Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • Kerminen, Kaisa (Helsingin yliopisto, 2017)
    The wide use of pesticides has led to the contamination of soils, subsoils, surface and ground waters. This motivated research on pesticide dissipation and remediation of pesticide contaminated soils and groundwater. The herbicide dissipation was studied in boreal surface soils, subsurface sediment slurries and pilot-scale sediment columns. The sediments were from a groundwater area that was contaminated with atrazine, desethylatrazine (DEA), simazine and 2,6-dichlorobenzamide (BAM). The aim was to enhance dissipation by microbes (indigenous / Pseudomonas ADP), sonication (0, 5, 10, 20 or 30 min, 43 kHz, 320 W) or the following additives: surfactant methyl-β-cyclodextrin, a mixture of zero-valent iron and organic matter (EHC®), peat or a compost-peat-sand (CPS) mixture. Microbes enhanced atrazine (half-lives 57–181 d) and terbutryn (70–291 d) degradation in surface soils. Atrazine was also degraded chemically in four soils (half-lives 120–183 d). Oxygen did not affect atrazine half-lives significantly, while terbutryn was only degraded in aerobic soils. Herbicide dissipation was poorest in the soil that had the lowest amounts of organic matter and nitrogen. Sonication did not decrease the atrazine concentrations, compared with the non-sonicated controls, despite of indications of microbial and chemical degradation. Surfactant did not stimulate atrazine degradation by indigenous sediment microbes, and Pseudomonas ADP degraded atrazine even without surfactant. EHC® enhanced chemical atrazine dissipation under aerobic conditions and, in columns, cleaned atrazine-, DEA- and BAM-contaminated groundwater for about a month. Peat and CPS enhanced the chemical dissipation of atrazine and simazine. Peat also enhanced hexazinone dissipation. Only trace amounts of atrazine, simazine and hexazinone could be extracted from peat and sediment, which indicates that the dissipation was caused by chemical degradation and/or unextractable bound residue formation. In conclusion, the addition of peat, CPS and Pseudomonas ADP were the best approaches for reducing pesticide concentrations. EHC® could also be useful in remediation of small quantities of pesticides, preferably in the presence of oxygen. However, the usability of peat, CPS and EHC® in remediation should be further studied to avoid the possible adverse effects of organic matter additions to drinking water quality.
  • Keto, Antton (Helsingin yliopisto, 2017)
    Water-levels of lakes in Finland are artificially regulated for energy production, flood protection, navigation and recreational use. There is a need for changing water-level regulation practices, due to changing climate, increasing recreational use of lakes, and implementation of legally binding national targets for electrification of renewable sources. To obtain more knowledge-based assessments of new water management regulations, we need to develop water-level regulation assessment tools and to increase the sensitivity of ecological classification systems for hydromorphological pressures, as the European Union Water Framework Directive (WFD)requires. The main objectives of this study were to 1) develop criteria and threshold values for assessing the ecological status in regulated lakes, 2) identify both high-hydrological status and heavily modified lakes and 3) estimate the role of helophytes in the uppermost littoral zone. Impacts of water-level fluctuation on macrophytes, macrozoobenthos, and littoral fish fauna were clearly evident, and the threshold value between moderate and good ecological status was a 3.5 m winter water-level drawdown with the mean ecological quality ratio assessment method (1.8 m with the one-out-all-out principle). The vertical extension of Phragmites was most strongly associated with the water-level fluctuation of open water period (OWP), followed by Carex spp. and Equisetum. Overall, the RF models explained 4--41% of the variation observed in the helophytes zones. The models indicated that OWP fluctuation, slope, openness and cover of other macrophyte groups were key factors explaining the extent of the helophyte zones. The hydrological regime could be classified as having high hydrological status in 20% of the regulated lakes. Quite often, the ecological status was poorer, implying that high-hydrological status lakes often face other anthropogenic pressures, such as eutrophication that degrades high ecological status. Provisional designation with hydrological criteria seemed to work quite well, because 13 of the 15 lakes were estimated similarly with simple hydrological criteria, compared with the national HMWB designation only later produced by the environmental authorities.
  • Davidsson, Pär (Helsingin yliopisto, 2017)
    Necrotrophic phytopathogens, such as soft rot bacteria, cause large losses in agriculture. Unlike biotrophic pathogens, these typically rely on toxins and plant cell wall-degrading enzymes (PCWDEs) to kill and degrade the host tissue. As such, the methods utilised by the plants to defend themselves against biotrophs, such as the hypersensitivity response (HR), could instead be beneficial for necrotrophic pathogens. One key component in plant defence against necrotrophic pathogens is the recognition of oligogalacturonides (OGs), a breakdown product of the pectin in the plant cell wall, formed by the action of PCWDEs. Similar to direct recognition of the pathogen itself, recognition of OGs trigger a wide array of defence responses, resulting in improved protection against pathogens. Long OGs with a degree of polymerisation (DP) between 10 and 20 have been well studied. In this study, we explored the role of the relatively less understood short OGs (DP < 9). We utilised trimeric OGs to study the changes induced by short OGs on the transcriptome of Arabidopsis thaliana. We established that, similarly to long OGs, short OGs up-regulate genes related to defence and down-regulate genes related to plant growth and development. Phenotypic assays confirmed that pre-treatment with short OGs could improve resistance in A. thaliana against the soft rot bacteria Pectobacterium carotovorum, to the same degree as long OGs. Furthermore, we showed that treatment with both types of OGs results in seedling growth retardation. As part of investigating the signalling triggered by short OGs, we confirmed that trimeric OGs do not trigger the characteristic initial ROS (reactive oxygen species) burst, but do trigger expression of a large set of peroxidases. Similar to long OGs, part of the signalling in response to short OGs goes via phosphorylation of Mitogen-activated protein kinases (MAPKs). Our results show that short OGs are indeed biologically active elicitors of plant defence, with a signalling pathway that appears to be in part distinct from long OG signalling. We used the established trade-off between plant defence and plant growth and development to develop screens for mutants with altered OG sensitivity. One mutant line exhibiting hypersensitivity to OGs, resistance to the necrotrophic pathogens Botrytis cinerea and P. carotovorum, as well as sensitivity to the hemibiotrophic pathogen Pseudomonas syringae, was chosen for further studies. We established that the observed phenotypes were due to overexpression a cell wall-localised apoplastic peroxidase (class III peroxidase, CIII Prx) – PEROXIDASE 57 (PER57). We detected increased levels of ROS and increased cuticle permeability, associated with downregulation of genes involved in cutin formation and biosynthesis. We also observed a priming of OG related response genes. The phenotypes could be recaptured by overexpression of several CIII Prxs, indicating a general phenomenon. ABA treatment of these lines restored the phenotypes to wild-type. This appears to be mediated via removal of ROS. Noticeably, the peroxidase activity remained high in the peroxidase overexpression lines, indicating that while exogenous application of ABA was able to remove the ROS produced by the peroxidases it only had a minor direct effect on the activity of the peroxidases. Our results, combined with previous research on cuticular and ABA mutants, led us to propose that cuticle integrity is influenced by a positive feed-back loop. A disturbed cuticle leads to elevated ROS levels via increased peroxidase activity, which in turn impairs cuticle formation and biosynthesis. Under normal circumstances this loop is regulated by ABA. In the situation where a necrotrophic pathogen is invading the plant recognition of cell-wall derived DAMPs, such as OGs, it leads to activation of peroxidases that further promote resistance signalling via the creation of ROS.
  • Keskitalo, Salla (Helsingin yliopisto, 2017)
    A decade after identification of the human kinome, only a fraction of the kinome has been systematically studied. This clearly illustrates the lack of knowledge regarding the functions and cellular effects that these proteins have in the establishment of cellular phenotypes. Surprisingly, recent evidence suggests that approximately 23% of all kinase genes were estimated to function as cancer genes. The overall aim of this thesis project was to shed light on the mechanisms controlling protein kinase activity and function, particularly in human cancers. A global and comprehensive interactomics analysis of the signaling networks of the evolutionarily conserved CMGC-protein kinase family, consisting of cyclin-dependent kinases [CDK], mitogen-activated protein kinases [MAPK], glycogen synthase kinases [GSK3] and CDC-like kinases [CLK]) was performed. From this physical and functional interaction analysis, hundreds of novel interactions, kinase-substrate relationships and previously unknown links to human diseases, such as cancer were identified. The unprecedented sensitivity and specificity of this approach was also illustrated, and highlighted, for example, by the purification and identification of the complete translational co-activator complex (the Mediator complex) with two of the CMGC kinases (CDK8 and CDK19). At the same time, the Mediator complex was identified mutated in benign uterine human tumors (uterine leiomyomas). To further deepen the understanding of the role of CDK8 and CDK19 kinases in controlling human disease pathways, we studied the functional role of two MED12 mutations in uterine leiomyoma and prostate cancer. Based on these studies, MED12 was found essential for the kinase activity of CDK8 in the context of the Mediator kinase module. Furthermore, disruption of the Mediator kinase module subunit interactions was shown as a common mechanism contributing to the formation of uterine leiomyoma. The MED12 mutants in leiomyoma and prostate cancer were shown functionally different. Finally, a novel MED12 nuclear localization signal was identified, and its importance in the correct nuclear localization of MED12 and subsequent proper assembly and function of the Mediator kinase module was experimentally proven. The described results from the multidisciplinary studies clarify the cellular roles of CMGC kinases and Mediator subunits, facilitating the design of targeted future therapies/therapeutics against human diseases.
  • Kilpinen, Lotta (Helsingin yliopisto, 2017)
    Human mesenchymal stromal cells (hMSCs) are currently used in many advanced cellular therapies. The clinical use of hMSCs requires extensive cell expansion, but the consequences of expansion, especially at the molecular level, are not fully understood. The therapeutic effect of hMSCs is mediated paracrine interactions with immune cells modulating both innate and adaptive immune response. Membrane glycerophospholipids (GPLs) provide precursors for signaling lipids, which modulate cellular functions, including immunological effects. In this thesis, I investigated the effect of the donor’s age and cell doublings on the GPLs, gene expression and microRNA (miRNA) profiles of human bone marrow MSCs (hBM-MSCs). In order to gain more insight into the functional mechanisms of hMSCs, I investigated the extracellular vesicle secretion from human umbilical cord blood derived MSCs, and evaluated their immunosuppressive capacity in vitro as well as their possible immunomodulative and protective effect in kidney ischemia-reperfusion injury in vivo. In this study, I was able to demonstrate that the hBM-MSCs, harvested from 5 young adults and 5 old donors, showed clear compositional changes in their GPL profiles during expansion. Most strikingly, the molar ratio of arachidonic acid (20:4n-6) containing species of phosphatidylcholine and phosphatidylethanolamine accumulated, while the species containing monounsaturated fatty acids decreased during passaging. The lipid changes correlated with the decreased immunosuppressive capacity of hBM-MSCs suggesting a connection between lipid signaling and immunomodulatory functions. Although there were clear alterations in gene expression levels and lipid profiles, the miRNA expression levels were more stable. The expression levels of 37 miRNAs were changed in the old donors group and 36 miRNAs were changed in the young donors group. Of these, only 12 were differentially expressed in both young and old donor BM-MSCs and their predicted target mRNAs, the expression of which was changed, were mainly linked to cell proliferation and senescence. This thesis provides a detailed analysis of molecular changes during MSC expansion. The combination of in vitro and in vivo models accompanied with a detailed analysis of molecular characteristics is essential to understand the complexity of the MSC paracrine mechanisms and functionality.
  • Laakso, Senja (Helsingin yliopisto, 2017)
    This dissertation examines local experimentation from a practice theoretical perspective. By doing this, the dissertation bridges the gap between two fields of research: one relating to the governance of experiments and the other to the dynamics of practices. In this way the dissertation contributes to the timely issue of steering consumption in a more sustainable direction by utilising experiments and interventions at multiple societal levels – an issue attracting wide interest within both research and policy communities. The dissertation focuses on the role of participants in accommodating novel technologies and services into their everyday lives, and the role of social interplay between individuals and their collectives in supporting or opposing the change and diffusion of practices. These factors – how everyday practices are linked together, how change in one practice affects other surrounding practices, and how individuals adjust and evaluate their performances with respect to social norms, expectations, standards and rules – are fundamental to both stability and change in practices. The dissertation comprises of five articles that illustrate, firstly, what can be expected from a local experiment and what the role of each experiment is and, secondly, what can be learnt from an everyday practice perspective on experiments and how the experiments are accommodated into the system of everyday practices. The study draws on a meta-study on 25 papers on climate governance experiments and on three empirical case studies on local experiments in Jyväskylä, Finland. This dissertation asserts that a practice approach and a participant perspective can provide new opportunities for experimental governance by illustrating the complexities of everyday practices and how to acknowledge them in experimentation. Although sustainability transitions require changes in practices as entities, a focus on the performances of practices is crucial for any intervention, as it sheds light on individual learning and experiences. The findings highlight the interdependencies and path dependencies of practices, as well as the collective perceptions of normality steering understandings of acceptable or unacceptable actions. The results also demonstrate that the participants are active contributors in experimentation, adjusting the new configurations of elements and practices in the prevailing system and reflecting on their performances in relation to others. Addressing the dynamics between individual performers of practice and their communities in (re)producing practices, and then targeting the interventions at the collective underpinnings preventing (or accelerating) change might be the key to stabilising emerging, sustainable practices.
  • Teesalu, Mari (Helsingin yliopisto, 2017)
    Simple carbohydrates constitute a big part of our everyday diet, as significant consumption increases have occurred in recent decades. This has coincided with a dramatic rise in people suffering from metabolic disorders, such as diabetes and obesity. However, the genetic factors ensuring a healthy response to sugar intake remain poorly understood. To keep blood glucose in a healthy range even upon overnight fasting or following a rich meal, animals need to be able to adapt quickly. In a healthy organism, high sugar intake leads to rapid conversion of excess sugars into stored glycogen and triacylglycerols, while starvation triggers glucose production through gluconeogenesis and glycogen breakdown. To cope with these fluctuating nutritional conditions organisms possess glucose-sensing mechanisms. Such pathways have a key role in monitoring changes in cellular and organismal nutrient status and readjusting animal physiology accordingly to maintain homeostasis. Intracellular sugar metabolites are sensed by the conserved Mondo family transcription factors (TFs)(MondoA and MondoB/ChREBP in mammals, Mondo in Drosophila), which act together with TF Mlx. Together, they control the expression of metabolic target genes by binding to the carbohydrate response elements present in their promoters. The known Mondo-Mlx targets include genes involved in carbohydrate metabolism and biosynthesis of fatty acids. Yet, the physiological output of these transcription factors has remained largely elusive. As these TFs are very well conserved in Drosophila, this model organism has been used in this thesis to understand the physiological role of Mondo-Mlx and their target genes in vivo. We show that Mondo-Mlx interact in the fly and are crucial for dietary sugar tolerance. Loss of either transcription factor leads to impaired growth and lethality upon high sugar diet. We further characterize the mlx mutant phenotype to reveal high circulating glucose, and increased glycogen levels. We uncover transcriptional repressor Cabut as a direct target of Mondo-Mlx. The Cabut promoter is directly bound by Mondo-Mlx in a sugar-dependent manner. Loss of Cabut similarly results in dietary sugar intolerance, pointing to a crucial function in carbohydrate metabolism. Mondo-Mlx through Cabut are essential for repressing the expression of pepck – the rate limiting gene in gluconeogenesis and glyceroneogenesis. A failure to regulate this step results in pepck over-expression, leading to several fold higher levels of circulating glycerol, and pupal lethality of mlx mutants. Moreover, we reveal that Cabut interconnects nutrient sensing with the circadian clock, and contributes to circadian gene expression oscillation. We also identify Salt inducible kinase 3 (SIK3) as a direct transcriptional target of Mondo-Mlx required for dietary sugar tolerance. Moreover, we show that the activity of the rate-limiting enzyme in the pentose phosphate pathway, glucose-6-phosphate dehydrogenase (G6PD), is increased following sugar feeding. The sugar-augmented increase in G6PD activity is achieved through SIK3-dependent activating G6PD phosphorylation. Collectively, Mondo-Mlx-mediated transcriptional upregulation, as well as SIK3-dependent phosphorylation promote G6PD enzyme activity in response to high high sugar diet. The increased G6PD activity is required for elevating NADPH/NADP+ ratio in order to reduce glutathione in high sugar conditions. We determine that upregulating G6PD activity through Mondo-Mlx and SIK3 is essential for redox balance maintenance, and dietary sugar tolerance. In sum, thesis demonstrates that maintaining redox balance, directing the flow of carbon backbones, and regulating the expression of metabolic circadian genes is essential for dietary sugar tolerance. We highlight the central role of Mondo-Mlx in orchestrating the necessary transcriptional response required for safe glucose utilization, and ultimately, for maintaining metabolic homeostasis.
  • Li, Ling (Helsingin yliopisto, 2017)
    The increasing use of titanium dioxide nanoparticles (TiO2 NPs) and their consequent release into the environment, make it important to understand the behaviour, fate and potential adverse effects that TiO2 NPs may have upon organisms. After being introduced into the aquatic environment, TiO2 NPs will undergo transformation processes, which will affect their properties, including, chemical composition, size, surface charge and coating, and these may also have substantial implications on the fate and toxicity of the NPs. This highlights the importance of physiochemical characterization of the NPs in conjunction with a toxicological assessment. The transformation processes are dependent both on the physicochemical properties of the NPs and on the physicochemical properties of the ambient environment. However, these properties have been seldom studied in complex natural waters. Therefore, the research done for this PhD dissertation aimed to investigate the behaviour of TiO2 NPs in natural waters, and to associate the NPs colloidal stability with various water properties. The toxicity tests of TiO2 NPs were performed on two aquatic organisms each of which represent different trophic levels: Lemna minor (L. minor) and Daphnia magna (D. magna) according to ISO 20079 and OECD test 202, respectively. The specific aim was to assess the possible toxic effects of TiO2 NPs with maintained colloidal stability in an optimized ecotoxicological test medium. Given the potential of TiO2 NPs to carry other pollutants, the mixture toxicity of TiO2 NPs with cadmium (Cd) and lead (Pb) on D. magna were also investigated. TiO2 NPs exhibited different colloidal stability, which depend on the physicochemical properties of the natural waters. Total phosphorus, total nitrogen, alkalinity, pH, electrical conductivity and turbidity were shown by experimental and linear regression analysis to be the main water properties that negatively influence NPs stability among 14 water properties that were compared. All six of these physicochemical properties of water had positive correlations on the deposition of TiO2 NPs in lake waters. TiO2 NPs showed low colloidal stability in standard ecotoxicological test media, but modification of the current standard medium enabled the steady exposure of L. minor and D. magna. TiO2 NPs showed no adverse effect on the growth rate or chlorophyll a content of L. minor, or immobility of D. magna. However, TiO2 NPs were found to become attached to the cell wall of L. minor and to the body surface of D. magna, both of which may cause the potential transfer of TiO2 NPs into the aquatic food chains. Such a transfer would lead to an exposure of other organisms and contribute to the environmental fate of NPs. The presence of TiO2 NPs also influenced the bioaccumulation and toxicity of Cd and Pb in D. magna. TiO2 NPs increased the bioaccumulation and toxicity of Cd in daphnia, whereas it reduced the toxicity of Pb regardless of the 3- to 4-fold increase of bioaccumulation found. Surface attached TiO2 NPs combined with adsorbed heavy metals, caused adverse effects on D. magna swimming and moulting behaviour, which was assumed to lead to chronic toxicity. The research findings presented in this thesis elucidate the water physicochemical properties that control the aggregation and deposition of TiO2 NPs in complex natural waters, and offer an insight into their biological effects and accumulation potential upon aquatic organisms.
  • Tigistu-Sahle, Feven (Helsingin yliopisto, 2017)
    The application of human bone marrow derived mesenchymal stromal cells (hBMSCs) for regenerative or immunomodulatory therapies, e.g. treatment of the graft-versus-host disease, requires in vitro expansion of the cells. The hBMSCs undergo subtle changes during expansion which may compromise their functionality. In order to evaluate these changes lipidomics techniques were applied and the fatty acid (FA) and glycerophospholipid (GPL) profiles of hBMSCs were determined. During the cell passaging, arachidonic acid (20:4n-6) -containing species of phosphatidylcholine (PC) and phosphatidyl-ethanolamine (PE) accumulated while the species containing monounsaturated fatty acids (MUFA) or n-3 polyunsaturated fatty acids (n-3 PUFAs) decreased. The accumulation of 20:4n-6 and deficiency of n-3 PUFAs correlated with the decreased immunosuppressive capacity of the hBMSCs, which suggests that extensive expansion of hBMSCs harmfully modulates membrane GPLs profiles, affects lipid signaling and eventually impairs the functionality of the cells. Experiments, in which hBMSCs were cultured with different PUFA supplements revealed that the cells may limit the proinflammatory 20:4n-6 signaling by elongating this precursor with high biological activity to the less active precursor, 22:4n-6. It was also found that the ability of hBMSCs to produce long chain highly unsaturated fatty acids from C18 PUFA precursors was limited apparently due to the low desaturase activity of the cells. Thus, when the n-3 PUFA precursor, 18:3n-3, had little potency to reduce the GPL 20:4n-6 content, the eicosapentaenoic (20:5n-3) and docosahexaenoic (22:6n-3) acid supplements efficiently displaced the 20:4n-6 acyls, allowing attenuation of inflammatory signaling. These findings call for specifically designed optimal PUFA supplements for the cultures with sufficiently 20:5n-3 and 22:6n-3 but moderately 20:4n-6. Studies on the dynamics of PUFA incorporation into the major GPL classes revealed that the PUFAs in PC are remodeled at first, then those of the PEs and phosphatidylserines (PS). These results demonstrate that not only the type of PUFA administered but also the treatment time largely determines the resulting composition of the membrane GPL species, which serve as PUFA donors for the synthesis of lipid mediators. This thesis work highlights the importance of using lipidomics data to complement genomics or proteomics approaches when aiming at understanding of the therapeutic mechanisms of stem/stromal cells. The work provides tools to develop the protocols of hBMSCs culture and manipulate the functionality of the cells.
  • Pavón Jordán, Diego (2017)
    Climate change has become a major threat for biodiversity in recent decades. Waterbirds, in particular, are very responsive to climate change compared to other avian species and have already shown changes in phenology and distribution. Such strong and rapid response of some species to climate change has motivated debate about the effectiveness of the site-safeguard network, as climate change may ultimately push species of conservation concern out of the protected areas. One such network, which aims to protect all European bird species, is the Special Protection Area (SPA), designated under the EU Birds Directive. My thesis overviews the most important environmental factors acting upon Nordic waterbird populations now and in the future. In addition, I studied (i) the spatial changes in wintering abundances of 25 waterbird species in Europe in relation to weather conditions, (ii) the effectiveness of the SPA network delivering climate change adaptation for a protected waterbird species and (iii) the effects of weather conditions and habitat type on the abundance of 17 waterbird species breeding in Finland. Results show differential response of 25 waterbird species (classified into five guilds) to inter-annual variation in weather conditions. The centre of gravity in abundance of dabbling ducks, diving ducks, swans and other waterbird species (non-Anatidae) moved southwestwards in cold winters. On the other hand, only the centre of gravity in abundance of dabbling and diving ducks moved northeastwards in warm, and a priori beneficial, winter weather conditions. In this case, diving ducks responded the fastest. There was no link between the movement of the centre of gravity in abundance of geese with winter weather conditions. These differences in responses to weather conditions are probably related to different food and habitat requirements during winter as well as to life-history traits. Furthermore, while the centre of gravity in abundance of diving ducks showed a steadily long-term shift northeastwards over the past three decades, that of other waterbird species shifted southwestwards in recent years probably due to several consecutive cold winters. Dabbling ducks, swans and geese did not show long-term shifts. A detailed study about the wintering distribution of the smew Megellus albellus supports the above-mentioned findings and shows that the wintering numbers of this protected diving duck in the northeastern part of the wintering range increased from 6% of the total wintering population in the early 1990s to 32% in the early 2010s. In this context of climate-driven redistribution of wintering waterbirds, the EU s SPA network facilitated the redistribution of wintering smew towards the northeast: smew wintering numbers increased twice as fast inside than outside SPAs. However, results also pinpointed big gaps in the SPA network in north European countries, as most of the individuals winter outside the network in Sweden (79%) and Finland (95%). This findings call for an urgent assessment of the network in northern Europe, where wintering numbers are rapidly increasing. Furthermore, due to the high flexibility in migration of this and other waterbirds according to current weather conditions, it is of paramount importance to maintain a cohesive and coherent site-safeguard network throughout the flyway, including cold weather refuge sites. Lastly, the abundance of waterbird species breeding in Finland was higher after mild winters in western and northern Europe likely due to improved survival. This beneficial effect of mild weather conditions was more apparent in eutrophic wetlands than in oligotrophic ones. However, my analysis of population trends in different habitat types revealed faster population declines in wetlands surrounded by agricultural and urban areas, possibly due to hyper-eutrophication processes that renders such wetlands unsuitable for waterbirds to breed. These findings suggest that the impact decreased habitat quality can overcome the positive effects of milder winters and cause populations to decline.
  • Fraixedas, Sara (Helsingin yliopisto, 2017)
    The combined effects of climate and land-use change constitute a major threat to global biodiversity. Accurate tools to track changes in biodiversity have been largely called upon in order to address global conservation targets. In response to this, a range of ecological indicators have been developed to measure the state of biodiversity in a changing world. Because of their sensitivity to environmental changes, birds are increasingly used in the construction of multi-species indicators, which represent a powerful tool for decision-makers to assess conservation effectiveness. This work aims to further our understanding of the general state of bird populations in Finland and the underlying ecological processes behind corresponding trends, covering different environments and with a special focus on some of the most threatened ecosystems of northern Europe. Using data on common bird species, the effects of climate change and anthropogenic habitat degradation on bird populations are quantified for different habitat types and seasons of the year. Habitat-specific indicators are also produced to deepen knowledge about large-scale impacts taking place in the environment while allowing an evaluation of the conservation status of bird populations, thus helping target the most critical conservation issues. Although the effects of climate and land-use change on bird populations vary significantly with the habitat type and the life-history traits of the species (e.g. migration strategy), the conservation status of nearly all studied communities is considerably deteriorating in both Finland and its neighbouring Northern European countries. Peatlands and forests are of particular concern, given that intensive management actions are severely impacting the inhabiting bird communities.
  • Kaartinen, Tanja (Helsingin yliopisto, 2017)
    T cells are a promising therapeutic target and remedy in modern medicine. Various ways of modifying T-cell response are under development with a view to treating cancer, autoimmune diseases, and transplantation-related complications. T-cell function can be steered by altering target recognition or cosignaling receptors as well as by inducing immunological memory or regulatory T cells (Tregs). Unwanted immune responses can be curtailed by administering Tregs and, perhaps, long-lasting immunological tolerance can be induced. Cytotoxic T cells can be directed against cancer cells. Considerable T-cell numbers are required for clinical efficacy. Therefore, in vitro cell expansion is often necessary and cultures are commonly supplemented with interleukin (IL)-2. As T-cell activation, proliferation, effector differentiation, and the development of memory are inherently coupled to each other, excessive stimulation during expansion may lead to exhaustion. Hence, cells with weaker therapeutic potency may be produced. In this thesis, various methods of T-cell activation and in vitro cell expansion were evaluated particularly in the context of personalized medicine and cell therapy. Good therapeutic response to T-cell therapy in cancer depends in part on the survival of T cells and T-cell memory. The present study demonstrated that the proportion of memory T cells could be increased by limiting the length of in vitro T-cell expansion and by reducing the amount of IL-2. This study further showed that as a result of in vitro expansion Tregs expressed higher levels of the Cytotoxic T lymphocyte-associated antigen 4 (CTLA4) cosignaling receptor. CTLA4 is a central molecule for the Treg-mediated inhibition. The level of CTLA4 expression in Tregs correlated with higher inhibitory function of the cells. Apparently, high CTLA4 receptor expression after cell expansion was in part a result of changes in the alternative splicing of CTLA4 messenger RNA (mRNA). It was also found that the splicing preferences and the expression levels of CTLA4 mRNAs were associated with genetic variation in the T-cell cosignaling receptor gene region. This thesis provides new knowledge that can be applied in the evaluation of individual variation in T-cell immunity and the production of therapeutic T cells. The T-cell expansion method that was developed here is directly applicable in T-cell manufacturing, and the findings may have substantial clinical relevance.
  • Survila, Mantas (Helsingin yliopisto, 2017)
    To survive, plants must recognize the presence of danger and establish effective defenses against invading pathogens. Most plants are resistant to the majority of plant pathogens. This passive protection is provided primarily by the cell wall and waxy cuticular layer that limit the progress of most attackers. If these barriers are overcome, the second line of defense is triggered upon detection of pathogen-associated molecular patterns or damage-associated molecular patterns by pattern recognition receptors. The activation of PRRs induces multifaceted intracellular signaling pathways that ultimately initiate defense responses. Many molecular components by which plants perceive pathogens and the downstream signaling cascades have been characterized on a molecular level. However, the mechanisms by which plants protect themselves from phytopathogens (in particular necrotrophs) remain to be elucidated. Three aspects of plant immunity to phytopathogens are addressed in this thesis: (I) the role of glucosidase II β-subunit AtGCSIIβ in EFR receptor-mediated defense signaling, (II) the role of F-box protein AFB4 in plant innate immunity against necrotrophic pathogens, and (III) the role of class III peroxidases in cuticle formation that governs very strong and local resistance against necrotrophic bacterial and fungal pathogens. Plants exploit membrane-localized PRRs for specific and rapid detection of the potential pathogens. Many eukaryotic membrane-localized proteins undergo quality control during folding and maturation in the endoplasmic reticulum, a process termed endoplasmic reticulum quality control. The biogenesis of EFR, and to a lesser extent FLS2 receptors, is regulated by this mechanism. Study I demonstrated that the glucosidase II β-subunit AtGCSIIβ is pivotal for the function of the plant innate immunity receptor EFR. Loss-of-function in AtGCSIIβ results in elf18-insensitive phenotype, confirming the importance of AtGCSIIβ in biogenesis of the EFR receptor. F-box proteins are important components in plant hormone responses. They target regulatory proteins to the ubiquitin proteolytic machinery and mediate hormone signaling transduction. In study II, we demonstrated that auxin signaling F-box protein mutant plants are enhanced in their resistance to bacterial and fungal necrotrophic pathogens. This was accompanied with altered sensitivity to methyl jasmonate, indole-3-acetic acid, and abscisic acid phytohormones, thus providing evidence that ABF4-mediated signaling is involved in balancing growth and defense responses via coordination of hormone-mediated signaling pathways. The ability to maintain the barrier properties of the epidermis is largely due to the cell walls, which are covered with specialized lipids. This fine structure at the outermost region of the cell walls of epidermal cells is called the cuticle, which has been the subject of many studies. Plants perceive and ultimately activate defense mechanisms in response to cuticular and cell wall structural components e.g. oligogalacturonides released by the action of degradative enzymes secreted by pathogenic bacteria or fungi. Cuticle alterations induce a battery of reactions that often result in reactive oxygen species production and resistance to necrotrophic pathogens. However, the source of ROS generated upon altered cuticle status and the acute downstream defense signaling pathways involved in such defense remains elusive. Study III provides evidence that ROS produced by class III apoplastic peroxidases suppress the expression of cuticle-biosynthetic genes, and together with ABA, regulate the formation of the cuticle envelope. However, resistance to necrotrophic pathogens in cuticle-depleted plants is a result of activated OG signaling components and function independently of salicylic acid and jasmonic acid signaling pathways. This thesis demonstrates the use of Arabidopsis in studying the genetic basis of plant defense mechanisms. It provides novel insights on plant resistance to pathogens, and reveals how cuticular defects activate defense via OG signaling pathway.
  • Alanko, Teija (Helsingin yliopisto, 2017)
    Archaeobotany combines botany, archaeology and history, and studies useful plants and interactions between humans and plants in the past, including horticulture. Garden history has been studied in Finland mainly through historical sources, but not much with archaeological or archaeobotanical methods, although the importance of multidisciplinary work has been noted, since written sources available are often not sufficient. Archaeobotany in Finland has revealed garden plant remains, but garden soils have not been investigated much. Archaeobotanical material, obtained from soil samples, i.e. macrosubfossil plant remains, is interpreted in archaeological and historical contexts. Excavations are, however, often restricted for practical reasons, determining also sites for macrofossil analyses. An alternative sampling method may be one solution to carry out macrofossil studies in sites unlikely to be excavated, such as historical gardens. The aims of this study were to elucidate a part of Finnish and Swedish garden history by means of archaeobotany, and to test archaeobotanical sampling in gardens in the absence of excavations with a sampler and applying AMS-radiocarbon dating. The research comprises four case studies and a review from five sites; Naantali Cloister, Kumpula Manor, and academic gardens in Uppsala, Turku and Helsinki. The sites are partly linked historically to each other, and they reach from the 15th century to the 21st century. Soil samples were collected at four sites with a sampler from different levels from narrow pits, one by one in vertical series. At one site, samples came from excavations. The samples were floated and sieved in a laboratory, and macrofossil remains were identified and counted. Altogether 8,404 macrofossil plant remains belonging to 154 plant taxa were obtained. In total 30 AMS-radiocarbon dates were measured from seeds, charred grains, and pieces of charred wood. The oldest dated seeds and grains were medieval, the youngest were modern. Macrofossil plant remains included cereals, berries, ornamental, medicinal and garden plants, and cultural or garden weeds, indicating both consumption and garden cultivation at the sites. Other soil contents, such as fish scales and chips of wood and charcoal, referred to fertilization and thus also gardening. The sampling method worked reasonably well. Sampling was independent of excavations, and relatively quick. Still, the maximum size of a sample was limited, although larger samples could have yielded more macrofossils and species. Written sources were necessary for the background, but in the cases of historical gardens, the literature gave historical contexts well enough. Garden history can and should be studied with both written sources and archaeobotanical methods. Informative macrofossil sampling can be carried out both from excavations and straight from garden soil. Plant lists, when existing, give information of cultivated species, but not of plants consumed or having grown as garden weeds at the sites. Still, quite few species that were mentioned in the plant lists were obtained as macrofossils in this study, perhaps due to the relatively poor state of preservation of the seeds in garden soil, and the probable scarce accumulation of seeds of cultivated species into the garden soil. Nevertheless, in sites with no comprehensive plant lists, archaeobotany revealed valuable information of plants that could not be gained otherwise. The Naantali Cloister case showed the importance of searching remains of garden plants also from structures outside of gardens.
  • Kärpänoja, Pauliina (Helsingin yliopisto, 2017)
    The increasing trend of antimicrobial resistance in bacteria is a global problem, although resistance varies between geographical regions significantly. Today, common bacterial pathogens can be resistant to all known antimicrobial agents. The growing resistance has been linked to increasing use of antimicrobials in humans, food industry ant veterinary medicine in several studies. The battle against antimicrobial resistance is highly dependent on the knowledge of resistance rates in different bacterial species and accurate methods to measure the resistance. Finnish laboratories provide resistance data annually for the national FINRES report. This data is forwarded to the European EARSNet database and from 2016 also to the Global Antimicrobial Resistance Surveillance System (GLASS, organised by WHO). The solidity and uniformity of this data depend on the primary results of laboratories. This thesis is composed of four studies, which cover methodolgical issues in the susceptibility testing of the main respiratory pathogens and the connection between antimicrobial use and resistance. Susceptibility testing methods and their quality were examined for Haemophilus influenzae and Streptococcus pneumoniae. The connection between sulfamethoxazole-trimethoprim use and resistance was investigated among H. influenzae, S. pneumoniae and Moraxella catarrhalis using the FINRES data and drug consumption data provided by Finnish Medical Agency. As a result of this study the susceptibility testing method for H. influenzae with good sensitivity and specificity was launched for the Finnish susceptibility testing guideline (FiRe standard), the focus was in identifying the difficult to detect non-β-lactamase mediated ampicillin resistance. In addition, evaluation of the quality of susceptibility testing in Finnish laboratories showed good reproducubility with two indicator organisms H. influenzae (ATCC49247) and S. pneumoniae (ATCC49619) when recommended guidelines were followed. The quality was assessed from internal quality control results of the laboratories. An automated method (Vitek2®, AST GP-74, bioMerieux) for susceptibility testing of S. pneumoniae provides highly comparable results with the reference broth dilution method. Time to results is considerabely shorter than with the traditional methods. Regional sulfamethoxazole-trimethoprim consumption was found to have a positive connection with resistance in S. pneumoniae but the change of resistance was not significant. The change in resistance over time in H. influenzae was border-line significant, but the drug use did not explain the change. Change in resistance among M. catarrhalis was not statistically significant and there was no significant connection between the drug consumption and resistance. Sulfa-trimethoprim consumption fell throughout the country during the investigation period. Conclusions: The accuracy of the susceptibility testing of bacteria requires evidence-based standardization and continuous quality controlling. Clinical laboratory automation can be implemented safely in pneumococcal susceptibility testing. The impact of sulfamethoxazole-trimethoprim consumption on resistance varies for different bacterial species. A reduction in its use in the long run has not led to a significant reduction in resistance.