Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • Zhao, Xiang (Helsingin yliopisto, 2015)
    Vertebrate brain is one of the most complex and mysterious objects for biological research. Embryonic brain development involves stereotypic brain structure formation, and a vast number of precise intercellular connections are established for the generation of the highly complex circuitry of the brain. This work aims at explaining HMGB1 and AMIGO1 function in modulating vertebrate brain development. Hmgb1 knockdown zebrafish morphants produced by injection of morpholino oligonucleotides display severe defects in the forebrain and gross deteriorated catecholaminergic system. The morphant is also deficient in survival and proliferation of neural progenitors. Similar central nervous system (CNS) developmental defects have been observed in HMGB1 knockout mouse embryo. The HMGB1 null mouse embryonic brain cells showed much lower proliferating and differentiating activities compared to wild type animals. HMGB1 knockdown and knockout model respectively from zebrafish and mouse have confirmed that AMIGO1 expression is directly regulated by HMGB1. AMIGO1 regulates expression of Kv2.1 potassium channel during development, but the colocalization of AMIGO1 and Kv2.1 has only been observed in mouse and zebrafish adult brain. Furthermore, knockdown of amigo1 expression using morpholino oligonucleotides impairs the formation of fasciculated tracts in early fiber scaffolds of brain. The same defect can be also induced by mRNA-mediated expression of the Amigo1 ectodomain that inhibits adhesion mediated by the full-length protein. The impaired formation of neural circuitry is reflected in enhanced locomotor activity and attenuated escape responses. Our data demonstrate that HMGB1 is a critical factor for embryonic CNS development involved in many important developmental events. HMGB1 is essential for the neurogenesis and differentiation occurring at the developmental stage when forebrain structures are forming. Amigo1 is required for the development of neural circuits under the regulation of HMGB1. The mechanism involves homophilic interactions within the developing fiber tracts and regulation of the Kv2.1 potassium channel to form functional neural circuitry that controls locomotion. HMGB1 and AMIGO1 are both crucial for embryonic brain development and neural circuit formation.
  • Helenius, Laura (Helsingin yliopisto, 2015)
    Zooplankton are considered an important link between the zooplanktivores that consume them and the lower trophic levels, yet their specific ecological role in littoral brackish ecosystems is still relatively unstudied. In general, ecological interest in zooplankton derives from their roles as grazers or as a food source. As grazers, their role is coupled with predicting future densities and composition of the algal community, while alternatively as prey they provide information on fish stocks in terms of the zooplankton production available to fish. This thesis aimed to unravel aspects related to these roles in the littoral zones of the Baltic Sea, by shedding light on the themes of zooplankton composition and diversity, the interactions between zooplankton and their predators, and the general feeding ecology of components of zooplankton. The first objective of the thesis was to gain baseline information on zooplankton community composition and diversity in the littoral Baltic Sea via field sampling on a salinity gradient. The thesis also aimed to investigate how salinity and other abiotic factors, such as turbidity, temperature and wave exposure, affect zooplankton communities and the predation that structures them. Predation via two types of feeding by zooplanktivorous fish was studied experimentally as a regulator of zooplankton communities. Finally, the thesis investigated the role of copepod nauplii as grazers in laboratory conditions. Salinity was found to be the most significant abiotic driver of spatial patterns of composition and diversity of zooplankton. Turbidity/chl a also influenced community structure to a lesser extent. The spatial patterns of species heterogeneity remained relatively constant regardless of temporal turnover, and there was an abrupt change in species composition at an intermediate salinity of 4 (on the Practical Salinity Scale) on the salinity gradient. Functional diversity of zooplankton was found to be related to salinity, but also to factors related to productivity after a certain threshold. Zooplankton diversity was also affected by predation, but this effect was regulated by the initial composition of the zooplankton community, which was in turn directly related to seasonality. Predation itself was found to structure the community through direct removal of crustacean zooplankton, as well as cascading effects on microzooplankton. These effects, as well as the extent of the disturbance generated by turbidity on zooplanktivorous feeding, were all closely related to predator type. In the final section of the thesis, which concentrated on zooplankton as consumers, the functional responses of stage NII nauplii of the calanoid copepod Paracartia grani to various microalgae were found to be either Holling type II or III responses. Highest maximum clearance rates were found on a diatom and a dinoflagellate of a size of ~12 µm, indicating an optimal prey:predator size ratio of 0.08. In plurialgal mixtures, feeding patterns were largely dependent on prey type. Zooplankton are irrevocably linked to phytoplankton and fish through food web interactions. Changes in the abiotic environment inevitably lead to a response in the biotic environment as well, and a bottom-up resource level response reflects on top predators, in this case the littoral fish. Therefore, understanding the abiotic and biotic factors determining zooplankton diversity and density is a precondition to understanding the links between phytoplankton, zooplankton, and coastal zooplanktivores.
  • Nurmi, Katariina (Helsingin yliopisto, 2015)
    The innate immune system responds to infection or injury by initiating nonspecific inflammation, which functions to limit the spread of harmful microbes or the damage caused by tissue injury. The cells of the innate immune system are the first to encounter danger signals, and they mediate the rapid local immune response. Inflammatory reactions are normally beneficial for the host, and inflammation is usually resolved when the threat has been removed. However, in chronic inflammatory diseases, the danger signals either are not cleared or continue to be formed. Pathogen-derived molecules and danger signals induce the activation of pattern recognition receptors (PRRs) in the innate immune cells. Several families of PRRs exist, and their interplay is needed for the induction of efficient immune defense reactions. Nucleotide-binding domain and leucine-rich repeat-containing receptors (NLRs) are intracellular receptors that respond to a plethora of danger- and pathogen-associated molecular patterns. Their activation induces the assembly and activation of cytosolic multiprotein complexes called inflammasomes. Inflammasomes act as a primary checkpoint for the activation and secretion of the strong proinflammatory cytokines interleukin (IL)-1β and IL-18. Similar to other cellular functions, innate immune responses are operated via a complicated interplay between signalosomes. To become activated inflammasomes require the coordinated activation of Toll-like receptors (TLRs) and NLRs, which induce the activation and assembly of inflammasome complexes. The consequent secretion of inflammasome-derived cytokines is, in turn, modulated by autophagy. Inflammasome activation and autophagy also interact with cellular death pathways. Cellular death acts to limit the spread of intracellular pathogens by denying a protective niche to these pathogens, thereby inhibiting their replication and predisposing them for detection by the immune system. The aim of this study was to investigate the roles of ethanol and hemin in the modulation of innate immune cell functions, as well as the mechanisms underlying the reported protective effects of ethanol and hemin against chronic inflammatory diseases. Alcohol is the most commonly and widely used drug in the world. The consequences of alcohol consumption depend on both the pattern of consumption and the amounts consumed. Alcohol abuse predisposes to more frequent and severe infections, whereas the light to moderate consumption of alcoholic beverages has been associated with a reduced incidence of chronic inflammatory conditions, such as cardiovascular diseases and rheumatoid arthritis. These seemingly different responses may both derive from attenuated reactions of innate immunity. In the present thesis study, ethanol was shown to reduce the viability and proliferation of mast cells. This reduced viability resulted from the immunologically silent apoptotic death of mast cells. In macrophages, ethanol reduced the pyroptotic cell death induced by inflammasome activation and instead directed cell death toward apoptosis. Excessive inflammasome activation is a prominent feature of several chronic inflammatory diseases. The mechanisms that restrain inflammasome activation were studied in greater detail in cultured macrophages. Ethanol dose-dependently inhibited inflammasome activation and the secretion of IL-1β in human macrophages. It was further shown that the inhibitory effect of ethanol was mediated by a reduction in lysosomal disruption and the release of active cathepsin B, which thus contributed to diminished inflammasome assembly. The majority of mammalian cells are constantly renewed. Enormous numbers of senescent red blood cells are phagocytosed daily by macrophages. In certain pathologies, such as malarial infection, massive hemolysis occurs that exceeds the capacity of the scavenging and degradation systems of hemoglobin. As a consequence, free heme and hemin are released into the circulation. Free heme and hemin are cytotoxic and proinflammatory compounds. However, heme and hemin are also potent inducers of the heme oxygenase-1 (HO-1) enzyme, which possesses anti-inflammatory and cytoprotective effects. In the present thesis study, hemin and its synthetic derivative cobalt protoporphyrin (CoPP) blocked inflammasome activation and assembly. Decreased secretion of IL-1β was also observed in vivo in a nucleotide-binding domain and leucine-rich repeat-containing family, pyrin domain-containing 3 (NLRP3)-dependent peritonitis model in mice. The inhibitory effects of hemin and CoPP were partially dependent on the induction of HO-1 transcription by NF-E2-related factor-2 (Nrf2) and the enzymatic activity of HO-1. The inhibitory effects of hemin and CoPP were mediated by increased degradation of inflammasome components, which was due to elevated autophagy. Overall, the results of this study demonstrate that ethanol and hemin markedly prevent inflammatory cellular responses in macrophages and mast cells. This inhibition may contribute to the cardioprotective effect of ethanol and the anti-inflammatory effects of hemin. An enhanced molecular understanding of the mechanisms by which ethanol and hemin inhibit inflammation may help reveal new therapeutic options in the treatment of chronic inflammatory diseases.
  • Ylä-Anttila, Päivi (Helsingin yliopisto, 2015)
    Eukaryotic cells contain membrane-bound organelles to carry out specialized cellular functions. These organelles are inherited in cell division as templates and are augmented by proliferation through production of protein and lipid components by the cell, and the trafficking of these components within the cell. Autophagy is an evolutionarily conserved degradation pathway for cells to maintain homeostasis, produce nutrients for energy production, degrade misfolded proteins or damaged whole organelles, and fight against intruding pathogens. The process of autophagy entails the isolation of cargo by a specialized organelle, called the phagophore, which closes to form a sealed double membrane bound autophagosome. This organelle then undergoes maturation by fusion with endosomes and lysosomes to obtain its degradation capacity. Hence, there are many dynamic membrane modifications that need to take place during the autophagic process. The origin of the autophagic limiting membrane, as well as the clearance of the degradative structures, are yet to be defined. This study utilized high resolution electron microscopic methods and three dimensional modeling to reveal nanometer scale interactions of phagophores and autophagosomes with other organelles. Immunolabeling techniques at both light and electron microscopy level were utilized to determine which organelles should be sampled at an ultrastructural level. Direct membrane communication was detected between the phagophore and endoplasmic reticulum (ER), (putative) ER exit sites, mitochondria, the Golgi complex, as well as late endosomes or lysosomes. ER was the most frequent proximal organelle to phagophores and autophagosomes and this suggests an involvement of ER in the nucleation process of phagophores. This study also reveales a role of the small GTP-binding protein RAB24 in the clearance of autophagic structures in cells. Biochemical and microscopic methods in combination showed that RAB24 is needed in the clearance of autophagic structures in nutrient rich conditions i.e. during basal autophagy. RAB24 was confirmed to localize in both of the autophagosome limiting membranes. GTP binding and prenylation of RAB24 were found to be necessary for the targeting of the protein to LC3 positive autophagic structures, whereas tyrosine phosphorylation was less important for this targeting. Electron microscopy revealed that autolysosome-like structures accumulate in cells when RAB24 is silenced, suggesting that it has a role in the clearance of autolysosomes.
  • Milardi, Marco (Helsingin yliopisto, 2015)
    Fish introductions, unlike many other clades, are often carried out purposefully. This is a worldwide practice, which has been ongoing since ancient times and has found new powerful ways to increase in magnitude and scope through the development of more effective transport and with increasing population wealth. Even though the literature is building up pace fast with this relatively recent phenomenon, information is still lacking on the mechanisms and results of the impact that introduced fish have on freshwater ecosystems. Remote small lakes at high-latitudes can be used to evaluate some of these impacts, as they are of limited size and often host relatively simple food webs with a single species of introduced fish, which makes them ideal model systems. Many areas are not as easy to investigate, as they present much more complex ecosystems where complex species interactions take place. For example, artificial lotic systems with a high number of species interactions can be particularly challenging to tackle as other anthropogenic/environmental stressors might be challenging to disentangle. This thesis focused on three main themes which addressed the reliance of introduced fish on terrestrial energy, their cascading effects on the food web and their interaction with native species. The first two themes used brown trout introduced in remote small lake ecosystems at high latitudes as a model, whereas the last theme used a complex lotic system at low latitudes where multiple species were introduced at different times. The chapters of this thesis used neo- and paleolimnological techniques to investigate the impacts of introduced fish, sometimes in combination. In particular, the first theme was tackled through the use of stomach content, fatty acids and stable isotopes to unravel the feeding ecology of introduced brown trout. The second theme was instead addressed through multiple paleo-proxies in combination with neolimnological analyses and models. The last theme was investigated through the analysis of long-term environmental and fish-assemblage data. Our findings suggest that terrestrial sources could be highly important in supporting introduced brown trout populations in small lakes at high latitudes. Despite challenges inherent to the turnover rates of fish liver and muscle tissues, which were longer than previously thought, this support did not vary across different years or fish densities, but was affected by seasonal factors over the course of the open-water season. Our results also suggest that introduced brown trout affect the food web of host lakes through trophic cascades, altering the abundance of pelagic and benthic micro- and macroinvertebrates, probably through a modification of the distribution of macro-invertebrate communities. According to a bioenergetic and a mass balance model, introduced brown trout nutrient regeneration should have increased lake productivity; however paleo-proxies indicated no such change but rather a shift from pelagic to benthic productivity. Finally, our results suggest that, in artificial lotic systems at low latitudes, environmental chemistry did not play a role in the decline of the native fish species communities. Rather, this was a result of the interaction between some of the introduced fish species and the native ones, enhanced by the habitat simplification and the peculiar water fluctuation regime.
  • Laakkonen, Hanna (Helsingin yliopisto, 2015)
    The Northern Pacific and Atlantic Oceans share a faunal element consisting of pairs of closely related vicariant taxa or populations and known as the amphi-boreal fauna. The inter-oceanic systematic affinities reflect a history of shared ancestry since past dispersal through the Bering Strait and across the Arctic basin, starting from the initial opening of the Bering Strait at the end of the Miocene. This thesis examines the biogeographical history of the amphi-boreal faunal element using information from molecular marker characters. The aim is to document the dynamics and consequences of the faunal interchange between the two oceans, spanning from the end of Miocene to the present. This is done by comparing differences in the mitochondrial gene sequence variation in different taxonomic groups and across the circum-boreal geographical scale, encompassing 70 taxa. The consequences of dispersal to genetic diversity was examined more closely and with additional markers in two exemplary genera, herrings and bivalve molluscs of the genus Hiatella. The phylogeographical histories of the vicariant Pacific-Atlantic populations and taxa are found remarkably variable. A simple vicariant history, with a single early invasion in the Pliocene or Early Pleistocene, was inferred only in about 50% of the examined taxa and in 30% signatures of more than one trans-Arctic invasion were found in the molecular data. Overall the estimates of inter-oceanic divergence within each of the broader taxonomic groups studied (fishes, molluscs, crustaceans, echinoderms, polychaetes) varied greatly, up to 10 20 fold, and suggest that trans-Arctic faunal dispersal has been a dynamic and repeated process through the entire time frame considered. Nevertheless, from the molecular divergence, several instances of putative cryptic vicariant species were revealed in invertebrates. In the nearly cosmopolitan bivalve mollusc Hiatella, altogether 11 cryptic taxa were discovered in the Northern Hemisphere and a hypothesis of their repeated inter-oceanic movements was presented. In some 40% of the amphi-boreal genera a close inter-oceanic relationship was found, often seen as incomplete mtDNA lineage sorting and implying recent trans-Arctic dispersal or ongoing migration. The consequences of secondary dispersal from the Pacific to Atlantic were examined more closely in the model cases of the genera Clupea and Hiatella. The Pacific herring C. pallasii, of East Asian origin, invaded the Northeast European seas after the last glacial period and then differentiated into separate regional populations. In Europe, the species has hybridized with the native sister species C. harengus, the Atlantic herring. The amount of introgression from the Atlantic to the Pacific herring has varied between the various contact regions of the two taxa. Particularly the Norwegian local Balsfjord herring stock seems to represent a heavily introgressed hybrid swarm. Secondary contacts of differentiated lineages were found to be a common phenomenon in all of the broader taxonomic groups studied. The introgression between old lineages, but also the effects of shorter isolation-dispersal cycles, may be important but so far overlooked phenomena in shaping the genomic composition and adaptive properties of taxa that inhabit the post-glacially colonized marginal habitats of the northern seas. Due to the current global warming and changing navigation practices in the Arctic, trans-Arctic inter-oceanic faunal exchange is expected to increase. The topic requires closer studies in the near future, in order to understand what kind of ecological and genetic consequences the exchange will have on the present day faunal communities.
  • Ramiadantsoa, Tanjona (Helsingin yliopisto, 2015)
    Habitat loss and fragmentation is the main culprit behind the current decline in biodiversity. The estimated current rate of extinction is two or three orders of magnitude higher than the background extinction rate. This thesis analyzes existing data and develops models to improve our understanding of the role of spatial processes in the dynamics of populations and communities. This work is focused on the features of habitat destruction that causes decline of biodiversity as well as the traits that make species vulnerable to habitat loss. First, I attempt to infer relationships between spatial heterogeneity, rate of diversification (speciation and extinction), and the dynamics of geographical ranges from a reconstructed phylogeny. I build a flexible comparative method to analyze adaptive radiation and range dynamics that extends the current models in two directions by allowing more than two regions and by assuming diversity-dependent diversification rates. In a five-region system stimulated by the biogeography of Madagascar, processes that increase and decrease diversity are strongly correlated. Therefore, it is not possible to estimate independently region-specific speciation and extinction rates, though their ratios can be successfully estimated. When applied to Malagasy dung beetles, we found that diversification rate is highest in the northern (very heterogeneous) and lowest in the southern (most homogeneous) parts of Madagascar. Thus it appears that landscape heterogeneity promotes diversification and thus biodiversity. The two other chapters investigate the consequences of habitat loss and fragmentation for generalist and specialist species. We aim to understand how generalist and specialist species respond to habitat loss and fragmentation. In particular, we ask why generalist species often increase in abundance following an intermediate level of habitat destruction. I develop a modular modeling approach that allows one to switch on and off various mechanisms as needed. This approach one to assess the marginal and joint effects of different mechanisms by comparing model outcomes. Our analyses confirm that a high level of specialization leads to high sensitivity to habitat loss and fragmentation. When landscape quality is high, specialists are competitively superior, but when landscape degrades, generalists gradually become superior. In previous models, competitive hierarchy is usually thought to be an intrinsic property of species, but we show that a shift in competitive capacity is caused by extrinsic factors. Comparing deterministic versus stochastic models, we find that a key extrinsic factor is increase in demographic stochasticity in degraded landscapes that affects specialists more than generalists. In the third chapter, I ask about the role of large- scale habitat corridor for biodiversity conservation. We analyzed a community of 300 species belonging to 6 taxonomic groups inhabiting more than 2000 km2 forest, composed of two large national parks in Madagascar, Ranomafana and Andringitra, and connected by a corridor. We found that in 2000 the corridor was still functional, but since then it has degraded substantially and may lose its corridor function in the coming decades. Our spatially realistic simulations show that species with passive mode of dispersal suffer the most from corridor destruction. This thesis emphasizes the role of different mechanisms that should be considered while analyzing species responses to changes in habitat structure. The most important ones are the mode of dispersal, ecological specialization, temporal and spatial stochasticity, and competition. As such, tropical regions, like Madagascar, are in double trouble due to high ecological specialization of most species and high rates of habitat destruction. Effective measures need to be enforced to ameliorate the conditions within and outside protected areas so they can truly enhance biodiversity protection.
  • Savola, Sakeri (Helsingin yliopisto, 2015)
    Approximately 75% of Finland is covered by boreal forest. Intensive commercial forestry has shaped the Finnish landscape as well as the animal communities that inhabit it. It has been suggested that commercial forestry increases the density of voles in boreal ecosystems. Voles, especially those belonging to Microtus, are important prey items for many avian and mammalian predators and are susceptible to numerous pathogens, e.g., Puumala virus In this thesis, I studied the effects of a changing landscape on vole populations and the influence of dynamic vole population densities on other trophic levels in the ecosystem. The main questions in the thesis are: how is commercial forestry affecting small mammal populations?; how does habitat and the small mammal community influence the prevalence of Puumala virus?; what are the main factors regulating red fox (Vulpes vulpes) population density?; and what are the habitat preferences of red fox? In our vole study in Taivalkoski northern Finland we found that the early stages of forest succession are preferred by Microtus and, thus, commercial forestry is increasing the amount of habitat used by Microtus voles. In the Finnish forest landscape, Puumala virus is found in forests of all ages as is its main host, the bank vole. However, the highest bank vole densities are found in mature forests. We also found evidence of a dilution effect in that the incidence of Puumala virus antibodies in breeding bank voles was lower when the abundance of other small mammal species was high. Our results based on Finnish long-term wildlife monitorings suggest that the red fox population is regulated by its main predator, the Eurasian lynx, in addition to its own abundance in the environment. The red fox hunting bag was surprisingly related positively to the red fox population growth. We also found a negative relationship between autumn vole density and fox population growth in the next year. We suggest that the red fox population is affected by both top-down and bottom-up factors. In our study on GPS-collared red foxes we found that foxes favour agricultural areas, and that home range size is smaller in regions dominated by crop fields. Within the home range, foxes prefer open forests that have been recently clear-cut and replanted, where Microtus voles can be found more abundantly. In comparison to lynx, foxes tend to range within more modified habitats, e.g., agricultural and urban areas, where predator densities are lower and alternative resources can be found. Commercial forestry is affecting vole population density and other trophic levels in boreal forests. The increasing abundance of apex predators (e.g., lynx) is limiting the density of the vole predators (e.g., red fox) and thereby driving the system and its trophic interactions in a new level.
  • Kiiski, Kirsi (Helsingin yliopisto, 2015)
    Nemaline myopathy (NM) and related disorders constitute a heterogeneous group of congenital myopathies. Mutations in the nebulin gene (NEB) are the main cause of the recessively inherited form. NEB is one of the largest genes in the human genome consisting of 249 kb of genomic sequence. NEB contains 183 exons and a 32 kb homologous triplicate region (TRI) where eight exons are repeated three times. The aims of this Doctoral Thesis study were to develop and implement into diagnostics new efficient variant analysis methods for NEB and other NM-causing genes. The first aim was to design and validate a custom copy number microarray targeting the NM-causing genes for the detection of copy number variations. MLPA (multiplex ligation-dependent probe amplification) and Sanger sequencing were also used. The second aim was to utilise whole-exome sequencing to search for novel disease-causing variants in the known NM genes and try to identify novel NM genes. Lastly, the aim was to collect more data in order to try to find genotype-phenotype correlations of NEB-caused NM. The design and validation of the NM-CGH microarray was successful. Of the total sample cohort of 356 NM families, 196 NM families were studied using the custom-made NM-CGH array. Nine different novel large causative variants were identified in ten NM families. The size of these variants varies greatly, covering only a part of one NEB exon on up to dozens of NEB exons (72bp - 133 kb). In addition, a novel recurrent variation of the NEB TRI region was identified in 13% of the NM families and in 10% of the studied 60 control samples. Deviations of one copy are suggested to be benign but gains of two or more copies might be pathogenic. One novel homozygous deletion was also identified in another NM gene, TPM3, in a patient with severe NM. Furthermore, ten samples were studied using exome sequencing, and for six of those samples, novel disease-causing variant(s) were identified. Two variants were identified in one family in a novel, putative NM gene that is currently under further investigation. 165 NM families from the total cohort of 356 NM families have been identified thus far with two pathogenic NEB variants. Altogether 220 different pathogenic variants were identified in these 165 families, accentuating that the patients in the majority (84%) of the families are compound heterozygous for two different NEB variants. Most of the variants are small single nucleotide changes whereas large variants are more rare. However, copy number variations are much more frequent than previously thought: pathogenic copy number variants were identified in 16% of these 356 NM-families. Genotype-phenotype correlations between the type of NEB mutation and the NM subtypes remained, however, unobtainable. The NM-CGH microarray has been implemented into molecular diagnostics of NM. Using the NM-CGH microarray followed by exome-sequencing has accelerated mutation detection. This combination has increased the coverage of the NM genes and thus improved the diagnostics of NM and NM-related disorders.
  • Sheehy, Jatta (Helsingin yliopisto, 2015)
    Soils comprise more carbon (C) than any other terrestrial source and hence even a small change in the C content can be significant in regards to atmospheric CO2 concentration. Cultivated soils have lost soil organic carbon (SOC) during the latest decades in Finland. New cereal crop management practices, like no-till (NT) and reduced tillage (RT), can affect not only soil organic carbon (SOC) stocks and stabilization, but also nitrous oxide (N2O) emissions. The aim of this study was to gain better understanding about the changes in soil C dynamics and N2O emissions as a result of management practice changes in the boreal region, and the implications of these changes to climate change mitigation. Changes in SOC stocks and stabilization rates under different tillage (NT, RT, CT (conventional tillage with a moldboard plow)) and straw management (straw retention, straw removal, straw burning) practices, were studied at different sites with clayey and coarse textured soil across southern Finland. This was done by soil fractionation method (wet sieving and microaggregate isolation) to elucidate the composition of different soil fractions, namely large and small macroaggregates, microaggregates, silt and clay and macroaggregate-occluded soil fractions, and where the C is stored within them. The effects of Lumbricus terrestris on SOC were studied using the same method. Nitrous oxide fluxes were monitored biweekly for 2 years under CT, NT and RT practices using closed chambers. Measurements of several environmental and soil parameters were taken to study the underlying factors controlling the observed changes in soil C stocks and N2O emissions under the different management practices. Climate change mitigation potential through the studied cereal crop management practices seems small in the humid boreal region based on the results of this study. The minimum tillage treatments did not sequester SOC at any of the study sites which had been under NT or RT for a decade and the total C stocks were lower in the 0 15 cm topsoil layer at one clayey site under RT compared to CT after implementing RT for 30 years. All clayey sites had a fairly high SOC content originally and all sites had higher decomposition rate of crop residues in NT compared to CT, possibly hindering C sequestration. However, the aggregate stability was enhanced in NT cropping systems compared to CT, and NT increased the amount of SOC in large macroaggregates at several sites and in microaggregates within macroaggregates in the coarse textured site. L. terrestris mediated the formation of soil aggregates and the increase of SOC in the topsoil but possibly enhanced the decomposition rate in the soils. Cumulative N2O emissions were higher under NT compared to both CT and RT at the clayey sites and lower at the coarse textured site. However, the coarse textured site under NT received slightly less N fertilizer compared to CT. Increased N2O emissions under NT on clayey soils were likely due to denser soil structure with consistently higher soil moisture content and poor aeration. Therefore, mitigating N2O emissions requires special attention to soil structure and drainage. This study suggests that RT is a notable option to control N2O emissions. In the future, climate change could increase precipitation and freeze-thaw cycles in boreal agroecosystems possibly enhancing N2O fluxes and C losses of cultivated soils which puts pressure on finding new mitigation measures.
  • 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.