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Suuresta tarpeesta huolimatta, ei työvälineitä geeniekspression endogeeniseen säätelyyn ole nykypäivänä tarjolla lääketieteellisiin eikä tutkimuksellisiinkaan tarkoituksiin. Vuonna 2017 karakterisoitiin uuden CRISPR-Cas tyypin VI kompleksit. Nämä kompleksit hyödyntävät endonukleaasiaktiivisuudessaan uudenlaista Cas13 -efektoria, jonka kohteena toimii yksijuosteiset RNA-molekyylit. Cas13 tunnistaa kohteensa opas-RNA:n (gRNA) avulla. Tätä komplementaarisuutta hyödyntämällä on onnistuttu kohdistamaan Cas13:n aktiivisuus spesifisiin lähetti-RNA molekyyleihin nisäkässolukokeissa ilman kohde-RNA:n ulkopuolisia hajoamistuotteita. Tämän lisäksi nukleaasiinaktivoituja Cas13 efektoreita (dCas13) on käytetty esimerkiksi kohdennettuun nukleotidien deaminaatioon ja vaihtoehtoisen silmikoinnin indusointiin. Tämä todistaa dCas13 efektorien kyvyn toimia ohjelmoitavina apuproteiineina, joiden avulla voidaan ohjata kompleksiin liitetyn proteiinin toiminta spesifisille kohde-RNA:n alueille. Tässä tutkimuksessa, kaksi eukaryoottien translaatioon osallistuvaa proteiinia, ELAVL1 ja EIF4E, yhdistettiin dCas13b efektorin kanssa C- ja N-terminaalisesti, tarkoituksena lisätä kohteena olevan lähetti-RNA:n ekspressiota parantamalla tämän translatiivisuutta tai stabiliteettia. Koeasetelmassa vertailtiin näiden neljän fuusioproteiinin sekä aktiivisen Cas13b:n vaikutusta lusiferaasin ekspressioon käyttäen kuutta eri gRNA:ta aktivaation ohjaamisessa. Kokeet suoritettiin in vitro ympäristössä HEK293T-soluissa. Natiivi Cas13b vähensi merkittävästi lusiferaasisignaalia, kun taas samassa asetelmassa C-terminaalinen dCas13b-ELAVL1 fuusio lisäsi tätä tilastollisesti merkittävästi eli aikaansai kasvaneen lusiferaasiekspression. Vastaavaa vaikutusta ei ollut havaittavissa muissa fuusioproteiineissa. Tulokset todistavat onnistuneen Cas13b-välitteisen degradaation, sekä dCas13bELAVL1-välitteisen lisääntyneen lusiferaasitranskriptin translaation. Jatkotutkimusta vaaditaan fuusioproteiinin toiminnallisuuden ja varsinaisen kohteen ulkopuolisen aktiivisuuden määrityksessä. Siitä huolimatta tutkimuksessa esitelty fuusoproteiinikonstrukti voisi hyvin olla toimiva työkalu geeniekspression spesifin lisäyksen mahdollistamisessa endogeenisessa kontekstissa

Bamboos are very relevant for ecosystem dynamics in tropical and subtropical forests worldwide. Madagascar holds 35 endemic species of woody bamboo, mainly found in forested areas. Six species of bamboo lemurs endemic to the island are highly specialized to exploit such bamboo species. Bamboo lemurs are highly threatened with extinction, and recent translocations of individuals to protected areas have failed, resulting in the death or emigration of all translocated individuals. The distribution, dynamics, and conservation status of the bamboo species they depend on is poorly known, while rising deforestation rates and direct exploitation of bamboo present important threats. Remote-sensing techniques, used often to map vegetation classes over large scales can potentially be used to map the extent of bamboo in a forested area, given the distinct structural and phenological characteristics of these grasses. In this study, I integrated ecological and remote sensing approaches to understand the diversity of bamboo species in the Ranomafana region of Madagascar, and to determine whether their distribution can be mapped through remoted sensing, if their occurrence is limited to particular habitat types, whether the national park presents suitable patches of bamboo for bamboo lemurs, and whether vegetation changes over the last 15 years have diminished the potential availability of bamboo in the area. I conducted an expedition to Ranomafana National Park (RNP), in south-eastern Madagascar, in November 2023, and collected 123 vegetation plots, including 45 plots revisited after an expedition in 2008. I used this field data to train a random forest classifier conducting supervised classifications based on Sentinel-2 imagery. I used these classifications to map the extent of different vegetation types and two genera of bamboo in RNP and its surroundings and evaluated their spatial and temporal distribution. The classification model accurately predicted the distribution of genus Cathariostachys, an endemic giant bamboo which is the main food source for bamboo lemurs in Ranomafana. Plots with Cathariostachys grew in the highest densities of all bamboo assessed in the field plots, and its distribution was projected over secondary and degraded forest areas, including areas outside RNP. Instead, the distribution of the endemic climbing bamboo of genus Sokinochloa, a secondary food source for bamboo lemurs, was captured with lower accuracy, mostly in the forested areas inside RNP, where it grew in low densities in the field plots. Comparing forest extent based on remote sensed classifications from 2008 and 2023, I show that a big proportion of forest has been lost in unprotected areas. RNP provided protection against forest loss, but the promotion of primary forest conservation and the disturbances through illegal activities are likely not providing habitat to secondary forest dwelling Cathariostachys bamboo. Small, sparse Sokinochloa patches within the continuous forest can assist bamboo lemur connectivity when moving through clustered patches of Cathariostachys. Nonetheless, because bamboo lemurs are affected by poaching in unprotected areas, the availability of good-quality Cathariostachys bamboo stands inside RNP is crucial for their conservation. However, no evidence of sexual reproduction or establishment of new patches of Cathariostachys was found in the field. Therefore, habitat restoration measures focused on securing new growth of this bamboo genus inside RNP could have a great impact on the conservation of bamboo lemurs. The success of such conservation measures could be assessed remotely with the mapping model developed in this study.

Introduction: High anthropogenic pressure exercised on the Baltic Sea causes a decline in valuable reproduction areas of coastal fish, such as the northern pike (Esox lucius L.). Hence, the conservation and restoration of the reproduction areas of pike are increasingly of importance. The Kvarken Archipelago, located in the Gulf of Bothnia, presents valuable reproduction habitats for fish. The pre-flads, flads, glo-flads and glo-lakes provide warm and sheltered areas that are preferred by spring-spawning fish, such as pike. However, the precise environmental factors influencing pike reproduction in the region have not yet been identified. In this study, different environmental factors influencing pike reproduction in the Kvarken Archipelago were assessed. Furthermore, as technology advances, there is a need to evaluate the use of new techniques alongside the generally time consuming and expensive traditional research methods applied for surveying the pike reproductive areas. Henceforth, the present study assessed the suitability of the high-resolution aerial photography for identifying potential reproduction areas of northern pike. Methods: The data of pike fry density, the vegetation, the abiotic and biotic environmental factors, as well as the aerial images of the 45 sampling sites were collected by Natural Resources Institute Finland and Metsähallitus Parks and Wildlife Finland as part of the Kvarken Flada -project. Pike fry were sampled with a flat dipnet amongst vegetation along a 100 m sampling line during spring. Concurrently, the vegetation, the occurrence of sticklebacks (Gasterosteidae) and the abiotic factors affecting water quality, including salinity, pH, oxygen content and turbidity were determined. The temperature was recorded with temperature loggers from early spring until late summer. The temperature sum for June showed the greatest effect on pike fry densities and was thus used in the analyses. The archipelago zones, which are based on previously modelled temperature sums, were defined for the sampling sites in the geographic information system (QGIS). Additionally, factors describing the morphology, the vegetation and bottom substrate coverage of the sampling sites were utilized in the analyses. The presence of pike fry was analysed with binary logistic regression. The pike fry densities were studied using non-parametric analyses due to the high number of zero observations in the data. The aerial images were taken in late summer of 2017 and 2018, when the vegetation was fully developed. The vegetation types, i.e. reed, fallen reed, wetland grasses, submerged vegetation and filamentous algae, identified in the images were compared to the vegetation data gathered during field survey in QGIS. The performance of the aerial images was assessed by calculating the accuracy, sensitivity and specificity for the different vegetation classes, first for the whole dataset and then for the sampling points with pike fry observations. Results and conclusions: This study determines two key factors defining suitable reproduction areas of pike, the temperature sum for June and the morphology of the sampling site. The results indicate that pike prefer warm and sheltered areas with suitable vegetation, such as reed and wetland grasses. In particular, glo-lakes provide favorable conditions for pike and the temperature sum for June was significantly higher in the glo-lakes compared to the pre-flads. The temperatures of the glo-lakes were constant throughout the archipelago, providing suitable conditions for pike reproduction also in the outermost archipelago. In all of the glo-lakes pike fry were observed and generally the highest pike fry densities were found in glo-lakes. However, the year class strength of pike can be affected by the possibility of the juvenile pike to emigrate from the enclosed glo-lakes back to the sea. Salinity reflects the connectivity of the site to the surrounding sea and had a significant negative effect on pike fry density. Additionally, the presence of sticklebacks affected negatively the presence of pike fry, which might be traced back to the different use of the archipelago zones and site morphologies of these species. Increasing pH negatively influenced the pike fry density. However, pike fry were observed also in the highest pH conditions and therefore pH alone is not sufficient to explain the presence and density of pike fry. Due to the small sample size of the dataset, it can be assumed that not all of the factors influencing pike reproduction were identified and thus the use of a larger dataset is recommendable in future studies. This study provides new methodological information on reproduction area surveying of pike with high-resolution aerial photography. The different vegetation classes were successfully identified from the aerial images. The seasonal differences were noticeable in the results, as in the aerial photographs taken in late summer, the vegetation was fully developed compared to the field study in early spring. Nevertheless, aerial photography proved to be an effective method for identifying reproduction areas of pike based on the vegetation. Furthermore, reproduction areas in need of restoration could be assessed with aerial photography.

The objective of this thesis is to study resilient urban housing business ecosystems and the role and use of nature-based solutions (NBS) in these ecosystems. Thesis aims to gather knowledge on how nature-based solutions are perceived in urban residential building and planning regime and how these solutions are valued to increase urban resilience. Thesis aims to provide knowledge on who are the actors in key role in designing, implementing, or using nature-based solutions in the case cities urban built environment and residential buildings of the business ecosystem. The benefits from nature-based solutions are presented and challenges hindering the mainstreaming of nature-based solutions as well as ways to overcome them are addressed. This thesis is a qualitative study with an empirical research approach. The empirical part of the study consists of data collected from 11 expert interviews, and two expert workshops. Altogether the empirical data corpus consisted of 15 transcripts. The interviews were semi-structured, thematic interviews where experts from different organizations of urban planning and construction industry were interviewed. Two separate workshops were held during August of 2023 in both case cities Helsinki and Turku. Workshops consisted of researcher presentations and focus group work, and the expert participants represented versatility of the field. Study applies reflexive thematic analysis method for qualitative data analysis. It is a systematic and flexible method that is used for identifying, analysing, and reporting meaning-based multifaceted and conceptual patterns within data by generating codes and themes. Several actor groups and key actors were identified based on the analysis. Also, an open role for a champion was recognized from the analysis. Several benefits derived from NBS and barriers for mainstreamed use were identified. Multiple solutions such as land use planning, urban governance practices including green factor, and economical incentives help to increase use of NBS in urban settings, and to answer the future of more resilient city. Urban resilience can be increased through inclusion of NBS and the associated delivery of ecosystem services in urban areas. Urban greenery and green spaces are highly relevant for well-being of residents. A holistic approach for urban planning and residential housing building is called for with increase in implementation of NBS. City should be designed for people as well as to other species. Experts share a vision of greener and more sustainable city where nature becomes one with the city, and city with the nature. There is still need for more research on long-term review of follow-ups and next steps taken from pilot projects to answer how nature-based solutions could be transferred from experimentations for everyday use and how this knowledge could be transferred for wider audiences.

Land-use change stands behind the current biodiversity crisis and all it entails in terms of ecosystem services. Guinea-Bissau, in West Africa, is originally characterized by a forest- savanna mosaic biome. However, while savannas have long been planted with rice, both rice paddies and forest remnants are now being converted into cashew monocultures – the only cash crop in the country – at unprecedented rates. The ecological impact of such rapid change is largely unknown. To help fill this gap, we examined how three diversity metrics – rarefied species richness, abundance and composition – varied across forest remnants, cashew orchards and rice paddies for amphibians and reptiles in northern Guinea-Bissau. To do so, visual encounter surveys were carried across 21 sampling sites, seven of each habitat type. A total of 703 amphibian and 266 reptile encounters was recorded from nine and 14 taxa, respectively. The results show class-specific responses to habitat type. Amphibians’ diversity in forest remnants and cashew orchards was similar across all metrics, but rice paddies had a higher abundance and unique composition compared to forest remnants. Reptiles’ abundance was highest in cashew orchards and this habitat had a distinct composition, when compared to forest remnants. Rice paddies sustained both lower reptile richness and abundance. Overall, our results are not in agreement with the expected detrimental impacts of cashew expansion, which might be due to the still high heterogeneity of habitat types within the landscape. Rice paddies proved particularly important for amphibians, and for open-habitat reptiles, boosting overall species diversity. In face of the eminent habitat conversion, maintaining heterogeneous landscapes, including the persistence of both forest remnants and rice paddies, will allow minimizing biodiversity loss in West Africa.

Tiivistelmä – Referat – Abstract Celiac disease (CD) is a serious lifelong condition, in which the immune system attacks an individual’s own tissue when eating gluten. This leads to inflammation and damage to the small intestine. Celiac disease often goes undiagnosed because many of its symptoms are nonspecific. The prevalence of combined undiagnosed and diagnosed CD is estimated to affect 1 in 100 people throughout Europe and USA. CD is a polygenic disease, it is known that the human leukocyte antigen (HLA) system plays a crucial role. HLA-DQ2/DQ8 risk allele genotyping screening test from a whole blood sample (B -HLAKeli) is routinely used to estimate the genetic risk of a patient having CD. HLA genotyping test result is routinely used to rule out celiac disease rather than confirming it; if an individual does not have celiac disease related risk alleles, it is very unlikely that he or she has celiac disease. The Celiac disease diagnosis decision making process is based on the classic triple combination of serological antibody tests, the HLA-DQ2/DQ8 genotyping test and duodenal biopsies. The aim of this master’s thesis was to study evaluate how the two different risk classification praxis for HLA-DQx.5 allele used for celiac disease diagnostics in SYNLAB Finland and Estonia central laboratory and in SYNLAB Suomi central laboratory might influence the clinical process and final diagnosis. In SYNLAB Suomi central laboratory HLA-DQx.5 is classified and interpreted as a risk allele predisposing to celiac disease. In SYNLAB Finland and Estonia central laboratory this allele is classified as CD-non-risk-allele based on recommendations in international guideline. In addition, the aim was to get a general understanding of celiac disease prevalence and risk allele distributions among the study population. From the study population of 196 celiac disease suspect patients, 9% had a celiac disease positive laboratory result and the HLA risk genotype distribution among positive cases was well aligned with the expected values described in the literature. Study results indicated that there’s no additional clinical value if HLA-DQx.5 is classified as a celiac disease predisposing risk allele; the study data implies that it is very unlikely to find celiac disease positive cases from laboratory test perspective among HLA-DQx.5 carriers. Based on the study, approximately 7% of the celiac disease suspects carry the allele HLA-DQx.5 and therefore probably go through additional celiac disease related laboratory testing if this allele is interpreted as a risk allele. According to the study findings and general recommendations based on international guideline of celiac disease diagnosis, it seems that there is no clear clinical benefit if HLA-DQx.5 is classified as a CD risk allele.

High-grade serous carcinoma (HGSC) is the most common and lethal subtype of ovarian cancer. To date, HGSC has typically been diagnosed late, and the survival rate is poor. Relapses are common despite standardised treatment options, and platinum-based chemotherapy resistance remains frequent. The tumours are generally heterogeneous, which makes HGSC complex. Molecular mechanisms of tumour initiation, progression and chemoresistance are insufficiently understood. Thus, efficacious treatment is challenging, and current options do not help some patients. In addition, a population of cancer cells having stem cell-like properties are suggested to play a role in tumour initiation, progression and chemoresistance. There is an urgent need to better understand prognostic biomarkers and treatment responses in HGSC. With diverse analytical methods, the treatment-unresponsive patients and their outcomes could be identified by predictive biomarkers. This thesis aimed to validate potential tissue biomarkers associated with cancer stem cells and poor prognosis in HGSC, evaluate the usability of the RNAscope technique and briefly review the hypotheses on cancer stem cells. Four putative biomarkers were studied: ALDH1A1, BMI1, MYC and SOX2. The RNAscope technique was used to detect and quantify the biomarker expression. Using diagnostic tumour tissue specimens from 95 patients allowed capturing the expression in situ. With comprehensive clinical information, we could test whether the biomarkers distinguished patients with similar background information but different outcomes. This thesis shows that BMI1 could be a potential prognostic biomarker in high-grade serous carcinoma. The results provide information about the expression patterns of previously identified potential HGSC stemness markers. Proteomics studies such as immunohistochemistry could provide complementary information. When the molecular mechanisms and prognostic markers are better understood, they will provide a promising opportunity to develop novel diagnostic methods for predicting the outcomes and deciding treatments for this complex disease.

The lymphatic system is a network of vessels that permeate a substantial part of the whole body. It plays an essential role in fluid homeostasis by the drainage of interstitial fluid from the blood capillaries, after which the fluid, now called lymph, is transported through the vessel network and back to the blood circulation. The lymphatic system also plays an important role in the transportation of immune cells and in activation and maintenance of the immune system. Due to these crucial functions, there is a growing interest in exploiting the lymphatic system in the treatment of many immunological and inflammatory diseases. In many cases, an ideal treatment method would be to induce lymphatic growth (lymphangiogenesis) to boost immunological functions, facilitate resolution of inflammation and reduce the harm from lymphatic vascular abnormalities. However, there is a gap in knowledge in how to induce lymphangiogenesis in a controlled manner, with the major lymphangiogenic growth factor, vascular endothelial factor C (VEGF-C), tending to create disorganized lymphatic networks. The purpose of this thesis is to investigate factors influencing lymphangiogenesis, in an attempt to find ways to control it. Vaahtomeri research group has preliminary results showing a role of planar cell polarity (PCP) in control of dermal lymphatic vessel sprouting (the initial step for the formation of new lymphatic branches) and lymphatic network expansion. The focus of Vaahtomeri research group has been the core PCP protein Van Gogh-like protein 2 (VANGL2), which together with the other core PCP proteins is known to play an important role in the collective cell polarization and morphogenesis in many tissue types. The role of VANGL2 has previously been studied in the lymphatic system, and so far, VANGL2 has been implicated in both lymphatic valve morphogenesis and in flow-induced control of lymphatic endothelial cell (LEC) polarization. However, there still remains a gap in knowledge in what role VANGL2 plays in lymphangiogenesis and the lymphatic network as a whole. In this thesis, I investigated the role of VANGL2 in lymphangiogenesis, firstly by the use of an in vivo lymph node experiment, which offered a robust model to investigate the role of VANGL2 in the mature lymph node lymphatic network. In the experiment, I induced growth of the lymph node lymphatic network by means of an immunization reaction, and then I compared the lymphatic networks of Vangl2-deleted and control mice. Despite some minor differences between the Vangl2-deleted and control lymphatic networks, this experiment did not show a role for VANGL2 in the mature lymph node lymphatic network. Secondly, I investigated the potential mechanistic role of VANGL2 in control of dermal lymphatic vessel sprouting in growth conditions. This experiment showed a specific role for VANGL2 in sprouting of the lymphatic network, thus providing valuable research in understanding how lymphangiogenesis is regulated. Altogether, the results presented in this thesis work as a steppingstone for finding new treatments relating to the safe induction of lymphangiogenesis.

The increased rates of population growth and urbanization worldwide raises the question of food security and self-reliance in cities. In view of this situation, in recent years there has been a re-emergence of urban agriculture in its traditional form and in new variations, such as on urban rooftops. A number of rooftop urban farms exist in the world; however, very few studies have been done to establish the quality of crops they produce, specifically concerning the concentrations of contaminants. The main purpose of this study was to investigate levels of contamination in edible plants grown on urban rooftops. I determined concentrations of polycyclic aromatic hydrocarbons (PAH) and trace metals in the biomass of three types of horticultural crops grown in the city of Helsinki, Finland. Lettuce, radish and peas were planted on five rooftops in various areas of Helsinki and control samples were acquired from local food stores and markets. Both groups of crops were analyzed for concentrations of 11 trace elements using the Elan 6000 ICP-MS and 16 PAHs using Shimadzu GC-MS-QP2010 Ultra system with the AOC-20i /AOC-20s autosampler. Additionally, lettuce and pea samples from the roofs were analyzed washed and unwashed to establish levels of particulate contamination on the surface of plants that can be mechanically removed through washing. Results obtained suggest that concentrations of PAHs and trace metals in rooftop vegetables in Helsinki are very low and the differences in their concentrations compared to control (store) samples are insignificant. This demonstrates that the consumption of vegetables produced in uncontaminated soil on urban roofs in Helsinki is safe. All samples showed concentrations well below the safety limits for heavy metals and PAHs established in the European Union (EC, 2006). Finally, there was a difference in concentration of PAHs and trace metals between washed and unwashed samples, however most of the results did not show statistical significance.

Social behaviour can be divided into neutral, positive, and negative, depending on the social context. Positive social behaviour involves affiliative prosocial interactions that encourage social and emotional cohesion. Rat (Rattus norvegicus) is a globally distributed common rodent species adapted to living near humans. Rats are intelligent and social animals with reciprocal prosocial behaviour. However, research on the social behaviour of rats is concentrated in laboratory settings and very little is known about the social behaviour of free-living rats. Rats arouse strong prejudice in humans and are considered aggressive. Despite a long history of coexistence, there are still strong conflicts between humans and rats. In this study, I used camera trap data to investigate the types of social behaviour in free-living rats and the time allocation of different behaviours. I investigated how the rats' behaviour is divided into socially neutral or positive and negative behaviour in relation to the total time spent on the behaviour. I also investigated the types of social behaviour that occur when rats approach each other and the frequencies of these different behavioural models. For the behavioural analyses, I used data-driven ethograms that I made and the behavioural analysis software BORIS. I found that the majority (over 96.2 %) of the social behaviour of the free-living rats in my study population was neutral or positive behaviour as measured by the duration of the behaviour categories. I also found that the most significant proportion of social behavioural models in rats was socially neutral or positive. Agonistic behavioural models were rare and occurred mostly between adults. In contrast, rats exhibited a moderate amount of prosocial behaviour, particularly in the form of food sharing and muzzle touching. My study brings new information to the limited previous research on the behaviour of free-living rats. The results suggest that most of the social behaviour in free-living rats would be neutral or positive behaviour, and agonistic behaviour in rats would be relatively rare. To the best of my knowledge, this work is the first study to analyse the social behaviour of free-living rats from camera trap data. Objective research data on the social behaviour of rats may mitigate prejudice against rats and attitudes towards rats may become more positive. This can mitigate conflict between humans and rats and promote peaceful coexistence. This work can be used as a pilot for future studies. The information this work provides can also be used, for example, to educate people about their attitudes towards rats.