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  • Taskinen, Juuso (2019)
    Human umbilical vein endothelial cells are responsible for maintaining and forming new vessels from existing ones, in a biological process called sprouting angiogenesis. Sprouting angiogenesis is a crucial mechanism for the resolution of hypoxia and normal development of tissues. It also plays a key role in internal plague hemorrhages, which can lead to embolisms and other cardiovascular complications. Angiogenesis is also crucial for cancer development. Sprouting angiogenesis is initiated by hypoxic tissue excreted vascular endothelial growth factor gradient, which induces normal endothelial cells into either a proliferative stalk cell or a signal sensing tip cell phenotype. Both of these cell types depend on the rapid flow of lipids to their plasma membrane, either to form plasma membrane protrusions in tip cells or as new plasma membrane material in dividing stalk cells. This flow is envisioned to involve both vesicle-mediated and non-vesicular mechanisms. A major non-vesicular route of lipid transfer occurs at membrane contact sites via lipid transport proteins. Furthermore, lipids can be transported to the plasma membrane by the direct fusion of vesicles or endosomes with the plasma membrane This thesis set out to explore the role of two membrane contact site proteins, oxysterol-binding protein- related protein 2 and protrudin, in angiogenesis and lipid transfer. Their role was examined by RNA-sequencing transient knock-down samples of these proteins in HUVECs. The RNA-sequencing data was examined by differential expression, gene ontology overrepresentation and gene set enrichment analyses. Gene expression analysis provided almost 10 000 significantly changed transcripts (adjusted p-values < 0.05), in each silenced cell type. The distribution of differentially expressed genes in oxysterol-binding protein- related protein 2 silenced cells, is skewed toward negative fold changes, whereas the distribution of differentially expressed genes in protrudin silenced samples is normally distributed. The results also show significant changes in gene ontologies related to proliferation, cell cycle, angiogenesis as well as hypoxia in both sample types. Gene set enrichment analysis showed upregulation in angiogenesis related pathways, such as the PI3K-Akt and MAPK pathways, in both samples. Significant downregulation was present in cell cycle related pathways and cholesterol biosynthesis pathway in both ORP2 and protrudin silenced samples.
  • Kuivala, Tea (2023)
    Lynch syndrome (LS) is the most common cancer predisposition disease caused by dominantly inherited pathogenic variant (PV) of a mismatch repair (MMR) gene leading to a defective gene allele. The four major MMR genes encode MMR proteins – MSH2, MSH6, MLH1 ja PMS2 – that participate in the proofreading and repairing of the daughter strand for mismatches after every replication. The inherited PVs predispose to cancer development as only one somatic allele loss is required for biallelic loss according to the Knudson’s “two-hit” hypothesis. The biallelic loss of an MMR-gene leads to disrupted protein function altering the MMR process. When mismatches are left unrepaired, genomic instability is caused, which can eventually lead to tumorigenesis. Especially, the risk of colorectal cancer (CRC) and endometrial cancer (EC) is increased in LS. The predisposition syndrome, LS, is important to detect as early as possible to decrease the risk of cancer by prevention and surveillance. The MMR genes and their defects vary in their consequences to the repair process considerably, and thus, it is crucial to know the different characteristics and functional effects of them when estimating the level of cancer risk. Variants of uncertain significance (VUS) are especially prevalent among LS variants. More information about their impact to the disease can be acquired by in vitro and in silico methods, for instance. The main goal of the efforts for early detection and prevention is to reduce cancer morbidity and mortality. In this thesis, the pathogenicities of MSH2 and MSH6 variants were studied with DiagMMR assay, which has been developed for studying the protein function of these genes. In addition to the traditional agarose gel electrophoresis (AGE), the samples were also analyzed by a fragment analyzer, Labchip, that bases its function on capillary electrophoresis. This way the MMR detection efficiency of the methods could be compared. Samples were collected as skin biopsies from controls and LS patients with known MMR gene variants by Helsinki University Central Hospital (HUCH). InSiGHT database, that collects the different MMR-gene variants and their pathogenicity classification, was used to ensure that different kinds of variations, both pathogenic (class 5) and currently internationally unlisted variants, were analysed. The skin samples were cultured to acquire primary fibroblasts for nuclear protein extraction. The level of pathogenicity was revealed by MMR-protein activity when substrate DNA with a mismatch was added to the extract. Then, restriction enzymes were used for producing fragments of different lengths, depending on the repair action, and the MMR efficiency was visualized by both electrophoretic methods. Additionally, MAPP-MMR tool was used for studying the MSH2 mismatch variants in silico. By comparing the results from these two methods, we show that the more quantitative Labchip brings diagnostic value to DiagMMR suggesting 100% specificity (n=10) and 90,9% (n=11) sensitivity in reference to the variant information. For example, MSH6 c.3103C>T, which is listed as pathogenic in InSiGHT, was more consistent in giving a MMR deficient (dMMR) result with Labchip. Difference in the functional detection could be seen particularly with the MSH6 variants, but the differences were less notable when Labchip results were compared to the previous interpretations of the samples made based on the validated DiagMMR protocol. With the unlisted MSH6 variants, c.3139dupT was detected as dMMR by Labchip which was in unison with the previous interpretation. Another one, MSH6 c.551delA, was seen as MMR proficient (pMMR) in all the results by both the methods, and with the previous interpretation being unclear, which highlights the importance of further testing of this variant. There was also one unlisted variant (c.1805T>C) among MSH2 for which we got uniform dMMR results in two patients. The high MAPP-MMR score (25.150) for the MSH2 p.Leu602Pro amino acid change also supported the evidence gained of the pathogenic nature of this variant. As a conclusion, DiagMMR can be used reliably for MMR efficiency analysis, especially when performed together with a more quantitative analysis method.
  • Muranen, Sampo (2019)
    Tree shoot architecture research is important due to its significance in fields such as timber production, fruit and nut production and aesthetics of common areas. Also, research on genetic factors that regulate shoot and root system architecture might provide novel methods to store more carbon in forests and, hence, mitigate global warming in the future. LAZY1 is one of the major genes that affects branch and tiller angle in herbaceous and woody species such as Arabidopsis, rice and peach tree. LAZY1 has been under scrutiny over a decade but its molecular function remains unknown. However, it is known that lazy1 mutation affects polar auxin transport. Here it is studied how LAZY1 affects initial branch angle, fiber length and reaction wood development in silver birch (Betula pendula). Also, transcript levels of few shoot architecture related genes were analyzed. LAZY phylogenetic analysis provided evidence of a duplication of LAZY1 in three studied tree species (Betula pendula, Prunus persica, Populus trichocarpa), duplicated genes are here named LAZY1a and LAZY1b. Plant material employed in this study was a segregating population (50:50) of back-cross 1 of weeping birch (B. pendula ´Youngii´) which has a truncated lazy1a. Histological samples of branches were prepared by cryo-sectioning, stained with carbohydrate binding Alcian Blue and lignin binding Safranin dyes to reveal patterns of tension wood development. Due to the large size of branch sections, samples were imaged with a microscope and the images were merged together in a Photoshop application. Branch angles were measured manually with a protractor (angle) tool from stem to the middle of a branch. The data was analyzed using mixed linear models due to the nature of used plant material. We could not use clones because of major issues in in vitro propagation. Branch samples were macerated, fibers imaged and measured by ImageJ software. LAZY1a gene expression levels were analyzed by RT-qPCR method. RNA-sequence analysis indicated that the expression pattern of LAZY1a and LAZY1b is similar in B. pendula. However, one should construct a promoter-reporter line to study with better resolution if their expression is spatially analogous. Initial branch angle was significantly different in wild type compared to lazy1a mutant. For future, one could generate single and double knock out lines of lazy1a/b to study if they have cumulative effect on the branch angle, an important factor in timber quality. Tension wood formation was difficult to quantify with the employed method, due to issues in segregating G-layered tension wood from thick-walled reaction wood. A chemical analysis of cellulose content might provide a more objective method to observe tension wood in branches. RT-qPCR method indicated that LAZY1a transcript levels are higher in wild type compared to mutant. A complementation or knock down experiment would provide sound evidence that lazy1a induces the weeping phenotype. X-ray diffraction method could be employed to study the orientation of cellulose microfibril angle in branches of the wild type vs. mutant. Generation of effective tensional stress requires a cellulose microfibril angle less than 10 and this angle is affected by auxin concentration. It is possible, that this angle is larger in lazy1a due to defect in polar auxin transport.
  • 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.
  • Kuoppalaakso, Timo (2023)
    Women have exhibited higher levels of math anxiety (MA) compared to men. Despite the relationship between MA and sex differences being topic of interest for over twenty years, the focal point has mostly been on the psychological causes. This review investigates the biological underpinnings of the social phobia and identifies numerous possible correlates which could inform future efforts to support students experiencing math anxiety and encourage more females to pursue STEM related careers. Articles that investigated sex differences in the context of MA were selected for the study using PRISMA guidelines. Females were found to experience higher levels of math anxiety compared to males. Age was shown to influence the prevalence of MA between sexes, with sex differences in MA being more infrequent in children and increasing towards adulthood. The findings suggest that a diverse set of biological sex differences related to to brain function, cognition and sex hormones can, in part, explain the higher prevalence of MA among females and age-related deviations. By shedding light on possible biological factors contributing to sex differences in MA, this review represents a valuable step toward a more comprehensive understanding of this complex issue.
  • 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.
  • Lappalainen, Siiri (2023)
    Progressive retinal atrophy or PRA is a collective term for a group of hereditary degenerative retinal diseases in dogs. PRA affects the photoreceptor cells of the eye ultimately progressing into complete vision loss. Documented in over 100 breeds, it is the most common type of canine retinal diseases. PRA is considered a homologous disease to human retinitis pigmentosa, thus providing a large animal model for studying retinal biology and genetic aetiology of its diseases. The objective of this thesis was to study the genetic cause of a novel form of PRA in young Finnish Lapphunds. Analysis built upon a combination of gene mapping methods and analysis of next­ generation sequencing data. Gene mapping was performed with two analysis methods, genome­-wide association study and homozygosity mapping, utilising single nucleotide polymorphism microarray based genotype data. Identifying a clinical phenotype from the canine biobank at the University of Helsinki resulted in a study cohort of six case and 10 control dogs. Combined with pedigree information, this early­-onset PRA was most likely a new autosomal recessive condition in the breed. Genome­-wide analyses resulted in the discovery of a disease­-associated locus on chromosome 27. Findings of single nucleotide variant filtering of one whole-­genome sequenced affected dog led to the prioritisation of an intronic substitution variant (T > C) in SOX5 gene as a potential cause of PRA. Genetic validation of the variant with 23 dogs showed promising results. Four out of five affected dogs were homozygous for the variant, while controls were either wild-type or heterozygotes. As a result, a previously unknown disease locus was successfully identified, suggesting a possible new spontaneous canine model of retinitis pigmentosa. By better understanding the patho­physiological processes of disease, improved diagnostics and marker­-based testing as well as novel therapies can be developed for both dog and man. However, further studies are needed to understand the underlying molecular mechanism of the candidate disease variant.
  • 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.
  • Koppelomäki, Krista (2023)
    Good understanding of animal emotions is vital for improvement of animal welfare. Emotions are affective states that are defined by positive or negative valence depending on the pleasantness of the situation, as well as the state of arousal or excitement. As subjective experiences, emotions are hard to measure directly. Lateralization, a phenomenon in which emotion processing is done asymmetrically in different hemispheres of the brain, has been used to study changes in valence. The state of arousal is known to cause changes in the activation of the autonomic nervous system, which lead to changes in peripheral blood circulation. These neurologically mediated changes in blood flow can lead to changes in surface temperature that can be detected by infrared thermography (IRT). IRT is a technology that’s based on converting infrared radiation to images. From these images, the surface temperature of an animal can be quantitatively measured. Previous studies have focused mostly on negative emotions, which are known to affect surface temperatures. Positive and neutral affective states are in need of more research, as they have been studied less. Lateralization is also still a fairly new area of research. In this thesis I investigated if there would be detectable surface temperature patterns in riding horses at Cypis-talli, Espoo, that could be linked with mainly positive and neutral emotional states. I also explored the possibility of finding lateralization effects related to emotional states in horses. Additionally, I wanted to know if these changes in surface temperature would be situational or dependent on individual variation. We used naturally occurring situations in the horses’ lives to observe them in three situations: one where the horses got fed, one where they were taken outside to the paddocks after feeding, and one where the horses were momentarily separated from their paddocking buddies. During all situations the horses’ eyes and nasal region were measured with a thermal camera. Numerical data was collected from the images and analysed with linear mixed models and post-hoc pairwise comparisons. I found that there were significant changes in surface temperature in the eyes and nasal region of the horse that were likely related to changes in arousal. The surface temperature of the eyes and nasal region dropped when the horses got their feed, got taken outside to the paddocks and when they were separated and reunited with another familiar horse. Another finding was that there appeared to be a lateralization effect in the eyes and nasal region on the nasal cavities. There seemed to be a lot of individual variation in temperature throughout. An interesting finding was that the health condition of the horse significantly affected the temperature changes in many cases. My results suggest that surface temperature effects that have been previously seen in other species via IRT can also be detected in horses, and that the changes in temperature are most likely related to the emotional state and health status of the animal. Nasal temperature could be useful for measurement in future studies, but further research to validate its use in detection of emotional or health related states is required.