Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • 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.
  • Lampi, Mirka (Helsingin yliopisto, 2019)
    Viruses are the most abundant entities in the biosphere, the estimated amount of viruses is more than 10^30. The number is incomprehensible and exceeds the amount of host cells at least by one order of magnitude. Viruses are extremely diverse entities by means of morphologies, sizes, genomes and biochemical and biophysical properties. As obligate parasites, viruses can only be propagated in living cells. This sets challenges for the virus purification, since the starting material contains host and growth media derived impurities. Medical applications such as phage therapy, vaccine development, and gene therapy require large amounts of highly purified viruses and virus-like particles (VLPs). Nanotechnology utilizes viruses and VLPs as building blocks for nanoscale materials and devices and also requires virus purification methods which maintain the biophysical and biochemical properties of the particles. Viruses are often purified with combinations of different methods. The most common ones are precipitation and ultracentrifugation. Precipitation does not lead into high purities and is generally applied as a pre-step for purification. Ultracentrifugation leads to high purity but it exposes viruses to high shear forces possibly leading to losses of infectivity. The large size of many viruses may restrict utilization of traditional chromatography. However, monolithic matrices are applicable for virus purification. In this work asymmetrical flow field-flow fractionationation (AF4) method was developed for virus purification. AF4 is a highly versatile size-based separation method applicable for samples with sizes ranging between ~1‒500 nm. The separation in AF4 is conducted with the aid of liquid flows. Solid stationary phase is not applied at all, thus no strong interactions during the separation occur making the method gentle. Several parameters in the AF4 system are adjustable, making the method highly versatile and an attractive alternative for virus purification. In this study, AF4 conditions were optimized for purification of six prokaryotic viruses, having different morphologies and properties. Analytical sample channel and preparative UV-detector were utilized. Yields of infective viruses were high and purity levels comparable to the ones obtained with a method based on precipitation and ultracentrifugation. AF4 was proven to be applicable for all tested viruses, also the ones requiring high ionic strength conditions were amenable for AF4 purification. The AF4-method is fast and obtained virus preparations were homogenous. As the system is highly versatile, it is expected that it can be tailored for other viruses as well, to meet the further needs of virus purification.
  • Siebenhühner, Felix (Helsingin yliopisto, 2019)
    Neuronal processing is distributed into anatomically distinct, largely specialized, neuronal populations. These populations undergo rhythmic fluctuations in excitability, which are commonly known as neuronal oscillations. Electrophysiological studies of neuronal activity have shown that phase synchronization of oscillations within frequencies characterizes both resting state and task execution and that its strength is correlated with task performance. Therefore phase-synchronization within frequencies is thought to support communication between oscillating neuronal populations and thereby integration and coordination of anatomically distributed processing in cognitive functions. However, it has remained open if and how phase synchronization is associated with directional flow of information. Furthermore, oscillations and synchronization are observed concurrently in multiple frequencies, which are thought to underlie distinct computational functions. Little is known how oscillations and synchronized networks of different frequencies in the human brain are integrated and enable unified cognitive function and experience. In the first study of this thesis, we developed a measure of directed connectivity in networks of coupled oscillators, called Phase Transfer Entropy (Phase TE) and tested if Phase TE could detect directional flow in simulated data in the presence of noise and signal mixing. Results showed that Phase TE indeed reliably detected information flow under these conditions and was computationally efficient. In the other three studies, we investigated if two different forms of inter-areal cross-frequency coupling (CFC), namely cross-frequency phase synchrony (CFS) and phase-amplitude coupling (PAC), could support integration and coordination of neuronal processing distributed across frequency bands in the human brain. In the second study, we analyzed source-reconstructed magneto- and electroencephalographic (M/EEG) data to investigate whether inter-areal CFS could be observed between within-frequency synchronized networks and thereby support the coordination of spectrally distributed processing in visual working memory (VWM). The results showed that CFS was increased during VWM maintenance among theta to gamma frequency bands and the strength of CFS networks predicted individual VWM capacity. Spectral patterns of CFS were found to be different from PAC, indicating complementary roles for both mechanisms. In the third study, we analyzed source-reconstructed M/EEG data to investigate whether inter-areal CFS and PAC could be observed during two multi-object visual tracking tasks and thereby support visual attention. PAC was found to be significantly correlated with object load in both tasks, and CFS in one task. Further, patterns of CFS and PAC differed significantly between subjects with high and low capacity for visual attention. In the fourth study, we analyzed intracerebral stereo-electroencephalographic data (SEEG) and source-reconstructed MEG data to investigate whether CFS and PAC are present also in resting state. Further, in order to address concerns about observations of CFC being spurious and caused by non-sinusoidal or non-zero mean signal waveforms, we introduced a new approach to identify true inter-areal CFC connections and discard potentially spurious ones. We observed both inter-areal CFS and PAC, and showed that a significant part of connections was unambiguously true and non-spurious. Spatial profiles differed between CFS and PAC, but were consistent across datasets. Together, the results from studies II-IV provide evidence that inter-areal CFS and PAC, in complementary ways, connect frequency-specific phase-synchronized networks that involve functionally specialized regions across the cortex to support complex functions such as VWM and attention, and also characterize the resting state. Inter-areal CFC thus may be crucial for the coordination and integration of spectrally distributed processing and the emergence of introspectively coherent cognitive function.
  • Kalliola, Maria (Helsingin yliopisto, 2019)
    Phytohormones affect all the developmental stages of plant from germination to flowering but also plant responses to biotic (e.g. pathogens) and abiotic stresses (e.g. drought and cold) and furthermore, acclimation to environmental changes. Phytohormones form a signalling network affecting both directly and indirectly many functions in plants; for example stomatal openness is affected by phytohormones. Stomata allow gas-exchange between air and leaf, thus optimizing between CO2 intake i.e. effectiveness of photosynthesis, and the inevitable evaporation of water through the open stomata. Stomata furthermore provide an entrance for pathogens but also for example air pollutants, like tropospheric ozone that causes oxidative stress in plants, employing stomata to enter the plant. Phytohormones also have a central role in pathogen responses and innate immunity in plants. Thus, it can be concluded that stress and pathogen responses, innate immunity, oxidative stress tolerance and stomatal responses are all tied together via the phytohormone signalling network. This thesis concentrates mainly on effects of two phytohormones; auxin and the rather newly discovered class of phytohormones, strigolactones. Auxin is historically known for its role in plant growth and development, but it also affects stress and defence responses by interacting with other hormones; auxin and the most important hormone in bacterial pathogen responses, salicylic acid, act in a mutually antagonistic manner and many pathogenic micro-organisms produce auxin within their interactions with plants. Interestingly, auxin is also the target of strigolactone pathway and strigolactones act by dampening auxin transport. Thus, both strigolactones and auxin affect lateral branching in plants – auxin by classical polarity of auxin transport and strigolactones via affecting auxin. Strigolactone and auxin furthermore share other commonalities since also strigolactone was recently discovered to affect stress and pathogen responses in plants. Strigolactone signalling is complex and all the details are still not known. In strigolactone perception the F-box protein MAX2 functions together with the strigolactone receptor, D14 protein. Other MAX proteins (MAX1, 3 and 4) function in strigolactone synthesis. In this thesis first MAX2 and later also all the other strigolactone-related proteins were discovered to have a role in susceptibility to pathogens. However, MAX2 was found to have an exceptional role compared to the other strigolactone-related proteins; only max2 plants have higher stomatal conductance than the wild-type plants and only max2 was found to contribute to sensitivity to oxidative stress. MAX2 also affects hormonal signalling; ABA levels in max2 were particularly high in excised leaves that were left to dry. Interestingly, it was concluded that MAX2 acts in a parallel signal pathway to the well characterized guard cell ABA signalling pathway, which was discovered by crossing max2 with the well-known guard cells affecting mutants (ABA biosynthesis mutant aba2, guard cell ABA signalling mutant ost1, and ghr1 required to regulate ion channel activity).
  • Spoljaric, Inkeri (Helsingin yliopisto, 2019)
    Spontaneously arising network events are a characteristic feature of all developing neural networks. This activity is crucial for normal neuronal development and the establishment of appropriate synaptic connectivity. In the developing hippocampus, depolarizing GABAergic drive is essential in generation of early network events, known as giant depolarizing potentials (GDPs). Blockade of GABAergic signaling leads to hypersynchronization of the network and emergence of ictal-like events, pointing to dual, both excitatory and inhibitory roles for GABA, in regulation of these events. In Studies I-III of this thesis, we examined the role of GABAA receptor (GABAAR) -mediated neurotransmission with some parallel work on glycinergic signaling as well as neuronal Cl- regulation in modulation of GDPs in the developing rodent hippocampus. In Study I, we demonstrate that low levels of GABA and glycine suppress GDPs by activating extrasynaptic receptors. This implies that regardless of the depolarizing drive for Cl- currents at this developmental stage, a low conductance via Cl- -permeable GABAARs and glycine receptors (GlyRs) can cause efficient shunting and inhibition of the network events. In Study II, we discovered that sustained activation of a subset of hippocampal interneurons, caused by the neuropeptide arginine vasopressin (AVP), silences the network events in the perinatal hippocampus, regardless of the maturational level of the GABAergic system as compared across species. This is attributed to decreased synchronous interneuronal input that is essential for the GDP generation. In Study III, we demonstrate that transport-functional K-Cl cotransporter 2 (KCC2) is present in the CA3 pyramidal neurons already in the perinatal stages in mice and rats. Cl- extrusion by KCC2 counteracts the dominant Na-K-2Cl cotransporter 1 (NKCC1) -mediated Cl- uptake and restrains the depolarizing GABAergic drive onto the CA3 pyramidal cells. Thereby, function of KCC2 limits pyramidal neuron spiking and synchronization during GDPs and participates in the modulation of GDPs from their developmental onset. This work describes novel physiological GABAergic mechanisms that control GDPs in the perinatal rodents and establishes a role for KCC2 in regulation of pyramidal neuron excitability and synchronization during GDPs starting from their developmental onset.
  • Camarena Gómez, María Teresa (Helsingin yliopisto, 2019)
    Global warming is one of the most alarming pressures affecting marine ecosystems worldwide. One of the indirect effects of the increasing surface-water temperature is the change in phytoplankton community composition, shifting in some ecosystems from diatom predominance towards the dinoflagellate predominance or co-occurrence with diatoms during blooms. These distinct phytoplankton groups vary in the quality and/or quantity of the dissolved organic matter (DOM) they release, which may have contrasting effects on the associated bacterioplankton communities, in terms of structure and function, and also on the carbon flux passing through the microbial loop. The main objective of this thesis was to assess the effect of diatoms and dinoflagellates on shaping the bacterial community composition and dynamics in different ecosystems in which either one or both of these two groups dominate the phytoplankton bloom, such as the Baltic Sea and the Humboldt Current System (HCS) off Chile. This was achieved by conducting both experimental and field studies in these areas. Phytoplankton community composition and the stage of the bloom phase clearly affected to the bacterial community composition and dynamics in both ecosystems. Alphaproteobacteria, dominated by SAR11 and Rhodobacteraceae, was the most abundant bacterial class in all studies. The oligotrophic SAR11 dominated in pre-bloom conditions and was associated with dinoflagellates. In contrast, copiotrophic bacteria belonging to the classes Flavobacteriia, Gammaproteobacteria, Betaproteobacteria and the family Rhodobacteraceae (genera Loktanella, Planktotalea, Planktomarina and Amylibacter) were associated with diatom species such as Achnanthes taeniata, Chaetoceros spp., Skeletonema costatum and Thalassiosira levanderi in the Baltic Sea and with Thalassiosira spp. in the HCS. In addition, in the Baltic Sea, bacterial communities dominated by copiotrophs had higher bacterial production rates than in SAR11 dominated bacterial communities. Hence, the diatom-released DOM boosted the development of more productive bacterial communities during phytoplankton blooms. Further differences in the bacterial community composition were driven by the different salinities in these two ecosystems; Betaproteobacteria, Planctomycetes and Actinobacteria were more abundant in the brackish Baltic Sea than in the HCS. The results of this thesis highlight that the shift to the dinoflagellate dominance or co-occurrence with diatoms may affect the bacterial community composition and activity during bloom events. Certain diatom species promote the growth of copiotrophic bacteria, which contribute largely to high bacterial production rates and recycling of carbon. In contrast, the increase in dinoflagellate abundance associated with global warming may potentially change the pelagic remineralization of organic matter, which could reduce the carbon flux to higher trophic levels.
  • Misiewicz, Zuzanna (Helsingin yliopisto, 2019)
    Anxiety disorders manifest themselves as a prolonged or exaggerated response to a threatening situation, which can be either real or perceived. Their high prevalence (14%) places them as one of the most common mental disorders within the European Union. This conveys an important message about the necessity of finding new clinically relevant drug targets leading to the development of novel personalized treatment practices. To facilitate this process, efforts should be focused on gaining a deeper understanding of the complex molecular, biochemical, and system-level mechanisms behind the neurobiology of stress, and the role of stress as one of the main etiological factors in anxiety-related psychiatric disorders. The phenotypic heterogeneity of human populations and high variability of external environmental factors, along with limited access to brain tissue samples, presents some of the main challenges to studying anxiety disorders in humans. As these aspects can be controlled for in animals, animal models are often used to administer specific stressors in a uniform manner and to obtain brain tissue at a precisely chosen time point. Thereby, within the scope of this thesis, we take advantage of the fact that anxiety is an evolutionarily conserved response and address the integration of both human and mouse data obtained from a variety of approaches, including genomic, transcriptomic, and proteomic methods. First, to identify genetic loci predisposing to a specific phobia, the fear of heights, we conducted a genome-wide parametric and non-parametric linkage scan, followed by joint linkage and association analysis in a small population isolate with reduced genetic and environmental heterogeneity. Our results implicated three regions with suggestive evidence for linkage, including region 8q24.2-q24.3 (LOD = 2.09), which encompasses 49 genes, including several candidate genes for psychiatric disorders. Second, we identified molecules and biological pathways affected by chronic social defeat stress (CSDS), a mouse model of chronic psychosocial stress, in the following three brain regions: medial prefrontal cortex (PFCM), ventral hippocampus (HIPV), and bed nucleus of the stria terminalis (BNST). We used two inbred mouse strains with different basal anxiety levels, the innately non-anxious C57BL/6NCrl (B6) and innately anxious DBA/2NCrl (D2). Following analysis of RNA sequencing results, we discovered that differentially expressed (DE) oligodendrocyte-related genes were over-represented in gene set enrichment analysis (GSEA) of all studied brain regions. As oligodendrocytes are known for their function in axon myelination, we followed the results from transcriptomic analyses with transmission electron microscopy (TEM) and established that B6 stress-susceptible mice had thicker myelin in BNST axons compared to controls. Third, using the CSDS model, we further investigated the role of the BNST through additional studies of gene regulatory networks (GRN) of mRNAs and miRNAs and protein-protein interaction networks. Subsequently, we followed with an integration analysis of the results from both transcriptomic (mRNA sequencing, as well as AGO2 miRNA, and mRNA immunoprecipitation sequencing) and proteomic (liquid chromatography–tandem mass spectrometry) experiments. Furthermore, to translate our results to human anxiety disorders, we performed transcriptome profiling in blood cells of CSDS-subjected mice and compared it with gene expression patterns from blood cells of panic disorder patients who underwent exposure-induced panic attacks. We then followed with integrative gene set enrichment analysis of mouse and human data, which showed systemic genetic background-specific enrichment of mitochondria-related gene sets. Importantly, our results showed downregulation of the oxidative phosphorylation pathway in the CSDS-subjected D2 strain and panic disorder patients after a panic attack. To conclude, our results suggest (1) brain-region and mouse strain-specific differences in myelination in susceptibility and resilience to stress and (2) dysregulation of mitochondrial pathways associated with anxiety-related behavior in both mice and humans. Taken together, our results provide further insight into the complex genetic architecture of anxiety disorders and support the suitability of cross-species approaches to studying biological mechanisms underlying anxiety disorders. Keywords: anxiety disorders, chronic social defeat stress (CSDS), panic disorder, acrophobia, linkage analysis, gene expression, protein abundance, multi-omics studies
  • Uusheimo, Sari (Helsingin yliopisto, 2019)
    ABSTRACT Massive amounts of industrially-fixed reactive nitrogen (N) results in excess N amounts in the environment. High N loading from agricultural catchments and wastewater treatment plants can be mitigated by natural N removal processes in aquatic environments. These microbe meditated processes, mainly denitrification, remove the reactive N returning it back to the atmosphere mainly in the form of harmless N2 gas. These processes occur in anoxic sediments and are dependent on the surrounding temperature. Generally, microbial N removal has been found to be efficient in wetlands, compared with other aquatic environments. In a cold climate, the process rates of microbial N removal are assumed to be low, however they are poorly understood. In this study, N removal rates were measured in a shallow agricultural wetland and in a wetland polishing treated wastewater situated in southern Finland. In the agricultural wetland, the influence of environmental factors were studied by conducting the study in field conditions. Seasonal denitrification rates were governed mainly by sediment temperature, followed by sediment oxygen conditions and water turbidity. Diurnally, denitrification was regulated by light affecting sediment oxygen conditions. Rates measured in the field merely during daytime may lead to underestimations of N removal potential of shallow wetlands. Nutrient retention and the contribution of N removal processes to the total N retention was estimated in the wetland receiving treated wastewater. The efficient N retention found was estimated to be mostly based on microbial processes, mainly on denitrification and slightly on anammox. In addition, the interference arising from organic carbon to nitrate measurements with optical sensors was studied and the information was used in improving the accuracy of sensor nitrate results in an agricultural brook. Increasing organic carbon concentrations was found to increase the nitrate concentrations by sensors and the effect was manifold in bog water. The interference was resolved by taking account the dissolved organic carbon in the correction of the sensor results. This study increases the information of actual N removing process rates and improves the knowledge of the extent constructed wetlands can remove excess N in cold climate, and provides information for the use of optical sensors in monitoring N loading.
  • Amiryousefi, Ali (Helsingin yliopisto, 2019)
    Chloroplasts are cytoplasmic organelles chiefly responsible for the photosynthesis. Their genes have been used extensively during the past decades in phylogenetic analyses of various photosynthetic eukaryotes, particularly plants. The genomic content of this organelle and its very architecture can be used for a deeper insight in evolution and towards robust phylogenetic hypotheses. Ever since this importance was recognized concurrently with the advancements of methods in both providing a basic genetic material through sequencing and advanced methods to analyze the data, we have witnessed the introduction of a couple of thousands plastid genomes up to this date. This process, by no means is in its decline or even stationary state, as this pace is projected to be accelerated in the coming years, with the inevitable advances in our technologies and our need to understand the nature as accurate as possible. The aim of this study as represented in the sequel chapters is twofold; 1) to introduce the complete chloroplast genomes of two species from the euasterid clade and provide their phylogenetic analyses; Solanum dulcamara L. as a native Old World diploid member of the nightshade family, and Ambrosia trifida L. as a recognized invasive plant originated and evolved from North America. 2) To provide two analytical tools for more advanced treatment of the genetic information of plastids in bioinformatics. By comparative analysis for bittersweet and giant ragweed, the result show that synteny and the genomic content of both belonging to the families Solanaceae and Asteraceae, respectively, have a conserved structure. We also noted that many submitted annotations in the nightshade family are far from acceptable quality, and further on, we improved them with reannotation of the existing sequences. On the other hand, a novel tool (IRscope) to detect and plot the Inverted Repeat (IR) regions of the chloroplast genome was introduced. IRscope, with the help of iterative search algorithm, allows the depiction of genes in the vicinity of the Junction Sites (JS), of up to ten different chloroplast genomes of embryophytes (land plants). Moreover, we constructed an online calculative suite (iMEC) to return the result of the seven different molecular markers against the provided input file. This tool is useful particularly in studies aimed to assess the efficiency of different marker systems linked to plastid genome variation.
  • Aho, Velma T. E. (Helsingin yliopisto, 2019)
    Parkinson's disease is the second most common neurodegenerative disease in the world, and in spite of decades of research, the cause of the non-familial form of the disease is not known. There are currently no medications to slow down the progression of the disease nor good biomarkers for early diagnosis, even though the earliest non-motor symptoms can appear years or even decades before the onset of motor symptoms. The microbial inhabitants of the human body have recently been implicated in various medical conditions, including neurodegenerative disorders. They could offer new insight into the pathogenesis of Parkinson's disease, particularly since a microbial agent has long been suspected to play a part in the process. A typical question in studies surveying human microbiota is which specific microbial taxa differ between groups of interest, such as patients with a disease and control subjects. There are many statistical tools for performing these analyses, also known as differential abundance comparisons. The aim of my doctoral thesis was to explore the potential associations of Parkinson's disease and human microbiota, particularly of the mouth, the nose and the gut, with an additional focus on the statistical tools used for comparing differentially abundant bacterial taxa. All four publications included in my thesis were based on samples from the same subjects: 76 patients with Parkinson's disease and 76 control subjects with no signs of parkinsonism. The studies also used the same methodology, 16S rRNA gene amplicon sequencing, to compare bacteria from oral and nasal swab samples and fecal samples of these subjects. Over the course of the four publications and in a previously unpublished analysis, I compared differentially abundant taxa with six tools: Metastats, LEfSe, metagenomeSeq, DESeq2, ANCOM, and an approach based on random forests. Our results suggested that the bacterial communities of the gut and the mouth differ between Parkinson's patients and control subjects, with statistically significant differences in beta diversity and in the abundances of several bacterial taxa. Differences in gut microbiota could also be detected at a follow-up time point with samples collected two years after the initial sampling. Additionally, there were differences between the gut bacteria of Parkinson's patients with and without irritable bowel syndrome -like symptoms. For nasal bacteria, there were no differences between the patient and control groups in diversity nor the amounts of specific bacteria. Regarding the differential abundance analyses, comparing gut bacteria of patients and controls from the same samples with six different tools highlighted the wide variation in the lists of significant results, which often did not overlap except for a handful of taxa. While a few benchmarking studies have previously contrasted some of the tools, there is a definite need for further standardized testing to guide researchers in choosing between them. Despite these discrepancies, all tools tested in this thesis supported Parkinson's patients having a decreased abundance of the family Prevotellaceae in their gut. This difference in abundance could also be detected at the follow-up time point. As several other research groups have reported seeing a decrease in Prevotellaceae after our pilot publication, it is emerging as one of the key changes in microbiota associated with Parkinson's disease.
  • Kuony, Alison (Helsingin yliopisto, 2019)
    The lacrimal apparatus products the tear film protecting the eye surface. The lacrimal gland, located in the orbit, produces 80% of the tear film components. These include growth factors destined to the avascular cornea, necessary for corneal epithelium maturation and renewal. A defective tear film leads to dry eye diseases which affect an increasing percentage of the population (more than 35% in the elderly). Although dry eye diseases can lead to visual loss in extreme cases, no definitive treatment has been developed so far. My thesis work focused on unravelling lacrimal gland early development, postnatal maturation and subsequent function in mouse models. I notably used a dry eye disease mouse model to study the implication of Ectodysplasin (Eda) pathway in lacrimal gland development, maturation, function, as well as in the cornea/lacrimal gland feedback loop during corneal healing process. In addition of improving the general knowledge on lacrimal gland biology, my work gave some insights on the dry eye phenotype associated to Ectodysplasin loss-of-function mutation and on the resulting defective cornea wound healing.
  • Leppänen, Jaakko (Helsingin yliopisto, 2019)
    The mining industry has a critical role in modern societies. However, the environmental harm induced by mining activities may be drastic. One of the most important aspects of mining pollution is water contamination due to accidental or controlled waste water release, or due to harmful leachate originating from waste areas. Whereas the water quality in receiving water systems is usually monitored, the ecological impacts of mine waters are assessed more rarely. One of the challenges when ecological impacts are studied is the lack of long-term data regarding the pre-mining conditions. Palaeolimnological methods allow the reconstruction of historical conditions of water bodies. Sedimentary geochemistry and subfossil remains of biological communities (e.g. cladoceran crustacea, diatom algae) can be used to assess the natural pre-disturbance variability, the impact of the disturbance and the post-disturbance dynamics. In this thesis, mining pollution is assessed within three projects, conducted on two boreal lakes in Finland. In Lake Kirkkojärvi, the impact of historical mining activity, namely, the direct release of mineral tailings was studied from a sediment core covering also the pre-mining environmental conditions. The impacts of the mine pollutants were reflected in cladoceran communities as declining species richness and diversity. The lake Kirkkojärvi bay was studied by using a palaeolimnological top-bottom approach. The bay has been receiving acid mine drainage for nearly 50 years. However, the cladoceran community change in the bay does not reflect any changes in acidity or metal pollution. In Lake Kivijärvi the Na2SO4- and metal-contaminated mine water has had a clear impact on cladoceran and diatom communities as both groups exhibit changes due to mining pollution. Based on the results, the most important contaminants in the studied systems are saline effluents and mineral tailings. Cladocera hold great potential in palaeolimnological mining pollution studies due to their sensitivity to changes in the water quality and due to their central location in food-webs. However, more research is still needed: Most importantly, some taxonomic issues must be clarified and in-situ toxicity studies should be conducted in order to find the most sensitive indicator species for different types of pollution. The results of this work present important information regarding pollution impact assessment. In particular, this study highlights the utility of Cladocera as early warning indicators, while supporting the use of multiple sediment proxies in palaeolimnological pollution research in order to provide information about the timing, direction, and magnitude of ecosystem impacts caused by pollution events. This is of essence for environmental management as globally the exploitation of poor-grade large mine deposits will drastically increase in the near future. Only by providing such crucial information on the short- and long-term impacts of mining on aquatic ecosystems and their resilience, a technologically, socially and environmentally sustainable management of mines can be guaranteed in the future.
  • Viita, Tiina (Helsingin yliopisto, 2019)
    Actin is best-known from its functions in the cytoplasm, where it is a key component of the cytoskeleton. Nevertheless, functions of actin are not restricted to the cytoplasm, since actin is also present in the nucleus, where it has been linked to multiple functions from gene activation to chromatin remodeling. However, molecular mechanisms by which actin operates in the nucleus are still poorly understood. This is mainly because of the lack of well-characterized binding partners for nuclear actin. Therefore, the aim of this thesis was to identify and characterize novel nuclear actin-binding partners and elucidate the molecular mechanisms behind actin regulated transcription factors. To identify nuclear actin-binding partners, we used two complementary mass spectrometry (MS) techniques, affinity purification combined with MS (AP-MS) and proximity dependent biotin identification with MS (BioID). Analysis of our interactome data revealed that actin can form stable complexes with proteins related to chromatin remodeling but seems to function in a dynamic fashion in other nuclear processes, such as transcription and DNA replication. In our experimental setup actin seemed to be monomeric when it associated with nuclear complexes. We also discovered a novel actin-containing complex, human Ada-Two-A-containing complex (hATAC). HATAC is a histone modifying complex and actin directly binds one of it subunits, lysine acetyltransferase 14 (KAT14). We showed that actin-binding modulates histone acetyl transferase (HAT) activity of KAT14 in vitro and in cells. Our interactome data also indicated that actin could be involved in RNA splicing and mRNA processing. Further experiments showed, for the first time, that actin has a functional role in mRNA splicing, as alterations in nuclear actin levels disturbed survival motor neuron protein 2 (SMN2) alternative exon skipping. In addition, the nuclear actin interactome analysis provided new insights into nuclear processes already earlier linked to actin, such as chromatin remodeling, transcription and DNA replication, and hence this work provides a protein interaction platform for further mechanistic studies of nuclear actin-dependent functions. One well-known protein, which is known to bind nuclear actin and to regulate transcription is myocardin-related transcription factor A (MRTF-A), a co-activator of serum response factor (SRF). MRTF-A has a RPEL domain, which can regulate the localization and activity of MRTF-A in response to actin dynamics. Interestingly, also phosphatase and actin regulator (Phactr) protein family contains RPEL domain and binds protein phosphatase 1 (PP1). The molecular properties of MRTF-A intrigued us to study if the Phactr-proteins could be putative binding partners of nuclear actin. We revealed that the RPEL domain of Phactr4 do not regulate the subcellular localization of Phactr4. Instead, Phactr4 controls the activity of PP1 in response to actin monomer levels in the cytoplasm, thereby creating a feedback loop that maintains actin homeostasis in cells. In addition, we were able to show that MRTF-A subcellular localization is not solely dependent on actin, since DDX19, an ATP-dependent RNA helicase, can regulate nuclear import of full-length MRTF-A independently of actin dynamics. This thesis work has thereby broadened the knowledge of nuclear actin-binding partners as well as revealed novel regulatory properties of actin-regulated RPEL domain containing proteins.
  • Yadav, Leena (Hansaprint Oy, 2019)
    Nearly all eukaryotic processes are regulated by cyclic phosphorylation-dephosphorylation of cellular signaling proteins, catalyzed by protein kinases and phosphatases, respectively. Until now, the kinases dominated the scientific research, however, in recent years only, the protein phosphatases have emerged as crucial regulators for setting up the levels and amplitude of phosphorylation-driven signaling events. Nevertheless, our molecular and biological awareness of these enzymes is still poor. This thesis aims to gather information on these vital aspects of phosphatase biology. Through our high-throughput systematic affinity-purification coupled to mass spectrometry (AP-MS) approach, we provide the first glimpse on the cellular protein protein interactions and functional networks of human protein phosphatases from three broad families: phosphoprotein phosphatase, metal-dependent phosphatase, and protein tyrosine phosphatase. Next, we obtained the comprehensive view on their enzymatic structure-activity relationship by utilizing inhibitor Okadaic acid, revealing the effect of catalytic disruption on the phosphatase interaction profile and on the phosphorylation status of their various sub-complex components. From here, we expanded the thesis by investigating the functional relevance of unique phosphates-kinase interaction in the context of specific signaling. From dephosphorylation and luciferase assays we established the role of PTPRA phosphatase in negatively regulating RET kinase activities and its down-stream Ras-MAPK pathway, showing RET as novel PTPRA substrate. By including RET cancer mutants- MEN2A and MEN2B, we, further, shed light on the tumor suppressor functions of PTPRA in human cancers. Taken together, this thesis not only provides a global landscape of human protein phosphatase complexes and their functions but also furnish a reliable resource for futuristic investigations.
  • Zimm, Roland (Helsingin yliopisto, 2019)
    The turtle carapace has been considered one of the classic examples of an evolutionary novelty. It is diagnostic of the turtle clade and probably largely responsible for its success in evolution. In more detail, it consists of ossified dermal plates overlaying laterally extended ribs, as well as a regular array of epidermal scutes. Interestingly, the unique and complex mosaic pattern formed by the carapacial scutes is highly conserved amongst almost all extant turtle taxa. Since the morphogenesis of this remarkable pattern has not been studied much before, I present, in this dissertation, a novel computational approach to elucidating carapacial scute development. In a mathematical model, a combination of two mechanistically different reaction-diffusion systems together with growth reproduces scute formation in the carapace. In order to disentangle the underlying gene regulatory network, we disturb carapace development experimentally in embryos of Trachemys scripta and use the model to understand the resulting phenotypes. We show how the carapacial ridge acts as a signaling center which is required for the onset of scute development. Furthermore, the model suggests how phenotypic differences between species might arise and explains, in line with statistical data from different turtle species, how environmental stress, rather than genetic mutations, leads to the very specific patterns of variation found within turtle populations. Thus, our results suggest that environmental stress might be an underrated source of phenotypic variation within species. Developmental insight helps us understand why this particular variation occurs and at what frequencies. In order to further understand how environmental factors might interfere with development and to be able to account for more realistic tissue growth and biomechanics, I present a more general multiscale model of animal development that integrates biomechanics, GRN dynamics and cell behaviours in different, interacting cell types and tissues. Thus, this model does not only allow an advancement of our understanding of mechanisms by which phenotypic variation in the developing turtle scute might be generated, it is also a useful tool to understand more general features of development and variation. Finally, I discuss my work in the context of previous hypotheses about the origins of turtle scutes as well as their variation. By a comparison with the development of other ectodermal organs in different vertebrates, I try to integrate turtle scutes into a wider evolutionary background.
  • Parajuli, Anirudra (Helsingin yliopisto, 2019)
    Microbes play important roles in the development of the human immune system. Human commensal microbiota of the gut and skin have been shown to modulate the immune system, and high diversity of this microbiota is likely to confer protection against immune-mediated diseases. However, sufficient contacts with the diverse microbiota in our environment have also been thought to be equally important. It is suggested that the rising incidences of immune-mediated diseases such as allergies and asthma in the western urban society having less proportion of natural environment could be due to insufficient contacts with environmental microbes. This thesis aimed to find out the effect of living environment, including the coverage of built area, vegetation type and pollution, on environmental microbiota, their human exposure as well as the composition of human commensal microbiota. This thesis also aimed to study whether applying soil and plant based materials on skin is effective in establishing better contact with microbes. The effect of pollution on the composition of the environmental microbiota was studied by contaminating four different types of soils with polyaromatic hydrocarbons (PAHs). It was found that PAH-pollution altered the community composition of bacteria, increased the abundance of bacterial phyla shown to be unfavorable and reduced the abundance of those recognized to be favorable for the human immune system. Since exposure to environmental microbes affects human microbiota and the immune function, pollutants such as PAHs likely affect human exposure to environmental microbes and also lead to disturbances in the composition of the human commensal microbiota. The effect of land cover type on indoor exposure to environmental microbes was investigated by studying the composition of bacteria in the debris deposited in experimental doormats installed inside the main door of urban and rural houses in southern Finland. The quantity of environmental litter and bacterial diversity was significantly less in the doormats of houses in heavily built urban area compared to those in sparsely built rural areas. Stool samples from elderly volunteers living in those houses were analyzed to investigate the effect of land cover type and garden vegetation diversity on the composition of gut microbiota. The number of shrub and non-woody flowering plant species in the yard were associated with an increased abundance of several bacterial taxa known to promote the human immune system. The effect of built area was similar to the shifts in the gut microbiota observed in urban inhabitants from highly industrialized areas relative to rural hunter-gatherer population in previous studies suggesting that high incidences of immune disorders in western population could be associated with a greater coverage of built area. Urban volunteers were asked to apply soil and plant-based materials on their hands to see if the use of natural ingredients is effective in changing the composition of bacteria on the skin. This led to a significant increase in the diversity and biomass as well as the relative abundance of several bacterial taxa suggesting that microbial exposure via skin could potentially be employed as a route for preventing or even treating immune-mediated disorders by increasing the diversity of skin microbiota, which needs to be investigated. This thesis concludes that urban living environment characterized by increasing proportion of built areas and high pollution levels could lead to adverse changes in the environmental microbes, reduced indoor exposure to those microbes as well as unfavorable shifts in the composition of the gut microbiota. Shrubs and flowering plants could contribute positively to gut microbial homeostasis. Likewise, a direct contact with soil and plant based materials can be effective in increasing the diversity of the skin microbiota.

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