Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • Spirin, Viacheslav (Helsingin yliopisto, 2016)
    This dissertation deals with the basidiomycete genus Antrodia, one of the largest polypore genera, which embraces over 80 species. Together with some other genera of brown-rot fungi (Fomitopsis, Laetiporus, Postia etc.), Antrodia constitutes its own lineage within the Polyporales, the so called antrodia clade. However, the genus in its current scope is polyphyletic and in need of further splitting into several natural genera. The main aim of this study is to define what is the genus Antrodia as a monophyletic unity, and to revise species concepts in some of the most important species complexes in Antrodia sensu lato. In the strict sense, Antrodia is a small genus, with six species closely related to the genus type, Antrodia serpens. They are highly uniform morphologically but can be recognized based on meticulous pore and spore measurements, as well as ecological and geographic data. Morphological and DNA data also allowed to revise species concepts within the Antrodia crassa, A. serialis, and A. malicola groups, belonging to the antrodia clade. All these revisions were based on type studies, studies of available herbarium material, and DNA analyses. In total, specimens of 46 Antrodia species were sequenced, 36 of them for the first time. Twelve new species were described, and six new combinations were proposed. Neotypes and epitypes were designated for seven species, in order to fix the current use of the species names. Results of the present research can be applied to further taxonomic revisions of brown-rot polypores, as well as for introducing phylogenetically sound genus concepts in the antrodia clade. Re-evaluation of species concepts in the A. crassa group provided new data on the ecology and indicator values of some species, and therefore it can be useful for defining their status in regional Red Lists and lists of indicator species of old-growth forests.
  • Meinander, Outi (Helsingin yliopisto, 2016)
    Light-absorbing impurities in the cryosphere are of hydrological, environmental and climatic importance. The wet and dry deposition of black carbon (BC), organic carbon (OC), and dust particles affect the optical properties and melt of snow and ice. In the Arctic region, the climatic effects are amplified, and surface albedo feedback is often cited as the main contributor. The aim of this thesis is to fill in some of the gaps in our knowledge of the effects of BC, OC, and Icelandic dust on snow in the European Arctic through a series of field and laboratory experiments and an analysis of the resulting data, including modeling. The thesis presents a new hypothesis on the snow density effects of light-absorbing impurities, an important quantity for climate modeling and remote sensing. Three processes are suggested to explain the proposed BC density effect . Experimental results show that dirty snow releases melt water quicker than cleaner snow. The albedo of natural seasonally melting snow in Sodankylä, north of the Arctic Circle, is found to be asymmetric with respect to solar midday, thus indicating a change in the properties of the snow. The radiative transfer modeling results show that the observed solar zenith angle asymmetry results in a 2-4 % daily error for satellite snow albedo estimates. Surface albedo model results indicate that the biggest snow albedo changes due to BC are expected in the ultraviolet (UV) part of the electromagnetic spectrum. The albedo of natural seasonal snow measured in Sodankylä, is found to be lower than expected. Solar UV and visible (VIS) albedo values of 0.6-0.8 in the accumulation period and 0.5-0.7 during melting are observed. The low albedo values are explained to be due to large snow grain sizes up to ~ 3 mm in diameter, meltwater surrounding the grains and increasing the effective grain size, and absorption caused by impurities in the natural snow (87 ppb BC and 2894 ppb OC). The BC contents of the surface snow layer at the Sodankylä Arctic Research Center, Finland, is higher than expected. Increased BC in spring time suggests surface accumulation of hydrophobic BC during snow melt. Some of the high BC concentrations are related to anthropogenic soot transported from the Kola Peninsula, Russia. The origin of OC can be anthropogenic or natural, and may include pollen, seeds, lichens, natural litter or microorganisms that reside in snow and ice. Iceland is the most important Arctic dust source, but a scientific assessment of its impacts on the cryosphere is currently unavailable and scientific results are urgently needed to investigate the role of Icelandic dust in Iceland and elsewhere, in the past, present and future. Experimental results on Icelandic volcanic ash show that a thin layer increases the snow and ice melt but that an ash layer exceeding a certain critical thickness causes insulation. The Arctic results of this thesis have relevance to the assessment of Arctic climate change, including modeling and satellite applications.
  • Cypryk, Wojciech (Helsingin yliopisto, 2016)
    Extracellular vesicles (EVs) are small, membranous entities secreted from most eukaryotic cells at both homeostatic and stress conditions. Carrying active biological molecules nucleic acids, lipids and proteins EVs serve as important means of intercellular communication. In the immune system, EVs circulting in body fluids play important modulatory roles in coordination of responses. EVs are integral part of secretome all proteins secreted by cells. EVs provide means for secretion of proteins that are not trafficked through conventional, ER/Golgi-mediated mechanisms. Analysis of EV proteome provides basis for fundamental discoveries in understanding the biogenesis, secretion and delivery of these nanosized messengers to target cells. Macrophages are principal tissue-resident effector cells of innate immune system, performing surveillance of their neighborhood in search for danger. Macrophages express pattern recognition receptors (PRRs) which recognize conserved pathogen-associated molecular patterns (PAMPs) conserved range of molecules expressed by pathogens. PRRs also recognize endogeneous ligands that appear in the human body in other dangerous conditions and diseases. These are collectively called danger-associated molecular patterns (DAMPs). Recognition of PAMPs and DAMPs by PRRs triggers intracellular signaling, leading to activation of macrophage defense mechanisms. These begin with inflammation and secretion of pro-inflammatory cytokines, but many other proteins are also actively secreted by activated macrophages. Although inflammatory cytokine secretion is a well-studied process, very few studies investigating overall and EV-mediated protein secretion from human macrophages were performed. This thesis aims at broadening our understanding of EV-mediated protein secretion from human macrophages activated in response to selected innate immune activators, namely extracellular adenosine triphosphate (ATP), a potent DAMP released during cell damage; (1,3)-β-glucan, a polysaccharide component of fungal cell wall, activating dectin-1-mediated signaling and influenza A virus (IAV) - common seasonal pathogenic virus targeting lung epithelia and macrophages. Total secretome and purified EVs were analyzed using different high-throughput mass spectrometry-based methods and further explored using bioinformatic and biochemical studies. The presented results provide evidence that EV-mediated protein secretion is an integral part of responses of human macrophages to studied stimuli. Its activation is demonstrated with quantitative and comparative proteomic approaches. The secreted vesicles are characterized by a broad size range consistent with both exosomes and microvesicles, demonstrating that both types of vesicular structures are involved in protein secretion. The EVs carry distinct set of immunologically important proteins, and bioinformatic analysis suggests that the secreted EVs may exert immunomodulatory effects on recipient cells. It is shown that during IAV infection, EVs are mediators of pro-inflammatory and antiviral cytokine release, thus they may serve as protective capsules of targeted cytokine delivery. Proteomic analysis identified also a broad set of DAMPs unconventionally secreted in association with EVs, further extrapolating their function towards danger signaling in cellular immune responses. The study on ATP-mediated responses further investigates the intracellular signaling involving calpains, abundant cytosolic proteases, identifying their crucial roles downstream P2X7 receptor: in EV release, as well as inflammasome activation and IL-1β secretion. The data presented here indicate that EVs serve as unconventional means for secretion of a broad range of proteins secreted in PRR-mediated responses in human macrophages. Bioinformatic and functional analysis identifies potential processes involved in their generation as well as their roles in intercellular communication. Together, the presented thesis contributes to our understanding of unconventional, EV-mediated protein secretion in macrophage responses towards common, physiologically releveant threats. The studies presented here will serve as basis for further detailed functional analysis of the roles of EVs in communication between macrophages and other immune system cells. It will also lay the grounds for future studies involving EV-mediated macrophage responses in patients with fungal and viral infections.
  • Jakobson, Maili (Helsingin yliopisto, 2016)
    Studies in the past three decades have provided a detailed understanding of the key mechanisms mediating apoptosis (a type of programmed cell death) in eukaryotic cells. Our knowledge of the molecular regulation of apoptotic factors is, however, incomplete.Recent evidence from genetic and molecular studies demonstrate that possibilities to activate cell death machinery in post-mitotic cells is more restricted than in most dividing cell types. The aim of our studies has been to better understand the unique features regulating apoptotic factors in neurons. Apoptosis in mammalian cells is controlled by Bcl-2 family proteins. Of those, the BH3-only subgroup and pro-apoptotic effectors Bak and Bax are particularly important in initiating apoptosis. In most types of neurons Bak expression is affected by an alternative splicing mechanism. Neuronal bak variant, N-Bak, encodes a putative BH3-only protein, but its existence has remained controversial. N-Bak mRNA is abundantly expressed, suggesting that post-transcriptional mechanisms may control N-Bak protein expression in neurons. This thesis addresses the molecular mechanisms, which regulate neuronal Bak expression in more detail. Using immunoblot analysis, we show that endogenous N-Bak protein is not constitutively expressed in healthy neurons. N-Bak protein expression remained undetectable upon nerve growth factor deprivation induced apoptosis in cultured sympathetic neurons. Similar results were obtained using primary cortical neurons in etoposide-induced intrinsic apoptosis model. Challenging neurons with cytotoxic drug, thapsigargin, did not reveal N-Bak protein expression, suggesting that its mRNA is translationally silent also in stressed primary neurons. The absence of N-Bak protein was further confirmed using quantitative mass spectrometry analysis, which did not reveal any peptide form samples representing healthy, stressed or apoptotic neurons. We also show that accelerated proteosomal degradation is not responsible for the absence of N-Bak protein in neurons. The open reading frame of N-Bak mRNA is prematurely terminated, being potential target for the nonsense mediated mRNA decay (NMD) pathway. We found that N-Bak mRNA is not a constitutively targeted by NMD, but instead, is relatively stable in neurons. Luciferase reporter assays showed that N-Bak mRNA is translationally repressed via cis-acting contextual elements in its untranslated regions. Finally, we demonstrate that N-Bak mRNA localizes into the uncharacterized granular structures in sympathetic neurons, and this distribution remains unchanged in apoptotic neurons. Our findings collectively demonstrate that multiple post-transcriptional mechanisms control N-Bak expression in neurons. These mechanisms may be part of the program that governs tight control over apoptosis in neurons. Our results also highlight the importance to further characterize diverse, still neglected post-transcriptional regulation mechanisms that can modulate apoptotic pathways in a various post-mitotic cells.
  • Autio, Sari (Helsingin yliopisto, 2016)
    Sari Autio: Do we listen to earthworms? Tools for evaluating the Finnish National Action Plan on the sustainable use of plant protection products Qualitative programme evaluation procedures for the Finnish National Action Plan on the Sustainable Use of Plant Protection Products (NAP) were developed in this study. The purpose of the NAP is to reduce the risks to human health and the environment from the use of plant protection products. The NAP was studied using systems thinking as a complex, purposeful system with goals defined within the framework of the European legislation concerning plant protection products. Due to the multidisciplinary nature of the NAP, the research approach is integrating. Soft Systems Methodology was used to analyse the goals of stakeholders involved in the preparation and implementation of the NAP to make the implicit pre-assumptions behind it visible, and an explicit programme logic was formulated for it. A range of evaluation questions were derived to focus on gathering data and evidence needed to support qualitative evaluation of the programme s achievements in adequate detail and from multiple perspectives. Existing heuristic tools were explored that initially appeared to be appropriate for framing the goal-setting for a qualitative assessment of the NAP. Four models of heuristic tools were selected for the NAP tool box: 1) Critical Systems Heuristics, 2) sustainability screening of National Sustainable Development Strategies, 3) Limiting Factors Analysis and 4) Systemic Programme Logic. These heuristic tools were adapted to consider the specific characteristics of the use of plant protection products, in order to improve their applicability in this purpose. The heuristic tools were aggregated as a separate guidance for practical evaluation needs of governance. The NAP was reviewed also from the perspective of stakeholder participation, as a process of collective learning. Users are in prime position to adopt safer application techniques in reducing environmental and health risks in the long term. The quality of training, extension services and information for the users, as well as the mutual atmosphere of the actors influence the willingness to adopt the knowledge provided. A joint co-production of knowledge between all stakeholders should be considered so as to keep the influence from accumulating solely on limited high-level expert circles. Halfway through the first programme period, the actors involved still have time to prepare for the evaluation, which will take place around the year 2020. Finland has to report to the European Commission and other Member States about achieving the goals of the NAP. Key words: National Action Plan (NAP), sustainable use of plant protection products, reducing environmental and health risks, evaluation, heuristic tool, programme logic, collective learning, participatory action research, system
  • Wolf, Jana (Helsingin yliopisto, 2016)
    Abstract Size is a feature that is often connected to different life history-traits and individuals can vary in many fitness aspects related to size, such as reproductive strategies, dispersal and mating behaviour, dominance and many more. If size variation is not continuous in a species, individuals can be divided into two or more distinct size morphs. In social insects, queen size dimorphism (QSD) is an interesting phenomenon as it separates queens into two different morphs, with macrogynes defined as the larger and microgynes as the smaller morph. The aim of this thesis is to improve our understanding of this phenomenon in social insects with a special focus on a palaeartic ant species, Myrmica ruginodis. This thesis demonstrates how several taxa differ in their cause, prevalence and evolutionary processes involved in QSD. Four different hypotheses have been identified as reasons to QSD. First, intraspecific polymorphism in connection with alternative reproductive strategies. Second, inquilinism, where microgynes mainly produce sexual offspring and forego worker production. Third, speciation, where the two morphs represent separate species with intraspecific polymorphism as an ancestral state and speciation processes often combined with inquilinism. Fourth, selfish larval development, which has only been observed in stingless bees so far. This thesis shows how the first three scenarios represent transitional stages and are valid in ants, which provide the necessary evolutionary framework via high levels of obligate secondary polygyny. This thesis also examines the cause for QSD in Myrmica ruginodis by analyzing several traits. These are morphology, offspring production, dispersal and mating behaviour, as well as gene flow. Overall my results suggest that macrogynes and microgynes in the ant M. ruginodis represent an intraspecific polymorphism with alternative reproductive strategies without inquilinism involved in it. Incomplete mating isolation among morphs indicate that this species is at a very early transitional stage from intraspecific polymorphism along the divergence continuum.
  • Rydman, Elina (Helsingin yliopisto, 2016)
    Common materials acquire new properties when manufactured in the nanoscale. The same properties that are responsible for the exciting new possibilities are also a cause for some concern. The high surface area to volume ratio is a feature of engineered nanomaterials (ENM) that causes the amount of surface area to dominate their possible effects. In the case of carbon nanomaterials and other fibers, also the shape and length of the particle play important roles. The two ENM studied in this thesis, nanosized titanium dioxide (TiO2) and carbon nanotubes (CNT), are among the most widely used ENM in the world which means that they hold a high potential of occupational and possible customer exposure. Inhalation is the most likely exposure route in occupational settings. For this reason, inhalation exposure of mice was the main route of administration. The study settings were chosen to mimic occupational exposure as far as possible. Different immunological parameters were examined in the lungs of the exposed mice, such as the influx of different leucocytes, expression of cytokine and chemokine messenger molecules and changes in the lung tissue. The results from TiO2 studies indicated that even a normally inert material when nanosized may become inflammogenic. In addition, even small changes in the structure, or even a coating, may modify radically the nature of a material. Exposure to most nanosized TiO2 caused only modest to no inflammation, whereas a silica (SiO2) coated TiO2 triggered an inflammation characterized by pulmonary neutrophilia and mRNA expression of neutrophil chemoattractant CXCL1 and proinflammatory TNF-α. In tissues and bronchoalveolar lavage (BAL), TiO2 was readily engulfed by macrophages. In a model of allergic asthma, it was found that exposure to both nanosized and larger TiO2 seemed to prevent asthmatic symptoms. This underlines the importance of bearing in mind the heterogeneity of the human population when assessing the toxicity of ENM. CNT have raised some serious concerns in the scientific community and the media due to their similarity in structure to asbestos. Here, a remarkable new type of eosinophilic inflammation was observed in long rigid CNT exposed mice after a week of inhalation to these particles. This inflammation was characterized by strong eosinophilia, goblet cell hyperplasia, Th2 type cytokines and increased airway hyper-responsiveness to methacholine. All of the above symptoms have previously been described as symptoms of classical asthma. Transcriptomic analyses revealed radical up-regulation of innate immunity and cytokine/chemokine pathways. There were also roles found for mast cells and alveolar macrophages in orchestrating the inflammation. Lastly in the only exposure conducted by aspiration, mice were exposed to two long CNT (rigid/R and tangled/T) and to crocidolite asbestos. From a few hours to 28 days after a single exposure, there was a striking inflammatory cascade starting with macrophages and neutrophils, progressing to eosinophilic inflammation and eventually terminating as granulomas, goblet cell hyperplasia, Charcot-Leyden-like crystals and the mRNA expression of IL-1β, TGF-β, TNF-α and IL-13. The most dramatic inflammation was seen in the R/CNT group, followed by asbestos with T/CNT being clearly more weakly inflammogenic. In summary, inhalation exposure especially to certain fibrous nanomaterials seems to cause strong pulmonary inflammation. This may put exposed individuals at risk of developing lung diseases. In addition to the material of the nanoparticle, two important factors in risk evaluation are the shape of the particle and the possible modification made (e.g. coating) to the particle. The model of allergic asthma demonstrated that an underlying inflammatory condition can greatly affect the inflammatory outcome seen after nanoparticle exposure. The results of this thesis help to understand the underlying mechanisms in nanoparticle induced pulmonary inflammation.
  • Oikkonen, Jaana (Helsingin yliopisto, 2016)
    Most people have the capacity for music perception and production, but the degree of music competency varies between individuals. In this thesis, I studied abilities to identify pitch, tone duration and sound patterns with Karma s test for auditory structuring (KMT), and Seashore s tests for time (ST) and pitch (SP). These abilities can be considered as basic components of musicality. Additionally, I studied self-reported musical activities, especially composing and arranging. Musical ability is a diverse phenotype that includes both acquired and innate abilities. Earlier studies have shown that genetic component affects musical traits; here, heritability was estimated as 21-68%. Genetic predisposition of musical abilities was studied in family material (N=915) using linkage and linkage disequilibrium analyses. The best association for musical aptitude (KMT, SP and ST) was obtained at 3q21.3 near GATA2 and the best linkage at 4p14 adjacent to PCDH7. For musically experienced individuals without creative activity in music, linkage was found at 18q21. Interestingly, regions near 4q22.1 and 16p12.3 were linked with multiple musical traits. The genes within the resulting regions showed enrichment of inner ear development, schizophrenia and the long-term depression pathway, which is a molecular pathway important in learning and memory. Using three selection signature methods, FST, haploPS and XP-EHH, over 100 candidate genomic regions were detected to be under positive selection in individuals with high music test scores in the music tests. Enrichment analysis pointed to the development of the inner ear, corresponding to the enrichment results from the musical aptitude linkage analysis, even though there were no common regions between these two studies. The fourth part of this thesis integrates our musical ability gene mapping results with other music-related studies, including also animal model studies. A convergent genomics approach ranked EGR1, cortisol, FOS and FOXP2 as the most prominent molecules that affect musical abilities. The best 40 genes showed enrichment of cognition. Previous studies have shown that musical abilities share a common background with cognitive abilities, such as intelligence, and this study is the first to suggest the associated molecules. In conclusion, with these studies, I suggest many new genes and pathways to be associated with musical traits. The genetic predisposition for music is affected by a large number of genes of which only a few have been identified. Musical abilities were linked to multiple different chromosomes of which the 4q22 region is especially interesting. We made a literary survey combining information of molecules related to musical traits that can be used to evaluate genomics results in the future.
  • Vaahtera, Lauri (Helsingin yliopisto, 2016)
    The air pollutant ozone (O3) enters plant leaves through stomata and activates apolastic reactive oxygen species (ROS) signaling. Depending on growth conditions and genotype, this results in large transcriptional reprogramming,closure of stomatal pores and activation of cell death programs. These responses are also regulated through plant stress hormones. This thesis sheds light on how stress hormone signaling is connected with apoplastic ROS signaling in the model plant Arabidopsis thaliana, and investigates regulatory mechanisms which generate specificity among sequence-specific transcription factors (TFs), the executers of apoplastic ROS -induced transcriptional reprogramming. The essential methods of the thesis include O3 exposures of Arabidopsis wild type and mutant plants followed by quantification of cell death and characterization of transcriptional responses supplemented with several protein-level analyses of selected WRKY family TFs. The O3-induced cell death was found to be inhibited by plant hormone salicylic acid, and genes RESPIRATORY BURST OXIDASE HOMOLOG F (RBOHF) and WRKY70 were found to be required for O3-induced cell death in jasmonic acid insensitive genetic background. Even though stress hormones were verified to play important roles in the regulation of cell death, the transcriptional response to apoplastic ROS in a hormone deficient/insensitive mutant was highly similar to wild type, suggesting that much of the signaling involved is independent of the studied hormones jasmonic acid, salicylic acid, and ethylene. The potential major executers of transcriptional response to apoplastic ROS, WRKY family TFs, were studied for their transcriptional regulation, DNA-binding preferences, protein-protein interactions, subcellular localization, and effects on transcriptome. The results showed that the DNA-binding preferences of WRKYs vary substantially between phylogenetic groups, implying that the specificity in signaling between different WRKYs can be partly achieved through DNA binding preferences. Transcriptomic analyses of mutants with altered expression levels of the strongly ROS-inducible WRKY75 implicate this TF as a positive regulator of well-known pathogen-responsive genes, such as PATHOGENESIS-RELATED GENE 1 (PR1) and PATHOGENESIS-RELATED GENE 2 (PR2), and as a negative regulator of several hormone signaling pathways and TFs.
  • Aarnos, Hanna (Helsingin yliopisto, 2016)
    As dissolved organic matter (DOM) constitutes a vast reservoir of carbon and nutrients in lakes, rivers and ocean, it plays an important role in the global carbon and nutrient cycles. Only a part of DOM is directly biologically utilizable by bacteria, but solar radiation induced photochemical reactions may mineralize DOM to inorganic forms such as dissolved inorganic carbon (DIC) and ammonium (NH4+), and also degrade non-labile DOM molecules to labile organic substrates available for bacteria. This dissertation examined the photochemical transformation of DOM in the surface water in different scales of aquatic environments; from a Finnish boreal lake and the Baltic Sea to the coastal areas of ten globally big rivers. This dissertation studied photochemical reactions such as photoproduction of DIC, NH4+, and labile substrates supporting bacterial growth, and determined the photoreactivity of DOM, i.e., apparent quantum yields for the photoreactions in each environment. To consider the relevance of photochemistry of DOM, an optical model was used to quantify the photoreaction rates taking into account for the determined photoreactivity of DOM and solar radiation incidental to each environment studied. In the Baltic Sea, the pelagic heterotrophic bacterioplankton was carbon-limited indicating low bioavailability of DOM in the surface water. Irradiations of the waters with natural or simulated solar light resulted in photobleaching of chromophoric dissolved organic matter (CDOM) and phototransformation of DOM to DIC and NH4+ as well as to labile DOM substrates. This dissertation showed that across the entire Baltic Sea, the annual photoproduction of NH4+ corresponded to 9 18% of the annual river loading of DON, but the photoproduction of DIC exceeded the annual river loading of photoreactive terrigenous DOC. Furthermore, the studies along the salinity transects indicated that terrigenous DOC was more photoreactive than marine DOC but the marine DON was more reactive than terrigenous DON. The photoproduced labile substrates supported bacterial production and biomass leading to a 3-level trophic transfer of non-labile DOM and a simultaneous stimulation of autotrophic algae and primary production. The annual amount of photostimulated bacterial biomass corresponded to 3 5% of total bacterial biomass across the entire Baltic Sea. In the Baltic Sea as well as in the mesohumic lake studied, the photolytic water layer was shallow and limited the phototransformation of DOM to the top 30 cm. In the global scale, the annual DIC photoproduction from terrigenous CDOM in front of the ten rivers studied (12.5 ± 2.1 Tg C y-1) corresponded to 18 ± 4% of annual flux of terrigenous DOC of the rivers. When extrapolated to a global estimate, 44.5 ± 10.6 Tg of terrigenous DOC was annually mineralized to DIC by solar radiation in coastal waters. Globally, the amount of photomineralization of terrigenous DOC was larger in coastal ocean than in lakes and reservoirs. However, the areal rates of DIC photoproduction were larger in the lakes and reservoirs than in the coastal waters indicating that phototransformation of terrigenous DOC was likely limited by relatively short residence times in inland waters. To conclude, the phototransformation in coastal waters formed the final sink for riverine terrigenous CDOM and DOC, but was restricted in general, to a few hundred kilometres from river mouths to the ocean with the exception of largest discharging rivers.
  • Puntila, Riikka (Helsingin yliopisto, 2016)
    Translocation of non-indigenous species is a global threat to the structure and functioning of coastal ecosystems. Coastal ecosystems and estuaries are particularly prone for invasions due to impacts from a variety of anthropogenic stressors and frequent propagule pressure, notably from shipping. In addition, species poor environments, especially when already impacted by multiple anthropogenic stressors, such as the Baltic Sea, are thought to be particularly susceptible to invasions. In the Baltic Sea, to date more than 130 non-indigenous species have been reported and about 80 have been able to become established. Few have become invasive, spreading rapidly and/or begun to impact the native ecosystem. In this thesis the aim was to study how invasive benthic non-indigenous species, specifically the Harris mud crab (Rhithropanopeus harrisii) and round goby (Neogobius melanostomus) have settled in their new environment, how they have affected the ecosystem and how this information of the species can in future be used in management practices (e.g., risk assessments) in the Baltic Sea. The results show that the interactions between the two non-indigenous species and the environment are highly complex and may involve both generic and strictly context-specific components. The native predators and parasites in the area have begun to exploit the new species, although they are currently unable to control the growing mud crab and round goby populations. Furthermore, the FISK (Fish Invasiveness Scoring Kit) risk assessment exercise for the southern coastal areas of Finland showed that many non-indigenous fish species, some of which have already established, do have potential for becoming pests in the area. However, the continuously changing environment (incl. due to climate change) modi- fies both the non-indigenous and invasive biota in the area as well as may alter the nature and magnitude of ecosystem changes caused by the non-indigenous species. The infor- mation gathered in the thesis can be used in further risk assessments and aiding future management decisions.
  • Kylväjä, Riikka (Helsingin yliopisto, 2016)
    For understanding the interaction between bacteria and the host, it is essential to identify and characterize bacterial adhesive proteins, adhesins, and other bacterial molecules that interact or interfere with the host. Adhesins mediate the initial colonization steps of bacteria. The colonization may lead to infection or commensalism. When the molecular mechanisms are known, new treatments to prevent the infections can more easily be designed. For assessment of the functions of bacterial proteins in vitro, the proteins are usually purified from the cells or displayed on the surface of a heterologous host. Various surface display techniques, such as phage or fimbria-assisted display, have been developed for the analysis of polypeptides complicated to overproduce by conventional expression methods. Secretion of recombinant proteins to the culture medium of E. coli is an appealing approach since the purifying step is simple. However, reports on high-level extracellular protein secretion in bacteria are scarce. In the first part of this study, a random chromosomal library of Staphylococcus aureus was created in the secretion-competent E. coli strain MKS12. S. aureus expresses several adhesins, some of which are well characterized. Here, we wanted to identify possible new adhesins or proteins with novel functions. All the extracellularly secreted staphylococcal polypeptides of this study were tested for binding to some well-known receptors of S. aureus such as fibronectin, fibrinogen, collagens, and plasminogen. We found three putative moonlighting proteins i.e. proteins with functions additional to their conventional functions: a universal stress protein and an ATPase subunit of phosphoribosylaminoimidazole carboxylase, which both bound to fibronectin and fibrinogen, and the penicillin binding protein 3 capable of binding and activating plasminogen. Adhesins have been studied at the molecular level in many human pathogenic bacteria, such as S. aureus, but the knowledge on the surface molecules mediating adhesion of commensals, such as Lactobacillus, has not drawn as much attention. The second part of this study dealt with the interaction of Lactobacillus crispatus ST1 with the epithelium of the chicken crop and the human vagina. We investigated the molecular mechanisms underlying the interaction of L. crispatus ST1 with the epithelium and identified a novel high-molecular-mass adhesin that was named as lactobacillus epithelium adhesin (LEA). LEA was shown to bind efficiently to the stratified squamous epithelium of the crop and to the similar type of epithelium in the human vagina. In this thesis work we have applied a novel secretion method for heterologous protein expression and characterized novel adhesive proteins of two Gram-positive bacterial species.
  • Laitinen, Anita (Helsingin yliopisto, 2016)
    Mesenchymal stem/stromal cells (MSCs) are multipotent cells that can be found in various tissues. These cells have the capacity to differentiate into bone, adipose, and cartilage. They also have the capacity to suppress immune reactions and the capacity to support angiogenesis. The utilization of these cells in cell based therapies has therefore been intensively studied. There are several clinical studies on going to demonstrate the therapeutic potential of these cells. The utilization of MSCs has been studied in for example graft-versus-host-disease (a severe complication after hematopoietic stem cell transplantation), stroke, myocardial infarction, and cartilage lesions. The frequency of MSCs is variable in different tissues. The number of these cells in tissues is so low that these cells need to be cultured outside of the body, in vitro, to obtain adequate numbers of MSCs for cell therapy purposes. It has been demonstrated that different in vitro culture conditions have effects on the properties of MSCs. Traditionally cells are cultured in growth medium containing fetal bovine serum (FBS). There is a great interest to find alternative supplements to replace FBS for clinical grade production of MSCs to avoid the patients to become predisposed to xenogenic infectious agents or antigens. Platelet-derived supplements might be one potential alternative for FBS. An efficient method to culture MSCs from cord blood was established in this thesis. Additionally a method to produce clinical-grade bone marrow MSCs in platelet-derived supplement containing culture medium was established. Different culture conditions were demonstrated to have an effect on proliferative and immunosuppressive capacity of MSCs as well as on their capacity to support angiogenesis. In this thesis it is also indicated that MSCs can suppress immunoreactions producing an immunosuppressive molecule, adenosine, via a cell surface enzyme, CD73. The knowledge of the impact of culture conditions on the properties of cells as well as understanding the functional mechanisms of the cells is a prerequisite to produce safe and efficacious cell therapy products.
  • Kumar, Anmol (Helsingin yliopisto, 2014)
    Neurotrophic factors such as brain¬-derived neurotrophic factor (BDNF) and glial cell line¬¬¬-derived neurotrophic factor (GDNF) are a family of proteins which play an important role inside and outside central nervous system. While precise regulation of BDNF and GDNF levels in time and space in an organism is crucial in determining the biological outcome, mechanisms involved in controlling their levels are not fully understood. Messenger RNAs (mRNAs) play a critical role in gene expression by conveying genetic information from DNA to protein synthesis. 3ʹ untranslated region (3ʹUTR) is a part of mRNA sequence which regulates gene expression by binding to microRNAs (miRs), RNA-binding proteins (RBPs) and other trans-acting factors. In this thesis, we investigated the 3ʹUTR mediated regulation of BDNF and GDNF. We demonstrate the presence of regulatory elements in the 3ʹUTR of BDNF and GDNF and, show that BDNF is regulated by four different miRs, namely miR-1, miR-10b, miR-155 and miR-191 and, RBP tristetraprolin (TTP) in different cell lines. Further, we show that GDNF is regulated by multiple miRs in cell lines and identify binding sites for miR-146a and miR-96 in the GDNF 3ʹUTR. Finally, we demonstrate that replacement of GDNF 3ʹUTR in mice with a 3ʹUTR with reduced responsiveness to negative regulators including miRs leads to elevated level of endogenous GDNF mRNA and protein in various organs with profound biological effects including in the brain dopamine system function in mice. We conclude that 3ʹUTR mediated regulation of BDNF and GDNF is biologically important and propose that 3ʹUTR replacement is an informative way to study gene function in vivo.
  • Magalhães, Ana Cathia Dias (Helsingin yliopisto, 2016)
    The time of arrival of interneurons and oligodendrocytes to the neocortex is critical for proper functional brain development. Aberrances in this sequence can be detrimental, and involved in different developmental diseases. Thus, understanding the mechanisms for temporal control of the genesis and migration of neural cells is crucial. The aim of this study was to focus on the ventral telencephalon, a major source of interneurons and oligodendrocytes, in more detail. A more sensitive method was developed for detecting and quantifying oligodendrocyte precursor cells, e.g. Olig2. The device decloaking chamber was compared to the microwave oven-based heat-induced epitope retrieval (HIER) method by studying the labeling of Olig2 marker in paraffin-embedded sections from embryonic mouse brain. The results demonstrated that the decloaking chamber-based HIER method is the most suitable technique for the detection of single Olig2-labeled cells in the ventral telencephalon. This qualitative result was reflected in the quantitative analyses: more Olig2-labeled cells were quantifiable with the decloaking chamber- than with the microwave oven-approach. Thus, the decloaking chamber-based HIER method constitutes a sensitive technique for the detection of oligodendrocyte precursor cells, and therefore for its quantification in the developing ventral telencephalon. The development of telencephalon depends on fundamental processes, which include proliferation and migration of neural cells. The Na-K-Cl cotransporter isoform 1 (NKCC1) is an important protein for the process of volume regulation, and has been implicated in cell division. Within the developing brain, the ventral telencephalon showed the highest expression of NKCC1. This expression corresponded to neural progenitor cells in the lateral ganglionic eminence (LGE). Using NKCC1 knockout mice, it was demonstrated that NKCC1 influenced cell cycle reentry. Consequently, mice lacking NKCC1 have impaired Sp8-expressing interneurons and Olig2-labeled cells. Thus, NKCC1 is crucial in vivo for cell cycle decision, thereby altering the production of oligodendrocyte and interneuron progenitor cells in the LGE. Once interneurons are born, they migrate to the neocortex. The implication of syndecan-3 was assessed in their tangential migration. The results showed that the Glial cell line-derived neurotrophic factor GDNF interacts with syndecan-3 to promote the tangential migration of calbindin-expressing interneurons within the telencephalon. Consistently, mice lacking syndecan-3 have an accumulation of migrating interneurons in the LGE. In summary, two important mechanisms were found for temporal and spatial control of cortical oligodendrocytes and interneurons.