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(2022)Fear has far-reaching physiological and behavioural effects for animals, altering their foraging efficiency, parental care and breeding success. Extensive research shows that an animal’s perceived risk of predation, for example, can have fitness effects equivalent to direct killing. However, less work has explored the effects of fear induced by other natural enemies. Here I investigated by field experiment how the perceived risk of brood parasitism by common cuckoos (Cuculus canorus) affects behaviour of reed warblers (Acrocephalus scirpaceus), one of the favourite host species. Previous work shows that reed warblers upregulate behavioural defences based on social information about parasitism risk, but it is not known whether this alters their behaviour outside of an encounter with a cuckoo. Therefore, I manipulated social information about parasitism risk using models and alarm-call playbacks, and measured differences in vigilance behaviour depending on the amount of social information provided (high, medium, low, no risk). I found that vigilance increased when the perception of parasitism risk increased, both during social information presentations and 6 days later during incubation (when the nest is no longer at risk of parasitism). The findings suggest that when perceived risks are high, incubation behaviour is adapted to reduce parasitism risk. Additionally, the cues indicating increased parasitism risk reduced the fledging success, possibly due to the increased stress and the time allocated into vigilance rather than parental care. Therefore, these changes in incubation behaviour impact individual fitness. Further study is required into the behavioural changes in parenting during chick rearing from the increased perception of parasitism risk.
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(2020)Influenza A viruses are pathogens infecting birds and selected mammals. They are responsible for around 500 000 human deaths each year and pose a substantial economic burden to the healthcare system. The most important pathway in influenza virus detection is a retinoic acid-inducible gene I pathway, which recognizes the 5’-triphosphate in viral RNA. Its activation leads to the production of interferons: a group of cytokines important in overcoming viral infection. In order to replicate successfully, viruses had to develop mechanisms to overcome host defences. They include, among others, regulation of interferons and interferon stimulated genes expression. During influenza A virus infection, this function is performed by viral non-structural protein 1 (NS1). The aim of this study was evaluating the effect of NS1 of five different avian influenza strains and one seasonal influenza strain on activation of type I and III interferon gene promoters. The NS1 of seasonal virus H3N2 shown the highest suppression of both interferon I and III promoters, while NS1 originating from avian H9N2 and H7N7 strains had limited effect on interferon promoter activation. NS1 of H5N1/04, H5N1/97 and H7N9 was very effective at suppressing interferon type I promoter, which correlates with the severity of the infection in humans. When it comes to interferon type III promoter, H7N9 was very efficient at the suppression, while NS1 of H5N1/04 had little impact on promoter activation. The study has provided more information on the efficiency of potentially pandemic avian influenza strains at inhibition of interferon response and may be a base for further research. The project was conducted at the Finnish Institute of Health and Welfare.
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(2022)Kiihtyvän ilmastonmuutoksen aikana on entistä tärkeämpää löytää tapoja vähentää päästöjä ja sitoa hiiltä. Biohiilen käyttö on yksi keino ilmastonmuutoksen hillitsemiseen, ja sillä on potentiaalia parantaa maatalouden satoja. Ennen kuin biohiilen käyttö voi yleistyä, sen mahdolliset ulkoisvaikutukset, kuten vaikutukset maaperän eliöstöön, on kuitenkin ensin selvitettävä. Tässä opinnäytetyössä tutkittiin biohiilen käytön vaikutuksia mikrobien suhteelliseen runsauteen, kastematoyhteisöihin ja mikrobibiomassaan. Vain lauhkean ja boreaalisen vyöhykkeen kenttätutkimukset olivat osana tutkimusta. Biohiilen vaikutukset mikrobiryhmien suhteelliseen määrään selvitettiin kirjallisuuskatsauksella. Kirjallisuuskatsaus tehtiin myös selvittäessä biohiilen vaikutuksia kastematoihin. Biohiilen vaikutukset mikrobibiomassaan selvitettiin meta-analyysillä. Meta-analyysissä käytetyt tutkimukset luokiteltiin muuttujien, kuten biohiilen raaka-aineen, pyrolyysilämpötilan, maaperän pH:n, SOC:n, maaperän rakenteen ja biohiilen levitysmäärän perusteella. Tätä kautta voitiin selvittää, voisiko jokin näistä muuttujista selittää meta-analyysin tulokset. Mikrobien suhteellisen runsauden havaittiin muuttuvan biohiilen lisäyksen myötä, mutta reagoivat organismiryhmät vaihtelivat suuresti ja vaikutus yleensä haihtui ajan myötä. Biohiilen lisääminen ei vaikuttanut kastematoihin merkittävästi. Meta-analyysien tulokset viittaavat siihen, että biohiilellä ei myöskään ole merkittävää vaikutusta mikrobien kokonaisbiomassaan. Eri muuttujilla tehdyt meta-analyysit viittaavat siihen, että biohiilen lisäyksellä on positiivisin vaikutus mikrobien biomassaan happamissa maaperissä, joissa on karkea rakenne ja korkea SOC-pitoisuus, kun biohiiltä tuotetaan 500 °C–700 °C:ssa ja levitetään määrinä, jotka ovat suurempia tai yhtä suuri kuin 30 t ha-1. Biohiilen raaka-aineella ei havaittu olevan merkittävää vaikutusta. Yhteenvetona voidaan todeta, että mikrobi- ja kastematoyhteisöt pysyvät yleensä vakaina biohiiltä käytettäessä. Tämä mahdollistaisi biohiilen käytön mm. hiilen sitomiseen ja maaperän hedelmällisyyden lisäämiseen maaperän eliöstöä vahingoittamatta. Lisätutkimusta kaivataan kuitenkin erityisesti boreaalisilla alueilla sekä biohiilen ja pääviljelykasvin mahdollisista vuorovaikutuksista. Tutkia kannattaisi myös mahdollisuuksia käyttää biohiiltä yhdessä muiden orgaanisten käsittelyjen, kuten lannan tai kompostin kanssa biologisen monimuotoisuuden ja sadon parantamiseksi.
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(2021)The general structure of the vertebrate brain is highly conserved. However, a large amount of variation exists in brain size and shape, both regarding the whole brain and its subdivisions. This variation is caused by selection acting on species’ behavioural traits and shaping the evolution of the brain in the same process. It is known that one of the factors affecting vertebrate brain morphology is ecology, including habitat complexity, activity patterns and diet. The effects of diet on brain size have been studied in primates, bats and small mammals, where frugivory in primates and bats and insectivory in small mammals, are linked to larger brains. The effect of diet on brain morphology has not been studied in squamate reptiles (lizards and snakes) and the ecological factors behind size and shape variation are largely unknown in squamates compared to other vertebrates. Squamates show large diversity in diet preference as well as feeding behaviour in general, which makes them a suitable model organism to study brain evolution. Further, squamates have highly developed nasal chemical senses that are important for feeding behaviour. These factors in mind, it would be expected that diet has an effect on squamate brain morphology, and especially the brain regions important for feeding behaviour, such as the olfactory bulbs in the forebrain. To study the effects of diet on squamate brain size and shape, the brains of 51 squamate species were micro-CT scanned and 3D-brain surfaces were generated for each species. The species were categorized into four diet groups: carnivorous, herbivorous, omnivorous and insectivorous. To analyse shape and size change across species and diet groups, 73 landmarks were placed on each 3D-brain surface, covering all brain regions: olfactory bulbs, cerebral hemispheres, telencephalon, diencephalon, midbrain, cerebellum and hindbrain. The results from this study show that diet affects significantly the shape of the whole squamate brain, as well as the size of the telencephalon. Telencephalon size differed significantly between the herbivorous and carnivorous groups. Diet had no significant effect on the other brain subdivisions studied here, including the olfactory bulbs. Diet is a large part of a species’ ecology and it is very complex behaviour involving several senses and brain regions, which could explain the results obtained from this study. The results from this study are preliminary, but they indicate that diet could be one of the factors affecting brain morphology in squamates. In the future, including other factors of feeding behaviour than food choice and analysing the effects of diet on a deeper level, such as including brain regions within the brain and analysing cellular organization, could shed some new light on how diet affects squamate brain morphology.
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(2022)Sex determination in humans occurs via the sex chromosomes, X and Y. Females carry two X chromosomes while males are XY individuals. Due to this X chromosome distribution the expression of X-linked genes is balanced with a process called X chromosome inactivation (XCI) where one of the X chromosomes is silenced, selected either randomly or preferentially, in early female embryogenesis. X-linked disorders are more prevalent in males as, generally, in females the effects of a disease-causing variant in other of the X chromosomes can be compensated with the normal allele on the other X whereas male express the allele on their only X chromosome. However, cases of heterozygous females manifesting an assumed recessive X-linked disorder have been reported although the symptoms are usually milder in these cases than in males. One suggested reason behind this is a skewed XCI where the majority of female’s cells express the mutated allele. The main goal of this thesis was to examine how often heterozygous female carriers have symptoms of X-linked disorders. To achieve this goal, likely pathogenic and pathogenic X-chromosomal variants were retrieved from the ClinVar database and their global allele frequencies were examined from The Genome Aggregation Database (gnomAD). The genetic and phenotypic data of 500,000 individuals from the UK Biobank (UKB) were used to conduct genetic association analyses between the ClinVar variants and quantitative traits related to their reported phenotypes. The associations were tested in males and in females separately to allow for examination of sex-specific effects and inheritance models via the comparison of effect sizes. 89 (likely) pathogenic variants were detected from UKB, and the majority of these were extremely rare with minor allele frequency below 0.01% in the global population. 11 and 27 of them were selected for the association analyses for the male and female populations of UKB, respectively, after filtering out variants that did not meet requirements such as enough carriers. One to five quantitative traits were chosen for each variant resulting in 28 tests among males and 87 among females. These analyses showed few significant associations while the majority of the tested variants were observed to have no effects on the chosen trait. The most statistically significant association was observed with variant rs137852591 on the gene AR (androgen receptor) in males. The variant was related to lower muscle mass and shorter height that are associated partial androgen insensitivity syndrome reported in ClinVar for this variant. Nominally significant associations were seen with this variant and the same traits in heterozygous females suggesting that there might be, indeed, symptoms of the syndrome in females as well. Additionally, in both sexes variants on gene G6PD seemed related to traits that are characteristics of glucose 6 phosphate dehydrogenase deficiency. The limitations of these databases must be taken into account when conducting studies utilizing them. However, this thesis demonstrated that heterozygous female carriers may have symptoms of X-linked disorders assumed to have recessive inheritance pattern. In the future, a wider set of phenotypes could be used to investigate the impacts of the X-linked variants more broadly.
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(2020)Anthropogenic activity has enhanced global warming at alarming rates, causing temperatures to increase and heat waves to occur more frequently. The effects of global warming are prominent in aquatic ecosystems, particularly in the Baltic Sea. Temperature increases and fluctuations in the Baltic Sea create a changing environment and this can affect inhabiting species’ behaviors, specifically behaviors during reproduction. Reproductive behavior influences both the number and quality of offspring born into a population therefore making behavior changes during reproduction important to study. The three-spined stickleback (Gasterosteus aculeatus), an ectothermic animal, inhabits the Baltic Sea and is an ideal species to study reproductive behavioral changes. Although previous studies have researched three-spined sticklebacks in changing environments, none had specifically looked into the effects of rising temperatures and temperature fluctuations on male three-spined stickleback reproductive behavior. The three-spined stickleback is of particular interest because it reproduces in shallow waters which tend to be more affected by temperature changes. In this study, I aimed to investigate behavioral responses of stickleback males to higher temperatures and to temperature fluctuations during reproduction, as well as the consequences the responses have for reproductive success and the viability of offspring. In order to see how this species would cope with rising temperatures and heat waves during reproduction, a comparative climate chamber experiment was executed in Southern Finland at Tvärminne Zoological Station. Males were housed in either 19°C or 14°C for two breeding cycles, and for the second breeding cycle eight males switched temperatures to experience a temperature fluctuation. Results show that during reproduction, three-spined sticklebacks respond to higher temperatures with increased courtship activity, increased parental activity, quicker breeding cycles, and more weight lost. Parental care activity in constant high temperature decreases from the first to the second breeding cycle, while parental activity in constant low temperature increases. During temperature fluctuations, males experiencing a rise in temperature increase their parental care activity, while males experiencing a drop in temperature demonstrate the opposite. However, no significant consequences of temperature and temperature changes for reproductive success and the viability of offspring were detected during the two breeding cycles. Overall, the results of this study would indicate that the three-spined stickleback will prove to be a resilient species, and maintain population growth in the face of increased temperatures and temperature fluctuations in the Baltic Sea.
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(2012)The non-lethal effects of predation, i.e. predation risk, can significantly affect the prey population by inducing changes in behavior to reduce the risk of predation. Vigilance, hiding, and fleeing are common responses in order to lower predation risk while changes in habitat selection, habitat use, and changes in activity patterns are more severe changes and can profoundly affect prey fitness. Prey may begin to avoid habitats frequented by predators and may begin to reduce their activity during the time of day when predators are active. Human disturbance can be comparable to predation risk as it may induce similar changes in behavior. Therefore, human activity can be compared to predation risk even though the risk posed by humans may rarely be lethal. For many large vertebrates, however, humans do pose a direct and lethal threat. This is especially true for large predators whose severe decline has been attributed to centuries of persecution and habitat loss and whose populations have only recently began to increase following more favourable management plans and conservation efforts. Similarly, brown bear (Ursus arctos) populations have only recently began to increase in many parts of Europe and North America. In Finland brown bears survived extinction only in the wilderness areas in the north and in the east but have recolonized much of the country in the past decades. These solitary, opportunistic omnivores prefer forested habitats and usually try to avoid humans who they may view as predators. The limited availability of ideal habitats and extensive human activity means that bears may have to use spatio-temporal avoidance of humans rather than large scale spatial avoidance in order to reduce the risk of encountering humans. This should be evident in bear daybed selection whereby bears should select daybed sites away from human activity and select sites that provide good cover against humans while the bear rests during the day i.e. peak period of human activity. Additionally the daybed concealment should be higher closer to human activity. I studied bear daybed selection using GPS location data from collared bears from Central Finland and North Karelia regions and identifying possible daybed sites. Habitat of the daybeds was studied both by visiting daybeds in the field to assess the tree height, tree species composition, and concealment (visibility and canopy cover) and by using GIS software to identify large scale habitat preference. Effects of human activity (house, small roads, large roads) were studied by comparing the concealment of the daybed to a nearby random site and by comparing the bears' early morning locations' distance to human activity with subsequent daybed locations. Further tests were performed to test if season, bear sex, or the study area affected bear daybed selection. The results indicate that bears strongly preferred forested habitats in daybed selection and preferred mixed forests and woodland shrub habitat over the dominant coniferous forests possibly due to their higher proportion and availability of spruce (Picea abies) and deciduous trees (e.g. Betula spp. and Populus tremula) that can offer better cover than pine (Pinus sylvestris) which is dominant in coniferous forests. Mixed forests and woodland shrub may also be preferred as they provide bears with more nutritious vegetation as a food source. Both males and females preferred sites with shorter trees for better concealment while females with cubs preferred sites with taller trees with less concealment. Thus females with cubs may have to trade high concealment for better escape chances for the cubs to avoid potentially infanticidal males. Human activity was shown to affect daybed selection as daybed sites were more concealed than nearby random sites and bears were also closer to human activity during early morning but selected their daybeds farther away. Daybeds were considerably farther away from houses and large roads than from small roads which were often scarcely used forestry roads. Concealment did not change with distance to human activity indicating that bears may not be able to avoid human activity at a large spatial scale even in areas of low human population density. Due to low sample sizes and individual bias the results of this study should be considered more indicative than of high probability. Nevertheless they provide largely new information on bear daybed selection that may be of public interest in reducing human bear conflicts and of use in bear conservation and management.
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(2019)Environmental stress caused by heavy metal contamination of the sediment can threaten ecosystem functioning. Sediment macrofauna are often used to study the effects of environmental stress factors over time, as they are relatively sedentary and thus reflect the ambient conditions in an area. This study investigates whether heavy metal pollution influences the macrofaunal community adjacent to a former steel works factory in Koverhar, in the western Gulf of Finland. Various indices based on macrofaunal community composition and diversity are used in the Baltic Sea to evaluate the environmental status. This thesis evaluates the performance of three of these indices, Shannon-Wiener’s Index (H’), Benthic Quality Index (BQI) and Brackish water Benthic Index (BBI), in detecting the influence of heavy metal pollution on the marine environment. Two macrofaunal sampling methods, GEMAX corer and van Veen grab, are also compared to each other to investigate if there are differences in the structure of the macrofaunal communities that they capture. The study found that while there were indications of environmental stress, such as a lack of sensitive species and an abundance of tolerant species at the more heavily polluted stations, the heavy metal pollution could not be definitively proven to be the cause. H’ and BBI failed to find the differences potentially associated with heavy metal pollution between the stations, while BQI detected some of the differences found by the macrofaunal community analysis. The two sampling methods were found to not be significantly different from each other in terms of macrofaunal communities, but yielded significantly different macrofaunal index values, with the GEMAX results displaying a larger variance between replicates while the van Veen results were more consistent.
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(2019)The gut microbiome of mammals plays many important roles in the host, including preventing colonization of pathogens, maintaining intestinal homeostasis, helping digest nutrients and even affecting host behavior. The composition of mammalian gut microbiota varies greatly between individuals, species and in time. When a mammal is born, it acquires its first, mostly anaerobic, gut microbiota through maternal transmission in the birth canal. After the initial transmission of bacteria, host genotype, especially genes related to immunity, become an important factor that helps determine which species get to stay in the gut and prosper. In adulthood age, sex, diet, disease and contact with others all become important shapers of microbiome composition. Since microbial communities are comparable to any macroecological communities, they can be explained through ecological theories. For example, community assembly theory can help distinguish the effects of input (e.g. transmission) from selective processes (e.g. filtering host genotype) on gut microbiome composition. Community assembly can lead to multiple stable equilibria determined by which species colonized the area first (“priority effect”), emphasizing the importance of early transmission, such as that maternal transmission birth. Metacommunity theory on the other hand, views a large ecosystem as a mosaic of patches and can be helpful in describing the composition of the microbiome in adult individuals. In this thesis, I use community assembly theory and metacommunity theory as a framework to explore determinants of individual gut microbiome composition in wild European wood mice (Apodemus sylvaticus). Specifically, I set out to investigate how much of the gut microbial community variation was accountable for host relatedness and how much of this effect is due maternal transmission (input) versus host genotype (filtering). To find out more about what affects the composition of the gut microbiome in wild animals, I collected both tissue and microbiome samples from wood mice in the Wytham woods research area near Oxford, Great Britain. In addition to the data collected in Wytham, I was given another similarly collected dataset from Silwood Park. My study questions were: What proportion of gut microbiome composition in wood mice is determined by host genotype? Do mothers affect their offspring’s microbiome more than fathers through maternal transmission of bacteria? DNA extractions and mouse genotyping were done by me in the MES laboratory at the University of Helsinki. Sequencing of microbial DNA was done by my co-supervisor at Royal Veterinary College in London. Microbiome similarity was compared to host genetic relatedness using Mantel test and likelihood ratio tests on linear models with dyadic data (comparing relatedness and microbiome similarity of each pair). According to the results, related individuals had a significantly more similar microbiome in Wytham, but not in Silwood. In both populations, microbiome similarity was also affected significantly by age and home range area. The general trend was, that mother-pup and fullsib pairs had more similar microbiome than unrelated pairs (though this effect was significant only in Wytham) and father-pup pairs had a more different microbiome than unrelated pairs (though this effect was significant only in Silwood). All data combined, mice had significantly more similar microbiome with their mother than father. The higher similarity between mother-pup pairs and full siblings can be explained by maternal transmission and postnatal physical contact. Since the father’s effect is purely genetic, their microbiome differing from their offspring even more than from unrelated individuals could be explained by lack of physical contact and different age. Alternatively, females could even be choosing to mate with males with different immunogenotypes, and thus more different microbiome from themselves than expected by chance. Based on my results, transmission of bacteria during and shortly after birth is a key factor shaping microbiome composition and it might even account for the “genetic” effect seen in previous studies.
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(2022)Research conducted on neural oscillations have paved the way to unravel the complexities of the brain dynamics underlying behavior and cognition. Neuronal oscillations characterize neuronal activity and processing at all spatial scales from neuronal microcircuits to large-scale brain dynamics and hence link cellular and molecular mechanisms to circuit dynamics underlying behavior. Large-scale oscillations and their inter-areal synchronization can be identified from in vivo electrophysiological data from animal models as well as from human magneto- and electroencephalography (M/EEG) data. Large-scale oscillation dynamics identified from human M/EEG data has been critical for resolving whole-brain oscillation dynamics view but is hindered by the indirectness of the measures. In contrast, rodent in vivo electrophysiology has been conventionally used to resolve oscillation dynamics locally in brain microcircuits. Although these measurements yield critical information of the mechanisms behind local oscillation dynamics, they are difficult to link with whole-brain dynamics view obtained from human M/EEG data. The newly established setup at the Neuroscience Center aims overcome these limitations and allows the measurements directly from the brain of awake head-fixed mice with over 1000 channel measuring simultaneously from both cortical and subcortical structures. This Master’s thesis project objective was to obtain proof-of-concept data to characterize oscillation dynamics during resting-state (RS) from awake behaving mice and to investigate whether these dynamics could be modulated by the manipulating E/I balance. More specifically, the current project aimed to investigate the oscillatory profile of the default-mode network (DMN) activity while manipulating the E/I balance with pharmacological mediums. Electrophysiological data was collected from RS activity from awake mice with two µECoG grids comprising together 512 channels and two laminar Neuropixel probes with each consisting 348 channels. The areas of interest were targeted to capture the DMN activity, covering anterior cingulate cortex (ACC), secondary motor cortex (M2), retrosplenial areas, visual cortical layers, pre- and infralimbic areas, hippocampal areas such as CA1 and dentate gyrus as well as lateral and posterior thalamic areas. The network activity was modulated with pharmacological mediums (sedative, stimulant, control) administered in low acute doses to see their effects on the oscillatory profile. Data from four mice were included into this Master’s thesis work and each mouse was recorded first for 30-minute daily baseline, following a 30-minute pharmacological measurement. This Master’s thesis included the data obtained from the µECoG data to the data analysis focusing on the large-scale cortical activity of the DMN. Power spectral density analysis showed a prominent alpha peak, also seen in humans, across condition with a mild decrease in volume in the stimulant condition. Synchronization was assessed with imaginary part of the phase locking value (iPLV), and the results showed increased synchronization in the stimulant condition and decreased in sedative condition in comparison to the control condition. The amplitude correlation coefficient showed also expected results in both pharmacological conditions, namely higher correlation in stimulant and lower in sedative. This project was able to obtain valuable information of the newly established in vivo electrophysiology setup and the results were in line with our expectations. This promising outcome solidifies the translational potential of the setup and its ability to serve as a translational counterpart in numerous research designs in health and disease.
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(2023)Suot ovat tärkeä osa maailmanlaajuista hiilen kiertokulkua, koska ne varastoivat suuria määriä hiiltä eloperäiseen materiaaliin turpeen muodossa, joka muodostuu biomassan hitaasta hajoamisesta kylmän, hapettoman ja matalan pH:n ympäristön vuoksi. Soista vapautuu myös metaania (CH4), joka on voimakas kasvihuonekaasu, jonka lämmityspotentiaali on 28 kertaa voimakkaampi kuin hiilidioksidin (CO2). Turvemaiden netto-C-päästöt riippuvat suotyypistä ja ympäristöolosuhteiden muutoksista, kuten pohjaveden korkeudesta tai turpeen lämpötilasta, ja niistä johtuvasta tasapainosta CH4-päästöjen ja turpeen muodostumisesta johtuvan hiilinielun välillä. Tämän tutkimuksen tavoitteena oli selvittää, miten kasviyhteisöt ja muut säätelevät tekijät, kuten lämpötila, pohjaveden korekus, LAI ja suotyyppi vaikuttavat sekä ilmakehän hiilivirtaan että turpeen CH4- ja CO2-pitoisuuksiin. Lisäksi tehtiin stabiiliin hiili-13 isotoopin mittauksia, jolla saadaan lisätietoa metanogeneesin biogeokemiasta. Mittaukset otettiin rahkasammalvaltaisista mättäistä ja saravaltaisista välipinnoista. Mittauspisteille tehtiin kolme kasvillisuuden manipulointia, joilla selvitettiin kasvillisuuden vaikutuksia hiilidynamiikkaan 1. putkilokasvien ja sammaleiden poisto, 2. pelkkä putkilokasvien poisto, 3. Kaikki kasvillisuus tallella. Tutkimuspaikka sijaitsee Etelä-Suomessa Siikanevan suoalueella. Mittaukset tehtiin vuonna 2018 touko-syyskuussa ombrotrofisessa keidasrämeessä ja oligotrofisessa saranevassa. Mittauskausi oli poikkeuksellisen kuiva ja pohjavedenkorkeus oli keskiarvoa matalammalla. Tästä johtuen monia aikaisemmin havaittuja korrelaatioita ei löytynyt. CH4-virtojen suuruus riippui suotyypistä ja kasvillisuuden manipuloinnista. Keskimääräiset turpeen CH4 ja CO2 pitoisuudet olivat hieman korkeammat mittauspisteissä saranavevalla. Pitoisuudet kasvoivat nopeasti syvyyden myötä, 50 cm:n syvyydessä pitoisuudet olivat useita suuruusluokkia suurempia kuin 7-20 cm:n syvyyksissä korkeimpien, mittausten ollessa yli 500 000 ppm. δ13C-CH4-arvot muuttuivat negatiivisemmiksi tyypillisesti syvyyden myötä, kun hydrogenotrofinen metanogeneesi yleistyi. Kasvillisuuden manipuloinneilla oli vaihtelevia vaikutuksia CH4-vuohon, eikä lehtipinta-alaindeksi osoittanut vahvaa lineaarista korrelaatiota CH4:n kanssa. CH4-virtaus oli myös epäherkkä pohjaveden korkeudelle, mutta kasvien välittämä CH4-kuljetus ei todennäköisesti ollut syynä, koska kasvillisuuden poistokäsitellyt mittauspisteet osoittivat myös samanlaista epäherkkyyttä veden korkeudelle. Putkilokasvien ja sammaleiden poistaminen vähensi yleensä CH4-virtoja. Mättäissä, joissa putkilokasvit oli poistettu, mutta sammaleita ei, oli alhaisimmat CH4-virrat. Yhteenvetona voidaan todeta, että useimmat ympäristömuuttujat eivät osoittaneet vahvaa korrelaatiota CH4:n kanssa. Mikään yksittäinen muuttuja ei selittänyt selvästi eroja CH4-vuossa. Turpeen CH4 ja CO2 pitoisuudet riippuvat voimakkaasti syvyydestä ja suotyypistä. Kasvillisuuden poistaminen tyypillisesti vähensi CH4-virtoja.
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(2021)The immune system is crucial in the central nervous system (CNS), protecting sensitive tissues, promoting regeneration, and maintaining homeostasis. It is involved in CNS-disorders, such as neurodegenerative diseases and neurological insults related to stroke. Critical myeloid leukocytes in the CNS are microglia, divided into pro-inflammatory M1 and anti-inflammatory M2 phenotypes. This polarization achieves modulation of the inflammatory response by amplifying or dampening it. Therefore, microglia are widely investigated in CNS-disorders. β2-integrins are adhesion proteins that mediate inflammation. They are expressed explicitly on leukocytes, including microglia. Important processes, such as phagocytosis and cell motility, are regulated by β2-integrins. They also relay downstream signals, altering inflammation in many settings, although their effects on microglial properties and stroke are currently poorly understood. We here aimed to investigate the role of β2-integrins in stroke-related injury and microglia polarization in vivo using knock-in (KI) mice, which lack functional β2-integrins. Our results show that in a mouse model of haemorrhagic stroke, the functional outcome was less severe in β2-integrin KI versus wild-type (WT) mice (P = 0.0147), suggesting that β2-integrins are involved in stroke pathophysiology. Furthermore, by using flow cytometry we observed significantly lower frequencies of M1 microglia in the KI mouse brain (P = 0.0096). Therefore, our findings reveal neuroprotective aspects by inhibiting β2-integrins in neuroinflammation. Investigating microglial properties mediated by β2-integrins could contribute to the understanding of neuroinflammatory events, leading to the development of therapies for poorly treated CNS-disorders. Our results suggest that β2-integrins should be further explored as molecular targets for novel stroke treatments.
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(2022)Pathogenic variants in BRCA-associated protein 1 (BAP1) cause BAP1 tumour predisposition syndrome (BAP1-TPDS) with increased risk of several cancers including uveal melanoma (UM). UM originates from the melanocytes of the choroid, iris or ciliary body in the eye. UM is a rare cancer with a high metastatic rate and is usually seen in Caucasian people. BAP1 is a deubiquitinating enzyme and to function as a tumour suppressor it needs to retain enzymatic activity. To retain its enzymatic activity, it needs a functioning UCH-domain and nuclear localisation signal. Loss of function variants in BAP1 are easily interpreted as pathogenic, however, many missense variants remain as unclear on their status of pathogenicity. We aimed to study the enzymatic activity of missense variants in the UCH domain of BAP1. We selected 22 missense variants near or in the BAP1 UCH domain (aa1-240). Nineteen were identified in patients with UM and three rare variants from gnomAD database detected in the general population. The variants were cloned to a bacterial expression vector and expressed as a GST-fusion protein. Then we assayed the purified proteins for their ability to cleave ubiquitin. Ten patient derived variants reduced the deubiquitinating activity of BAP1. Seven mutants with variants from patients with familial BAP1-TPDS, retained <20% of their activity. Three variants previously classified as Variant of unknown significance (VUS) and one pathogenic decreased the activity to half. The function of twelve variants was interpreted as normal (80-120%). Of these, two were previously interpreted as pathogenic. Functional studies are needed for accurate BAP1 missense variant classification. Although BAP1 variants are dominant, penetrance might be affected by variants effect on enzymatic activity and patients with pathogenic variants might not exhibit familial BAP1 -TPDS. If enzymatic activity is retained and patient exhibits familial BAP1-TPDS, further studies need to be conducted on effects on splicing and protein-protein interactions. However, if patient exhibits only familial UM and harbours a BAP1 VUS with normal activity, other genes predisposing to UM should be considered.
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(2021)Recent studies have associated ER stress with various types of hearing loss, such as drug- and noise-induced, age-related, and hereditary hearing loss. However, the research has mostly focused on auditory sensory cell (hair cell) death, and it is not well understood if other molecular mechanisms can drive ER stress-dependent hearing loss. We used Manfflox/flox;Pax2-Cre conditional knockout (cKO) mice under the C57BL/6J (B6) mouse strain to study the effects of genetically-induced chronic ER stress on hearing function. In these mice, the gene coding for mesencephalic astrocyte-derived neurotrophic factor (Manf) has been silenced specifically in the cochlea. Manf is thought to act as an ER homeostasis regulator, and it has shown cytoprotective properties in different disease models both in vitro and in vivo. However, Manf’s mode of action is still poorly understood and even less is known about its function in the inner ear. Previously, cKO mice were found to upregulate ER stress markers in the cochlear hair cells. These mice develop progressive high-frequency hearing loss characterized by high-frequency outer hair cell (OHC) death. However, they have elevated hearing thresholds already at postnatal day 22 (P22) before any OHC death takes place and have elevated hearing thresholds in hearing frequencies where OHCs are retained. Therefore, there has to be another pathological mechanism besides OHC death accounting for the elevations in their hearing thresholds. Hence, we wanted to study the effect of ER stress on the outer hair cell hair bundle structure. The hair bundle is located at the apical pole of the hair cells, and it consists of filamentous actin (F-actin)-filled stereocilia. In mechanotransduction (MET), sound stimuli-induced motions of cochlear fluids cause stereocilia to deflect towards the tallest stereocilia row, allowing for depolarization of hair cells and transformation of mechanical force into electrical signal. Therefore, hair bundle is an essential structure for the hearing function. We used scanning electron microscopy (SEM) and fluorescent microscopy to study OHC hair bundles of cKO mice. We saw disorganization of the bundle structure already at P22. It progressed with age and advanced to strong stereocilia fusion by P56. At this age, all of the high-frequency OHCs of cKO mice displayed stereocilia fusion. We used cochlear whole mounts and immunostainings to study the protein composition of OHC stereocilia of Manf-deficient mice. The base of the stereocilia, termed as the tapering region, contains proteins that link the plasma membrane of stereocilia to their F-actin core, ensuring the cohesion of individual stereocilia. Mutations in these proteins have been associated with stereocilia fusion and hair bundle disorganization. At P56, we saw that stereocilia tapering region proteins radixin (RDX) and myosin 6 (Myo6) were mislocalized from the tapering region towards the apical tips of stereocilia in the high-frequency OHCs of cKO mice. Additionally, we saw that PTPRQ – a tapering region protein that is under normal conditions expressed only in the IHCs of mature cochlea – was upregulated in OHCs of cKO mice, yielding an expression pattern similar to RDX and Myo6. In addition, we used the F-actin probe phalloidin to quantitatively compare F-actin densities in the cuticular plates of cKO and WT mice. Cuticular plate is a structure responsible for attaching stereocilia to hair cell body. It consists of a dense F-actin network and prior studies have associated defects in the cuticular plate composition with hearing loss and stereocilia bundle abnormalities. We found a significant decrease in phalloidin staining intensity in the cuticular plates of high-frequency OHCs of cKO mice, indicating that their cuticular plate F-actin rigidity had been reduced. Together our data shows that Manf deficiency promotes diverse impairments in the OHC hair bundles, consequently inducing hearing loss. To conclude, our study presents novel insights into the complexity of ER stress-induced cochlear pathology. We show that ER stress impairs MET by inducing structural changes in the OHC hair bundle. It appears to be the major reason for hearing loss in the cKO mice, rather than hair cell death. In the future, the impact of Manf deficiency to the inner ear should be further studied. For example, younger and aged cKO mice could be studied to better characterize the progression of Manf deficiency-induced cochlear pathology and hearing loss. Similarly, Manf’s effect on hearing should be studied in other ER stress models to determine its role in the hearing function.
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(2019)Biodiversity is declining across the globe. The IUCN Red List, which is often used to measure species’ risk to go extinct, is showing alarming biodiversity declines both globally and within Finland. The most commonly used tool for biodiversity conservation is the establishment of protected areas. The Conference of Parties (COP) of the international treaty for biodiversity conservation (The Convention on Biological Diversity), has set a target to expand the international protected area network to cover 17% of the terrestrial area of the world. However, the designation of protected areas carries costs in terms of both land-use and money. Relatively little is known about what protected areas can achieve at the species level, and only limited evidence exists that links the establishment of protected areas to an improved conservation status of species. The lack of knowledge is because protected area establishment and its effects are often hard to study due to inadequate data. In this thesis, I created a framework to study the link between the increase in protected areas and protected area investment in relation to the conservation status change of one taxonomic group, the breeding birds in Finland. I first investigated the general trend in conservation status of Finnish birds using the Red List Index 2015. I then studied the effect of increasing the protected area on Finnish bird species’ range and the monetary investment on protected areas on bird species’ range in comparison to change in their IUCN Red List assessments. The timeframe of the study was 1996-2010 for protected area establishment and 2010-2015 for bird species’ conservation status change. My results show that the conservation status of birds in Finland is considerably worse than before, with Red List Index being 0.779. This is approximately 9.2% decline from the Red List Index in 2010. The species that gained more protected area on their range during 1996-2010 did not fare better in terms of conservation status than the birds that gained less protected area on their range on the same period. This is possibly because the threshold where the protected areas would cover the species’ range sufficiently to enable the conservation of the whole population is still not reached even for species with the higher protection levels. Also, the species that had higher estimated monetary investment on the protected areas on their range did not acquire better conservation status development than the species on whose range there was less estimated monetary investment. The expansion of the Finnish protected area network in 1996-2010 did not help to change the negative trend of Finnish birds in 2010-2015. The species that gained more protection in terms of land or monetary investment during this period, were not showing better results than the species that gained less protection. These results hint that the protected areas in Finland are not effective in terms of bird conservation. This does not mean, however, that we can claim that they are ineffective in all aspects, as we don’t know what would have been the situation if there were no protected areas established at all. There are also several other factors that affect the conservation status development of birds in Finland. These include degradation of matrix habitats, hunting and climate change, which might all overrun the possible positive effects of the protected areas and protected area investment.
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(2020)Alzheimer’s disease is the most common form of dementia and one of the highest causes of death worldwide. Recent discovery of lymphatic vessels from the dura mater, the outermost meningeal layer covering the central nervous system, has led to reassessment of the role of lymphatic vessels in neuropathological diseases. The meningeal lymphatic vessels drain macromolecules from the cerebrospinal fluid into the deep cervical lymph nodes and their proper function could be crucial for preventing amyloid-beta aggregation into the brain parenchyma. The function of the meningeal lymphatic vessels is still partly unknown. They have been hypothesized to function as an immune cell hub for the brain and dysfunction of the meningeal lymphatic vessels could lead to immune cell changes in the brain parenchyma. In my thesis, the role of the lymphatic vessels in Alzheimer’s disease was investigated by inducing atrophy of the meningeal lymphatic vessels with VEGF-C depletion in an APdE9 mouse model of Alzheimer’s disease. Single cell sequencing was used to identify the cell types present in the dura mater and in the deep cervical lymph nodes of an Alzheimer’s disease mouse model with and without atrophy of the meningeal lymphatic vessels. The amyloid-beta accumulation was immunohistochemically assessed from the brain and the cognitive decline was studied with behavioral tests. The results showed that atrophy of the meningeal lymphatic vessels did not increase the amount of amyloid-beta in the brain or affect the cognitive decline. The single cell sequencing from the meninges provided a more comprehensive cell atlas than has been published before. It was also found that the atrophy of the meningeal lymphatic vessels was associated with changes in the number of immune cells in the dura mater. The biggest changes were in the number of neutrophils and B-cells, which increased. Further studies are needed to evaluate the role of the meningeal lymphatic vessels in Alzheimer’s disease progression, as the results in this thesis were opposite to the results published before.
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(2023)Chondrodysplasia is a disease caused by defects in endochondral ossification. Chondrodysplasia affects the growth of long bones and causes disproportionate dwarfism. In addition to humans, chondrodysplasia has been discovered from multiple dog breeds. Chondrodysplasia in Alaskan Malamutes has been discovered already in the 1970s, but the genetic background of the disease is still unknown. This master’s thesis was conducted in Professor Hannes Lohi’s research group. The aim of this thesis was to identify a locus associated with chondrodysplasia in Alaskan Malamutes, and to find and validate candidate variants. All samples used in this study were collected from private owners with their consent. The study cohort consisted of four families of Alaskan Malamutes with affected individuals. Data used in the study included genotype data, and data from whole exome and whole genome sequencing. A significant locus on chromosome 8 was discovered, using genome-wide association study. However, some of the families with affected Alaskan Malamutes did not share this locus. A candidate variant in GALNT16 was identified by filtering NGS data from the families sharing the risk locus. Validation of the candidate variant showed that the variant was not causative for chondrodysplasia in Alaskan Malamutes. Based on the results, it can be possible that the causative variant for chondrodysplasia in all affected Alaskan Malamutes is not the same, and chondrodysplasia in Alaskan Malamutes may be more heterogonous than previously thought.
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(2019)Canine hip dysplasia (CHD) is a complex developmental orthopedic disorder particularly common in large size breeds. CHD is characterized by the development of a loose and incongruent hip joint. Affected dogs often suffer from secondary osteoarthritis. Radiographic examination reveals flattening of the femoral head and joint widening. An analogous disorder exists in humans. CHD is inherited quantitatively with suggested involvement of the genes of major effect. Genetic studies utilizing dense SNP arrays have revealed few candidate loci and genes for CHD, including the intronic deletion variant of fibrillin 2 (FBN2) gene in Labrador Retriever breed. FBN2 is a promising candidate gene having a functional role in bone and joint development. Therefore, the objective of this study was to investigate the role of FBN2 in the development of CHD in the Finnish dog population and in additional breeds. The specific aims included establishment of well-phenotyped cohorts of samples from four high-risk breeds, namely Labrador Retriever, Golden Retriever, German Shepherd dog and Bernese Mountain Dog and the assessment of the presence and prevalence of the FBN2 deletion in the Finnish dog population affected by CHD. The study cohorts established here will be later utilized also in genome-wide association studies to identify additional CHD loci. Altogether 220 dogs, out of which 53 were Labrador Retrievers, 41 Golden Retrievers, 79 German Shepherd dogs and 47 Bernese Mountain Dogs, were included in the case-control study. For the German Shepherd dogs, the hip status of each dog was further confirmed of by screening the radiographs available from the Finnish Kennel Club archive. All dogs were genotyped by fragment analysis for the FBN2 deletion. The results revealed the presence of the deletion in all four breeds with highest prevalence in the Retriever breeds, in which the deletion haplotype was more common than the wild type. In our study, all CHD-affected dogs in the Labrador Retriever breed had at least one copy of the deletion allele. However, since the deletion allele was common also in the unaffected Labrador Retrievers, no statistically significant allelic association with the deletion and CHD was detected in statistical analysis. In the three other breeds, no association in statistical analysis was found either. Thus, the previously reported positive allelic association between the intronic deletion in the FBN2 gene and CHD was not replicated. Larger genome-wide studies are warranted to identify the major effect CHD loci.
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(2021)The supervisory expectations directed towards banks and other financial institutions to integrate, identify and manage climate-related risks has increased substantially during the past decade. The transition towards a de-carbonized economy creates risks and opportunities for financial institutions. The European Central Bank (ECB) has identified climate-related risks as one of the key drivers in the euro area requiring a forward-looking approach to be taken into consideration while dealing with these risks. One of the main ongoing tasks in the area is the identification and classification of environmentally sustainable activities. The objective of this Master’s thesis is to examine the effect that the reported greenhouse gas (GHG) emissions and the implementation of an emission reduction strategy have on corporate repayment capacity, calculated through external credit ratings. Previous literature has found a relationship between companies’ creditworthiness and environmental factors, but the results vary depending on the applied variables. The typical approach used in prior studies is the application of aggregated values of environmental, social and governance (ESG) factors or limiting the analysis to specific industries or countries. The theoretical framework for this thesis rests mainly on previous academic research on the topic and publications by supervisory bodies. The data comprises 593 corporations from 37 countries operating in different industries over the years 2015-2019. The value of the probability of default (PD) is deployed as a measure of corporate repayment capacity. The climate-related variables and financial ratios were provided by the Carbon Disclosure Project (CDP) and Standard and Poor’s (S&P). The relationship between corporate repayment capacity and the climate-related variables was analysed using a panel data multivariate regression model, specifically the ordinary least squares (OLS) method. The results of this study indicate that emission intensity levels contribute statistically in a negative and significant way to corporate credit ratings, implying that higher levels of emissions lead to a higher PD. On the other hand, having an emission reduction target contributes positively and significantly to corporate repayment capacity, indicating that having this target leads to a lower PD. The analysed climate-related variables were statistically more significant in industries considered to consist of high emitting companies, as opposed to low emitting ones.
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(2019)Background: Despite the well-established link between diabetes and dementia risk, the impact of prediabetes and diabetes on the prodromal dementia phase remains controversial. In this study, we investigated whether prediabetes and diabetes increase the risk of cognitive impairment–no dementia (CIND) and accelerate its progression to dementia, as well as the possible underlying mechanisms. Methods: In the Swedish National Study on Aging and Care-Kungsholmen (SNAC-K), one cohort of cognitively-intact individuals (n=1,837) and one cohort of individuals with CIND (n=671) aged ≥60 years were followed for up to 15 years. At baseline and each follow-up (every 3 or 6 years), a neuropsychological test battery was administered, and the domains of episodic memory, processing speed, executive function, visuospatial abilities, and language were derived. CIND was defined as having no dementia and cognitive performance ≤1.5 SDs below age group-specific means in at least one cognitive domain. Dementia was diagnosed according to DSM-IV criteria. Diabetes (controlled and poorly-controlled) was diagnosed by physicians through medical assessment, clinical records, and glycated hemoglobin (HbA1c) ≥6.5%. Prediabetes was identified as HbA1c 5.7-6.4% in diabetes-free participants. Clinicians diagnosed heart disease and collected blood samples used to measure C-reactive protein (CRP). Data were analyzed with Cox regression models adjusted for possible confounders. Results: At baseline, in the cognitively-intact cohort, 133 (7%) participants had diabetes and 615 (34%) had prediabetes. During follow-up (mean 9.2 ± 3.0 years [range=2.2-15.5 years]), 544 (30%) individuals in the cognitively-intact cohort developed CIND. Poorly-controlled diabetes (HbA1c ≥7.5%) was associated with 2-times higher risk of CIND (HR 2.0, 95% CI:1.11-3.48) than diabetes-free participants. In the CIND cohort, 84 (13%) had diabetes and 238 (36%) prediabetes. During follow-up (mean 7.7 ± 4.0 years [range=0.2-15.2 years]), 132 (20%) individuals progressed to dementia. Poorly-controlled diabetes was associated with 3-times higher risk of dementia progression (HR 3.3, 95% CI: 1.29-8.33). Furthermore, comorbid heart disease and diabetes was associated with 2.5-times higher risk of progression to dementia (HR 2.5, 95% CI: 1.17-5.47), particularly if the diabetes was poorly-controlled (HR 5.8, 95% CI: 1.72-19.3). Similarly, having elevated CRP levels and diabetes was associated with increased risk of progression to dementia (HR 4.1, 95% CI: 1.15-14.2), especially in participants with poorly-controlled diabetes (HR 13.6, 95% CI: 1.89-98). No associations between prediabetes and CIND were detected in either cohort. Conclusions: Diabetes, especially if poorly-controlled, increases the risk of cognitive impairment and accelerates its progression to dementia. The diabetes-associated progression from CIND to dementia is further exacerbated by the presence of heart disease and elevated levels of systemic inflammation.
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