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The Effects of Soil Treatments and Yellow Rattle on the Soil Properties of Newly Established Meadows (2024)My master’s thesis aims to determine the impact of soil treatments and the hemi-parasite Rhinanthus minor (yellow rattle) on the soil properties of newly established perennial wildflower meadow. As urbanization and urban green spaces increase, the need for viable methods for establishing biodiverse meadows on existing lawns grows. I joined a lawn to meadow project based at Lammi Biological Station wherein four soil treatments (untreated, scarified, overturned, and replaced with meadow substrate) were employed in eight meadow blocks. Within those blocks, yellow rattle was sown into half of the plots to determine if it can hamper the growth of competitive grass species. My aim was to explore the meadow blocks’ chemical soil properties (phosphate, nitrate + nitrite, ammonium, total carbon, total nitrogen, and pH). The soil properties were measured using LECO analysis, photometric analysis, and a pH meter. In the newly established meadows at Lammi biological stations, there is evidence that soil properties do change as a result of different soil treatments and the introduction of a hemi-parasitic plant. The initial soil properties show that soil turnover results in increased nitrate + nitrite and decreased total nitrogen compared to untreated meadow soil and lawn controls, respectively. Meadow soils replaced with a substrate exhibited nutrient poor conditions typical of low nutrient preferring meadow plants. The effects of yellow rattle on aboveground community structure are not investigated here, but after the first growing season, its presence increased nitrate + nitrite in the first ten cm of soil. Nitrogen mineralization as a result of grass introduced to soil microbes and nutrient dense yellow rattle leaves may be the cause of these changes to the soil properties. Meadow establishment can take 3 – 5 years, so the use of these methods should continue to be observed. I would expect larger differences to manifest as the experiment continues, namely, decreased soil nutrients as more growing seasons pass.
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(2021)The immune system is crucial in the central nervous system (CNS), protecting sensitive tissues, promoting regeneration, and maintaining homeostasis. It is involved in CNS-disorders, such as neurodegenerative diseases and neurological insults related to stroke. Critical myeloid leukocytes in the CNS are microglia, divided into pro-inflammatory M1 and anti-inflammatory M2 phenotypes. This polarization achieves modulation of the inflammatory response by amplifying or dampening it. Therefore, microglia are widely investigated in CNS-disorders. β2-integrins are adhesion proteins that mediate inflammation. They are expressed explicitly on leukocytes, including microglia. Important processes, such as phagocytosis and cell motility, are regulated by β2-integrins. They also relay downstream signals, altering inflammation in many settings, although their effects on microglial properties and stroke are currently poorly understood. We here aimed to investigate the role of β2-integrins in stroke-related injury and microglia polarization in vivo using knock-in (KI) mice, which lack functional β2-integrins. Our results show that in a mouse model of haemorrhagic stroke, the functional outcome was less severe in β2-integrin KI versus wild-type (WT) mice (P = 0.0147), suggesting that β2-integrins are involved in stroke pathophysiology. Furthermore, by using flow cytometry we observed significantly lower frequencies of M1 microglia in the KI mouse brain (P = 0.0096). Therefore, our findings reveal neuroprotective aspects by inhibiting β2-integrins in neuroinflammation. Investigating microglial properties mediated by β2-integrins could contribute to the understanding of neuroinflammatory events, leading to the development of therapies for poorly treated CNS-disorders. Our results suggest that β2-integrins should be further explored as molecular targets for novel stroke treatments.
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(2024)Agriculture is known to have major environmental impacts through intense use of resources and occupation of land, and it is a significant contributor to climate change and biodiversity loss. Extensive agriculture, as High Nature Value (HNV) farming, benefits biodiversity while providing food and other ecosystem services (ESS). The environmental impacts of HNV ruminant production systems utilizing semi-natural grasslands (SNG) have until now been unknown for Finland and Estonia. SNGs are characterized by high biodiversity and a need for constant management. As livestock production, especially ruminant production, HNV farming on SNGs in the respective countries has potentially considerable environmental impacts whilst simultaneously supporting biodiversity through maintenance of the endangered SNGs. This thesis aims at quantifying and comparing the environmental parameters of global warming potential (GWP), land occupation (LO), and biodiversity, through life cycle assessment (LCA) of HNV livestock production systems in the two neighboring countries of Finland and Estonia and disentangling the drivers for the environmental parameters in both countries. In addition, a GWP for production output (meat) is quantified, and the environmental parameters are considered in relation to the production output of the farms. The results indicate that the HNV ruminant farming systems of Estonia are more extensive and self-sufficient to their production than their Finnish counterparts. Enteric fermentation drives the GWP on the farming system as well as on the product level, while the impact of imported inputs is observed in GWP and LO of Finnish HNV farms. Future research shall focus on determining the environmental impacts of water use and carbon sequestration, as well as the effect of HNV farming on below ground biodiversity. In addition, future research shall include animal welfare aspects to gain a comprehensive understanding of the sustainability of HNV ruminant farming systems.
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(2022)Pathogenic variants in BRCA-associated protein 1 (BAP1) cause BAP1 tumour predisposition syndrome (BAP1-TPDS) with increased risk of several cancers including uveal melanoma (UM). UM originates from the melanocytes of the choroid, iris or ciliary body in the eye. UM is a rare cancer with a high metastatic rate and is usually seen in Caucasian people. BAP1 is a deubiquitinating enzyme and to function as a tumour suppressor it needs to retain enzymatic activity. To retain its enzymatic activity, it needs a functioning UCH-domain and nuclear localisation signal. Loss of function variants in BAP1 are easily interpreted as pathogenic, however, many missense variants remain as unclear on their status of pathogenicity. We aimed to study the enzymatic activity of missense variants in the UCH domain of BAP1. We selected 22 missense variants near or in the BAP1 UCH domain (aa1-240). Nineteen were identified in patients with UM and three rare variants from gnomAD database detected in the general population. The variants were cloned to a bacterial expression vector and expressed as a GST-fusion protein. Then we assayed the purified proteins for their ability to cleave ubiquitin. Ten patient derived variants reduced the deubiquitinating activity of BAP1. Seven mutants with variants from patients with familial BAP1-TPDS, retained <20% of their activity. Three variants previously classified as Variant of unknown significance (VUS) and one pathogenic decreased the activity to half. The function of twelve variants was interpreted as normal (80-120%). Of these, two were previously interpreted as pathogenic. Functional studies are needed for accurate BAP1 missense variant classification. Although BAP1 variants are dominant, penetrance might be affected by variants effect on enzymatic activity and patients with pathogenic variants might not exhibit familial BAP1 -TPDS. If enzymatic activity is retained and patient exhibits familial BAP1-TPDS, further studies need to be conducted on effects on splicing and protein-protein interactions. However, if patient exhibits only familial UM and harbours a BAP1 VUS with normal activity, other genes predisposing to UM should be considered.
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(2021)Recent studies have associated ER stress with various types of hearing loss, such as drug- and noise-induced, age-related, and hereditary hearing loss. However, the research has mostly focused on auditory sensory cell (hair cell) death, and it is not well understood if other molecular mechanisms can drive ER stress-dependent hearing loss. We used Manfflox/flox;Pax2-Cre conditional knockout (cKO) mice under the C57BL/6J (B6) mouse strain to study the effects of genetically-induced chronic ER stress on hearing function. In these mice, the gene coding for mesencephalic astrocyte-derived neurotrophic factor (Manf) has been silenced specifically in the cochlea. Manf is thought to act as an ER homeostasis regulator, and it has shown cytoprotective properties in different disease models both in vitro and in vivo. However, Manf’s mode of action is still poorly understood and even less is known about its function in the inner ear. Previously, cKO mice were found to upregulate ER stress markers in the cochlear hair cells. These mice develop progressive high-frequency hearing loss characterized by high-frequency outer hair cell (OHC) death. However, they have elevated hearing thresholds already at postnatal day 22 (P22) before any OHC death takes place and have elevated hearing thresholds in hearing frequencies where OHCs are retained. Therefore, there has to be another pathological mechanism besides OHC death accounting for the elevations in their hearing thresholds. Hence, we wanted to study the effect of ER stress on the outer hair cell hair bundle structure. The hair bundle is located at the apical pole of the hair cells, and it consists of filamentous actin (F-actin)-filled stereocilia. In mechanotransduction (MET), sound stimuli-induced motions of cochlear fluids cause stereocilia to deflect towards the tallest stereocilia row, allowing for depolarization of hair cells and transformation of mechanical force into electrical signal. Therefore, hair bundle is an essential structure for the hearing function. We used scanning electron microscopy (SEM) and fluorescent microscopy to study OHC hair bundles of cKO mice. We saw disorganization of the bundle structure already at P22. It progressed with age and advanced to strong stereocilia fusion by P56. At this age, all of the high-frequency OHCs of cKO mice displayed stereocilia fusion. We used cochlear whole mounts and immunostainings to study the protein composition of OHC stereocilia of Manf-deficient mice. The base of the stereocilia, termed as the tapering region, contains proteins that link the plasma membrane of stereocilia to their F-actin core, ensuring the cohesion of individual stereocilia. Mutations in these proteins have been associated with stereocilia fusion and hair bundle disorganization. At P56, we saw that stereocilia tapering region proteins radixin (RDX) and myosin 6 (Myo6) were mislocalized from the tapering region towards the apical tips of stereocilia in the high-frequency OHCs of cKO mice. Additionally, we saw that PTPRQ – a tapering region protein that is under normal conditions expressed only in the IHCs of mature cochlea – was upregulated in OHCs of cKO mice, yielding an expression pattern similar to RDX and Myo6. In addition, we used the F-actin probe phalloidin to quantitatively compare F-actin densities in the cuticular plates of cKO and WT mice. Cuticular plate is a structure responsible for attaching stereocilia to hair cell body. It consists of a dense F-actin network and prior studies have associated defects in the cuticular plate composition with hearing loss and stereocilia bundle abnormalities. We found a significant decrease in phalloidin staining intensity in the cuticular plates of high-frequency OHCs of cKO mice, indicating that their cuticular plate F-actin rigidity had been reduced. Together our data shows that Manf deficiency promotes diverse impairments in the OHC hair bundles, consequently inducing hearing loss. To conclude, our study presents novel insights into the complexity of ER stress-induced cochlear pathology. We show that ER stress impairs MET by inducing structural changes in the OHC hair bundle. It appears to be the major reason for hearing loss in the cKO mice, rather than hair cell death. In the future, the impact of Manf deficiency to the inner ear should be further studied. For example, younger and aged cKO mice could be studied to better characterize the progression of Manf deficiency-induced cochlear pathology and hearing loss. Similarly, Manf’s effect on hearing should be studied in other ER stress models to determine its role in the hearing function.
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(2019)Biodiversity is declining across the globe. The IUCN Red List, which is often used to measure species’ risk to go extinct, is showing alarming biodiversity declines both globally and within Finland. The most commonly used tool for biodiversity conservation is the establishment of protected areas. The Conference of Parties (COP) of the international treaty for biodiversity conservation (The Convention on Biological Diversity), has set a target to expand the international protected area network to cover 17% of the terrestrial area of the world. However, the designation of protected areas carries costs in terms of both land-use and money. Relatively little is known about what protected areas can achieve at the species level, and only limited evidence exists that links the establishment of protected areas to an improved conservation status of species. The lack of knowledge is because protected area establishment and its effects are often hard to study due to inadequate data. In this thesis, I created a framework to study the link between the increase in protected areas and protected area investment in relation to the conservation status change of one taxonomic group, the breeding birds in Finland. I first investigated the general trend in conservation status of Finnish birds using the Red List Index 2015. I then studied the effect of increasing the protected area on Finnish bird species’ range and the monetary investment on protected areas on bird species’ range in comparison to change in their IUCN Red List assessments. The timeframe of the study was 1996-2010 for protected area establishment and 2010-2015 for bird species’ conservation status change. My results show that the conservation status of birds in Finland is considerably worse than before, with Red List Index being 0.779. This is approximately 9.2% decline from the Red List Index in 2010. The species that gained more protected area on their range during 1996-2010 did not fare better in terms of conservation status than the birds that gained less protected area on their range on the same period. This is possibly because the threshold where the protected areas would cover the species’ range sufficiently to enable the conservation of the whole population is still not reached even for species with the higher protection levels. Also, the species that had higher estimated monetary investment on the protected areas on their range did not acquire better conservation status development than the species on whose range there was less estimated monetary investment. The expansion of the Finnish protected area network in 1996-2010 did not help to change the negative trend of Finnish birds in 2010-2015. The species that gained more protection in terms of land or monetary investment during this period, were not showing better results than the species that gained less protection. These results hint that the protected areas in Finland are not effective in terms of bird conservation. This does not mean, however, that we can claim that they are ineffective in all aspects, as we don’t know what would have been the situation if there were no protected areas established at all. There are also several other factors that affect the conservation status development of birds in Finland. These include degradation of matrix habitats, hunting and climate change, which might all overrun the possible positive effects of the protected areas and protected area investment.
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(2020)Alzheimer’s disease is the most common form of dementia and one of the highest causes of death worldwide. Recent discovery of lymphatic vessels from the dura mater, the outermost meningeal layer covering the central nervous system, has led to reassessment of the role of lymphatic vessels in neuropathological diseases. The meningeal lymphatic vessels drain macromolecules from the cerebrospinal fluid into the deep cervical lymph nodes and their proper function could be crucial for preventing amyloid-beta aggregation into the brain parenchyma. The function of the meningeal lymphatic vessels is still partly unknown. They have been hypothesized to function as an immune cell hub for the brain and dysfunction of the meningeal lymphatic vessels could lead to immune cell changes in the brain parenchyma. In my thesis, the role of the lymphatic vessels in Alzheimer’s disease was investigated by inducing atrophy of the meningeal lymphatic vessels with VEGF-C depletion in an APdE9 mouse model of Alzheimer’s disease. Single cell sequencing was used to identify the cell types present in the dura mater and in the deep cervical lymph nodes of an Alzheimer’s disease mouse model with and without atrophy of the meningeal lymphatic vessels. The amyloid-beta accumulation was immunohistochemically assessed from the brain and the cognitive decline was studied with behavioral tests. The results showed that atrophy of the meningeal lymphatic vessels did not increase the amount of amyloid-beta in the brain or affect the cognitive decline. The single cell sequencing from the meninges provided a more comprehensive cell atlas than has been published before. It was also found that the atrophy of the meningeal lymphatic vessels was associated with changes in the number of immune cells in the dura mater. The biggest changes were in the number of neutrophils and B-cells, which increased. Further studies are needed to evaluate the role of the meningeal lymphatic vessels in Alzheimer’s disease progression, as the results in this thesis were opposite to the results published before.
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(2023)Chondrodysplasia is a disease caused by defects in endochondral ossification. Chondrodysplasia affects the growth of long bones and causes disproportionate dwarfism. In addition to humans, chondrodysplasia has been discovered from multiple dog breeds. Chondrodysplasia in Alaskan Malamutes has been discovered already in the 1970s, but the genetic background of the disease is still unknown. This master’s thesis was conducted in Professor Hannes Lohi’s research group. The aim of this thesis was to identify a locus associated with chondrodysplasia in Alaskan Malamutes, and to find and validate candidate variants. All samples used in this study were collected from private owners with their consent. The study cohort consisted of four families of Alaskan Malamutes with affected individuals. Data used in the study included genotype data, and data from whole exome and whole genome sequencing. A significant locus on chromosome 8 was discovered, using genome-wide association study. However, some of the families with affected Alaskan Malamutes did not share this locus. A candidate variant in GALNT16 was identified by filtering NGS data from the families sharing the risk locus. Validation of the candidate variant showed that the variant was not causative for chondrodysplasia in Alaskan Malamutes. Based on the results, it can be possible that the causative variant for chondrodysplasia in all affected Alaskan Malamutes is not the same, and chondrodysplasia in Alaskan Malamutes may be more heterogonous than previously thought.
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(2019)Canine hip dysplasia (CHD) is a complex developmental orthopedic disorder particularly common in large size breeds. CHD is characterized by the development of a loose and incongruent hip joint. Affected dogs often suffer from secondary osteoarthritis. Radiographic examination reveals flattening of the femoral head and joint widening. An analogous disorder exists in humans. CHD is inherited quantitatively with suggested involvement of the genes of major effect. Genetic studies utilizing dense SNP arrays have revealed few candidate loci and genes for CHD, including the intronic deletion variant of fibrillin 2 (FBN2) gene in Labrador Retriever breed. FBN2 is a promising candidate gene having a functional role in bone and joint development. Therefore, the objective of this study was to investigate the role of FBN2 in the development of CHD in the Finnish dog population and in additional breeds. The specific aims included establishment of well-phenotyped cohorts of samples from four high-risk breeds, namely Labrador Retriever, Golden Retriever, German Shepherd dog and Bernese Mountain Dog and the assessment of the presence and prevalence of the FBN2 deletion in the Finnish dog population affected by CHD. The study cohorts established here will be later utilized also in genome-wide association studies to identify additional CHD loci. Altogether 220 dogs, out of which 53 were Labrador Retrievers, 41 Golden Retrievers, 79 German Shepherd dogs and 47 Bernese Mountain Dogs, were included in the case-control study. For the German Shepherd dogs, the hip status of each dog was further confirmed of by screening the radiographs available from the Finnish Kennel Club archive. All dogs were genotyped by fragment analysis for the FBN2 deletion. The results revealed the presence of the deletion in all four breeds with highest prevalence in the Retriever breeds, in which the deletion haplotype was more common than the wild type. In our study, all CHD-affected dogs in the Labrador Retriever breed had at least one copy of the deletion allele. However, since the deletion allele was common also in the unaffected Labrador Retrievers, no statistically significant allelic association with the deletion and CHD was detected in statistical analysis. In the three other breeds, no association in statistical analysis was found either. Thus, the previously reported positive allelic association between the intronic deletion in the FBN2 gene and CHD was not replicated. Larger genome-wide studies are warranted to identify the major effect CHD loci.
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(2021)The supervisory expectations directed towards banks and other financial institutions to integrate, identify and manage climate-related risks has increased substantially during the past decade. The transition towards a de-carbonized economy creates risks and opportunities for financial institutions. The European Central Bank (ECB) has identified climate-related risks as one of the key drivers in the euro area requiring a forward-looking approach to be taken into consideration while dealing with these risks. One of the main ongoing tasks in the area is the identification and classification of environmentally sustainable activities. The objective of this Master’s thesis is to examine the effect that the reported greenhouse gas (GHG) emissions and the implementation of an emission reduction strategy have on corporate repayment capacity, calculated through external credit ratings. Previous literature has found a relationship between companies’ creditworthiness and environmental factors, but the results vary depending on the applied variables. The typical approach used in prior studies is the application of aggregated values of environmental, social and governance (ESG) factors or limiting the analysis to specific industries or countries. The theoretical framework for this thesis rests mainly on previous academic research on the topic and publications by supervisory bodies. The data comprises 593 corporations from 37 countries operating in different industries over the years 2015-2019. The value of the probability of default (PD) is deployed as a measure of corporate repayment capacity. The climate-related variables and financial ratios were provided by the Carbon Disclosure Project (CDP) and Standard and Poor’s (S&P). The relationship between corporate repayment capacity and the climate-related variables was analysed using a panel data multivariate regression model, specifically the ordinary least squares (OLS) method. The results of this study indicate that emission intensity levels contribute statistically in a negative and significant way to corporate credit ratings, implying that higher levels of emissions lead to a higher PD. On the other hand, having an emission reduction target contributes positively and significantly to corporate repayment capacity, indicating that having this target leads to a lower PD. The analysed climate-related variables were statistically more significant in industries considered to consist of high emitting companies, as opposed to low emitting ones.
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(2019)Background: Despite the well-established link between diabetes and dementia risk, the impact of prediabetes and diabetes on the prodromal dementia phase remains controversial. In this study, we investigated whether prediabetes and diabetes increase the risk of cognitive impairment–no dementia (CIND) and accelerate its progression to dementia, as well as the possible underlying mechanisms. Methods: In the Swedish National Study on Aging and Care-Kungsholmen (SNAC-K), one cohort of cognitively-intact individuals (n=1,837) and one cohort of individuals with CIND (n=671) aged ≥60 years were followed for up to 15 years. At baseline and each follow-up (every 3 or 6 years), a neuropsychological test battery was administered, and the domains of episodic memory, processing speed, executive function, visuospatial abilities, and language were derived. CIND was defined as having no dementia and cognitive performance ≤1.5 SDs below age group-specific means in at least one cognitive domain. Dementia was diagnosed according to DSM-IV criteria. Diabetes (controlled and poorly-controlled) was diagnosed by physicians through medical assessment, clinical records, and glycated hemoglobin (HbA1c) ≥6.5%. Prediabetes was identified as HbA1c 5.7-6.4% in diabetes-free participants. Clinicians diagnosed heart disease and collected blood samples used to measure C-reactive protein (CRP). Data were analyzed with Cox regression models adjusted for possible confounders. Results: At baseline, in the cognitively-intact cohort, 133 (7%) participants had diabetes and 615 (34%) had prediabetes. During follow-up (mean 9.2 ± 3.0 years [range=2.2-15.5 years]), 544 (30%) individuals in the cognitively-intact cohort developed CIND. Poorly-controlled diabetes (HbA1c ≥7.5%) was associated with 2-times higher risk of CIND (HR 2.0, 95% CI:1.11-3.48) than diabetes-free participants. In the CIND cohort, 84 (13%) had diabetes and 238 (36%) prediabetes. During follow-up (mean 7.7 ± 4.0 years [range=0.2-15.2 years]), 132 (20%) individuals progressed to dementia. Poorly-controlled diabetes was associated with 3-times higher risk of dementia progression (HR 3.3, 95% CI: 1.29-8.33). Furthermore, comorbid heart disease and diabetes was associated with 2.5-times higher risk of progression to dementia (HR 2.5, 95% CI: 1.17-5.47), particularly if the diabetes was poorly-controlled (HR 5.8, 95% CI: 1.72-19.3). Similarly, having elevated CRP levels and diabetes was associated with increased risk of progression to dementia (HR 4.1, 95% CI: 1.15-14.2), especially in participants with poorly-controlled diabetes (HR 13.6, 95% CI: 1.89-98). No associations between prediabetes and CIND were detected in either cohort. Conclusions: Diabetes, especially if poorly-controlled, increases the risk of cognitive impairment and accelerates its progression to dementia. The diabetes-associated progression from CIND to dementia is further exacerbated by the presence of heart disease and elevated levels of systemic inflammation.
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(2022)Colorectal cancer (CRC) is one of the most common types of cancers, encompassing approximately 10 % of all cancer cases worldwide. Regulation of cell proliferation and cell fate decisions is crucial for maintaining cellular homeostasis and preventing CRC initiation, a process in which the Wingless (Wnt)/β-catenin signalling pathway is known to play an important role. For instance, somatic mutations occurring in the Apc gene lead to aberrant activation of the Wnt/β-catenin pathway, which further leads to the accumulation of β-catenin into the nucleus where the TCF/LEF transcription factors, including TCF1, TCF3, TCF4, and LEF1, bind β-catenin to activate downstream Wnt target genes and promote CRC development. TCF1 is encoded by the gene Tcf7 that can be alternatively spliced to produce long (p45) and short (p33) isoforms whose function in CRC development has remained poorly understood. Previously, deletion of Tcf7 has been found to increase intestinal adenoma formation in mice with one mutated Apc allele (ApcMin/+), which are predisposed to development of multiple intestinal adenomas. To study how heterozygous deletion of the p45 isoforms affects intestinal adenoma formation and the cellular transcriptome, we have studied ApcMin/+ mice, which have a heterozygous mutation of Tcf7 gene encoding only the p33 isoform (AmTp45∆/+). In our study, we used immunohistochemistry and RT-qPCR together with a single-cell RNA sequencing (scRNA-seq) analysis. Heterozygous deletion of the p45 isoforms in the ApcMin/+ mice dramatically increased the numbers of intestinal tumours, spleen size and its white pulp areas but it had no effect on cell proliferation or expression of the Wnt-target gene Prox1 in intestinal adenomas. In addition, ApcMin/+ mice with both heterozygous p45 and Lef1 deletions developed significantly more intestinal tumours. Without the Apc mutation, neither of these mouse models developed intestinal adenomas or spleen abnormalities. RT-qPCR analysis showed decreased expression of Tcf7 in the small intestine of the AmTp45∆/+ mice. scRNA-seq analysis revealed that the AmTp45∆/+ mice downregulated various Wnt antagonists and stem cell markers and upregulated several genes that function in different metabolic pathways. Overall, these results support the concept that Tcf7 functions in synergy with Apc to repress intestinal malignancy. Our results establish a basis for comparison of the relative importance and specific functions of the TCF/LEF1 family members in CRC development.
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(2023)Non-native species can have complex effects on the abundance of native species potentially altering the functioning of ecosystems negatively. Invasive species can outcompete local species competing for resources, ultimately causing the extinction of local species. Inter- and intraspecific competition can be especially vigorous for limited resources. Invasive species have been thought to be a leading cause in native species extinction, and their effects on native species can be especially pronounced during reproductive crucial life-history stages, such as nest-building. Based on previous information about invasive species and their effects on ecosystems, and previous studies conducted related to invasive species, I conducted an experiment at the Tvärminne zoological station in Hanko, southern Finland during May and June of 2021. I conducted a laboratory experiment in which the test species used were the invasive fish species round goby, that has increased its range across the Baltic Sea rapidly, and the native fish species sand goby. The purpose was to see, if there was any effect the invasive species has on the nesting success and motivation of the native species. Methods included five different treatments in aquariums. The results did not differ statistically between different treatments, length was close to statistical significance. However, these results do not demonstrate, that the round goby has no effect on the nest building motivation of sand gobies. Some factors of the experimental setup might have been faulty, and future studies with a larger sample are needed to examine the effects of competition on native species’ abundance.
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(2020)Iron is a trace element but indispensable for all photosynthesizing organisms. It is unevenly distributed in the world’s oceans, limiting production in offshore high nitrogen low chlorophyll (HNLC) seas. The Caribbean Sea periodically receives high amounts of iron-carrying aeolian dust originating in the African desert. This aerosol Fe is estimated to contribute three times as much as riverine input to the total iron in the seawater, a considerable fraction of it being soluble ferrous Fe(II) due to photochemical reactions. It has been hypothesized that the excess iron in the Caribbean Sea is one of the reasons why the Caribbean coral reefs are less resilient to degradation. The algae that are not limited by iron have the potential to efficiently utilize the macronutrients from e.g. anthropogenic sources and overgrow the corals. In this study Fe, N & P enrichment experiments were conducted in situ in Guadeloupe to find out if iron limitation can be detected and to contemplate the role of atmospheric iron and the anthropogenic impact. Sargassum polyceratium and Dictyota spp. (Phaeophyceae) were collected from four locations that had degraded coral reefs with macroalgae growing on them. The samples’ fluorescence was measured using Pulse Amplitude Modulator (PAM) fluoroscope to detect nutrient-induced fluorescence transients (NIFTs), rapid changes in chlorophyll fluorescence caused by nutrient assimilation in the algal specimen. Iron limitation was detected in all of the study locations but it was weak, which gives limited support to the hypothesis about iron deteriorating the Caribbean reefs’ chances against disturbance. Comparison of the locations did not result in differences in iron limitation according to the anthropogenic impact level. The difference was statistically significant in P limitation, the algae from high impact sites expressing greater demand. Ammonium and nitrate enrichments did not result in significant differences, but NH4 limitation did occur, as well as co-limitation of N & P. Iron has an important role in the phosphorus flux in the sediments and high Fe availability benefits N-fixing cyanobacteria. Redox conditions in the sediment control both Fe and P availability in the water column. Nutrient leaching does affect the local nutrient dynamics but the effects of eutrophication depend on both the species and the community. Notable differences in the NIFT responses were detected between the species that may indeed exert differing nutritional strategies. Coral reef ecosystem complexity emphasizes the importance of timing as well as consistence in quantification of the environmental parameters. The applicability of NIFT results would improve if they were combined with nutrient concentrations data. The fluorescence method appears to be useful in studying iron limitation but more research on iron-induced NIFTs is needed.
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(2022)The main motivator of this thesis was to discover the importance of Chaoborus in a eutrophic and dystrophic lake and evaluate suitable restoration methods to enhance the state of the study lake. The role of Chaoborus in the study lake, Lake Jouttenus, was studied with sampling of both the water column and the sediment, echo-surveys, and diet analyses of fish. The sampling was planned as comprehensive, and the sampling stations were distributed across the whole lake area to examine the density and distribution of Chaoborus. The deeper areas of the lake were emphasized more in sampling because Chaoborus tend to favor those areas. The Chaoborus density was calculated with stratified sampling, which gives a more precise mean density estimate than simple random sampling. In addition, fish were caught on four (4) study occasions to find out if they had included Chaoborus in their diets. The mean density of Chaoborus in Lake Jouttenus was a little lower than expected, only 271 individuals/m2 in areas ≥2 m depth. The highest density of larvae was found from mid-depths between 6.0-7.9 m in the sediment. Only the deepest areas (≥8 m depth) had limnetic Chaoborus and more limnetic than benthic larvae. The mean length of larvae was 8.4 mm in the sediment and 9.0 mm in the water column. The length distributions appeared to be unimodal. Echo-surveys confirmed that the larvae occurred in the water column only in the deepest area in the north of the lake where the hypolimnion had a low oxygen concentration below 4 m depth. The diet analyses showed that roach and perch had eaten Chaoborus but the number of Chaoborus was high only in the diet of roach in early July. In comparison with other studied lakes, the density of Chaoborus was the lowest in Lake Jouttenus. In addition, the mean length of benthic Chaoborus in Lake Jouttenus was lower than in the other studied humic lakes. The distribution of limnetic Chaoborus appeared as restricted to the deepest areas in the lake and elsewhere the larvae occurred only in the sediment. The slow growth of Chaoborus and their low mean density could be explained by the lack of an efficient refuge and probably also the lack of resources. The larvae were unable to reach the epilimnion and their prey safely at daytime and/or the amount and quality of food items for the larvae were poor. The darkness caused by humic substances and low oxygen concentration in the hypolimnion created a refuge for the limnetic larvae only in the deepest area of Lake Jouttenus. Roach and perch ate Chaoborus occasionally. However, mass removal of fish is not recommended as it would decrease the predation pressure by fish on Chaoborus and increase the risk of Chaoborus population growth at the deepest areas and enable their range to extend. Instead of mass removal of fish all methods that aim in reducing the humic substances in the water especially at the lake catchment area might enhance the state of the lake. The clarification of water would diminish the living conditions for Chaoborus in long-term and help with controlling the other troubling factors such as Gonyostomum semen blooms in the study lake.
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(2022)Exchanges between DOM and POM play an important role in the carbon cycling of freshwater ecosystems. Flocculation is a process where aggregates of DOM are formed and moved from a liquid phase to a solid phase. For colloids to form flocs, the negative surface charge of the present organic colloids needs to be destabilized. This process is generally dependent on salinity, but other compounds affecting the ionic strength of the solution can influence these processes. Gypsum is applied to Finnish fields to reduce the amount of nutrient leaching from agricultural soils. Gypsum treatment effectively reduces the runoff of both particulate and dissolved phosphorus from agricultural fields. Gypsum treatments are performed in areas where the soil contains over 30% clay minerals, making gypsum usage highly relevant in the Archipelago Sea area. This thesis aimed to find out how gypsum additions influence flocculation processes and DOM characteristics of terrestrial organic matter in boreal rivers. The study focused on the implications of gypsum use in waterways from areas with agricultural activities. Three core experiments were conducted to investigate the effects of several variables on flocculation dynamics. This study provides some preliminary insights into the influence of gypsum on biogeochemical processes in rivers. Gypsum additions were found to influence the flocculation processes of terrestrial organic matter in boreal aquatic environments. The most notable effect of gypsum additions was the enhanced floc formation, creating an increased flux of organic material onto the sediment surface. This has potential implications for microbial and benthic food webs, meaning that gypsum use is something that may need to be considered when assessing the impact of agriculture on the biogeochemical processes of waterways. Gypsum additions were also found the influence the characteristics of the remaining DOM pool. With the current knowledge, the positive aspects of gypsum use heavily outweigh the negative ones.
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(2024)Background and objectives: Since early adolescence, the bedtimes and wake-up times begin to delay gradually until the early adulthood. This so-called shift to eveningness reaches its maximum at around the age of 20, and it usually occurs earlier in girls than boys. Eveningness has been previously associated with depression, anxiety, sleep problems, somatic symptoms, and other health-related issues in adolescents and adults. The aim of this study is to examine the associations between adolescents’ chronotype and their physical and mental well-being. Methods: This study examined how the self-reported chronotype was associated with self-reported problems related to adolescents’ physical and mental well-being. The chronotypes were divided into 5 types: Definitive Morning-types, Moderate Morning-types, Intermediate-types, Moderate Evening-types, and Definitive Evening-types. The participants were 7th, 8th and 9th graders, and the sample consisted of 6522 students from 83 schools in Finland. Some of the data was gathered at three time points, some at two time points, and some at one time point during the academic year. The associations between chronotype and well-being variables were studied cross-sectionally and some of them also longitudinally. Results: The main findings were that eveningness was associated with difficulty concentrating in lessons, susceptibility to give up easily on difficult tasks, school burnout symptoms, feelings of nervousness and anxiety, excessive worrying, difficulty relaxing, irritability, restlessness, difficulty falling asleep, waking up at night, daytime tiredness, and low mood as compared to morningness. Eveningness was also associated with neck and shoulder pain, lower back pain, and headache, as well as pain in the head and lower back due to the use of digital devices. Eveningness was associated with decreased concentration in lessons and increased susceptibility to give up on difficult tasks across time. On the other hand, feeling lonely and not being accepted as part of the group were associated with morningness. Conclusions: In conclusion, the physical and mental health problems were emphasized among Evening-type adolescents, as compared to Morning-type adolescents. Since adolescents shift toward eveningness, the need for thorough management of sleep and circadian problems should be highlighted, in order to intervene and improve the mental and physical well-being of adolescents both at school and at home.
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(2014)Sexual signals, that are part of animal signalling systems, are important in attracting and competing for mates. Costly sexual signals can vary in honesty. Honest sexual signals convey truthful information about the signaller's condition and quality, reflecting reliably the direct and/or indirect benefits. Eutrophication of the Baltic Sea, which arises from an increased input of nutrients into an ecosystem by human, alters the water turbidity, especially in coastal areas, which affects visual sexual signalling in the three-spined stickleback (Gasterosteus aculeatus). Boosted algal growth increases water turbidity and decreases the amount of light that penetrates the water column, and thus reduces visibility. This change in visibility can affect the honesty of sexual signals. My aim was to study if the three-spined stickleback sexual signals honestly reflect a direct benefit of mate choice, male parenting ability, when the environment changes due to increased water turbidity and if the maintenance of honesty depends on the social setting in the presence of competing males. I studied the maintenance of signal honesty by having two experimental treatments; turbid water treatment and clear water treatment. I had two males interacting in a same experimental aquarium. I showed the males a female and recorded courtship activity twice for 15 minutes. The female was then released and the male followed as well as the time it took to follow the male to the nest were recorded. I photographed the males in days one, two, three and six of the experiment to be able to observe the change in the nuptial colouration. The males were let to spawn and the egg mass was weighted for the eggs received and the eggs hatched. I found that the courtship activity tended to be reduced in turbid water. Increased water turbidity relaxed the association between female mate choice and courtship activity. Increased water turbidity had no significant effect on male red nuptial colouration or on female preference for redness but it reduced the difference between the two males in redness during courtship. Hatching success was found to be higher in clear water. The difference between the chosen and the not chosen male in hatching success tended to be reduced in turbid water. According to my results the honesty of courtship seemed to be maintained by adjusting courtship activity to reflect the lowered hatching success. On the other hand nuptial colouration was not adjusted and was not honest. The hierarchy between males was also weakened in turbid water which gave males an advantage to cheat. I showed that, as in many other species, such as in different bird and whale species, environmental change influences three-spined stickleback signalling and reproduction outcome. It remains to be seen whether sticklebacks will adopt an alternative signalling method, such as size or olfaction, or adjust the present visual signalling system to turbid conditions. Future will show if the changed signalling system can maintain sexual selection of good parental ability. More research is needed to understand the effect of turbidity on reproduction and population viability and uncover the broader influence of changes in the stickleback ecology to the Baltic Sea habitats.
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(2018)The motivation of this study was to find new treatment options for the rare cancer pseudomyxoma peritonei (PMP). PMP is a slowly progressing mucinous adenocarcinoma that originates from the appendix and disseminates into the peritoneum where the cancer cells secrete large amounts of MUC2, the main component of intestinal mucus, into the peritoneum. The disulfide isomerase AGR2 helps MUC2 with forming the correct intramolecular disulfide bonds prior secretion, and is essential to MUC2 protein production. The mucus build-up into the peritoneum causes stress on vital organs, and eventually death. Therefore, inhibiting MUC2 production in PMP cancer cells might slow down the disease progression significantly. MAPK/ERK and cAMP/PKA signaling pathways stimulate MUC2 production, and activating mutations in KRAS and GNAS of these pathways are common in PMP. The aim of this study was to elucidate how MUC2 and AGR2 affect each other’s expression levels, and how the MAPK/ERK pathway and the cAMP/PKA pathway targeting substances caffeine, theophylline, cromolyn, fudosteine, octreotide, and lanreotide, affect MUC2 expression in vitro. This study was conducted on human colorectal adenocarcinoma cell lines LS174T, LoVo, and HT29 that all produce large amounts of MUC2. In addition, LS174T and LoVo cell lines carry activating heterozygous mutations in their KRAS genes. MUC2 and AGR2 expression levels were measured on mRNA level with real-time quantitative reverse transcriptase polymerase chain reaction. The effects of MUC2 on AGR2 expression, and vice versa, were tested by silencing each at a time with the appropriate siRNA. MUC2 siRNA suppressed both MUC2 and AGR2 mRNA levels down to 50 % in LS174T cells and down to 40 % in LoVo cells in respect to their control groups. AGR2 siRNA suppressed AGR2 mRNA levels down to 50 % in LS174T cells and even down to 30 % in LoVo cells in respect to their control groups, while there were no statistically significant changes in MUC2 mRNA levels. Caffeine and theophylline inhibit phosphodiesterase of the cAMP/PKA signaling pathway, and in consequence, the hydrolysis of the secondary messenger cAMP, prolonging the activation of the pathway. Caffeine stimulated MUC2 production in LS174T and LoVo cells. In addition, AGR2 mRNA levels increased in LoVo cells, in which the fold change in MUC2 mRNA levels was much greater. Theophylline, a compound found in tea, and used for the treatment of asthma, did not affect MUC2 production. PMP cancer cells express protein S100P. Cromolyn is a pharmaceutical substance used for the treatment of asthma, and it inhibits S100P, and thereby S100P/RAGE signaling -dependent activation of MAPK/ERK pathway. Fudosteine, on the other hand, is a mucoactive pharmaceutical substance that lowers the production of MUC5AC, the main component of lung mucus. Since activating GNAS mutation stimulates the production of both MUC2 and MUC5AC in HT29 cells, the expression of both must be at least partially controlled by same mechanisms. In addition, Somatostatin analogues octreotide and lanreotide inhibit ERK1/2 of the MAPK/ERK pathway, as well as protein kinase A of the cAMP/PKA pathway, and hence cAMP production. However, none of these four tested pharmaceutical substances were able to inhibit MUC2 production in the cell lines used this study in vitro.
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(2019)One of the first cellular response to a variety of stress inducers is the inhibition of cap-dependent protein synthesis. This also occurs as a first defense mechanism against viruses, which must evolve counter-defense strategies to overcome the attempt of the cell to block viral protein production. On the other hand, viruses have developed strategies to overcome the host translational shutoff and are resistant to cellular stress. Some viruses use specific proteins that interfere with PKR activation and prevents eukaryotic initiation factor 2 alpha (eIF2a inactivation, while others utilize the internal ribosome entry site (IRES) to achieve translation independently of eIF2a. Following the lead of a previously performed genome-wide screen, I found that ouabain, a potent cardiotonic steroid that specifically inhibits the cellular Na+ K+ ATPase pump leading to decreased intracellular levels of K+ and inhibition of cellular bulk protein synthesis, inhibits viruses at post entry step of their life cycle. Three viruses were used: Respiratory syncytial virus (RSV, Paramyxoviridae), Semliki forest virus (SFV, Togaviridae), and Vesicular stomatitis virus (VSV, Rabdoviridae). Of the three viruses, VSV was the less inhibited by ouabain. The effect of the drug was specific for the Na+K+ATPase because point mutations that disrupted the ouabain binding site in the pump abrogated the antiviral effect of ouabain. In addition, the drug-induced inhibition of virus infection was reversed by exogenous addition of K+ ions, indicating the effect is dependent of the activity of the Na+K+ATPase. Follow up experiments using the small molecule regulator of proteostasis ISRIB, an inhibitor of the integrated stress response, indicated that the antiviral effect of ouabain does not involve the inactivation of the eIF2a, a central regulator of protein synthesis and stress responses. The finding that VSV can replicate in the presence of concentrations of ouabain that strongly inhibit other viruses suggest a mechanism of resistance that could be further investigated to shed light into the regulation of viral protein synthesis and mRNA regulation and potential use of cardiotonic steroids as antivirals or in oncolytic therapy.
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