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  • Berglund, Nora (2022)
    In Finland and in many other European countries, indoor housing of dairy cattle has been increasing at the expense of grazing. According to Finnish legislation, only dairy cows housed in tie-stalls are obligated to graze for 60 days per year between May and September. Pressure to intensify production leads to increase in herd sizes, regional concentration, lack of suitable pastureland near large barns, and automation of milking. Conversely, grazing is regarded as important for animal welfare, maintenance of biodiversity and cultural landscapes. Farmer perceptions towards grazing have not been studied in Finland comprehensively, which need to be understood better in order to provide adequate support for sustainable management of grazing. The research aims at gaining understanding of the external and internal factors driv- ing the farm-level decision making related to grazing regimes. Concept of good farming ideal is used to examine farmers’ decision-making. The data was collected from 26 cattle farms with a gradient of grazing from zero to maximum. Firstly, an online questionnaire was sent out to farmers and secondly, semi-structured inter- views were conducted with 7 dairy producers, to further explore farmer views about grazing, biodiversity, and animal welfare. The results show farmers who practice grazing to perceive it more positively than the farmers who do not graze. Some of the farmers who grazed seemed to consider it almost as an intrinsic value, whereas farmers with no grazing saw it as an inef- ficient production method, which they were afraid would become an obligation. The most im- portant internal factors driving decision-making about grazing based on the questionnaire and interviews, were animal welfare, decreased workload because of grazing, infrastructure of the farm, economic aspects, and benefits of grazing to biodiversity and landscape values. Exter- nal factors found to affect the decision of grazing were incentives, regulations, and consumer expectations. Animal welfare was found to be a basis for production for many and the most important feature valued for good farming, to which grazing was seen to contribute. The re- sults imply subsidies regarding grazing should be higher for grazing to be considered profita- ble and more enjoyable by farmers.
  • Heilala, Maria (2019)
    Despite the advances in the management of breast cancer, discovery of novel and targeted drugs remains a challenge. It has been suggested that drug failure rates in clinical trials might be diminished by improving the predictive potential of preclinical cancer models. Three-dimensional (3D) scaffold-based cell culture has emerged as an attractive platform for mimicking tissue-like microenvironment, since it is well-known that cells respond to the cues in the extracellular matrix (ECM). The aim of this thesis was to develop fibrin-based hydrogels and evaluate their performance in 3D cell culture of breast cancer cells. The fibrin gel formulation was first optimized by testing the effect of different buffers on gel properties. Structural properties were examined with scanning electron microscopy and mechanical properties measured with oscillatory rheometry. Three different fibrin concentrations of the optimized formulation were then used as scaffolds for DU4475 breast cancer cells. After seven days of culture, the morphology, phenotype and proliferation of the resulting cell structures were assessed by using techniques such as light microscopy, immunofluorescent confocal microscopy and Western blot analysis. The desired properties for 3D cell culture were obtained by preparing fibrin gels at high pH in the absence of calcium. The main finding of the thesis was that fibrin concentration strongly affected the phenotype of DU4475 cells, with cells cultured in the softest gel retaining their original characteristics to the greatest extent. In the future, the developed scaffold could possibly be used in drug discovery and personalized medicine by culturing tumor explants from patients. However, the methods used in the study must be further optimized and the results validated with other breast cancer cell lines and with primary tissues.
  • Väyrynen, Pia (2017)
    Follicle-stimulating hormone (FSH) regulates mammalian reproduction. The hormonal function of FSH is exerted through its receptor, FSHR. Hormone binding leads to signal transduction by the synthesis of the second messenger (intracellular cAMP) and the activation of other downstream signaling pathways. FSH receptors are mainly found in ovaries and testes where FSH stimulates e.g. follicular growth and spermatogenesis, respectively. It has been previously shown that FSHR mutations are linked to infertility through abnormalities in the receptor function. For example, inactivating FSHR mutation (Ala189Val) leads to arrest of follicular development in females and reduced sperm counts in males. FSH action seems to be especially critical for folliculogenesis and essential for female fertility. The development of gonads and dysfunctions affecting reproduction are the focus of our research group. Studies of recent years have demonstrated extragonadal FSHR expression, including endothelial cells of female reproductive tract and developing placenta. The physiological relevance and function of this extragonadal FSHR is still not well known, especially during embryogenesis. In addition, the expression or function of the mutated FSHR has not been studied in any cells endogenously expressing the receptor. As a consequence, the purpose of this thesis was to study FSHR expression and function in human pluripotent stem cells (hPSCs) as a model for early human development. The study was conducted in a human embryonic stem cell line (hESC H9, 46, XX) and two human induced pluripotent stem cell lines (hiPSC HEL127.6 and HEL128.5; 46, XX). iPSCs were obtained from female patients carrying the A189V mutation in the FSHR gene. Cells were differentiated for 8/12 days using two in vitro cell culturing protocols for distinct differentiation attempts. The first protocol (protocol D) was designed for embryonal cell differentiation, the other (trophoblast protocol) for extraembryonal differentiation. Cells at different stages of differentiation were studied with qRT-PCR and immunocytochemistry. At d8, cells were stimulated with FSH for qPCR studies and for cAMP assay. Control cells (H9) differentiated by protocol D endogenously expressed functional FSHR. These cells responded dose-dependently to FSH stimulation by substantially increasing cAMP production, downregulating FSHR mRNA expression and altering inhibin gene expression. Patient-derived iPSCs carrying the mutation expressed FSHR as well but the receptors were non-functional as expected. Both H9 and patient-derived cells that differentiated into trophoblast-like cells with the other protocol, also expressed FSHR at low level but did not respond to FSH stimulation. Preliminary results with protocol D indicate that the cells resemble extraembryonic cell types. The study has revealed novel information and insight about extragonadal FSHR expression and function during differentiation. However, the exact identity and the biological role of these cells is yet to be confirmed.
  • Aapio, Fanny (2020)
    Food literacy is a noteworthy topic to be studied due to food’s considerable environmental and health effects. When food literacy and its characteristics are known, food literacy can be used as a tool to improve people’s health and the condition of the environment. Thus, this thesis aims to reveal the extent of food literacy among Finnish upper secondary school students. In this context, food literacy emphasises food-related environmental and health knowledge. Environmental knowledge is understanding of the global environmental impact of food. Health knowledge, on the other hand, is the familiarity with the relationship between excessive meat consumption and Finnish common diseases along with beliefs regarding diets and food products as a source of protein. This thesis also aims to identify to what extent does the food literacy differ based on gender, study year and living area. This study was performed as a quantitative sample survey and the data was collected using an online Typeform -questionnaire. The questionnaire reached respondents from many different Finnish localities, mainly from cities. The final data consisted of 1320 individuals and it was analysed using IMB SPSS Statistics 24 software. The following methods were used to analyse data: frequency analysis, an Independent Samples t Test, a One-way ANOVA, and a Post-hoc LSD test. Gender, study year and living area were used as grouping variables to examine the differences between groups. The results show that the students named school as the main source of food literacy. Moreover, the results indicate that awareness regarding food production, dietary health and proteins increase significantly from the first to the third study year. The students acknowledged food production causing environmental problems and that the share of food in the consumer’s climatic impact is considerable. Nevertheless, the students underestimated the climatic impact of cheese and they were unaware of the more specific characteristics of food’s environmental impacts. They also had food-related environmental misconceptions considering packaging, transportation and meat consumption. Moreover, approximately half or more of the students were aware of the connection between excessive meat consumption and the increased risk of distinct common diseases. Most of the students acknowledged a versatile vegetarian diet as being a healthy choice. The study also reveals that female students had notably higher dietary health knowledge than male students. This Master’s thesis study mainly supports the findings of previous studies on food-related knowledge. The results elucidate the extent, characteristics, gaps and misconceptions of students’ food literacy. These findings may be utilized to improve school education on food literacy, alter misconceptions and fill the gaps of knowledge in pursuit of improving the health of people and the condition of the environment.
  • Jokinen, Toni (2019)
    In this thesis I focus on a novel disaster response and preparedness mechanism called forecast-based financing. The mechanism is linked to the changing paradigm of humanitarian response that calls for more localized and more resilience building solutions to addressing and preventing humanitarian crisis. It is also in the core of the anticipation agenda which argues that waiting for disasters to happen is not a sustainable option and that forecast data and pre-agreed triggers and actions should be used in order to prevent both loss of lives and mitigate the cost and impact of disasters. Main hypothesis is that climate related hazards to livelihoods and food security seems to be the sector where forecast-based financing could have most potential for increasing resilience and sustainability. Slow onset crises with long lead-time allow for better targeting and more variety of actions. As the lifetime of the action is longer, there is less chance of action which is in vain. Furthermore, the actions which are more localized, for example direct support to farmers, can decrease their vulnerabilities. I aim at taking a critical approach to assessing this potentiality associated with the forecast-based financing mechanism through case study. The three cases (Mongolia, Kenya, Zimbabwe) were selected from pilots implemented by the main actors: the Red Cross, World Food Programme (WFP) and Food and Agriculture Organization (FAO) and Start Network. This thesis uses a combination of evaluative and heuristic approach to qualitative case study analysis. To answer the first research question, 1) is the forecast-based financing mechanism successful in prioritization of actions in a way that best address the needs and resources of vulnerable populations, I aim at finding out if mechanism is effective (or potentially effective) in delivering impact. For the second research question, 2) are the actions sustainable and do they bring socio-economic benefits that go beyond meeting acute humanitarian needs, I will see if new pathways are found for confirming the defined hypothesis. I am using heuristic approach in terms of finding new links e.g. between actions and needs of either donors, actors or beneficiaries. I asses and analyse available reports and evaluations (secondary data) of the selected operations. I conducted eleven (11) semi-structured key informant interviews (primary data) using practitioner’s perspective for retrieving qualitative data, for further understanding and for triangulation. All key informants were affiliated to the cases. My analysis show that the potentiality for development impacts and long-term transformation of the forecast-based financing is there but it is not utilized in the cases reviewed nor is it perceived in a same way across practitioners of different backgrounds. Currently the mechanism is used more for effective response, not for addressing the root causes of vulnerability. In general, the entitlement or empowering of a person who is affected by disaster currently does not go beyond securing bridge over lean season, avoiding negative coping mechanisms or e.g. better yield or survival of livestock. Sustainability potential of the forecast-based financing seems to be currently underutilized and international funding envelopes do not offer an alternative to the humanitarian funding launched case-by-case. Most of the practitioners interviewed were clearly in favour of linking and using forecast-based financing in some way to long-term programming, thinking outside of the framework of humanitarian response, extending lead time significantly and adding positive reinforcement inputs. I argue that with a lead time that goes long in advance, towards development actions, the mechanism needs to be reframed for the donors and the sources of funding might need to be reconsidered. To implement meaningful resilience actions in slow onset cases, triggers need to be early enough and actions in two phases: 1) anticipatory and benefiting from forecast and 2) early response. At beneficiary level the actions should be geared up to better address underlying socio-economic vulnerabilities and take advantage of the long lead time.
  • Raitanen, Henna (2020)
    In this study, the goal was to determine which nutrient, phosphorus or nitrogen, limits the phytoplankton growth at the Vanajavesi freshwater site. The aims were to detect spatial and temporal changes and find out if the wastewater treatment plant (hereafter, WWTP) located by the study site affects the nutrient concentrations and the limiting nutrient. The reliability of determining limiting nutrient by bioassays and measuring the phytoplankton response to different treatments as fluorescence was also evaluated. The study was conducted because knowledge of nutrient limitation is essential when allocating resources to reduce nutrient loading and planning other remediation practices in eutrophicated waterbodies. According to the EU Water Framework Directive, all waterbodies in the EU must be in a good ecological status by the year 2027. This goal is yet to be achieved in Vanajavesi; the ecological status of the river Vanajanreitti is poor and that of lake Vanajanselkä is moderate. The samples for bioassays were taken from five different locations. Three sampling sites were in the river and two by the lake. Based on the direction which the water flows, one of the sampling sites was before the outlet from the WWTP and the rest after it. The bioassays were carried out with the water and natural phytoplankton community taken from the study site. The experiment was conducted five times: in November, March, May, July and August. The temperature and light conditions in the incubation room were set to mimic those in Vanajavesi at each given time. Part of the preparations was to filter out the zooplankton using 50 μm plankton net. There were four different treatments: control without nutrient additions, nitrogen addition, phosphorus addition and nitrogen and phosphorus additions. Fluorescence from the 2 litre incubation bottles was measured every 1-3 days during each experiment. Chlorophyll a was determined in laboratory before and after the experiments. Nutrient concentrations were also determined before each experiment. Small seasonal and temporal changes were observed in the nutrient concentrations and the limiting nutrient. These changes were most likely due to changing seasons, effluent from the WWTP and denitrification at lake Vanajanselkä. Phosphorus limited phytoplankton growth year around at all places. At the end of the summer also nitrogen was limiting. In July co-limitation was detected in all sampling sites. In situations of co-limitation there was either no secondary limiting nutrient, or it was phosphorus. Only once, in August at the sampling point before the outlet from the WWTP, was the secondary limiting nutrient nitrogen. On average the nutrient concentrations were higher in the river than in the lake. Chlorophyll a concentrations and some nutrient concentrations were higher after the WWTP. However, no significant negative impact due to WWTP could be detected, especially at lake Vanajanselkä and the WWTP did not result in a change from phosphorus limitation to nitrogen limitation. Bioassays and the phytoplankton yield measured with a fluorometer was a reliable way of determining the limiting nutrient. Chlorophyll a concentrations verified the fluorescence results. The probe used in this study measured only the fluorescence of chlorophyll a. Even more accurate result of the phytoplankton biomass would have been obtained with a probe that measures also the fluorescence of phycocyanin, the photosynthetic pigment in cyanobacteria, because cyanobacteria has less chlorophyll a than other phytoplankton groups. As Vanajavesi is phosphorus limited or co-limited by phosphorus and nitrogen year around, reductions in phosphorus loading will likely improve the water quality. The main source of phosphorus to Vanajavesi is the nutrient loading from agricultural practises on the drainage basin. Efficient management of this diffuse loading will cause the phytoplankton biomass, especially the biomass of harmful cyanobacteria, to decrease. Nitrogen-fixing cyanobacteria is not dependent on the nitrogen concentrations in the water column, but the concentration of phosphorus. Significantly reducing the phosphorus loading is a prerequisite for the Vanajanreitti and Vanajavesi to be in a good ecological status by the year 2027.
  • Myyryläinen, Jerry (2020)
    Hypolimnetic withdrawal and purification is a new method developed to restore eutrophic lakes, which enables the removal and capture of nutrients such as phosphorus from hypolimnetic water. The method is currently being studied in a pilot-scale project at Lake Kymijärvi, Lahti, Finland. The project employs a closed-circuit system, in which the hypolimnetic water is pumped into a filtering system onshore, where the dissolved phosphorus is first precipitated. There are two possible methods for precipitation: aeration of water, in which dissolved phosphorus is precipitated by iron hydroxides as the water aerates, and addition of calcium hydroxide (Ca(OH)2) (hereafter “chemical treatment”), in which dissolved phosphorus is precipitated as hydroxyapatite. The water then flows through a nutrient filter, which traps the precipitate. The nutrient filter consists of two parallel filters, which enables the simultaneous comparison of two different filter materials. Finally, the water is returned to the lake via a wetland. A closed hypolimnetic withdrawal and purification system like this has not been previously studied as a restoration method. The aim of this master's thesis is to study the operation of the hypolimnetic withdrawal and purification system of Lake Kymijärvi by comparing the phosphorus retention capacity with 1) two different filter materials and 2) two different precipitation methods. The compared filter materials were fine gravel (manufactured by Rudus) and calcitic waste rock (manufactured by Nordkalk). Additionally, the thesis investigates the ratio of phosphorus fractions (Ca-P and Fe-P) of the phosphorus trapped in the filters, the distribution of trapped phosphorus between different filter layers and the effect of the filter materials on the concentrations of calcium, iron, manganese and sulfur of the water flowing through the filters. The operation of the hypolimnetic withdrawal and purification system was tested during four hypolimnetic water test pumping periods in summer 2019. The material for this thesis consisted of water and filter material samples collected from the system during the test pumping periods. The water samples were used to determine the capacity of the filter materials to capture phosphorus and other elements. The filter material samples were used to study the ratio of different phosphorus fractions and the distribution of trapped phosphorus between different filter layers. Both filter materials captured phosphorus efficiently via both precipitation methods. At their highest efficiency, both materials captured over 90 % of dissolved phosphorus and over 75 % of total phosphorus. No statistically significant difference was found in the phosphorus retention capacity between the filter materials, nor the precipitation methods. Of other elements, both filter materials captured iron very efficiently during both precipitation methods, and manganese during the chemical treatment. The phosphorus trapped in the filters was not evenly distributed between different filter layers and most of the phosphorus was trapped in the bottom-most layer in both filters. The phosphorus fractions between the two precipitation methods differed less than expected. After water aeration, all the phosphorus trapped in the filters was bound to iron. Even after the chemical treatment, less than half of the trapped phosphorus was bound to calcium, with the remainder bound to iron. According to the results, it is possible to remove phosphorus efficiently from hypolimnetic water with the system, using whichever of the studied precipitation methods or the filter materials.
  • Mäkinen, Theresa (2022)
    The topic of forest fires has gathered a lot of media attention in recent years as it relates closely to climate change and other sustainability issues. The media has an important role in communicating these issues as it affects, how the public percieves them, how different sustainability problems are defined and what kind of solutions are seen plausible. I became interested in how the media represents the issue of forest fires. My aim in this thesis is to find out, how the Colombian news media has framed the Amazon rainforest fires. As my material I used the news articles from the Colombian news media El Tiempo. I definined my timeframe from July 2019 to september 2019 because at that time the news subject was of high interest. After the initial search I went through the articles and left out any irrelevant ones. I was left with 24 news articles. As an analytic tool I utilized qualitative frame analysis guided by Robert Entman´s definition of frames and used ATLAS.ti to make an initial thematic coding. After that I mapped out all the actors that were cited in the news articles and divided them into groups. Using these actor groups, I searched for the frames. There were eight actor groups, politicians and political organizations being the most prominent one. Looking at how these actors talked about the forest fires, two main frames came out: populist and scientific. The populist frame concentrated mainly on Jair Bolsonaro. In this frame there was a lot of nationalist and economic arguments and responsability was directed away from him. There seemed to be a lot of enemies also. The second frame concentrated in deforestation, climate change and the forest fires being a global issue. In this frame international actors used economic and political pressure in order to affect Bolsonaro´s policy solutions. The research showed, how difficult it can be to solve shared global problem and made visible a historical political division between authoritarianism and democracy. An other important notion is the lack of marginalized groups in the news media.
  • Österblad, Ika (2016)
    Parasitoid host interactions are intimately associated with food web dynamics as well as with evolutionary change. The parasitoid s possibility to expand its host range or switch to different hosts is affected by parasitic strategy. Strong specialization to a narrow host repertoire can arise e.g. if the larva spends considerable time in close contact with an active, developing host (koinobiosis). In contrast, an ectoparasitic larva, growing rapidly on a sessile host, does not have to be equally tightly adapted to host physiology. This may permit a wider host range. However, there are other restricting factors, such as egg production capacity. Extant parasitoids show a staggering species diversity, most notably among the Hymenoptera. Theories concerning speciation in association with host range have been developed, but draw from knowledge of merely a small part of this diversity. This study adds information by showing a number of radical host shifts in the evolutionary history of the ichneumonid wasp genus Gelis. Species of this genus exploit either insect prepupae or spider eggs. These are similar in being rather defenceless, aside from a protective silk covering. Nonetheless, differences are large enough to restrict Gelis species to each utilise only one of the two groups. In order to trace ancient host group shifts, host data was mapped onto a phylogeny constructed through bayesian analysis of sequence data. Sequences from the COI (mitochondrial) and ITS2 (nuclear, noncoding) regions were used. The results suggested at least four host group shifts within the genus. In addition, wing reduction was found to have occurred in two different lineages. Through COI barcode sequence clustering supported by morphological traits, a previously undescribed species from the G. bicolor-species complex was detected. The phylogenetic analyses also indicated the existence of further cryptic species, and the genus Thaumatogelis Schwarz was found to be nested within Gelis.
  • Jeltsch, Markku Michael (1997)
  • Zhou, Quan (2020)
    Leaf senescence is a developmental and physiological phase in plants to end leaf development. Environment factors such as drought stress, extreme temperature, and pathogen threat and internal factors including age and reactive oxygen species induce leaf senescence. Some phytohormones such as jasmonic acid and salicylic acid play a key function in cell death in plants. WRKY transcription factors is known as one of the largest transcription factor family in plants which regulates a variety of plants processes. WRKY75 which belong to WRKY transcription factors has shown multiple functions in plant development like regulation of Pi starvation responses and root development and flowering. In my thesis, I focused on the role of WRKY75 in senescence and stress responses. WRKY75 was identified as a positive regulator of cell death in Arabidopsis. WRKY75 can promote salicylic acid biosynthesis by promote transcript levels of SID2 and also cause hydrogen peroxide accumulation by suppressing the transcription of CAT2. Hydrogen peroxide and salicylic acid can promote WRKY75 transcription at the same time. To evaluate the function of WRKY75 transcription factor in SA signalling and cell death, three lesion mimic mutants acd5, cat2, dnd1 and their corresponding wrky75 double mutant were used. Interestingly, no different phenotypes were found between acd5, cat2, dnd1 and their corresponding wrky75 double mutants in cell death and hydrogen peroxide accumulation detection in Arabidopsis leaves. Meanwhile, marker genes transcription levels were not different in both short day and long day growth condition. However, different phenotypes were observed in botrytis infection. Based on these results, we formed a hypothesis that gene redundancy could influence genetic characterization of WRKY75. To overcome this problem, SRDX-WRKY75 chimeric repressor transgenic lines were generated. The SRDX domain act as a dominant negative regulator to suppress WRKY75 target genes. In future research, these new lines can be used to test transcript levels for putative WRKY75 target genes.
  • Taskinen, Juuso (2019)
    Human umbilical vein endothelial cells are responsible for maintaining and forming new vessels from existing ones, in a biological process called sprouting angiogenesis. Sprouting angiogenesis is a crucial mechanism for the resolution of hypoxia and normal development of tissues. It also plays a key role in internal plague hemorrhages, which can lead to embolisms and other cardiovascular complications. Angiogenesis is also crucial for cancer development. Sprouting angiogenesis is initiated by hypoxic tissue excreted vascular endothelial growth factor gradient, which induces normal endothelial cells into either a proliferative stalk cell or a signal sensing tip cell phenotype. Both of these cell types depend on the rapid flow of lipids to their plasma membrane, either to form plasma membrane protrusions in tip cells or as new plasma membrane material in dividing stalk cells. This flow is envisioned to involve both vesicle-mediated and non-vesicular mechanisms. A major non-vesicular route of lipid transfer occurs at membrane contact sites via lipid transport proteins. Furthermore, lipids can be transported to the plasma membrane by the direct fusion of vesicles or endosomes with the plasma membrane This thesis set out to explore the role of two membrane contact site proteins, oxysterol-binding protein- related protein 2 and protrudin, in angiogenesis and lipid transfer. Their role was examined by RNA-sequencing transient knock-down samples of these proteins in HUVECs. The RNA-sequencing data was examined by differential expression, gene ontology overrepresentation and gene set enrichment analyses. Gene expression analysis provided almost 10 000 significantly changed transcripts (adjusted p-values < 0.05), in each silenced cell type. The distribution of differentially expressed genes in oxysterol-binding protein- related protein 2 silenced cells, is skewed toward negative fold changes, whereas the distribution of differentially expressed genes in protrudin silenced samples is normally distributed. The results also show significant changes in gene ontologies related to proliferation, cell cycle, angiogenesis as well as hypoxia in both sample types. Gene set enrichment analysis showed upregulation in angiogenesis related pathways, such as the PI3K-Akt and MAPK pathways, in both samples. Significant downregulation was present in cell cycle related pathways and cholesterol biosynthesis pathway in both ORP2 and protrudin silenced samples.
  • Muranen, Sampo (2019)
    Tree shoot architecture research is important due to its significance in fields such as timber production, fruit and nut production and aesthetics of common areas. Also, research on genetic factors that regulate shoot and root system architecture might provide novel methods to store more carbon in forests and, hence, mitigate global warming in the future. LAZY1 is one of the major genes that affects branch and tiller angle in herbaceous and woody species such as Arabidopsis, rice and peach tree. LAZY1 has been under scrutiny over a decade but its molecular function remains unknown. However, it is known that lazy1 mutation affects polar auxin transport. Here it is studied how LAZY1 affects initial branch angle, fiber length and reaction wood development in silver birch (Betula pendula). Also, transcript levels of few shoot architecture related genes were analyzed. LAZY phylogenetic analysis provided evidence of a duplication of LAZY1 in three studied tree species (Betula pendula, Prunus persica, Populus trichocarpa), duplicated genes are here named LAZY1a and LAZY1b. Plant material employed in this study was a segregating population (50:50) of back-cross 1 of weeping birch (B. pendula ´Youngii´) which has a truncated lazy1a. Histological samples of branches were prepared by cryo-sectioning, stained with carbohydrate binding Alcian Blue and lignin binding Safranin dyes to reveal patterns of tension wood development. Due to the large size of branch sections, samples were imaged with a microscope and the images were merged together in a Photoshop application. Branch angles were measured manually with a protractor (angle) tool from stem to the middle of a branch. The data was analyzed using mixed linear models due to the nature of used plant material. We could not use clones because of major issues in in vitro propagation. Branch samples were macerated, fibers imaged and measured by ImageJ software. LAZY1a gene expression levels were analyzed by RT-qPCR method. RNA-sequence analysis indicated that the expression pattern of LAZY1a and LAZY1b is similar in B. pendula. However, one should construct a promoter-reporter line to study with better resolution if their expression is spatially analogous. Initial branch angle was significantly different in wild type compared to lazy1a mutant. For future, one could generate single and double knock out lines of lazy1a/b to study if they have cumulative effect on the branch angle, an important factor in timber quality. Tension wood formation was difficult to quantify with the employed method, due to issues in segregating G-layered tension wood from thick-walled reaction wood. A chemical analysis of cellulose content might provide a more objective method to observe tension wood in branches. RT-qPCR method indicated that LAZY1a transcript levels are higher in wild type compared to mutant. A complementation or knock down experiment would provide sound evidence that lazy1a induces the weeping phenotype. X-ray diffraction method could be employed to study the orientation of cellulose microfibril angle in branches of the wild type vs. mutant. Generation of effective tensional stress requires a cellulose microfibril angle less than 10 and this angle is affected by auxin concentration. It is possible, that this angle is larger in lazy1a due to defect in polar auxin transport.
  • Martins, Beatriz (2020)
    According to the latest estimations, cancer is the second leading cause of death worldwide. Despite the significant advances in the range of drugs and treatment modalities to treat cancer, the number of deaths is estimated to continue rising, posing serious challenges for the patients, their families, and the healthcare systems. Conventional treatments tend to be associated with severe adverse side effects and treatment resistance. Consequently, safer and more efficient therapy options are urgently needed, especially for the treatment of metastatic tumors refractory to conventional treatments. A new and revolutionizing field in oncology is immunotherapy, in which oncolytic viruses are included. Oncolytic viruses have an inherent or acquired selectivity to replicate exclusively in tumor cells, ultimately destroying them. Simultaneously, they also activate the dormant host’s immune system to fight against the tumor. Adenoviruses, particularly, have shown to be safe, inducing only mild adverse side effects in clinical trials, making them a great candidate for further clinical development. Adenoviruses can be genetically modified to increase their infectivity or improve the anti-cancer immune responses induced by the virus, e.g., through the expression of immunostimulatory molecules. The focus of this thesis was to develop and characterize several genetically modified oncolytic adenoviruses expressing either OX40L alone or OX40L and CD40L, two co-stimulatory molecules capable of engaging both the innate and adaptive arms of the immune system to fight the tumor. The insertion of the transgenes into the E3B-14.7k region of the Ad5/3-∆24 adenovector plasmid was performed using Gibson Assembly® cloning approach. After successful cloning, the recombinant viral genomes were transfected into A549 cells for viral amplification, followed by CsCl purification to produce a high titer viral preparation. The expression of the transgenes was studied in vitro by ELISA and functional assays, showing promising expression levels of functional OX40L and CD40L. However, when the infectivity and virus killing potency were analyzed, in vitro by immunocytochemistry and MTS assay; and in vivo using an immunodeficient mouse model, the data showed that the cloned viruses performed sub-optimally when compared to the control unarmed virus (Ad5/3-∆24). These findings suggest that the insertion of the two transgenes in place of the E3-14.7k gene was detrimental to the fitness of the virus.
  • Lehtinen, Oskari Jouko (2022)
    Lifespan is a key fitness trait, together with fecundity, dispersal, and growth. In addition to environmental factors shaping variation in lifespan, it is also influenced by genetic components. Based on theory, genetic variation in lifespan is expected to be reduced due to its high relevance to fitness. However, due to trade-offs between different life-history traits and the variable or unstable environmental conditions organisms face in nature, life-history traits are also expected to sustain higher genetic variation. From studies in model organisms, such as the fruit fly and the roundworm, researchers have uncovered key insights into the genetic basis of lifespan. Some genes have been shown to contribute more to lifespan than others and different species seem to share homologous genes influencing lifespan that have been conserved. Many of these genes relate to the insulin receptors and insulin signaling processes. The allelic variation and over- or under-expression of these genes have been shown to be associated with changes in lifespan. However, regardless of our accumulating knowledge of these genes in impacting lifespan under laboratory conditions, we have little understanding of the role of these genes impacting variation in lifespan under more natural conditions. In general, assessment of genes affecting variation in lifespan in natural populations is rare, even under circumstances where we know that the lifespan has a heritable component. The Glanville fritillary (Melitaea cinxia) is a butterfly that inhabits most of Europe. It is used as a model species in ecology and evolution in relation to metapopulation dynamics and spatially structured habitats. It has been studied extensively both under experimental conditions and via observational studies in the field. The Glanville fritillary butterfly works as a good model organism for assessments of genetic components of life-history variation, as vast amounts of genomic and ecological data are already available. In this thesis, I aim to shed light on the genetic background of lifespan by using the Glanville fritillary as a model organism. More specifically, I will test the association of some well-known lifespan-related candidate genes with a phenotypic variation on the butterfly’s adult lifespan based on previously obtained experimental data on individuals collected from the natural metapopulation during the larval stage.
  • Heinonen, Maria (2021)
    Skeletal dysplasias are a group of rare monogenic bone disorders affecting joints and the skeleton. An increasing number of gene defects have been associated with skeletal dysplasias, but many cases remain without a known cause or a clear diagnosis. Exome sequencing data of the family with two siblings affected with an undiagnosed type of bone dysplasia was examined in this study with the aim of determining the genetic cause behind the phenotype. The causal variant was assumed to be in a novel disease-causing gene, since a previously performed gene panel of skeletal disease-causing genes had not revealed any positive results. The search for potential rare pathogenic variants in genes linked to the skeleton was done with VarAFT filtering software. The search revealed a short list of candidate variants confirmed first with Broad Institute’s Integrative Genomics Viewer (IGV) and then with targeted Sanger sequencing. Conservation analysis on the affected amino acids, in silico functional analysis on the variants and a comprehensive literature review on all candidate genes were performed to evaluate the likelihood of them being the variant behind the phenotype. A shortlist of three genes were obtained with the analyses, with one of them seeming to be the most likely candidate. However, to assuredly identify the disease-causing variant, further testing should be performed. Functional analyses should be done to test the functions of the proteins encoded by the candidate genes and the consequences of the pathogenic variants.
  • Laiho, Elina (2021)
    The European rabbit (Oryctolagus cuniculus) is a small mammal native to the Iberian Peninsula, but introduced by humans to all continents except Antarctica. The rabbit has been a remarkably successful invasive species due to its generalist nature and fast reproduction. Its spreading has mostly been destructive to the local nature, and humans have used fatal rabbit diseases such as rabbit haemorrhagic disease (RHD) to control harmful populations. The rabbit population in Helsinki is one of the most northern annually surviving rabbit populations in the world. It is believed to have originated from escaped pet rabbits in the late 1980s, and in the early 2000s, the rabbits spread rapidly around the Helsinki area. RHD spread unintentionally to Finland in 2016, and the disease caused a significant reduction in the Helsinki rabbit population. Rabbit population genetics has previously been studied in several countries, but never before in Finland. The aim of the thesis was to examine the genetic diversity and population structure of the Helsinki rabbit population before and after the RHD epidemic, and to compare the results to similar preceding rabbit population genetic studies. Rabbit populations have previously been found to recover from major population crashes without a notable loss in genetic diversity using DNA microsatellite markers. The recent RHD epidemic in Helsinki provided an opportunity to study, whether a rabbit population can recover from a population crash even in a harsher environment without losing genetic diversity. To conduct genetic analysis, fourteen DNA microsatellite loci were genotyped from individuals caught during two distinct time periods, in 2008-2009 (n=130) and in 2019-2020 (n=59). Population structure was observed in both temporal rabbit populations with small but significant FST values. The 2019-2020 population was more diverse than the 2008-2009 population in terms of allele numbers and expected heterozygosity. This result was unexpected considering the recent RHD-epidemic but could be explained by gene flow from new escaped rabbits. Compared to other wild rabbit populations around the world, the Helsinki area rabbits exhibit significantly lower genetic diversity. Bottleneck tests showed a significant signal separately in both temporal populations, but the RHD bottleneck cannot be distinguished based on the tests. The results could be biased by new gene flow, or the initial bottleneck caused by the founder effect of only a few pet rabbits. The rabbits have demonstrated their adaptation and survival skills in the cold climate of Helsinki. The population has significantly lower genetic diversity compared to other wild populations, yet recovered from a major RHD epidemic without reduction in genetic diversity under these more extreme environmental conditions. It has been proven again; the rabbit is a thriving invasive species.
  • Kerminen, Sini (2015)
    Studies of population structure are motivated by the need to understand population history and to have well-characterised groups of individuals in studies of genetics of diseases and traits. A standard method to analyse genetic population structure is principal component analysis (PCA). A disadvantage of PCA is that it can reliably handle only independent genetic markers. This means that the genetic markers that are correlated with other genetic markers have to be excluded from the data. This leads to a loss of information. In 2012, Lawson et al. published a chromosome painting method that can utilise haplotype information, i.e. information from correlated markers, and thus it can detect more subtle differences in populations than the standard PCA. This thesis studies two questions. The first question is whether the chromosome painting method can provide more precise genetic clustering of geographically defined Finnish groups than the standard PCA method. The second question is whether the chromosome painting method can reveal new details of population structure in Finland. The data used in this study are from the FINRISK Study survey of 1997. This cohort includes the genotype data of about 4,000 individuals and the information about individuals and their parents birthplaces. 345 Individuals were randomly chosen from the cohort in such a way that both of their parents were originated from the same province. Ten provinces of Finland were used as study groups for the method comparison. First, the data were analysed with SmartPCA (a standard PCA method) and ChromoPainter (the chromosome painting method) and the results were compared both visually and quantitatively. Finally, the individuals were assigned to populations based on the ChromoPainter result using FineSTRUCTURE program and these genetic populations were compared to the geographic origin of the individuals. The results showed that the chromosome painting method clustered seven out of ten groups significantly tighter than the standard PCA. Nevertheless, SmartPCA was faster and easier to use than ChromoPainter. The main population genetic division was found between the eastern and western parts of Finland, which was consistent with earlier studies. All in all, 15 populations were detected and the results revealed that they were geographically clustered. The genetic populations correlated well with the borders of Finnish provinces and counties. As the first conclusion, the chromosome painting method was able to give more precise results than the standard PCA but the standard PCA is still more suitable for quick preliminary analyses of genetic data. As the second conclusion, the chromosome painting method was able to detect detailed subpopulation structure in Finland and these populations are geographically clustered. Results provide an excellent basis for the future studies of population structure and genetic diseases in Finland.
  • Rahnasto, Johanna (2019)
    Preeclampsia is a vascular pregnancy disorder characterized by new-onset hypertension and proteinuria and/or new-onset preeclampsia associated symptoms during the second half of pregnancy. The pathophysiology of the disorder is not fully understood, but incomplete placentation and maternal tolerance towards fetal tissue are known to play a part in the disease pathogenesis. Predisposing factors include nulliparity, obesity, diabetes, chronic hypertension and autoimmune diseases. Furthermore, women who have experienced preeclampsia are more susceptible to cardiovascular disease later in life. One established biomarker for preeclampsia is the increased concentration of the soluble Fms-like tyrosine kinase 1 (sFlt1) in the maternal serum. sFlt1 is frequently overexpressed in preeclampsia and it is linked with angiogenic imbalance and endothelial dysfunction, although its role in the disorder is not completely clear. Preeclampsia has a genetic background. There are protective and predisposing variants in and near the Fms related tyrosine kinase 1 gene (FLT1; coding for sFlt1) that have been associated with preeclampsia either in the mother or in the fetus. In this study, five genetic polymorphisms over a 2.3 kb region in the 3’ untranslated region of FLT1 were genotyped by Sanger sequencing and fragment analysis in altogether 1200 individuals consisting of case and control mother–child pairs of the Finnish Genetics of Pre-eclampsia Consortium (FINNPEC) cohort. These polymorphisms were tested for association with various preeclampsia-related phenotypes by Fisher’s exact test. In the maternal genome, the minor alleles of rs17086497 and rs57760154 were associated with extreme hypertension (systolic blood pressure >180 mmHg) (p=0.004, OR=1.77) and obesity (p=0.023, OR=1.63). Homozygosity for these minor alleles was associated with pregnancy complications in general (p=0.026, OR=2.53) and the early-onset form of preeclampsia (p=0.004, OR=3.34). Additionally, the minor alleles of rs9554314, rs3138582 and rs149279513 were associated with extreme hypertension (p=0.045, OR=1.63) and obesity (p=0.023, OR=1.78). Moreover, a suggestive association to severe proteinuria (> 5 g/24h) was found in the maternal genome. In the fetal genome, significant negative associations were reached for rs17086497 and rs57760154 in terms of the serum concentration of sFlt1 in the preeclampsia group (p=0.008, OR=0.23). Overall, the results seem to link the studied region in the maternal genome to preeclampsia with severe features. This supports the idea of preeclampsia as a heterogeneous disorder with varying etiology and mechanisms and thus highlights the importance of differentiating between the various sub-phenotypes. For example, the association of the same allele in the fetal genome with lower maternal sFlt1 levels and in the maternal genome with severe symptoms of preeclampsia suggests that the sFlt1 level might not be a good measure in all patients. Additionally, the observed associations with extreme hypertension and obesity point to the possibility that this region might be relevant for the endothelial damage that is thought to be a central factor in creating the later-in-life disease susceptibility.
  • Almusa, Henrikki (2013)
    The next-generation sequencing (NGS) platforms create a large amount of sequence in short amount of time, when compared to first generation sequencers. An overview of the NGS platforms is provided with more in-depth look into Illumina Genome Analyzer II as that is used to create the data for the thesis. There were two main aims in this thesis. First, to create a pipeline which can be used to analyse genomic sequencing. Second, to use the pipeline to compare whole human exome capture methods from two manufacturers, Roche Nimblegen and Agilent. The pipeline is describe in detail in material and methods. All the inputs for the pipeline are described and examples shown. In the pipeline the given sequences are first aligned against the reference genome. Then various separate analysis is performed to retrieve variants and coverage of the sequencing. Supplementary results include paired-end anomalies, larger insertion and deletion polymorphisms and assembly of non-aligned sequences. The two capture methods are also described and changes to the manufacturers' recommended protocols are listed. Finally, the section has the options and various inputs used in the pipeline runs of the exome data. The results of the pipeline is a basic level of analysis of the sequencing as well as various graphs showing the quality of the run. All the output files intended for user are described. By using the results of the pipeline, the user can do more in-depth analysis as required by the project. When comparing the two exome capture methods, the Nimblegen capture was shown to be more efficient in capturing the CCDS exome. While the Agilent capture kit provided better one fold coverage over the exome, higher fold coverage (over 10 fold), which is required for reliable variant calling in nextgeneration sequencing, was better reached using the Nimblegen capture kit. Also, significantly fewer false positive paired-end anomalies were observed in the library created by using the Nimblegen capture.