differing in their distribution patterns. The Finnish cytotypes exhibit differences in morphology but there is also evidence for ecological differences between the cytotypes. In addition, there is an atypical tetraploid population which differ significantly morphologically from other tetraploid populations. The objective of this master’s project was to examine the growth of bulbils from three different origins of Allium oleraceum. Another objective of the experiment was to give information on differences between the cytotypes in Finland, tetra- and pentaploids, but also the atypical tetraploid cytotype. Furthermore, I investigated whether the bulbils exhibit a dormancy-like phenomenon, with a special focal point on dormancy according to Vegis’ theory (1964). Earlier findings have shown considerable capability of growth during winter in Allium oleraceum, which is also examined in this project. The experiment included collected bulbils from two localities. Tetra- and pentaploid bulbils were collected from a mixed population of both cytotypes in Tvärminne, Hangö, and tetraploid bulbils were also collected from the atypical tetraploid population on Sveaborg, Helsingfors. Growth experiments were done outside and in growth chambers with controlled temperature and light conditions. The bulbils were planted outside in early autumn. Of each origin one group was kept outside during the entire winter, one group was put in growth chambers in December and one group was put in growth chambers in February to examine the effect of differing winter length on growth. During the experiment, the timing of growth onset in bulbs and leaf growth was followed up. The origins included in this project exhibited considerable differences. The pentaploid cytotype from Tvärminne had bulbils of greater size than the tetraploid cytotypes, between which there was only an indication of a difference. For the bulbils from the atypical tetraploid population growth onset took place early in the autumn and the vast majority of the bulbils started growing in a short period of time. For the two origins from Tvärminne the growth onset took place later and a considerable number of bulbils started growing in the spring. The tetraploid cytotype from Tvärminne exhibited earlier growth onset and a higher share of bulbils started growing in the autumn than the pentaploid cytotype from Tvärminne. In the growth chambers the differences between the three origins were not as obvious but the two cytotypes from Tvärminne were affected by the timing of the experiment more than the atypical tetraploid cytotype from Sveaborg. The observed differences between the origins in the experiment are thought reflect the different distribution patterns of the cytotypes and could hence be adaptations to different conditions. The atypical tetraploid population could be of Central European origin which would mean that it could have adaptations to mild winters which would explain the big difference between this origin and the two other origins. Between the two experiments in the growth chambers significant differences were observed. The growth was considerably greater in February than in December for all origins, especially in the midmost temperatures. The observed differences between the two experiments signifies that bulbils of Allium oleraceum exhibits a dormancy-like phenomenon and according to Vegis’ theory. In contrary to earlier findings, only little growth was observed during winter. The lack of considerable growth could be explained by the thick snow cover which made the amount of light that reached the plants very low which then led to little growth. The results from this project suggest that there are differences between the three different origins of bulbils included. Further studies are needed to find out if the observer differences are adaptations to local conditions or if there are differences on a higher level between the Finnish cytotypes.
  • Renvall, Valtteri (2021)
    Energy consumption of apartment buildings account for a significant part of European Union’s total greenhouse gas emissions and improving the energy efficiency of buildings is a major part of reaching Union’s climate goals. To reach these goals the EU has revised some of its legislation and one of the latest reforms is the complete revision of Energy Efficiency of Buildings directive in 2018. Directives article 14 decreed that member states need to implement energy efficiency measures on large apartment buildings and to meet these measures member states were given three options on how to implement article 14. Finland implemented the article with so called voluntary advice method. The goal of this study is to understand the conclusion of the national implementation of article 14 and explain it with implementation theory. The study tries to understand what factors led to the implementation of voluntary advice method and whether this selection can be explained with implementation theory. Study design is one case explanatory case study. Seven semi-structured interviews were conducted for this research and the material was analysed with qualitative methods. All the interviewees were either officials in charge of the implementation or experts and researchers who took part in the implementation process. The study shows that the factors leading up to the selected implementation method were earlier experiences from other implementations, the straightforward nature of implementing advice method and the cost estimates between the given implementation options. It also became clear that the method was favoured by the officials, experts and target group and this volition might have affected the result. Study helps to understand the process of implementing EU legislation in a member state, what challenges officials face during the implementation and what kind of expectations steer the process. The study found out that previous implementation methods may have a significant impact on the implementation of revised directives. Study also verified the factors affecting implementation defined by implementation theories.
  • D' Assunção Castro, Beatriz (2022)
    Tiivistelmä – Referat – Abstract The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase is a master regulator of cell growth. In the presence of environmental cues, such as nutrients and growth factor, mTORC1 is transported to the lysosome where it is activated by a small GTPase Rheb. Dysregulation of mTORC1 has been linked to several diseases such as cancer and neurodegeneration. Despite our growing understanding of the nutrient-driven activation mechanism of mTORC1, we still do not fully understand how nutrients are transported out of the lysosome or how nutrient sensing is connected to nutrient transport. Recently, SLC38A9, a small lysosomal transmembrane protein, was identified as a mediator of the efflux of essential amino acids from the lysosome to the cytosol. It also acts as an amino acid sensor for mTORC1, playing a role in its activation. Due to poorly vascularized tumor cores, cancers such as pancreatic ductal adenocarcinoma, have access to very scarce amounts of free nutrients. Consequently, they rely on scavenging of protein macromolecules from the extracellular environment, followed by digestion inside lysosomes. The digested nutrients are released to the cytosol via transporters such as SLC38A9 and activate the mTORC1 pathway which carries out the growth processes. In fact, recent studies in mouse xenograft models have shown a severely slowed down growth of PDAC tumors with SLC38A9 knocked out. Blocking of SLC38A9 activity with pharmacologics or biologics would prevent the release of digested amino acids from the lysosomes, starving cancer cells of nutrients, while sparing normal cells that do not feed on extracellular proteins. However, SLC38A9 is still poorly understood, and development of selective inhibitors first requires mechanistic understanding of the protein and knowing what its binding pockets look like. In order to obtain this information, we aimed to determine the three-dimensional structure of SLC38A9 through cryogenic electron microscopy (cryo-EM). However, two significant challenges hindered our ability to obtain high-resolution images of this membrane protein: (i) its small size, and (ii) its constant conformational changes. To address this, I proceeded to develop a set of nanobodies that would bind SLC38A9 with high affinity and specificity. Nanobodies allow for locking of target proteins in specific conformational states, and they can also serve as chaperones for visualizing proteins in cryo-EM. To obtain these nanobodies, I used a library of 100 million unique nanobodies, displayed on the surface of yeast cells. Specific SLC38A9 binder nanobodies were obtained through multiple rounds of selection and sorting, using decreasing concentrations of fluorescently- labeled SLC38A9. After the final selection round, single colonies were picked and the strength of binding to SLC38A9 was evaluated. High-throughput screening results showed that we were able to obtain specific SLC38A9 binders and that there was variation in binding strength among the selected nanobodies. These nanobodies will enable the determination of the cryo-EM structure of SLC38A9 and also serve as tools to further dissect the function and mechanisms of SLC38A9 in amino-acid efflux from lysosomes to cytosol, providing further insights for the development of novel cancer therapeutics.
  • Ordax Sommer, Nicolás (2021)
    Trace element analysis is a useful tool for the study of migration and migratory connectivity in birds. Trace elements are present in the environment and, through the food chain, can be incorporated into tissues such as growing feathers. Since the concentrations of elements remain stable after the feather has stopped growing, and trace element abundances can vary at very small geographical scales, the concentration of trace elements in feathers can provide information on the location where a feather was moulted. Trace element analysis is still rarely used and there are important gaps in our understanding of how trace elements can vary at different organizational levels such as within a feather, between individuals or even between species. It is also not clear if large-scale geographical patterns can be detected by the method, as trace element concentrations can vary a lot even at small scales, which could make it impossible to see larger-scale patterns. To address that, my objectives were (1) analysing the variability of trace element concentrations within feathers, between individuals and between species and (2) determining whether trace element levels differed in feathers grown in Africa compared to feathers grown in Europe. This would shed insight on the suitability of trace element analysis for the study of migration and migratory connectivity. I analysed the concentration of 18 trace elements in the rachis of feathers from willow warblers (Phylloscopus trochilus) and barn swallows (Hirundo rustica) collected in Finland. I plucked three belly feathers from willow warblers collected in spring, whose feathers had grown in Africa. These feathers were used to analyse variability of trace element concentrations within feathers and between individuals. They were also compared to feathers plucked from barn swallows collected in spring (two feathers per bird) to analyse variability between the feathers of two species that winter in the same region. Finally, African-grown feathers of willow warblers were compared to European-grown feathers of willow warblers collected in autumn (two feathers per bird) to look for differences in trace element concentrations in feathers grown on two different continents. Trace element concentrations were analysed using Laser-Ablation Inductively-Coupled-Plasma Mass-Spectrometry (LA-ICP-MS), which allowed to measure concentration at hundreds to thousands of points along the feather rachis. The concentration of each of the 18 elements was used as the response variable in linear mixed models (LMM). To model variation in concentration within the feather I used location along the feather rachis as the explanatory variable and explored how well it predicted concentration of each element. To compare variation between feathers and individuals I fit models including and excluding the feather and individual that each measurement belonged to as random effects and compared them using AIC. To compare between willow warbler and barn swallow feathers grown in Africa I included species identity as the explanatory variable and looked at how the concentration of the 18 elements differed between them. Finally, I followed the same approach to compare willow warbler feathers moulted in Africa and in Europe. For most elements there was little variation along the feather rachis, with concentration remaining stable from feather base to tip. Zn and S showed an increase in concentration starting at the feather base until the central part of the feather and then remained constant toward the tip. Feathers belonging to the same individual showed mostly similar trace element concentrations, although there were exceptions and differences between feathers of different willow warbler individuals were also little. 10 out of 18 elements showed significant differences in feathers of willow warblers and barn swallows grown in Africa. Eight of those elements were more abundant in willow warbler feathers, while only two were more abundant in barn swallow feathers.12 out of 18 elements showed significant differences between their level in African-grown feathers and European-grown feathers. Of those, 10 elements showed higher levels in African-grown feathers, while only two were higher in European-grown feathers. My results suggest that trace elements can show variation at different organizational levels. Variability within feathers was important in at least two elements, which could be caused by physiological processes. This means that when designing sample collection for trace element analysis, unless we know that an element does not vary along a feather, it is important to consider which part of feathers we are sampling. Variability between feathers and individuals was lower than within feather variability, but still significant. Future studies should account for possible within and between individual differences in their design. Differences between barn swallows and willow warblers were large, which was expected based on the literature. It is still unknown what drives these differences between species: some explanations suggested have been physiological and dietary differences or differences in their habitats. I also found clear differences between feathers of willow warblers grown in Europe and Africa. While the exact cause is still not known, this means that at least in willow warbler feathers it is possible to study large scale geographical patterns by trace element analysis. LA-ICP-MS has potential to be a powerful tool to study migration and migratory connectivity in birds. It allows to detect variation in trace elements at continental scales while also allowing to control for different levels of variability in the study design. I encourage researchers to adopt its use in their research.
  • Williamson, Adam (2024)
    For a better understanding of global climate change we need evidence allowing us to track changes in the environment. Pollen is geologically stable, making it a key option as a potential proxy for tracing historic environmental changes. To quantify past environmental changes, it is necessary to test proxies under today’s climate. The amount of UV-B radiation reaching the surface of the Earth has varied throughout the Earth’s history. These variations are ecologically important because changes in UV-B radiation impact plant regulation, growth, defense, and decomposition. The availability of fossil pollen and spores has resulted in significant interest in the potential of using the relationship between UV-B radiation and the accumulation of phenolic sunscreens as a proxy to trace past changes in UV-B radiation. Fossil pollen from Pinus sylvestris is readily available and proven techniques exist to quantify levels of UV-B absorbing compounds from both fossil and extant pollen. We investigated how levels of UV-B-absorbing compounds in Pinus sylvestris pollen change after strobili developed under UV attenuating filters. Fifteen Pinus sylvestris trees were selected from a seed orchard of trees in Nurmijärvi, Finland. The treatments used were Rosco 226 film – filtering solar UV-A and UV-B light, polyester film – filtering solar UV-B, polyethylene film – acting as a transparent control, and an open control condition with no filter. The filters were installed in April 2022 and 2023 and remained in place each year beyond dehiscence towards the end of May. The pollen was analysed using Fourier-transform infrared spectroscopy. Principal component analyses and linear regression models were used to simplify the multivariate data and then describe the levels of UV-B absorbing compounds in the different treatment groups. A sample of needles from underneath the filters was used to verify the effectiveness of UV treatments across the experimental design by analysing their epidermal flavonol content. Our results found no clear link between UV-B exposure and accumulation of UV-B absorbing compounds in Pinus sylvestris pollen. However, we did find statistically significant differences in concentrations of UV-B absorbing compounds in pollen between the different trees. The needle analyses verified that the experimental design had the potential to affect the biochemistry of these branches by revealing significant differences in relative absorbance by epidermal flavonols due to UV treatment type. Multifactorial drivers affect the concentrations of UV-B-absorbing compounds in plants, and viewing the response of these compounds to a single driver may be an oversimplification complicating their use as a proxy. We argue that methodologies used in previous research have inconsistencies which fail to account for environmental factors that either covary with UV radiation or diverge from it. This may explain why our results go against the trend. Finally, we examine our own research experimental design and suggest improvements and avenues by which this research can move forward.
  • Sartamo, Laura (2017)
    Baltic Sea has undergone major changes in the last few decades and its ecological condition has changed. Paleolimnology provides methods to detect changes in the past, mostly from the times when no surveillance was conducted. This Master's thesis is about the response of a common Cladocera, Eubosmina maritima to the past environmental change in Sandöfjärden, Gulf of Finland. I studied past isotopes, δ13C and δ15N to detect past changes in the eutrophic changes from sedimented subfossil remains to detect how the E. maritima population abundance and morphology have changed due to eutrophication and increased predation pressure. I analyzed a 30 cm sediment core of which I counted E. maritima remains. I also measured the lengths of carapaces, mucros and antennules in order to detect changes in their morphology. I used carbon nitrogen ratio, total carbon, total nitrogen, and their stable status of the sea area. To indicate predation pressure on E. maritima, I used the resting egg data of a predatory cladocera Cercopagis pengoi, that was introduced to the area at the beginning of the 1990's. The sediment core is stratigraphic, meaning that the layers are connected to each other and therefore cannot be treated as independent samples. The data was first viewed graphically to reveal correlations. I applied redundancy analysis (RDA) to find out if changes in the Eubosmina-populations are explained by the environmental changes. Associated is Monte Carlo permutation test to check which explanatory variables are the most important. Finally I performed variance partitioning to separate the effects of the environment caused by time in the sediment time series. My results show that E. maritima population has increased in number since the 1950's and a positive correlation with δ15N suggests that this has a connection to increased nutrient levels. It also seems that big E. maritima individuals became more common in eutrophic conditions. Increased predation pressure affected E. maritima populations the strongest right after C. pengoi was introduced to the area when also the longest mucros were found. There also was a slight decrease in the E. maritima abundance at that time. The changes of the lengths of the appendages seem to be more connected to predation pressure, whereas the abundance and the overall body size seem to have a connection with eutrophication. Along with the eutrophication increased the number of E. maritima in the Gulf of Finland. The effect of predation pressure was the clearest right after the introduction and then later smoothened.