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Lipids are fat soluble compounds that are derived from living tissues. Lipids have many important physiological functions. Developing methods for efficient lipid analysis is important since lipids can function as biomarkers in diseases. Additionally these methods can be used for the discovery of the biological processes of disease development. Lipids comprise of molecules with different polarity and structure. Several mass spectrometric ionization methods have been used in the analysis of lipids but they usually require sample preparation prior to the analysis. Desorption electrospray ionization-mass spectrometry (DESI-MS) and desorption photoionization-mass spectrometry (DAPPI-MS) are novel ionization methods that allow sample analysis straight from the matrix, such as tissue, usually without any sample preparation. DESI-MS has already been used in the analysis of different lipids, but DAPPI-MS has only been used in the analysis of steroids. The ionization of a range of lipid compounds (phospholipids, triglycerides, fat soluble vitamins, fatty acids, and steroids) by DAPPI-MS and DESI-MS was studied. Analysis conditions were optimized for all the different lipid classes with both DAPPI and DESI using standard samples. Some lipids were also analysed straight from pharmaceutical preparations. There were differences in the suitabilities of DAPPI-MS and DESI-MS for the ionization of different lipid classes. DAPPI-MS worked well for the ionization of nonpolar lipids like triglycerides, vitamins and fatty acids, but the phospholipids fragmented in the DAPPI-MS process and showed no molecular ion. Previous studies have shown that DESI-MS works well in the ionization of phospholipids, and this study showed that it works reasonably well for other lipid groups as well, with the exception of some of the nonpolar lipids. New knowledge was acquired especially about the suitability of DAPPI-MS for the analysis of different lipids. Based on the results it can be said that DAPPI-MS works equally well or better than DESI-MS in the ionization of most lipid classes. The DAPPI method should still be further developed so that phospholipids, which are very important lipids in human physiology, could be analysed by DAPPI-MS. As lipids were not analysed straight from a tissue sample, there are no conclusions about the suitability of DAPPI-MS for the analysis of lipids straight from tissue samples.

Parkinson´s disease (PD) is the second most common neurodegenerative disease in the world after Alzheimer´s disease. There is still no drug that alters the state of the disease. It has been found that Endoplasmic reticulum (ER) stress is one mechanism in PD. ER stress occurs due to accumulation of unfolded proteins. ER stress triggers Unfolded protein response (UPR) that protects against ER stress by decreasing unfolding of proteins. In the beginning, UPR has protective effect, but in prolonged ER stress UPR triggers apoptotic cell death. There are several key mediators in the UPR pathway. Characterisation of ER stress in PD models may be important for the current and future drug development of PD. If ER stress is a significant factor that affects the disease development, it would be important to find a drug that alters these mechanisms and UPR. This may be a way to halt the disease development. Different animal models of PD, like 6-OHDA (6-hydroxydopamine) and MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) model, have similarities in their mechanisms. It has been found that ER stress occurs both in the brain of PD patients and animal models of PD. That is why studying and further characterisation in animal models is relevant. The aim of this study was to characterize ER stress in 6-OHDA rat model. The expression of some key mediators of the UPR were determined in this study. There were male and female Spraque Dawley rats in this experiment. 6-OHDA or saline was injected intrastriatally in 3 spots by stereotaxic surgery. Two weeks after 6-OHDA lesions, amphetamine-induced rotation test was conducted to the rats. The rats were divided into groups based on lesion size according to the results. For this study, the rats were euthanised at week 2 or week 4 post lesion. The rats were euthanised by carbondioxide, and the death was confirmed by decapitation. The brains were collected and stored in -80°C. Striatum and substantia nigra were collected later. Total RNA was isolated from these samples. Part of the RNA sample was used to conduct cDNA synthesis. Finally, the gene expression of Atf4, Ire1α, Xbp1s, Xbp1t, Grp78 and Chop was measured from these cDNA samples by qPCR (quantitative polymerase chain reaction). The qPCR data describes the expression of exact gene. The data was processed prior to statistical analysis. By statistical analysis, it was possible to compare the expression of these genes between 6-OHDA group and vehicle group. In addition, comparison was made between 6-OHDA treated groups at week 2 and 4. According to the results, only Chop expression had increased in 6-OHDA lesioned rats at week 2 compared to the vehicle group. In other genes there were no statistical differences, unlike in several other studies where the expression was found to be increased. Thus, the characterisation of this model requires further studying, possibly by increasing the sample size and studying later time points as well.

We have developed a software for homology modelling by satisfaction of distance restraints using MODELLER back-end. The protocols used extend exploration of distance restraints and conformational space. We drive the models in optimization cycle towards better structures as assessed by the used metrics on DOPE score, retrospective distance restraint realization and others. Hydrogen bond networks are optimized for their size and connectivity density. The performance of the method is evaluated for its ability to reconstruct GPCR structures and an extracellular loop 2. The software is written in object-oriented Python (v.2.7) and supports easy extension with additional modules. We built a relational PostgreSQL database for the restraints to allow for data-driven machine and deep learning applications. An important part of the work was the visualization of the distance restraints with custom PyMOL scripts for three-dimensional viewing. Additionally, we automatically generate a plethora of diagnostic plots for assessing the performance of the modelling protocols. The software utilizes parallelism and is computationally practical with compute requirements on an order of magnitude lower than those typically seen in molecular dynamics simulations. The main challenges left to be solved is the evaluation of restraint goodness, assigning secondary structures, restraint interconditioning, and water and ligand placement.

Mild traumatic brain injury (TBI) is defined as an injury that disrupts the normal functioning of the brain and is the result of external force to the head. It is the most common type of traumatic head injury, and it is common especially in contact sports and within military personnel. Mild TBI typically causes no clear structural changes to the head, but it can induce persistent clinical symptoms, as well as microscopic pathological changes to the brain that may eventually lead to neurodegeneration and increase the risk for several diseases. Mild TBI is a risk factor for several neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, and chronic traumatic encephalopathy. The primary objective of this study was to develop a repetitive mild TBI mouse model for future research purposes in the field of head trauma and neurodegeneration. The injury was induced as a closed head injury with an electromagnetic impactor. Literature and pilot experiments were used to define the parameters of the impactor required to induce a brain injury of desired severity. The characterization criteria of the mild TBI model considered the criteria used to define human mild TBI, as well as long term effects often reported after repetitive mild TBI: neurodegeneration as tau protein related pathology, neuroinflammation, and memory deficits. The secondary objective of this study was to tentatively test a prolyl oligopeptidase (PREP) inhibitor on the behavioral and histological effects of mild TBI. The functioning of the mild TBI model was studied by histopathological and behavioral assessments. After baseline behavioral assessment and repetitive (1 injury every 24 hours altogether 5 times) mild TBI inductions, the mice were monitored for approximately 3 months, during which several rounds of behavioral tests were performed. Barnes maze and novel object recognition tests were used to assess memory functions, and locomotor activity test was used to assess general locomotor activity. After euthanasia, brain histopathology was performed to study the amount of tau protein and the level of neuroinflammation. Due to the low number of animals in the study, the results are directional and need to be confirmed in subsequent studies. The histopathology showed greater amount of neuroinflammation and tau protein in the brains of injured mice, but statistical evaluations could not be made. Memory functions were slightly worse in the injured mice compared to controls, but significance of the results is unclear. Locomotor activity was not influenced by the mild TBIs. PREP inhibition treatment increased the locomotor activity of the mice, but the significance is unclear. The mild TBI model seems promising and the characterization criteria were partially met. The results of the study need to be verified in subsequent studies with a greater amount of animals. The model developed here can be used to study the involvement of head trauma in neurodegeneration, as well as treatment alternatives to changes caused by mild TBIs. As there currently are no curative treatments to neurodegenerative diseases, research regarding neurodegeneration and its risk factors is highly important.

Cancer immunotherapy refers to therapy strategies that utilise the mechanisms of the immune system to treat cancer patients. The benefits of the approach include the possibility for specific targeting and utilisation of the host immune system. The treatment methods include cancer vaccines, oncolytic viruses (OVs), cell-based immunotherapies and antibodies. The interplay between the cancer and the immune system has been observed crucial for the progress of the cancer and the success of immunotherapies. An immune inflamed tumour microenvironment has been observed beneficial for the success of several therapy methods. Many immunotherapy methods rely on detecting tumour specific antigens that are used to guide the therapy agent to the target site. This strategy poses challenges when considering tumour immune evasion mechanisms, which can cause downregulation of target antigens, and heterogeneity of tumour cells and patients. OVs have the advantage of not requiring predetermined target structures to exert their effect to the tumour cells. They cause direct tumour cell lysis and induce immune responses, and may be modified to express additional genes, including immunostimulatory agents. However, virus-related immunosuppressive mechanisms and a rapid viral clearance may limit their effects. A Western Reserve (WR) Vaccinia virus (VACV) is a highly oncolytic virus strain but the virus has been observed to suppress the function of the cyclic guanosine monophosphate adenosine monophosphate synthase – stimulator of interferon genes (cGAS STING) innate immune pathway which has been shown to have a significant role in anti-tumour immune responses. The aim of this study was to create a WR VACV encoding a dominantly active (D A) STING and to determine whether the virus is capable of activating the cGAS STING pathway. The effects were compared to a corresponding virus vvdd tdTomato that does not have the STING encoding gene. The pathogenicity of viruses was controlled by a double deletion of the thymidine kinase and vaccinia growth factor genes which restricts the virus replication to tumour cells. Transgene fragments were cloned from template plasmids by polymerase chain reactions (PCRs) and joined together in a Gibson Assembly (GA) reaction to form a STING-P2A-eGFP gene insert. The insert was attached to a shuttle vector pSC65-tdTomato by restriction enzyme digestion, ligation and transformation in Escherichia coli. The correct transgene plasmid construct was verified by Sanger sequencing and PCRs. The transgene was inserted to a modified WR VACV vvdd-tdTomato-hDAI by a homologous recombination. The newly created VVdd STING-P2A-eGFP virus was purified by plaque purification. The STING protein expression was studied by an immunocytochemistry (ICC) assay. The immune signalling pathway activation was examined by testing nuclear factor kappa-light chain-enhancer of activated B cells (NF-κB) activation in RAW-Blue cells and dendritic cell activation and maturation in JAWS II cells. The cell viability after iinfection was studied with four cell lines; A549, B16-F10, HEK293 and MB49. The D-A STING expressing virus was produced successfully. The ICC experiment verified the capability of the VVdd STING-P2A eGFP to produce the STING protein in the infected cells. The preliminary findings indicate that the VVdd STING-P2A-eGFP virus activates the NF-κB signalling in the RAW-Blue cells and that the activation is dependent on the STING expression. The activation level is relative to the infection concentration at MOI range 0,001 to 0,1. The findings suggest that the VVdd-STING-eGFP virus can induce innate immune signalling via the STING pathway. The reference virus did not activate the signalling. The in vitro experiments also indicated that the STING virus may induce DC activation and maturation. We observed a trend of CD86 and CD40 expression upregulation on the JAWS II DCs. The effects to the cell viability were inconclusive. More studies should be conducted to verify the results. The effects of the virus should be studied in more advanced cancer models that take into account the complexity of the immune system. These preliminary results indicate the that the VVdd-STING-P2A-eGFP virus could stimulate the immune signalling through the STING pathway.

The potential of extracellular vesicles (EVs) as diagnostic markers and drug delivery vehicles has been studied increasingly in recent years. One of the challenges in this field has been the isolation of EVs from complex biological fluids such as blood. The methods widely used for the isolation process include for example size exclusion chromatography (SEC) and ultracentrifugation (UC). As these methods use size and density of the particle, the have not been efficient enough in isolating EVs from certain particles such as lipoproteins. Due to the challenges related to these methods, other isolation methods have been sought to improve the efficiency of EV isolation. One of these methods is ion-exchange chromatography (IEC). From the two forms of IEC, anion-exchange chromatography has been studied more in EV isolation due to the negative net charge on EV particles. However, in this study the functionality and efficiency of cation-exchange chromatography (CEC) in EV isolation was studied as very little research has been done on this method. In this study, two CEC-resins were studied to define their applicability in EV isolation. A standard strong cation-exchange chromatographic resin SP Sepharose Fast Flow was compared to a strong tentacle-type resin. In addition to this, we studied the possibility to use a magnesium gradient to separate different forms of lipoproteins from EVs through dextran-sulfite precipitation. Tentacle-type CEC-resin was found to be more efficient in capturing EVs compared to the standard-type resin without magnesium. These EVs could then be eluted from the column with sodium chloride. The use of magnesium gradient allowed the separation of apolipoproteins in the samples. Higher concentrations of magnesium also reduced the number of lipoproteins in the samples altogether but resulted in the loss of EVs as well. These results were promising and showed that cation-exchange chromatography can be used in EV isolation. Tentacle-type resin seemed to be most efficient in removing impurities and capturing EVs. While more research is needed before these findings can be applied to clinical use, these results prove that cation-exchange chromatography can be used in EV isolation as a new, efficient and up scalable method.

Diabeetikoiden määrä lisääntyy jatkuvasti. Samalla hoitokulut ovat kasvaneet merkittävästi. Paras tapa hillitä kustannusten kasvua on hoitaa diabetesta mahdollisimman hyvin. Näin voidaan ehkäistä myös diabetekseen liittyvien oheissairauksien syntyä. Diabeteksen hoidossa on tärkeää kiinnittää huomiota hoidon jatkuvuuteen ja potilaan hoitoon sitoutumiseen. Apteekin henkilökunnan asema on noussut yhä keskeisemmäksi diabeetikon hoitoon sitoutumisen edistäjänä. Tämän pro gradu -tutkielman tavoitteena oli selvittää, mikä on apteekin farmaseuttisen henkilökunnan rooli diabetespotilaan hoitoon sitouttamisessa, elämäntapamuutosten toteuttamisessa ja niiden pysyvyyden varmistamisessa. Asiaa tarkasteltiin voimaantumisen teorian näkökulmasta. Tarkoituksena oli selvittää, miten voimaantuminen yksilössä tapahtuu, miten sitä voidaan apteekkineuvonnalla edistää ja mikä on apteekin rooli ulkopuolisena voimaannuttajana. Tämän tutkimuksen aineisto on kerätty Mäntyharjun Havu apteekissa ja se on osa laajempaa tutkimusta, jonka päätavoitteena on kehittää ja testata apteekkeihin soveltuva yksilökeskeinen toimintamalli tyypin 2 diabeteksen hoidon tukemiseen. Toimintamalli perustuu säännöllisiin neuvontatapaamisiin apteekissa. Pro gradu -tutkielmaan analysoitavaksi valittiin tutkimusjoukosta (n=19) ne, joilla tapahtui apteekkiohjelman aikana eniten positiivisia muutoksia yksilötasolla sekä elämäntapamittareilla mitatuissa arvoissa että kliinisissä parametreissa (n=4). Kvaliatiivisessa analyysissä käytettiin sekä deduktiivista että induktiivista lähestymistapaa. Vaikka diabeetikoilla oli tietoa sairaudesta ja elämäntapojen merkityksestä, niin käytännön tasolla jokainen henkilö kaipasi hoitoon ja erityisesti muutosten toteuttamiseen tukea ulkopuoliselta taholta. Apteekin rooli ulkopuolisena voimaannuttajana koettiin erityisen keskeiseksi. Tapaamiset loivat oikeanlaisen ympäristön ja ilmapiirin elämäntapamuutosten toteuttamiseen ja voimaantumisprosessin etenemiseen. Voimaantuminen ruokavaliomuutoksiin oli koko intervention aikana melko nousujohteinen prosessi. Sen sijaan voimaantuminen liikunnalliseen elämäntapaan oli aaltoilevaa. Apteekkitapaamiset sosiaalisena tapahtumana paransivat asiakkaan hoitoon sitoutumista. Asiakas koki, että häntä kohdellaan yksilönä kokonaisvaltaisesti. Voimaantuakseen yksilö tarvitsi aikaa. Vuoden mittaisen intervention aikana voitiin saavuttaa pysyviä muutoksia elämäntapoihin, mikäli yksilöllä itsellään oli halu ja motivaatio sitoutua tukiohjelmaan. Tämä tutkimus osoitti, että tämänkaltaista apteekkiohjelmaa tarvitaan. Nykyisessä kiireyhteiskunnassa ihmiset arvostavat, jos jollakin on aikaa paneutua yksilöön itseensä ja hänen sairautensa hoitoon kokonaisvaltaisesti.

Hepatotoxicity is an undesired feature of many drugs and is one of the main reasons for attrition during the drug development process. Although an in vitro model can never totally correspond to or replace a whole organism, a reliable in vitro model for liver toxicity screening would help to detect liver toxicity earlier in the development process. Effective and early in vitro screening would reduce the need of animal subjects and clinical trials and thus would be both ethically more acceptable and more cost-effective. Currently mostly used models for liver metabolism and toxicity studies are primary hepatocytes, hepatic cell lines and animal models. However, these models have many drawbacks and are not considered reliable. Human embryonic stem cells (hESCs) are pluripotent cells that can be differentiated into many specialized cell types including hepatocytes. They are also self-renewable and thus represent an unlimited and promising source of hepatocytes to be used as a tool in in vitro liver toxicity testing of drug candidates. The aim of this study was to produce hepatocytes from hESCs via multiple steps following the in vivo pathway of developing hepatocytes: first hESCs were differentiated into definitive endoderm cells, after which they were differentiated into hepatic progenitor cells. Finally, hepatocyte-like cells (HLCs) were induced from the progenitor cells. Our specific interest was the use of hepatic cell derived acellular matrix as a differentiation basis for hepatic progenitors and hepatocytes. We also studied the effect of Matrigel overlay on the hepatic differentiation. Differentiation method without the Matrigel overlay was promising. HLCs showed correct hepatocyte-like morphology and expressed hepatocyte markers such as albumin, α-antitrypsin, CYP3A4 and HNF4α both on mRNA and protein level shown by qPCR and flow cytometry and immunofluorescence staining, respectively. Accordingly, the expression of stem cells marker SSEA-3 showed a tendency to decrease as the differentiation proceeded. HLCs also functionally resembled hepatocytes shown by albumin production. However, we could not detect other hepatocyte functions such as urea production or CYP activity. With Matrigel overlay, the hepatocyte-like morphology of the cells was lost, no albumin production was shown and the expression of several hepatocyte markers was lower than in the experiment done without the Matrigel overlay. Thus, Matrigel overlay was shown to be unbeneficial for hepatocyte differentiation. In conclusion, we showed that differentiation of hESCs on the acellular matrix with specific growth factors and without the Matrigel overlay seems promising as a method to produce HLCs. This preliminary study serves as a basis for future studies, in which the differentiation method should still be further studied and developed to yield functional HLCs of uniform quality.

Posterior eye segment diseases, such as age-related macular degeneration, are leading causes of preventable visual impairment in the developed countries. Direct intravitreal injections are currently routinely used to deliver therapeutic agents most efficiently to posterior eye segment. Regular injections can however cause ocular complications and some drugs may also be toxic to ocular tissues at high local concentrations of free drug. Different nano-sized particulate systems have been extensively studied as possible drug delivery systems for intravitreal administration offering sustained, local drug action with controlled release. The vitreous gel can form a barrier for diffusion of particles due to its macromolecular structure and composition. Furthermore, ageing and different disease states cause changes in the vitreous structure possibly resulting in shift in the intravitreal movement of particulate systems. In the literature part of this Master's thesis ocular drug delivery is reviewed with main focus on drug targeting in the posterior eye segment. In the experimental work liposomes with different lipid compositions and surface charges were prepared as model particulate systems to evaluate the intravitreal diffusion of nanoparticles with confocal microscope. Furthermore, the influence of aging on the intravitreal diffusion was modeled by enzymatic degradation of the vitreous gel structure. It is discovered that vitreous gel hinders the movement of nanoparticles. Level of hindrance depends on particle's characteristics. 100-200 nm anionic particles move quite freely in the negatively charged vitreous gel. Similarly sized cationic particles are immobile in the vitreous due to electrostatic interactions between surface of the cationic particle and anionic glycosaminoglycans in the vitreous. 1 µm anionic and cationic particles are sterically trapped inside the vitreous meshwork created by the 3-dimensional biopolymer network of the vitreal macromolecules. Vitreous liquefaction increases the diffusion rate of nanoparticles but the clinical impact on ocular pharmacokinetics needs further research.

Neurodegenerative diseases and neuronal injury after trauma are common causes of neuronal loss. Adult brain has only a limited regenerative capability to replace the lost neurons caused by several distinct brain diseases. Direct reprogramming of brain resident cells into neurons could provide a promising strategy for efficiently replacing non-functional neurons. To date, the focus has been put largely on astrocyte-to-neuron reprogramming despite the relatively low yield of newly generated neurons reported in vivo. According to our hypothesis oligodendrocytes possess a more diverge transcriptomic profile when compared to neurons and astrocytes thus allowing better cell-specific targeting of reprogramming. Here, we establish the molecular tools for direct neuronal reprogramming of human oligodendrocytes to neurons. We investigate whether the expression of a known neural fate specification factor under selected oligodendrocyte-specific promoters is sufficient to induce oligodendrocyte-to-neuron transformation. Furthermore, we test the established tools in vitro using an immortalized human oligodendrocyte cell line. Our preliminary data shows that the human ERBB3 promoter and a single transcription factor transfected cells express doublecortin (DCX), an early marker of neuronal identity. Only recently, the direct in vitro reprogramming of human oligodendrocyte precursor cells into functional neurons has been reported. The direct reprogramming of oligodendrocytes into neurons provides an exciting alternative of neuronal replacement for astrocyte-to-neuron reprogramming. Overall, the field of direct reprogramming offers interesting possibilities for regenerative medicine providing a method for the production of newly generated disease and patient-specific cells.