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Autophagy is a cellular recycling and quality control process that eliminates cellular material in a non-selective or selective fashion. Macroautophagy is non-selective, and degrades macromolecules or damaged organelles to sustain cellular homeostasis. The selective autophagy of dysfunctional or excess mitochondria is known as mitophagy. The clinical importance of functional degradation is exemplified by the lysosomal storage disorders (LSDs), where lysosomal hydrolytic enzymes are absent or dysfunctional. Previous investigations of a rare infantile LSD indicated a change in autophagy and decreased mitochondrial content. The aim of this MSc thesis was to quantitatively compare macroautophagy and mitophagy in a cellular model of this rare LSD, by generating fluorescent macroautophagy and mitophagy reporter-expressing cell lines from patient material. Fibroblasts derived from patients diagnosed with a rare infantile LSD were transduced with lentiviruses carrying either mCherry-GFP-LC3 or mito-QC reporters, for the microscopic analysis of autophagy and mitophagy, respectively. I also monitored autophagic flux by traditional biochemistry in untreated and starved cells, in the presence or absence of lysosomal inhibitors (bafilomycin A1). Basal and iron-depletion induced mitophagy was profiled using confocal microscopy, quantitative cell biology and biochemistry. My findings suggest differential autophagic turnover in LSD patient-derived fibroblasts, with a marked accumulation of non-acidified autophagic structures. Basal mitophagy was elevated in two out of three LSD patient cell lines compared to unaffected controls. LSD patient cells exhibited altered mitochondrial content and network architecture compared to controls. These phenotypes were accompanied by distinct changes in the endo-lysosomal system and increased cell size. The patient-derived cells exhibit a profound accumulation of lysosomes and autophagic structures. My findings are in accordance with previous research in the field, suggesting perturbed macroautophagy in this rare LSD. The observations of altered mitochondrial homeostasis in this LSD provide a basis for future investigation. The reporter-expressing cells, generated as part of this MSc thesis project, will enable future studies of mechanisms that underlie phenotypic changes, and will complement essential in vivo work in this area.

Immunopeptidomics research, focused on HLA-presented peptides, indicates that identifying neoantigens – unique peptides from cancer cell mutations – holds potential for personalized cancer treatment. PeptiCHIP, a compact microfluidic device from ValoTx, facilitates neoantigen identification in small tumor samples. This study evaluates PeptiCHIP against traditional immunopurification methods, assessing its advantages and commercial potential through stakeholder interviews guided by the double diamond model of design thinking. The aim is to establish PeptiCHIP’s unique advantages in immunopeptidomics research and precision oncology. Data for this research were gathered through semi-structured interviews and comparative laboratory analyses. The interviews revealed a positive reception among 19 stakeholders towards PeptiCHIP, highlighting a strong interest in its potential to accelerate workflows and enhance the personalization of cancer treatment. Laboratory comparisons confirmed that PeptiCHIP offers greater sensitivity than competitor products in detecting antigens, pinpointing the most immunogenic peptides from individual tumor samples. This suggests that the data could be effectively utilized as a targeted treatment approach in precision oncology therapies. The results indicate an eagerness to adopt PeptiCHIP, driven by its enhanced detection speed and accuracy. This research not only underscores the technological and commercial potential of PeptiCHIP in impacting precision oncology but also highlights the importance of aligning technological innovations with user needs and market demands. For ValoTx, a strategic commercial approach is needed to set a benchmark in precision oncology innovation.

Populations of forest grouse – capercaillie (Tetrao urogallus), black grouse (Lyurus tetrix) and hazel grouse (Tetrastes bonasia) - have been declining through all of Europe. Habitat loss, fragmentation and degradation are recognized to be the most important ultimate causes behind this trend. In Fennoscandia, there is a general consensus that forestry practices have a primary role, even though the mechanisms are still not fully understood. Nest predation is generally thought to be an important proximate cause of the declines, but how nest predation relates to habitat changes remains poorly understood. I combined long-term data provided by the Natural Resources Institute Finland (LUKE) from inventory studies, both for grouses and predators, with an artificial nest experiment. I investigated a) how predation rate varies with forest age and landscape structure; b) what is the possible role of non-native mesopredator species as predators; c) how nest predation rate relates to larger scale reproductive success. In spring 2021, I placed 141 nests with two hen eggs each, in the regions of Kainuu and North Karelia for 14 days with camera traps. The nests were equally divided between mature forests (>80 years), young forests (<40 years) and edges of mature forests (in a mature forest 5m from a clearcut or a field). I found that the overall predation rate was low (~13 %) and similar in the three sites, but predation time was faster in mature forests, suggesting that when these are scarce, they can act as an ecological trap by increasing nest detectability. However, nest predation decreased with the increasing of mature forests in the landscape around the nest, supporting the hypothesis that on a larger scale forestry may increase generalist predator densities. Areas with higher predator densities suffered higher nest losses. The main predators were pine martens, badgers and magpies, followed by bears and ravens. No nests were predated by raccoon dogs or American minks. There was no correlation between areas with higher nest predation and areas where grouse had lower reproductive success which may result from other factors, e.g., chick predation. My results add to the diverse outcomes of several studies of grouse nest predation in Europe, which together indicate large variation in nest predation, no consistency in predatory species, and weak effects of landscape composition on nest predation.

Behavior change can be seen as one cornerstone in transiting to more sustainable energy cultures. Various implemented behavioral intervention experiments have been popular and successful in creating behavioral change during and/or right after the intervention period, however follow-up research examining the persistence of changed behavior has been limited. The empirical material of this thesis builds on a set of data collected in a European research project ENERGISE. The analysis utilizes the data collected from two Finnish living lab experiments performed in 2018, focusing the examination on the closing interviews conducted by the research team and the participants’ self-reported practices in the follow-up survey three months after the intervention. The analysis examines the formation of new practices in relation to their persistence in everyday life. Answers to open questions presented in the follow-up survey are also examined in the analysis, to fuller the representation of events. The sample of the research is not enough to make comprehensive statistical generalizations, instead it gives interesting insight on the durability of the effects of one energy intervention. The research questions guiding this thesis are: How did household practices change when households participated in an intervention? How persistent are the observed changes in practices post-intervention? What contributes to the persistence of treatment effects? This examination observed persistence of behavioral change post-intervention. This examination suggests that these encouraging results may be supported by a number of different factors; the broad perspective of energy practices that the intervention designed on practice theory provided and the making of household routines visible to participants to question and experiment with. In addition, the intervention techniques used as making commitments, goal setting, social comparison elements and providing energy feedback, which corroborate with prior intervention follow-up studies that have noted the importance of a carefully thought intervention design with these techniques, to support creating permanent behavioral change. Intervention designs should also in-clude a longer-term evaluation and further study investigating the factors contributing to creating permanent change should be implemented.

Quantitative food webs have been used since the 1990s to describe the ecology of ecosystems. Such webs describe not only 'who eats whom' but also how many individuals get eaten, giving a detailed picture of the connections in an ecosystem. This detail allows far-reaching ecological conclusions to be drawn, for all manner of questions ranging from the influence of abiotic and biotic factors on population dynamics to the effect of latitude on ecosystem structure. Currently the webs' greatest limitations are their incompleteness and lack of geographic coverage: most published webs focus on a tiny fragment of the total food web, and there are few webs from higher latitudes. In this thesis I address these limitations, by extending a parasitoid-lepidopteran web which is being collected in the High Arctic. I add data on bird and spider predation of the web's Lepidoptera, and on the lepidopterans' herbivory of their food plants. Specifically, I ask what the relative strengths of predation and parasitism are in this community, and what effect herbivory has on the plants' seed production. I measured predation rates using both live caterpillars and modelling clay dummies as bait. The former, caterpillars of Sympistis nigrita tethered to threads, gave an estimate of both spider and bird predation. The latter showed bird predation only, but gave a larger sample size than tethered caterpillars. For the herbivory rates, I measured the seed production of avens flowers (Dryas octopetala x integrifolia, one of the main lepidopteran food plants) when damaged by feeding caterpillars. I found that predation is an important cause of mortality for S. nigrita, comparable to the high rates of parasitism already observed. During the larval period, some 38% of S. nigrita caterpillars are killed by spiders, 8% by parasitoids and 8% by birds. The caterpillars ate highly variable amounts of avens flowers, with 14.4% of flowers damaged by feeding in a set of 743 flowers, and 8.3% in another set of 672 flowers. The damaged flowers produced fewer and smaller seeds than did undamaged ones, causing overall avens seed production to drop by 7%. Overall, my findings show spider predation to be a relevant addition to the current parasitoid-lepidopteran food web. Bird predation, however, is relatively light – both when compared to spider predation and also to earlier predation rates reported from warmer latitudes. It is nevertheless comparable to the (naively twice as strong) parasitism since almost half the parasites die when their host is predated. When comparing food webs in order to address large scale ecological questions, such as the effect of latitude on food web structure, broader webs may be required instead of the mere parasitoid-host webs produced to date.

Animal personality is described as consistent behavioural variation between individuals over long periods of time. Behaviours often connected to animal personality are such as boldness, aggressiveness, and anxiety. In this thesis, the focus was on the behaviours along the shy-bold axis, containing various degrees of boldness expressing behaviour. The study was conducted by using long-term data from the past 30 years on the banded mongoose (Mungos mungo) population in the Mweya Peninsula in the Queen Elizabeth National Park in Uganda. In particular, I used the data on regular weighing events done within the population. As the weighing is not forced on these individuals, the participation percentage on these events can be used to describe an individual’s boldness. I used the participation percentage as a boldness index (values between 0 and 1) for each individual to describe their position on the shy-bold axis. This index was then used to analyse the differences between sexes, and the fitness effects boldness had on the individuals of this population by using proxies of survival, weight at sexual maturity and lifetime reproductive success (LRS). To determine long-term consistency between individuals, I analysed the repeatability of the boldness index. The repeatability of these values showed we can consider this behaviour as an animal personality. From the fitness analyses, it was concluded that boldness had significant positive effects on the fitness proxies used, proposing that bold individuals have higher fitness in this population. While sex did not affect an individual’s boldness, it had significant interactions with boldness, affecting the strength of fitness effects on individuals in weight at sexual maturity and LRS.

Työssä kuvataan eri puolilta Suomea toukokuussa 1976 eläinsuojista kerättyjen talvehtineiden hibernaatiossa olleiden naaraiden insektaariossa munimien munien morfologiaa. Valomikroskoopilla munista määritettiin yläpinnan kirjailu, mitattiin munan kokonaispituus, yläpinnan leveys,kellukkeiden pituus sekä laskettiin kellukkeiden kaarien määrä. Munan yläpinnan kirjailuun ja yläpinnan leveyden - munan kokonaispituuden väliseen suhteeseen perustuvien määritysten avulla aineistosta oli todettavissa kaksi lajia: Anopheles messeae messeae Falleroni sekä Anopheles beklemishevi beklemishevi Stegnii & Kabanova. A. b. beklemishevi määritetään Suomesta ensimmäistä kertaa. SEM- ja TEM-kuvauksissa tutkitaan Hintonin (1968) mainitsemia piirteitä, joiden hän katsoo eroavan eri Anopheles lajeilla. Lajinmäärityksen kannalta SEM-tarkastelu ei ole tarpeellinen, sillä mainittavia eroja ei löytynyt kuin yläpintaa ympäröivän reunuksen ja kellukkeiden liittymäkohdasta. Lisäksi työssä esitetään em. lajien levinneisyys ja vertaillaan saatuja levinneisyyskarttoja vanhoihin malarian levinneisyyttä Suomessa ja muualla Pohjoismaissa käsitteleviin tietoihin.

Caged photolysable compounds have served to be pivotal to neuroscientific investigations; allowing the cognizing of molecular kinetics and properties of neuronal micro-machinery such as neurotransmitter receptors. Precision in terms of temporal and spatial resolution of neurotransmitter release endowed by photolysis has multitudinal applicabilities in the realm of GABAA receptors (GABAARs), their neuronal niche and effects on neuronal and network activity. Caged compounds, in their caged form, may display certain unideal traits such as undesired interactions with the system and antagonistic activity on the target receptor. This study aims to reevaluate the GABAAR antagonistic actions of caged Rubi-GABA, which was found to antagonize these receptors at significantly lower concentrations than those reported in the literature. Furthermore, this study electrophysiologically characterizes the possible antagonistic properties of a novel quinoline-derived UV-photolysable caged GABA compound, 8 DMAQ GABA, whose activity, in its caged form appears to have a much more favorable antagonism profile compared to the widely used RuBi-GABA. To assess the antagonistic effects of these compounds on GABAAR-mediated miniature inhibitory postsynaptic currents (mIPSCs) patch-clamp recordings were carried out in the whole-cell voltage clamp configuration on cortical layer 2/3 cortical pyramidal neurons in acute neocortical slices prepared from 16-18 day-old rat rats. The results of this study indicate a revised antagonism profile for caged Rubi-GABA, with marked GABAAR toxicity in the low micromolar range. The study also scrutinizes the photo-kinetic properties of both caged GABA compounds and reveals that the rate of GABA release from 8-DMAQ is slower than from RuBi-GABA.

The human gut is inhabited by gut microbiota, a complex and diverse ecological community of trillions of microbes that affect both the normal human physiology and countless disease states and susceptibilities. Understanding the composition, functions and the causes and effects of changes in the microbiota is invaluable for understanding diseases that are connected to the microbiota and developing better treatments to the diseases. The gut microbiota varies between individuals and keeps changing over time. Behind the variability are e.g. the person’s age, genetics, diet, environment, and especially diseases and the use of antibiotics. When antibiotic use disrupts the gut microbiota, the changes can persist for years. Antibiotic resistance tends to increase after the use of antibiotics. Since antibiotic resistance in bacterial pathogens is considered a major health threat, the characterization of the human gut resistome (the antibiotic resistance genes (ARGs) found in the gut microbiota) is of great medical interest. Next-generation sequencing techniques have enabled studying also those microbe species that cannot be cultured at the moment. Metagenomics provides information on all genetic material collected from a given environment and enables searching for any sequences of interest within it, e.g. ARG sequences. The development of Parkinson’s disease (PD) is suspected to begin in the enteric nervous system and spread from there toward the central nervous system. The use of antibiotics could be linked to PD through their effects on gut microbiota, and since these effects are modified by the gut resistome, the aim of this study was to find gene sequences coding antibiotic resistance in human gut metagenomics data originating from stool samples of PD patients and healthy controls, and to find out potential differences in the occurrence of antibiotic resistance genes in the gut microbes of the two study groups. DeepARG was the chosen method for searching antibiotic resistance gene sequences in the metagenomics data. The statistical data analyses, including alpha diversity, multivariate analyses, and differential abundance analysis, were performed with the R statistical programming language in RStudio. DeepARG found 840 different ARGs in 192 samples. The ARGs belonged to 29 different ARG classes. The alpha diversity analysis showed a small estimated difference between PD and control groups indicating a possible slightly higher ARG diversity in the PD group. Multivariate analysis did not give any strong suggestions of definite biologically meaningful differences between the study groups. 16 ARGs were deemed differentially abundant in the study groups. BepE, cmeA, cmlv, dfrE, mefC, msrB, opcM, oprM and RbpA seemed to have increased abundance, and arnC, BN537_02049, dfrK, mgrA, murA, tet35 and tetT were suggested to have decreased abundance in PD patients compared to the healthy controls. These ARGs do not appear interconnected in any other way except for some sharing antibiotic types to which they offer resistance, and some having similar resistance mechanisms. In the light of an ongoing, unpublished epidemiological study of the connection between PD and the use of antibiotics it would seem that only three ARGs (msrB, mefC and dfrE) might be somehow relevant in PD development, but their effects, if any, are most likely minor. Eight ARG classes were shown to have differential abundance between PD patients and healthy controls. Bacitracin, fosfomycin and polymyxin classes showed decrease and chloramphenicol, fosmidomycin, puromycin, rifampin and sulfonamide classes showed increase in abundance in PD compared to controls. The change in the abundance of a certain ARG could reflect change in the abundance of the bacteria carrying that resistance gene. If so, the follow-up questions would be how much change in the abundance of bacteria is due to the use of certain antibiotics and how much is caused by environmental factors. It also remains to be studied whether specific antibiotics associated with the ARGs that in this study showed differential abundance in PD patients and healthy controls might have an actual role in PD development. The results of this thesis study are later to be combined with and further studied alongside information coming from ongoing studies on antibiotics use in general population and in PD patients. While this study did not concentrate its efforts into finding novel ARGs, the metagenomics dataset could also in the future be applied for that purpose.

Coxsackievirus A9 (CVA9) is a member of the Picornaviridae family of viruses and Enterovirus genus. CVA9 is mostly associated with milder Enterovirus symptoms such as rashes, but there are also individual cases of more serious diseases caused by CVA9 infection, including hepatitis. The picornavirus capsid structure is largely conserved and composed of 3-4 viral proteins (VP). At the base of VP1 there is a hydrophobic pocket occupied by a lipid factor. The expulsion of that lipid factor leads to expansion of the capsid, viral uncoating and genome release into the cell. To prevent that expansion, an ongoing study has been screening and synthesizing hundreds of potential molecules to target the VP1 pocket and replace the pocket factor. One such molecule is CL300, an N-phenyl benzamide, which has an antiviral effect on CVA9. The purpose of this study was to validate the proposed mechanism of action of CL300 on CVA9 by confirming its binding location with cryogenic electron microscopy and single-particle processing methods. Through processing, 31,050 particles were narrowed down to 21,230 particles that were reconstructed into a 2.26 Å resolution density map of CVA9 with a heterogeneous density in the VP1 pocket. Due to features present in that density and the presence of multiple rotamer densities in a nearby residue, Y210, it was concluded that either CL300 or lipid factors were present in different VP1 pockets, resulting in an averaged density in the map. The final result of this study was a model of CVA9 with CL300 in the hydrophobic pocket. These results, in conjunction with the ongoing study into the antiviral effect of CL300, have implications for the potential future production of antivirals and vaccines to combat CVA9 and other Enterovirus infections where there is conservation of the binding pocket.