Bio- ja ympäristötieteellinen tiedekunta

 

Recent Submissions

  • Jokinen, Maarit (Helsingin yliopisto, 2019)
    Research and evaluation are crucial components of evidence-based policy, decision-making and effective conservation management. As research consumes the same limited resources that could be used for conservation, it should provide as valuable and useful information as possible. This requires framing research questions to be relevant to both researchers and users of the information. A general problem is that researchers may be detached from conservation policy and practice, and thus do not recognize information needs. Furthermore, measuring and predicting effects of conservation is not an easy task. The spatial scale considered, and whether the costs and side effects are taken into account, may affect the conclusions. Effective conservation has population-level effects, but accurately measuring population change requires adequate resources and both ecological and statistical expertise. In addition, as societal actions and change in human behaviour are needed to bring about the desired changes, interdisciplinary approaches are needed for finding solutions to conservation problems. In this thesis, I use the conservation of the Siberian flying squirrel (Pteromys volans) in Finland as a model case for developing more effective conservation research. As an arboreal species, the flying squirrel is threatened by forest habitat loss and degradation. I evaluate the ecological effectiveness of species protection regulation along with the side effects it has had on forest owner attitudes toward the species. I use species distribution modelling (SDM) to predict the occurrence probability of the species in Finland. I also evaluate the methods and results of the species monitoring scheme by using information from the SDM and modelled relationship between the species observed occurrence and abundance. I found that the effectiveness of the prior approval system for forest management on flying squirrel nest sites was low but made the species a symbol of broader socio-political disputes. Conservation ineffectiveness is partly due to insufficient restrictions for forest management, but also due to lacking occurrence information. I found that species occurrence probability is explained by several environmental variables, but the ability of SDM to predict occurrence at specific sites and years remains limited with available data. I also found that the design of the population monitoring scheme does not allow reliable inference of the change in population size from the collected occurrence data. To conclude, the effectiveness of both conservation measures and research related to the evaluation and monitoring of the effects of conservation − including the population monitoring scheme – have suffered from shortcomings. Certain relevant study questions have been ignored, the monitoring scheme suffers from methodological problems, available data are not analysed or synthetized, or results have not been provided in usable form. In addition, the connection between available information and conservation policy and practice is very weak: even the most usable and objectively relevant information may not have substantial instrumental value. Much stronger partnerships between policymakers, managers and researchers of various disciplines is needed to increase the effectiveness of conservation and conservation research.
  • Vainio, Elisa (Helsingin yliopisto, 2019)
    Methane (CH4) is a strong greenhouse gas, and its ecosystematmosphere exchange depends on the consumption and production rates. The boreal zone includes nearly one third of the world’s forests, and boreal forest soil is the largest carbon stock among different ecosystem types. Upland soils are a globally important sink of CH4 due to microbes oxidizing atmospheric CH4. During the last decades, the understanding of the CH4 dynamics of forests has been reshaped and increased substantially, as the trees have been shown to contribute to the CH4 exchange. The newly-found aerobic CH4 emissions from plants have also revealed the existence of previously unknown processes. Meanwhile, the ecosystem-scale studies on CH4 exchange have shown that forests may occasionally be net sources of CH4. In this thesis, the objective was to quantify the CH4 exchange in a boreal pine forest, regarding the contributions of soil, ground vegetation and trees. The effects of soil water conditions and the CH4-consuming and -producing microbes were also studied. The research included the most abundant boreal tree species: Scots pine, downy birch and Norway spruce. The effect of ground vegetation on the forest floor CH4 flux was studied by classifying the vegetation into four groups, and by measuring the CH4 fluxes of three common shrubs (bilberry, lingonberry, and heather) in the laboratory. The forest floor CH4 flux was upscaled to the whole research site from topography-modelled soil moisture. The results demonstrated that the CH4 flux of the forest floor is strongly dependent on the soil moisture. All the studied tree species emitted CH4 from the stems and the branches, and the stem-emissions were significantly higher from trees growing at wet soil compared to drier soil. The ground vegetation species and soil moisture are strongly connected, and based on the results, both affect the CH4 flux. In the laboratory, heather shoots resulted in mean CH4 emissions, while bilberry and lingonberry shoots indicated uptake. Thus, the studied shrub species seem to have different CH4 dynamics. In addition, the shrubs increased the amount of CH4-consuming microbes and thus CH4 uptake in the soil. While the forest floor at the site was on average a sink of CH4 throughout the growing season, the upscaled forest floor CH4 flux revealed high spatial variation and CH4-emission patches at the area. The size and CH4 flux of these patches was related to temporal variation in the soil moisture.
  • Lindström, Stafva (Helsingin yliopisto, 2019)
    Biotic and abiotic characteristics shape the microbial communities in the soil environment. These characteristics vary both spatially and temporally, depending on variations in temperature, water availability and plant coverage, which on a larger scale are driven by topography, soil type, land use, vegetation and the ruling climate. In a sub-arctic climate, the seasonal fluctuations in temperature, precipitation and plant cover force the microbes in the top soil to adapt or decline. For many organisms trying to survive the cold winters, a nest can provide protection from the harsh environment. For example, the mound building wood ants, such as the Formica exsecta, selectively choose both the spot, and the building material for their nest mounds, in which they overwinter. These ants are also able to generate extra heat by using their lipid reserves during early spring, to secure the brood development. The higher and steadier temperature inside the nest is further enhanced by the decomposing process, intensified by the constant addition of organic plant material carried out by the ants, and the availability of nutrients. This creates a unique microclimate inside the nest mounds, in which the microbes can stay largely protected from the environmental drivers of the microbial communities in the surrounding top soil. I hypothesized, that the nest environment would promote the formation of unique bacterial and fungal communities in the nests, compared with the surrounding soil. I also hypothesized that the nest communities are stable in time, and that they would show less temporal than spatial variation. Furthermore, I expected to see nest-characteristic, temporally stable taxa, which could be identified as the core microbiome of the F. exsecta nests. However, to ensure a robust methodological approach, I first tested the combination of Next Generation Sequencing (NGS) and a classical community fingerprinting method, Terminal Restriction Fragment Length Polymorphism (T-RFLP). I sampled nests of the mound-building ant F. exsecta, and generated NGS (Illumina MiSeq), and T-RFLP data of the bacterial and fungal communities. I used ordination techniques and network analysis to disclose the community structures in the nests, and compared them with the ones in the reference soil. I assessed the variation in diversity, evenness and enrichment of taxa in the nests, and evaluated their spatial and temporal variations. I also identified significantly nest characteristic and temporally stable taxa, which represent a potential core microbiome of the nests. The results show that the bacterial and fungal communities, in the rigorously curated nest environment, are significantly different from those in the reference soils. I demonstrate that the nests represent a niche, where microbial species can adapt and diverge from the communities in the surrounding soils. The findings in my thesis work contribute to our understanding of the composition, function and adaptation of microbial communities in patchy, secluded habitats, and open up for further studies in a multilayered ecological system.
  • Ciuba, Katarzyna (Helsingin yliopisto, 2019)
    Fundamental processes of essentially each cell of the human body depend on structures built of actin. This relatively small (MW=42 kDa) protein is a central building block of the cytoskeleton. Actin-based structures contribute to diversified processes, including cell migration, morphogenesis, and intracellular transport. Above-mentioned activities are crucial in multiple basic physiological events, for example embryonal development, wound healing and immunological responses. Moreover, abnormal regulation of actin networks has implications in various diseases, such as cancer. Although extensively studied over the years, the field of actin-based structures still lacks answers for many important questions. For example, contractile actomyosin bundles of non-muscle cells, stress fibers, are essential for cell morphogenesis, adhesion and mechanosensing. However, the precise mechanisms regulating their assembly and function remain unclear. Studies included in this thesis reveal novel aspects underlying regulation of contractile structures in non-muscle cells. Assembly and organization of stress fibers depend not only on biochemical signals, but also on mechanical ones. Study I identifies mechanosensitive Ca2+-dependent CaMKK2-activation as an upstream regulator of AMPK-VASP pathway, which is crucial for contractile stress fiber maturation. Studies II and III unravel how two distinct proteins, calponin-3 and caldesmon, contribute to regulation of stress fiber organization and contractility in non-muscle osteosarcoma cells. We show, that calponin-3 is a dynamic component of all stress fiber subtypes. Moreover, its presence is essential to manage their proper contractility, as calponin-3 deficiency leads to uncontrolled behavior and breakage of stress fibers due to increased tension. We also show for the first time that non-muscle caldesmon is present exclusively in contractile stress fibers, where it colocalizes with myosin II motor domains. Moreover, we demonstrate an important role for caldesmon in regulation of stress fiber contractility, as lack of this protein leads to lower number of thick contractile bundles and reduced traction forces. Together, these studies broaden our knowledge on the mechanisms underlying assembly and regulation of contractile stress fibers in non-muscle cells.
  • Laitila, Jenni (Helsingin yliopisto, 2019)
    The nemaline myopathies (NM) are a group of genetic muscle disorders, ranging in severity from severe, early lethal forms to milder muscle disorders with onset in childhood, sometimes presenting in adulthood. Nemaline myopathies present with usually non-progressive or slowly progressive generalised muscle weakness and are pathologically characterised by the presence of cytoplasmic inclusions called nemaline bodies or rods. So far, mutations in twelve genes have been identified underlying the disorder. This Thesis aimed at elucidating the expression of the nebulin gene (NEB) and the function of the protein, in order to gain insight into the pathogenetic mechanisms leading to NM. Approximately half of NM cases are caused by mutations in NEB, and the vast majority of these are inherited recessively. NEB consists of 183 exons, giving rise to transcripts up to 26 kb in length. Nebulin is an enormous protein, with important roles in maintaining the structure and function of skeletal muscle. It is localised in the thin filament of the muscle sarcomere, and one nebulin protein spans the entire length of the filament. Nebulin structure is highly modular, consisting of actin-binding simple repeats, and super repeats formed by seven simple repeats. In NEB, more than 240 different pathogenic variants have been published, causing myopathies with no cure currently available. Furthermore, most NEB-NM patients have a compound heterozygous genotype, with two private mutations anywhere along the gene, which further hampers the discovery of any genotype-phenotype correlations. Many of the NEB exons are alternatively spliced. In this study, we investigated NEB expression at the RNA level, in 21 different skeletal muscles and in brain. We demonstrated co-expression of several different nebulin isoforms in all the muscles studied, but no isoforms specific for certain muscles were identified. The results also indicated that all 183 NEB exons are expressed in adult brain, and that the expression levels were comparable with expression in skeletal muscle. Further studies are warranted to elucidate the expression in brain. We however, went on to further investigate the expression and function of NEB in skeletal muscle. Exons 143 and 144 are mutually exclusive, encoding the super repeats S21a and S21b, respectively. The amino acid sequences of the alternative region differ in both charge and hydrophobicity. We developed specific antibodies for these two isoforms, enabling studies of their expression at the protein level. Our results showed differences in the usage of these isoforms between various myofibres, and during muscle development. S21b was the only isoform present in early myotubes, whereas regulated expression of S21a appeared later, mainly in fast myofibres. These results form a basis for studying the functional differences between the isoforms, and add to the basic knowledge of normal muscle function. The size of nebulin complicates studies at the protein level as well as genetic studies. As the super-repeat region encompasses nearly the entire protein, we constructed a panel of 26 mini-genes, corresponding to all the different nebulin super repeats, to enable protein interaction studies. The studies covering the entire nebulin super-repeat region revealed differences in actin binding between the seemingly similar super repeats, depending on their location in the protein. Actin binding was significantly stronger towards the end of the protein, while the entire central region bound actin weakly. This finding constitutes an important step in understanding nebulin function, and may facilitate the interpretation of the effects of various NEB mutations, depending on their location along the protein. Furthermore, the super-repeat panel can be utilised for studying mutational effects functionally at the protein level. To shed light on the pathogenetic mechanisms underlying NM, and to enable the study of nebulin function in normal and defective muscle, we developed the first murine model of NM with compound heterozygous Neb mutations. The aim was to produce a model recapitulating the most common form of NM, i.e. the typical congenital form. By studying the new compound heterozygous model, and the parental lines, we have gained valuable insight into the effects of Neb mutations on muscle function. The mouse models will be useful in deciphering the pathogenetic mechanisms of NEB-NM, and will be suitable for the assessment of potential therapeutic approaches. The results of this Thesis shed light on the expression and function of nebulin in health and disease. This brings us closer to understanding the pathogenetic mechanisms of NM, and how the disorder evolves, which in turn will enable providing more accurate diagnosis and prognosis for NM patients. Understanding the pathogenetic mechanisms underlying NM is also a prerequisite for developing effective therapies for NM in the future.
  • Jokinen, Mikko (Helsingin yliopisto, 2019)
    Väitöskirja Lapin ympäristökiistojen kulttuuriset tekijät tarkastelee millaisia kulttuurisia merkityksiä Lapin luonto ja sen käyttö saa paikallisten ihmisten ja maankäyttöä ohjaavan hallinnon parissa. Sosiaalinen ja kulttuurinen kestävyys sekä konfliktinhallinta ovat väitöskirjan läpäiseviä peruskäsitteitä ja teemoja, joiden toteutumista tarkastellaan useiden eri tapaustutkimusten kautta. Tutkimuksen maantieteellinen pääpaino on saamelaisten kotiseutualueella Ylä-Lapissa, ei kuitenkaan tiukasti sinne rajautuen. Väitöskirja koostuu seitsemästä erillisartikkelista, jotka on julkaistu kotimaisissa ja ulkomaisissa tieteellisissä sarjoissa. Artikkeleiden teoreettinen viitekehys ankkuroituu luonnonvarojen ja ympäristökiistojen hallintaa koskeviin sekä kulttuurintutkimuksen jaettujen merkitysten teorioihin. Käytetyt aineistot ovat kysely- ja haastattelututkimusaineistoja – aineistot sekä analyysimenetelmät ovat siten määrällisiä ja laadullisia. Tutkimus asettuu yhteiskuntatieteellisen ympäristötutkimuksen kenttään. Tutkimuksen keskeisiä havaintoja on, että Lappiin sijoittuvia ympäristökiistoja ja niiden hallintaa luonnehtii toimijoiden moninaisuus ja kohtaamattomuus. Osapuolten roolit ja motiivit ympäristökiistojen käsittelyssä ovat usein epäselvät tai ongelmalliset, eikä jaettua ymmärrystä kiistan luonteesta, syistä ja mahdollisista seurauksista useinkaan synny. Suomalaiselta yhteiskunnalta ja valtion maita hallinnoivalta Metsähallitukselta on puuttunut sellaisia institutionaalisia rakenteita ja toimintatapoja, jotka ovat kulttuurisensitiivisiä ja kykenevät sosiaalisesti kestävästi hallinnoimaan Lapin luonnonvaroja ja niitä koskevia kiistoja. Uusia aiempaa parempia toimintatapoja on kuitenkin viime vuosina otettu käyttöön. Lapissa korostuu perinteisten elinkeinojen kuten poronhoidon ja luonnonvarojen kotitarvekäytön merkitys ja arvostus, mutta niiden saamia kulttuurisia sisältöjä ei aina tunnisteta. Väitöskirjan teesi on, että luonnonkäytön ja ympäristökiistojen hallinnassa tarvitaan kulttuurisensitiivistä otetta. Nopean kulttuurimuutoksen läpikäyneessä Ylä-Lapissa menneisyys on vahvasti läsnä ja selittää paikallisten ihmisten luonnonkäyttöön liittämiä arvostuksia ja merkityksiä. Luonnonsuojelu on varsinkin Ylä-Lapissa merkittävä maankäyttömuoto, jonka toteuttaminen kaipaa kulttuuriset tekijät tunnistavia ja avoimempia lähestymistapoja saavuttaakseen paikallisväestön hyväksynnän ja tuen. Luonnonsuojeluhankkeissa kannattaa jatkossa hyödyntää luontoon ja sen käyttöön liittyvää kulttuurista tietoa yhdessä ekologisen tiedon kanssa, jotta hankkeet saavat myönteisen vastaanoton. Avainsanat: Lappi, ympäristökiista, kulttuurinen kestävyys, luonnonsuojelu, luonnonvaro­jen hallinta, saamelaiset.
  • Lyytinen, Outi (Helsingin yliopisto, 2019)
    Viruses are obligate parasites infecting the cells from all the three domains of life: Bacteria, Archaea and Eukarya. Ribonucleic acid (RNA) viruses contain ribonucleic acid as their genomic element instead of deoxyribonucleic acid (DNA). There are three main types of RNA viruses: positive-sense single-stranded [(+)ssRNA], negative-sense single-stranded [(-)ssRNA] and double-stranded RNA (dsRNA) viruses. This Thesis is focused on revealing molecular details of replication and assembly of two dsRNA viruses: Pseudomonas phage phi6 (phi6) and human picobirnavirus (hPBV). Double-stranded RNA viruses need to carry an RNA-dependent RNA polymerase (RdRp) inside their virion to the host in order to be able to replicate their genome. We characterized the hPBV RdRp enzymatically and structurally and revealed the similarities of this RdRp to the other known small dsRNA virus RdRps like phi6 RdRp, which has been extensively studied. We showed that hPBV RdRp has a canonical cupped right-hand polymerase structure, it can replicate and transcribe homologous and heterologous template RNA in the absence of capsid proteins and it also possesses terminal nucleotidyl transferase activity. This is only the second dsRNA virus RdRp reported with this activity. The assembly of these two viruses is relatively different due to the differences in their structures. Phi6 has three layers and a lipid-protein envelope as its outermost layer whereas hPBV does not have any lipids in its structure and is composed of only one layer of capsid proteins surrounding the dsRNA genome. The assembly of the inner protein layers of phi6 is very well-known whereas as the envelope formation and the assembly of hPBV capsid layer is largely uncharacterized. Our results suggest that hPBV might use a co-assembly of its capsid proteins and genomic RNA precursors as its assembly strategy. The envelope assembly of phi6 was studied expressing phi6 membrane proteins in Escherichia coli bacteria. Our results revealed that only one small membrane protein P9 can induce phi6-specific vesicle formation in E. coli cells. Also, heterologous green fluorescent protein can be added to the vesicles by co-expressing non-structural P12 protein. This study reveals interesting molecular details about the genome replication and assembly of hPBV, a relatively unknown opportunistic human pathogen, and the envelopment process of phi6. These results are biologically interesting and may have also biotechnological applications in the future.
  • Hlushchenko, Iryna (Helsingin yliopisto, 2019)
    This thesis explores the role of several actin-binding proteins in the regulation of brain physiology with a focus on dendritic spines. Dendritic spines are considered the plausible physical substrate for learning and memory, as their morphology allows for modulating incoming signals. Disruptions in spine density and morphology are also often associated with neuropsychiatric disorders. The two cellular processes representing neuronal learning are long-term potentiation (LTP) and long-term depression (LTD). Here, I show that the actin-severing protein gelsolin transiently relocates to dendritic spines upon LTD induction, but not LTP induction or spontaneous neuronal activity. It is plausible that the modest – but relatively long-lasting – LTD-induced elevation of Ca2+ concentration increases the affinity of gelsolin to F-actin, thus inducing the relocalization of gelsolin to dendritic spines. Proper spine regulation is crucial for learning in live animals. MIM is an I-BAR containing membrane curving protein, shown to be involved in dendritic spine initiation and dendritic branching in Purkinje cells in the cerebellum. Behavioral analysis of MIM knock-out (KO) mice revealed defects in both learning and reverse-learning, alterations in anxiety levels and reduced dominant behavior, and confirmed the previously described deficiency in motor coordination and pre-pulse inhibition. Anatomically, we observed a decreased density of thin dendritic protrusions, enlarged brain ventricles and decreased cortical volume. Genetic studies have pointed out that genes often disturbed in neuropsychiatric disorders encode synaptic actin regulators. We selected five genes encoding different actin-regulating proteins and induced ASD-associated de novo missense mutations in these proteins. These mutations induced changes in the localization of α-actinin-4, which localized less to dendritic spines, and for SWAP-70 and SrGAP3, which localized more to dendritic spines. Among the wild-type proteins studied, only α-actinin-4 expression caused a significant change in dendritic spine morphology by increasing mushroom spine density and decreasing thin spine density. We hypothesized that mutations associated with ASD shift dendritic spine morphology from mushroom to thin spines. An M554V mutation in α-actinin-4 (ACTN4) resulted in the expected shift in dendritic spine morphology by increasing the density of thin spines. In addition, we observed a trend toward higher thin spine density with mutations in myosin IXb and SWAP-70. Myosin IIb and myosin IXb expression increased the proportion of inhibitory synapses in spines. The expression of mutated myosin IIb (Y265C), SrGAP3 (E469K), and SWAP-70 (L544F) induced variable changes in inhibitory synapses.
  • Marwah, Veer Singh (Helsingin yliopisto, 2019)
    Toxicology is the scientific pursuit of identifying and classifying the toxic effect of a substance, as well as exploration and understanding of the adverse effects due to toxic exposure. The modern toxicological efforts have been driven by the human industrial exploits in the production of engineered substances with advanced interdisciplinary scientific collaborations. These engineered substances must be carefully tested to ensure public safety. This task is now more challenging than ever with the employment of new classes of chemical compounds, such as the engineered nanomaterials. Toxicological paradigms have been redefined over the decades to be more agile, versatile, and sensitive. On the other hand, the design of toxicological studies has become more complex, and the interpretation of the results is more challenging. Toxicogenomics offers a wealth of data to estimate the gene regulation by inspection of the alterations of many biomolecules (such as DNA, RNA, proteins, and metabolites). The response of functional genes can be used to infer the toxic effects on the biological system resulting in acute or chronic adverse effects. However, the dense data from toxicogenomics studies is difficult to analyze, and the results are difficult to interpret. Toxicogenomic evidence is still not completely integrated into the regulatory framework due to these drawbacks. Nanomaterial properties such as particle size, shape, and structure increase complexity and unique challenges to Nanotoxicology. This thesis presents the efforts in the standardization of toxicogenomics data by showcasing the potential of omics in nanotoxicology and providing easy to use tools for the analysis, and interpretation of omics data. This work explores two main themes: i) omics experimentation in nanotoxicology and investigation of nanomaterial effect by analysis of the omics data, and ii) the development of analysis pipelines as easy to use tools that bring advanced analytical methods to general users. In this work, I explored a potential solution that can ensure effective interpretability and reproducibility of omics data and related experimentation such that an independent researcher can interpret it thoroughly. DNA microarray technology is a well-established research tool to estimate the dynamics of biological molecules with high throughput. The analysis of data from these assays presents many challenges as the study designs are quite complex. I explored the challenges of omics data processing and provided bioinformatics solutions to standardize this process. The responses of individual molecules to a given exposure is only partially informative and more sophisticated models, disentangling the complex networks of dynamic molecular interactions, need to be explored. An analytical solution is presented in this thesis to tackle down the challenge of producing robust interpretations of molecular dynamics in biological systems. It allows exploring the substructures in molecular networks underlying mechanisms of molecular adaptation to exposures. I also present here a multi-omics approach to defining the mechanism of action for human cell lines exposed to nanomaterials. All the methodologies developed in this project for omics data processing and network analysis are implemented as software solutions that are designed to be easily accessible also by users with no expertise in bioinformatics. Our strategies are also developed in an effort to standardize omics data processing and analysis and to promote the use of omics-based evidence in chemical risk assessment.
  • Mennesson, Marie (Helsingin yliopisto, 2019)
    Anxiety disorders are the most prevalent mental illnesses in Europe, yet, their molecular basis is poorly understood. Unraveling the molecular mechanisms underlying the occurrence and maintenance of anxiety is crucial for effective drug development to treat anxiety disorders. In this thesis work, I focused on the NETO1 and NETO2 auxiliary proteins for kainate receptors (KARs) that tightly modulate the functional properties of the receptor. Because variants in KAR genes have been associated with psychiatric diseases in humans, and with anxiety-like behavior in mice, we hypothesized that NETO1 and NETO2 regulate anxiety through their modulation of KARs. Therefore, the aim of this thesis was to investigate the role of NETO1 and NETO2 in the regulation of anxiety and fear, and to evaluate their potential as novel treatment targets for anxiety disorders. To test our hypothesis, I first carried out a comprehensive behavioral screen of Neto1+/+, Neto1-/-, Neto2+/+ and Neto2-/- mouse anxiety-like and fear-related behaviors. We showed that neither NETO1 nor NETO2 regulated anxiety-like behavior in mice. However, Neto2-/- mice had reduced activity in novel environments without effect on locomotor activity in familiar environments, stress physiology or depression-like behaviors. In cued fear conditioning, Neto2-/- but not Neto1-/- mice had increased fear expression and delayed extinction. To establish the molecular and cellular mechanisms modulating the fear phenotype of the Neto2-/- mice, I investigated its expression pattern by in situ hybridization in the core fear network, composed of the medial prefrontal cortex, the amygdala and the hippocampus. Neto2 was widely expressed in all of these regions and in both excitatory and inhibitory neurons. Accordingly, the NETO2 protein was detectable in the same regions. We next established that in the synapses of these brain regions, the abundance of GLUK2/3 and GLUK5 KAR subunits was reduced 20–40% in the absence of NETO2. By focusing on the amygdala, the central brain region for the processing of fear-inducing stimuli and fear learning, we observed immature features of parvalbumin-expressing inhibitory neurons in Neto2-/- mice. Furthermore, we found a higher amplitude and frequency of miniature excitatory post-synaptic currents specifically in the basolateral amygdala, which is a critical brain region for fear memory consolidation. Concurrent with these results, dendritic spine density in thin dendrites was higher in Neto2-/- compared to Neto2+/+ mice. Taken together, these findings imply stronger glutamatergic synapses within the amygdala in the absence of NETO2. Finally, using the c-Fos immediate early gene as a marker for neuronal activation, we found increased activation of amygdala neurons in Neto2-/- compared to Neto2+/+ mice after fear acquisition. Higher activation of the amygdala may be related to stronger associative learning and be represented behaviorally by higher levels of fear expression during fear conditioning. To summarize, we showed that in the absence of NETO2, mice demonstrate higher conditioned fear expression and extinction delay suggestive of a higher overall conditionability, which is a symptom of posttraumatic stress disorder (PTSD). Furthermore, we established that neither Neto1 nor Neto2 is required for innate anxiety-like behaviors. We propose that the reduced KAR abundance at the synapses of Neto2-/- mice, together with the immaturity and increased excitability of the amygdala, and with the stronger activation of local circuits within the amygdala during fear acquisition underlie the higher conditionability and delayed fear extinction phenotype. Our findings suggest directions for future mechanistic studies on the role of NETO2 in fear conditionability. Taken together, this work showed for the first time that Neto2 is required for normal fear expression and conditioning, and that it modulates amygdala function during associative fear learning, findings with putative therapeutic significance for PTSD.
  • Vaattovaara, Aleksia (Helsingin yliopisto, 2019)
    For plants as sessile organisms effective signaling mechanisms are essential. Plants utilize signaling networks to receive cues from the environment and signal between cells. Various proteins and protein families are involved in the signaling networks in plants including receptor-like kinases (RLKs) and their related receptor-like proteins (RLPs). RLKs are typically located in the plasma membrane and transfer signals from the apoplastic space to the interior of the cell. The domain of unknown function 26 (DUF26) is a cysteine-rich protein domain involved in signaling. DUF26-containing proteins are a plant-specific protein family containing both RLKs and RLPs, including cysteine-rich receptor-like kinases (CRKs), plasmodesmata-localized proteins (PDLPs) and cysteine-rich receptor-like secreted proteins (CRRSPs). To facilitate investigation of the functions of DUF26 proteins, comprehensive phylogenetic and evolutionary analyses were combined with broad phenotypic analyses of crk mutants and structural investigation of two PDLPs from the model species Arabidopsis thaliana. These analyses revealed that DUF26-containing genes have a complex evolutionary history, including several steps of domain rearrangements and differential expansion and contraction patterns in different groups of plants and between different groups of CRKs, PDLPs and CRRSPs. CRKs were found to be involved in stress responses and development based on their loss-of-function phenotypes. The crystal structure of the AtPDLPs revealed a close structural homology between the DUF26 domain and fungal lectins, suggesting that DUF26 could be a carbohydrate-binding unit in plants. Annotation quality is crucial for virtually any type of sequence-based analysis, including phylogenetic estimation of relationships between genes, proteins and species. For this reason, the annotations of DUF26-containing genes were carefully curated in such a way as to facilitate the subsequent evolutionary analyses. Since most functional data is obtained from model species, only through thorough estimation of the relationships between proteins from different species we can reliably transfer information among species. In the future, as more functional information becomes available, the knowledge gained from this study will be applied in translational research between model species and crop species.
  • Kumar, Darshan (Helsingin yliopisto, 2019)
    The endoplasmic reticulum (ER) is the largest membrane bound organelle in a cell and has multiple responsibilities. Execution of the various duties performed by the ER requires it to be shaped in a rather complex and intricate manner. ER’s two major structural motives, namely sheets and tubules, play very complex yet not fully understood role in giving ER its overall structure and function. The ratio of sheet and tubule conformations differ significantly within cell types and during cell cycle. Such a balance is possible only with a well-functioning set of factors that constantly communicate with each other throughout a cell cycle. These factors are specifically responsible for either shaping the ER sheets or tubules in addition to factors that keep the dynamic nature of the ER sound. During mitosis, ER undergoes a major transformation in its structure, where the sheet-tubule ratio shifts more towards tubules. Specific factors keep this process sound by acting actively during the stage of mitosis for proper cell division to occur. Although research on such factors are still on-going, many in-depth details on such factors (e.g. their precise localization) and their mechanism of action plus novel factors for ER shaping still needs to be resolved using techniques involving high end light and electron microscopy. In addition, a constant battle in data analysis for answering key questions also persists. Development of tools to study and analyse data on the lines of image analysis and processing is an unmet need that needs simultaneous attention. The research in this thesis focuses on three family of proteins that we uncover as responsible candidates in shaping the ER. To aid the study, this thesis also discusses the development of a software platform for analysis of microscopic data generated during this study. In this research, Reticulon family of proteins (RTN) were characterised using high-end microscopic techniques. We showed RTN4A and RTN4B to localize to ER tubules and sheet edges using pre-embedding immuno electron microscopy (immuno-EM) and electron tomography. Using qPCR, RTN4A and RTN4B were observed to be the most expressed isoforms in neurons and epithelial cells respectively. FAM134C, a poorly characterised protein was identified as one of the RTN4B interacting proteins. FAM134C localised to the ER where it specifically resided at high curvature ER (sheet edges and tubules) similar to RTN4B. FAM134C, similar to the RTN4B also had the capability to promote ER tubules upon overexpression. In addition, another family of proteins belonging to receptor expression enhancing protein (REEP), namely REEP3 and REEP4 were studied for shaping ER during mitotic stage of cell cycle. REEP3 and REEP4 collectively were observed both in tubulating peripheral ER during mitosis and clearing tubular ER from the chromatin for a normal mitosis to take place. Collectively, this work elaborates on proteins belonging to three classes that shape and position the ER specifically either in interphase or during stages of cell division. Our findings also throws light on the role of different domains in each of these proteins such as the reticulon homology domain (RHD) that was observed to be present in all these proteins under study. The RHD previously known for inserting partially and unsymmetrically in the outer leaflet of the ER gives a strong indication for proteins like RTN4B and FAM134C to localize to ER thus tubulating ER upon overexpression conditions. We uncovered the RHD’s crucial role in ER shaping and positioning in REEP3/4 during mitosis.
  • Liu, Ying (Painosalama Oy, 2019)
    In nature, animals often live in an environment with unpredictable food availability and abundance. In response to these changes in nutrient landscape, animals coordinate growth rate and metabolism. A key signaling pathway mediating the nutrient-dependent responses is the insulin/insulin-like growth factor signaling (IIS). IIS controls growth and metabolism through regulating a large number of target genes. Thus, to understand the mechanisms by which nutrient-dependent control of physiology occurs, it is important to address the transcriptional regulation involved in IIS. However, our understanding of the transcriptional regulators involved in IIS, as well as their mechanism of action, remains incomplete. Drosophila is a powerful model organism to analyze gene regulatory mechanisms involved in IIS, due to its genetic toolkit and high conservation of the IIS pathway. Drosophila has eight insulin-like peptides (dILPs), which are homologous to mammalian insulin and insulin-like growth factors (IGFs). Binding of dILPs to their receptors induces IIS and activates downstream PI3K/AKT, MAPK/ERK and TOR pathways, which control the expression of a large group of genes, regulating metabolic homeostasis and tissue growth. In this study, we systematically explored the transcriptional regulators involved in the regulation upstream and downstream of IIS. We identified ten candidates that regulate dILP transcription, and nine that mediate gene expression downstream of IIS. Among the IIS downstream regulators, we identified a chromatin-binding protein, PWP1. The activation of PWP1 is controlled by nutrition levels through the TORC1 pathway. PWP1 associates with RNA Pol I, and enriches in rDNA and 5S rRNA gene regions to maintain the chromatin in a transcription-competent state to promote the expression of rRNAs. Besides, we showed that the expression level of PWP1 in human head and neck squamous cell carcinoma tumors associates strongly with patient prognosis, suggesting its important role in tumorigenesis. Among the regulators of dILP transcription, we found a novel transcription factor that promotes dILP6 expression, and it is likely a new component of the starvation-responsive gene regulatory network. In addition, we explored the Hyd-mediated regulation of transcription factor Myc, and the role of this regulation in tissue growth control and cancer. In conclusion, our studies identified important but poorly studied regulators of IIS, and further revealed novel mechanisms of how IIS is involved in metabolism and growth regulation. These findings not only establish the groundwork for the molecular basis of IIS function, but also provide opportunities for the therapeutic treatment of IIS-related diseases in humans. For instance, we observed that PWP1 is a potential therapeutic target and a useful marker for grading cancer aggressiveness. Hence, our findings opened a new research avenue for further studies of PWP1 in tumorigenesis and cancer therapy, providing the opportunity to help prognosis and treatment, and ultimately improve the quality of life of cancer patients.
  • Sevilem, Iris (Helsingin yliopisto, 2019)
    The vascular system of plants functions as a transportation route for water, nutrients and signaling molecules while also forming a support structure and generating most of the radial growth by increasing the number of cell files through periclinal cell divisions. These features have transformed life on Earth by enabling plants to colonize land and grow larger. In mature plants, the conductive tissues xylem and phloem are produced from stem cells in the vascular cambium, which develops from the procambium formed during early development. The vascular cylinder of the Arabidopsis root comprises a central xylem axis with a peripheral phloem pole on either side and procambial cells located between the xylem and phloem. Formation of the vascular pattern requires high auxin and cytokinin signaling domains in the xylem and phloem/procambium positions, respectively. However, the gene regulatory network acting downstream of these hormonal cues has remained unknown. I investigated procambium patterning in the Arabidopsis root. Our research group discovered that radial growth is activated in the peripheral phloem domain by six mobile DOF transcription factors that we named PHLOEM EARLY DOF (PEAR) proteins, consisting of PEAR1, PEAR2, and their four homologues. PEAR proteins form an inverse concentration gradient to the HD-ZIP III transcription factors, which inhibit periclinal cell divisions in the central domain partially by inhibiting the movement of PEAR proteins. HD-ZIP III expression is promoted by auxin in the xylem axis and inhibited by endodermis-derived mobile microRNA165/166 in the periphery. The PEAR and HD-ZIP III genes form a feedback loop in which the PEAR proteins promote HD-ZIP III transcription while the HD-ZIP IIIs inhibit PEAR transcription and protein movement. The PEAR-HD-ZIP III regulatory module decodes hormonal and microRNA signals to result in the formation of a highly active peripheral zone and a more quiescent central zone during procambium development. We also determined that a member of the DOF family, DOF2.1, acts downstream of TARGET OF MONOPTEROS 5/LONESOME HIGHWAY-dependent cytokinin biosynthesis to regulate periclinal cell divisions in the outer procambial cells in contact with the xylem axis. Together, PEAR and DOF2.1 proteins control all of the periclinal divisions in the procambium through their activity in partially distinct domains. We also identified SUPPRESSOR OF MAX2 1-LIKE 3 (SMXL3), a member of SMXL subclade 2 which is expressed in the early phloem and procambium cells, as a putative direct target of PEAR2 that is sufficient to promote periclinal divisions. Characterization of SMXL subclade 2 identified SMXL3, 4 and 5 as essential regulators of phloem formation that act very early in development and thus are required for all aspects of phloem development. Phloem specification requires periclinal divisions in the procambium. SMXL3, 4 and 5 act in both the periclinal divisions and phloem specification in a partially redundant manner. Furthermore, analysis of regulators downstream of the PEARs revealed that they not only promote cell proliferation but also specify the identity of the surrounding cells non-cell autonomously, including procambial and phloem pole pericycle identity. Our work highlights the importance of cell-to-cell communication in plant development. The interaction of mobile hormones, transcription factors and microRNAs originating from different tissues is required to coordinate developmental processes in the vascular cylinder. We have assembled the most complete understanding to date of the regulatory network coordinating procambial development and have identified the protophloem sieve elements as the organizers of radial growth during the early stages of vascular development in the Arabidopsis root. These findings can potentially be used to increase yields in forestry and agriculture.
  • Hellemann, Dana (Helsingin yliopisto, 2019)
    Benthic nitrogen (N) cycling in sandy sediments in the stratified aphotic coastal zone (> 15 m) of the Baltic Sea was investigated along a north–south environmental gradient of N loading, trophic status, coastal geomorphology and sediment permeability. The aim was to establish a more comprehensive view of the Baltic Sea coastal N filter, where N transformation processes remove (via denitrification and anaerobic ammonium oxidation) and retain (via dissimilatory nitrate reduction to ammonium) land-derived N and thereby reduce its availability to the open sea; so far these processes have not been quantified in the deeper, aphotic sandy sediments. The main results are that a) not all sandy sediments were permeable enough to experience advective pore-water flow – mass transport in non-permeable sands functions via diffusion and fauna-mediated fluxes only, which simplifies biogeochemical measurement design; b) N removal rates were affected by the availability of labile particulate organic matter as a source of labile organic carbon and N, resulting in higher removal rates in eutrophic than in oligotrophic conditions, as well as similar removal rates in non-permeable sands and muds when also the substrate availability was similar; c) seasonal N removal in the stratified aphotic coastal zone is largely driven by the hydrography-controlled development of bottom water temperature, and differs from the seasonal pattern observed in the mixed photic coastal zone; and d) the role of dissimilatory nitrate reduction to ammonium in the aphotic coastal sandy sediments of the Baltic Sea is presumably more important than previously anticipated. These results indicate that the sandy sediments in the aphotic coastal zone of the Baltic Sea have an important role in N removal and retention, and are thus an integral component of the Baltic coastal N filter. The results further show the strong influence of the local environment on N cycling rates, emphasizing the need for context dependent data analysis, particularly in a diverse coastal setting such as in the Baltic Sea.
  • Gammal, Johanna (Helsingin yliopisto, 2019)
    The rapid rates of global biodiversity loss and the serious anthropogenic pressures currently affecting our marine ecosystems have increased the interest in and importance of understanding the role of biodiversity for ecosystem functioning. It is well known that biodiversity contributes to a plethora of ecosystem functions, and that benthic macrofauna have an influence on several functions that sedimentary ecosystems provide. Biodiversity-ecosystem function relationships can however be very context dependent, which complicates our ability to generalize on the role of biodiversity and to predict the consequences of environmental change for ecosystem functions and services. In this thesis, biodiversity-ecosystem functioning (BEF) relationships were examined in a variety of field studies in different ecosystems to elucidate the context-dependence of these relationships in heterogeneous real-world coastal zones. This included testing the effects of hypoxia, habitat characteristics and background biodiversity on the link between the fauna and the functioning in terms of benthic nutrient recycling. Hypoxia is a serious threat both in open and coastal waters, and its consequences for the benthic macrofauna-function link was investigated through sampling along natural gradients of increasing hypoxia, in a low-diversity as well as a higher-diversity coastal system. In both systems, the benthic macrofaunal communities were clearly decimated with declining oxygen conditions, although some species did show a higher tolerance of low oxygen concentrations. These species were likely important for the solute fluxes as long as the species could prevail, but during severe hypoxia and anoxia nutrient recycling processes were heavily altered, with markedly larger effluxes of ammonium and phosphate. A large variation in macrofaunal communities and solute fluxes was also observed between normoxic sites, with indications that even small variations in sediment organic material content and carbon/nitrogen ratio affected the relationships. The effects of environmental context in mediating ecosystem functioning were further assessed through sampling 18 sites on a gradient of grain size, from coarse sand to silty sediments, with varying organic material content and vegetation. Benthic macrofaunal community abundance, biomass and species richness was higher in coarser sediments and in habitats with more vegetation. Biomass and abundance of a few dominant species together with organic content, amount of roots and vegetation were indicated to contribute to nutrient recycling processes across the sedimentary gradient. Closer analyses suggested that the benthic macrofauna had a stronger influence on the ecosystem functions in muddy and medium sediments than in sandy sediment, despite the richer communities in the sandy sediments. Species redundancy is hypothesised to be important for the stability of ecosystems. Therefore redundancy patterns over space and their ability to reflect natural biodiversity-ecosystem function relationships across an extensive sandflat were explored. Redundancy over space was observed within the investigated functional groups, but the dominant species were indicated to drive the spatial distribution of the functional groups and the ecosystem functioning. In summary, these correlative field studies indicated that abundance and biomass of benthic macrofauna are important for nutrient recycling processes at the sediment-water interface, but the relationships are significantly mediated by environmental context. Hypoxic conditions in coastal zones are especially problematic because the heavily altered nutrient recycling processes and decimated macrofauna communities, can have severe consequences for overall functioning of the ecosystems. Furthermore, a few dominating species were suggested to be especially important for the investigated ecosystem functions regardless of large variations in species richness across studies. Hence, it is important to consider natural variability, as well as several measures of biodiversity, not only species richness, in BEF studies in order to obtain a more realistic understanding of the biodiversity-ecosystem function relationships in heterogeneous coastal areas. An improved understanding of the complex links within coastal ecosystems is a prerequisite for improved management and conservation.
  • Kivioja, Jarno (Helsingin yliopisto, 2019)
    The objective of this thesis was to facilitate molecular detection and treatment of acute myeloid leukemia (AML) patients with recurrent t(5;11)(q35;p15.4) translocation, which joins nucleoporin 98 (NUP98) and nuclear receptor binding SET-domain protein 1 (NSD1) genes together. These patients suffer from a malignant disease with highly unfavorable prognosis and no evidence regarding efficient therapeutic options. In study I, we investigated NUP98-NSD1 transcript variants from AML patients with t(5;11) to facilitate its molecular detection from newly diagnosed AML patients and post-treatment samples. We focused on this topic since, comparably to many AML-defining translocations, the detection of t(5;11) relies on accurate molecular screening methods. This translocation cannot be captured using conventional cytogenetic methods (G-banding) due to its subtelomeric localization and small size. Moreover, potential for alternative fusion transcripts may complicate detection and quantification of NUP98-NSD1. In this study, we discovered three chimeric NUP98-NSD1 transcripts from an index patient, which were later validated from two additional patients. The transcripts harbored two alternative fusion junctions joining NUP98 exon 11 as well as exon 12 to NSD1 exon 6, alternative 5’ donor site of NUP98 exon 7, and skipping of NSD1 exon 7. Intriguingly, residual levels of the previously unknown fusion gene between NUP98 exon 11 and NSD1 exon 6 was found to increase in two patients during disease progression. In study II, our aim was to identify novel, more efficient, and less toxic small-molecule inhibitors for the treatment of NUP98-NSD1+ AML using high-throughput drug sensitivity and resistance testing together with RNA sequencing. By screening over 300 anti-cancer drugs on patient cells and experimentally generated mouse cell models, we found that multikinase inhibitor dasatinib and pan-BCL-2 inhibitor navitoclax effectively and specifically target BM MNCs expressing NUP98-NSD1 and FLT3-ITD. In combinatorial drug screens, strong synergistic interactions were found between dasatinib and navitoclax. Gene expression analysis revealed up-regulation of genes encoding for targets of dasatinib and navitoclax, LCK, FGR, and BCL2A1. Furthermore, we discovered that NUP98-NSD1+/FLT3-ITD+ BM MNCs are highly resistant to topoisomerase II inhibitors such as mitoxantrone. It remains to be investigated whether replacing topoisomerase II inhibitors with dasatinib and navitoclax in AML induction therapy could lead to improvements in long-term survival in patients with NUP98-NSD1 and concomitant FLT3-ITD.
  • Chrysafi, Anna (Helsingin yliopisto, 2019)
    Stock assessment is a critical step in fisheries management, since it directly estimates reference points that help determine whether a population’s size is acceptable and subsequently, to set harvest levels. Therefore, many international agreements require that all exploited aquatic populations are assessed quantitatively. However, for the majority of the worlds’ harvested fish stocks, data is lacking. Such fisheries are often referred to as data-poor or data-limited and are a major challenge for stock assessment scientists and fisheries managers, since the traditional approaches to stock assessment cannot be implemented. The necessity to assess the status of all fisheries, led to the development of models tailored to data-limited situations. In this thesis, I first introduced the characteristics of data-limited fisheries, and then described the various quantitative indicators and models developed to assess them, some of which are widely used in real assessment schemes. I reviewed the approaches by their input requirements and their biological realism. Compared to the models used to assess data-rich stocks, models tailored to data-limited stock assessment contain a large degree of uncertainty and therefore, I recommended further exploration of the existing datalimited approaches. This thesis continued by focusing on a particular group of data-limited assessment methods, which are based on stock reduction analysis. Although such models can cope with low data availability, at the same time, they are particularly sensitive to the misspecification of relative stock status (expressed as the current biomass level relative to virgin biomass), a critical input requirement. However, stock status is unavailable for the majority of data-limited stocks. Therefore, I explored different sources of information used to estimate stock status under such circumstances. First, I considered the use of fisheries experts’ opinion and presented a method to elicit expert knowledge using a novel, user-friendly on-line application. To evaluate the experts’ ability to predict stock status, I compared the elicited distributions to stock statuses derived from data-rich models. In this work, I explored the performance of experts with different levels of experience in stock assessment, since scientific expertise is not evenly distributed throughout the world, and quantified how well they performed relative to each other. The results indicated that the true stock status is the most significant factor accounting for bias in expert opinions, followed by their experience level. Nevertheless, expert opinions are often used to inform management decisions and this thesis revealed that for data-limited stock assessment, expert elicited stock status priors potentially can be highly biased, leading to highly biased harvest recommendation levels. A way to overcome this issue is by calibrating expert judgment. To achieve this, my coauthors and I developed a hierarchical Bayesian model for expert calibration. The model’s main assumption is that experts’ biases vary as a function of the true value of the parameter, as identified in the expert elicitation experiment. Experts’ bias function was explicitly modeled, following the supra-Bayesian approach, using Gaussian processes to construct the prior, and the results of the expert elicitation experiment were used as calibration data to infer the posterior. The constructed models were tested both with simulated data and with the expert elicitation results. The tested models for expert judgment calibration, substantially improved stock status predictions compared to those that were uncalibrated and in comparison to vague uniform guesses, thereby demonstrating the value of calibration in minimizing expert bias. In the last article included in this thesis, uncalibrated and calibrated expert opinion derived stock status priors were compared to productivity and susceptibility (PSA) vulnerability scores and catch trend-derived (Boosted regression trees; BRTs) stock status priors. Furthermore, the performance of each of these methods was evaluated and compared to a commonly used prior that assumes a stock is at B40% (i.e. 40% of the virgin biomass). First, I evaluated the degree of bias in estimating true stock status and then, the effect of bias on the estimation procedure of overfishing limits (OFLs) in the specific assessment models for ten data-rich stocks. All, with the exception of fisheries experts with no experience in stock assessment, provided more accurate priors about stock status than the B40% rule. Experts with experience in stock assessment produced particularly informative and accurate priors, exemplifying their important role in the assessment procedure. Based on the performance evaluation and the data requirements for constructing a stock status prior, I recommended a procedure for selecting the most appropriate prior(s).
  • Gehrmann, Friederike (Helsingin yliopisto, 2019)
    Climate change will be most pronounced at high latitudes where it will affect autumn, winter and spring disproportionally more than the growing season. Increasing or decreasing precipitation as snow, rising temperature and more frequent freeze-thaw cycles raise uncertainties about how the timing of snowmelt and the length of the growing season will change for northern plants. The timing of plant developmental stages (phenophases) in relation to snowmelt timing is important for avoiding harsh weather conditions in spring and ensuring a long growing season. In this doctoral dissertation, I investigate the effect of snowmelt timing and temperature conditions on plant phenology and plant stress. The first objective was to determine the natural variation in snowmelt timing on a small spatial scale in subarctic-alpine Finland. Such variation in the microclimate is created by the landscape topography and show the range of conditions plant populations are currently adapted to. Snowmelt timing varied by up to seven weeks within a few metres distance, so that early-melting plots were exposed to more frequent and more severe spring freezing events. This implies that plant populations are already exposed to the kind of climatic conditions which would be predicted from climate change. Secondly, I studied how the physiology of Vaccinium vitis-idaea and the phenology of seven subarctic-alpine plant species are affected by this natural variation in microclimate. The higher numbers of freezing events in early-melting plots were related to a higher reduction in the quantum yield of photosystem II (ΦPSII) in V. vitis-idaea, but not to increases in frost damage. This species therefore does not suffer substantial damage from the natural climatic variation in this habitat, implying that in this location it is likely highly resistant to the predicted changes in climate. Differences in snowmelt timing also led to three distinct patterns of phenological timing in subarctic-alpine plant species along the snowmelt gradient. These patterns can raise ideas about the mechanisms underlying the rate of plant development and can help researchers classify past and future phenological responses. Lastly, I compare the effect of natural versus experimental gradients of snowmelt timing on the timing of autumn senescence in High Arctic plants. The results show that the two gradients lead to different conclusions regarding the effect of snowmelt timing on the timing of autumn senescence. Selective warming only in the beginning of autumn had a delaying effect on autumn senescence in Dryas octopetala, despite the short duration of the warming treatment. Previous studies have commonly employed a warming treatment over the entire growing season. The results of this dissertation highlight that we need to integrate different approaches to studying climate change effects on plants. Natural gradients, although often disregarded, can give additional insight into plants’ adaptation to climate variation and therefore complement experiments. Experimental treatments simulating climate change need to be very selective in which period of the plant life cycle they are applied as expected changes in climate strongly depend on the season. Due to the variable sensitivity of different phenophases and plant species to climate and the importance of plants in the ecosystem carbon balance, further detailed research is needed to understand the drivers and mechanisms underlying plant phenology.
  • Nevalainen, Maisa (Helsingin yliopisto, 2019)
    The risk of a major oil spill in the Arctic has become a matter of global concern, since climate change is extending the ice-free period and bringing more shipping to the area. The Arctic is already under great pressure from climate change, and an oil spill in this unique and sensitive environment could be a catastrophe for its biota. Fortunately, no major oil spill has happened in the true Arctic yet, but as the probability of one is increasing, we need to prepare for the potential consequences. Understanding the likely impacts of Arctic oil spills could greatly benefit conservation of the area as, for example, spatially and temporally varying risk could be taken into account when selecting shipping routes. Hence, comprehensive knowledge about the impacts of oil spills on Arctic ecosystems is needed. So far, however, knowledge about the likely impacts of oil on Arctic biota is scarce and insufficient for comprehensive risk assessment. The thesis constructs and applies a probabilistic framework for assessing the environmental risk oil spills pose for marine biota in the data-poor Arctic. The work consists of the summary and four research papers. Paper I brings together the current understanding about Arctic oil spills and their environmental impacts, and conceptualizes that knowledge as a probability-based framework that can guide further risk assessment. It further identifies the key Arctic marine functional groups that environmental risk assessment should focus on. Paper II carries out an expert elicitation to quantify the acute oil spill -induced mortality of adult and offspring individuals belonging to each functional group. Paper III develops a vulnerability index describing the acute mortality and the longer-term recovery potential of the functional groups based on scientific and grey literature. Paper IV uses the information collected in papers I–III and combines it with estimates of oil spreading and species distributions to compare the spatiotemporally varying mortality risk for polar bears, ringed seals and walrus in a case study area, the Kara Sea. The results of the thesis suggest that, in general, polar bears and marine birds are most at risk from spilled oil in the Arctic, but there is great variation in the risk depending on the timing of the spill and the type of oil spilled. Moreover, the distribution of biota in relation to shipping routes can have a major impact on the risk the spilled oil poses to them. Furthermore, the amount of ice present at the spill site can alter the risk to biota, as ice cover affects both the spreading of oil and the abundance of species in the vicinity of the oil spill. On an acute scale, medium density oil spilled when ice concentration are relatively low seems to be the worst-case accident scenario when considering the joint impact on all biota, but determining the safest shipping route may prove to be challenging. This thesis offers new insights into the risk that oil spills pose to Arctic biota, and is a step on the way towards a comprehensive understanding of the impact of Arctic oil spills. However, there are still great knowledge gaps, which this thesis both identifies and aims to minimize by suggesting different methods for efficient data collection to benefit risk management related to Arctic shipping. Additional research is needed to evaluate the longer-term impacts of spilled oil and the persistence of oil in cold environments in particular. Furthermore, the need for a valuing method to guide both risk assessment and management is recognized.

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