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  • de Sena, Sofie (2022)
    The analysis of gaze behaviour is nowadays commonly employed to help with the diagnosis and exclusion of differential neurological conditions as well as to help researchers better understand cognition in the early stages of life. However, its application in the developmental evaluation and follow-up of children with early-onset epilepsy has not been profoundly studied yet. Therefore, the current study aimed to investigate the association between the gaze behaviour of infants with early-onset epilepsy and their future neurodevelopmental outcome. To study the association and its predictive ability, three models were created. Sixty-three infants with epileptic seizure onset before 12 months of age participated in the study with the voluntary consent of their parents. Infants’ gaze behaviour was recorded with Tobii Pro-X3-120 at two measure points. The results showed infants’ initial ability to fixate their gaze, changes in their gaze shift probability in the first 12 months of life, and structural aetiology to be significantly associated with the infants' developmental outcome at 24 months of age. Where the structural aetiology was significantly associated with poorer developmental outcome, good initial fixation ability and improvements in the infants’ gaze shift probability during their first year of life were significantly associated with more positive outcome. These findings suggest that gaze behaviour at an early age is an essential predictor of later development in infants with early-onset epilepsy. Hence, eye-tracking could provide means to evaluate the later neurocognitive outcome of infants with early-onset epilepsy at an early age.
  • Martins, Beatriz (2020)
    According to the latest estimations, cancer is the second leading cause of death worldwide. Despite the significant advances in the range of drugs and treatment modalities to treat cancer, the number of deaths is estimated to continue rising, posing serious challenges for the patients, their families, and the healthcare systems. Conventional treatments tend to be associated with severe adverse side effects and treatment resistance. Consequently, safer and more efficient therapy options are urgently needed, especially for the treatment of metastatic tumors refractory to conventional treatments. A new and revolutionizing field in oncology is immunotherapy, in which oncolytic viruses are included. Oncolytic viruses have an inherent or acquired selectivity to replicate exclusively in tumor cells, ultimately destroying them. Simultaneously, they also activate the dormant host’s immune system to fight against the tumor. Adenoviruses, particularly, have shown to be safe, inducing only mild adverse side effects in clinical trials, making them a great candidate for further clinical development. Adenoviruses can be genetically modified to increase their infectivity or improve the anti-cancer immune responses induced by the virus, e.g., through the expression of immunostimulatory molecules. The focus of this thesis was to develop and characterize several genetically modified oncolytic adenoviruses expressing either OX40L alone or OX40L and CD40L, two co-stimulatory molecules capable of engaging both the innate and adaptive arms of the immune system to fight the tumor. The insertion of the transgenes into the E3B-14.7k region of the Ad5/3-∆24 adenovector plasmid was performed using Gibson Assembly® cloning approach. After successful cloning, the recombinant viral genomes were transfected into A549 cells for viral amplification, followed by CsCl purification to produce a high titer viral preparation. The expression of the transgenes was studied in vitro by ELISA and functional assays, showing promising expression levels of functional OX40L and CD40L. However, when the infectivity and virus killing potency were analyzed, in vitro by immunocytochemistry and MTS assay; and in vivo using an immunodeficient mouse model, the data showed that the cloned viruses performed sub-optimally when compared to the control unarmed virus (Ad5/3-∆24). These findings suggest that the insertion of the two transgenes in place of the E3-14.7k gene was detrimental to the fitness of the virus.
  • Lehtinen, Oskari Jouko (2022)
    Lifespan is a key fitness trait, together with fecundity, dispersal, and growth. In addition to environmental factors shaping variation in lifespan, it is also influenced by genetic components. Based on theory, genetic variation in lifespan is expected to be reduced due to its high relevance to fitness. However, due to trade-offs between different life-history traits and the variable or unstable environmental conditions organisms face in nature, life-history traits are also expected to sustain higher genetic variation. From studies in model organisms, such as the fruit fly and the roundworm, researchers have uncovered key insights into the genetic basis of lifespan. Some genes have been shown to contribute more to lifespan than others and different species seem to share homologous genes influencing lifespan that have been conserved. Many of these genes relate to the insulin receptors and insulin signaling processes. The allelic variation and over- or under-expression of these genes have been shown to be associated with changes in lifespan. However, regardless of our accumulating knowledge of these genes in impacting lifespan under laboratory conditions, we have little understanding of the role of these genes impacting variation in lifespan under more natural conditions. In general, assessment of genes affecting variation in lifespan in natural populations is rare, even under circumstances where we know that the lifespan has a heritable component. The Glanville fritillary (Melitaea cinxia) is a butterfly that inhabits most of Europe. It is used as a model species in ecology and evolution in relation to metapopulation dynamics and spatially structured habitats. It has been studied extensively both under experimental conditions and via observational studies in the field. The Glanville fritillary butterfly works as a good model organism for assessments of genetic components of life-history variation, as vast amounts of genomic and ecological data are already available. In this thesis, I aim to shed light on the genetic background of lifespan by using the Glanville fritillary as a model organism. More specifically, I will test the association of some well-known lifespan-related candidate genes with a phenotypic variation on the butterfly’s adult lifespan based on previously obtained experimental data on individuals collected from the natural metapopulation during the larval stage.
  • Heinonen, Maria (2021)
    Skeletal dysplasias are a group of rare monogenic bone disorders affecting joints and the skeleton. An increasing number of gene defects have been associated with skeletal dysplasias, but many cases remain without a known cause or a clear diagnosis. Exome sequencing data of the family with two siblings affected with an undiagnosed type of bone dysplasia was examined in this study with the aim of determining the genetic cause behind the phenotype. The causal variant was assumed to be in a novel disease-causing gene, since a previously performed gene panel of skeletal disease-causing genes had not revealed any positive results. The search for potential rare pathogenic variants in genes linked to the skeleton was done with VarAFT filtering software. The search revealed a short list of candidate variants confirmed first with Broad Institute’s Integrative Genomics Viewer (IGV) and then with targeted Sanger sequencing. Conservation analysis on the affected amino acids, in silico functional analysis on the variants and a comprehensive literature review on all candidate genes were performed to evaluate the likelihood of them being the variant behind the phenotype. A shortlist of three genes were obtained with the analyses, with one of them seeming to be the most likely candidate. However, to assuredly identify the disease-causing variant, further testing should be performed. Functional analyses should be done to test the functions of the proteins encoded by the candidate genes and the consequences of the pathogenic variants.
  • Laiho, Elina (2021)
    The European rabbit (Oryctolagus cuniculus) is a small mammal native to the Iberian Peninsula, but introduced by humans to all continents except Antarctica. The rabbit has been a remarkably successful invasive species due to its generalist nature and fast reproduction. Its spreading has mostly been destructive to the local nature, and humans have used fatal rabbit diseases such as rabbit haemorrhagic disease (RHD) to control harmful populations. The rabbit population in Helsinki is one of the most northern annually surviving rabbit populations in the world. It is believed to have originated from escaped pet rabbits in the late 1980s, and in the early 2000s, the rabbits spread rapidly around the Helsinki area. RHD spread unintentionally to Finland in 2016, and the disease caused a significant reduction in the Helsinki rabbit population. Rabbit population genetics has previously been studied in several countries, but never before in Finland. The aim of the thesis was to examine the genetic diversity and population structure of the Helsinki rabbit population before and after the RHD epidemic, and to compare the results to similar preceding rabbit population genetic studies. Rabbit populations have previously been found to recover from major population crashes without a notable loss in genetic diversity using DNA microsatellite markers. The recent RHD epidemic in Helsinki provided an opportunity to study, whether a rabbit population can recover from a population crash even in a harsher environment without losing genetic diversity. To conduct genetic analysis, fourteen DNA microsatellite loci were genotyped from individuals caught during two distinct time periods, in 2008-2009 (n=130) and in 2019-2020 (n=59). Population structure was observed in both temporal rabbit populations with small but significant FST values. The 2019-2020 population was more diverse than the 2008-2009 population in terms of allele numbers and expected heterozygosity. This result was unexpected considering the recent RHD-epidemic but could be explained by gene flow from new escaped rabbits. Compared to other wild rabbit populations around the world, the Helsinki area rabbits exhibit significantly lower genetic diversity. Bottleneck tests showed a significant signal separately in both temporal populations, but the RHD bottleneck cannot be distinguished based on the tests. The results could be biased by new gene flow, or the initial bottleneck caused by the founder effect of only a few pet rabbits. The rabbits have demonstrated their adaptation and survival skills in the cold climate of Helsinki. The population has significantly lower genetic diversity compared to other wild populations, yet recovered from a major RHD epidemic without reduction in genetic diversity under these more extreme environmental conditions. It has been proven again; the rabbit is a thriving invasive species.
  • Kerminen, Sini (2015)
    Studies of population structure are motivated by the need to understand population history and to have well-characterised groups of individuals in studies of genetics of diseases and traits. A standard method to analyse genetic population structure is principal component analysis (PCA). A disadvantage of PCA is that it can reliably handle only independent genetic markers. This means that the genetic markers that are correlated with other genetic markers have to be excluded from the data. This leads to a loss of information. In 2012, Lawson et al. published a chromosome painting method that can utilise haplotype information, i.e. information from correlated markers, and thus it can detect more subtle differences in populations than the standard PCA. This thesis studies two questions. The first question is whether the chromosome painting method can provide more precise genetic clustering of geographically defined Finnish groups than the standard PCA method. The second question is whether the chromosome painting method can reveal new details of population structure in Finland. The data used in this study are from the FINRISK Study survey of 1997. This cohort includes the genotype data of about 4,000 individuals and the information about individuals and their parents birthplaces. 345 Individuals were randomly chosen from the cohort in such a way that both of their parents were originated from the same province. Ten provinces of Finland were used as study groups for the method comparison. First, the data were analysed with SmartPCA (a standard PCA method) and ChromoPainter (the chromosome painting method) and the results were compared both visually and quantitatively. Finally, the individuals were assigned to populations based on the ChromoPainter result using FineSTRUCTURE program and these genetic populations were compared to the geographic origin of the individuals. The results showed that the chromosome painting method clustered seven out of ten groups significantly tighter than the standard PCA. Nevertheless, SmartPCA was faster and easier to use than ChromoPainter. The main population genetic division was found between the eastern and western parts of Finland, which was consistent with earlier studies. All in all, 15 populations were detected and the results revealed that they were geographically clustered. The genetic populations correlated well with the borders of Finnish provinces and counties. As the first conclusion, the chromosome painting method was able to give more precise results than the standard PCA but the standard PCA is still more suitable for quick preliminary analyses of genetic data. As the second conclusion, the chromosome painting method was able to detect detailed subpopulation structure in Finland and these populations are geographically clustered. Results provide an excellent basis for the future studies of population structure and genetic diseases in Finland.
  • Rahnasto, Johanna (2019)
    Preeclampsia is a vascular pregnancy disorder characterized by new-onset hypertension and proteinuria and/or new-onset preeclampsia associated symptoms during the second half of pregnancy. The pathophysiology of the disorder is not fully understood, but incomplete placentation and maternal tolerance towards fetal tissue are known to play a part in the disease pathogenesis. Predisposing factors include nulliparity, obesity, diabetes, chronic hypertension and autoimmune diseases. Furthermore, women who have experienced preeclampsia are more susceptible to cardiovascular disease later in life. One established biomarker for preeclampsia is the increased concentration of the soluble Fms-like tyrosine kinase 1 (sFlt1) in the maternal serum. sFlt1 is frequently overexpressed in preeclampsia and it is linked with angiogenic imbalance and endothelial dysfunction, although its role in the disorder is not completely clear. Preeclampsia has a genetic background. There are protective and predisposing variants in and near the Fms related tyrosine kinase 1 gene (FLT1; coding for sFlt1) that have been associated with preeclampsia either in the mother or in the fetus. In this study, five genetic polymorphisms over a 2.3 kb region in the 3’ untranslated region of FLT1 were genotyped by Sanger sequencing and fragment analysis in altogether 1200 individuals consisting of case and control mother–child pairs of the Finnish Genetics of Pre-eclampsia Consortium (FINNPEC) cohort. These polymorphisms were tested for association with various preeclampsia-related phenotypes by Fisher’s exact test. In the maternal genome, the minor alleles of rs17086497 and rs57760154 were associated with extreme hypertension (systolic blood pressure >180 mmHg) (p=0.004, OR=1.77) and obesity (p=0.023, OR=1.63). Homozygosity for these minor alleles was associated with pregnancy complications in general (p=0.026, OR=2.53) and the early-onset form of preeclampsia (p=0.004, OR=3.34). Additionally, the minor alleles of rs9554314, rs3138582 and rs149279513 were associated with extreme hypertension (p=0.045, OR=1.63) and obesity (p=0.023, OR=1.78). Moreover, a suggestive association to severe proteinuria (> 5 g/24h) was found in the maternal genome. In the fetal genome, significant negative associations were reached for rs17086497 and rs57760154 in terms of the serum concentration of sFlt1 in the preeclampsia group (p=0.008, OR=0.23). Overall, the results seem to link the studied region in the maternal genome to preeclampsia with severe features. This supports the idea of preeclampsia as a heterogeneous disorder with varying etiology and mechanisms and thus highlights the importance of differentiating between the various sub-phenotypes. For example, the association of the same allele in the fetal genome with lower maternal sFlt1 levels and in the maternal genome with severe symptoms of preeclampsia suggests that the sFlt1 level might not be a good measure in all patients. Additionally, the observed associations with extreme hypertension and obesity point to the possibility that this region might be relevant for the endothelial damage that is thought to be a central factor in creating the later-in-life disease susceptibility.
  • Almusa, Henrikki (2013)
    The next-generation sequencing (NGS) platforms create a large amount of sequence in short amount of time, when compared to first generation sequencers. An overview of the NGS platforms is provided with more in-depth look into Illumina Genome Analyzer II as that is used to create the data for the thesis. There were two main aims in this thesis. First, to create a pipeline which can be used to analyse genomic sequencing. Second, to use the pipeline to compare whole human exome capture methods from two manufacturers, Roche Nimblegen and Agilent. The pipeline is describe in detail in material and methods. All the inputs for the pipeline are described and examples shown. In the pipeline the given sequences are first aligned against the reference genome. Then various separate analysis is performed to retrieve variants and coverage of the sequencing. Supplementary results include paired-end anomalies, larger insertion and deletion polymorphisms and assembly of non-aligned sequences. The two capture methods are also described and changes to the manufacturers' recommended protocols are listed. Finally, the section has the options and various inputs used in the pipeline runs of the exome data. The results of the pipeline is a basic level of analysis of the sequencing as well as various graphs showing the quality of the run. All the output files intended for user are described. By using the results of the pipeline, the user can do more in-depth analysis as required by the project. When comparing the two exome capture methods, the Nimblegen capture was shown to be more efficient in capturing the CCDS exome. While the Agilent capture kit provided better one fold coverage over the exome, higher fold coverage (over 10 fold), which is required for reliable variant calling in nextgeneration sequencing, was better reached using the Nimblegen capture kit. Also, significantly fewer false positive paired-end anomalies were observed in the library created by using the Nimblegen capture.
  • Koivumaa, Minna (2020)
    Tiivistelmä – Referat – Abstract Ewing sarcoma is a rare bone and soft tissues cancer that occurs mainly among children and young adults. It is an aggressive cancer. Treatment of Ewing Sarcoma Family of Tumours (ESFT) primarily includes surgery, radiation and chemotherapy. The treatment protocol depends on the presence of tumour metastases at the time of diagnosis. In the treatment of local tumours, the 5-year patient survival rate has increased from 50% to 70%. However, patients that have tumour metastases at the time of the diagnosis or have a recurrent disease, the five-year survival rate is only 25%. As the current treatment options have reached their limits, it is important to develop more advanced therapies. DNA methylation is an epigenetic event that affects gene expression. By comparing the methylation level of the DNA in gene promoter regions in ESFT cancer cells to the methylation level of DNA in gene promoter regions in normal cells it could be possible to discover genes and signalling pathways that are important in the development of ESFT and that could be potential drug target molecules. The aim of this study is to find out the genome-wide gene promoter DNA methylation status in Ewing sarcoma cell line samples and Ewing sarcoma patient tumour samples compared to a normal reference sample. Another aim is to find gene promoter regions that are differentially methylated in the Ewing sarcoma cell line samples and the Ewing sarcoma patient tumour samples compared to the normal reference sample. Materials and Methods The Ewing Sarcoma cell line samples (12) were obtained from the Laboratory of Oncologi Research, Instituti Ortopedici Rizzoli Laboratory, Bologna, Italy. The Ewing sarcoma patient tumour samples were pre-isolated DNA samples already in Finland. The normal reference sample was a commercial mesenchymal cell line sample. From the Ewing Sarcoma cell line samples and the normal reference sample, DNA isolation was done by using phenol-chloroform method. DNA methylation profiling of the samples was performed by combining MeDIP (methylated DNA immunoprecipitation) protocol with 2-set promoter microarray hybridization protocol provided by Agilent Tecnologies company. DNA methylation data that was received from the microarrays was normalized and pre-processed with the Feature Extraction software provided also by the Agilent Technologies company. Visualization of the DNA methylation data was performed by using Chipster analysis software provided by CSC. To measure the level of DNA methylation at the gene promoter regions, a log2ratio value was calculated for every gene promoter region in all the sample types. To find gene promoter regions that were differently methylated, a log2 fold change value was calculated from the log2ratio values between the Ewing Sarcoma cell line cancer samples and the normal reference sample and between the Ewing sarcoma patient tumor samples and the normal reference sample for each gene promoter region. The log2 fold change value was also calculated between the Ewing Sarcoma cell line cancer samples and the Ewing Sarcoma patient tumor samples. After this a t-test was performed to determine the statistical significance of the log2 fold change values. Detection of genome-wide DNA methylation levels at the gene promoter regions in the Ewing sarcoma cell line samples and the Ewing sarcoma patient tumour samples compared to the normal reference sample was performed by averaging log2 fold change values. The same calculation method was used to detect the differences in the genome-wide DNA methylation levels at the gene promoter regions between the Ewing sarcoma cell lines and the Ewing Sarcoma patient tumour samples. Results Differences in the DNA methylation levels at the gene promoter regions were detected between the Ewing Sarcoma cell line samples, patient tumour samples, and the normal reference sample. Genome-wide measurement of the DNA methylation levels at the gene promoter areas showed that the Ewing sarcoma cell lines had more DNA methylation at the gene promoter regions than the patient tumour samples and the normal reference sample. The patient tumour samples showed less DNA methylation at the gene promoter regions compared to the Ewing sarcoma cell lines and the normal reference sample. Differentially methylated gene promoter regions between the Ewing sarcoma cell lines and the reference sample were found 16. In the patient tumour samples, also 16 differently methylated gene promoter regions were found compared to the normal reference sample. Differentially methylated gene promoter regions between the Ewing sarcoma cell lines and the patient tumour samples were 56.
  • Duru, Ilhan Cem (2017)
    Lactobacilli are gram-positive lactic acid bacteria with wide beneficial properties for human health and food production. Today most of the fermented products and probiotic foods are produced by lactobacilli species. One of the most using area of lactobacilli species is fermented products especially dairy products. Lactobacilli species can be used as starter or adjunct cultures in dairy products and play important role for preservation and quality, texture and flavor formation. Additionally, probiotic properties of lactobacilli species provide several health effect for human by stimulation of immune system and protection against pathogens. Lactobacillus rhamnosus LC705 is a facultatively heterofermentative type lactobacilli which is used in production of dairy products as adjunct starter and protective culture. The complete and annotated genome sequence of L. rhamnosus strain LC705 published on 2009. Known characteristics of L. rhamnosus strain LC705 are food preservation, toxin removal and health benefits when combined with other probiotic strains. However, molecular mechanism behind these characteristics are not known or not clearly understood. To get further insight on these properties and roles in cheese ripening of strain LC705, we re-annotated genome of the LC705 with updated methods and databases, analyzed metabolic pathways of LC705, and performed RNA-seq experiment to determine gene expression changes of LC705 during warm room (25 °C) and cold room (5 °C) cheese ripening process. Several un-characterized proteins of LC705 were annotated (77) and 1197 enzyme commission (EC) numbers are added to annotation file with re-annotation of genes of LC705. More importantly, re-annotation provided us 72 new pathways of LC705 which is 35% of the entire collection of 201 pathways. Analyzes of pathways showed that genome of LC705 has responsible genes for production of flavor compounds such as acetoin and diacetyl which are provide buttery flavor to dairy products, and hydrogen sulfide which is a volatile sulfur compound that cause unlikeable odor. Additionally to flavor compounds, we defined genes that produce anti-fungus compounds and bacteriocin which provide food preservation characteristic to LC705. Determination of gene expression respond of LC705 during warm room and cold room cheese ripening process with RNA-Seq showed that central metabolism genes that responsible for lyase activity, degradation activity, disaccharides and monosaccharides metabolism are warm induced genes. The genes play role in citrate metabolism pathways were significantly down-regulated during cold room, citrate degradation pathways are critical for buttery flavor products, therefore buttery flavor compounds are produced by LC705 during warm room. Finally, during cold room ripening, the genes of LC705 that produces ethanol and acetyl-CoA from pyruvate was up-regulated, so we may say that LC705 uses pyruvate to produce ethanol and acetyl-CoA instead of lactic acid.
  • Ollonen, Joni (2020)
    The skull represents the most highly diversified and evolutionarily adapted anatomical aspect of metazoans, and its development and evolution have been a major driving force in the expansion of vertebrates. The evolution of skull and lower jaw bones have led to the adaptive radiation of jawed vertebrates, and skull tissues have changed rapidly over time and were finely tuned to meet functional and ecological demands with tremendous precision. Because of the long-lasting interest in conventional animal models, there is no general genetic or developmental model of skull evolution and diversity in vertebrates. Squamate reptiles represent the best model to study those aspects because of their key basal phylogenetic position within amniotes (i.e., mammals, birds, reptiles) and their exceptionally high levels of morphological variation (including their kinetic skulls). In particular, their lower jaw bones display tremendous variation. In order to assess this variation and the ecological and developmental factors connected to it, several methods from different fields of biology have to be used. In this study, morphometric, embryology and developmental approaches are used to investigate the ecological and developmental factors associated with the diversification of lower jaw bones in snakes and lizards. The shape diversity of squamate lower jaw bones was approached in a systematic way, using geometric morphometrics. Embryological methods were used to compare the embryonic stage of available squamate model animals at oviposition and to assess the order of ossification of embryo with earliest developmental stage at oviposition (bearded dragon, Pogona vitticeps). In addition, expression of major conserved candidate genes at different stages of lower jaw development (pharyngeal arches, mesenchyme patterning, ossification) were assessed in this species. The results indicate that the lower jaw bones of snakes versus lizards but also of fossorial squamates versus other habitats are significantly different. Heterochrony was also detected at both early stages (pharyngeal arche development at oviposition) and at the onset of ossification in lizards and snakes. Coherent with that, alterations in the expression pattern of Dlx genes in pharyngeal arches were observed in bearded dragon in comparison to earlier studies with mice, while other conserved markers of skeletogenesis were rather conserved. This analysis of the genotype and phenotype map of the reptilian skull provides some new insights into the development, origin and divergence of vertebrate tissues. The results will establish a good basis for future studies involving comparative developmental biology of bearded dragon. Future studies will offer excellent new opportunities to link craniofacial morphology, genetics/genomics and development to both ecological adaptation and evolutionary biology.
  • Haikonen, Joni (2019)
    Kainate receptors are known to regulate neuronal function in the brain (Li, H., & Rogawski, M. A. (1998), Braga, M. F. et al. (2004), Lerma & Marques (2013), Carta, M (2014)). In the amygdala, they have been shown to affect synaptic transmission and plasticity, as well as glutamate and γ-aminobutyric acid (GABA) release (Li, H. et al. (2001). Braga, M. F. et al. (2003), Braga, M. F. et al. (2009), Aroniadou-Anderjaska, V. et al. (2012), Negrete‐Díaz, J. V. et al. (2012)), however, their role during development of the amygdala circuitry is not known. In the present study, we wished to understand how GluK1 kainate receptors regulate synaptic population activity and plasticity in the developing amygdala by using extracellular field recordings in P15-18 Wistar Han rat pup brain slices. Since field excitatory postsynaptic potentials (fEPSPs) are not commonly measured from the amygdala, we first sought to pharmacologically characterize the basic properties of the extracellular signal, recorded from the basolateral amygdala in response to stimulation of the external capsulae (EC). Having confirmed the validity of the fEPSP as a measure of postsynaptic population response, we were able to show that blocking GluK1 with (S)-1-(2-Amino-2-carboxyethyl)-3-(2-carboxy-5-phenylthiophene-3-yl-methyl)-5-methylpyrimidine-2,4-dione (ACET), a selective GluK1 antagonist, had no effect on the fEPSP. Furthermore, activation of GluK1 with RS-2-amino-3-(3-hydroxy-5-tert-butylisoxazol-4-yl) propanoic acid (ATPA), a GluK1 agonist, reduced the amplitude of the fEPSP, without affecting its slope, suggesting an increase in inhibitory signaling within the network. Blocking GABAergic activity with GABAA- receptor antagonist picrotoxin significantly reduced the effects of ATPA. Additionally, the increase in inhibitory signaling due to the activation of GluK1 was confirmed with whole-cell voltage clamp, by measuring spontaneous inhibitory postsynaptic current (sIPSC) frequency. Activation of GluK1 heavily increased sIPSC frequency in the basolateral amygdala neurons. Finally, we were also able to show that activation of GluK1 with ATPA strongly attenuates LTP induction. These results show that GluK1 kainate receptors play a vital role in the modulation of synaptic transmission and plasticity in the developing amygdala.
  • Viitanen, Arto I. (2019)
    The intestinal stem cells (ISC) are responsible for the regeneration of the intestine epithelial barrier after acute injury and for the replenishment of its cells overall. How the ISC activation and resulting proliferation is controlled is complex and still under study. The ISCs of the midgut, which is the functional analogue to mammalian small intestine, are also highly responsive to changes in nutrition, and with proper methodologies it is possible to study the effects of diet on stem cell activation. The metabolic flux of the nutritional components of the diet can then shed light on which metabolic pathways are necessary for nutrient-dependent proliferation. One nutrient that has garnered interest is glutamine (Gln). It is well established that glutamine supplementation can in parenterally fed patients diminish intestinal barrier atrophy, extend the time the patient can be kept under the regime, and increase survivability of critically ill patients. Consequently, glutamine or its downstream metabolites may have stem cell activating characteristics. However, the exact regulatory mechanisms and specific effects of Gln are not well known, and studies have found contradictory results on the beneficial effects of Gln supplementation. Glutamine itself is a conditionally essential amino acid that has a variety of functions: it is an important source of nitrogen and cellular energy and contributes carbon into the tricarboxylic acid cycle (TCA) and is involved in protein and nucleotide synthesis. In this thesis, the effects of Gln supplementation on the cell populations of D. melanogaster were studied via microscopy and computational analysis. Cross-breeds of fruit fly were established to lineage label the ISC with a GAL4/UAS driver system. Confocal microscope was used to image the midguts which were then analysed with Imaris software. A novel analysis method was developed to study population changes and varying features of the cells in the midgut in an unprecedented region-by-region bulk analysis. Earlier studies into nutrient control of ISC have had limited focus within the midgut and might have consequently given a restricted view of ISC activation. This new Longitudinal Analysis of Midgut (LAM) can be utilized in a diverse set of further studies to describe conditional variation within midgut, and possibly other tissues. Gln was found to increase total cell numbers to comparable levels with well-fed midguts, and to drive limited endoreplication in enterocytes. Lineage labelled cell population grew primarily in the R3 and R4 regions of the midgut. Additionally, enteroendocrine cells (EE) were greatly increased in the posterior part of R3 but had conceivable minor increases along the whole length of the midgut. Improved nutrition was also found to affect the proportions of the midgut, presenting itself as elongated posterior and stunted anterior. Overall, the pipeline and analysis method established during this study enable more expeditious research of effects of other nutritional components and allows for study of effects of other mechanisms, for example how gene knock-downs or altered gene activities affect cell populations of the midgut.
  • Virtanen, Tia-Maria (2020)
    Earth’s overshoot day marks the date when humanity’s ecological footprint exceeds Earth’s biocapacity for the year. As the day fell on earlier every year it shows that our current consumption pattern is unsustainable. One of the main human sources of greenhouse gas emissions is related to household consumption and thus companies play an important role in developing consumption practices more sustainable for consumers as they are the main providers of products and services. This research examines the ways three Finnish companies guide consumers towards environmentally sustainable choices as well as drivers and barriers related to consumer guidance. The objective is to enlighten companies’ consumer guiding methods as part of corporate responsibility and understand which factors encourage and hinder companies to guide consumers. The research was conducted as a qualitative multiple-case study. The case companies were Valio, S Group’s grocery stores and Fazer. The research data was collected via companies’ sustainability reports and focused semi-structured interviews by interviewing the case companies’ employees working with corporate responsibility, environmental management and communication. The data was analyzed by data-driven content analysis. The findings show that the case companies use guiding methods to steer consumers to environmentally sustainable choices: information provision, choice editing, nudging and financial incentives. The current trends related to sustainability and responsibility as well as a potential competitive advantage, the protection of brand image, the benefits of a forerunner, and a corporate strategy in which sustainability is an integral part encourage companies to guide consumers. Whereas, the principle of consumers’ freedom of choice, the responsibility of a big operator as well as risks related to the development of innovations and being a forerunner cause tensions in consumer guidance. The results confirm that various tensions are related to guiding consumers towards sustainability. Especially, the concept of consumers’ freedom of choice is firmly embedded in the mindset of business. Therefore, future research could examine the ways to bring these tensions and underlying contradictions more strongly into the public discussion to find solutions to promote sustainable consumption for consumers among companies.
  • Pakarinen, Tytti (2019)
    On a global scale the amount of meals consumed outside home setting continues to increase, which means that food service sector has a significant role in reaching global sustainability goals. Finland has a long tradition of public food services and a significant part of Finnish people enjoy a government-subsidized daily lunch. As a student restaurant UniCafe participates in Kela-funded meal scheme, thus UniCafe’s meals follow Finnish Nutrition Recommendations’ nutritional criteria for meals. This research examines the ways UniCafe guides its customers to making environmentally sustainable choices in their restaurants. This thesis also reviews UniCafe’s environmental sustainability measures, most significant of which are offering sustainable meal options, sourcing responsible ingredients and products, proper waste sorting and reducing food waste. This research also dwells in to the reasons behind these environmental measures and examines UniCafe as a forerunner company in the food service sector. The level of acceptability of different customer guidance ways are also evaluated on a general level and within UniCafe clientele. This research was conducted via qualitative case study research approach. The data for this research was col-lected via semi-structured theme interviews by interviewing UniCafe and Ylva restaurant and support services staff. Additionally, primary research data also comprised of Ylva’s online publications on responsibility and business operations. The data was analyzed by qualitative theory-guiding content analysis. According to the results, UniCafe is a forerunner company due to its unique customer and ownership base. UniCafe is expected to take environmental sustainability into account in their daily operations and selections. Five different customer guidance ways used by UniCafe were identified in this research: forced choice re-striction, choice editing, nudging, financial incentives and informational strategies. Most UniCafe customers accept the use of these different customer guidance methods but UniCafe perceives forced choice restriction as problematic, particularly on campuses that do not have many UniCafe restaurants. The results show that UniCafe guides its customers in many ways to promote environmental sustainability of their operations and their customers. In addition, the results confirm that methods such as informational strat-egies are perceived as more acceptable but simultaneously less effective than methods that restrict freedom of choice. In general, UniCafe customers approve environmental sustainability measures and customer guidance. On the other hand, UniCafe’s unique position in the student lunch market in Helsinki metropole area means that the results of this research cannot be generalized to apply to other food service sector operators.
  • Klemelä, Anna (2022)
    The Baltic Sea consists of islands, islets, and underwater nature. The sea’s species and habitats form a complex, interdependent network. The Baltic Sea is a challenging environment due to its low salinity, slow water turnover, and the densely populated catchment area. Species in the Baltic Sea have adapted to these circumstances, but climate change, eutrophication and different human induced pressures threaten the sea’s biodiversity. Biodiversity loss can be mitigated through protection areas. However, protection is not always successful. For example, insects and fungi often lack sufficient protection, whereas animals such as birds are more eagerly protected. Humans tend to protect charismatic or beautiful species and ignore others, even when other species’ need for protection is more dire. Establishing effective marine protected areas (MPAs) is difficult as information on underwater life is lacking. Finland’s underwater nature is better known, as it has been explored in the VELMU programme since 2004. In this thesis I study the governing documents of privately owned MPAs established during the last ten years in the Baltic Sea. Privately owned MPAs are the most common MPA type in Finnish marine areas. My research questions are: 1) Which nature values are represented in the privately owned MPAs? 2) How well is the underwater nature represented? The number of governing documents is 63. My method is qualitative content analysis and quantification of data. The material was coded using Atlas.ti. The nature values in the governing documents formed three categories: vegetation, birds, and underwater nature. Protecting vegetation was mentioned in 52 documents, birds in 39 documents, and underwater nature in 28 documents. The protection of underwater nature was most often based on protecting underwater habitats outlined in the EU’s habitat directive, instead of protecting underwater species. Birds and vegetation in the archipelago are somewhat comprehensively protected in privately owned MPAs. Although all 63 MPAs included a water area, underwater nature is mentioned in less than half of the governing documents. Underwater nature values are not always mentioned even when the MPA consists mostly of water, or when the governing document mentions the beauty or value of the water area. Descriptions of underwater nature are also often lacking in detail compared to the descriptions of vegetation and birds. To ensure biodiversity both underwater and above, underwater nature values should be protected more efficiently. Especially from the perspective of bird protection, it is noteworthy that protection usually does not cover their underwater food sources.
  • Uski, Isa (2015)
    Hampaat kehittyvät epiteelin ja mesenkyymin vuoropuheluna, vetovastuun ollessa ensin epiteelillä ja sitten mesenkyymillä. Ajatellaan, että ensin muodostuu ylä- ja alaleukaa reunustava epiteelijuoste eli hammasjuoste. Hammasjuoste paksuuntuu paikallisesti tulevilla etu- ja poskihampaan alueilla hammasplakodeiksi. Plakodit kasvavat muodostaen mesenkyymiin tunkeutuvat hammassilmut. Mesenkyymi tiivistyy silmun ympärille ja muodostaa vuorovaikutuksessa epiteelin kanssa kaikki hampaan kudokset epiteeliperäistä kiillettä lukuun ottamatta. Hampaan muodostumiseen vaikuttavat solubiologiset mekanismit ovat verraten huonosti tunnetut, etenkin hammasjuosteen ja plakodien osalta. Epiteelin ja mesenkyymin vastavuoroisesta signaloinnista taas on kertynyt runsaasti tutkimustietoa. Hyvin tunnettuja ovat esimerkiksi epiteelin primäärinen kiillekyhmy - ei-jakautuvista soluista koostuva signaalikeskus, joka ohjaa epiteelin kasvua silmuvaiheesta lakkivaiheeseen - sekä sekundääriset kiillekyhmyt, jotka määräävät hampaan nystermien paikat. Lisäksi jo 1990-luvun lopulla on saatu viitteitä varhaisemman, plakodivaiheen signaalikeskuksen olemassaolosta, mutta keskus on edelleen huonosti tunnettu eikä käsite ole vakiintunut kirjallisuudessa. Tämä Pro gradu-työ antaa lisätukea edellä mainitun varhaisen signaalikeskuksen olemassaololle. Työssä pyritään myös saamaan lisää tietoa varhaisimpien hampaan kehitysvaiheiden syntytavasta. Työssä hyödynnetään FUCCI-solusykli-indikaattorihiirtä ei-jakautuvien ja jakautuvien solujen erottamiseksi ja K17-GFP-siirtogeenisiä hiiriä hammasepiteelin erottamiseksi. Työssä tutkitaan hammasalueiden kehittymistä kuvantamalla alkiosta irrotettujen siirtogeenisten leukojen kehitystä hetki hetkeltä (ex vivo-aikapistekuvantaminen). Lisäksi tutkitaan hampaiden kehitystä kestävöityjen alaleukojen eri ikävaiheiden sarjoista sekä yhdistetään FUCCI-mallin antama tieto solujen jakautumisesta ja jakautumattomuudesta tunnettujen hammasalueen geenien ilmentymiseen whole mount in situ-hybridisaatiolla. Työssä etsitään myös parasta vasta-ainetta hammasepiteelin erottamiseen näytteistä, joilla fluoresoivaa hammasepiteelimarkkeria ei ole. Tässä työssä osoitetaan, että varhainen epiteelin signaalikeskus alkaa muodostua jo hammasjuostevaiheessa. Tällöin hammasalueelle ilmestyy yhtenäinen ei-jakautuvien solujen populaatio, joka myöhemmin rajoittuu kunkin plakodin alueelle. Nämä ei-jakautuvat solut ovat hammasepiteelin osajoukko ja ne ekspressoivat tunnettujen signaalireittien jäseniä Shh ja Dkk4, joiden ilmentyminen on liitetty varhaiseen signaalikeskukseen. Ei-jakautuvan solujoukon muoto muuttuu edelleen hampaanalun saavuttaessa silmuvaiheen. Vaikuttaa siltä, että varhaisen signaalikeskuksen solut päätyvät lopulta kiille-elimen varteen, joka aikanaan häviää. Ei-jakautuvien solujen alueen muodonmuutoksen mekanismi ei tässä työssä selvinnyt, vaikka sitä yritettiin ex vivo-kuvantamisella selvittää. Muussa leuassa solunjakautuminen on runsasta kaikissa tutkituissa kehitysvaiheissa ja ex vivo-kuvantaminen paljasti, että silmuvaiheessa ei-jakautuvien solujen populaation vieressä havaitaan erityisen voimakas solunjakautumisen aalto. On mahdollista että ei-jakautuvien solujen muodostama varhainen epiteelin signaalikeskus ohjaa tätä solunjakautumista ja siten silmun kasvua mesenkyymin sisään. Jatkossa tulee tarkemmin selvittää varhaisen signaalikeskuksen roolia hampaan kehityksessä. Kun tarkastellaan aiempia tutkimuksia tässä Pro gradu-työssä paljastuneiden seikkojen valossa, on syytä epäillä, että silmun kasvun lisäksi valmiiden hampaiden lukumäärä, sijainti ja koko ovat ainakin osittain riippuvaisia tämän varhaisen signaalikeskuksen säätelystä.
  • Huhtinen, Kaarina (2006)
    The aim of this thesis is to explain how Finland and Denmark have implemented the EC directive of Environmental Impact Assessment (EIA). Requirements of EIA in Denmark are a part of the Planning Act. In Finland EIA requirements are implemented through separate EIA legislation. The Danish EIA process is more openly political: final decisions of projects are made by politicians. Besides, decisions can be appealed to The National Protection Board of Appeal which has members from all political parties. In Finland the environmental permit decisions are made by the competent authority and decisions are appealed to the Administrative Courts. Decision-making procedures differ in these two countries. In Denmark, the final alternative of a project is chosen already in the EIA process, whereas in Finland the project can alter after EIA process before the permit decision. In the Finnish EIA procedure the developer is responsible for preparing the Environmental Impact Statement (EIS), but in Denmark the responsible actor is the regional authority. Yet, in practice, it's often the developer who prepares the EIS. What the law requires and how things are in practice differ more in Denmark than in Finland. In this study EIA is examined from the perspective of Planning theories. Communicativeness is one of the core elements of EIA. Still, in both countries examined, filling the minimum requirements of EIA legislation doesn't guarantee communicative planning. However, single cases can be communicative. At first there was no need and also no eagerness either to concentrate on the communicative side of EIA process in Denmark. Denmark has developed further participation and communicativeness in the field of urban planning. EIA has changed the participation practices of planning in Finland. Attempts to avoid EIA are a problem in both countries. It means that the public suffers form inadequate information of projects and the combined effects of projects are not evaluated. Important decisions are made before the EIA-phase. There s much pressure on the strategic environmental impact assessment of plans and programmes. There s a reform coming for animal husbandry projects, because they are the most typical EIA projects in Denmark. EIA in Finland could also be developed through examining different types of projects. The objectives of EIA and strategic environmental assessment in different sectors should be clarified.
  • Mäkelä, Mirka (2015)
    Archaea are known to thrive in different kinds of extreme habitats. Halophilic archaea are found in environments where the salt concentration is high, like in salt lakes and solar salterns. The habitats of halophilic archaea have salt concentration varying from higher than sea water to the saturation of salt. In high salinity habitats, the biodiversity is typically low and archaea are dominant microorganisms. The cell density of haloarchaea can be up to 107 cell/ml.When there are no predators for archaea and other halophilic microbes, viruses are thought to be the driving agents for their evolution. To this date, 130 archaeal viruses are described and 90 of them are known infect halophilic archaea. Most of the isolated haloarchaeal viruses are head-tailed. These head-tailed viruses can be divided into three different groups by the properties of the tail structure. Those three types of head-tailed viruses are myo-, sipho- and podoviruses. The infection cycles, receptors or lysis mechanisms used by archaeal viruses are still poorly known. Few studied archaeal viruses use seemingly similar strategies to attach to the surface of the host cell, to penetrate the cell surface and to release new virions, as bacteriophages and viruses of eukaryotic cells do. Since archaeas differ so much from eukaryotic or bacterial cells, their viruses must have developed different strategies to carry out their infection cycle. Several filamentous viruses of archaea are known to attach to the pilus structures of their host cells and some of the enveloped archaeal viruses attach straight to the cell membrane of the host. These strategies are seemingly similar to those used by bacteriophages and viruses of eukaryotic cells. Strikingly different mechanism to release virions has been seen on SIRV-2, virus of a hyperthermophilic archaeon. The SIRV-2 infection induces pyramid shaped extrusions on the surface of the host cells. In the end of the infection cycle these pyramids open and release new virions from the cell. This is the first lysis mechanism described for an archaeal virus. In this work, the infection cycle of a head-tailed virus infecting extremely halophilic Haloarcula vallismortis was studied. The Haloarcula vallismortis tailed virus 1 (HVTV-1) is head-tailed siphovirus with a double stranded DNA genome. In previous studies the infection cycle of HVTV-1 is described to be lytic. The genome sequence, 3D-structure of the capsid and the major capsid protein of HVTV-1 is known. HVTV-1 infection has been seen to induce large, roundish structures on the surface of the infected cell. These structures may have a role in the course of the infection cycle. Several animal viruses are known to cause massive rearrangements in the host cell so that replication proteins, viral genome and the replication agents needed from the host are concentrated in specific locations. These rearrangements facilitates and enhances the viral replication. The roundish structures induced by HVTV-1 might play the same role as the virus factories of animal viruses do or these structures may be involved in the release of new virions in somewhat similar manner as those virus induced pyramid structures. In this study two main goals were set: 1.) To explore the adsorption of HVTV-1 in more details and see if the host cell receptor could be solved. 2.) To solve the possible role of the virus induced structure seen in the host cell and to find out, in which point of the infection cycle those structures appear. Based on this study, it can be said that the adsorption of HVTV-1 is efficient and very fast. The virus attaches to the archaella structures of the host cell and the attachment is mediated by the tail of the virus. One archaella may serve as a receptor for several viruses and they are not saturated. The intracellular phase of the infection cycle of HVTV-1 is long and the virus production starts 8 hours after infection. Virions are released when the host cells is lysed 12 hours after the infection. Two hours before the lysis, two virus induced structural changes of the cell are seen. The roundish structures at the surface of the cell and wide areas in the cytoplasm filled by a structure looking similar as lipid membranes. At the same time when the virus production begins, at least two virus induced or coded proteins are produced in the cell. The other one of these proteins was identified and it is predicted to be the virus encoded ribonucleotide reductase. Ribonucleotide reductase is an enzyme known to catalyse the synthesis of deoxyribonucleic acids from ribonucleic acids. If the ribonucleotide reductase is a part of seen structures, the timing of their appearance and the known function of the enzyme, could suggest those structures to play a role in the maturation or release of the virions. Many questions still remains and there would be lot more details to study in the HVTV-1 infection. Especially interesting would be the identification of the other virus induced protein, purifying those roundish structures and analysing them in more details.