Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • Honkonen, Olga (Helsingin yliopisto, 2015)
    Urbanization is progressing worldwide, with approximately 50% of the Earth s population currently living in urban areas, and this number is expected to increase to 60% by 2025. In Finland, as well as anywhere else, the population is gathered in the cities. At the moment, over 80% of Finns are living in urban areas. Urban areas are also known to produce a significant load of various pollutants to the surrounding environment. One of the significant forms of urban-derived pollutants emission to the surrounding environment is surface runoff. Pollution in urban surface runoff often comes from non-point sources, including motor vehicle emissions, coal and wood burning, tire wear, coal tar, creosote and asphalt leaching, oil spills, and runoff from building sites and other surfaces Our research was focused on distribution and toxicity of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and oil hydrocarbons. Previous studies in other countries indicated that above mentioned pollutants are often present in sediments adjacent to urban areas, may be toxic to aquatic life and recognized as priority pollutants for stormwater. In our study, notable amounts of hydrophobic organic compounds were found in the Lake Vesijärvi sediments and water column as well is in stormwater, urban air and runoff sediment from stormwater traps. Contaminant concentrations in the lake tended to decline with the distance from the urban shore. Toxicity of the sediments, determined with luminescent bacteria test was found to be lower in the Lake Vesijärvi than in the stormwater wells, however no clear gradient with the distance from the urban shore was found. In urban area degree of contamination and toxicity of the sediments depended on traffic intensity in the area. Toxicity of the both lake and stormwater well sediments was also found to correlate partly with organic contaminant content of the samples. These findings suggest that runoff from Lahti urban area has a notable impact on the Lake Vesijärvi condition. Comparison with Finnish contaminated soil guideline values displayed that present contaminant concentrations might be harmful for the natural ecosystem. It indicates that hydrophobic organic pollutants are important contributors to the Lake Vesijärvi sediment contamination and their inputs should be regularly monitored in order to avoid possible decline in the lake sediment quality.
  • Rajamäki, Kristiina (Helsingin yliopisto, 2015)
    Atherosclerosis is the underlying cause of myocardial infarction and stroke, the leading causes of death worldwide. It is a complex multifactorial disease closely linked with obesity, type II diabetes, and metabolic syndrome and, together, these conditions comprise the global epidemic of metabolic disorders that are becoming more and more prevalent, affecting adults and children alike. Atherosclerosis affects the large arteries that gradully loose their normal structure and function via a degenerative process involving lipid accumulation and chronic inflammation in the arterial wall. The lipid accumulation is driven by high circulating levels of cholesterol-carrying low density lipoproteins that become trapped and modified in the arterial wall. This causes an inflammatory reaction characterized by abundant immune cell infiltrates, mainly monocyte-derived macrophages. The macrophages scavenge large amounts of lipids and become activated to secrete a host of proinflammatory mediators and matrix-degrading enzymes that drive the progression of the disease. These processes result in the focal development of fatty lesions or plaques along the arteries. Over time, more complex lesions develop as a result of inflammatory and fibrotic responses, matrix remodeling, calcification, cholesterol crystallization, neovessel formation, and microhemorrhages. Ultimately, the plaques may rupture, causing thrombosis and acute complications. Although inflammation is recognized as a major driving force in atherosclerotic lesion development, the mechanisms triggering and maintaining the arterial wall inflammation remain incompletely understood. The aim of this thesis was to study the role of a key innate immune signaling pathway, the inflammasome, in atherosclerosis. The inflammasomes are large cytoplasmic signaling complexes that trigger the proteolytic maturation and secretion of two proinflammatory and proatherogenic cytokines, interleukin(IL)-1beta and -18. The inflammasome pathway can be triggered by microbial components or by sterile endogenous danger signals that elicit the activation of cytoplasmic sensor molecules from the NLR (nucleotide-binding domain and leucine-rich repeat containing) or PYHIN (pyrin and HIN domain containing) families. Despite the established roles of IL-1beta and -18 in driving atherosclerotic lesion development, the triggers of inflammasome activation in atherosclerotic plaques remained unknown. Macrophages are the prototypical inflammasome pathway-expressing cells, and thus cultured human macrophages were utilized to identify and characterize atherosclerosis-associated triggers of the inflammasome pathway. Cholesterol crystals and acidic environment were both found to trigger a strong inflammatory response via the activation of NLRP3 inflammasome and secretion of IL-1beta and IL-18. Cholesterol crystals are a hallmark of atherosclerotic lesions, yet they have been considered an inert material that merely acts as a sink for excess free cholesterol in the arterial wall. These new data suggested, however, that cholesterol crystals act as a potent sterile danger signal that may directly link pathological lipid accumulation and inflammation in the lesions. Local extracellular acidosis arises in the growing plaque due to the hindered diffusion of oxygen and the highly active glycolytic metabolism of macrophages. Acidic environment not only triggered the NLRP3 inflammasome, but even a very mild acidification from the physiological pH of 7.4 to 7.0 was sufficient to greatly amplify the IL-1beta response to other NLRP3 activators, including cholesterol crystals. Having showed that the atherosclerotic lesions harbour potent activators of the inflammasome pathway, we further analyzed the expression of this pathway in atherosclerotic human coronary specimens obtained from 10 explanted hearts. For this purpose, we utilized a quantitative PCR array targeting 88 inflammasome pathway-related molecules. Significant upregulation of 12 target genes was found in advanced coronary plaques compared to early lesions from the same coronary trees, including many of the very core components of the inflammasome pathway. Moreover, p38delta mitogen-activated protein kinase (MAPK), a poorly characterized isoform of the stress- and cytokine-activated p38 MAPK family, was consistently upregulated in advanced coronary plaques. Immunohistochemical stainings of human coronary lesions showed strong expression of NLRP3 inflammasome components and p38delta MAPK in macrophages surrounding the cholesterol crystal-rich lipid core. Furthermore, the p38delta MAPK was activated in cultured human macrophages upon NLRP3 inflammasome activation by cholesterol crystals and extracellular ATP, and required for NLRP3-mediated IL-1beta secretion. Taken together, the data presented in this thesis propose novel inflammasome-mediated mechanisms that may trigger sterile inflammation in atherosclerotic lesions and thus drive lesion progression.
  • Fabritius, Henna (Helsingin yliopisto, 2015)
    A noticeable fraction of the World s species inhabit disturbed or early-succession habitats. In Finland, 23.3 % of the endangered species are species of traditional agricultural biotopes or otherwise human-modified habitats. These habitats are, after forests, the second most important habitat for endangered species in Finland. When conservation plans have to be designed for early-succession habitats and their species, specific complexities emerge due to their transitional nature. Protected areas are vulnerable to discontinuities in maintenance funding, and alternative strategies for site maintenance vary in terms of maintenance type, intensity and frequency. Besides the establishment of protected areas, species persistence may sometimes be better supported by altering the dynamics of transitional habitats or by establishing new habitat sites. My thesis focuses on the challenges of conservation planning that are related to the maintenance of specific successional stages or disturbance frequencies in dynamically changing environments. My study species is an endangered butterfly, the false heath fritillary (Melitaea diamina), an endangered Finnish butterfly. The false heath fritillary has the status of a species of strict protection in Finland due to the rapid shrinkage of its distribution during the past decades. I have used the false heath fritillary and its habitats as a case study to develop methods to estimate habitat destruction rates, habitat maintenance effects and the spatial emergence pattern of dynamic habitats from field data. We use metapopulation models to study how changes in the patterns of patch emergence and destruction affect population viability and how habitat dynamics affect conservation success. Finally, we contrast our results against the institutional constraints in false heath fritillary conservation. Our results show that false heath fritillary habitats, which occur on multiple land use types, have high destruction rates and reach their best quality 2-3 years since maintenance. In simulations, the habitat turnover rate and the spatio-temporal pattern of habitat patch emergence have a significant effect both on population viability and on the effectiveness of conservation actions. The institutional constraints of false heath fritillary conservation have led to unpredictability in habitat maintenance resourcing. Conservation planning for early-successional species requires monitoring of habitat dynamics and prediction of changes in the future availability of habitat. The availability of site maintenance funding should be taken into account already during the conservation planning phase.
  • Llano, Olaya (Helsingin yliopisto, 2015)
    Dendritic spines are the main site of reception of glutamatergic -excitatory- neurotransmission in the central nervous system. According to the current view on neuronal function, dendritic spines play a pivotal role in the formation of synaptic networks for memory storage. Consequently, dendritic spines are crucial for cognitive processes, e.g. learning. Numerous disorders such as intellectual developmental disorders, schizophrenia and cognitive impairment are associated with functional and structural abnormalities of dendritic spines. The main objectives of this project were to identify molecular regulators of the structure and function of dendritic spines and to characterise novel mechanisms leading to dendritic spine development and synapse formation. Actin is the most abundant protein in dendritic spines. Rearrangements of the actin cytoskeleton are responsible for the morphological changes of dendritic spines, making actin a major player in the regulation of glutamatergic synaptogenesis. Increasing evidence shows that dendritic filopodia are crucial in the formation of dendritic spines. Often filopodia act as precursors of mature dendritic spines. While filopodial protrusions in other cell types have been widely studied, the molecular mechanisms regulating the emergence and maintenance of dendritic filopodia are poorly understood. In this thesis work, we show that the polymerizing factor mDia2 promotes initiation and polymerization of actin in the filopodial tip. We also describe a novel observation of filopodial root polymerization. Spine maturation is accompanied by expansion of the spine head. We propose here that the actin polymerizing factor Arp2/3 complex takes active part in the branched actin polymerization during spine head expansion. Spine heads are dynamic structures, with long protrusions often visible on their surface. Our results demonstrate that the actin depolymerizing factor cofilin-1 has a double function in the regulation of dendritic spine actin dynamics. On one hand cofilin-1 replenishes the actin monomer pool, and on the other hand it shapes the spines by severing the actin filaments and therefore controls actin filament length. The maturation of synaptic networks is strictly dependent on the synchronous development of both inhibitory and excitatory transmission. Within this context the formation of and stabilization of dendritic spines is an important step in the maturation of glutamatergic transmission. However, in terms of functional maturation, chloride regulatory proteins, such as the K-Cl cotransporter KCC2, are crucial regulators of GABAergic -inhibitory- transmission. Interestingly, previous studies have identified KCC2 as an important agent required for the maturation of dendritic spines and consequently glutamatergic transmission. The mechanism how KCC2 exerts its chloride-extrusion independent effect on dendritic spines and excitatory synapses remained obscure. In this thesis work we have identified the molecular interaction between the potassium-chloride cotransporter KCC2 and the guanine nucleotide exchange factor βPix. Importantly, KCC2 inhibits the action of βPix towards the GTPase Rac1, a major regulator of the actin cytoskeleton in dendritic spines. The inhibition of βPix by KCC2 leads to decreased cofilin-1 inactivation and subsequent reduction in the fraction of actin that is stable. This novel molecular pathway leads to the regulation of glutamatergic synaptogenesis and spine formation by KCC2 via βPix. Synaptic cell adhesion molecules orchestrate trans-synaptic recognition as well as specification of glutamatergic synapses. Fine-tuning of synaptic networks requires a delicate balance between positive and negative signalling mechanisms that regulate dendritic spine formation. The intercellular adhesion molecule ICAM-5 negatively regulates the maturation of dendritic spines. We have found that ICAM-5 binds to pre-synaptic β1 integrins in filopodia and immature dendritic spines, preventing spine maturation. We have characterized the molecular mechanisms leading to the diminished interaction of ICAM-5 and β1 integrins during spine maturation. Moreover, genetic manipulation of ICAM5 affected the morphology and function of dendritic spines. The results included in this thesis work contribute to the deeper understanding of the molecular mechanisms regulating the development of dendritic spines. We have studied molecules that control all steps of these processes, from filopodia formation to mature spine regulation; encompassing structural and functional synaptogenesis.
  • Hauru, Kaisa (Helsingin yliopisto, 2015)
    In this thesis I combined perspectives from urban forest ecology, environmental psychology and empirical aesthetics to determine whether ecologically beneficial urban forest planning and management can also be experientially good. The thesis consists of four interrelated papers, three of which are empirical research papers and the fourth a theoretical review article. All empirical work was performed in boreal forests in Helsinki, the capital of Finland. In the ecological part of the thesis I concentrated on studying planning and management options that contribute to the ecological quality of urban forests, especially tree regeneration and biodiversity, as well as the vitality of native forest species. Previous studies have shown that urbanization, increasing edge effects as a result of forest fragmentation, and intensive recreational use affect the ecological quality of forests negatively. These negative effects can be reduced by keeping forest patches large enough to provide habitats for forest species, and maintaining the forest edge vegetation dense and multilayered to reduce edge effects. Furthermore, leaving natural barriers, e.g. decaying logs, on the forest floor to guide people s movement and to restrict intensive trampling, are likely to be ecologically sound options. In the first empirical paper, I introduced a new ecological forest management option called sheltering group . It is a thicket of saplings occurring in forests that suffer from heavy wear, which can be used as a barrier against trampling to provide safe regeneration microsites for other saplings and forest vegetation. Ecological forest management options may not always be favored in urban forest planning and management because they are generally thought to affect people s recreational, e.g. restorative and aesthetic, experiences negatively. In this thesis I examined whether this assumption is supported when people are taken into forests and their multisensory experiences investigated on-site. In two empirical papers I examined, using survey techniques, how closure of view to the urban matrix from the forest interior, which indicates dense edge vegetation minimizing ecological edge effects, affects the restorative experiences of residents, and do ecologically beneficial decaying logs on the forest floor affect aesthetic experiences of forest visitors. I showed that restorative experiences were better in forest interiors with closed views to the urban matrix than at the edges or edge zones with open or semi-closed views. Furthermore, decaying logs did not, in general, affect the aesthetic experiences of people in urban forests, and logs were well accepted by urban forest visitors. My results indicate that at least these ecological forest management options enhance or maintain experiential qualities of the studied urban forests. In this thesis my aim was also to clarify concepts related to restorative and aesthetic experiences to better determine, assess and measure the experiential quality of green spaces in the future. In the fourth paper I concentrated on operationalizing aesthetic experiences and explored, through a literature review, what is a multisensory aesthetic experience in natural or semi-natural environments, and what dimensions it consists of. I concluded that aesthetic experience in natural environments is not the same thing as general preference and it is more than scenic beauty. I also suggested that aesthetic experiences consist of at least the following dimensions perceived in the environment: coherence reflecting care and congruence of the environment, complexity reflecting diversity and mystery, multisensory beauty, as well as sublimity. All these dimensions should be taken into account when assessing the aesthetic quality of green spaces. I also provided recommendations for pluralistic planning and management aiming at eco-experientially good quality urban forests.
  • Yli-Hemminki, Pirjo (Helsingin yliopisto, 2015)
    Mineral concretions or nodules are found from the Oceans, lakes and in soils. Their element content has been studied well due to possible commercial use, but interest in their bacterial communities has risen due to environmental implications. Iron manganese (Fe Mn) concretions cover vast bottom areas in the Gulf of Bothnia and the Gulf of Finland (GoF). These mineral precipitates sequester several times higher amounts of Fe, Mn, phosphorus (P) and arsenic (As) than the surrounding sediment. Despite their large occurrence, the environmental significance of the concretion bottoms has been a somewhat understudied issue. The aim of the present study was to investigate the bacterial community structure, and possible microbial contributions to the formation and decay of concretions in the Baltic Sea. The further aim was to study how concretions respond to different environmental stresses, such as anoxia and crude oil contamination, which the concretions may encounter in GoF bottoms. The methods used were determination of solid and dissolved Fe, Mn, P and As during microcosm incubations under oxidising or reducing conditions, also with crude oil and 14C naphthalene added. Bacterial community structure was studied by cloning and sequencing taxonomic marker gene (partial 16S rRNA gene), and quantification of polycyclic aromatic hydrocarbon degradation (PAH RHDα) gene copy number. Morphologically and taxonomically diverse bacteria colonise both the pitted surface and the porous interior of spherical concretions. Half of the population was affiliated to uncultured Proteobacteria, and one third was unclassified bacteria. Concretion bacteria populations appeared typical for this habitat. Bacteria may significantly affect the formation of the concretions in the GoF, because known Mn oxidising bacteria were enriched in Mn2+ containing liquid and semi solid media. The Fe2+ oxygen gradient favoured the enrichment of species which are known to reduce Fe and to degrade petroleum hydrocarbons. Concretions released Fe and Mn during anoxic conditions only if they were supplied with labile carbon source, indicating bacterial metal reduction. The dissolution of Mn was the highest, but the release of P and As followed Fe. The release rates (µmol m-2 d-1) from the concretions were within the range of the previously estimated fluxes out of the GoF sediment. Still, the concretions released only minor proportions (0.1 0.4%) of their total Fe, Mn, P and As content during a prolonged anoxic period. Concretions and sediment had a very similar capacity to remove petroleum compounds and mineralise naphthalene under oxic as well as anoxic conditions, and over one half of the added crude oil disappeared from the microcosms. Copy numbers of PAH degradation genes increased, indicating biological degradation potential of PAHs by the concretion bacterial community. Both concretions and sediment had rich and clearly different bacterial communities prior to and also past the exposure to crude oil. Only 9% of the OTUs were shared between the initial concretions and the sediment. Concretion bacterial sequences were affiliated to bacterial groups previously found from concretions and metal rich environments (ecotypes) even after the crude oil exposure, whereas sediment bacterial sequences were similar to those originating from sediments and oil contaminated sites.
  • Aivelo, Tuomas (Helsingin yliopisto, 2015)
    Parasite community dynamics is one of the central themes in contemporary parasitology. While between-host dynamics has been studied for a long time, within-host dynamics is less well studied. My aim was to identify which factors affect the parasite community during the lifetime of individual hosts by following longitudinally several individuals from a long-living species. Specifically, I was interested in how the dynamics of infra- and component communities differ from one another and which traits explain the variation in infracommunities. I studied rufous mouse lemur (Microcebus rufus), which is a primate living in the eastern montane rainforests of Madagascar. Mouse lemur is a well-suited study species as it can live for up to ten years in the wild. Due to its small size, the population density is high and trapping straightforward. Nematodes are the most common helminths found in mouse lemurs, but their identification is difficult. Typically, the nematodes are identified from adult specimens, but for longitudinal studies, this is not possible, as we cannot dissect the host individuals. In addition, morphological differences between species are small and we expected to encounter previously undescribed species. These difficulties led to the development of a new method, based on metabarcoding, to identify parasitic nematodes from fecal samples. The method I developed encompasses all steps from fieldwork to sequence analysis. Despite numerous confounding factors, the method managed to amplify and analyze half of the samples collected. Whilst there is room for further improvements, the main advantage is that the method works well for different host species, for example mouse lemurs and gastropods. In principle, this method works for all species of nematode, including free-living soil nematodes. Nevertheless, the resolution of identification do not allow for species-level identification. The variation in the parasite community inside individual hosts was extensive, but at the population level remained stable. Most of the parasites belonged to the putative species thought to be Strongyloides sp. The reason for this species success might be its lifecycle, the parasite can live in the intestine or as a free-living form in the soil. Due to the limited number of samples, the factors affecting the dynamics in individual mouse lemurs are difficult to analyze. It appears that sex and age do not have an effect on either parasite load or variation in parasite dynamics. Nevertheless, body condition appears to bear a consequence with the individuals in better condition having more parasite species in addition to higher fecal egg loads. The reason may be that those individuals are able to sustain larger populations of parasites, or that they are more tolerant to parasites. Hibernation could lead to the extinction of the nematode community, whereas higher precipitation appeared to lead to higher prevalences. This work gives insights into the dynamics of parasite communities both at the host individual and population level. It highlights the need for longitudinal studies as parasite community dynamics in host individual-level cannot be inferred from the host population-level The method I have developed can be used to perform more efficient and faster surveys of previously unknown parasite communities, though further development is necessary for better reliability.
  • Välimäki, Elina (Helsingin yliopisto, 2015)
    Pathogenic micro-organisms have the potential to invade the body and damage the host. The innate immune system is the first defense mechanism to respond in such case. Principal innate immune effector cells macrophages detect the presence of microbe-derived, or endogenous molecules in inappropriate compartments. This recognition leads to the activation of macrophages triggering their defense reactions including secretion of proteins. Inflammasome is an intracellular protein complex that is assembled in macrophages promoting the secretion of an important inflammatory cytokine, interleukin(IL)-1β. Activation of the innate immune response is crucial in immediate host defense, and it also regulates the activation of the adaptive immune response later in infection. However, secretory responses from activated macrophages, or molecular signaling pathways leading to the activation of the inflammasome have not been fully characterized. This study aimed for exploring proteins secreted from human macrophages exposed to endogenous danger signals alone, and in combination with microbe-derived signals. Macrophages were activated with endogenous molecules monosodium urate (MSU) and adenosine triphosphate (ATP). MSU and ATP encountered in extracellular environment are both danger signals to the innate immune system, indicating tissue damage or metabolic dysfunction. The results show that exposing macrophages to MSU or ATP induces a robust protein secretion. Simultaneous detection of MSU with bacteria-derived lipopolysaccharide activates the secretion of inflammatory and defense proteins. Macrophages exposed to ATP display a rapid secretion of vesicles, and this secretion is dependent on the activity of proteins called calpains. Calpains are also required for ATP-induced inflammasome activation in macrophages. Second aim of this study was to explore inflammatory response of macrophages from healthy subjects with a history of reactive arthritis (ReA), an inflammatory joint disease, upon detection of microbe-derived signals. The results show that inflammasome activation is normal, but the secretion of two inflammatory cytokines, tumor necrosis factor and IL-23, is lower from macrophages of former ReA subjects compared to the release of these cytokines from cells of healthy controls. Thirdly this study aimed for unraveling signaling pathways activated by fungal-derived trichothecene mycotoxins in human macrophages. Trichothecene mycotoxins represent an exogenous danger signal to the innate immune system evoking an inflammatory response. The results of this study reveal that trichothecene mycotoxins activate the NLRP3 inflammasome in macrophages. This study provides new information about early innate immune responses that is useful in the discovery of treatments for diseases whose pathogenesis is associated to disturbances in the innate immune system.
  • Natri, Heini (Helsingin yliopisto, 2015)
    Sex chromosomes are involved in several fundamental biological processes such as sex determination, sexual selection and dimorphism, as well as speciation. Structurally distinct sex chromosomes have evolved multiple times independently in various taxa, and different sex determination and sex chromosome systems are often found in closely related species of non-mammalian vertebrates. While the evolution of heteromorphic sex chromosomes from an ordinary pair of autosomes that obtain a sex-determining role has been hypothesized, the exact process and mechanisms of sex chromosome differentiation are not well understood. The restriction of recombination is known to be a crucial step in the process of sex chromosome evolution, and two main models have been proposed to explain the process of recombination suppression: (1) the gradual reduction of cross-overs driven by genetic modifiers of recombination rates, and (2) a stepwise model based on chromosomal rearrangements, such as inversions. It has been hypothesized that chromosomal transitions are connected with the formation of new species. However, it is unknown whether such transitions lead to, or result from, the restriction of genetic exchange between groups that ultimately results in speciation. Sex chromosomes may have a substantial role in speciation by contributing to reproductive isolation between different taxa, particularly through hybrid sterility. Sex chromosomes are a plausible source of the effects of Haldane s rule one the most consistent rules of evolutionary biology which states that the heterogametic sex (XY or ZW) is more likely to exhibit hybrid incompatibility than the homogametic sex. Furthermore, genetic factors associated with reproductive isolation are often located on sex chromosomes. In this thesis I have investigated the molecular evolution of sex chromosomes specifically the molecular process of recombination suppression and sex chromosome differentiation and the role of sex chromosomes in speciation by using stickleback fishes as a model system. By utilising various genetic methods, I have investigated the inter- and intraspecific variation in sex chromosome differentiation in three-spined and nine-spined sticklebacks. I have examined the neo-sex chromosomes of the Japan Sea lineage of the three-spined stickleback in order to gain insight into the process of recombination suppression and genetic differentiation of sex chromosomes at the initial stages of their evolution. Furthermore, through comprehensive breeding experiments and genetic analyses, I studied the evolution of sex determination and sex chromosome systems, as well as the genetic mechanisms of hybrid incompatibility in nine-spined sticklebacks. The results presented in this thesis illustrate a striking variety in sex chromosome and sex determination systems between and within these stickleback species. My findings suggest that recombination suppression and genetic differentiation of sex chromosomes may develop in various ways: my results show that the differentiation process has proceeded in a gradual manner in the earliest stages of neo-sex chromosome evolution in three-spined sticklebacks, yet they demonstrate a rapid process of sex chromosome evolution within the nine-spined stickleback species driven by a chromosomal inversion. Moreover, this thesis provides evidence for the role of sex-chromosomal inversions in the formation of postzygotic reproductive isolation and thus speciation.
  • Meller, Laura (Helsingin yliopisto, 2015)
    Anthropogenic pressures have pushed both climate and ecosystems to the point that their stability and functioning is at risk. Halting the loss of biodiversity by 2020 is one of the goals of the European Union. Climate change has been identified as one of the key challenges for biodiversity conservation in the EU. Empirical observations of climate change impacts, predictive tools and approaches, and appropriate policy responses are developed in separate fields of research with different methodologies and cultures. My thesis aims at bringing these three aspects together to explore responses to climate change from the perspective of biodiversity in the European Union. The thesis consists of a summary and five chapters. Chapter I looks into EU biodiversity policy in light of needs arising from climate change, with a focus on bridges between climate change impacts to appropriate conservation responses and further to policy. Chapter II evaluates approaches to reducing uncertainty in conservation prioritization based on ensemble modelling of species distributions. Chapter III builds methodologically on the findings of chapter II to explore the balance between various aims of biodiversity funding in the EU and how allocations of the funds reflect those aims. Chapters IV and V explore the balance between mitigation benefits and adaptation drawbacks of bioenergy as regards biodiversity conservation. The existing EU biodiversity policy has more potential to support effective adaptation than what its current interpretation and practice allows, although there seem to be gaps that cannot be addressed with the existing policies. The numerous scientific recommendations for conservation responses to climate change mainly address species range shifts. There is a mismatch between future conservation needs and the current practice of allocating funds for biodiversity conservation in the EU. For birds of European conservation concern, climate change drives larger changes in range size than land use for short-rotation woody bioenergy. However, bioenergy was predicted to have a negative impact on a larger proportion of the species than climate. Three policy recommendations arise from my thesis. First, compliance with strategic environmental assessment and green infrastructure guidance should be ensured for biodiversity projects receiving funds from the EU Structural and Cohesion funds. Second, biodiversity project funding from the SCF funds needs to be explicitly linked to the biodiversity strategy goals and assessed from the perspective of biodiversity needs. Indicators of project success should include an indicator relevant for biodiversity. Third, mitigation of climate change is a key strategy for biodiversity conservation, as it makes effective adaptation more feasible.
  • Rajakylä, Kaisa (Helsingin yliopisto, 2015)
    An essential transcription factor Serum response factor (SRF) and its co-activators, Myocardin related transcription factors (MRTFs) regulate the expression of many target genes required for normal growth and actin cytoskeleton regulation. MKL1 (also known as MRTF-A and MAL) is one family member of MRTFs and mediates the signals from the cytoplasm to the nuclear SRF in response to changes in actin dynamics. Although it is well established that actin regulates nucleo-cytoplasmic shuttling of MKL1, the molecular mechanism of this regulation has not been characterized. Therefore the aim of this thesis was to reveal the mechanisms of MKL1 nuclear import. RNA interference (RNAi) screen identified two proteins as putative proteins mediating MKL1 nuclear localization: Importin-β (Ipoβ), which is the main import receptor in cells, and mRNA export factor Ddx19. The main purpose of this study was to confirm the hits from the RNAi screen and assess their specificity in regulating MKL1 localization. This work revealed that both Ipoβ and Ddx19 are specific and necessary factors for MKL1 nuclear import and thus required for SRF activation. We show that Ipoβ together with its adaptor protein Importin-α (Ipoα), binds to a bipartite nuclear localization signal (NLS) of MKL1, which is located in the actin-binding RPEL repeat and composed of two basic elements. Furthermore, the biochemical assays demonstrate that actin competes with Ipoα/Ipoβ heterodimer for access to the MKL1 NLS, thus explaining the inhibitory effect that actin binding has on MKL1 nuclear localization. By using advanced microscopy techniques, we show that Ddx19 adds an additional regulatory step for MKL1 nuclear import by modulating the conformation of MKL1, which affects its interaction with Ipoβ for efficient nuclear import. The ATPase cycle of Ddx19, which is crucial for its role in mRNA export, is not required in MKL1 nuclear import. In contrast, the RNA-binding activity of Ddx19 seems to be required. My work thus proposes a novel role for Ddx19, a well-known mRNA export factor and regulator of translation, in nuclear import of MKL1. In addition to MKL1, the conserved actin-binding RPEL repeat is also present in the Phosphatase and actin-regulating proteins (Phactrs). Our work demonstrates that the RPEL repeat of Phactr4 does not determine its localization in cells, but instead facilitates the competitive binding of monomeric actin and Protein phosphatase 1 (PPI) to Phactr4. This mechanism is required to control the phosphorylation status of cofilin, one of the downstream targets of PPI. Upon decrease in the cellular G-actin levels, Phactr4 activates cofilin through its binding to PPI, which leads to increase in the cellular levels of monomeric actin. Therefore our data pointed to an important role for Phactr4 in a feedback system, where actin monomers can locally regulate their own abundance. Thus this work highlights the role of RPEL repeat as a universal actin-binding site, which regulates actin homeostasis in cells.
  • Gruber, Christina (Helsingin yliopisto, 2015)
    Both the ability to gain a high dominance status and having an efficient immune defence are favourable qualities that typically increase fitness in social and host-parasite interactions. Individuals with a high dominance status are predicted to gain fitness-related benefits from prior access to limited, defensible resources, such as food and matings. Immune defence mechanisms, on the other hand, have evolved to minimize the fitness costs of parasitic infections. The relative significance of a high dominance status and strong immune defence for individual fitness is, however, affected by the quality of the environment. The aim of this thesis is to improve the understanding of environmentally determined variation in dominance status, immune defence and their consequences for individual fitness. I use the native noble crayfish (Astacus astacus), the invasive signal crayfish (Pacifastacus leniusculus) and the highly virulent, invasive Aphanomyces astaci, the causative agent of the crayfish plague, as my study models. I first experimentally test theoretical predictions on how major ecological factors, including food availability, predation risk and population density, influence behavioural decision-making in fight contests, especially with regard to the maintenance of dominance hierarchies between size-matched crayfish. Using natural noble crayfish subpopulations with different crayfish plague history, I then explore whether variation in immune defence and crayfish plague resistance is potentially explained by local adaptation to the disease, or alternatively by geographical divergence. By keeping noble crayfish experimentally under constant environmental conditions, I finally determine whether seasonal variation in immune defence is endogenously regulated. My results show that individuals that had achieved dominant status in non-resource fight contests have an advantage in monopolising a limited, defendable food resource in a future contest. Furthermore, I find evidence that as population density increases, the division of the resource between dominants and subdominants becomes more unequal. Generally, my results suggest that due to ecological factors the dominance status of individuals can be more dynamic than theory predicts, especially when the contestants have similar fighting ability. For example, in line with the asset-protection principle, individuals having achieved dominant status in a non-predation risk contest increase their submissive behaviours in the presence of a predation threat, giving subdominants the opportunity to win a larger percentage of bouts in the predation risk contest. My results also reveal evidence for geographical variation in resistance to the crayfish plague and immune defence that is, however, independent of historical disease outbreaks in the study subpopulations. Furthermore, for the first time in invertebrates, my results demonstrate reproduction-related endogenous seasonal variation in the immune defence of noble crayfish. Overall, my results suggest that ecological factors, such as population density, predation risk and disease history, have to be taken in to account to better understand the causes and consequences of dominance status and immune defence in any individual species.
  • Tumiati, Manuela (Helsingin yliopisto, 2015)
    Breast cancer is the second most common cancer in the world and the most common cancer among women. Germ-line mutations in the DNA repair gene RAD51C (RAD51 paralog C) predispose women to breast and ovarian cancers, yet the mechanisms by which a lack of RAD51C causes tumorigenesis are poorly understood. RAD51C deficiency is thought to promote cancer by preventing correct repair of DNA double-strand breaks, leading to accumulation of somatic mutations and genomic instability, a cancer hallmark. Similarly, defects in other genes involved in repair of DNA double-strand breaks, such as BRCA1 (breast cancer 1, early onset), BRCA2 (breast cancer 2, early onset), or PALB2 (partner and localizer of BRCA2), are linked to breast cancer, suggesting that the mammary gland is particularly susceptible to genomic instability. We know that RAD51C-null cells from several organisms present a number of chromosomal aberrations, and Rad51c knockout mice die during early embryogenesis from massive Trp53-mediated apoptosis. A previously generated mouse model demonstrated that when Rad51c is lost together with Trp53, multiple tumors develop approximately at one year of age. However, while Trp53 knock-out mice predominantly develop osteo- and myosarcomas, a spontaneous loss of both Rad51c and Trp53 in double-mutant mice leads mostly to development of epithelial-derived carcinomas, especially in mammary glands, skin, and skin-associated specialized sebaceous glands. While suggesting a possible role for Trp53 in the Rad51c-mediated tumorigenesis, this study left several questions unaddressed. First, the ability of Rad51c loss to induce tumor formation independently of Trp53 stood as an open question. Second, the mechanisms by which Rad51c might cause malignant transformation remained unclear. Last, there was complete absence of information about the role of RAD51C in the mammary gland. We set out to fill these gaps by generating a skin and skin-associated Rad51c knock-out mouse model. For this purpose, we conditionally deleted Rad51c and/or Trp53 from basal cells of the epidermis and ectodermal-derived glands using Keratin 14 Cre-mediated recombination. With this model, we demonstrated that deletion of Rad51c alone is not sufficient to drive tumorigenesis but impairs the proliferation of sebaceous cells and causes their transdifferentiation into terminally differentiated keratinocytes. In addition, we reported that Rad51c/p53 double mutant mice develop multiple tumors in skin and mammary and sebaceous glands at around six months of age, while Trp53-mutants have a tumor-free survival of 11 months and a lower tumor burden. We also observed that in situ carcinomas are detectable in Rad51c/p53 double mutant mice as early as four months of age, which provided a tool for studying the early phases of tumorigenesis. Notably, we reported that mouse mammary tumors recapitulate several histological features of human RAD51C-associated breast cancers, especially a luminal-like, hormone receptor-positive status. Finally, we described that loss of RAD51C causes chromosomal aberrations in both mouse and human cells, providing a direct translational link between the phenotype observed in the two species.
  • Silvennoinen, Reija (Helsingin yliopisto, 2015)
    Atherosclerosis is a multifactorial progressive disease characterized by the appearance of inflamed lesions in the inner arterial wall (intima). The clinical manifestations of atherosclerosis afflict more than half of the population globally. The main component of an atherosclerotic lesion is a cholesterol-filled macrophage (a foam cell); the degree of cholesterol accumulation within these cells is a major determinant of the disease process. In addition to macrophages, the inflamed intima contains numerous mast cells which, upon activation, acutely secrete serine proteases and other mediators that can influence the progression of atherosclerotic lesions. HDL-mediated removal of cholesterol from the lipid-filled macrophages and its transfer to the liver and feces for ultimate excretion, a process termed macrophage- reverse cholesterol transport (m-RCT), is an important anti-atherogenic mechanism. The multi-step m-RCT pathway appears to be modulated at the various steps. Mast cell-derived proteases, by degrading HDL lipoproteins, may affect the early steps of m-RCT, a possibility that has not been investigated in vivo. Psychological stress, an established risk factor for cardiovascular diseases and a potent activator of mast cells, might also interfere with m-RCT. With an aim to answer the question whether cholesterol flux through the m-RCT pathway could be physiologically modulated by mast cell activation and stress, this thesis assessed the functionality of the various components of the m-RCT pathway using the mouse as the experimental model. In the first study, a short-term m-RCT in vivo analysis was validated and performed to investigate the consequence of local mast cell activation for the functionality of HDL in m-RCT. The following study utilized the same method to address the effects of acute psychological stress on m-RCT. In the third study, the effects of stress on m-RCT were assessed in a chronic setting. An inhibitory role of peritoneal mast cell activation in vivo on the initial step of the m-RCT was established. Conversely, stress exposure, both acute and repetitive, induced multiple m-RCT-promoting responses in the liver and intestine. Mice exposed to acute psychophysical stress exhibited accelerated m-RCT due to compromised intestinal absorption of cholesterol, uncovering a novel functional connection between the stress hormone corticosterone and m-RCT. Repeated exposure to the same stressor resulted in increased fecal excretion of bile acids which also stimulated the rate of m-RCT. Altogether, the results presented in this thesis demonstrate that the m-RCT pathway is effectively modulated by two physiological factors, psychological stress and mast cell activation, which are involved in the pathology of atherosclerosis.
  • Morandin, Claire (Helsingin yliopisto, 2015)
    Understanding how the interaction of genotypes and environment may result in distinct phenotypes from similar sets of genes is a central theme in evolutionary biology. Social insects have been important study organisms for this question, with sociality evolving in parallel in unrelated taxa. The defining feature of advanced sociality, the separate reproductive queen and non-reproductive worker castes of social insects, is central to social evolution. Queens and workers share, most of the time, a similar genome, suggesting that the basis of this dimorphism must result from differences in expression of the same genes. Furthermore, workers forgo their own reproduction to help raise the offspring of the queen, thus queen and worker genes are expected to experience natural selection in unique ways. Yet, the regulatory architecture that governs queen and worker phenotypes remains largely unknown in social insects. This thesis demonstrates the plasticity of caste-biased expression patterns in ants at several levels. It shows that few genes retain their caste-biased expression patterns across closely related species, lineages, or development stages. For the first time, this thesis shows that biological functions, through conserved sets of genes, are strongly associated with caste phenotypic differences across the ant phylogeny. These sets of genes also appear to be co-opted for other types of key social phenotypes and likely serve as building blocks of phenotypic innovation. My thesis furthermore focuses on the interactions between caste-biased expression patterns and rates of molecular evolution to comprehend the origins and results of caste-biases. The work presented in this thesis shows that evolutionary constraints strongly affect evolutionary rates of protein-coding genes, gene expression evolutionary stability, and the ability of a gene to become caste-biased. These constraints are significant features that have been greatly under-appreciated in previous studies. The work in this thesis takes advantage of the power of genomic methodologies and technologies to provide new insights into mechanisms of social evolution, and the evolution of plastic gene expression in a more general framework. It builds on existing knowledge to provide the field of social insect research with novel concepts (e.g. co-expressed network) to understand the molecular mechanisms behind the origin and the maintenance of the two female castes.