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Lichens are symbioses between fungi, photosynthetic algae and other organisms. The fact that several different fungi may occur in the same lichen thallus adds a further dimension to the diversity of these miniature ecosystems. Calicioids are a polyphyletic group of predominantly lichenised fungi which includes many species with stalked ascomata, topped with a persistent spore mass (mazaedium). One such species is Chaenotheca chrysocephala, a relatively common crustose lichen with a wide distribution. The lichenicolous fungus Chaenothecopsis consociata grows on the thallus of C. chrysocephala and is generally considered to be a parasite. This study aims to map the temporal and geographical distribution of C. chrysocephala and C. consociata in Europe in order to find out whether the parasite was present there before the year 1942, when the species was described, and to identify possible patterns which may affect the population dynamics of these two species. This study found that C. consociata was indeed present in Europe before 1942, at least in Norway, Sweden and Finland. Additionally, the percentage of infected C. chrysocephala thalli seems to have increased in Europe since the parasite was first found. The GBIF dataset showed a significant increase in infected C. chrysocephala thalli in northern Europe (N-EU) compared to central-southern Europe (CS-EU). Although the exact reason is unclear, this increase may be related to differences in forest structure across Europe. Firstly, the host lichen seems to prefer Picea and Pinus as its substrate, these being typical trees of needleleaf forests in Europe. Furthermore, the decrease of old-growth forest stands in Sweden and Finland may have reduced suitable habitat for the host, while the concurrent increase of disturbed stands may have favoured the dispersal of the parasite.

Prostate cancer is one of the most common cancers diagnosed in men. Somatic copy number alterations (SCNA), such as the deletion of PTEN or NKX3.1 and the amplification of MYC, have been associated with prostate cancer progression and could serve as potential biomarkers during diagnosis. One approach to utilize this information would involve screening a large number of prostate tissue sections for SCNAs and subsequently validating the findings using a secondary method. This process could enable more personalized treatment options for cancer patients. This thesis aimed to create a robust and reproducible workflow for SCNA identification. This was achieved by optimizing a chromogenic immunohistochemistry (IHC) protocol using immunostaining chambers and open-source 3D-printed laboratory hardware. The optimized protocol was then transferred to an automated liquid handling robot, and a panel of three antibodies for PTEN, NKX3.1, and MYC was developed for SCNA screening with IHC. Additionally, a chromogenic in situ hybridization (CISH) protocol was optimized to validate the results of the IHC. The immunostaining chambers required a lower antibody dilution to perform comparably to the manual IHC stainings. The automated protocol using the liquid handling robot produced high-quality stains with optimized dilutions. The optimized CISH protocol successfully identified the presence of the target gene, but unclear signals and merging of the signals obstructed detailed analysis. While complete deletion of PTEN was detectable, determining the number of gene copies per cell proved challenging due to signal variability and sample-dependent problems. Further optimization of the CISH protocol or development of an automated analysis workflow tailored to address these challenges is needed for more accurate analysis.

Schizophrenia, a mental disorder affecting over 1% of the world’s population, has a 41-65% chance of being acquired in monozygotic twins, and shows a complex heritable pattern. Research has shown the involvement of various neuronal and glial cell types in the disorder’s progression. Recent studies are focusing on cortical interneurons, as clinical features of schizophrenia such as working memory deficits emerge due to the abnormal activity of these cells . The advent of induced pluripotent stem cell (iPSC) technology has made it easier to study schizophrenia disease mechanisms, with studies revealing differences in morphological and physiological properties of cortical interneurons in patients with schizophrenia. In this thesis , the aim was to optimize iPSC-interneuron differentiation protocol and live-cell imaging method suitable for disease modelling. Interneurons were differentiated from iPSCs with overexpression of inducible transcription factor, Achaete-scute homolog 1 (ASCL1). The iPSCs were derived from twin pairs discordant for schizophrenia and from healthy controls. Expression of interneuron-specific markers was verified using RT-qPCR and validated at the protein level by an immunocytochemistry (ICC) assay in the control cell lines first. Additionally, to estimate the formation of neurites and differences in neurite length and branching, the differentiated interneurons from the controls were subjected to live-cell imaging by IncuCyte S3 live-cell imaging system. Imaging parameters such as cell body cluster filter was optimized to visualize the neurites. To study interneuron involvement in schizophrenia, iPSCs from one twin pair discordant for schizophrenia were successfully differentiated. Interneurons strongly expressed Gamma-aminobutyric acid (GABA) neurotransmitter related neuronal markers: glutamate decarboxylase 67 (GAD67) and GABA at protein level. The neurons were identified as somatostatin (SST) subtype GABAergic neurons by their mRNA and protein expression. While it was possible to observe differences in gene expression, there were no clear differences in the morphology of the differentiated cells as well as the localization of markers in comparison to the healthy controls. Further studies should focus on having a protracted time for differentiation where more mature interneurons can be produced by establishing co-cultures with excitatory neurons. This will help replicate the in vivo cortical machinery which in turn will aid in better understanding of disease mechanisms.

Alzheimer's disease (AD) is a degenerative brain disorder that exhibits deterioration as one gets older. Although much remains to be learned about the pathophysiology of AD, there is strong evidence links amyloid beta (Aβ) plaques, which are responsible for cognitive impairment, to GABAergic interneurons. Model systems are of prime importance for adequately studying the pathophysiology of this disorder; however, existing in vitro models have limitations in producing patient-specific cells. The development of induced pluripotent stem cell (iPSC) technology has provided a novel opportunity for the effective production of disease-relevant cell types while preserving the molecular traits of the patient. In this thesis, the differentiation protocol established by Nicholas et al. (2013) was used to promote the development of interneurons derived from iPSCs. To enhance the efficiency of differentiation, the protocol was modified with the use of small molecules combined in different ways. The end result of the differentiation was characterized using immunocytochemistry (ICC) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The combination of molecules that produced greater efficiency in differentiation was selected, and the optimized protocol was carried out with iPSCs derived from an AD patient harbouring the APP Swedish mutation. The differentiation of cortical interneurons, demonstrated by the expression of pan-neuronal and specific GABAergic neuronal markers, signifies the successful generation of differentiated interneurons in the context of AD. AD iPSCs upregulated several markers related to AD pathology, such as APP and BACE1. However, the cell lines tolerated the small molecules differently, and thus, the protocol needs more optimization in the future. In summary, iPSC-based differentiation protocols are capable of producing disease-specific cell types that would be helpful in developing accurate AD models for revealing the mechanisms of Aβ pathology.

The many symbiotic microbes associated with plants can represent the first line of defence against viral pathogens, which can have profound impacts on plant health and productivity. Unfortunately, although countless studies have investigated variations in the composition of microbial communities associated with crops, showing benefits in the plants’ nutrient acquisition, stress tolerance or growth promotion, much less is known about how viruses might affect the composition of the microbiota associated with plants, and especially non-crop plants. Furthermore, we also often lack an understanding of how plant viruses are transmitted across their environment. Addressing these knowledge gaps is bringing us closer to better describe and manage the complex relationships between plant microbiota and viral pathogens in their natural environment. The main objective of my Master’s study is to examine variations in the bacterial community associated with a plant in the agricultural landscape, and to identify potential players in microbial community changes. With this in mind, I chose to work with the ribwort plantain, Plantago lanceolata, because it has a widespread distribution, it is present around cultivars, and there is extensive knowledge of its biology and genetics. Thus, P. lanceolata, represents an excellent system for investigating the causes of variation in the plant-associated microbiota. More precisely, I worked with the P. lanceolata population evolving in the Åland Islands, in Southwestern Finland, which has been the target of long-term ecological and evolutionary metapopulation studies. The population is also known for co-evolving with several viral pathogens, and with diverse Hemiptera insects (plant sucking-insects) that have been suggested as possible vectors of the viruses between plants. I collected P. lanceolata leaves, and insects found on P. lanceolata specimens from 28 habitat patches, or meadows, from five localities across the Åland Islands (Geta, Sund, Lemland, Finström, Eckerö). I extracted DNA from a total of 10 leaves per patch, as well as 60 Hemiptera specimens (of several uncharacterized species). I screened for viral infection in all samples by amplifying the viral loci for reverse transcriptase form Plantago latent caulimovirus (cauV) and the replication associated protein gene from Plantago lanceolata latent virus (PlLV). In parallel, I characterized the bacterial communities associated with each plant and insect through metabarcoding of the highly variable V5-V6 region of the 16S rRNA bacterial gene. My MSc's project shows that bacterial species richness (alpha-diversity metric) and community composition (beta-diversity metric) vary between plant and insects. But that they do not vary between the virus-infected and uninfected plants tested, and neither between geographical locations within the Åland Islands. This is the first study investigating the effects of two virus infections on the microbiota of a common weed from the Åland Islands. It provides preliminary data for the study of how the bacterial microbiota of P. lanceolata might respond to virus infections, and how viruses might be transmitted between individual plants.

The planetary health approach emphasizes the interconnectedness between human health and natural systems. Urban planners also have the opportunity to promote planetary health through their work by reducing the negative environmental impacts of planning solutions and by increasing decisions that support residents' health and wellbeing. Numerous studies have shown that nature promotes human physical, mental, and social health, underscoring the importance of accessible nearby nature, especially in growing cities. This thesis examines urban planning in the city of Lahti from the perspective of planetary health. The study aims to investigate how nearby nature and its health and wellbeing effects, particularly for children and young people, have been considered and identified in land use planning. Additionally, the goal is to determine how conflicting land use interests are prioritized in decision-making. The research material consists of interviews with officials from the Lahti Urban Environment service area, and the data is analyzed with qualitative content analysis and thematization. The results indicate that nearby nature is perceived as an important part of Lahti's urban structure. Urban greenspaces and nearby nature areas are most concretely taken into account by zoning them as green areas in general and detailed plans. Furthermore, urban planning utilizes surveys of nearby nature conducted in early childhood education institutions and schools to ensure accessibility of nearby nature for children and adolescents. The appreciation of Lahti's planners, nature-friendly organizational culture, functional planning practices, and the recognition of the city's environmental efforts support the preservation of nearby nature areas in the urban structure. However, green areas without zoning are constantly at risk of being allocated for other land use purposes in a growing city. Planners describe their work as a continual search for compromises between conflicting desires, goals, and land use interests. They hold a central position of power and responsibility in making sustainable planning decisions, which can also be guided by planners' own values, attitudes, and expertise. Systems thinking required by planetary health approach along with research findings on the health and wellbeing effects of nearby nature, should be more effectively integrated into urban planning, political decision-making, and public discourse. Although this study focuses on planners in one city, it offers interesting insights into effective urban planning practices and current challenges within the framework of planetary health.

The taxonomy of the green macroalgal genus Monostroma is poorly known in the Baltic Sea region and worldwide.Two species of Monostroma are currently reported from the Baltic Sea: the cosmopolitan spring species Monostroma grevillei and a proposed endemic, free-floating summer species Monostroma balticum. However, previous work has highlighted the unclear taxonomic status of M. balticum, and some consider it a growth form of the cosmopolitan species M. grevillei or a monostromatic growth form of Ulva spp. No molecular data exists of M. balticum, and the morphological characteristics distinguishing this species from M. grevillei and similar species are unclear in the literature. The aim of this thesis is to explore the taxonomic status of M. balticum by firstly systematically reviewing the historical and contemporary literature, including the original description, to illuminate the current morphological circumscription of M. balticum and related species. Secondly, using DNA barcoding based on the tufA -marker, fresh collections of foliose monostromatic green algae from the Baltic Sea region are identified molecularly and put into an evolutionary context using phylogenetics. Thirdly, novel plastid genomes are produced from monostromatic green algae to explore the genomic features of these algae and to see if they aid in species delimitation or phylogenetic approaches. Based on the literature review, the morphological and ecological features used in specimen identification currently (micromorphology, free-floatingness and occurrence in summer) may not be enough for accurate identification, and especially the micromorphological features are quite vaguely described in contemporary literature making their use difficult in practise. All monostromatic specimens collected are identified using DNA barcoding as either M. grevillei, Kornmannia leptoderma or Ulva intestinalis, and those specimens mostly resembling the original description of M. balticum are recovered as U. intestinalis. Plastid genomes were produced from M. grevillei, K. leptoderma and U. intestinalis, from the latter species separate genomes were generated from a typical tubular-morphology specimen as well as a “M. balticum”-morphology specimen. M. grevillei and K. leptoderma plastids were unusual in being large, inflated by many introns and intrageneric regions and having many rearrangements. Produced U. intestinalis plastomes are similar and resemble previously published Ulva genomes. The accurate identification of M. balticum -like specimens is discussed, and for future work DNA barcoding is suggested to be the main tool for specimen identification. This thesis provides evidence towards a previous hypothesis that M. balticum is not a distinct species but a specific growth from of U. intestinalis. Investigating historical herbarium specimens, including original material, using molecular methods is proposed to verify if M. balticum should be synonymised formally with U. intestinalis. The potential drivers of the shift in growth form of U. intestinalis are discussed. Finally, the plastid genome landscape in these foliose green algae is discussed.

Background: The infant gut microbiome undergoes major temporal changes in the first year of life, crucial for supporting normal development and long-term health. The immense diversity of fiber structures in breast milk and later in solid foods pose unique selection pressures on the gut microbiome maturation by providing novel substrates for the microbiota. However, the longitudinal impact of complementary food-derived fibers on the taxonomic and functional maturation of the gut microbiome during the gradual transition from breast milk to solid foods is not well understood. Objectives: My objective was to examine how breast milk, its fiber and complementary food fibers in the broader context of overall infant diet may affect the gut microbiome bacterial species composition and support age-appropriate gut bacterial maturation trajectories during first year of life. Methods: Longitudinal and cross-sectional development of 68 infant gut microbiomes and 33 metabolomes were examined with linear mixed models to determine the impact of infant nutrition on gut microbiome taxa and functional development. Nutrition assessments were based on detailed quantitative weighted 3-day food records (months 3,6,9,12) and the intakes of total dietary fiber with its food sources and fiber fractions relied on current internationally approved CODEX-compliant values. Questionnaires were utilized to monitor when various complementary foods were introduced, enabling more comprehensive nutritional analyses. Bacterial species identification was based on MetaPhlAn2 quantification of bacterial species from metagenomic data and metabolomic profiles were generated using four liquid chromatography-mass spectrometry (LC-MS) methods. Results: My examinations place the previously described sequential trajectories in infant gut microbiome maturation into detailed fiber-dependent nutritional context relying on metagenomic species identification. I discovered 176 complementary food derived fiber-bacterial species associations. The majority of the associations (147, 84%) were positive whereas breastfeeding and related variables tended to be inversely associated with the same species, showing strongest inverse correlations to later trajectory species indicative of slower maturation. Both bacterial species and metabolomic profiles displayed pronounced longitudinal shifts in response to solid food fibers. Each introduction of novel dietary source of fiber associated to diversification of the microbiome revealing fiber-species specific temporal patterns. Conclusions: The longitudinal analyses highlight that sufficient fiber intake from appropriate sources during the weaning period likely function to build capacity for the species permanence in the more diverse and stable mature gut microbiome composition and function reached in later childhood.

Background and objectives: Since early adolescence, the bedtimes and wake-up times begin to delay gradually until the early adulthood. This so-called shift to eveningness reaches its maximum at around the age of 20, and it usually occurs earlier in girls than boys. Eveningness has been previously associated with depression, anxiety, sleep problems, somatic symptoms, and other health-related issues in adolescents and adults. The aim of this study is to examine the associations between adolescents’ chronotype and their physical and mental well-being. Methods: This study examined how the self-reported chronotype was associated with self-reported problems related to adolescents’ physical and mental well-being. The chronotypes were divided into 5 types: Definitive Morning-types, Moderate Morning-types, Intermediate-types, Moderate Evening-types, and Definitive Evening-types. The participants were 7th, 8th and 9th graders, and the sample consisted of 6522 students from 83 schools in Finland. Some of the data was gathered at three time points, some at two time points, and some at one time point during the academic year. The associations between chronotype and well-being variables were studied cross-sectionally and some of them also longitudinally. Results: The main findings were that eveningness was associated with difficulty concentrating in lessons, susceptibility to give up easily on difficult tasks, school burnout symptoms, feelings of nervousness and anxiety, excessive worrying, difficulty relaxing, irritability, restlessness, difficulty falling asleep, waking up at night, daytime tiredness, and low mood as compared to morningness. Eveningness was also associated with neck and shoulder pain, lower back pain, and headache, as well as pain in the head and lower back due to the use of digital devices. Eveningness was associated with decreased concentration in lessons and increased susceptibility to give up on difficult tasks across time. On the other hand, feeling lonely and not being accepted as part of the group were associated with morningness. Conclusions: In conclusion, the physical and mental health problems were emphasized among Evening-type adolescents, as compared to Morning-type adolescents. Since adolescents shift toward eveningness, the need for thorough management of sleep and circadian problems should be highlighted, in order to intervene and improve the mental and physical well-being of adolescents both at school and at home.

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive degeneration of upper and lower motoneurons (MN) within the central nervous system (CNS), leading to muscle atrophy and eventual paralysis. Cause of death is in most cases due to respiratory failures 3-5 years after diagnosis. ALS can occur idiopathically without any know causes or it can be associated with certain genetic mutations. One of these known factors is a point mutation in the superoxide dismutase 1 (SOD1) gene, particularly the G93A mutation is known to affect the functionality of SOD1. SOD1 is an enzyme that metabolizes reactive oxygen species (ROS) and the SOD1-G93A mutation limits this functionality and propagates endoplasmic reticulum (ER) stress signalling cascades. Mutated SOD1 cannot be broken down by the cell, and hence it is associated with activation of protein degradation (ERAD) system with a prolonged ER stress signalling, followed by apoptotic cellular response. Although SOD1-G93A mutation has been widely studied, the basic mechanisms of the disease are not fully understood. Mesencephalic astrocyte derived neurotrophic factor (MANF) is an evolutionary conserved protein with trophic properties. MANF has been researched as novel treatment in a range of neurodegenerative diseases, such a Parkinson’s. MANF has been shown to promote cell survival but has limitation as an administered drug treatment. In this study we used transgenic SOD1-G93A mouse model with male mice to study the effects of a novel MANF variant for ALS. Disease progression and histology were used to assess the treatment efficacy.