Faculty of Biological and Environmental Sciences

 

Recent Submissions

  • Herrero, Annika (Helsingin yliopisto, 2021)
    Large terrestrial carnivores are capable of long dispersal distances and thus have a potentially high rate of gene flow between populations. Even with such high mobility, discontinuous habitat and human-caused mortality may constrain dispersal and gene flow. Therefore, isolation of populations because of habitat fragmentation may cause genetic structuring in them because of genetic drift. In a continuous population, geographic barriers should not significantly affect dispersal and gene flow, so the effects of social, ecological and evolutionary forces are easier to detect. In large carnivores, males generally disperse more often and earlier than females and their dispersal distances are longer than those of females. The direction of sex-bias in dispersal is commonly explained by inbreeding avoidance, polygynous mating system and male-male competition. Remaining in, or near, the natal home range is explained by kin selection and inclusive fitness. Molecular evidence reveals the spatial genetic structure and clustering of relatives and family lines that may underlie these traits. We studied the spatial genetic relatedness, family structure, movement patterns and sex- bias of dispersal in the Eurasian lynx (Lynx lynx) in an unfragmented population in southern Finland. We used GIS and resource selection functions to analyse telemetry data of dispersing lynx and genetic methods to analyse data obtained from hunted lynx. Dispersal onset age, duration, distance, route or route linearity did not differ statistically between males and females that dispersed. However, the small number of females and the high variation in all dispersal parameters likely affected the outcome of analysis. Linear distance between the start and the end comprised only 20 % of the total dispersal route. Lynx selected their habitat non-randomly. During daylight hours lynx were more discerning in their habitat selection, while most of the traveling took place at night, reflecting the crepuscular and nocturnal activity of the lynx. According to the results of genetic analyses, the majority of females stayed close to their natal home range after reaching independence. Males dispersed and settled randomly in space. This led to genetic differentiation and spatial clustering of related females but not of males. Females form the backbone of the local populations, and genetic evidence is in line with the idea that females facilitate the settling of related females. In contrast to females, for males, relatedness is inversely important to avoid inbreeding. Hunting of adult lynx may disturb the forming of matrilineages and decrease genetic variation. Hunting should aim at mimicking a natural mortality pattern, which means hunting mostly young lynx, as the natural adult survival in Eurasian lynx is high.
  • Yan, Yan (Helsingin yliopisto, 2021)
    Blue and UV radiation are environmental cues or sources of information that can shape the morphology and development of plants. It was hypothesized that: H1) long-term treatments of solar blue (400–500 nm), long-UV (350–400 nm) and short-UV (290–350 nm) radiation (starting before seedling emergence) are perceived as different and can trigger distinct morphological, physiological and molecular responses; H2) parental long-term exposure to short-UV radiation before flowering affects response patterns to blue and UV radiation in the offspring; H3) long-term exposure to solar blue, long-UV and/or short-UV radiation enhances drought tolerance; H4) the responses in H1, H2 and H3 are accession-dependent and related to the environments where the accessions originate. To test these hypotheses, three experiments assessed morphological, physiological and molecular responses of accessions of two legume species, faba bean (Vicia faba L.) (I, II) and barrel medic (Medicago truncatula Gaertn.) (III). To impose radiation treatments by attenuating different wavebands of sunlight, four types of plastic filters were used in experiments I and III outdoors. Through pairwise filter comparisons, three different solar wavebands were assessed: blue, long-UV and short-UV radiation. In experiment I, two accessions of V. faba (Aurora; ILB938) originating from contrasting UV environments (southern Sweden; Andean region of Colombia and Ecuador) were grown under the four filters in sunlight. To study the transgenerational effect of solar short-UV radiation, experiment II was established using seeds produced by plants from experiment I and a factorial experiment design combining the two V. faba accessions, two parental UV treatments (full sunlight and exclusion of short-UV radiation) and four offspring light treatments, from the factorial combination of UVB and blue radiation manipulations in a controlled environment. In experiment III, the effect of long-term exposure to solar blue, long-UV and short-UV radiation during growth on the tolerance of subsequent progressive drought was studied in three M. truncatula accessions using the same filter treatments as in experiment I combined with progressive drought treatments imposed by withholding watering for 2 and 7 days to half the plants starting 40 days after sowing. The three M. truncatula accessions, Jemalong A17, HM006 and HM020, originate from Australia, France and Tunisia, respectively. After long-term natural light treatments (I, III), blue light but not long-UV or short-UV radiation, significantly regulated plant morphology and transcript abundance. In contrast, both solar blue and short-UV radiation, but not long-UV radiation, induced the accumulation of total flavonoids in leaves of V. faba (I) and M. truncatula (III). Moreover, simultaneous exposure to blue and UVB radiation had a synergetic effect on the induction of flavonoid accumulation (II). In V. faba, the variations of flavonoid composition and gene expression between the two accessions were consistent throughout the two successive generations (I, II). In V. faba, the transgenerational effect of short-UV radiation altered the morphological responses of the progenies to blue light, and it also affected flavonoid accumulation of the offspring in response to UVB radiation. Moreover, the transgenerational effects differed in the two accessions (II): in Aurora, the parental exposure to solar short-UV radiation led to a near-doubling of total quercetin concentration in response to UVB radiation in the progeny, while this was not observed in ILB938. The difference of responses to blue and UV radiation in these two accessions are consistent with adaptation to contrasting UV environments. In M. truncatula, long-term exposure to both solar blue and UV radiation pre-acclimated plants to subsequent slowly imposed drought, as observed in the transcriptomic result in accession Jemalong A17 that drought (2 and 7 days without watering) did not regulate differentially expressed genes (DEGs) under the filter transmitting blue and UV radiation. In contrast, drought increased transcript abundance of several previously described stress-inducible genes under all other filters. In the light of transcriptomic and flavonoid responses to filter and drought treatments, two processes potentially contribute to light-driven acclimation to drought: 1) increased flavonoid accumulation under blue and short-UV radiation could enhance the capability to scavenge drought-induced reactive oxygen species (ROS); 2) down-regulation of genes involved in light reactions of photosynthesis by blue light could reduce the generation of ROS when stomata close. In conclusion, under long-term sunlight treatment, blue light modified plants’ morphology and transcript change while both blue and short-UV radiation induced the accumulation of flavonoids; a transgenerational effect of short-UV radiation influenced offspring responses to blue and UVB radiation differently in the two accessions; both blue and UV radiation contributed to pre-acclimation toward subsequent drought by functioning as environmental cues rather than stressors even if the specific responses differed among accessions. Thus, the results support the four hypotheses.
  • Laine, Mikaela (Helsingin yliopisto, 2021)
    Psychiatric disorders are very common, with anxiety disorders being the most prevalent (16 % lifetime prevalence). While moderately heritable, their incidence is also strongly influenced by environmental risk factors, chiefly psychosocial stress. However, our knowledge of how, in neurobiological terms, these disorders arise is lacking, slowing down the development of efficient treatments. The aim of this thesis was firstly to identify which brain regions are recruited by chronic psychosocial stress, by using mice as model organisms. To model psychosocial stress we used chronic social defeat stress (CSDS), which involves short confrontations between intruder and resident-aggressor male mice, repeated daily for 10 consecutive days. A week after stress exposure C57BL/6NCrl (B6) mice had a higher number of cells expressing ΔFOSB, a marker of repeated neural activation, in several stress-related brain regions. These included the bed nucleus of the stria terminalis (BNST) and ventral hippocampus (vHPC). We also found significant correlations in the numbers of ΔFOSB+ cells between medial prefrontal cortex (mPFC) subregions (infralimbic and prelimbic cortices) and the vHPC of stress-exposed but not non-stressed control mice. Our second aim was to discover, by using unbiased RNA-sequencing (RNA-seq) of stress-related brain regions (the mPFC and vHPC), biological pathways perturbed by CSDS. Additionally, we used mice from two inbred strains, representing different levels of baseline anxiety-like behaviour: B6 (low-anxiety) and DBA/2NCrl (D2, high-anxiety). This enabled us to explore how genetic background modulates the response to stress. While some mice exposed to CSDS show social avoidance (called stress-susceptibility), others are behaviourally similar to non-stressed control mice. This phenomenon, known as resilience, is also observed in humans. We found that B6 and D2 mice showed vastly different behavioural responses to CSDS. B6 mice displayed a predominantly resilient phenotype (66.1 % of CSDS-exposed mice across several cohorts), while the majority (85.0 %) of D2 mice were susceptible. Pathway analysis of RNA-seq data suggested that differentially expressed genes (DEGs) were enriched in genes related to oligodendrocytes (OLGs), the myelin-producing cells of the CNS. For example, genes encoding myelin components were downregulated in the mPFC and vHPC of B6 susceptible mice compared to controls. Myelin is a lipid-rich ensheathment around axons, and it enables both fast nerve conduction and adjustment thereof via myelin plasticity. We followed up the gene expression findings with a structural analysis of myelinated axons using transmission electron microscopy (TEM). We found that in the vHPC, B6 susceptible mice had thinner myelin sheaths than controls. In the mPFC, B6 resilient mice had thicker myelin than controls, restricted to axons with small diameters. By contrast, D2 resilient mice had thinner myelin in this region than susceptible mice, indicating potential bidirectional dynamics of myelin plasticity in resilience. Lastly, we performed RNA-seq of enriched OLGs and myelin from the mPFC. The aim of this experiment was to identify pathways affected by CSDS specifically in these cells and in myelin. Additionally, we used this dataset to identify genes (24.8 % of all genes and 18.8 % of expressed micro-RNAs [miRNAs]) which were enriched in the myelin fraction compared to OLGs in nonstressed control mice. This suggests selective transport of certain mRNAs and microRNAs into the myelin sheath, potentially for local regulation. When comparing CSDS-exposed mice and controls, we found lower expression of myelin-related genes in B6 susceptible, D2 susceptible and D2 resilient mice compared to same-strain controls. In the B6 strain this was found in the myelin fraction, while in the D2 strain these genes were differentially expressed only in OLGs. Ingenuity Pathway Analysis (IPA) predicted TCF7L2, a transcription factor, to be an upstream regulator of these DEGs. In summary, we showed involvement of a broad but selective network of brain regions in CSDS. Genetic background had a large influence on the response to stress, highlighting a source of individual variation with implications for understanding human stress-resilience and -susceptibility. This moderation by genetic background was also seen at the level of gene expression in the brain. Finally, our findings suggest that myelin plasticity is an important part of the chronic response to stress. Future work will identify by which mechanisms stress influences myelin, and how this could be best harnessed for improving therapeutic strategies.
  • Ismail, Shamel (Helsingin yliopisto, 2020)
    Endoscopic retrograde cholangiopancreatography (ERCP) is a minimally invasive procedure for biliary and pancreatic disorders. It has evolved to predominantly therapeutic procedure with the diagnosis of primary sclerosing cholangitis (PSC) being one of the main exceptions. ERCP has the high potential for complications, like post ERCP pancreatitis (PEP), bleeding, cholangitis and perforation. Therefore, the data concerning the risk factors of ERCP is essential. The roles of preoperative laboratory testing and the new criteria of difficult biliary cannulation are poorly studied. ERCP plays also the major role in the endoscopic removal of papillary tumours (European Society of Gastrointestinal Endoscopy, European Association for the Study of the Liver, 2017). The main purpose of this study is to assess the safety of ERCP for different groups of patients, and the adverse effects that can follow. Additionally, the study examines the effect of using different tools during the procedure on the complication rate and the means to minimize the complication rates in the future. The main complications after ERCP are post ERCP pancreatitis (PEP), bleeding, cholangitis and perforation. The risk factors of ERCP complications in 441 consecutive PCS patients were retrospectively analysed. The outcome of 61 endoscopic papillectomies was retrospectively studied in study II. In the prospective study (III) of 821 consecutive patients with native papilla were evaluated the complication rates in difficult cannulation cases. To evaluate the relationship between ERCP complications and the need for routine preoperative laboratory tests (RPLT) before the ERCP procedure, we conducted prospective study (IV) with 1196 patients. In PSC patients (study I) the PEP and cholangitis rates were 7 and 1.4 %, respectively. PEP predictive factors are female sex (Odds ratio 2.6, p=0.015), and a guide wire slipping in the pancreatic duct (PD) (Odds ratio 8.2, p<0.01). The risk of PEP is directly proportional to the number of times the guide wire slips into the pancreatic duct. A previous endoscopic biliary sphincterotomy (EST) was found to be a protective factor from PEP (Odds ratio 0.28, p= 0.02). In benign tumours of the papilla (study II), the recurrence rate after resection was 25.5% (study II). Altogether 5 (9.5%) patients underwent a pancreaticoduodenectomy, and 46 out of 51 (90.5%) were treated endoscopically. Obstruction of the bile duct and jaundice as a manifestation were risk factors for malignancy (p<0.001). PEP occurred in 6 cases (9.8%). After a benign tumour resection and placing a stent, the PEP rate decreased (p=0.045). The bleeding rate was 18%. In study (III), when the primary cannulation method used to cannulate the bile duct succeeded, the PEP rate was 2.3%, but when the surgeon used advanced methods to achieve the cannulation, the PEP rate increased up to 13.5%. The primary cannulation success rate was 79% in the absence of difficult cannulation criteria compared to 20.4% when at least one criteria was present (p<0.001). Broad RPLT could not predict the adverse effects of ERCP in study (IV). In conclusion, the new criteria of difficult biliary cannulation are important because the complication risk increases with the complexity of cannulation. Endoscopic papillectomy for benign tumours is feasible and relatively safe. The role of RPLT in safety of ERCP is minimal.
  • Backer Johnsen, Hermanni (Helsingin yliopisto, 2020)
    This thesis studies the ecosystem approach (EA) which is a concept used in environmental science, policy, and law. It is widely referred to in protection of the world’s seas and oceans, including regional cooperation such as the work of The Baltic Marine Environment Protection Commission (HELCOM). In general, the ecosystem approach reflects the idea that management should be more integrated across different human activities but also that it should be based on, usually scientific, knowledge of ecosystems. More specifically, however, its substance remains a subject of debate. This thesis aims at contributing to the understanding of the ecosystem approach by studying and outlining a HELCOM interpretation as emerging from the implementation process 2003-2018. The thesis is based on the findings of five articles, four of which provide case studies on different aspects of EA implementation at HELCOM based on meeting records, literature research and first-hand knowledge. The fifth article is a study of HELCOM work 2003-2018 based on attendance and topics of 724 international meetings organised during the implementation period, types of organizational output and the outcomes of Ministerial Meetings. The summary derives a conceptual framework for EA with three elements, to report and discuss the findings of the five Articles. The thesis concludes that, as implemented within HELCOM, EA can be characterised by an element of quantification consisting of definitions and regulatory use of scientific targets of ecosystem quality, with roots in EU regulatory approaches and a different focus compared to the EA as defined within the Convention on Biological Diversity (CBD). A second element of integration is manifested in a significant expansion of new HELCOM activities in the fields of MSP, Fisheries, Agriculture and regional linkages to EU and global policies. However, regarding the third element, EA resulting in concrete management measures, has been a central component of implementation activities, but the main result seems to be in providing a more elaborate ways for proposing, justifying, specifying, and reporting the achievement of management action decided in other processes than HELCOM. The results of the fifth article indicate that the annual HELCOM work has doubled in volume during 2003-2018, measured as hours spent in meetings. This increase can be attributed to a general dilation, across all activities, as well as the new fields of work. Comparing the types of documents adopted by HELCOM in the beginning and end of the period 2003-2018 there is some evidence that a shift has taken place from technical specifications and concrete emission standards to more assessment products & indicators. Based on the data collected it is not possible to conclude whether these developments are a result of EA implementation as such, or primarily due to other factors such as the parallel, and closely intertwined, implementation of the EU Marine Strategy Framework Directive (MSFD). Due to its scientific nature the EA element of quantification is more an evolution of the traditional HELCOM monitoring and assessment work, however the integration element involves expansion of cooperation to new substance areas, professional groups, and worldviews. This work requires diplomatic effort and innovation for joint solutions to the environmental problems of the Baltic Sea. More focus on relevant human activities, drivers of change and monitoring progress in the implementation on key management measures affecting the state of the marine environment, but also scenarios and foresight could provide new avenues for the protection of the Baltic Sea. Keywords: sea, marine, ecosystem management, regional seas cooperation, Helsinki Convention, Baltic Sea, EU, Marine Strategy Framework Directive, marine spatial planning, MSP, international organization, meeting
  • Karki, Sudeep (Helsingin yliopisto, 2020)
    Synaptic adhesion molecules play a key role in the regulation of synapse development and maintenance. Several families of leucine-rich repeat (LRR) domain containing synaptic adhesion molecules have been characterized, including synaptic adhesion-like molecules (SALMs), and the LRR transmembrane (LRRTM) proteins. These proteins localize mostly in postsynaptic neurons in excitatory synapses and interact with presynaptic adhesion protein families; neurexin (NRXN) and leukocyte common antigen-related protein tyrosine phosphatases (LAR-RPTPs). Dysfunction of the synaptic adhesion molecules is linked to cognitive disorders, such as autism spectrum disorders and schizophrenia. This thesis work comprises the structural and functional study of SALM3 and SALM5 proteins from the SALM family, and their interaction with PTPσ from the LAR-RPTPs family. In addition, this thesis includes the work on the development of an inhibitory screening assay for synaptic adhesion molecules interactions, here targeting the LRRTM2-NRXN interaction. The SALM family proteins include five members, SALM1-5. We have solved the crystal structures of the mouse SALM5 LRR-Ig, and SALM3 LRR constructs at 3.1 Å and 2.8 Å resolution, respectively. Both the structures show the LRR domain mediating the dimerization, also verified by biophysical studies. We determined the binding affinity of SALM3 and SALM5 as 2-23 µM towards PTPσ, and solved the solution structure of the SALM3-PTPσ complex using small-angle X-ray scattering (SAXS), revealing a 2:2 complex formation similar to that observed for SALM5 and PTP. Based on our structure-function studies, SALM3 dimerization is vital for the SALM3-PTPσ complex to exert synaptogenic activity. We also developed an inhibitor screening method for the adhesion proteins interactions, focusing on the LRRTM2-NRXN interaction. We utilized the AlphaScreen technology to identify inhibitors with moderate IC50-values and established an orthogonal in-cell western blot assay to verify the obtained hits. This paves the way for the future development of high affinity compounds by further high throughput screening of larger compound libraries. The studies conducted in this thesis and the results have contributed to a better understanding of the role of SALM proteins in synapse formation, and possibly these structure-based studies will help to understand their implications in disease. The inhibitor screening assay developed can be adapted towards other synaptic adhesion interactions, and the inhibitors obtained could be used for functional studies, or towards drug discovery.
  • Sinha, Vishal (Helsingin yliopisto, 2020)
    The genetic aetiology of schizophrenia has been extensively studied in a nationwide collection of Finnish families since the late 1980s. Linkage and association studies of families ascertained for schizophrenia in Finland (SCZ) have continually identified the 1q42 region, and the Disrupted in Schizophrenia 1 (DISC1) gene in particular, as an important locus. Within the same SCZ cohort, an association at the genes for DISC1 interacting partners, the DISC1 network, including NDE1, PDE4D, PDE4B, and NDEL1, has also been observed, however, any true causal variants are yet to be identified. Thus, our research aims to identify variants at the DISC1 network of 27 genes, including DISC1, that can help us understand the origins of major mental illnesses, principally SCZ in Finland. We have used a three-stage sequencing and genotyping strategy to identify, validate, and replicate variants of interest. These were later studied in other cohorts ascertained for major mental illness, and in phenotypes with alternative traits. In total, 19,844 variants were identified through sequencing, and 93 variants were selected for genotyping in the larger SCZ cohort (n=1122) based on the association evidence and potential functional consequences. Variants associated in this larger cohort were again genotyped the rest of the SCZ cohort (n=1696), and in other major mental illness cohorts (n=2733). Through this work, we report a functional variant in the regulatory region of PDE4D associated with schizophrenia in a replicable manner, particularly in the psychotic and cognitive domains, with this variant significantly altering the amount PDE4D is expressed in the brain. We have further identified another sex-dependent functional variant in NDE1 gene associated within the females in the schizophrenia cohort, and is an eQTL for the NDE1 gene according to the GTEx database. Furthermore, a significant number of the gene expression changes are also significantly altered between the sexes, shedding light on to sex differences in psychiatric disorders and the sex-dependent association for NDE1. The analysis of DISC1 is currently ongoing, however, our initial findings have identified an exonic variant in DISC1 associating to both schizophrenia and anxiety disorders.
  • Virolainen-Arne, Eija (Helsingin yliopisto, 2020)
    Flooding stress and concomitant anoxia stress of plants has been in the focus of abiotic stress research for several decades. Despite that, there are several poorly studied areas in the field of flooding stress research such as responses of the anoxia-tolerant wild plant species and the function of plant mitochondria under oxygen deprivation stress. Contents and redox states of the small molecular antioxidants, that is ascorbate, glutathione and tocopherols, were determined in roots or rhizomes of four anoxia-tolerant and -intolerant plant species under anoxia and reoxygenation. Results of the study demonstrate that no correlation could be detected between the anoxia-tolerances of individual plant species and in the contents of given antioxidant induced by anoxia-reoxygenation stress but some correlation was observed between the redox states of glutathione pool and anoxia tolerances of the iris species of the study. Permeability transition was induced under high calcium ion concentration in wheat root mitochondria. Properties of the permeability transition in wheat mitochondria were characterized and results of the study demonstrated several similarities with the properties of the mammalian permeability transition. However, several features of the permeability transition observed in wheat root mitochondria diverge from the features found in plant mitochondria of different species or origin of tissue. Anaerobic ATP use of mitochondria isolated from roots of anoxia-sensitive wheat and anoxia-tolerant yellow flag iris was determined. Results of the study demonstrate that wheat mitochondria show high ATP hydrolyzing activity while mitochondria of yellow flag iris hydrolyze ATP molecules at a low rate under anoxia. Results of the study correlate well with the anoxia tolerances of the species referring to divergent survival strategies of the species under oxygen deprivation. While mitochondria of yellow flag iris, a species tolerating long-term anoxia, consume ATP at a sparing rate thus avoiding depletion of the ATP pool under anoxia, wheat mitochondria consume rapidly ATP molecules leading to abrupt ATP depletion and cell death. Investigating the mechanisms underlying plant anoxia-tolerance would benefit breeding of cultivated plants in order to have more flooding tolerant cultivars in future. Several aspects of plant anoxia-tolerance are still unknown and should be investigated such as properties and function of mitochondria in anoxia-tolerant wild plant species and function of the plant F1Fo-ATP synthase under anoxia.
  • Elovaara, Samu (Helsingin yliopisto, 2020)
    Cell lysis, as a consequence of adverse conditions, has been recognized as an important loss process among phytoplankton, in addition to the well-known loss processes of grazing and sinking. Cell lysis has been connected to increased release of carbon fixed by phytoplankton as dissolved organic carbon (DOC), the primary carbon source for pelagic heterotrophic bacteria. This has the potential to enhance pelagic remineralization at the cost of reduced sedimentation of organic carbon. Cell lysis may, therefore, have global consequences as the ratio of pelagic remineralization to sedimentation widely determines whether oceans function as a source or a sink of atmospheric carbon. However, the subject has been studied predominantly in oceans and oligotrophic marine regions. The Baltic Sea is different from these environments and the causes and consequences of phytoplankton cell lysis may, therefore, be expected to differ. The studies included in this thesis are the first attempt to study phytoplankton cell lysis and its effect on carbon cycling in the Baltic Sea. The focus of the thesis is mainly on elucidating the abiotic and biological controls of cell lysis and its relationship with pelagic DOC concentration. These were studied on a spatial scale during a spring bloom on an area covering the Gulf of Finland, the Åland Sea and the Baltic Proper, and on a temporal scale during a two-year long monitoring campaign in an estuary in the northern Gulf of Finland. In both studies the proportion of cells undergoing lysis was measured using a membrane impermeable nucleic acid stain to indicate cells with compromised membrane integrity. The spatial monitoring study revealed considerable variation in the proportion of cells undergoing lysis with generally higher proportion of dying cells in deep water (1-10 m: average 84%, range 67-91%; 30 m: average 77%, range 62-90%; 60 m: average 71%, range 58-86%) and among nanophytoplankton (surface water average: 64%), as compared to smaller eukaryotic picophytoplankton (surface water average: 88%) and picocyanobacteria (surface water average: 82%). No clear correlations between cell lysis and nutrient concentrations were found, although there was a weak correlation between the proportion of intact eukaryotic picophytoplankton and phosphate concentration (R2 = 0.13, p = 0.029). No connection between cell lysis and DOC concentration was found. Also during the temporal monitoring campaign variation of cells undergoing lysis was high (surface water average: 62%, range 18-97%). Again, no correlation between nutrient concentrations and cell lysis was found, although this time there was a weak negative relationship between the proportion of cells undergoing lysis and DOC concentration (R2 = 0.15, p = 0.0185). In both studies some indication was found that phytoplankton lysis is less prevalent in conditions where interspecific phytoplankton competition is low. Details of the flow of carbon from phytoplankton to pelagic heterotrophic bacteria was studied experimentally using two phytoplankton species (a dinoflagellate Apocalathium malmogiense and a cryptophyte Rhodomonas marina). Contrasting species specific differences were found in their ability to transfer carbon from the inorganic pool via DOC to bacterial biomass and in the composition of the emerging bacterial community. The smaller R. marina released more bioavailable DOC and attracted a bacterial community mainly consisting of copiotrophs (bacteria thriving when DOC is abundant and highly bioavailable), which likely directs more carbon towards microbial loop. The DOC released by the larger A. malmogiense was less bioavailable. If these results can be generalized to other taxa of similar size, the fast consumption of DOC released by R. marina may partially explain why no relationship between the lysis of small phytoplankton and DOC concentration was found. The overarching conclusion from the two field studies is that the environmental conditions, such as nutrient limitation, that have been shown to promote cell lysis in oligotrophic marine regions are not the main determinants of cell lysis in the Baltic Sea. Also, the high ambient DOC concentration and terrestrial runoff in the Baltic Sea seem to mask the effect of cell lysis on DOC concentration. The group and species specific differences in both cell lysis and carbon cycling indicate that investigating cell lysis on lower taxonomic levels will help to connect cell lysis to carbon cycling.
  • LaMere, Kelsey (Helsingin yliopisto, 2020)
    Today, the wicked socio-ecological problems facing the world, like climate change and food security, are far too large-scale and complex for any single institution or academic discipline to address alone. Further, these often-contentious issues affect various stakeholders. Therefore, progress requires socially sensitive solutions that take all relevant parties' knowledge and values into account. Hence, participatory problem-solving approaches, like inter and transdisciplinary science, which invite diverse perspectives into the problem-solving process, are attractive options for combatting wicked problems. By integrating diverse knowledge bases and modes of thinking, these approaches can produce more creative, credible, democratically accountable, and socially acceptable solutions. However, despite the benefits they provide, these approaches must be developed further to ensure they reach their full potential. As such, chapters I and II of this thesis aim to promote the incremental advancement of inter and transdisciplinary science on two dimensions: First, chapter I aims to draw attention to the critical process of strengthening communication via cognitive integration. Cognitive integration "bridges the gaps" in understanding between members of diverse problem-solving teams, which eases communication and promotes collaborative work. Chapter I uses a paired structural topic modeling and interview analysis approach to identify and describe different perspectives about "risk," a key concept for the operational interdisciplinary team studied. Within this team, diverse perspectives about ideas as fundamental as the definition of risk and potential conflict areas were found, like the idea of quantitative risk analysis. Transparently revealing and describing the differences in perspectives within diverse teams in this way at the beginning of their collaborative work could help facilitate cognitive integration and direct conflict resolution efforts, thereby enabling inter and transdisciplinary teams to begin their work more smoothly and effectively. The second area for development this thesis aims to address is the lack of peer-reviewed methods in inter and transdisciplinary research. Specifically, chapter II describes the development of a new method for mental model elicitation, which is a popular tool within transdisciplinary research. Mental model elicitation is intended to document a participant's causal understanding of a problem system. However, the academic literature rarely discusses the elicitation process, and those approaches it does describe, direct and indirect elicitation, are likely to either oversimplify the participants' ideas or introduce facilitator bias, respectively. Chapter II describes the Rich Elicitation Approach (REA), which combines both approaches in a single framework to maintain the benefits of each while compensating for their shortcomings. Unlike chapters I and II, the final chapter of this thesis, chapter III, focuses on a real-world transdisciplinary problem-solving effort. Specifically, chapter III reports the outcomes of a problem framing study to understand how climate change may affect salmon and their fishery in the Baltic Sea region and direct fishery management accordingly. Chapter III makes use of the REA developed in chapter II, as stakeholders' mental models form the basis of this study. By analyzing these models, 15 themes describing the problem, goals for the salmon management considering climate change, and strategies to help achieve those goals were found. Additionally, chapter III identified potentially conflicting values and ideas that salmon management may need to address moving forward. Problem framing is only the first step toward addressing the climate change issue for salmon management. Continuing efforts will require the cooperation of diverse problem-solving teams in a contentious management context, which could be facilitated by transparently acknowledging and describing perspective differences, as was done in chapter I.
  • Fang, Bohao (Helsingin yliopisto, 2020)
    How predictable is evolution? There is no fully satisfactory answer to this 100-year old question yet. However, within the past two decades, much progress has been made towards unravelling various factors that influence the predictability of evolution. Much of this work has focused on the similarity of evolutionary responses in replicate populations of a given taxon that have independently colonised similar environments – a phenomenon known as parallel evolution. The fish species in the family Gasterosteidae (sticklebacks) have become popular models to study the repeatability of evolution. This thesis focuses on evolutionary history and parallel evolution in two ecologically similar and geographically co-distributed species in the family Gasterosteidae, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius). Freshwater populations of both species evolved similar phenotypic traits after marine ancestors independently colonised freshwater environments. A highly resolved phylogeny is a prerequisite for untangling the processes that have shaped the underlying genomic divergence, including natural selection and population demographic history. Therefore, my thesis begins by resolving the worldwide phylogenetic relationships and demographic history of both focal species, using state of the art phylogenomic analyses. The results indicate that extant three-spined stickleback populations originated from the Eastern Pacific in the late Pleistocene, and the Atlantic populations were colonised from the Pacific ancestors via the Arctic Ocean. In contrast, nine-spined sticklebacks have a more ancient history, diversifying in the late Pliocene, and their current distribution is the result of multiple waves of trans-Arctic colonisation from the Far East, with several divergent lineages having evolved across their geographic range. The thesis then moves on to investigate the genetic basis of parallel freshwater adaptation in each of the two species, using the information gained in the previous chapter to set up specific hypotheses and define simulation parameters. For three-spined sticklebacks, the level of parallel evolution at the genotype level was 10 times higher among the freshwater populations in the ancestral Eastern Pacific region than anywhere else in the world. Empirical data and simulations demonstrate that these patterns are determined by a reduction in standing genetic variation outside the ancestral Eastern Pacific region, a result that can be explained by the demographic history of the species. A comparison of the two species revealed fundamental differences in the way standing genetic variation – the raw material upon which selection acts – is distributed among populations. This was exemplified by 2-fold higher degree of genetic structuring and 23-fold stronger isolation-by-distance in ninethan in three-spined sticklebacks. Conversely, the proportion of genetic parallelism in three-spined stickleback is 123.4 times greater than the nine-spined stickleback. Taken together, the thesis resolved the phylogenetic affinities and demographic history of stickleback fishes using state-of-art methods and a global sampling strategy. Based on this knowledge, the thesis further uncovered profound heterogeneity in the repeatability of evolution within and between the two model species in response to freshwater colonisation. Hence, the two stickleback species with their contrasting demographic and evolutionary histories constitute a model system to study how differences in the distribution of standing genetic variation can influence the predictability of evolution.
  • Käyhkö, Janina (Helsingin yliopisto, 2020)
    This thesis is a study of climate change adaptation as a human adjustment process in the context of Northern European agriculture. It deals with the human decision-making entailing uncertainty, risks and opportunities brought about by climate change and climate policies. Agricultural production of food in Northern Europe is under pressure. There are constant changes in societal structures, such as policies and economic markets, as well as climatic stressors. The climate impacts pose direct risks to production, such as increasing floods and droughts, as well as indirect pressures through, for example, the global demand for arable lands. This constantly changing and complex socio-environmental context of food production is expected to drive processes of adjustment in the agricultural sector. Recent assessments suggest that in most parts of Europe adaptation measures in the agricultural sector will increase significantly in the coming years. Agricultural adaptation research is focused on the climate risks with respect to production and on the development of technical solutions. Agricultural and food production sciences are at the front line of technical development of adaptation measures, such as new plant varieties, production environments and cultivation measures. There is also a growing body of literature on the systemic complexity of adaptation needs and options focused on climate impacts. Farm-scale adaptation is mainly studied in the development and management research fields among other applied research focused on developing countries, farm economics and local case studies. The current literature suggests that farmers will implement the adaptation measures in order to secure their livelihoods and to sustain the productivity of agricultural soils and lands. The perspective of agri-food system practitioners, nevertheless, is less represented in adaptation literature. This is also true of research on the societal drivers and outcomes of adaptation. That said, there is research suggesting that although adaptation is aimed at decreasing risks and vulnerability, the farm-scale adaptation measures may have unintended harmful impacts to different actors and resources. These are identified in yet few empirical studies to involve economic losses at farm scale, local environmental damage and short-term productivity decreases. This presents a gap in the research that should provide background knowledge for governing the complex field of adaptation in agriculture and food production sectors. From the perspective of environmental and social sciences, the adaptation measures call for focused assessment in terms of their social drivers and socio-environmental outcomes in all regions globally. This thesis sets out to address this gap and increase understanding on adaptation measures as an issue of decision-making within complex socio-environmental contexts and trade-offs. This thesis applies a qualitative empirical study with an interdisciplinary epistemological stand and methodological approach that draws on agri-food system practitioner perceptions. The focus is on crop farmers and on farm-scale adaptation. Furthermore, attention is paid to other professionals of the sector who deal with various agri-food systems, development and management, and in governance. The research starts with an analysis of adaptation measures and the drivers for their implementation at farm scale and the agricultural sector, followed by an analysis of the potential unintended harmful outcomes of these measures. Finally, the transformative adaptation measures that concern the food systems in the Nordic context are analysed. Key findings of this thesis show that climate change adaptation measures in the Nordic agri-food systems are currently aimed at reducing risks and increasing long-term adaptive capacity when it serves the highly contextual and often subjective needs. These do not always reflect the public policy goals and often involve harmful outcomes with respect to other actors and the sustainable development goals. To advance sustainable implementation of adaptation measures in Nordic agriculture inevitably requires governance interventions that include actors from various fields of society.
  • Paasinen Sohns, Aino (Helsingin yliopisto, 2020)
    Cellular transformation, the transition of normal cells into morphologically and functionally altered neoplastic cells, may be caused by a great variety of genetic and epigenetic alterations and ensuing aberrations in cellular signaling. The enzyme ornithine decarboxylase (ODC), the key regulator of the biosynthesis of polyamines and essential for cell proliferation, has often been associated with neoplastic transformation. In normal cells ODC activity is strictly controlled, but becomes constitutively activated during cell transformation induced by carcinogens, viruses or oncogenes. To test if ODC could be transforming by itself and potentially be a common mediator of cell transformation, rodent fibroblasts were engineered to overexpress ODC. The results showed that ODC is both necessary and sufficient for cellular transformation of immortalized rodent fibroblasts, and oncogenes, such as v-src may, at least in part, exert their effects via ODC. We compared signal transduction components in cells transformed by v-src, c-Ha-rasVal12 and ODC for common points of convergence. It was possible to exclude several signal transduction molecules, reported earlier to be activated in a transformation-specific manner. All transformed cell lines were found to display a constitutive increase in the phosphorylation of c-Jun. S-Adenosylmethionine decarboxylase, a second key polyamine biosynthetic enzyme was examined for its potential role in cell transformation. We showed that AdoMetDC overexpression surprisingly induces transformation both in sense and antisense conformations in rodent fibroblasts, and is highly tumorigenic in nude mice. AdoMetDC-induced transformation culminated in c-Jun phosphorylation. Mutants of MEK1, JNK1 and Jun reverted the transformed phenotype and Jun-mutant effectively inhibited the anchorage-independent growth of the AdoMetDC-transformed cells. AdoMetDC-transformed cells showed aggressive growth in nude mice and the resulting tumors were characterized by chaotic neovascularization. Angiogenic switch was triggered by an increase in VEGF expression and downregulation of thrombospondin-1 (TSP-1). The reintroduction of TSP-1 into AdoMetDC-transformed cells reverted the tumorigenic growth. Extracellular matrix degradation and invasive capacity required for invasion and metastasis were associated with induction of matrix metalloproteinase-2 and larger isoforms of Tenascin-C. In conclusion, our studies on polyamine biosynthetic enzymes in cell transformation of rodent fibroblasts suggest an important role for ODC and AdoMetDC. By comparing the signal transduction pathway of the ODC- and AdoMetDC-transformed cells to oncogenic Ras- and v-Src-transformed cells, we could determine c-Jun activation as a common point of convergence.
  • Holopainen, Minna (Helsingin yliopisto, 2020)
    Human mesenchymal stromal cells (hMSCs) are fibroblast-like cells that have an exceptional ability to modulate immune cells. Due to their immuno-modulatory properties, hMSCs have been employed in various clinical trials in the treatment of autoimmune or inflammatory diseases. Even though hMSC therapy has yielded multiple promising results, not all trials have been successful. Due to the discrepancies in the therapeutic response, hMSC therapy requires further development and standardisation. While optimisation of the culture conditions provides one method to improve the therapeutic efficacy of hMSCs, fine-tuning the culture conditions requires deep understanding of the hMSC immunomodulatory mechanisms. It has been established that hMSCs mediate their therapeutic effect via cell-cell contact and especially by secreting several paracrine factors that include lipid mediators and extracellular vesicles (EVs). Intriguingly, hMSC-derived EVs (hMSC-EVs) are able to mediate the therapeutic response of MSCs, which has led to a growing interest in and research on cell-free hMSC-EV therapy. In addition to EVs, lipid metabolism and especially the lipid mediator prostaglandin E2 (PGE2) are vital to the hMSC immunomodulation. Interestingly, the membrane lipid composition correlates with the immunosuppressive capacity of hMSCs, suggesting that membrane lipids play a role in mediating the immunomodulatory response of hMSCs. Lipid mediators are derived from polyunsaturated fatty acids (PUFAs) that can be stored in membrane phospholipids. Over the past few decades, the significance of PUFA-derived lipid mediators in orchestrating the dampening phase of inflammation, i.e., resolution, has been unravelled. These novel specialized proresolving mediators (SPMs) have several essential roles in modulating immune cells, including macrophages. The role of these SPMs in hMSC immunomodulation has received only marginal interest, and whether hMSCs produce multiple SPMs has not been determined. Keeping in mind that hMSC-EVs mediate the therapeutic response of MSCs, we investigated the lipid metabolism of hMSCs and their EVs after supplementing the cells with lipid mediator precursor PUFAs: arachidonic acid, eicosapentaenoic acid and docosahexaenoic acid (DHA). Due to the supplementation, the membrane phospholipid and fatty acid composition were notably modified and the downstream lipid mediator production was enhanced. Excitingly, we were able to demonstrate for the first time that hMSCs produce several SPMs, which may mediate the immunomodulatory response of hMSCs. Remarkably, we showed that the PUFA modifications in the phospholipid composition were transferred into the EVs, highlighting the importance of EVs as transporters of the immunomodulatory factors derived from hMSCs. Because of their importance in the resolution of inflammation, we investigated the effects of hMSCs and hMSC-EVs on macrophages with a focus on regulatory macrophages (Mregs). We elucidated that both hMSCs and hMSC-EVs enhanced the anti-inflammatory and proresolving properties of these less-studied macrophages, highlighting the importance of PGE2 in the function of hMSC-EVs. Moreover, the hMSC secretome increased the CD206 expression and Candida albicans phagocytosis activity of macrophages, demonstrating a functional change in the macrophage properties. Fascinatingly, the DHA-supplemented hMSCs even further skewed the macrophage phenotype in an anti-inflammatory direction. However, the change was limited, and the elucidation of the functional effects of PUFA supplementations on hMSCs require additional investigations. In conclusion, this thesis provides further evidence that the lipid metabolism has an essential role in hMSC functionality and that the SPM production may represent an additional mechanism in hMSC immunomodulation. For the first time, we have explored the impact of hMSCs and hMSC-EVs on Mregs and our results highlight the importance of EVs as the mediators of hMSC immunomodulation. Furthermore, we investigated the possibility of improving the hMSC immunomodulation with PUFA supplementations that would represent an easy and safe way to enhance the therapeutic potential of hMSCs or hMSC-EVs. A more detailed understanding of the complex immunomodulatory mechanisms of hMSCs is in key position when investigating new possibilities in the development of hMSC therapy.
  • Lehtimäki, Jaakko (Helsingin yliopisto, 2020)
    The motor protein myosin binding to filamentous actin and dislocating it, forms the basis for all eukaryotic cells and tissues to undergo higher order transformations such as cell division, migration and differentiation. Whereas e.g. fine motor skills and rhythmic contractions of the heart depend on highly organized sarcomeres, each undergoing similar degree of shortening through thin actin filaments sliding in-between the myosin filaments, the non-muscle cells exhibit much more dynamic actomyosin structures: the stress fibers. Although the composition, function and regulation of stress fibers have been studied quite extensively, we do not have a comprehensive understanding of how they are generated and maintained in various cells and tissues displaying diverse morphology and notable plasticity in the means of utilizing these contractile structures. In this thesis work, I studied the formation, maintenance and recycling of stress fiber structures in human osteosarcoma (U2OS), mouse embryonic fibroblast (MEF) as well as in canine kidney epithelial (MDCK) cells. First, I revealed that stress fiber assembly does not always need pre-existing stress fiber precursors as previously documented, but they can also coalesce directly from the actin cortex driven by non-muscle myosin II (NMII) pulses. Secondly, in-depth analysis of NMII assembly and its recruitment to stress fibers unraveled the role of a chaperone UNC-45a in regulating both of these events, and further extended its chaperone activity to assist the cortical myosin 1C assembly. Thirdly, we uncovered that stress fiber precursors are reorganized and packed into peripheral thin bundles upon epithelial cell-cell contact formation and this can be reversed by inhibiting AMPK-VASP pathway. Lastly, we demonstrated that actin stress fibers have an intimate and reciprocal, plectin-mediated relationship with vimentin intermediate filaments that extends to controlling the morphogenesis and nucleus positioning in migrating cells. Taken together, these studies bring forth the principal protein controlling the NMII-filament assembly and stability, broaden our understanding on the versatility in generating contractile actomyosin structures in different cell types and demonstrate how interconnected stress fibers are to other cytoskeletal elements.
  • Pokharel, Kisun (Helsingin yliopisto, 2020)
    The conservation, characterization, and sustainable utilization of farm animal genetic resources have far-reaching socioeconomic effects. Finnsheep, which is native to Finland, is globally known for its exceptional prolificacy and has been exported to several countries to improve the productivity of local breeds. Prolificacy, mainly determined by the ovulation rate and litter size phenotypes, has high economic importance in sheep farming systems. The ovulation rate is associated with the number of ovulatory follicles produced during the follicular growth phase of the estrous cycle, and successful implantation of the conceptus ensures maximum litters. The primary aim of this study was to evaluate the exceptional prolificacy of Finnsheep. Another important and overarching aim was to explore the genetic aspects of two important reproductive events leading to ovulation and successful pregnancy in sheep. To gain an insight into how these two processes are regulated genetically and non-genetically, the whole transcriptomes of selected reproductive tissues relevant to folliculogenesis (first phase, ovary) and early pregnancy prior to implantation (second phase, corpus luteum (CL) and endometrium) were analyzed. In the main experiment, the ovaries of 31 Finnsheep (n = 11) and Texel (n = 11) ewes as well as their F1 crosses (n = 9) collected during surgery were biopsied; other tissues, including the CL and endometrium, were collected at the slaughterhouse. Half of the animals were maintained on a flushing diet during the entire experiment to study the influence of nutrition during early pregnancy. In addition, the transcriptomes of the ovarian and endometrial tissues of Finnsheep ewes were compared to those of European feral mouflons. For transcriptomic analysis, cDNA libraries targeting mRNAs and microRNAs were sequenced using the Illumina HiSeq 2000 system with 100-base pair (bp) paired-end and 50-bp single-end techniques, respectively. Gene expression results from the first phase of the experiment revealed that the flushing diet strongly affected the Texel and, to some extent, the F1-crosses of sheep; however, Finnsheep were not affected by the diet. Likewise, the gene expression profiles of the F1 crosses were more similar to those of Finnsheep than of Texel, possibly because of the parent-of-origin effects, such as genomic imprinting. While no major candidate genes reportedly associated with prolificacy were differentially or highly expressed, FecGF polymorphism (V371M) in GDF9 was present in half of the experimental Finnsheep and F1 crosses but completely absent in the Texel sheep. The second phase of the experiment provided an insight on the cross-talk between the CL and endometrium, as revealed by both the shared and tissue-specific genes. Finnsheep had a higher embryo mortality rate than Texel. The top expressed genes were associated with progesterone formation and events (elongation and attachment), leading to blastocyst implantation. Several endogenous retroviruses (ERVs) were expressed in the endometrium samples. Immune-related genes and pathways appeared to be differentially expressed and/or regulated in the CL of pure-breds. During the preimplantation stage, the immune system of the Finnsheep ewes appeared superior to that of the Texel ewes. Owing to the influence of interferon tau in massive gene expression changes starting around day 13, the gene expression profiles of the endometrium samples in response to elongated embryos were remarkably different from those in response to spherical embryos. Moreover, several interferon-stimulated genes were upregulated in the endometrium samples having elongated embryos. In addition to differentially expressed genes between the reproductive tissues of domestic (Finnsheep) and feral (European mouflon) sheep, we identified novel genes and miRNAs and their regulatory mechanisms associated with reproductive traits. A few novel structural findings were obtained as part of this work. Maternally imprinted miRNA cluster on chromosome 18 (C18MC), which is conserved exclusively among placental mammals, was reported for the first time in sheep. With 46 expressed miRNAs, sheep C18MC may be the largest miRNA cluster among all mammalian species. The miRNAs (>500) quantified in this thesis are valuable, given that only 153 sheep miRNAs have been identified till date. A novel ERV transcript with high similarity to the genomic region within the FecL locus and known to affect prolificacy was identified, indicating that ERV plays an important role in reproduction and may even contribute to litter size differences. Overall, the work presented in this thesis explored two critically important aspects of reproduction, i.e., ovulation and preimplantation, in sheep using state-of-the-art genomics and bioinformatics tools. The resources and findings from this thesis are highly relevant to both breeders and researchers studying sheep. The comprehensive list of genes and miRNAs expressed in the three key reproductive tissues is a useful resource for understanding transcriptional patterns during the follicular growth phase and preimplantation stage leading to pregnancy in sheep. The diet- and F1 cross-related experimental results will be valuable for implementing sheep breeding strategies aimed at achieving an optimum reproductive capacity. Furthermore, these results will provide a foundation for future research, and the data may have additional applications following the advancement of analysis tools and technologies.
  • Rai, Neha (Helsingin yliopisto, 2020)
    Solar UV-B radiation (290–315 nm), UV-A radiation (315–400 nm), and blue light (400–500 nm) regulate multiple aspects of plant growth and development, and these are mediated by different photoreceptors. In plants, UVR8 is described as a UV-B photoreceptor, while cryptochromes (CRYs) are described as UV-A/blue photoreceptors, based on their absorption maxima and action spectra. However, these photoreceptors are also sensitive to other wavelengths outside the wavelengths of maximum absorption. Based on this property, their roles could differ in full-spectrum sunlight than those reported from experiments performed in controlled environments. In sunlight, both UV-B and UV-A/blue photoreceptors are simultaneously activated, and there is a possibility that their signaling pathways interact. However, an interaction between UVR8 and CRYs regulating transcriptome-wide responses remained unexplored. Furthermore, persistent high solar irradiance is often followed by drought in the field, and studies have indicated that UV and drought interact to regulate plant physiological responses. However, an interaction for metabolic and transcript abundance responses has not been well-described. These gaps in knowledge are addressed in my thesis through three main aims: (1) to identify the individual roles of UVR8 and CRYs in the perception of solar UV-B, short-wave UV-A (315–350 nm, UV-Asw), long-wave UV-A (350–400 nm, UV-Alw) radiation, and blue light by plants, (2) to test the interaction between UVR8 and CRYs under solar UV radiation, and (3) to determine if pre-exposure to solar UV radiation could provide acclimation to subsequent drought stress in plants. To achieve the first two aims, I used Arabidopsis thaliana wild type and mutants impaired in UVR8 and CRYs photoreceptors and exposed them to different ranges of wavelengths of solar or simulated solar UV radiation and blue light under optical filters. To achieve the third aim, I used two accessions of Medicago truncatula (Jemalong A17 and F83005-5). I exposed them to solar UV radiation using optical filters and subjected them to drought stress by restricting watering in a factorial experiment. The results indicated that UVR8 mediates the perception of both UV-B and UV-Asw radiation. In contrast, CRYs mediate the perception of UV-Alw radiation and blue light. A further novel finding is that UVR8 and CRYs interact antagonistically to regulate transcriptome-wide responses under UV-B and UV-Asw radiation. My thesis also provides evidence that UV-B+UV-Asw radiation and mild drought can interact positively to trigger acclimation through an increase in epidermal UV screening in the drought-intolerant accession, F83005-5, and through an increase in transcript abundance of CHALCONE SYNTHASE in the moderately drought-tolerant accession, Jemalong A17. Furthermore, all three studies showed a distinct response to solar or simulated solar UV-B+UV-Asw and UV-Alw radiation, suggesting a need to split UV-A into short and long wavelengths for future studies on UV-A radiation.
  • Koskelainen, Susanna (Helsingin yliopisto, 2020)
  • Jerney, Jacqueline (Helsingin yliopisto, 2020)
    Phytoplankton plays a pivotal role for aquatic ecosystem functioning and global biogeochemistry. Climate change has affected phytoplankton community composition and distribution in the last decades, including a higher prevalence for harmful algal blooms in many areas. The globally distributed dinoflagellate Alexandrium ostenfeldii has for example started to form dense toxic blooms in the Baltic Sea and a new bloom location was recently discovered in western Japan. To survive unfavorable conditions this species forms resting stages, which may accumulate in sediments, forming a “seed bank”. The aim of this thesis was to investigate the relevance of the seed bank for the ecology and evolution of A. ostenfeldii and to understand the implications of these findings for persistence and possible expansion under ongoing global change. A combination of field surveys in Finland and Japan, experimental work and genotyping were carried out to address these aims. The results indicate that the seed bank stores a large clonal diversity, underlining its importance for stabilizing local populations against environmental fluctuations. No population structure was detected in temporal parts of a pelagic population, showing that differentiation does not happen during one season. The life cycle of A. ostenfeldii was found to be highly versatile, allowing overwintering of asexual resting stages without a pronounced dormancy period, and sexual reproduction throughout the season. Predicted future temperature and salinity did not affect germination of A. ostenfeldii, but affected growth rates, demonstrating their selective effect on the pelagic part of the population when detached from the seed bank. In addition, the importance of resting stages for colonizing new habitats, was stressed by the close relationship found between a recently discovered bloom population in Japan and geographically distant populations of similar habitats. Low genetic diversity indicated a recent introduction, potentially due to anthropogenic dispersal of resting stages. In conclusion, the seed bank plays a pivotal role for evolution and ecology of A. ostenfeldii. It ensures survival of a genetically diverse population, and slows down evolution, by linking contemporary populations to past populations via frequent re-seeding of resting stages. Although selection is buffered by phenotypic plasticity, future temperature and salinity may affect the pelagic part of the population, in the long run. A generalist life cycle of A. ostenfeldii and the presence of a seed bank support persistence and potential future temporal and spatial expansion under global change.
  • Roslund, Marja (Helsingin yliopisto, 2020)
    The incidence of immune-mediated diseases has increased rapidly in developed societies. According to the biodiversity hypothesis, the core reason is the evident biodiversity loss in urban areas. This biodiversity loss limits exposure to a diverse microbiota, which is associated with the human commensal microbiota and immune regulation. In addition, urban pollutants, such as polycyclic aromatic hydrocarbons (PAHs), may alter microbial communities and interfere with immune regulation. However, studies linking urban biodiversity loss, PAH pollution, environmental and human commensal microbiota and immune regulation are lacking. This study is one of the first to estimate the connections between environmental exposure, the commensal microbiota, and the immune response of urban children using both intervention trials and comparative studies. The aim of this study was also to develop practices to reduce the risk of non-communicable immune-mediated diseases that are globally recognized as emerging public health problems. These diseases comprise over 80 inflammatory disorders including allergies, type 1 diabetes, asthma and inflammatory bowel disease. The research focused on two aspects: the effect of biodiversity and pollution on the commensal microbiota of children and immune regulation. First, I estimated PAH induced bacterial shifts in polluted urban landscaping materials, and whether environmental exposure to PAHs can affect children’s commensal bacterial communities on the skin and in the gut. Secondly, we set up a human intervention trial in which urban environmental biodiversity was manipulated and examined its effects on environmental and commensal microbiota and immune regulation in children. The PAH pollution studies showed that PAHs may induce shifts in environmental and human commensal bacterial communities that are associated with human health and immune regulation. Bacterial shifts in urban landscaping materials depended on soil material type, indicating that in the future it is possible to design gardening and landscaping materials that are more resilient to bacterial shifts induced by PAH pollution. Soil PAH pollution in day-care center yards was associated with altered Actinobacteria, Bacteroidetes and Proteobacteria communities on children’s skin and in day-care yard soils. However, altered genera differed between skin and soil, excluding Mycobacterium, the abundance of which increased on skin and in soil with increasing surface soil PAH levels. Associations were not found between gut microbiota and PAH levels in day-care yard surface soils or ambient air. However, gaseous chrysene levels in the ambient air were associated with the endocrine signaling pathways predicted from the gut bacterial metagenome with the Kyoto Encyclopedia of Genes and Genomes. The peroxisome proliferator-activated receptor (PPAR) is a crucial signaling pathway in the regulation of inflammation, metabolism, and tumorigenesis. The PPAR signaling pathway together with the adipocytokine signaling pathway can regulate immune cells and affect hormonally-mediated diseases, including obesity, insulin sensitivity, puberty, and fertility. The PPAR and adipocytokine signaling pathways both decreased among children, with higher gaseous chrysene levels in the day-care center’s ambient outdoor air. These findings indicate that PAH concentrations that are below the risk assessment safety limits may alter the human commensal microbiota and interfere with endocrine signaling. The imbalance in human microbiota and the decrease in endocrine signaling pathways might contribute to inflammatory disorders. Therefore, optimal risk assessments should take into account the possibility of the disruption of endocrine signaling pathways and the microbiota–health nexus. The 28-day biodiversity intervention trial included 75 children in three different day-care environments (standard urban, biodiversity intervention, and nature-oriented). During this intervention, the environmental and intervention children’s commensal microbiota was diversified, which in turn promoted their immune regulation and eventually may have beneficial health consequences. Surface soil bacterial communities differed between intervention and standard day-care yards and, in particular, differences were seen within alpha-, beta-, and gammaproteobacterial classes. The relative abundance of bacteria typically found in the forests of Finland increased in intervention day-care yards. These environmental changes in day-care yards remained for 2 years. The diversity of proteobacterial communities in soil and on the skin of the day-care children increased during the 28-day intervention. Importantly, an increase in skin gammaproteobacterial diversity was associated with beneficial effects in immune regulation, promotion of the plasma transforming growth factor-β level and proportion of regulatory T cells, and a decline in pro-inflammatory interleukin 17A (IL-17A) levels. In addition, among intervention children the ratio between anti-inflammatory IL-10 and pro-inflammatory IL-17A increased, indicating that the biodiversity intervention promoted children’s immune regulation. In addition, among intervention children, I observed shifts within gut Ruminococcaceae and Lachnospiraceae communities that have earlier been associated with gut health. Interestingly, the microbiota on the skin and in the gut of intervention day-care children shifted toward those in nature-oriented day cares. I followed the environmental and commensal bacterial shifts on the skin, in the saliva, and in the gut for a 2-year period among children in the intervention group. This long-term study showed that the biodiversity intervention shifted the environmental and commensal bacterial communities at the intervention day cares, and these shifts include important primers for the immune system. In particular, environmental shifts were permanent based on the 2-year period. These results are proving valuable since now that we understand the effect of biodiversity in the living environment, we can shape children’s commensal bacteria and thus affect immune regulation. The challenge will be to design novel pathogen-free nature-based solutions for urban people that include a high diversity and richness of anti-inflammatory health-promoting bacteria. Future research should target this challenge. The results of this thesis support the biodiversity hypothesis: environmental biodiversity is associated with the commensal microbiota of humans and immune regulation. Indeed, both biodiversity loss and pollution in the urban environment may lead to an altered environmental microbiome. This in turn can lead to an imbalanced immune system and consequently increase the prevalence of emerging public health problems, including allergies, asthma, type 1 diabetes, and inflammatory bowel disease. Importantly, this study has demonstrated that modifying the living environment of children with microbiologically diverse natural materials might provide a feasible approach for decreasing the risk of immune-mediated diseases in urban populations.

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