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Now showing items 79-98 of 961
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(2016)Pohjoismaissa syntypaikkalajitellun biojätteen kompostointi suurissa kompostointilaitoksissa on yleistynyt merkittävästi 2000-luvun aikana. Viime vuosina biojätteiden ja muiden orgaanisten jätteiden käsittelyssä on alettu suosimaan yhä enemmän mädätysprosessia sekä mädätyksen ja kompostoinnin yhdistävää osavirtamädätysprosessia. Mädätysprosessin avulla orgaanisten jätteiden sisältämästä energiasta pystytään tuottamaan biokaasua ja siitä edelleen uusiutuvaa energiaa. Tämän tutkimuksen lähtökohtana oli tarkastella biohiilen lisäyksen vaikutuksia kompostointiprosessiin, jossa yhdistyvät mädätys ja kompostointi. Aiempien tutkimusten perusteella biohiilen lisäyksellä on todettu olevan positiivisia vaikutuksia erilaisten orgaanisten jätteiden kompostointiprosessiin. Aiemmat tutkimukset on suurimmaksi osaksi tehty pienemmässä mittakaavassa ja ne ovat keskittyneet enemmän maatalousjätteiden kompostointiin. Tämän tutkimuksen tarkoituksena oli selvittää, voidaanko verrattain pienellä biohiilen lisäyksellä nopeuttaa orgaanisen aineksen hajoamista sekä parantaa typen pidättymistä kompostimassassa erilliskerätyn biojätteen osavirtamädätysprosessin kompostointivaiheessa. Tutkimuksen kokeellinen osuus koostui laboratoriomittakaavan kompostointikokeesta sekä laitosmittakaavan kompostointikokeesta Ämmässuon jätteenkäsittelykeskuksessa. Laboratoriomittakaavan kokeiden tarkoituksena oli saada tietoa eri biohiilipitoisuuksien vaikutuksesta kompostointiprosessiin ja toistomäärien kautta saada tuloksille tieteellistä pätevyyttä. Laboratoriokokeissa saatuja tuloksia sovellettiin laitosmittakaavan kokeissa. Tuloksia pyritään tarkastelemaan mikrobiologisen prosessin lisäksi osana jätehuoltoa ja sen kehittämistä. Tulosten perusteella biohiilen lisäyksellä oli myönteinen vaikutus kompostointiprosessiin osavirtamädätysprosessin kompostointivaiheessa. Laboratoriokokeissa biohiilen lisäyksellä oli merkitsevä vaikutus orgaanisen aineksen hajoamiseen ja siten kompostimassan mikrobiaktiivisuuteen. Vaikka laitosmittakaavan kokeessa biohiilen lisäys ei vaikuttanut orgaanisen aineksen hajoamiseen tilastollisesti merkitsevästi, voidaan kokonaisuutena arvioida, että biohiililisäsi kompostien mikrobiaktiivisuutta. Biohiilellä havaittiin merkitsevä vaikutus kompostien stabiloitumisnopeuteen ja ammoniumtypen pidättymiseen kokeen lopputilanteessa. Verrattain pienet biohiilipitoisuudet eivät vaikuttaneet haihtuneen ammoniakin määrään eivätkä kokonaistyppihäviöön kompostoinnin alkuvaiheessa. Biohiilikompostien stabiloitumisnopeudella ja mikrobiaktiivisuuden lisääntymisellä on kompostoinnin ympäristövaikutusten vähentämisen lisäksi kompostointilaitoksille myös taloudellinen merkitys, koska niiden avulla pystytään mahdollisesti säästämään tuotantokustannuksissa sekä säästämään kompostien jälkikypsytykseen tarvittavaa tilaa tai vastaavasti lisäämään kompostointilaitosten kapasiteettia. Tulevaisuudessa biohiili on teoriassa mahdollista saada osaksi orgaanisten jätteiden käsittelykokonaisuutta. Jäteperäisten biohiilten käytöllä voi tulevaisuudessa olla mahdollista parantaa resurssien kestävää käyttöä ja alueellisia kierrätysmääriä.
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(2022)Formation of template switching mutation has previously been proposed as a mechanism of RNA evolution. TSM mechanism may contribute to the creation, maintenance, and modification of the RNA Hairpin. The finding of de novo TSM in RNA sequences will provide evidence for this hypothesis. Ribosomal RNAs (rRNAs) appear in multicopy clusters on different chromosomes and evolve through concerted evolution. To study the properties of de novo TSM and the dynamics of the concerted evolution of rRNA, we developed a computational tool to analyze pairwise differences and the phylogenetic relationship of rRNA genes on different chromosomes. The genome assemblies that are based on traditional short-read sequencing methods have limitations on studying long tandem repeat rDNA, because the reading length is shorter than on the rRNA gene. To overcome this limitation. PacBio Hifi long-read sequencing data for human rRNA 18S and 28S genes were studied. By analyzing the diversity of rRNA genes between individuals and families, single nucleotide mutations, multiple nucleotide insertions, and deletions were identified. As expected, genetic variations in ribosomal genes were detected both within and between individuals. A larger sample size may be required for TSM identification. The finding of this research that related to the dynamics and concerted evolution of human rRNA may contribute to a better understanding of rRNA mutation-related genetic disorders.
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(2020)Tiivistelmä – Referat – Abstract Proteins differ from one another on the basis of their amino acid sequences, display a different spatial shape and structure, and have different functions. The linear order of amino acid residues are chained to one another by peptide bond. The ß-strands and α-helices can be considered as the key components present in the three-dimensional structure of a protein. There are several bioinformatic methods involved to predict structure and function of protein such as searching sequencing similarities, multiple sequence alignment, characterisation of domains, solvent accessibility, and modelling three-dimensional structures at atomic level. The main focus of this study was to build the three-dimensional structure models and then compare the homologues regions in different models. 36 reviewed capsid L1 and L2 protein sequences of human papilloma virus subtypes were selected based on 65% sequences similarity from Universal Protein database. We utilised several computational algorithms in this study for the analysis of protein sequences for the evolutionary relationship and modelled the three-dimensional structures of capsid L1 and L2 proteins of oncogenic human papilloma virus subtypes. For domains analysis in the protein sequences, we used Simple Modular Architecture Research Tool algorithms and predicted secondary structure of protein using Protein Prediction Protein 4.0 tool. I-TASSER Iterative threading assembly refinement algorithms were utilised for three-dimensional structure modelling of capsid L1 and L2 proteins. We found out a different evolutionary relationship and conserved residues in capsid L1 protein of human papilloma virus and L2 protein of human papilloma virus, and their different level of effect on the protein structure. We also predicted three-dimensional structure models for capsid L2 protein of human papilloma virus subtypes 41 and 13 which are folded completely differently from the rest L2 proteins. X-ray crystallography study is suggested for the determination of three-dimensional structure of L2 protein for understanding their contribution in viral assembly process.
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(2023)Tässä työssä tutkin, minkälaiset käyttäytymistä määrittävät tekijät koetaan esteiksi biojätteen lajittelulle sekä mitkä ihmisryhmät lajittelevat biojätteensä passiivisemmin kuin toiset HSY:n alueella. Analysoin tutkielmassani kyselytutkimusaineistoa klusterianalyysin avulla, jonka perusteella etsin mahdollisia lajittelua estäviä tekijöitä ja tarkastelen vastaajien demografisten tekijöiden jakaumaa passiivisten ja aktiivisten lajittelijoiden joukoissa. Lisäksi hyödynnän ympäristöpsykologian teorioita ja tutkimusta ympäristömyönteiseen käyttäytymiseen kannustamisesta. Tätä teoriataustaa ja tuloksiani soveltamalla ehdotan mahdollisia interventioita, joiden avulla voidaan tehostaa kotitalouksien biojätteen lajittelua pääkaupunkiseudulla ja Kirkkonummella. Biojätteen lajittelu kotitalouksissa on tärkeää, sillä lajitellulla voidaan lisätä jätteiden hyötykäyttöä, mikä edistää kiertotaloutta Suomessa. Biojäte on erityisen tärkeä jätelaji kierrättää, koska kompostoinnin ja mädätyksen avulla siitä saadaan lopputuotteina uusiutuvaa biokaasua, josta tuotetaan energiaa sähkönä yhteiskunnan tarpeeseen, sekä ravinnerikasta multaa, jota voidaan hyödyntää maanviljelyssä ja viherrakentamisessa keinolannoitteiden korvaajana. Kotitalouksissa syntyvä orgaaninen jäte sisältää runsaasti typpeä, joten biojätteen lajittelu edistää myös ekologisesti kestävää typen kiertoa. Analysoin työssäni HSY:n kuluttajakäyttäytymiskyselyn vastauksia monimenetelmällisesti hyödyntämällä kvantitatiivista klusterianalyysia sekä kvalitatiivista teema-analyysia. Tulosteni perusteella havaitaan, että passiivisten lajittelijoiden vastauksissa korostuu lajittelun vaivalloisuus, tiedonpuute sekä paikalliset deklaratiiviset normit käyttäytymistä rajoittavina tekijöinä. Lajitteluesteiden tunnistaminen ja kuvaileminen auttaa arvioimaan mahdollisia käyttäytymismuutostekniikoita, joilla kannustaa asukkaita lajittelemaan biojätteensä paremmin. Tuloksistani voidaan päätellä, että proseduraalisen tiedon saaminen, lajittelun ympäristövaikutuksista oppiminen sekä lajittelun helpottaminen voivat kannustaa asukkaita lajittelemaan biojätteensä huolellisemmin. Löydösten perusteella voidaan kohdentaa viestinnässä ja kampanjoinnissa käytettäviä tekniikoita, jolloin niillä voidaan tehokkaammin kannustaa ympäristömyönteiseen käyttäytymiseen ja saadaan HSY:n alueen lajitteluaste nousemaan biojätteen osalta.
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(2015)Viime vuosikymmeninä tiedonalakohtaista oppimista on tutkittu paljon käsitteellisen muutoksen näkökulmasta. Käsitteellinen muutos tarkoittaa oppijan tietorakenteiden muuttumista tai jäsentymistä virheellisistä kohti tieteellistä mallia. Käsitteellisen muutoksen teorioiden mukaan oppijoiden aikaisempien virhekäsitysten tunteminen ja huomioiminen on keskeistä oppimisen ja opetuksen onnistumisen kannalta. Tässä tutkimuksessa selvitettiin biologian yliopisto-opiskelijoiden fotosynteesiin liittyviä virhekäsityksiä, niiden muuttumista opetustekstin lukemisen seurauksena sekä biologian pääaineopiskelijoiden ja sivuaineopiskelijoiden virhekäsitysten eroja. Suomalaisten opiskelijoiden virhekäsityksiä on aiemmin tutkittu niukasti. Tämän tutkimuksen tavoitteena oli selvittää virhekäsityksiä suomalaisten opetussuunnitelmien mukaan opiskelleilta opiskelijoilta sekä selvittää virhekäsitysten yksityiskohtaista muuttumista käsitteellisen muutoksen näkökulmasta. Tutkimuksen aineistona oli yliopiston biologian peruskurssin opiskelijoiden (n=171) vastaukset fotosynteesiä ja sen ekologista merkitystä koskeviin avoimiin kysymyksiin. Opiskelijat vastasivat kysymyksiin ennen opetustekstin lukemista, heti opetustekstin lukemisen jälkeen sekä kaksi viikkoa lukemisen jälkeen. Aineisto analysoitiin laadullisin menetelmin kuvaamalla, tyypittelemällä ja tulkitsemalla havaittuja virhekäsityksiä. Virhekäsitysten tulkinnassa hyödynnettiin tiedon ja ajattelutaitojen tasojen luokittelua. Opiskelijoilla havaittiin yhteensä 58 fotosynteesiä koskevaa selkeästi virheellistä käsitystä ja 14 puutteellista tai epämääräistä käsitystä. Virhekäsitykset liittyivät fotosynteesireaktioon, kasvien rakenteisiin, kasvin energiatalouteen ja fotosynteesin ekologiseen merkitykseen. Lähes kaikki virhekäsitykset ja puutteelliset käsitykset olivat yleisempiä biologian sivuaineopiskelijoilla kuin pääaineopiskelijoilla. Virhekäsitykset vähenivät opetustekstin lukemisen seurauksena, ja monimutkaisempia tiedon ja ajattelutaitojen tasoja ilmentävät virhekäsitykset vähenivät vähintään yhtä paljon kuin muutkin. Lukuisia virhekäsityksiä kuitenkin säilyi oikeat vastaukset antaneesta opetustekstistä huolimatta. Kaksi viikkoa opetustekstin lukemisen jälkeen osa jo virhekäsityksensä korjanneista opiskelijoista vastasi jälleen virheellisesti. Tutkimus osoittaa, että suomalaisen peruskoulun ja lukion fotosynteesin oppimista koskevat tavoitteet eivät täyty edes monen biologian yliopisto-opiskelijan kohdalla. Suomalaisilla opiskelijoilla on pitkälti samoja virhekäsityksiä kuin kansainvälisesti tehdyssä tutkimuksessa on havaittu. Fotosynteesin oppimisen kannalta keskeisin tutkimuksessa havaittu ymmärryksen puute on vaikeus ymmärtää fotosynteesin merkitys Auringon valoenergian ja ravintoketjujen energian välisenä linkkinä. Opiskelijoiden vaikeudet korjata virhekäsityksiään selittyvät käsitteellisen muutoksen prosessin haastavuudella ja hitaudella. Fotosynteesiä koskevan oppimisen edistämiseksi opetuksessa tulisi aiempaa paremmin huomioida käsitteellisen muutoksen haasteet kognitiivisesta, sosiaalisesta ja motivaatioon liittyvistä näkökulmista. Tämä tutkimus tarjoaa tietoa niistä fotosynteesin oppimista koskevista erityispiirteistä, joita ilmiön tehokkaaseen oppimiseen pyrkivän opetuksen tulee huomioida.
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(2021)There are no comprehensive research data on Finnish matriculation examinations in biology. This type of data is needed, because evaluation guides what and how students learn and what they consider important. Genetics is one the most challenging topics in biology, and in the opinion of teachers it will continue to be an important discipline in the future. The importance of studying genetics can also be justified with philosophical, social and health reasons. This is why the present study focused on the genetics component of the matriculation exam in biology. The aim of the study was to provide information on the challenges and contents of past matriculation examinations in biology and how they have aligned with high school curricula. The results of the study could be used to evaluate this alignment in relation to genetics questions in the biology exam, and could help in designing new matriculation examinations that align better with the existing high or new high school curricula and their aims. The research questions were: 1. What knowledge and cognitive dimensions are measured with the genetics-related questions in matriculation examinations in biology? 2. How do knowledge and cognitive dimensions in genetics-related questions in biology matriculation examinations relate to high school curriculum aims? The data comprised matriculation examination papers in biology from spring 2011 to autumn 2020 (20 exams) and the aims of the Finnish national High School Curriculum in 2003 and in 2015. Qualitative content analysis was performed on the knowledge dimensions (factual, conceptual or procedural knowledge) and the cognitive process dimensions (remembering, understanding, applying, analyzing, evaluating or creating). The basis of this qualitative content analysis was Bloom’s revised taxonomy. The analysis was conducted on genetics-related matriculation examination questions and on the aims of the high school curriculum. The test questions and the aims were compared to determine whether they aligned. Classified questions were divided into two subcategories depending on which high school curricula they corresponded to. Genetics-related questions from spring 2011 to autumn 2017 corresponded to the High School Curriculum in 2003 and questions from spring 2018 to autumn 2020 corresponded to the High School Curriculum in 2015. Questions from the previous period were divided into all knowledge dimensions. All questions, except one, incorporated lower cognitive dimensions (remembering, understanding and applying). The main combined class was understanding conceptual knowledge. Questions from the later time period were also divided into all knowledge dimensions. Mostly lower cognitive dimensions were incorporated into the questions, but a few subquestions addressed higher cognitive dimensions (analyzing, evaluating and creating). The main combined class was understanding conceptual knowledge. All the aims were classified into conceptual or procedural knowledge classes. The aims were also divided between all cognitive dimensions, except remembering. Using constructive alignment as the basis for matching aims with questions, two aims in the High School Curriculum of 2003 and six aims in the High School Curriculum of 2015 had no questions that matched them. These aims mostly measured the cognitive dimension of creating. Several aims appeared to incorporate higher cognitive dimensions, but the questions were less well aligned with the aims than with those incorporating lower cognitive dimensions. The results concerning knowledge and cognitive dimensions were mostly as expected. Lower cognitive dimensions were highlighted in genetics-related matriculation examination questions in biology. The challenge of interpretation brought ambiguity to the aims and cumulative levels of cognitive dimensions when aligning questions with aims, as some of the questions aligned with aims did not assess such high cognitive dimensions as would be expected based on the aims, but were nonetheless aligned with them. Furthermore, there may be several reasons behind the absence of the creating dimension in matriculation examination questions. The alignment of questions and aims would be important to consider in the future, because evaluation has a considerable impact on studying.
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(2017)No comprehensive research has been conducted on matriculation examinations in biology. This kind of data are needed, however, as evaluation (e.g. challenges and contents of test assignments) direct the way students study and learn and what they consider important in the taught matter. Thus, it is impossible to say, if the tests really measure core knowledge of biology, or just fragmentary facts. The aim of this study was to provide information on the challenges and contents of matriculation examination in biology and to provide, for the first time, comprehensive information on the factors affecting competence. The results of the study can be used to evaluate the impact of the new curriculum of upper secondary school and to support the development of the new electronic matriculation examination assignments. The research questions were: 1. How do the test tasks of biology matriculation examination measure the core content and the levels of both knowledge and cognitive dimensions? 2. Are the types of test assignments, knowledge and cognitive dimensions distributed equally between all core contents? 3. Do the results vary among a) the examinations, b) the type of tasks, c) the core contents or d) the knowledge and cognitive dimensions? 4. Is the competence of a) task type or b) knowledge or cognitive dimension levels, subject to the different types of core contents? 5. How does gender explain the choice and competence of different tasks? The qualitative content analysis was used to identify the different aspects; the task types (selected response, brief constructed response or performance-based assessment), the knowledge dimensions (factual, conceptual or procedural knowledge) and the cognitive process dimensions (remember, understand, apply, analyze, evaluate or create). The content variation of matriculation exam was examined and classified using the biological core contents. The data comprised matriculation examinations in biology from spring 2011 to spring 2015 (9 exams, 108 tasks). Additionally, statistical analyses were used to examine how the test subjects (n = 28,777) succeeded in these different assignments and whether girls and boys were equally successful. The task type "selected response" was considered only in four (out of 108) tasks. All levels of knowledge dimensions were found but higher level cognitive processes, such as "analyse" or "create" were not required; the main emphasis in the tasks was in the understanding of conceptual knowledge. The majority of the tasks dealt with the core content "From the molecules to the organisms", i.e. the focus was on biological structures and processes. The analysis of scores obtained in the tests showed that the total scores were higher in the autumn examinations than in the spring examinations and that the scores had been steadily declining. The achievement in the task was most influenced by the type of task and the required level of cognitive process. The interest and knowledge varied between different core contents. Biological evolution appeared to be the most interesting topic to students and had also the highest scores. The girls mastered biology generally better than the boys, but the difference between the sexes was minimal in tasks requiring some form of applied aspect. In particular, the boys excelled the girls in tasks related to ecosystems which mostly required applications. The study also showed other factors affecting student achievement, one of the most significant being the impact of the use or non-use of verbs in the assignment. If the assignment lacked a verb describing what the task requires (e.g. distinguish, subtract, describe), the candidates managed the task poorly. Structural aspects of the task seem to have a great impact especially on the boys' level of knowledge. Future research should classify assignments, for example through assignment instruction guidance or visual interaction on knowledge.
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(2021)Effective population coding is dependent on connectivity, active and passive postsynaptic membrane parameters but how it relates to information transfer and information representation in the brain is still poorly understood. Recently, Brendel et al. (2020) showed how spiking neuronal networks can efficiently represent a noise input signal. This "D_Model” successfully showed that spiking neural networks can recreate input signal representations and how these networks can be resilient to the loss of neurons. However, this model has multiple unphysiological characteristics, such as instantaneous firing and the lack of units related to physical values. The aim of the present study is to build upon the D_Model to add biological accuracy to it and study how information transfer is affected by biophysical parameters. We first modified the D_Model in the MATLAB environment to allow for the simultaneous firing of the neurons. Using our CxSystem2 simulator in a Python environment (Andalibi et al. 2019), we built a network replicating the one used in the D_Model. We quantified the information transfer of Leaky Integrate-and-Fire units that had identical physiological values for both inhibitory and excitatory units (Comrade class) as well as more biologically accurate physiological values (Bacon class). We used various information transfer metrics such as granger causality, transfer entropy, and reconstruction error to quantify the information transfer of the network. We examined the behaviour of the network while altering the values of the capacitance, synaptic delay, equilibrium potential, leak conductance, reset potential, and voltage threshold. Broad parameter searches showed that no single set of biophysical parameters maximised all information transfer metrics, but some ranges fully blocked information transfer by either saturating or stopping neuronal firing. This suggests theoretical boundaries on the possible electrophysiological values neurons can have. From narrow searches within electrophysiological ranges, we conclude that there is no single optimal set of physiological values for information transfer. We hypothesise that different neuronal types may specialise in transferring different aspects of information such as accuracy, efficiency, or to act as frequency filters.
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(2023)The anthropause following the beginning of the COVID-19 pandemic in 2020 was followed by a heavy decline in people’s mobility and outdoor activities, which has had differing effects on biodiversity in urban areas. In Finland, outdoor activities were allowed, and as a result, the use of greenspaces increased notably in relation to pre-pandemic times. My objective was to study how people’s outdoor activities developed during the pandemic in the form of recreational bird-watching in the Helsinki metropolitan area (including Espoo, Vantaa, and Kauniainen). To accomplish this, I retrieved data on the number of bird observers from Tiira (a Finnish bird information service focused on bird observations), and related this data to the pandemic periods, also taking into account variables such as daily temperature and the use of parks. I found the highest number of bird-watchers during both lockdowns in 2020 and 2021. I also found that the number of bird-watchers was significantly higher after all restrictions were lifted, in 2022, when contrasted with pre-pandemic times. It is notable that the lockdowns happened at the same time as the bird Spring migration, a naturally popular time among bird-watchers. Thus, I consider that this may have had a synergistic role in people taking the opportunity to dedicate more time for bird-watching since they had more time to go outside due to strict restrictions. After all the restrictions were lifted in 2022, some bird-watchers continued to spend more time in bird-watching due to habit or increased appreciation for the activity or outdoors. The findings highlight the importance and potential of citizen science in observing birds and enabling more efficient conservation efforts for them. The results showing the development of bird-watching activities during the pandemic could also potentially be used as a proxy for other outdoor activities, and combined with other studies on the relations of COVID-19 on humans and other species could help to better understand the complex socio-ecological relationships in cities and greenspaces.
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(2023)The aim of this study was to identify which bird impact types are considered significant in practice in Finnish environmental assessment reports regarding wind power. Increasing numbers of wind turbines can impact birds directly and indirectly, which could contribute to the loss of bird diversity. Amid climate change mitigation attempts, biodiversity loss should not be overlooked. Environmental impact assessment is an example of a policy tool for identifying and reducing the negative environmental effects of a project, including bird impacts. All wind power-related EIA reports with significant bird impacts were collected from the joint website of Finland’s environmental administration and analyzed with the help of qualitative content analysis. The 18 cases were divided according to the types of impacts found in the literature. Although all four impact types including collisions, displacement due to disturbance, barrier effect, and habitat change were considered significant in the EIAs, collisions were the most frequent. Very little comparable data about the significance of different impact types were found. However, collisions were the most researched impact type, which could have also contributed to the evaluation of its significance. The results corresponded to previous literature for the most part as Accipitriformes (diurnal birds of prey excluding falcons), according to several studies, are more vulnerable to the impacts of wind turbines. They were estimated to face significant impacts more often compared to other bird orders present in the materials. The reasonings between the cases were quite similar, despite the ambiguity of the significance assessment. In the cases where the reason for significance was stated, the level of protection of the species was the most common. The results also support the argument about how the impact type, the object of the impact, and the significance of an impact vary depending on the locations. The findings of this thesis suggest that scientific data is used at least partially in significance assessments. The results are useful in future research, developing EIA practices, and enhancing bird protection. Looking at significant impacts is relevant also in the future as the assessment of significance is not uncomplicated.
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(2020)Uterine leiomyomas are benign tumors originating in the smooth muscle cells of the uterine wall. Leiomyomas represent one of the most common tumor types in women affecting up to 80% of pre-menopausal women. Besides having extensive implications on women´s health through the numerous symptoms they cause, leiomyomas are a cause of remarkable financial burden worldwide. Bivalent promoters are defined by the co-occurrence of two histone modifications with opposite functions: trimethylation of lysine 4 on histone 3 (H3K4me3) and trimethylation of lysine 27 on histone 3 (H3K27me3). H3K4me3 is associated with promoters of actively expressed genes, whereas H3K27me3 is frequently found at promoters of silenced genes. The genes controlled by the bivalent promoters are reversibly silenced or expressed at low levels and remain poised for fast activation or full repression as a response to external cues. Bivalent chromatin is gaining more and more importance as new roles are identified in tumorigenesis and cell differentiation. Despite this, the vast majority of data available was obtained from cell lines, and not from human tissue. The aim of this thesis work was to map the genomic location of bivalent promoters in uterine leiomyoma and myometrium tissue, and to characterize the functions of bivalently-controlled genes in differentiated tissue. This would provide novel information about bivalent promoters’ distribution in human tissues and also their potential role in myomagenesis. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) against H3K4me3 and H3K27me3 was performed on fresh frozen tissue samples of uterine leiomyomas and corresponding myometrium. A promoter was defined as bivalent, if it showed overlap between H3K4me3 and H3K27me3 peaks within a 2 kb region of a gene’s transcription start site in all samples. Altogether 951 bivalent promoters were found in myometrium and leiomyoma. Strikingly, only 231 (24.3%) promoters were present in both tissue types, most bivalent promoters being tissue-specific. These findings indicated bivalent promoters regulating a substantial number of genes also in differentiated tissue and the presence of extensive alterations in bivalent promoter distribution during myomagenesis. Gene ontology analyses of the bivalently-controlled genes in myometrium revealed the highest score for developmental processes. Instead, for leiomyomas, the highest enrichment was detected in stem cell fate specification-related processes. The data presented in this thesis suggests that bivalent chromatin plays an important role during myomagenesis, as it undergoes a significant reorganization during the process. Future experiments will provide novel insights about the role for these changes, i.e.: if they underlie the process.
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(2020)Cornea is transparent layer of cells lying in front of lens. The corneal epithelium, a squamous epithelium, covers the ocular surface and ensures proper vision by preserving the integrity of the eye. Corneal epithelium is renewed continuously throughout life from a pool of stem cells (SC). There are still conflicting theories about the localization of stem cells required for the growth, renewal and maintenance of the corneal epithelium. Previous studies demonstrated that the limbus, located in the periphery of the cornea, serves as the stem cell niche (SCN) in adults. However, contrasting evidence from clonal analysis proposes that, in early postnatal life, renewal is fuelled by SCs located in the basal layer of the central cornea. There are alternate patterns of renewal in young and adult mouse cornea and that there is an important, transitional time frame called cornea maturation, when the adult patterns of gene expression, cell dynamics and tissue renewal are established. In the cornea, solid SC markers are still missing, yet studies on human limbal cells have suggested Bmi1 and C/EBPδ as limbal SC markers. There are, indeed, long-lived SCs in the central cornea and that the gene Bmi1 plays a role in these central corneal SCs. However, the physiological importance of these Bmi1+ cells remains obscure. The main aim of this project is to understand the fate and dynamics of these Bmi1+ cells and study the chronology of maturation of the cornea. In this study, I have also tried to correlate the growth of eye size with proliferation of corneal epithelial cells This study was conducted using few different kinds of transgenic mice (Mus musculus). To study the fate of Bmi1+ cells, two different mouse lines were crossed: Bmi1-CreER and ROSA26-LacZ. Mice carrying both alleles were used for lineage tracing experiments. Moreover, Hematoxylin-eosin staining was used to follow the eye morphology. Immunohistochemistry was performed to follow the chronology of maturation of the cornea, proliferation of corneal epithelial cells and the location of Bmi1+ cells in corneal epithelium. From this study, we can propose that cornea maturation is completed by the time of eyelid opening, which take place two weeks after birth. Krt19 is perfect for studying the chronology of the corneal epithelium, immunostaining of Krt19 separates the territory of limbus from central cornea enabling to distinguish limbus distinctly. Proliferating cells reside in basal layer of cornea. Bmi1+ cells found throughout the basal layer of the cornea that locally renews the corneal epithelium concluding Bmi1+ cells as the progenitor cells.
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(2019)Tiivistelmä - Referat - Abstract Background. Platelets are known to contain ample amounts of brain derived neurotrophic factor. Previous spectrophotometric studies carried out in Pia Siljander’s lab have shown that BDNF is secreted from activated platelets packed in extracellular vesicles. For this project we wanted to 1) confirm that BDNF really is secreted in extracellular vesicles (EVs)2) find out how the choice of agonist affected the BDNF cargo of the platelet derived EVs, and 3) find out if the BDNF is packed into EVs of certain densities rather than others. Methods. The platelets were isolated from platelet concentrates by size exclusion chromatography. The isolated platelets were then activated by thrombin and collagen co-stimulation (TC) and by Ca2+ionophore, respectively. The platelet activation produced extracellular vesicles (PEVs) which were isolated by differential ultracentrifugation. The isolated PEVs were then analysed by flow cytometry, ELISA and Western blot for EV typical membrane surface proteins and for their BDNF content. As we were interested finding out whether BDNF is enriched in PEVs to certain populations, density gradient centrifugation was performed. These samples were also analysed by Western blot and by ELISA. The size distribution and concentration of PEVs in all samples was analysed by Nanoparticle tracking analysis. Results and conclusions. This study confirmed that platelets secrete PEVs as a response to agonists. PEVs with higher BDNF concentration were produced using TC co-stimulation as compared to PEVs derived from the Ca2+ionophore. The result implies that BDNF is actively packed into PEVs for instance as a thrombogenic response. Based on the density gradient results it seems that BDNF was packed into certain population of PEVs with a density between 1.112 g ml-1 and 1.132 g ml-1 corresponding to a particle diameter of less than 500 nm. The finding that BDNF is actively packed into TC co-stimulation derived PEVs of a certain population is interesting from a theragnostic point of view, since EVs are likely to be key players in the development of new cell-based therapies. Had there been more time, it would have been interesting to optimize both the density gradient protocol and the ELISA analysis. This optimization of methods would make the process more efficient, less prone to sample loss, not to mention that there would be less intra-assay variation.
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(2018)This master’s thesis addresses the role of intermediary organizations in sustainability transitions, specifically in the field of energy. The thesis discusses how intermediary organizations can diffuse and support the development of novel sustainable socio-technical niche-innovations through experiments. Theoretically, this thesis draws mostly upon the sustainability transition literature, particularly strategic niche management theory. Empirically, this thesis focuses on a case study of joint procurement of solar power plants that was implemented as a part of “New and innovative low-carbon business generates competitive advantage for companies and municipalities” (Välke) project in South-western Päijänne during 2016. Välke is a sub-project of Carbon-neutral municipalities (HINKU) and therefore the case study of this thesis links to other similar experiments in the HINKU network. The material of the thesis was collected through 9 semi-structured interviews with different stakeholders involved in the experiment and by using pre-existing secondary material. The material was analysed by qualitative content analysis using an analytical framework adopted from a previous study. The findings show that intermediaries support niche development by aggregating, circulating and applying lessons learned between and within joint procurement experiments. This was done by producing and disseminating documents, but more importantly through personal contact between intermediaries. The network of intermediaries showed hierarchical features as the coordinator of HINKU, the Finnish Environment Institute (SYKE), maintained the repositories of the learned lessons and also formed a link between municipal intermediaries involved with the experiments. Also, during the experiments the more experienced higher profile intermediaries – mostly SYKE – provided assistance to lower profile municipal intermediaries. This support included providing knowledge, but also raising the confidence of lower profile intermediaries. Following, the lower profile intermediaries provided similar assistance to the participants of the experiments. However, the intermediary roles were not stable as lower level intermediaries were adopting some of the roles of the higher profile intermediaries after gaining experience during the experimentation. In order to support the Finnish solar niche, the intermediaries went beyond mere aggregating, circulating and applying lessons between and within experiments. They were actively initiating new experiments in adjusted formsin new geographical locations and advocating the niche. This was partially linked to the strategic nature of the intermediaries, as they were established to catalyse activities that would lead to mitigation of greenhouse gas emissions. However, this active support for a particular socio-technical innovation contradicted the pursuit of intermediaries to be viewed as neutral and credible actors. Partially as a consequence – but also because of the phase of solar niche development in Finland and lack of resource and interest – SYKE chose to withdraw from future joint procurements of solar power plants for private actors. However, SYKE was planning to utilize the governance innovation of joint procurements in order to support other niche-innovations with sustainability gains. The findings show that intermediaries can accelerate energy transitions, at least on a regional scale. They emphasize the importance of cooperation and personal contact between intermediaries and the ability of intermediaries to utilize governance innovations. Also, the findings support stronger inclusion of intermediaries in governance frameworks to hasten energy transition and achieve wider sustainability goals. However, the thesis shows that particularly public intermediary organizations have to work under unclear mandates.
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(2022)During the time of ecological crisis, it is important to find new approaches on how to produce welfare within planetary and ecological boundaries. Besides focusing on technical and societal changes I state in this thesis that there is a need for focus on human’s spiritual side to solve wide sustainability issues. Immaterial welfare is highlighted with people who are practicing spirituality, in this case meditation with Buddhist background. Enhancing immaterial welfare is important in the world in which overconsumption is dwindling biodiversity and planetary resources. In this master’s thesis I discuss how acknowledging peoples’ inner worlds is an essential part of holistic sustainability transition towards sustainable welfare and society. According to previous research spiritual practices such as meditation and mindfulness can support sustainable behaviour in many ways. People practicing meditation with Buddhist background try to live in a way that reduces their own suffering and suffering of living beings around them. When living in a mindful state it may be easier to make daily choices that are aligning with one’s values. Those who practice meditation may feel stronger connection to nature which can foster ecological behaviour. In this thesis I conducted nine interviews with nine meditation practitioners who are regularly practicing meditation with Buddhist background. I focused on their lifestyle that takes environmental aspects into account and how do they perceive that the meditation practice helps them to live in sustainable way. Central questions in the interviews included connectedness to nature, values and adapting and reacting to ecological crisis. I analysed the interviews using content-guiding theory analysis reflecting previous research. Meditation itself does not transform one to become more environmentally friendly but it can for example help to live by own values. Buddhist philosophy and spiritual lessons based in Buddhism play important roles in the meditation practices of the people I interviewed. Those lessons can motivate them to act respectfully towards all kinds of living beings and reduce their suffering. The people in this study live out environmentally friendly lifestyle in multiple ways. The interviewees highlighted many immaterial factors in their wellbeing from relationships to being in silence. In addition, spiritual practice can support them with difficult emotions that can arise from the news about the environment and climate. Altogether the sustainability science could benefit from considering human’s spiritual sides and the lost connection to self and the surrounding world.
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(2023)Three-dimensional (3D) cellular cultures have been shown to represent tissue formations and functions more accurately than two-dimensional (2D) cultures and have been successfully utilized more accurately in model organisms, e.g., to understand cellular modular functions. However, the applications in non-model organisms are limited, and to our knowledge have not been implemented in ectotherms. At an ecological scale, the technique can enhance our understanding by providing insights on cellular and tissue level molecular mechanisms. A potential implementation of this method in Atlantic salmon is to elucidate the molecular function of the vestigial-like 3 (vgll3) gene, which plays a central role in salmonid maturity, potentially by regulating energy allocation via regulating adipogenesis. In this thesis, a proof of principle study was implemented, where the feasibility of obtaining and maintaining a suspension 3D adipose tissue culture in Atlantic salmon (Salmo salar) was assessed. The harvested visceral white adipose tissue from around the intestinal tissue of mature Atlantic salmon (salmon past smolt stage) was first separated into stromal vascular fraction (SVFs) and mature adipose fraction (MAFs). SVFs contain preadipocytes (precursors of adipocyte cells) in addition to a variety of other cell types. MAFs are mature adipocytes. Both MAFs and SVFs were successfully maintained in-vitro for over four weeks. SVFs were then successfully differentiated into mature adipocytes, demonstrating the feasibility of studying adipogenesis in Atlantic salmon. Proof of this methodology and its further implications may help us to understand the cellular functions of vgll3 and may subsequently help to better understand its causal relation to the maturation process in Atlantic salmon.
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(2022)Bumblebees are important pollinators globally and especially in Fennoscandia, yet they are declining. The amount of natural vegetation in cities is decreasing with urbanisation. Hence suitable habitats for urban bumblebees are diminishing. Brownfields can be important habitats for bumblebees in cities because they resemble natural habitats. I studied bumblebee communities in urban brownfields. My main aims were to evaluate how local and landscape scale environmental factors affect the suitability of a brownfield to be a habitat for bumblebees. I also evaluated whether certain bumblebee functional traits are filtered in the brownfields. I expected that especially local characteristics and primarily the amount of flowering plant cover and the size of a site would affect bumblebee richness and abundance. I also expected the bumblebee communities to be characterised by generalist feeders. I collected bumblebees using line tracking in 15 brownfield sites in the city of Lahti and sampled bumblebees six times during the summer of 2020. The share of ground cover types within each site was estimated, as well as the share of different habitat types within a 300 m buffer zone around the sites. The data were used to analyse which local and landscape characteristics affect bumblebee community composition, species richness, and abundance in a brownfield site. Trait analyses were used to test the relationship between bumblebee traits and environmental factors. I showed that bumblebee abundance and richness were affected by local site characteristics but not landscape-scale factors. However, community composition was associated with landscape characteristics, including forest and commercial or industrial areas. Unexpectedly, the size of a brownfield site did not affect community composition, richness, or abundance. Functional traits were filtered in brownfield sites, especially the prevalence of a short proboscis, which is linked to a generalist diet in these bees. Brownfield sites are rich in bumblebees. Brownfields are suitable habitats for bumblebees regardless of the scale of urbanisation, and even small sites can host a diversity of bumblebees. As the amount of natural habitat in urban areas is decreasing, brownfields should be considered important habitats for bumblebees and other pollinators in urban planning.
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(2023)Human induced pluripotent stem cells (hiPSCs) are derived from adult differentiated somatic cells and reprogrammed to an embryonic-like state. Pluripotent stem cells can be differentiated into almost any somatic cell type by using directed differentiation methods, but the differentiation efficiency often varies depending on the cell type. hiPSCs and cells differentiated from them can be used as a disease model carrying the patient’s phenotype and genotype. Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease where both upper and lower motor neurons degenerate, leading to paralysis. There is no curative treatment for ALS, and it leads to the death of the patient in 3 to 5 years on average from the first symptoms. The most common genetic cause of familial ALS is a hexanucleotide repeat expansion in C9orf72-gene. ALS pathology is strongly linked to endoplasmic reticulum (ER) stress, which affects cell homeostasis and proteostasis, and leads to apoptosis when prolonged. The primary aim of this research is to characterize the differentiation of four hiPSCs lines towards lower motor neurons and to study the neuroprotective effects of cerebral dopamine neurotrophic factor (CDNF) and CDNF-derived peptide on ER stress and cell viability. This experiment used two control cell lines from two healthy donors and two patient cell lines from two different ALS patients carrying the C9orf72-mutation. To evaluate the efficiency of the differentiation towards motor neurons, molecular markers for pluripotent and neural progenitor cells as well as for maturated motor neurons were analyzed. Relative gene expression levels were measured from weekly time points with qPCR. Immunocytochemical (ICC) antibody staining was performed during differentiation. Endogenic CDNF levels were analyzed from differentiating cells at weekly time points and the effect of CDNF on Thapsigargin (TG) -induced ER stress in motor neurons was analyzed. In addition, cell viability was analyzed in TG-CDNF treatment. All pluripotent and progenitor markers were downregulated in differentiated cells, and the expression of the mature motor neuron markers was upregulated. Mature motor neuron markers were also expressed at the protein level. The endogenous CDNF levels were highest at the progenitor cell stage. The ER stress response was upregulated in TG-treated cells, and there were no differences between treatments against ER stress. Furthermore, TG and growth factor treatments differentially affected the viability of the control and patient cell lines. Treatment decreased viability in control cell lines and increased viability in patient cell lines. Pluripotent stem cells were successfully differentiated toward motor neurons. The differentiation was performed twice, and the results were similar on both individual biological repeats. Analysis of endogenous CDNF expression levels was performed for the first time on hiPSCs lines. In this study, CDNF or its derivate didn’t reduce ER stress but it influenced cell viability, especially in patient cell lines with growth factor treatment. In the future, TG-treatment could be optimized regarding timing and growth factor treatment, or the toxin could be changed to another ER-stress inducing toxin. In addition, the C9orf72 pathology should be identified in order to use differentiated motor neurons as a pre-clinical disease model.
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(2020)Calsyntenin-3 is a type I transmembrane protein, that is mainly expressed on the post-synaptic cell membranes. It belongs to the calsyntenin family that is part of the cadherin superfamily. Calsyntenin-3 consists of a cytosolic C-terminal region, a transmembrane domain and an extracellular N-terminal part, that consists of a laminin G-like domain (LNS) and two cadherin domains (CAD). Calsyntenin-3 is mainly expressed in the brain, but it can also be found in the heart, liver, pancreas, lung, skeletal muscle and placenta. Calsyntenin-3 has an effect on neurogenesis by affecting the development of excitatory and inhibitory synapses. It might also play a role in Alzheimer’s disease, as it has been found to be able to bind β-amyloid peptide, that is known to play a key role in the development of Alzheimer’s disease. Calsyntenin-3 acts as a synaptic adhesion protein, that binds to the post-synaptic neurexins with its extracellular region. However, the previous studies have contradicting results regarding the calsyntenin-3 domains that mediate the interaction between the calsyntenin-3 and neurexins. There is also disagreement whether calsyntenin-3 binds neurexin-α, neurexin-β or both. Because of these discrepancies, the aim of this master’s thesis study was to produce the calsyntenin-3 ectodomain constructs that contained either the two CAD domains, the LNS domain or all three domains, using baculovirus mediated protein production in insect cell cultures. These purified protein constructs were meant to be used for the determination of the binding domains. Unfortunately, only the purification of the calsyntenin-3 LNS domain was successful and the purification of the constructs, containing the CAD domains, was unsuccessful. A SEC-MALLS experiment, that was performed for the calsyntenin-3 LNS domain, revealed that it forms dimers in a solution, which is consistent with experiments performed with the LNS domain of human sex hormone‐binding globulin. The second aim of this master’s thesis study was to express the calsyntenin-3 ectodomain constructs on the surface of HEK293T cells and to test the binding between calsyntenin-3 and neurexins in a cell surface binding assay. The results of the cell surface binding assay indicated that the binding is mediated by the calsyntenin-3 CAD domains and that calsyntenin-3 binds to neurexin-α, but the binding to neurexin-β was not detected. However, the results from the cell surface binding assay were conflicting: the binding between the calsyntenin-3 full ectodomain construct and neurexin-α was not detected, but the binding was detected between calsyntenin-3 CAD ectodomain construct and neurexin-α. Therefore, the cell surface binding assay cannot be considered entirely reliable and should be repeated before making further conclusions.
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(2022)Breeding-dispersal and philopatry are important life-history traits when it comes to the ecology of animals. A number of factors such as sex, age, habitat stability, population density, predation and various environmental factors influence the movement patterns of species. Philopatry, in general, can be used by organisms as a predator avoidance strategy and to improve feeding efficiency. Dispersal on the other hand has been shown to help avoid inbreeding and competition within groups or between kin. Among the different types of dispersal and philopatry, breeding dispersal and site fidelity to breeding sites have been studied in many vertebrates. Many birds and some ungulate species have been the focus of these studies and have shown that breeding success influences site fidelity. Among ungulates, the reindeer genus (Rangifer tarandus spp.) however, has received little attention for this topic. A species of special conservational value is the wild forest reindeer (Rangifer tarandus fennicus), which is a rare, and near-threatened subspecies of reindeer living in Finland. Knowledge of factors influencing the dispersal and site fidelity for this species is lacking but has important implications for the conservation and management of this and other vulnerable species. In my thesis I investigated the philopatry of wild forest reindeer females from eastern Finland and tested if the calving site fidelity was influenced by breeding success, predator pressure and the female’s age. Given the high densities of predators in the study area (Kainuu) and thus high predator pressure on reindeer, I expected (i) the philopatry of the wild forest reindeer female’s to be stronger in areas with higher predator pressure but (ii) higher dispersal movement when wild forest reindeer females had no breeding success the previous year. Additionally, I expected (iii) the dispersal distances of wild forest reindeer females to be negatively correlated with their age. For this study I used long-term GPS monitoring data of 53 collared wild forest reindeer females, which were followed for varying periods (2-6 years) between 2010-2021 from Eastern Finland. I found that the inter-year distances between calving sites per female had a median distance of 2.84 km, confirming that female wild forest reindeer show philopatry to calving sites, as do other reindeer subspecies. Even though the movement ranged from 4.8 m to 36.99 km, showing substantially longer dispersal for some individuals. The model outcomes indicate some association between predation pressure and site fidelity, and reduced philopatry following calf mortality, although none of these associations were significant. The age of the mother did also not show any significant influence on a female’s site fidelity. Nonetheless, these results would suggest that a mother's choice to leave or return to the same calving site might be influenced by the previous year's calf mortality but more complex variables like anthropogenic disturbances, environmental factors, as well as intrinsic factors and the physical condition of the mother most likely also play a role in this.
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