Bio- ja ympäristötieteellinen tiedekunta

 

Recent Submissions

  • Yan, Lijuan (Helsingin yliopisto, 2016)
    Soil pollution by petroleum hydrocarbons (PHCs) as a result of anthropogenic activities poses significant threats in the environment. In particular, used motor oil that contains high concentrations of aliphatics, polycyclic aromatic hydrocarbons (PAHs) and heavy metals (e.g. lead, zinc, chromium, barium and arsenic) contribute to chronic hazards including carcinogenicity. Microorganisms are able to degrade and utilize many recalcitrant compounds as carbon and energy sources in a natural attenuation process. However, in boreal regions this process is limited by the cool climate. The main goal of most bioremediation designs should be an optimization of environmental conditions for microbial growth and metabolic activities. Plant growth can stimulate the activities of soil microflora in the rhizosphere, thus enhancing the bioremediation of oil-polluted soil. Nitrogen deficiency is a frequent limiting factor of biomediation in oil-contaminated soils. Legumes that form symbiotic association with N-fixing bacteria are able to assist the biodegradation of PHCs. The planting of oil-tolerant perennial crops, especially legumes, in oil-contaminated soil holds promise for great economic benefits for bioenergy production while accelerating the oil degradation process. Fodder galega (Galega orientalis Lam.), a perennial forage legume, and smooth brome (Bromus inermis L.), a cool-season perennial sod-forming grass, are both persistent in boreal zones and have been shown to grow well together in crop mixtures without N-fertilizer supply. The oil tolerance and oil-rhizoremediation potential of G. orientalis and its microsymbiont Neorhizobium galegae have been demonstrated at microcosm and mesocosm scales. Plant growth promoting bacteria (PGPB) have potential to increase nodulation of galega, mitigate plant stress response and increase the bioavailability of soil contaminants, therefore enhancing the degradation of contaminants. These components can form a powerful combination to be used for bioremediation of oil-contaminated soil. However, the competitiveness and effectiveness of the crop- and PGPB-assisted bioremediation system need to be evaluated in field conditions. To date, there were no systematically described studies on bioremediation of oil-contaminated soil combined with crop biomass production in boreal regions. This multidisciplinary research project was conducted to fill this knowledge gap by evaluating the sustainability of the legume-cropping bioremediation system economically in terms of crop yield, and environmentally in terms of oil degradation rate and the dynamics of bacterial communities. To reach these aims, we established a multi-year bioremediation field experiment at the Viikki Experimental Farm, University of Helsinki, Finland (60°14'N, 25°01'E, 8 m AMSL) with crop treatments (brome grass, fodder galega, their mixture and bare fallow) as the main plots in four replicated blocks, and used motor oil treatments (7000 ppm +/-) and PGPB (+/-) treatments as the sub-plot factors. Soil samples were taken from the top 20 cm layer at six time points (July 2009, May 2010, November 2010, May 2011, May 2012 and October 2012). Soil chemical properties e.g. pH, electrical conductivity (EC), total C, total N and C:N ratio of three sample sets (July 2009, November 2010 and May 2012) were measured. Oil concentration was determined based on the difference of total solvent extractable material (TSEM) concentration between the oil-spiked plot and the average of control plots at each sampling time using the gravimetrical method. Crop physiological properties e.g. annual DM yield, total C, total N, C: N ratio, chlorophyll and BNF of the legume were measured. Soil-borne bacterial communities were investigated using i) LH-PCR community fingerprinting technique (all samples) and ii) Illumina s MiSeq sequencing (spring-summer samples). Oil contamination had a significant impact on soil chemical properties, e.g. pH, EC, total C and C:N ratio. The oil degradation was incomplete 40 months after the oil spike, with a dissipation of 73% - 92% of oil concentration (Paper I). As the field soil condition was good for oil degradation, the advantage of using crops to assist oil degradation was not evident. The oil degradation followed firstorder kinetics with the reduction rates decreasing as follows: bare fallow > galega-brome grass mixture > brome grass > galega. Oil, surprisingly, increased crop dry matter and nitrogen yield, particularly in the fourth year (Paper I). The legume-grass mixture produced significantly higher crop dry biomass than the pure stands. For instance, the unfertilized galega-brome grass mixture out-yielded the Nfertilized pure grass swards over years by an average of 32% (Paper I), suggesting that the inoculated galega could fully replace N-fertilizer for brome grass. PGPB enhanced the efficiency of biological nitrogen fixation of the legume, especially in legume-grass mixture plots (Paper I). The LH-PCR community fingerprinting technique produced similar results as the 16S rRNA gene amplicon sequencing. Both time and oil contamination were the main drivers of bacterial community dynamics (Papers II and III). The effect of oil was initially negative on overall bacterial diversity (Papers II and III), but variable on the diversity of bacterial sub-communities (Paper III). The bacterial communities responded quickly to oil contamination, but the effect of oil on community composition was recoverable over time (Papers II and III). Crop cultivation had a small impact on the composition of bacterial community (Paper III). The oil-favored taxa that discriminated bacterial communities between oil-contaminated and non-contaminated soils were mainly assigned to the two prevalent phyla Actinobacteria and Proteobacteria (Paper III). The operational taxonomic units (OTUs) with significantly different oil-specific abundance changes over time were all favored by oil; therefore, these oil-specific taxa were suggested as suitable bio-indicators to monitor the ecological impact of oil contamination (Paper III). Besides oil concentration, the changes in soil chemical properties, e.g. soil pH and EC, significantly affected bacterial community structure (Paper II and III). To summarize, oil contamination affected soil chemical and biological properties (e.g. crop growth and bacterial community), but the impact of oil decreased with time. The cultivation of oil-tolerant perennial crops, especially galega-brome grass mixture, in oil-contaminated soil can hopefully produce considerable biomass for bioenergy industry. Bacterial communities underwent a significant time- and season-dependent succession, regardless of oil contamination. Therefore, studies restricted to a single snapshot of time without any non-contaminated samples as reference cannot reveal oil contaminationrelated changes in the dynamic patterns of bacterial communities in the field soil. With the development and decreasing cost of high-throughput sequencing (NGS), NGS-based metagenomics analysis has become the mainstream method in microbial ecology research, providing in-depth view on bacterial populations at different taxonomic levels in the community. However, the LH-PCR technique is still suggested as a cost-effective method to monitor microbial community dynamics for assessing the ecological impact of oil contamination. Oil degradation was rather slow in the boreal climate. Long-term stimulation and monitoring of soil chemical properties, oil concentration, crop growth and microbial community are still needed for risk control. All these suggestions can be applied to soil contaminated by PHC contaminants other than used motor oil, despite hydrocarbon compositional differences.
  • Tynell, Janne (Helsingin yliopisto, 2016)
    Respiratory virus infections are a major cause of morbidity and mortality worldwide. Decades of research have yielded many breakthroughs in our understanding of virus-host interactions, but many aspects of viral pathogenesis still remain unresolved. Vaccines and antiviral treatments have been developed, but they are imperfect or completely lacking for many viral agents. Novel emerging viruses form an additional challenge, which can only be overcome by proper preparation and quick response against these unexpected infectious threats. Understanding virus-host interactions is critical for elucidating aspects of viral pathogenesis and devising better treatment strategies against viral pathogens. Our research has focused on the virus-host interactions of two major respiratory pathogens with a recent history of outbreaks by a novel viral agent, the influenza A virus and coronavirus. Influenza A virus has plagued humankind throughout human history and continues to cause annual epidemics and occasional pandemics associated with significant mortality. NS1 protein is one of the major virulence factors of influenza A virus. It has a multitude of different interactions with host cell components that either aid viral replication or hamper the antiviral response exhibited by the host cell. These interactions are located both in the host cell nucleus and the cytoplasm, and three signals regulating the intracellular localization of NS1 protein have been identified. While the critical impact of nuclear localization signal 1 is well known, the other two localization signals have remained poorly characterized. In this work we provide a detailed description of the NS1 nuclear export signal (NES), showing that the NES region is well conserved within different influenza A strains and that certain mutations within the region cause attenuation of virus replication. Through the use of different mutant viruses, we show that the attenuated phenotype is not due to impaired localization alone, but rather involves defects in the functions of NS1. We also show that NS1 is not exported through the classical CRM1-dependent pathway and we establish the nucleolar proteins that bind NS1 and thus guide its nucleolar localization. Human coronaviruses are a major cause of the common cold. For a long time coronaviruses were thought to cause only mild upper respiratory tract infections in humans. However, this view changed with the emergence of the highly lethal SARS coronavirus in 2002 and the identification of MERS coronavirus in 2012. While the SARS outbreak was efficiently contained, MERS coronavirus continues to circulate in camels and causes repeated introductions into the human population in the Middle East. Our MERS coronavirus research concentrated on characterizing MERS infection of human macrophages and dendritic cells, two important cell types of the innate immune system. We show that MERS coronavirus does not replicate productively in these leucocytes, but a significant innate immune response is generated. Altogether this work identifies important aspects of virus-host interaction of two important respiratory pathogens. We provide new information on the mechanisms and impact of influenza A virus NS1 intracellular localization and we characterize MERS coronavirus infection in primary human leucocytes as well as highlight important differences in the host cell responses between MERS and SARS coronaviruses.
  • Wong, Swee Chong (Helsingin yliopisto, 2016)
    In the past decade, advances in next generation sequencing (NGS) and genotyping technology have enabled merging of genetic analyses in ecological field studies of natural populations. The development of transcriptome sequencing such as RNA-seq provides a golden opportunity for researchers studying non-model organisms. In the design of genetic analyses in the context of ecological studies, genetic relationships among individuals are often overlooked, especially when sampling wild populations. In ecological studies, studies of e.g., life-history traits, environmental and ecological factors are often the main issues of interest, and genetic analyses remain a secondary consideration. Samples from ecological studies often represent different types, such as inbred samples, samples with complex family structure, and samples with unknown relationships. These distinctly different experimental setups present a challenge for genetic association studies, as the underlying relationships among samples could affect allele frequency distributions in populations, leading to spurious associations. The primary aim of this thesis is to devise protocols for quantitative genetic studies of samples from experimental designs intended for ecological studies, using a non-model organism, the Glanville fritillary butterfly, as the study species. Strategies and methods were implemented to discover potential genetic factors affecting trait variation in the Glanville fritillary. Interactions between the organism and the environment, such as effects of temperature on flight metabolic rate, on phenotypic plasticity and on larval development were studied. All samples were obtained from a large metapopulation of the Glanville fritillary in the Åland Islands in Finland. Flight metabolic rate, life history, female reproductive traits, and phenotypic plasticity were measured in family-based material, while the study of larval development was implemented using a population-based model. Problems tied to to relatedness of samples in each experimental setting were addressed with various strategies. The key findings of this thesis include discovery of a novel association between a SNP in the sex chromosomal gene triosephosphase isomerase and flight metabolic rate in females. This discovery was confirmed with one additional material: a dataset with 16 population samples. This gene is potentially another candidate gene in regulating the complex flight metabolic pathway. An interaction between temperature treatment preceding flight activity and SNP genotypes in the phosphoglucose isomerase gene was found to influence flight metabolic rate. Individuals with the genotype AC performed better when treated with low temperature, but individuals with genotype AA showed superior performance in high temperature treatments. Moreover, in another experiment, individuals with the AA genotype were more tolerable to heat shock than the AC individuals. Three SNPs in the cytochrome P450 337 gene were associated with the total number of eggs and caterpillars produced by females in their life-time. Further sequencing showed that regions prior to the coding region displayed similar association pattern with the three candidate SNPs, suggesting that causal variants might be located in the 5 regulatory region. Finally, SNPs from the vitellin-degrading protease precursor were associated with the incidence of the extra eighth larval instar (a development stage of insects), though the result was not significant after adjusting for multiple testing. This work contributes to developing procedures for samples originating from ecological studies and which might have sub-optimal experimental design for genetic analyses. Rigorous steps such as relatedness control, confidence interval calculation, and genetic power estimation were performed in this thesis to help interpret results from different chapters. The thesis shows that sound protocols can be developed to address problematic issues related to relationships among the samples.
  • Valo, Satu (Helsingin yliopisto, 2016)
    Lifestyle and diet have a major effect on the development of colorectal cancer (CRC). Dietary habits of Western populations in particular are recognized as a risk factor for CRC. However, the mechanisms that mediate the effects of Western-style diet (WD) on colorectal tumor development are largely unknown. CRC develops via multiple steps which involve genetic changes, such as mutations in growth-regulatory genes, and epigenetic alterations, such as CpG island hypermethylation. Lynch syndrome (LS) is one of the most common inherited cancer susceptibility syndromes. It is caused by inherited defects of the DNA mismatch repair genes (MMR), which together with other genetic and epigenetic changes are known to accelerate tumorigenesis. MMR defects are known to accelerate tumor progression in LS but the early events leading to polyp formation and the timing and order of the molecular hits remain unknown. A long-term feeding experiment with mouse models for LS and sporadic CRC was conducted to characterize tumor-promoting changes in normal colonic mucosa caused by WD and/or genetic predisposition. Changes in the proteome of histologically normal colonic mucosa were monitored at different time points of feeding experiment (5 weeks, 12, 18 and 21 months) with two high-throughput proteomic methods followed by analysis of affected pathways. Data from proteomic analysis indicated that the proteome was more consistently changed by diet and aging than by genotype. Overall, 21 out of 26 colonic tumors were detected in mice fed with WD. Proteomic analysis indicated disrupted lipid metabolism and increased oxidative stress in the normal-appearing tissue in association with WD. Moreover, proteome analyses revealed increased cell proliferation and decreased apoptotic processes in the normal colon mucosa of mice fed with WD, which may promote colorectal tumorigenesis. Finally, proteomic data coupled with measurement of bile acids in tissue specimens indicated that WD induces downregulation of intracellular bile acid transport, resulting in disrupted bile acid homeostasis which may provide a possible mechanism underlying the tumor-promoting effects of the diet. Studies on sporadic CRC have demonstrated that promoter hypermethylation leading to gene silencing can act as an alternative mechanism to mutations in early stages of tumor development but its importance in hereditary CRC remains unknown. We analyzed tissue specimens gathered during colonoscopy surveillances and colectomies performed on human LS mutation carriers to define changes in CpG island methylation that occur at different stages of the tumor progression sequence. Methylation changes at different stages of tumor progression were analyzed in relation to MMR gene expression, and normal tissue biopsies were studied for carcinogenic fields . In addition, we aimed to clarify the role of CpG island hypermethylator phenotype (CIMP) in the LS-associated tumorigenesis. Results indicate that the expression of the MMR protein corresponding to the gene mutated in the germline decreases along with dysplasia but occurs as a relatively late event in the tumor progression sequence, suggesting the presence of other somatic events that drive neoplastic transformation. Indeed, significant increase in the average degree of methylation of two candidate genes (SFRP1 and SLC5A8) was observed in normal colonic mucosa biopsies from patients with CRC (high-risk mucosa) when compared to those without (low-risk mucosa), indicating a possible carcinogenic field. Moreover, methylation was found to increase in LS adenomas and carcinomas along with dysplasia. These findings emphasize the importance and early appearance of epigenetic alterations in LS-associated tumorigenesis. In summary, the results offer new insights into the initiating molecular mechanisms through which Western-style diet and DNA methylation contribute to hereditary and sporadic colorectal carcinogenesis.
  • Ozan, Martina (Helsingin yliopisto, 2016)
    Individuals opt to breed cooperatively to increase their chances of successful propagation when resources are scarce or unpredictable. Yet, these same individuals are not genetically identical and come into conflict over limited resources they are to utilize for own reproduction. In spite of the predicted reproductive conflicts, many species, notably social insects, have evolved to become obligate cooperative breeders unable to propagate solitarily. So how do individuals share reproduction? In social insects, reproduction and work is divided among the society members i.e. the queen(s) and workers. The evolution of a non-reproductive caste - workers, can be explained by kin selection theory, which holds that individuals gain fitness indirectly by helping their kin queen, to reproduce. In many species of ants, however, colonies permanently contain multiple reproductive queens (polygyny). Queens compete for limited colony resources, which may lead to a conflict over personal reproduction and unequal reproductive shares. The reproduction by several queens also dilutes within-colony relatedness, which comes at a cost to worker indirect fitness. Hence, underneath the exemplary cooperation among colony individuals, both queens and workers, are predicted to act to enhance their own inclusive fitness. The aim of my dissertation was to disentangle mechanisms underlying reproductive partitioning in a polygynous black ant, Formica fusca, within the framework of kin selection theory. I examined queen traits that likely impact queen fitness including timing of oviposition, queen presence during brood rearing, her fecundity, and viability and size of queen offspring, along with the underlying chemical communication, as well as workers ability to utilize and exploit the available information to manipulate queen reproduction to own fitness advantage. My thesis has revealed that both, queens and workers, have the means and ability to influence the outcome of reproductive competition by actively utilizing chemical cues present on ant cuticle to pursue selfish actions. At the same time, the results suggest that passive feedback mechanism between the queen reproductive output and worker behaviour, nevertheless, ensures alignment of fitness interests between both parties. Overall, my dissertation highlights that complex within-group interactions govern the reproductive partitioning in social insects and contributes to better understanding of how reproductive conflicts are resolved to ensure peaceful coexistence.
  • El-Showk, Sedeer (Helsingin yliopisto, 2016)
    The evolution of vascular tissues was a critical innovation in the colonization of land by plants. We investigated how vascular tissues, in particular xylem, are patterned in the root of the model plant Arabidopsis. The vascular tissues of the Arabidopsis root tip are consistently patterned as a xylem axis flanked by procambial cells, with phloem poles developing perpendicular to the xylem axis. Cytokinin signalling inhibits the specification of protoxylem; the AHP6 gene inhibits cytokinin signalling at the protoxylem position during normal vascular development. We sought to understand the factors regulating AHP6 expression in the root tip. Cytokinin signalling is known to flank the xylem axis; we discovered a complementary domain of auxin signalling throughout the xylem axis. Based on this, we showed that auxin upregulates AHP6, creating a domain of low cytokinin signalling, and also acts to specify protoxylem. We used a combination of mutants and pharmacological treatments to investigate how mutually exclusive auxin and cytokinin signalling domains are maintained in the Arabidopsis stele. We discovered a feedback loop between the hormones, in which cytokinin activates auxin exporters, while auxin represses cytokinin signalling. The mutual inhibition between auxin and cytokinin regulates the extent of their domains during vascular patterning. We turned to computational simulations to investigate the sufficiency, stability, and dynamics of this network. Our simulations confirmed that the network is sufficient to maintain the hormone domains during vascular patterning, but also revealed a role for auxin importers, which we confirmed through experiments. While cytokinin is frequently thought to form gradients guiding developmental processes in the Arabidopsis shoot and root, we showed that an informative cytokinin gradient cannot form on the scale of these tissues via diffusion. While auxin is patterned through the activity of polarly localised transporters, there is no evidence for similar transport of cytokinin. Nevertheless, our findings highlight the need for a cytokinin patterning mechanism, such as directed cytokinin transport or patterning of the cytokinin perception machinery, since diffusion cannot form the observed cytokinin patterns. Finally, we discovered a potential link between the auxin-cytokinin feedback loop in the root tip and the initiation of lateral roots. Since our experimental data are equivocal on whether or not PIN1 is polarly localised in the procambium, we investigated both possibilities in our computational model. We discovered that polar localisation of PIN1 results in a regular flux of auxin towards the centre of the stele and back out via the xylem axis. This circuit privileges pericycle cells flanking the xylem axis to accumulate auxin if they experience a brief activation of an auxin importer; activation of the importer AUX1 in the xylem-pole pericycle cells is one of the earliest steps in lateral root initiation. Altogether, my thesis reveals a key role for mutually inhibitory auxin-cytokinin interactions in vascular development and links these findings to other developmental contexts. This work also demonstrates how the combination of experimental & computational approaches enables us to critically evaluate our models and develop more general insights.
  • Kallio, Katri (Helsingin yliopisto, 2016)
    All positive-strand RNA viruses replicate their RNA genomes in close association with cellular membranes. A great variety of cellular membranes are utilized by different viruses and those membranes are extensively modified to support viral replication and to protect the viral RNA from host cell defense mechanisms. Alphaviruses, including Semliki Forest virus (SFV), are positive-strand RNA viruses replicating their RNA on membranes derived from endosomal and lysosomal compartments. SFV induces small invaginations called spherules on plasma membrane and on endosomal membranes. Viral replication complex assembly, spherule formation and initiation of replication are carefully orchestrated events and are guided by specific sequence elements within the genomic RNA as well as by important enzymatic activities of nonstructural proteins (nsPs). The aim of this research was to study in detail how alphavirus replication complexes are assembled and to define the minimum requirements for spherule formation by using a plasmid-derived transreplication system mimicking SFV replication. The role of the genomic RNA in replication was deciphered by using RNA templates, which were either modified or differed in length. Use of RNA templates differing in length clearly showed that they define the spherule diameter suggesting that the template has a significant role in spherule formation. By modifying or deleting specific sequences from the template it was shown that highly conserved RNA elements are important for SFV replication and do not tolerate modifications without compromising replication. Study with the nsPs of SFV showed that the enzymatic activities essential for virus replication are also needed for spherule formation and that enzymes like helicase, protease and polymerase are absolutely essential for replication. Membrane association of the replication complex is also required to establish virus replication in the cells. The work with mutated nonstructural proteins and modified templates revealed a clear correlation between the minus-strand synthesis and spherule formation. This work describes the alphavirus replication processes in detail and provides new principles, which may be generally applicable to study the positive-sense RNA virus replication and the formation of virus-induced membranous replication spherules.
  • Söderholm, Sandra (Helsingin yliopisto, 2016)
    Phosphorylation is one of the most important post-translational modifications of proteins. Phosphorylation is a rapid and reversible way of modifying proteins; it is involved in the regulation of many cellular processes, serving as the main transducer of intracellular signaling cascades. It is possible to identify thousands of protein phosphorylation sites from a single sample with mass spectrometry (MS)-based phosphoproteomics. This is the main reason why MS-based phosphoproteomics is such an excellent method for revealing global changes in phosphoproteomes. Computational analysis of the MS data is vital for identifying the proteins and post-translational modifications. The data analysis steps in the phosphoproteomics workflow are also crucial for biological interpretation, e.g. identifying activated kinases and kinase substrates, as well as unravelling signaling pathways and networks. Cells of the innate immune system are central players in the host defence against pathogens such as viruses. Their pattern-recognition receptors (PRRs) recognize pathogen-associated molecular patterns (PAMPs), which are conserved structures present in pathogens. The most important PAMPs in viral infections are the viral genomes and replication intermediates, and their detection evokes pro-inflammatory and antiviral responses in the infected cell. Host factors and signaling cascades that promote or inhibit virus infections can serve as potential drug targets. Since protein phosphorylation is vital for the progression of nearly all signaling cascades, there is an increasing interest in applying phosphoproteomics and combining it with bioinformatics in studying the regulation of cellular signaling under various conditions, including viral infections. The main aim of the studies included in this PhD thesis was to characterize the global changes in the cellular phosphoproteomes of virus infected and dsRNA stimulated innate immune cells, and to identify the host proteins and cell signaling pathways involved in the early stages of the host response to Sendai virus (SeV), influenza A virus (IAV), and viral dsRNA. A computational analysis tool, named PhosFox, was developed for processing and comparing MS-based phosphoproteomic data generated by multiple database search algorithms. PhosFox was used for cross-sample comparisons of phosphopeptide identifications. PhosFox also facilitated the identification of those proteins whose phosphorylation was different between samples, and the clarification of phosphorylation sites not described in the literature. The findings from the phosphoproteomic data were explored further by implementing functional studies involving small interfering RNAs (siRNAs) and kinase inhibitors. There were extensive alterations in the phosphorylation of proteins in human epithelial cells and macrophages that were transfected with the synthetic dsRNA-mimic polyinosinic:polycytidylic acid (pI:C) or infected with SeV or IAV. Many of these proteins were determined to be members of pathways with little or no previously known role in the antiviral response to these particular viruses and viral PAMPs. Two novel host factors, RelA-associated inhibitor (RAI) and sirtuin 1 (SIRT1), were identified as negative regulators of dsRNA-induced apoptosis and NF-κB regulated cytokine expression by combining 14-3-3 interactome and phosphoproteome characterizations. The p38 mitogen-activated protein kinase (MAPK) signaling pathway was found to be regulating cytokine expression and apoptosis in dsRNA-transfected human keratinocytes. MAPK signaling pathways were also regulated in SeV and IAV infected cells. The mTOR signaling pathway was shown to be critical for the interferon response and virus replication in SeV infected human lung epithelial cells. A substantial number of those cellular proteins whose phosphorylation status changed after SeV or IAV infection or viral dsRNA challenge were involved in Rho GTPase signaling. Major changes in protein phosphorylation in IAV infected primary human macrophages were linked to cyclin-dependent kinases (CDKs). CDK activity was shown to be required for efficient viral replication and host response in IAV infection. Administration of one specific CDK inhibitor, SNS-032, also protected mice from IAV-induced death. The studies included in this PhD thesis are some of the first to apply phosphoproteomics for characterizing host-virus interactions. They emphazise the benefit of applying phosphoproteomics and bioinformatics in innate immunity and viral research, i.e. it is possible not only to identify cell signaling pathways, but also the specific host factors that regulate the cellular responses to viral infections. The results of these studies underline the importance and the potential MS-based phosphoproteomics has in the discovery of novel host factors, which can serve as possible antiviral drug targets. In conclusion, the MS-based phosphoproteomics approach led to the discovery of novel host factors and cell signaling circuits in virus infected innate immune cells.
  • Venesjärvi, Riikka (Helsingin yliopisto, 2016)
    Maritime transport is an efficient way to ferry goods, oil, and chemicals but shipping poses a threat to marine ecosystems. Oil spills have a potential to extinguish or debilitate fish and wildlife populations and habitat types important to the marine ecosystem. In this thesis, I study the resources and methods for collecting data and knowledge about the adverse impacts of oil on sensitive species and habitat types. Furthermore, I study how ecological knowledge could be passed to decision-makers and how the risks should be communicated. Finally, I discuss future policy improvements and scientific needs for ecological knowledge in oil spill risk management. This forms a synthesis of what kind of ecological information is required for the environmental risk management and conservation of marine ecosystems under oil spill threat. The thesis includes five papers, where we develop methods to assess the environmental impacts of oil spills and the effectiveness of management practices to mitigate their adverse ecological effects. Improved strategies combine theoretical disciplines, such as population biology with practical oil spill response. The results demonstrate that environmental risk assessment models can be used to structure problems, integrate knowledge and uncertainty, and persuade decision-makers by visualizing the results. Since the objective of risk assessment is to synthesize information for environmental management and policy design, which should rely on the extensive use of scientific evidence, communication between academia and decision-makers is of great importance. The use of Bayesian networks would improve the current oil spill risk management in the Baltic Sea, since all the variables affecting oil spill risk can be presented in one framework in a transparent manner. Many geospatial services work as tools of informative policy instruments, as they deliver ecological data and knowledge for oil spill risk management. Researchers could also participate more often in the contingency planning or practical management of oil spills as experts. Thus, all the relevant knowledge could be integrated into the decision-making process. This thesis offers new insights into oil spill risk management in the Baltic Sea and provides examples showing how evidence-based management actions should be chosen and carried out in order to minimize the risks. Policy recommendations are also provided. First, in oil spill risk management, the marine ecosystem should be prioritized based on its conservation value, recovery potential and protection effectiveness. Second, because preventive measures against oil accidents are considered cost-effective, maritime safety should be increased, with stricter and regional ship inspection practices. The effects of policy innovations should be assessed using probabilistic policy-support tools.
  • Eklund, Johanna (Helsingin yliopisto, 2016)
    Protected areas are a key tool for conserving biodiversity and an increase in their coverage has long been the aim of international conventions and initiatives. With progress to achieve target 11 of the Convention on Biological Diversity of protecting 17 % of terrestrial areas, the focus has now shifted towards assessing the protected area effectiveness in maintaining species or avoiding land conversions. In my doctoral thesis I develop a novel way of assessing PA effectiveness, based on the counterfactual thinking, and use this to link it to different management and ecological factors. I link different aspects of PA effectiveness conceptually to the quality of governance and show how spatial prioritizations can change with the inclusion of these socio-political factors. Using Madagascar as a case study, and in line with other studies elsewhere, I find that the protected area network is effective to some extent in mitigating the pressure of deforestation. I show the importance of considering the temporal dimension of protected area effectiveness measures and how protected area effectiveness changes over time due to increasing or decreasing pressures. These results link directly to considerations of vulnerability and irreplaceability in Systematic conservation planning and I show that accounting for governance factors in a global spatial prioritization analysis change the identification of areas. My thesis shows the relative nature of protected area effectiveness measures and how important it is to get the assessments right, especially because of the massive focus on protected area effectiveness as a panacea to stopping biodiversity declines. Improving protected area effectiveness needs to be linked to governance factors affecting not only the management but also the drivers of threat, something that previous studies have overlooked. With my thesis I make an attempt to bridge the themes of protected area effectiveness, considerations of quality of governance, and how it all links to conservation prioritizations. Our methodology has been developed with the aim to be computationally efficient and conceptually more robust than existing matching methods, with the potential to be scaled up for larger studies. However, how the two methods perform needs to be tested in the future. My dissertation has clear practical implications for the conservation of Madagascar s biodiversity and the results are of potential interest for both NGOs and the Madagascar National Park administration. The conceptual contribution of this thesis should be incorporated into mainstream thinking and the discourse of setting global priorities for biodiversity conservation, such as by the International Union for Conservation of Nature and Natural Resources (IUCN), the World Parks Congress (WPC) and ultimately the Convention on Biological Diversity (CBD).
  • Howlader, Mohammad Sajid Ali (Helsingin yliopisto, 2016)
    Amphibians are the most threatened class of vertebrates. About 48% of the known amphibian species are threatened by extinction, and many species still remain undescribed, especially from tropical and sub-tropical countries such as Bangladesh. In contrast to India and Sri Lanka, amphibian diversity in Bangladesh is poorly known, and little effort has been put towards documenting the species diversity and resolving evolutionary affinities among amphibian taxa in this country. Hence, the actual diversity of amphibians in Bangladesh remains unknown. The aim of this dissertation work was to improve our knowledge of amphibian diversity in Bangladesh by identifying and describing new amphibian species and investigating their evolutionary relationships with closely related taxa. I used morphological and molecular phylogenetic methods to identify and describe one new genus and five new species from different genera. In addition to using traditional morphological comparisons, I also utilized mitochondrial gene fragments to estimate phylogenetic affinities among the studied taxa, with Maximum-likelihood and Bayesian methods. The first two chapters of the thesis focus on the amphibian genera Fejervarya and Zakerana, the latter which was previously embedded within Fejervarya. These chapters also include descriptions of two new species Fejervarya asmati sp. nov. (now Zakerana asmati), as well as Fejervarya burigangaensis sp. nov. , respectively. In the third chapter, a new species (Zakerana dhaka sp. nov.) is described from the urban core of Dhaka, the capital of Bangladesh and one of the most densely populated mega cities in the world. In the fourth chapter, I describe Euphlyctis kalasgramensis sp. nov., which was earlier recognized as E. cyanophlyctis, and show that it is genetically highly divergent from the E. cyanophlyctis described from southern India. In the last and fifth chapter, I describe Microhyla nilphamariensis sp. nov. as a new species. It is a member of a highly genetically heterogeneous group of frogs that have been recognized as M. ornata for the past 173 years. In general, the results of the studies included in this dissertation advance our understanding of amphibian diversity in Bangladesh and adjacent regions, and show that discovery and description of new amphibian species from this region is still fairly easy. Consequently, it seems likely that more thorough sampling and further investigations in this region can uncover additional new amphibian species to science. Such studies, together with the discoveries described in this thesis, should also provide useful information for understanding and conserving the amphibian biodiversity in this poorly studied region.
  • Mathijssen, Paul (Helsingin yliopisto, 2016)
    Peatlands contain approximately a third of all soil carbon (C) globally and as they exchange carbon dioxide (CO2) and methane (CH4) copiously with the atmosphere, changes in peatland C budgets have a large impact on the global C balance and on the concentration of greenhouse gases in the atmosphere. How peatlands will react to future climate changes, however, is still relatively uncertain and as such there has been a growing interest in the reconstruction of past peatland C dynamics and linking these to past climate variations. In order to increase the understanding of peatland development and response patterns, I quantitatively reconstructed the Holocene (the last c. 11700 years) C dynamics of three different peatlands in Finland: a subarctic rich fen, a boreal poor peatland complex and a boreal managed pine bog. Several cores from each peatland were studied in order to reconstruct peatland succession, lateral expansion, peat and C accumulation rates, long term uptake of atmospheric CO2, CH4 fluxes and radiative forcing (RF). Peatland lateral expansion was most rapid during periods with relatively cool and moist climate conditions. The peatlands showed distinct successional pathways, which were sometimes triggered by fires. Successional stages were partly reflected in C accumulation patterns. In some cases, variations in C accumulation rates coincided with autogenic changes in peat type and vegetation, although accumulation rates were also related to the large-scale Holocene climate phases. The warm and dry conditions during the Holocene Thermal Maximum (between c. 9000 and 5000 years ago) reduced C accumulation rates in the subarctic fen and the boreal peatland complex. Reconstructed CH4 emissions suggest that CH4 emissions played a major role in the total C budget of the peatlands throughout the Holocene. The RF models based on long term CO2 uptake and CH4 emissions showed that the two boreal peatlands had a warming effect on the atmosphere for the first 4000-7000 years after the start of peat accumulation, after which they had an increasing cooling effect as a result of the long term effect of C uptake and storage. In contrast to the two southern sites, the subarctic fen had a warming effect through its entire history as a result of very low C accumulation rates. The results of my study show that peatland processes react differently to allogenic factors, such as climate and fire, depending on peatland type, microtopography and local hydrology. It highlights the necessity to study multiple peat cores per site before making exhaustive conclusions on historical development patterns and implications. The combination of lateral and vertical peat growth data with reconstructed CO2 and CH4 fluxes provided the necessary information for a comprehensive quantification of the climate - peatland feedback. In the studied sites this feedback seemed to be very sensitive to short term variations in CH4 emissions and lateral expansion.
  • Sakha, Prasanna (Helsingin yliopisto, 2016)
    Neurons have distinctive polar morphology with distinctive subcellular features comprising of cell soma, axons and dendrites. Primary objective of this study was to develop a novel microfluidic device for spatial isolation of axons from the somatodendritic compartment of cultured hippocampal neurons. A new method was developed for asymmetrical genetic manipulation improving specificity in studies of how individual proteins affect axonal morphology, presynaptic development and function. Subsequently, the microfluidic culture system was used to study the signaling events involved in synaptogenesis, focusing on the roles of kainate type of glutamate receptors (KARs). Functional studies have shown that KARs are present in axons and may regulate presynaptic function. However, the molecular composition and detailed subcellular localization of axonal KARs as well as their roles in presynaptic differentiation are largely unknown. The results show that axonal KARs promote early stages of synaptogenesis. Expression of low (GluK1-3) and high affinity (GluK4-5) KAR subunits promoted filopodiogenesis function at the isolated axons. In addition, axonal low affinity subunits enhanced clustering of synaptic vesicles and transmission efficacy at nascent glutamatergic synapses, an effect which was associated with widening of presynaptic active zone. High affinity KAR subunits had no effect on synaptic vesicle clustering, nor presynaptic transmission efficacy. However their heteromerization with low affinity subunits completely prevented the synapse promoting effects and instead lead to strong inhibition of presynaptic transmission efficacy. The presynaptic effects of GluK1-3 on synaptic vesicle clustering involved both PKA and PKC pathways. GluK1 expression was developmentally regulated in neonatal and juvenile hippocampus and heteromeric combination of GluK1c with high affinity subunits suppressed glutamatergic synaptic transmission. KARs are linked to various neurological and neuropsychiatric disorders. Our observations and previous findings strongly suggest that KARs are involved in morphological maturation of neurons and in refinement of neuronal circuitry in the brain. The present results provide novel insights into the involvement of different types of KAR subunits in synaptic development and morphological differentiation. Hence, they are potential therapeutic targets in various developmentally originating neurological disorders.
  • Mäkeläinen, Sanna (Helsingin yliopisto, 2016)
    Anthropogenic land use has caused detrimental impacts especially on forest ecosystems, and native forested landscapes have been lost and fragmented worldwide. Forest-dwelling animals are generally susceptible to habitat loss and fragmentation because of their strict habitat requirements and dependency on forests for food, nest sites and movements. Consequently, forest specialists, such as arboreal squirrels and gliding mammals, provide a worthy group of model species in order to assess the influence of landscape modification. The Siberian flying squirrel (Pteromys volans) is an arboreal rodent inhabiting spruce-dominated mature forests and due to destruction of its most suitable breeding habitat, the population has been decreasing in Finland. In my thesis, I investigate the effects of landscape modification on the occurrence, space use and survival of this species at multiple spatial scales. The occurrence probability of flying squirrel increased with a proportion of suitable movement forests on a 400-m-scale and was negatively associated with the isolation of occupied sites in a partly urban study area. However, no negative effects of urban habitat types were found, which indicates that the species is not disturbed by urbanization. It was found that regional environmental authorities were unaware of the presence of flying squirrel in most cases of forest harvesting in southern Finland. Despite occupied sites were delineated according to given guidelines, many of these sites became deserted after forest harvesting. This shows that the legal habitat protection of flying squirrel is ineffective and to improve this conservation practice, larger forested areas should be maintained around inhabited sites. The presence of urban habitats on movement routes increased movement distance and speed whereas urban habitats within home-range impeded only male movements. Structural forested connections had varying effects on nest-site switching and their importance remained unclear, which points out that defining and maintaining a species-specific connectivity is challenging in human-modified landscapes. Regional variation in flying squirrel survival was most likely caused by differences in predation pressure, predator community and landscape composition. Male mortality increased with a proportion of low-quality habitats in the surrounding landscape, whereas fine-scale habitat composition of the most used areas did not show any survival impacts. Natal dispersal distances of juveniles did not increase their mortality. Results of this thesis indicate that the effects of landscape modification on forest-dwelling animals are varying, sex-specific and depend on the scale. As landscape modification can also affect species indirectly, it is important to investigate the costs and risks of animal movements in human-modified environments.
  • Merikanto, Ilona (Helsingin yliopisto, 2016)
    Many existing and emerging microbial infectious diseases are caused by environmentally growing opportunist pathogens. These pathogens are, contrary to obligatory pathogens, able to survive and replicate in the outside-host environment as free-living microbes that use within-host growth as an alternative replication strategy. This disease class has eco-evolutionary implications in natural populations and causes a serious health and economical threat to humans, our food production and to wildlife. Because of the ability of environmentally growing opportunists to survive and replicate independently of hosts, these diseases are hard to eradicate with conventional methods. The conditions that favor or disfavor environmental opportunism are still poorly understood. Better understanding of the dynamics of these diseases is needed in order to develop proper control methods against them. In this thesis I have developed novel epidemiological models to describe the disease dynamics of environmentally growing pathogens. These models modify the traditional Susceptible-Infected host (SI-model) framework by combining it to the outside-host community of an environmentally growing pathogen. I have considered how the environmental growth of the pathogens and the antagonistic ecological interactions these pathogens face in the outside-host environment, such as competition, predation and parasitism, affect the disease dynamics, invasion of novel pathogens and biological control of environmentally growing infectious diseases. The analyses show that the disease dynamics of environmentally growing pathogens differ from obligatory pathogens. Importantly, ability to grow in the outside-host environment promotes disease outbreaks and can lead to the extinction of the host, which is untypical in the case of obligatory pathogens. Antagonistic interactions the pathogen faces in the outside-host environment can on the other hand limit disease outbreaks and prevent extinction of the hosts that would otherwise occur due to the disease. I conclude that the eradication can be accomplished 1) by increasing the outside-host competition, 2) through predation of pathogens, or 3) through viral infections in pathogens.