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  • Paranko, Birgitta (2019)
    Introduction and aims. Multiple different neurobiological alterations have been hypothesized to underlie Major Depression Disorder (MDD), but no unifying theory exists to explain the mechanisms of the disorder. The aberrant brain dynamics in MDD can be seen in the alterations of long-range temporal correlations (LRTCs), which have been proposed to be an indication of criticality in healthy brain. Alterations in LRTCs have been suggested to reflect deficiencies in excitation-inhibition (E/I) balance, neuromodulation or connectivity patterns, which have also been proposed to be the underlying mechanisms of MDD. There has been controversy whether the pathology is related to attenuated or increased LRTCs, and the sources of altered brain dynamics have not yet been localized. The aim of this study was to find in which frequency bands and where in the brain the neuronal LRTCs are altered in MDD on source level. In addition to analyzing the correlations between neuronal LRTCs and depression severity in parcel level, we studied correlations in functional networks to get a better understanding of the system level alterations in MDD. We also studied whether behavioral LRTCs correlate with depression severity or with behavioral performance. Methods. We investigated the long-range temporal correlations in a cohort of 19 depressed subjects by using magnetoencephalography (MEG) for recording brain activity during resting state and response inhibition task and performed DFA analysis on the amplitude envelopes of cortical oscillations. The depression severity was measured with BDI-21 questionnaire. Results and conclusions. We found the LRTCs to be positively correlated with depression severity in the alpha frequency band (8–12Hz) predominantly in the limbic system that underlies emotional control. This result was supported by the parcel level analysis in which correlations between alpha band LRTCs and depression severity were observed in the orbitofrontal cortex and temporal pole, indicating that the hyper-activation of limbic system could explain the negative bias characteristic to depression. Positive correlations were also found in frontoparietal, ventral, and dorsal attentional networks that support cognitive control. Alpha band LRTCs correlated also with behavioral LRTCs during both resting state and task conditions. However, we observed more wide-spread correlations between alpha range LRTCs and depression severity than between neuronal LRTCs and behavioral LRTCs. Behavioral LRTCs correlated with depression severity, but not with behavioral performance. These results indicate that depression is characterized by vast alterations in the brain dynamics and imply that the wide range of different symptoms in MDD could be explained by alterations in the excitation/inhibition balance in the limbic system and cognitive networks.
  • Komulainen, Anne (2013)
    Pulmonary arterial hypertension (PAH) is a progressive and devastating disease with poorly understood pathogenesis. It is characterized by abnormal remodelling of pulmonary vasculature due to uncontrolled apoptosis and proliferation of endothelial (ECs) and smooth muscle cells (SMCs) in vascular wall. In severe PAH pulmonary ECs exhibit hyperproliferative and apoptosis resistant phenotype contributing to the formation of neointima and development of plexiformic lesions. Structural changes promote occlusion of vascular lumen, and thus, increase in pulmonary vascular resistance. To date we lack efficient therapy to prevent vascular remodelling and restore normal vascular function in PAH. Purinergic signalling is potential modulator of pulmonary vascular homeostasis. It comprises of extracellular nucleotides, such as ATP, which signal through their receptors on cell membrane. Ectoenzymes with nucleotide hydrolyzing activity have an essential part in controlling homeostasis and physiologic concentration of extracellular nucleotides. Ectoenzyme CD39 plays a crucial role in dephosphorylating ATP, which is a known mediator of inflammation, angiogenesis, thrombosis and vasoconstriction according to previous research. Aims of this project were to study the role of extracellular ATP in pulmonary endothelial dysfunction during PAH pathogenesis. The goal was to evaluate the significance of ATPases, such as CD39, in the disease process and to identify significant ATP receptors on pulmonary ECs. We utilized a previously unused strategy to monitor ATPase activity in vivo in pulmonary endothelium of rats with PAH. With this strategy we could identify changes in a time-line manner. Our results indicate that ATPase activity is significantly attenuated in ECs during disease process. Similar finding was also observed in human pulmonary EC isolated from PAH patients suggesting that loss of ATPase activity mediated increase of extracellular ATP could play a role in disease pathogenesis. Our in vitro experiments reveal that loss-of CD39 in human pulmonary ECs leads to an apoptosis resistant and hyperproliferative phenotype. We also identify that purinergic receptor P2Y11 is a critical mediator of ATP responses in these ECs. Suppression of ATP mediated P2Y11 response in apoptosis resistant PAH patient ECs restores normal EC phenotype and thus, suggests a novel therapeutic strategy for pulmonary occlusive vasculopathy.
  • Suonto, Lotta (2019)
    Amelogenesis Imperfecta (AI) is a group of hereditary diseases where tooth enamel is abnormally formed. This disease has been found in Lancashire Heeler dogs. However, none of the mutations known to cause AI in canine, explain the disease in the Lancashire Heeler population. A research study was initiated to investigate the genetic background of the disease in the breed. Based on the pedigree data the disease was suggested to be inherited as an autosomal recessive disease. Whole-exome sequencing of two affected dogs was performed which revealed a plausible candidate variant in a gene regulating intracellular calcium concentration. The aim of this study was to examine whether the mutation in the candidate gene causes AI. The DNA were extracted from blood samples of 249 Lancashire Heelers. A genome-wide SNP genotyping was conducted on four cases and a homozygosity mapping was performed. The candidate variant was genotyped in a large cohort of Lancashire Heelers (n=249) and dogs from related breeds (n=91) to confirm the association with the disease. The expression of the candidate gene in lymphocytes was studied with RT-PCR. Clinical studies were performed to evaluate the clinical features and serum calcium levels were measured. The segregation of genotypes and phenotypes of the dogs was complete. The identified variant is predicted to cause a premature STOP codon, which, if translated, leads to a truncated protein lacking protein transmembrane domains. According to the results acquired from RT-PCR, it is possible that the protein will complete the translation despite the mutation. Clinical studies did not reveal other clinical features than enamel defects and serum calcium levels were normal. According to the results, we suggest that the identified variant is causal for AI in Lancashire Heelers. The results have significant impact because no other genetic connection between the gene and AI has been found before. Consequently, the development of a gene test is possible, creating multiple opportunities for researchers and veterinary medicine. The results are applicable also to human medicine. However, we need more research to achieve a complete understanding of the mutation and its effects.
  • Röhr, Emilia (2013)
    Typpi on perustuotantoa rajoittava ravinne lähes koko Itämerellä. Typen kierto perustuu mikrobien välittämiin hapetus-pelkistysreaktioihin, joissa typpeä muunnetaan erilaisiin muotoihin. Ammonifikaatiossa mikrobit mineralisoivat liuennutta tai partikulaarista orgaanista typpeä ammoniumiksi ja DNRA- prosessissa (dissimilatorinen nitraatin pelkistys ammoniumiksi)mikrobit pelkistävät nitraattia ammoniumiksi. Ammonium on biologisesti kaikkein käyttökelpoisin typen muoto ja siksi sen pitoisuudet ovat vesipatsaassa yleensä hyvin pieniä. Mikrobiprosessien mittaamiseksi myös pienten ammoniumpitoisuuksien määrittäminen on tärkeää. Pro gradu-tutkielmassa määritettiin DNRA:n ja ammonifikaation prosessinopeuksia Varsinaisen Itämeren vesipatsaassa hyödyntämällä stabiili-isotooppitekniikkaa. Tutkimuksen edellytyksenä oli selvittää kokeellisesti alin luotettava määritysraja ammoniumin 15N-pitoisuudelle. Menetelmäkehitystä varten valmistettiin koesarjoja ultrapuhtaasta vedestä ja tunnetun 15N:14N -suhteen omaavista ammoniumkloridijauheista. Minimimääritysrajakokeessa etsittiin eri ammoniumin ainemääriä sisältävän koesarjan avulla massaspektrometrisen analyysin tarvittava alin ammoniumin ainemäärä. Minimimääritysrajan alapuolelle pyrittiin pääsemään tekemällä kantoliuoskoe. Kantoliuoskokeessa valmistettiin eri ammoniumin ainemääriä (0,5 atom. %) sisältävä koesarja, joiden ammoniumin ainemäärää kasvatettiin lisäämällä näyteliuoksiin kantoliuosta, jonka määrä ja isotooppisuhteet tunnettiin. Kantoliuoslisäysten jälkeen näytteet analysoitiin massaspektrometrillä ja tuloksista seurattiin 15N:14N – suhteen muutosta eri laimennoksissa. Pienin luotettavasti määritetty ammoniumin ainemäärä oli 0,5 µmol. Kantoliuoskokeilla ei onnistuttu optimoimaan määritysrajaa pienemmäksi, eikä menetelmää siten hyödynnetty vesinäytteiden DNRA- ja ammonifikaatiomittauksissa. DNRA- ja ammonifikaatiomittauksia varten kerättiin vesinäytteitä Varsinaiselta Itämereltä neljältä eri näytteenottoasemalta (Läntisen Gotlannin, Itäisen Gotlannin , Fårön ja Landsortin syvänteet) toukokuussa 2011. Lisäksi Itäiseltä Gotlannin syvänteeltä otettiin vesinäytteet DNRA- ja ammonifikaatiomittauksia varten myös heinäkuussa 2011. Vesinäytteitä rikastettiin 15N- ammoniumilla siten, että näytteiden 15N- pitoisuudeksi saatiin 5 µM. Näytteitä inkuboitiin 24 tuntia in situ- olosuhteissa. Inkuboinnin jälkeen näytteistä mitattiin 15N- leima ammonium diffuusio- menetelmällä. Tuloksista laskettiin DNRA- potentiaalit sekä ammonifikaation in situ- prosessinopeudet. Keväällä mitatut ammonifikaation in situ- prosessinopeudet olivat matalia (0,36- 8,35 nM d-1). Tuloksia saattoi selittää se, ettei kesäisen perustuotannon tuottama partikulaarinen orgaaninen typpi ollut vielä ammonifioijien käytettävissä. Eri asemilta mitatuissa prosessinopeuksissa ei ollut tilastollisesti merkitsevää eroa. Tutkittujen ympäristömuuttujien ja ammonifikaation prosessinopeuksien välillä ei havaittu korrelaatiota. DNRA- potentiaalituloksia saatiin vain toukokuussa Läntiseltä Gotlannin syvänteeltä ja heinäkuussa Itäiseltä Gotlannin syvänteeltä kerätyistä näytteistä. Läntiseltä Gotlannin syvänteeltä mitattu DNRA- potentiaalinopeus (1,14 nM d-1) oli lähes nelinkertainen heinäkuussa Itäiseltä Gotlannin syvänteeltä mitattuun DNRA- potentiaaliin (0,38 nM d-1) nähden. Ammonifikaation merkitys Itämerellä on todennäköisesti pienempi ulapalla kuin estuaareissa, joissa suuri orgaanisen aineksen kuormitus tuo jatkuvasti substraatteja ammonifikaatiolle. Keväisen piileväkukinnan nopeasta sedimentoitumisesta johtuen saattavat ammonifikaation prosessinopeudet Itämerellä keväisin olla suurempia sedimenteissä kuin vesipatsaassa. Itämeren erityispiirteet, kuten alhainen suolapitoisuus todennäköisesti inhiboi vesipatsaan DNRA:n esiintymistä, jonka seurauksena mitatut DNRA- nopeudet jäivät mataliksi. DNRA: n kanssa nitraatista kilpailevan kemolitoautotrofisen denitrifikaation on sen sijaan havaittu olevan pääasiallinen typpeä pelkistävä prosessi Varsinaisella Itämerellä.
  • Kuitunen, Essi (2019)
    Glutamine, the conditionally essential amino acid, is a major carbon and nitrogen carrier required for a range of cell functions, such as protein synthesis and maintaining redox balance. While healthy cells adjust their activities in response to glutamine availability, tumor cells display deregulated glutamine uptake and metabolism allowing quick proliferation and survival in cellular stress conditions. Hence, further knowledge of the glutamine sensing network is of interest. Utilizing Drosophila melanogaster, the roles of formerly identified glutamine sensing regulator candidates, Forkhead box O (FoxO), Super sex combs (Sxc), Spalt major (Salm) and Spalt-related (Salr), were explored. Drosophila is an efficient model organism for analyzing gene regulatory mechanisms, with its simple genome but conserved genes and metabolic pathways. Loss-of function and gain-of-function mutants of the candidates were cultured with/without glutamine, and their physiological response and gene expression changes were analyzed. The results show the glutamine intolerant phenotype of FoxO and Sxc deficiency, not dependent on altered food intake levels of larvae. However, glutamine intolerance of Salr and Salm deficiency was not observed. Moreover, we aimed to gain further insight to the roles of FoxO and Sxc in glutamine metabolism. Since amino acid catabolism produces ammonia, and glutamine metabolism plays a vital role in ammonia detoxification, we performed a pH-based measurement of foxo and sxc mutant larvae hemolymph on food with/without glutamine. However, we could not associate FoxO or Sxc with regulation of glutamine-derived ammonia clearance. In addition, we explored FoxO downstream regulator candidates. Putative promoter areas of Paics, Uro, Sesn, salr, Prat2 and Gdh were cloned into reporter vectors and the luciferase activity was analyzed under the expression of foxo. The results indicate that FoxO is a regulator of all of the 6 genes. Next we could utilize the here constructed plasmids to see whether the FoxO-mediated regulation is affected by altered glutamine levels in cell culture.
  • Butkovic, Rebeka (2020)
    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.
  • Räisänen, Maritta (2019)
    Uterine leiomyoma (also known as myoma) is the most common neoplasia in women during reproductive age and it represents a burden for public health care. Approximately 70% of Caucasian women develop myomas, although only 25% of cases are symptomatic. The genetic background of myomas varies significantly and the most common genetic causes are mutations in genes Mediator complex subunit 12 (MED12), Fumarate hydratase (FH) or YEATS Domain containing 4 (YEATS4) , rearrangements affecting the High Mobility Group AT-hook 2 (HMGA2), and deletions in COL4A5/6 locus. MED12 mutations represent the most common genetic alteration in myomas, being present in approximately 70% of cases. Genome organization comprises different levels of complexity, spanning from regulation of individual genes to changes in the architecture of large portions of chromosomes. Literature offers massive evidence of changes in genome organization among different cell types and between several tumor and related healthy cells, but information about these changes in myoma is lacking. The aim of this study is to determine the main features of genome organization in myomas belonging to the aforementioned five genetic subclasses, in order to identify which are the underlying common pathways that are dysregulated in the neoplasia. This is achieved by mapping regions of open chromatin in myomas and related my-ometrium samples with ATAC-seq. Sample’s clustering seems not to be individual-dependent, while tumors belonging to FH, YEATS4 and COL4A5/6 subclasses form distinct clusters, unlike MED12 and HMGA2 subclasses. Six open chromatin regions located within genes were identified in 19/25 tumors and not in myometrium. Seven myometrium-specific open chromatin regions were identified in 21/25 myometria and in less than 10 tumors. As expected, Gene Ontology enrichment analysis revealed that myomas belonging to FH subclass are characterized by deregulation of metabolic pathways. Many of the identified genes in the open chromatin regions have been linked to other tumors in previous studies. Tumor-specific open chromatin regions locate within oncogenes, while myometrium-specific ones are found in proximity of tumor suppressor genes, suggesting a biological role in myomagenesis for these genes. Further investigation on the identified genes (e.g. transcriptional regulation, gene expression and protein level) and addi-tional studies on chromatin architecture are needed to fully unravel the mechanism of myomagenesis.
  • Raubenheimer, Marie-Claire (2020)
    Oil spillages represent a serious environmental hazard for flora and fauna of marine and coastal ecosystems. Though marine oil spills have decreased since the 1970s, the increasing production of petroleum goods remains a potential source of pollution due to its use and transportation. When aquatic organisms, including fish, are exposed to toxic oil compounds, this can cause sublethal morphological changes and increase mortality. In this context, herring have been frequently studied, and results suggest that particularly herrings eggs and larvae are highly susceptible to oil toxicity. In this thesis, a Bayesian meta-analysis was conducted to investigate the effects of crude and fuel oil on the mortality of herring eggs from the genus Clupea. Observations from laboratory studies, collected during a literature review, served as input for the statistical analysis. To this end, Bayesian inference modeling was applied to generate posterior probability distributions for additional mortality caused by exposure to oil mixtures. Also, oil concentration, oil type, exposure time, and temperature were analyzed to study possible correlations with mortality impacts. The results of this study suggest that acute mortality of exposed herring eggs is similar to mortality observed for individuals exposed to only small concentrations or none at all. Of all evaluated oil types, medium grade crude oil caused the most significant change in instantaneous mortality with increasing oil concentration. Generally, distinct oil types had a greater influence on mortality outcomes than temperatures at the given concentrations. For the lowest temperatures, some correlations for increased mortality were found. Overall, the unexplained variability between the reviewed studies has a relatively small influence on mortality outcomes. In conclusion, the mortality of exposed herrings eggs is most likely delayed due to sublethal effects, rather than immediate, at the modeled concentrations. Altogether, uncertainty amongst the posterior probability distributions is high, indicating a wide possibility range for the monitored parameters' actual values. The reasons for elevated uncertainty likely stem from diverse experimental setups, biological differences between tested species, relatively small sample sizes, and model-related issues. Thus, future research could consider additional variables, information from observational studies and other fish species to reduce uncertainty in mortality outcomes.
  • Zavattoni, Giorgio (2022)
    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.
  • Peltola, Sanni (2019)
    In recent decades, ancient DNA recovered from old and degraded samples, such as bones and fossils, has presented novel prospects in the fields of genetics, archaeology and anthropology. In Finland, ancient DNA research is constrained by the poor preservation of bones: they are quickly degraded by acidic soils, limiting the age of DNA that can be recovered from physical remains. However, some soil components can bind DNA and thus protect the molecules from degradation. Ancient DNA from soils and sediments has previously been used to reconstruct paleoenvironments, to study ancient parasites and diet and to demonstrate the presence of a species at a given site, even when there are no visible fossils present. In this pilot study, I explored the potential of archaeological sediments as an alternative source of ancient human DNA. I collected sediment samples from five Finnish Neolithic Stone Age (6,000–4,000 years ago) settlement sites, located in woodland. In addition, I analysed a lakebed sample from a submerged Mesolithic (10,000–7,000 years ago) settlement site, and a soil sample from an Iron Age burial with bones present to compare DNA yields between the two materials. Soil samples were converted into Illumina sequencing libraries and enriched for human mtDNA. I analysed the sequencing data with a customised metagenomics-based bioinformatic analysis workflow. I also tested program performance with simulated data. The results suggested that human DNA preservation in Finnish archaeological sediments may be poor or very localised. I detected small amounts of human mtDNA in three Stone Age woodland settlement sites and a submerged Mesolithic settlement site. One Stone Age sample exhibited terminal damage patterns suggestive of DNA decay, but the time of deposition is difficult to estimate. Interestingly, no human DNA was recovered from the Iron Age burial soil, suggesting that body decomposition may not serve as a significant source of sedimentary ancient DNA. Additional complications may arise from the high inhibitor content of the soil and the abundance of microbial and other non-human DNA present in environmental samples. In the future, a more refined sampling approach, such as targeting microscopic bone fragments, could be a strategy worth trialling.
  • Luomaniemi, Virve Kaarina (2020)
    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.
  • Hanstén, Magnus (2019)
    An increasing number of fisheries utilize rights-based management approaches for achieving economic, social and environmental sustainability. It is widely accepted that fisheries management is to a large extent about managing human behaviour, hence social acceptance is prerequisite for a successful management regime. Based on stakeholder interviews, this study analyses the opinions related to the recently implemented individual transferable quota (ITQ) system for the Finnish herring and sprat fisheries. Similarly, opinions were collected in 2007 by Kulmala et al. related to a possible implementation of ITQs, thus creating a unique opportunity to compile results from both a pre and post individual quota management implementation scenario. In 2007, it was suggested that fishers would largely support an ITQ system in Finland. Accordingly, this study implies that most of the Finnish stakeholders are content with the properties of the new system, however inequalities were perceived among fishers targeting fish for human consumption. In general, the system is expected to achieve its primary goal of improved economic efficiency within the fishery industry.
  • Hopkins, Tapani (2012)
    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.
  • Ragab, Basma (2020)
    Lymphedema is a progressive disease, resulting from abnormalities of the lymphatic system. It is characterized by swelling of one or more parts of the body, due to impaired lymph transport. Lymphedema has no definitive treatment and it can have serious effects on the patients' quality of life. However, the recent knowledge expansion of the molecular mechanisms regulating lymphangiogenesis provides new possibilities for the treatment of lymphedema. One of these mechanisms is the angiopoietin-TIE system. It has been shown recently that ANG2 is essential for the formation of lymphatic vasculature. Mice ANG2-deletion caused widespread lymphatic dysfunction, resulting in subcutaneous edema and chylous ascites. Lymphatic development is also regulated by TIE1 receptor, as its deletion in mice resulted in malformed jugular lymph sacs and severe edema. In this study, a model of autocrine TIE receptor activation has been established in endothelial cells to investigate the effect of the WT-ANG2 and four ANG2 mutants (T299M, N304K, C435S and R492Q) in TIE receptor phosphorylation and lymphedema. The role of these variants in direct cell adhesion has also been investigated in vitro using HeLa and lymphatic endothelial cells. The findings revealed that WT-ANG2 and soluble ANG2 variants induced both TIE2 and TIE1 activation in endothelial cells. We also found that N304K, C435S and R492Q mutants are secretion-deficients and retain the co-expressed WT-ANG2 inside the cells, causing a dominant negative effect in both TIE2 and TIE1 receptor activation which is likely associated with the lymphedema in the patients where the mutants were identified.
  • Pääkkö, Henna (2021)
    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.
  • Llach Pou, Maria (2019)
    Parvalbumin (PV) interneurons are GABAergic inhibitory neurons that shape neuronal network activity and plasticity. They are involved in both developmental and adult plasticity and have recently been divided into subpopulations that differ in birthdate, intrinsic properties and are involved in different types of learning; while late born PV neurons, expressing low levels of PV, are required for the acquisition of new information, early born PV neurons, expressing high levels of PV, are involved in the consolidation of the information. PV cells can be enwrapped with perineuronal nets (PNNs), an extracellular matrix structure that stabilizes synapses and indicates a mature state of the cell. The development of PNNs correlates with the closure of critical period of plasticity in development, and the enzymatic removal in adulthood can reopen those periods. Similarly, antidepressants like fluoxetine have been proven to reopen critical periods of plasticity in adulthood (iPlasticity) and decrease PNN structures in PV cells. However, whether the effect of fluoxetine is restricted to a subpopulation of PV interneurons is unknown. In addition, no previous studies have yet investigated the maturity state of the PV subpopulation by analyzing its PNN structures. In this thesis we aimed to elucidate differences in the maturity state of the subpopulations and the fluoxetine effect in those. To do that, we treated a cohort of adult mice with a chronic fluoxetine treatment previously reported to be capable of the reopening of critical periods. Following, we performed an immunohistochemistry analysis to detect PV and PNN levels in the CA3b hippocampal area. In addition, our mice line expressed TdTomato (TdT) in PV cells which allowed a more sensitive detection of PV neurons. After imaging the slices with a confocal microscope, we analyzed the PV and PNN intensity both by manual counting and with a semi-automatic macro script in ImageJ software that we developed and validated. The PV intensity of control mice was used to divide the cells in two groups; low PV and high PV expressing cells. PNNs in those subpopulations in both the control and fluoxetine treated group were analyzed and statistically compared. The low PV subpopulation showed a significantly low PNN intensity compared to the high PV subpopulation, indication a plastic or immature low PV subpopulation and a mature or consolidated high PV subpopulation. Interestingly, fluoxetine selectively decreased the PNN structures in the high PV subpopulation, by bringing the PNN intensity to comparable levels found in the low PV network. No effect of fluoxetine in the low PV network was detected. Fluoxetine induced a change towards a plastic state in the network believed to be involved in memory consolidation by decreasing its PNNs structures. This discovery gives new insights on the understanding of antidepressant plastic actions, suggesting that a chance for strong memories to change could be facilitated with the drug, and explain the antidepressant’s effects when combined with psychotherapy. However, supplementary experiments to compare and define PV subpopulations and a confirmation of the selective effect of fluoxetine are needed to confirm the preliminary hypothesis suggested by our data.
  • Andersson, Oliver (2020)
    This study focused on the spectral sensitivity of two Norwegian lake populations of opossum shrimp (Mysis relicta), with a common implantation history and a temporal separation of about 50 years. Previous findings have indicated a difference in the absorption maximum (λmax) between sea and lake populations of Nordic mysids that have been separated about 9 000 years. Between the population groups, the spectral sensitivity correlates to the Wavelength of Maximal Transmission (WLMT) in the habitats. This may be considered a form of adaptive tuning. It is not known if the species-specific mechanism is based on chromophore shift or opsin modification or a combination of both, neither is the timescale of the adaption well understood. The intent was to determine λmax of both populations, what chromophore(s) they use and possible variations of the opsin gene. By comparison to spectrometric data of the habitats, the study aimed to broaden the insight into the mentioned unknowns. The light conditions of the lakes were determined by spectrometry down to depths of three and five meters. As predicted a positive, lake-bound correlation between the attenuation coefficient (k) and WMLT was found. Single-rhabdom microspectrophotometry (MSP) was used to determine λmax of the visual pigment in situ. Absorbance spectra were analysed by manual fitting to mathematical pigment templates and by script-based automation. Neither the chromophore nor differences in λmax could be determined, due to a small sample size that limited the statistical power of the results. The opsin genes from both populations were sequenced. No differences expected to have an effect on spectral sensitivity were found. Spectral tuning could not be demonstrated to have occurred in the populations due to the limited sample size. Nor did the results give support for any new findings on the mechanism or the time scale of spectral tuning among mysids. To answer the proposed questions of the study, additional sampling of both populations is needed.
  • Srinivasan, Rakenduvadhana (2019)
    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.
  • Haapalainen, Samuli (2021)
    Biodiversity is decreasing globally due to human activity. At times, on-time monitoring of the state of habitats and biodiversity is challenging. One useful way to study these is to use certain species as indicators for the state of habitats and biodiversity. One group that are often used, are birds. They are easy to detect and they have specialized to most terrestrial ecosystems. Changes in the population sizes of different bird species can reflect changes in different habitats and their biodiversity. Therefore, it is essential that different bird monitoring practices produce reliable and comparable results. I compared datasets produced by two different Finnish bird census programs in my thesis. The census programs were national breeding bird survey program and Hanko Bird Observatory´s migratory bird census program. Both programs produce data on population abundances and changes in population sizes. Because methods between these programs differ greatly, their data may differ for some species. I compared the datasets by comparing population change indexes of the same species. I also tested whether species traits would be associated with the comparability of the datasets. These traits were mean body size, migratory behavior, favored habitats, and number of sightings for each species. I made models for all combinations of traits. I used a generalized linear model in my analysis. I compared the models by using Akaike´s information criterion (AIC) with correction for small sample sizes (AICc). My results showed that both national breeding bird survey program and Hanko Bird Observatory´s migratory bird census program produce parallel population trends for species. From the tested species traits, only migratory behavior was associated with comparability of the datasets. The datasets were highly comparable for long- and short-distance migratory birds but only moderately comparable for resident birds. This is likely due to migratory bird census program recording the local population dynamics of resident birds of Hanko peninsula. These local population trends may differ from the national trends of the same species. The breeding bird survey program should better reflect the national population trends. My results also showed that more numerous common bird species are declining faster than uncommon species. This is an alarming scenario because it points at extensive habitat degradation and biodiversity loss. Also, population trends of species favoring mires and mountains were clearly declining compared to species favoring other environments. This may be due to endangering of mire and mountain habitats due to climate change and human land use such as peatland drainage. Strong declines of species may also be explained by changes in the wintering areas of these species. Finnish breeding bird survey program and Hanko Bird Observatory´s migratory bird census program both produce overall comparable data on population trends of birds. They could be used to complement one another and to provide supporting evidence on the validity of bird population trends. Producing quality bird census data is highly important in tracking the state of biodiversity and when deciding on conservation acts. The data on the census programs provide support for the research on state of Finnish and European habitats and biodiversity.
  • Henttonen, Kaisu (2020)
    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.