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  • Srinivasan, Rakenduvadhana (2019)
    Caged photolysable compounds have served to be pivotal to neuroscientific investigations; allowing the cognizing of molecular kinetics and properties of neuronal micro-machinery such as neurotransmitter receptors. Precision in terms of temporal and spatial resolution of neurotransmitter release endowed by photolysis has multitudinal applicabilities in the realm of GABAA receptors (GABAARs), their neuronal niche and effects on neuronal and network activity. Caged compounds, in their caged form, may display certain unideal traits such as undesired interactions with the system and antagonistic activity on the target receptor. This study aims to reevaluate the GABAAR antagonistic actions of caged Rubi-GABA, which was found to antagonize these receptors at significantly lower concentrations than those reported in the literature. Furthermore, this study electrophysiologically characterizes the possible antagonistic properties of a novel quinoline-derived UV-photolysable caged GABA compound, 8 DMAQ GABA, whose activity, in its caged form appears to have a much more favorable antagonism profile compared to the widely used RuBi-GABA. To assess the antagonistic effects of these compounds on GABAAR-mediated miniature inhibitory postsynaptic currents (mIPSCs) patch-clamp recordings were carried out in the whole-cell voltage clamp configuration on cortical layer 2/3 cortical pyramidal neurons in acute neocortical slices prepared from 16-18 day-old rat rats. The results of this study indicate a revised antagonism profile for caged Rubi-GABA, with marked GABAAR toxicity in the low micromolar range. The study also scrutinizes the photo-kinetic properties of both caged GABA compounds and reveals that the rate of GABA release from 8-DMAQ is slower than from RuBi-GABA.
  • Haapalainen, Samuli (2021)
    Biodiversity is decreasing globally due to human activity. At times, on-time monitoring of the state of habitats and biodiversity is challenging. One useful way to study these is to use certain species as indicators for the state of habitats and biodiversity. One group that are often used, are birds. They are easy to detect and they have specialized to most terrestrial ecosystems. Changes in the population sizes of different bird species can reflect changes in different habitats and their biodiversity. Therefore, it is essential that different bird monitoring practices produce reliable and comparable results. I compared datasets produced by two different Finnish bird census programs in my thesis. The census programs were national breeding bird survey program and Hanko Bird Observatory´s migratory bird census program. Both programs produce data on population abundances and changes in population sizes. Because methods between these programs differ greatly, their data may differ for some species. I compared the datasets by comparing population change indexes of the same species. I also tested whether species traits would be associated with the comparability of the datasets. These traits were mean body size, migratory behavior, favored habitats, and number of sightings for each species. I made models for all combinations of traits. I used a generalized linear model in my analysis. I compared the models by using Akaike´s information criterion (AIC) with correction for small sample sizes (AICc). My results showed that both national breeding bird survey program and Hanko Bird Observatory´s migratory bird census program produce parallel population trends for species. From the tested species traits, only migratory behavior was associated with comparability of the datasets. The datasets were highly comparable for long- and short-distance migratory birds but only moderately comparable for resident birds. This is likely due to migratory bird census program recording the local population dynamics of resident birds of Hanko peninsula. These local population trends may differ from the national trends of the same species. The breeding bird survey program should better reflect the national population trends. My results also showed that more numerous common bird species are declining faster than uncommon species. This is an alarming scenario because it points at extensive habitat degradation and biodiversity loss. Also, population trends of species favoring mires and mountains were clearly declining compared to species favoring other environments. This may be due to endangering of mire and mountain habitats due to climate change and human land use such as peatland drainage. Strong declines of species may also be explained by changes in the wintering areas of these species. Finnish breeding bird survey program and Hanko Bird Observatory´s migratory bird census program both produce overall comparable data on population trends of birds. They could be used to complement one another and to provide supporting evidence on the validity of bird population trends. Producing quality bird census data is highly important in tracking the state of biodiversity and when deciding on conservation acts. The data on the census programs provide support for the research on state of Finnish and European habitats and biodiversity.
  • Henttonen, Kaisu (2020)
    The human gut is inhabited by gut microbiota, a complex and diverse ecological community of trillions of microbes that affect both the normal human physiology and countless disease states and susceptibilities. Understanding the composition, functions and the causes and effects of changes in the microbiota is invaluable for understanding diseases that are connected to the microbiota and developing better treatments to the diseases. The gut microbiota varies between individuals and keeps changing over time. Behind the variability are e.g. the person’s age, genetics, diet, environment, and especially diseases and the use of antibiotics. When antibiotic use disrupts the gut microbiota, the changes can persist for years. Antibiotic resistance tends to increase after the use of antibiotics. Since antibiotic resistance in bacterial pathogens is considered a major health threat, the characterization of the human gut resistome (the antibiotic resistance genes (ARGs) found in the gut microbiota) is of great medical interest. Next-generation sequencing techniques have enabled studying also those microbe species that cannot be cultured at the moment. Metagenomics provides information on all genetic material collected from a given environment and enables searching for any sequences of interest within it, e.g. ARG sequences. The development of Parkinson’s disease (PD) is suspected to begin in the enteric nervous system and spread from there toward the central nervous system. The use of antibiotics could be linked to PD through their effects on gut microbiota, and since these effects are modified by the gut resistome, the aim of this study was to find gene sequences coding antibiotic resistance in human gut metagenomics data originating from stool samples of PD patients and healthy controls, and to find out potential differences in the occurrence of antibiotic resistance genes in the gut microbes of the two study groups. DeepARG was the chosen method for searching antibiotic resistance gene sequences in the metagenomics data. The statistical data analyses, including alpha diversity, multivariate analyses, and differential abundance analysis, were performed with the R statistical programming language in RStudio. DeepARG found 840 different ARGs in 192 samples. The ARGs belonged to 29 different ARG classes. The alpha diversity analysis showed a small estimated difference between PD and control groups indicating a possible slightly higher ARG diversity in the PD group. Multivariate analysis did not give any strong suggestions of definite biologically meaningful differences between the study groups. 16 ARGs were deemed differentially abundant in the study groups. BepE, cmeA, cmlv, dfrE, mefC, msrB, opcM, oprM and RbpA seemed to have increased abundance, and arnC, BN537_02049, dfrK, mgrA, murA, tet35 and tetT were suggested to have decreased abundance in PD patients compared to the healthy controls. These ARGs do not appear interconnected in any other way except for some sharing antibiotic types to which they offer resistance, and some having similar resistance mechanisms. In the light of an ongoing, unpublished epidemiological study of the connection between PD and the use of antibiotics it would seem that only three ARGs (msrB, mefC and dfrE) might be somehow relevant in PD development, but their effects, if any, are most likely minor. Eight ARG classes were shown to have differential abundance between PD patients and healthy controls. Bacitracin, fosfomycin and polymyxin classes showed decrease and chloramphenicol, fosmidomycin, puromycin, rifampin and sulfonamide classes showed increase in abundance in PD compared to controls. The change in the abundance of a certain ARG could reflect change in the abundance of the bacteria carrying that resistance gene. If so, the follow-up questions would be how much change in the abundance of bacteria is due to the use of certain antibiotics and how much is caused by environmental factors. It also remains to be studied whether specific antibiotics associated with the ARGs that in this study showed differential abundance in PD patients and healthy controls might have an actual role in PD development. The results of this thesis study are later to be combined with and further studied alongside information coming from ongoing studies on antibiotics use in general population and in PD patients. While this study did not concentrate its efforts into finding novel ARGs, the metagenomics dataset could also in the future be applied for that purpose.
  • Voipio, Mikko Emil Olavi (2020)
    Nitric oxide (NO) is an important signalling molecule in the brain. NO regulates the function of many proteins by e.g. interacting with tyrosine and cysteine residues, thus inducing post-translational modifications. In animal models, inhibition of NO production triggers behavioural effects similarly to those induced by antidepressant drugs. Receptor tropomyosin-related kinase B (TRKB) has been identified as a key player mediating antidepressant drug (AD) induced effects, and it’s a potential target for NO since it displays multiple potential sites for nitration. Preliminary results from our group indicate that TRKB nitration impairs its signalling, and AD uncouple many proteins from TRKB and reorganizes TRKB protein complex. We examined the effect of selective nitric oxide synthase (NOS) inhibitor N⍵-propyl-L-arginine (NPA) in mice submitted to the contextual fear conditioning and found out that inhibiting NO production with NPA has an antidepressant-like effect on mice. We also found out that AD fluoxetine prevents nitration of TRKB receptors in vivo and antidepressant drugs fluoxetine, phenelzine and imipramine disrupt the interactions of TRKB, NOS1 and NOS1 adaptor protein (CAPON) in co-immunoprecipitation assay. To understand the nature of TRKB and NOS1 interaction, we thus examined the protein domains in NOS1 and TRKB using Uniprot database, and we were unable to identify sites that could interact directly. Literature search for NOS1 adapting proteins followed by Uniprot data mining indicated CAPON as a potential candidate to mediate NOS1: TRKB interaction. Our data shows for the first time that antidepressant drugs disrupt TRKB:CAPON:NOS1 interaction, thus protecting TRKB from NOS1-induced nitration. ADs might induce their behavioural effects by preventing NO-induced impair in TRKB signalling
  • Lahtela, Eero (2021)
    Municipal environmental authorities are required to conduct environmental monitoring. Unmanned aerial vehicles, UAVs, may be helpful in environmental monitoring but their applicability as a tool for municipal environmental monitoring has not been studied. In this thesis it was studied, how municipalities have been utilizing UAVs. Additionally, UAVs applicability for environmental monitoring and inspection work was tested using a litter monitoring experiment as an example. In the first part of the study, a questionnaire was sent to municipal environmental authorities in Finland, to municipalities in Sweden and to those participating in Eurocities WG Waste group (n = 512), covering the used applications, their utilization frequencies and successfulness, reasons for failures and future plans. The results were analyzed using descriptive statistics. In the second part of the study, a UAV was utilized in a litter monitoring experiment on four sites in Helsinki. Litter by category and leaves were counted based on visual observations from UAV imagery. The accuracy of UAV imagery detection was assessed by comparing its and ground assessment (GA) results. On one site, a control group also carried out UAV imagery detections in order to assess the magnitude of bias or offset occurring when both the GA and the litter detection from UAV imagery are conducted by a single individual. The Wilcoxon signed rank and Cronbach’s α reliability tests were used for statistical analysis of the results. Response rate of the questionnaire was low, 3.7% (n = 19). The pool of used applications was extensive and covered a variety of monitoring and inspecting targets with emphasis on the presumably manually piloted applications. Utilization was very successful. The most important reasons for failures were poor weather followed by lack of information and expertise. UAVs were included in the future plans of most participants for municipal environmental monitoring purposes. The UAV imagery detection accuracies of litter and leaves compared to the GA results were high, 90.5% for litter and 87.5% for litter and leaves, and no statistically significant differences existed between the assessment results. Especially leaves proved challenging to detect from UAV imagery. The control group’s detection accuracies were 67.9% without and 49.0% with leaves, and with leaves the results differed with statistical significance (p = 0.028). The internal reliability of the control group was relatively high, α = 0.776 without and α = 0.805 with leaves. UAVs are deemed sufficiently accurate and versatile as monitoring and inspecting tools for municipal environmental authorities. They have the capability to complement ground assessments or, with certain prerequisites, even function as an independent monitoring method. Further application and detection method development and research on municipal UAV utilization are needed.
  • Elf, Sonja (2019)
    Despite recent advances in understanding, diagnosis and treatment of cancer, this complex and versatile disease remains one of the leading causes of death worldwide. New and rapid diagnostic methods are needed to detect cancers at their early stages of development, thus enabling earlier prognosis, better risk assessment and more efficient treatment of the disease. There has been an increasing interest in specific molecular biomarkers as the hallmark for cancer research, and the detection of these markers from liquid biopsies using advanced molecular diagnostics methods provides major advantages over the conventional imaging methods currently used in oncology. The aims of this thesis were to examine the applicability of a novel molecular method, SIBA® (Strand Invasion Based Amplification), for the detection of cancer biomarkers, and to develop an assay targeting androgen receptor splice variant 7 (AR-V7) mRNA. The AR-V7 is proposed as a treatment-response biomarker in patients with castration-resistant metastatic prostate cancer (mCRPC). The expression of this variant can indicate resistance to hormonal therapies used for the treatment of advanced prostate cancer. Prostate cancer is the most common cancer after lung cancer in men worldwide and can gradually develop into a highly advanced lethal form, mCRPC, that is not responsive to androgen deprivation therapies. Positive AR-V7 status is suggested to represent the phenotype of this advanced stage of prostate cancer, and its detection can assist in treatment selection for the mCRPC patients. SIBA is a novel isothermal method for the amplification and detection of nucleic acids. The technology offers significant advantages over the more conventional molecular detection method, polymerase chain reaction (PCR), since the amplification reaction occurs at constant temperature and does not require sophisticated laboratory equipment for the thermal cycling. Reverse transcription SIBA (RT-SIBA) enables reverse transcription of RNA to cDNA as well as the simultaneous amplification and detection of the cDNA in one-step reaction under isothermal conditions. The method displays both high analytical sensitivity and specificity to the target nucleic acids. The RT-SIBA technology has not formerly been applied for the detection of human DNA or RNA. The main finding of this thesis was, that the RT-SIBA technology can be applied for rapid detection of specific molecular cancer biomarkers such as the AR-V7 mRNA. In this study, two RT-SIBA assays targeting the full-length androgen receptor (AR-FL) mRNA and the AR splice variant 7 mRNA were developed and optimized. Performance of the assays were evaluated by testing RNA isolates from AR-V7 positive and negative prostate cancer cell lines in the presence of human whole blood and plasma in the reaction. The developed RT-SIBA assays provided high analytical sensitivity and specificity: low copies of the target mRNA were amplified within 20 minutes without the production of non-intended amplicons. The results suggest that the RT-SIBA technology can be utilized for easy and rapid detection of AR-V7 and AR-FL mRNA directly from liquid sample material without a need for time-consuming sample treatment. Further performance evaluation using real AR-V7 positive clinical samples from mCRPC patients is necessary for the reliable validation of the developed assays.
  • Saarinen, Ronja (2023)
    Monen eri eläinryhmän edustajat käyttävät sosiaalista informaatiota sekä lajinsisäisesti, että lajienvälisesti erilaisten kelpoisuuteen vaikuttavien päätösten tekemisessä. Sosiaalinen informaatio voidaan jakaa tahallisiin ja tahattomiin signaaleihin ja informaation havainnoija voi käyttää tahattomia signaaleja hyväkseen johtaen siihen, että signaalin tuottaja kärsii huonommasta kelpoisuudesta. Tästä johtuvat valintapaineet voivat luoda informaation peittämisstrategioita signaalin tuottajassa. Tämä voi puolestaan johtaa osapuolten väliseen adaptaatioiden sykliin, jota kutsutaan myös koevolutiiviseksi kilpavarusteluksi. Pesäloiset ja niiden isäntälajit ovat klassinen esimerkki tällaisesta vuorovaikutussuhteesta. Leppälintu (Phoenicurus phoenicurus) on ainoa käen (Cuculus canorus) isäntälaji, joka pesii pelkästään koloissa. Kolopesintä tekee leppälinnusta erityisen isännän, eikä sen puolustautumiskäyttäytymistä ole laajalti tutkittu. Tutkimukseni päähypoteesi on, että leppälinnut piilottavat sosiaalista informaatiota käeltä puolustamalla niiltä pesäänsä vähemmän munintavaiheessa verrattuna haudontavaiheeseen. Aiemmissa tutkimuksissa näitä kahta vaihetta ei olla juurikaan vertailtu, vaikka käki loisii pesän pelkästään isännän munintavaiheessa. Testasin päähypoteesiani kenttäkokeilla, joissa ensin vertailin sitä, miten usein leppälinnut ovat läsnä pesillään muninnan ja haudonnan aikana sekä sitä, miten ne puolustavat molemmissa vaiheissa eri uhkia vastaan: pesäloinen, saalistaja ja kontrolli. Leppälinnut olivat enemmän pesillään haudonnan aikana ja tämä johtuu luultavasti siitä, että silloin linnut ovat panostaneet enemmän pesintäyritykseensä ja siitä, että naaraan täytyy pysyä pesällä pidempiä aikoja. Kaiken kaikkiaan, linnut puolustivat pesiään enemmän haudontavaiheessa, mutta niiden reaktio käkeä vastaan oli alhainen molemmissa vaiheissa. Jos siis leppälinnut peittävät informaatiota käiltä, ne eivät muuta tätä käyttäytymistä muninnan ja haudonnan välillä. Lintujen varoittelu lisääntyi saalistajan läsnä ollessa, mutta muu puolustautuminen ei vaihdellut uhkien mukaan. Tulokseni osoittavat, että saalistus saattaa olla pesäloisintaa suurempi uhka leppälinnuille tai että leppälinnut eivät tunnista käkeä uhkaksi. Kolopesintä vaikuttaa olevan leppälinnun paras puolustus käkeä vastaan, mutta lisää tutkimusta tarvitaan näiden kahden välisen dynamiikan tarkastelemiseksi.
  • Pitkänen, Stina (2018)
    The arylhydrocarbon receptor (AHR) is known for its xenobiotic role. In the last decades we have realized it has an important role even in normal physiology. Earlier studies have shown different circadian behavior in mice and rats when AHR is activated with the environmental toxoid TCDD. Also, AHR knock-out (AHRKO) mice have shown to adapt quicker to new lighting conditions. The aim of this study was to chart AHRs role on the circadian behavior in rats, by comparing daily eating and drinking habits under normal lighting condition for 7 days and for 7 days after a 12-hour light shift. Tissue samples to be used in continuing studies were taken after the 14 days long follow up. These studies will chart how the circadian timekeeping genes are expressed in the central (suprachiasmatic nucleus) and periphery (liver) cells in AHRKO rats after an adaptation to phase shift compared to wild type rats. This way the study will provide information that will help us understand the role of AHR in different species regarding behavior and in continuing studies gene expression. In our study no differences in drinking and eating activity could be seen between AHRKO and wild type rats. Both groups adapted to new lighting conditions equally fast.
  • Enberg, Emma (2021)
    Kiinnostus käyttää psykedeelejä, kuten lysergihapon dietyyliamidia (LSD) ja psilosybiiniä, erinäisten psykiatristen sairauksien hoidossa ei ole jättänyt huomiotta päihteiden väärinkäyttöä. Tutkimukset ovat osoittaneet alustavia positiivisia vaikutuksia LSD:n käyttämisessä erinäisten addiktioiden, kuten kokaiini-, nikotiini- ja alkoholiriippuvuuksien hoidossa. LSD:n on raportoitu auttaneen joitain alkoholismista kärsiviä pysymään raittiina jopa 6-12 kuukautta yksittäisen LSD annoksen jälkeen. Valitettavasti näitä tuloksia on hankala tulkita, ja vaikutusten taustalla olevat mekanismit tunnetaan huonosti. Tutkimme hiirimallimme avulla, kuinka yksittäinen LSD annos vaikuttaa ahmimiskäyttäytymiseen. Käytimme sukroosiliuosta ahmivaa eläinmallia palkkionottamiskäyttäytymisen mallintamiseen, mikä on yksi addiktioihin liittyvän käyttäytymisen tunnusmerkeistä. Tutkimuksemme tavoitteena oli selvittää vaikuttaako LSD palkkionottamiskäyttäytymiseen, ja siten mahdollisesti aivojen palkkiojärjestelmään. LSD -annostelu (0,05 ja 0,1 mg/kg, i.p.) vähensi akuutisti sukroosiliuoksen ahmimiskäyttäytymistä, mutta vaikutus loppui viikon kuluessa. Tästä havaitusta akuutista vaikutuksesta huolimatta erot ryhmien välillä eivät olleet tilastollisesti merkittäviä. Täten oletettiin, että nettovaikutukset aivojen palkkiojärjestelmään ovat epätodennäköisiä. Kuitenkin pelkän i.p. injektion (10 ml/kg) havaittiin vaikuttavan veden juomiseen. Havaitsimme merkittävän piikin veden juonnissa injektointipäivänä, mikä palautui normaalitasolle jo seuraavaan päivään mennessä. Nämä tulokset johtivat jatkotutkimukseemme, jossa osoitettiin injektion aiheuttavan piikin vedenjuontiin riippumatta siitä, injektoidaanko saliinia vai LSD:tä. Tätä vaikutusta ei enää havaittu, mikäli injektioita annettiin perättäisinä päivinä, mutta jopa yhden tai kahden päivän väli injektioiden välillä riitti palauttamaan injektion aiheuttaman piikin vedenjuontiin. Koska onnistuimme poistamaan vedenjuontiin aiheutuneen vaikutuksen toistetuilla saliini-injektioilla, eikä vaikutus palautunut injektoitaessa LSD:tä, voimme todeta, että vaikutus liittyi injektiotoimenpiteeseen. Keskeisin havaintomme tässä tutkimuksessa oli, ettei LSD:llä ole merkittävää akuuttia vaikutusta sukroosiliuoksen ahmimiskäyttäytymiseen tässä hiirimallissa.
  • Pietikäinen, Johanna (2007)
    The aim of this research is to find out why people recycle their old mobile phones lazily. The interest to recycle electronic equipment has enlarged in past few years; the reason for this is the aim of the European Union (EU) to increase recycling as a whole. In the background, there is the objective of the EU to reduce waste by delegating the responsibility of the products-waste handling to producers. The European Parliament and the Council have passed a directive on Waste Electrical and Electronic Equipment (WEEE) (2002/96/EC) and its amendment (2003/108/EC). This study is descriptive and aims at answering the questions about mobile phone owners recycling behaviour. The aim is to find reasons for consumers not recycling their phones, and hence, help to create measures to raise the takeback percentage. The results will be exploited in Nokia Corporation when they plan organizing the takeback system and possible future recycling campaigns. The primary research question is: What is a (non-)recycler like? For example, are there differences in mobile phone recycling behaviour between Finnish cultural areas? Theories concerning environmental behaviour (e.g. the Theory of Planned Behaviour) that were used to create a theoretical framework for the study are presented. The questionnaire was produced based on that framework, and so was the analysis. The questionnaires, 58 altogether, were filled in three Finnish cities, Helsinki, Turku and Lappeenranta, in February and March. The study is qualitative, but it is strongly supported by quantitative analysis. This means that the description of themes is to a great extent quantified. The results have shown that many phones are stored at home; only five people had recycled their phones. Usually phones were kept as spare phones, but also the lack of information about the takeback of used phones and laziness were reasons for not recycling phones. Most of the respondents considered recycling mobile phones important. Ten respondents have heard about the recent Finnish recycling campaign by Nokia and the WWF; the opinions were positive. By giving more information using, e.g., the internet or the mass media, about recycling mobile phones, the recycling percentage could be amounted. The non mobile phone recyclers were mostly women and over fifty. The capital city area could also need some specific attention as the mobile phone recycling activity was quite poor. Two questions were discovered needing more research: the best way(s) of informing people and people s limits in inconvenience when mobile phone recycling is concerned.
  • Preussner, Annina (2021)
    The Y chromosome has an essential role in the genetic sex determination in humans and other mammals. It contains a male-specific region (MSY) which escapes recombination and is inherited exclusively through the male line. The genetic variations inherited together on the MSY can be used in classifying Y chromosomes into haplogroups. Y-chromosomal haplogroups are highly informative of genetic ancestry, thus Y chromosomes have been widely used in tracing human population history. However, given the peculiar biology and analytical challenges specific to the Y chromosome, the chromosome is routinely excluded from genetic association studies. Consequently, potential impacts of Y-chromosomal variation on complex disease remain largely uncharacterized. Lately the access to large-scale biobank data has enabled to extend the Y-chromosomal genetic association studies. A recent UK Biobank study suggested links between Y-chromosomal haplogroup I1 and coronary artery disease (CAD) in the British population, but this result has not been validated in other datasets. Since Finland harbours a notable frequency of Y-chromosomal haplogroup I1, the relationship between haplogroup I1 and CAD can further be inferred in the Finnish population using data from the FinnGen project. The first aim of this thesis was to determine the prevalence of Y-chromosomal haplogroups in Finland and characterize their geographical distributions using genotyping array data from the FinnGen project. The second aim was to assess the role between Finnish Y-chromosomal haplogroups and coronary artery disease (CAD) by logistic regression. This thesis characterized the Y-chromosomal haplogroups in Finland for 24 160 males and evaluated the association between Y-chromosomal haplogroups and CAD in Finland. The dataset used in this study was extensive, providing an opportunity to study the Y-chromosomal variation geographically in Finland and its role in complex disease more accurately compared to previous studies. The geographical distribution of the Y-chromosomal haplogroups was characterized on 20 birth regions, and between eastern and western areas of Finland. Consistent with previous studies, the results demonstrated that two major Finnish Y-chromosomal haplogroup lineages, N1c1 and I1, displayed differing distributions within regions, especially between eastern and western Finland. Results from logistic regression analysis between CAD and Y-chromosomal haplogroups suggested no significant association between haplogroup I1 and CAD. Instead, the major Finnish Y-chromosomal haplogroup N1c1 displayed a decreased risk for CAD in the association analysis when compared against other haplogroups. Moreover, this thesis also demonstrated that the association results were not straightforwardly comparable between populations. For instance, haplogroup I1 displayed a decreased risk for CAD in the FinnGen dataset when compared against haplogroup R1b, whereas the same association was reported as risk increasing for CAD in the UK Biobank. Overall, this thesis demonstrates the possibility to study the genetics of Y chromosome using data from the FinnGen project, and highlights the value of including this part of the genome in the future complex disease studies.
  • Heikkilä, Sofi (2020)
    Conservation actions towards large carnivores have been successful in Europe, and the formerly lawfully persecuted species have started to reclaim their historical range. Coexistence with the predators is needed if their conservation should continue to succeed, as Europe does not host wilderness areas large enough to separate large carnivores from humans. As the importance of top-down regulation in ecosystems is recognized, the protection of these predators becomes essential. In Finland, all four large carnivore species, brown bear, grey wolf, Eurasian lynx and wolverine, have established populations, though their presence is not easily accepted by some. Large carnivores pose a threat to livestock and cause fear in the locals living in their territories. Wolf – hunting dog conflict is especially prominent in Finland south of reindeer husbandry area and the poaching of wolves hinders the population’s management. Attitudes towards large carnivores are often influenced by personal background, such as education level, ecological knowledge and respondent’s position in possible human – wildlife conflict. Residence can have an effect, as well, since conditions between living in urban or rural areas often differ. Hypothesis for this study are 1) attitudes towards large carnivores get worse while getting closer to protected areas, 2) attitudes towards large carnivores differ between eastern and western study areas, and 3) a higher education level increases positive attitudes towards large carnivores. The effect of ecological knowledge, prior experiences with large carnivores, age, sex and position in conflict was also explored. Study was conducted as a questionnaire, with face-to-face interviews and web survey distribution targeting two areas in Finland with large carnivore occupancy, one in the West and one in the East. A link between negatively perceived personal experiences and negative opinions towards large carnivores and their management was found. Living in the western area, where large carnivores have resided for a shorter time, predicted attitudes towards stricter management of the species. Third level education influenced attitudes positively. By understanding local attitudes towards large carnivores, it is possible to better understand the conflict between humans and predators, and so, find more likely solutions. Conservation actions where locals have been included, have been documented as successes. Regional differences in attitudes should be further studied and included in future decision making.
  • Sihvonen, Ida (2023)
    Research has identified the importance of understanding the connection between heat wave risk perception of elderly and their adaptation actions. In addition, developing more tailormade risk communication to elderly has been emphasized. The aim of this study is to understand how elderly citizens in the district of Töölö, Helsinki perceive the risk and adapt to increasing heat waves in a central part of the city and what the role of early warning systems (EWS) could be by collecting information through interviews on heat wave adaptation and risk communication. The qualitative data (N=6) consisted of transcribed interview data collected during February- March 2023. The data was analyzed through a thematic analysis and through using both a deductive and an inductive process, main themes and subthemes were identified within the data. The theory used in the deductive process was the Protection Motivation Theory in order to test if the theory could be used in this context. The results show that the personal risk perception and general risk perception varies for elderly and adaptive actions are in general taken to protect oneself from heat waves. However, Töölö as a high exposure area does not clearly increase the amount of adaptation actions but can rather offer benefits through its geographical position by the sea. The elderly’s interest in improving heat wave risk communication through an early warning system in Finland is noticeable. However, the final role of the system still remains open, and skepticism was expressed about the real need of a system in Finland. The results highlight that the elderly’s personal risk perception is rather independent of their adaptation actions, and they still adapt to heat waves, even when they perceive the threat as low. The results also highlighted that the elderly use multiple information sources to follow updates on heat waves, but the ideal risk communication media needs to be determined to develop an early warning system according to the needs of vulnerable risk groups such as elderly.
  • Anna, Leppänen (2023)
    Climate change and temperature rise in the Arctic is resulting in a decrease in sea ice extent and changes in sea ice variability. The impact of climate change on sea ice variability can be better understood when studying past events of climate change and sea ice extent change. Past environmental change can be reconstructed using bioindicators such as chrysophyte cysts, siliceous resting stages of chrysophyte algae. Archaeomonas spp., a genus of chrysophyte cyst, is often found preserved in Marginal Ice Zone sediments in the Arctic and its relationship with sea ice extent is explored here, to further understand its potential as a sea ice proxy. Diatom slides from three cores in the North Atlantic (Melville Bay, the North Water Polynya and Placentia Bay) were used to evaluate relationships between Archaeomonas spp. and known sea ice diatom species like Fragilariopsis reginae-jahniae. The Melville Bay core spans the last 8000 years, the North Water Polynya core spans the last 4000 years, and the Placentia Bay core spans the last 5800 years, providing a broad account of Archaeomonas spp. and diatom species abundances over the Holocene. It was concluded that Archaeomonas spp. was not directly correlated with known sea ice diatom species like F. reginae-jahniae at any of the three study sites. Archaeomonas spp. did display some similar relationships with cold water species like Thalassiosira hyalina, Thalassiothrix longissima, Thalassiosira nordenskioeldii and Fragilariopsis oceanica, and pack ice species like Actinocyclus curvatulus and Melosira arctica. Archaeomonas spp. can form in a range of conditions but prefers colder conditions where sea ice may form or drift to, as opposed to warmer, open water conditions. However, it is not directly linked to sea ice. Further research should focus on understanding whether Archaeomonas spp. forms in sea ice or not. There were some suggestions made to identifying Archaeomonas spp. at species level, but further research should be conducted on Archaeomonas spp.’s morphology to advance identification.
  • Nykänen, Sonja (2019)
    Colorectal cancer (CRC) kills more than half a million people a year worldwide. Usually the disease develops over several years via multiple steps which involve both genetic and epigenetic alterations. CRC is often diagnosed at late stage, when the cancer has already metastasized, and the prognosis is relatively poor. Several studies suggest that the first changes towards colorectal cancer occur and can be detected in histologically normal tissue before the appearance of any detectable lesion. The precancerous cells harbouring those changes may form a field of tissue, which is predisposed to malignant transformation. The study of pre-cancerous tissue might reveal the earliest changes in CRC development, which can be used as biomarkers for early detection and prevention of CRC. The aim of this thesis was to revise and investigate whether the aberrant expression of the six chromosomal segregation genes, Bub1, Mis18a, Pms2, Rad9a, Tpx2, and Mlh1, would signal carcinogenesis in mouse colon mucosa. Altogether fourteen mice, of which six had a proximal colon carcinoma, were selected for the study. The expression analysis was performed to histologically normal colon mucosa collected from the proximal and distal colon of each mice in order to investigate whether the possible pre-cancerous changes are found exclusively in the close proximity to the carcinoma. The expression was quantified with reverse transcription quantitative polymerase chain reaction (RTqPCR). No statistically significant gene expression differences were found between the carcinoma and control mice, indicating that the studied mice did not display cancer-preceding expression changes of the six studied genes in the carcinoma adjacent histologically normal colon mucosa. The results differed from the previously reported results, where the expressions of the six genes were found to be downregulated in the carcinoma adjacent mucosa. Here, the sample size was presumably not large enough to reveal statistically significant clustering of the expression patterns. However, Bub1 seemed to have a downregulated trend in the carcinoma adjacent mucosa, which supports the previously suggested role of Bub1 alterations in CRC initiation.
  • Kanerva, Sonja (2019)
    Increased intestinal permeability and its role in autoimmune, metabolic and chronic intestinal diseases is under extensive research as the “leaky gut” is considered as a potential target for preventive and therapeutic strategies in wide range of diseases. Zonulin, an eukaryotic analogue of Vibrio cholerae derived Zonula occludens toxin, which induces tight junction disassembly, has recently become a popular serum-based biomarker of intestinal permeability in biomedical research, even though the link between serum zonulin levels and functional measures of intestinal permeability has never been validated properly in humans. In addition, surprisingly little is known about the location and regulation of zonulin expression in the humans despite the protein was discovered almost two decades ago. Zonulin, also known as pre-haptoglobin-2, is an uncleaved precursor form of haptoglobin that is abundantly expressed in the liver. Zonulin, in turn, based on studies on rats, rabbits and monkeys, is expressed in the small intestine and stimulated by exposure to bacteria and gliadin, but no other stimulators have been described so far. It is also unclear, if different bacteria can induce different responses in zonulin secretion as only the effect of gram-negative enterobacteria has been documented so far. The aim of this study was to evaluate the effect of selected intestinal bacteria and of two known upregulators of haptoglobin, interleukin-6 (IL-6) and bacterial lipopolysaccharide (LPS), on zonulin secretion in vitro. The impact of two gram-positive probiotic bacteria (Lactobacillus rhamnosus GG & Bifidobacterium bifidum) and of two commensal gram-negative bacterial strains (Escherichia coli DH5α & Escherichia coli RY13) were tested for zonulin secretion in HT-29 intestinal epithelial cells, in addition to IL-6. Two separate lineages of immortalized human hepatocytes were tested for zonulin secretion by stimulation of LPS and IL-6. In addition, different immunological methods were assessed for quantification of zonulin, as the potential cross-reactivity of our primary analysis method, a commercial zonulin ELISA kit from Immundiagnostik AG that is also the main method used in the published zonulin studies, became more evident at the beginning of this thesis project. The main findings of this study were that the widely used commercial zonulin ELISA from Immundiagnostik AG is not specific for zonulin, but instead cross-reacts at least with complement C3, in line with the results published by other group during this work. Our further experiments comparing the signals of the above-mentioned zonulin ELISA and complement C3 ELISA for serum samples showed that there was only weak correlation between the obtained signals, suggesting that the zonulin antibody does not directly bind to complement C3. By using dot blot, western blot and immunoprecipitation, we found that the cross-reaction only occurred in native conditions. Based on zonulin ELISA measurements of the cell culture media from the in vitro experiments, very low signal was obtained for both intestinal and hepatic cells. Among the tested bacteria, only exposure to Lactobacillus rhamnosus GG led to a significant increase in the release of target protein. In hepatic cells, LPS had no effect, while IL-6 led to a significant increase of zonulin ELISA signal in one of the tested hepatic lines. However, it is currently difficult to differentiate if the low detected “zonulin” levels in this study are due to low level of secretion, or rather due to the lack of a proper method to detect zonulin. Taken together, these observations suggest that the most commonly used zonulin ELISA and other related, commercially available antibody-based methods for zonulin detection should be utilized with caution, as these antibodies cross-react with other protein(s). Hence, the serum “zonulin” cannot be considered as a biomarker of intestinal permeability until the captured protein(s) are identified, and similarly the anticipated effects of intestinal bacteria on zonulin expression cannot be reliably investigated with the currently available antibodies.
  • Toissalo, Emilia (2022)
    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by selective loss of upper and lower motor neurons (MN), which causes progressive muscle weakness and paralysis. ALS leads to death typically from 2 to 4 years after diagnosis. It is important to find more effective treatment options for this devastating disease, as the current treatments can prolong the survival by only a few months. Mesencephalic astrocyte-derived neurotrophic factor (MANF) belongs to an evolutionary conserved neurotrophic factor (NTF) family, whose mode of action differs from classical NTFs. MANF is an endoplasmic reticulum (ER) resident protein and is secreted upon ER stress from the ER, and it can protect the cells from ER stress-induced cell death. MANF has shown to be neuroprotective and –restorative in Parkinson’s disease and stroke rodent models. Adeno-associated viral (AAV) vectors can be used to express therapeutic genes in the target tissues for several months, which lessens the need for repetitive dosing. In this master’s thesis project, we aimed to investigate the neuroprotective effects of intrathecally injected AAV1-MANF gene therapy in a SOD1-G93A mouse model of ALS. We used two different MANF genes; full-length MANF and MANF with deleted ER retention signal (MANF-d), to assess the differences between normal and only secreted MANF. Red fluorescent protein (RFP) was used as a control and to further evaluate the transduction and expression of the viral vectors. Intrathecal injections were performed once on 13 weeks old mice, just before the disease onset. Clinical symptom analyses together with a set of behavioral tests were conducted once a week. Mice were sacrificed at the endpoint of the study when they could no longer use their hind limbs for forwarding propulsion. Immunohistochemical staining was performed on spinal cord paraffin samples, where MN count, microglia activation, and RFP expression were evaluated. AAV1-MANF and AAV1-MANF-d treatments improved the motor behavior of the SOD1-G93A mice one-week post- injection. More specifically, a statistically significant difference was seen in the turning times in the static rods test on two different diameter rods compared to control, but there was no difference between MANF groups. In addition, there was a notable difference between AAV1-MANF and the control group on week 16 rotarod scores. There were no statistically significant differences in other tests, survival of the mice, MN counts, or microglia activation between the groups. RFP expression was detected mainly in the ventral areas of the spinal cord with immunohistochemistry. Our results indicate the potential of MANF gene therapy in the treatment of ALS. Furthermore, we showed that intrathecal AAV1-MANF injections were well tolerated.
  • Mäkelä, Alexandra (2023)
    During recent years obesity has been under extra scrutiny due to its globally rising prevalence, multifaceted effects on the human body and common occurrence of comorbidities. It is estimated that one third of the Finnish population over age 40 will be obese by 2028 (THL, 2022). Consequently, development of mitigation strategies has become a high priority in today’s societies leading to a rising need for new treatments. Several studies have shown how pathological adipogenesis has deleterious effect on brain functionality. The neuropathology of obesity could be explained by increased blood-brain barrier (BBB) leakage, oxidative stress, neuroinflammation and glial activation. Pathologically activated astrocytes (astrogliosis) exhibit phenotypical and functional differences compared to healthy astrocytes, typically exhibiting enlarged cell bodies and swollen cytoskeleton. Astrogliosis has been mainly studied in the context of CNS diseases. Recent studies also shed light on the role of astrocytes in the progression of peripheral diseases including cancer metastasis or inflammation (Ma et al., 2023). However, the active astrocytic profile in obesity is relatively underexplored. In this study we report astroglial phenotypic shifts induced by high-fat diet (HFD) feeding and weight loss (WL). No significant change in GFAP expression was seen between mice that were given an HFD for different durations and their corresponding controls. However, we noted a non-significant trend for increased GFAP expression in response to shorter timepoints (5 days of diet change). This suggested an early astrocytic response to diet, which later normalizes over time. We reported healthy morphologies in astrocytes from chow group exhibiting typical simple thin cytoskeleton with long cell protrusions. Astrocytes in HFD-conditions exhibited reactive phenotypes evidenced by swollen cytoskeletal structures and high GFAP immunofluorescence, extensive lipid droplet (LD) accumulation and upregulated metabolic activity. These observations indicated stressful conditions caused by the diet. Astrocytes in WLconditions exhibited varying phenotypes displaying both reactive and healthy characteristics, slight increase of metabolic activity and lipid accumulation. In addition, we reported different immunofluorescence profiles between glial differentiation promoting marker Meteorin and ER stress regulated cytoprotective marker MANF between the experimental groups. These results show that HFD-induced obesity and consecutive weight loss induce a reactive-like phenotypic shift on astrocytes involving both morphological and functional changes.
  • Sridharan, Ravindran (2020)
    The brainstem monoaminergic neuronal systems are involved in regulation of mood, reward system, memory processing etc. Any defects or damage in these cells lead to many neurological disorders. The brainstem inhibitory GABAergic and excitatory glutamatergic cells in turn control these neuromodulatory neurons. The glutamatergic neurons are found in the Laterodorsal tegmental nucleus (LDTg), Interpeduncular nucleus (IPN) as well as in the Ventral tegmental are (VTA). The LDTg in particular sends these glutamatergic projections to the VTA to regulate their Dopaminergic (DA) neurons. During embryonic development, the brainstem GABAergic and glutamatergic neurons, that regulate the monoaminergic systems, are produced in the ventral rhombomere 1. Their subtypes are known to express various transcription factors (TFs), such as Nkx6-1, Vsx2 and Skor1 marking the glutamatergic neuron precursors in the ventral rhombomere 1. In this thesis project, I studied the expression of another TF, Skor2 in the embryonic brainstem precursors. The basis of the experiment came from an embryonic brainstem single cell mRNA sequencing study performed earlier, where Skor2 expression was observed in the cluster of neurons containing Nkx6-1, Vsx2 and Skor1 expressing cells. Based on this, I hypothesized that Skor2 expression could be seen in glutamatergic precursors in the ventral rhombomere (rV2) domain as well as later in the LDTg nucleus derived from these precursors. To test this, I performed immunohistochemistry (IMHC) studies on a transgenic mouse line expressing Green Fluorescent Protein (GFP) from the Skor2 locus. In the second part of the thesis, I hypothesized that the Skor2 positive cells need this TF for their differentiation. To study this aspect, I performed similar IMHC studies on homozygous Skor2GFP/GFP mice, where Skor2 had been inactivated. My study showed that Skor2 positive cells expressed markers Nkx6-1 and Vsx2 and represented a specific subgroup of early embryonic post-mitotic precursors in the rV2 domain. Later in the brainstem, in contrast to my initial hypothesis, I did not observe Skor2 expression in the LDTg glutamatergic region. Instead, I observed Skor2 positive cells in a region more lateral to the Ventral and Dorsal tegmental nuclei of Gudden. In the homozygous Skor2 mutants, I observed no changes in cell fate during embryonic development. Based on my results, the TF Skor2 is expresses in the glutamatergic precursors and neurons in the rhombomere 1, but form a part of a new cluster of cells away from the LDTg. These neurons have not been studied in detail. However, the Ventral and Dorsal tegmental nuclei of Gudden have been shown to regulate memory and navigation. It is possible that the Skor2 expressing neurons also participate in these functions. Identification of specific molecular markers, such as Skor2, for these neurons now allows their focused functional studies. Skor2 and Skor1 are related TFs belonging to Ski family of transcriptional repressors and are seen to be expressed together. Further investigations into the roles and functional redundancy of these two TFs can be performed using mice carrying mutations in both of these genes.
  • Annala, Heidi (2023)
    Luontopohjaiset ratkaisut (NBS, Nature-based solutions) ovat tietoisesti suunniteltuja ratkaisuja komplekseihin haasteisiin, ja niiden ytimessä ovat ”luonnon” elementit, kuten valikoidut mikrobit ja kasvillisuus. Nämä elementit ovat luontopohjaisen ratkaisun ytimessä, ja näin tekevät NBS:stä usein ekologisesti kestävämmän vaihtoehdon perinteisille teknisille maisemaratkaisuille. Suuri osa olemassaolevasta kirjallisuudesta on siten keskittynyt NBS:n ekologiseen ulottuvuuteen huolimatta niiden sisäsyntyisestä moniulotteisuudesta. Sosiaaliset elementit ovat kuitenkin paitsi olennainen osa NBS:n suunnittelua ja toimintaa, myös niiden pitkän tähtäimen onnistumisen edellytys. Aiempi tutkimus on osoittanut, että luontopohjaisten ratkaisujen menestys riippuu ennen kaikkea niiden paikallisen yhteisön saavuttamasta yhteydestä ja omistajuudesta. Näiden suhteiden muodostuminen tapahtuu usealla tasolla, mukaan lukien psykologisella ja asuinaluetasolla. Siksi tämä tutkimus tarkastelee luontopohjaisiin ratkaisuihin yhdistettäviä merkityksiä ja näkemyksiä paikallisen, karttapohjaisen, audio-visuaalisen kyselyn kautta. Vastauksista nousee esiin kaksi primääristä huomiota: Ensiksi, aineistosta on mahdollista erottaa NBS- ja äänimaailmamieltymysten, sekä avointen paikan merkitysten pohdintojen kautta vähintään kaksi paikallista arkkityyppiä, jotka lähestyvät luontopohjaisia ratkaisuja uniikeilla tavoilla. Toiseksi, erot näiden arkkityyppien reaktioissa paikallisiin luontopohjaisiin ratkaisuihinsa voivat selittyä osin luontosuhteen ja paikallishistorian kautta. Nämä löydöt korostavat yhtäältä olemassaolevan henkilökohtaiseen psykologiseen ulottuvuuteen keskittyvän NBS-tutkimuksen merkitystä, ja toisaalta paikallisen ja yhteisötason ymmärrystä kokonaisen