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(2016)Epidermolysis bullosa (EB) is a group of hereditary skin disorders caused by mutations in the genes that code for adhesion molecules in keratinocytes. The symptoms of the disease include blisters and erosions in the skin as well as abnormalities in the mucosal membranes, nails and tooth enamel. Depending on the causative mutation the severity of the disease ranges from mild to lethal. This master s thesis was carried out in professor Hannes Lohi s canine genetics research group. It is a case study aiming to identify the genetic cause of EB present in Central Asian shepherd dogs. Furthermore, the mode of inheritance, frequency of the mutation in the breed and the effect of the mutation on the tissue were also examined. Primary research material included blood and tissue samples from a family of Central Asian shepherd dogs. Additional samples were obtained from other Central Asian shepherd dogs as well as from dogs of closely related breeds. All dogs included in this study are owned by private persons, and participation in this study was voluntary. The research methods used in this study included both wet laboratory experiments and bioinformatic in silico procedures. The genome of one affected dog was sequenced in order to identify the gene causing EB, and data from the sequencing was filtered with multiple programs according to recessive model. The model was decided after analyzing the pedigree of the affected dogs. After finding the likely causative gene the mutation was validated in a larger cohort with Sanger sequencing. Protein expression in the tissue of affected dogs was also studied using immunofluorescence staining. As a result of this study, a new mutation causing recessive dystrophic EB was identified. The mutation is specific to Central Asian shepherd dogs. Affected dogs have a homozygous mutation in the COL7A1 gene, which codes for collagen VII α1 protein. The mutation causes a premature stop codon in the mRNA sequence, which results in abnormal protein production and separation of skin layers. The frequency of the mutation allele in the sample is approximately 18 % and more than a fourth of the dogs in the sample are carriers. Based on the pedigree analysis, the mutation is relatively new and it is only found in a small population. The disease can be prevented from becoming more common in the breed with the help of a gene test, and the test will be available in the commercial MyDogDNA gene test panel.
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(2021)Epigenetics is the study of changes in gene function without affecting the DNA sequence. Epigenetics studies the effects of the environment and behavior on the genome. Researchers have been able to detect several epigenetic modifications such as –DNA methylation, histone acetylation, and microRNA-associated gene silencing. Changes in the epigenome are essential for proper cell function and normal development and can also be induced by environmental factors. Stress is defined as a biological response to physiological and psychological demands which can affect cellular homeostasis. Factors such as prenatal life stress can affect gene function without directly altering the DNA nucleotide sequence. Elevated levels of stress can immobilize with the ability to impair cognitive function. There is evidence that suggests the involvement of epigenetic regulation in disorders such as addiction, depression, schizophrenia, and cognitive dysfunction. Therefore, this systematic review discusses recent findings of the role of epigenetics in prenatal exposure to stress. To achieve this, the thesis will cover different subtopics from genetics, neurobiology, and diseases, neuroscience, biological psychiatry, life sciences, medicine, behavioral brain research, biochemistry & molecular biology, as well as neuroendocrinology. Research questions are 1) Is there an association between epigenetics and prenatal stress? 2) What kind of mechanisms have been found? 3) What kind of techniques have been used in the identification of potential epigenetic mechanisms? What genes are associated with these epigenetic changes?. This study followed the "The Preferred Reporting Items for Systematic Reviews and Meta-Analyses" (PRISMA) guideline checklist. Eligibility criteria and search terms where be selected and documented to offer the widest range of articles covering the subjects of this study. A literature search was done using PubMed/Medline, Google scholar, and gray literature. The last sample comprised 59 articles. Data were extracted so that the participants, intervention, comparisons, and outcomes were included. The literature search conducted in this systematic review identified a few findings. First is that the majority of animal and human studies found a significant or moderate association between epigenetics and prenatal stress. Second, DNA methylation is the most studied epigenetic mechanism in maternal exposure to stress Third, genome-wide studies were more common in human studies than in animals and the most widely used method used is Infinium HumanMethylation450 Bead Chip. However, the common methods used in human and animal studies are most likely because of the small sample size and causation cannot be determined. Finally, NR3C1 and FKBP5 genes were the most studied in human studies where they showed the strongest association between prenatal stress and epigenetic modifications. While in animal studies, the most studied genes were Bdnf and Dnmt1 as they showed a significant methylation level after maternal prenatal stress exposure. In conclusion, maternal prenatal stress could trigger epigenetic alterations in neonates in both animals and humans. This holistic review detailed and evaluated locus-specific and studies exploring current knowledge about associations between maternal prenatal stress and epigenetic changes.
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(2023)The intestinal stem cells (ISCs) adapt in response to environmental factors and continually proliferate to renew the mammalian intestinal epithelium due to its rapid turnover. Overall, intestinal homeostasis is maintained by the differentiation and self-renewal of ISCs, which are regulated by different mechanisms, including epigenetic histone modifications. Earlier studies in the host laboratory have shown that the histone methyltransferase Su(var)3-9 is essential in the nutrient-induced activation of intestinal stem cells. Su(var)3-9 specifically trimethylates histone H3 on lysine 9 (H3K9me3), which is a repressive histone mark, responsible for transcriptional silencing at heterochromatin regions. It influences stem cell maturation, lineage specification, and many other cellular processes. However, the precise mechanisms behind its function in ISCs remain unknown – that knowledge is important for understanding the development of many diseases, including cancer and metabolic disorders. This thesis aimed to investigate the distribution of the heterochromatin mark H3K9me3 in the intestine with an emphasis on ISCs, using the Drosophila midgut and mouse intestinal organoids as models. Confocal microscopy was used together with cell-type-specific fluorescent staining, to obtain the expression of the H3K9me3 specific histone methyltransferase Su(var)3-9, in the midgut. An antibody was used for the detection of H3K9me3 distribution along the anterior/posterior axis in Su(var)3-9 overexpressed flies. Additionally, DNA adenine methyltransferase identification (DamID) was applied in order to find target genes of the H3K9me3 regulation in the genome with the specific chromo domain of M-phase phosphoprotein 8 (MPHOSPH8) that binds to H3K9me3. The number of lineage-labeled differentiated enterocytes was shown to be locally higher in the Su(var)3-9 overexpressed flies compared with the control, although the flies were on starvation without nutrient-induced activation. Moreover, the number of lineage-labeled progenitor cells was not remarkably altered between the samples. However, the intensity of H3K9me3 was significantly higher throughout the whole midguts in the Su(var)3-9 overexpressed flies in comparison to the control. According to one replicate, the DamID in mouse intestinal organoids revealed that the peaks of H3K9me3 were divergent between the samples grown in different conditions. The first sample was assumed to contain more ISCs, whereas the other one was assumed to contain more differentiated intestinal cells. According to my results, the Su(var)3-9 overexpression drives the stem cells against the differentiation of enterocytes. Furthermore, the MPHOSPH8 chromo domain in the organoids was successfully applied in DamID; thus, more replicates should be prepared for additional analysis, because I found several potential target genes of H3K9me3. In the future, it is important to further study the epigenetic regulation of ISCs, for applying the epigenetic marks as targets for the treatment of many human pathophysiological conditions, such as cancer, obesity, and metabolic disorders.
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(2019)In this master’s theses, Finnish biology teachers’ needs for material for continuing education and educational material for upper secondary school in epigenetics were studied. Two sets of educational materials, continuing educational material for teachers and educational material for upper secondary school teaching was produced accordant with the results. Epigenetics is used to describe stable alterations in gene expression which do not consider mutations in DNA sequence. DNA methylation, histone modifications and chromatin remodelling are the main epigenetic mechanisms to affect gene expression. Epigenetic modification patterns can alter de novo, or they can be originated by some environmental factor. Epigenetic regulation was introduced as a new subject matter in National Core Curriculum for General Upper Secondary Schools 2015 in Finland. Epigenetics is a relatively new branch in biology, and as a result many teachers have not studied the subject matter at the university. Continuing educational material is needed to update their knowledge. Biology teachers’ needs for material in epigenetics were studied with a survey which was distributed to the Biology and Geography Teachers’ Union’s e-mail list subscribers. Data was analysed qualitatively and quantitatively. In order to produce continuing educational material for teachers, literature regarding teacher competence, adult education and Finnish biology teachers’ subject expertise was examined. The concept of constructivist learning, and conceptual change were applied in the production of educational material for upper secondary school teaching. Relevant scientific literature in epigenetics was gathered and used to produce both sets of materials. In the study survey, the teachers reported specific individual educational needs which were acknowledged in the production of both sets of materials, alongside literature listed earlier. The survey showed that one of 33 biology teachers had studied epigenetics at the university, 20 of 33 teachers independently and 13 of 33 hadn’t studied epigenetics at all. The extent of the teachers’ studies in epigenetics was most often elementary and the main motivation to study epigenetics independently was a desire to handle the basics. The most common resource teachers used to study epigenetics was non-scientific magazines. Among the teachers who had not studied epigenetics at all, lack of time was the most common reason mentioned. However, 14 teachers described epigenetics as an important subject matter. Three teachers reported that they lack the expertise in teaching epigenetics and three felt that textbooks don’t offer support in teaching epigenetics. Online material and expert lectures were the most common continuing education material forms requested. Regarding the content of the continuing educational material for teachers, the most common requests were that the material should include the basics of epigenetics and practical examples. The form of educational material for upper secondary school teaching was most commonly requested to be online text or educational video. Regarding the content of the educational material for upper secondary school teaching, the most common requests among teachers were a summary of the theory of epigenetics and practical examples. The continuing educational material for teachers produced in this thesis consists of an introduction part and four parts about different subjects in epigenetics. The titles of the parts are: 1) What is epigenetics? 2) Molecular mechanisms of epigenetic gene regulation 3) Epigenetic gene regulation and 4) Epigenetic inheritance. The material was designed in a way that texts 3) and 4) are possible to comprehend without studying text 2) about molecular mechanisms of epigenetic regulation. The educational material for upper secondary school teaching consists of seven parts. At the beginning there is an introduction to teachers which is followed by six separate parts for students. Each part has a “Rehearse before reading”-box which introduces students to the subject and encourages rehearsal of biological concepts and vocabulary which are necessary for comprehending each part. After each part there are questions which test students’ learning as well as encourage to apply freshly acquired knowledge about epigenetics to other biological contexts. Titles for different parts are: 1) What is epigenetics? 2) Epigenetics and nutrition 3) Epigenetics and exercise 4) Epigenetics and mental health 5) Epigenetics and tortoiseshell cats and 6) Epigenetic inheritance. The material has been designed in such a way that the parts can be taught and learned separately. References are provided at the end of both material sets. Both materials produced in this thesis meet the teachers’ requests revealed in the survey. The form of the continuing educational material for teachers is online material, which was one of the most common requests among the teachers who answered the survey. The contents of the material correspond to the teachers requests as well, since most requested contents were the basics of epigenetics and practical examples. The educational material for upper secondary school teaching was requested as online material with a summary of the theory of epigenetics and practical examples, and all these requests were met. Both materials were produced considering relevant theories on pedagogy and adult education. Results of this study cannot be applied nationally in Finland since the sample size was small. Therefore, national relevance of the materials cannot be predicted. Predictions about the impact of the materials on teachers’ and students’ understanding about epigenetics cannot be made either, since learning is an active process which requires effort from the learner. However, a strong case can be made for the produced material, because materials include relevant information and their pedagogic choices can be justified by the literature. This thesis uncovered many questions for future research. For example, the efficacy of the materials could be studied in a practical classroom situation. Other possible questions for research or study designs could be about biology teachers’ expertise and continuing education in Finland.
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(2023)Lichens are sensitive organisms widely used for environmental biomonitoring. Urban environments have been under heavy pollution, especially sulphur dioxide and nitrogen oxides, due to human activity which has led to the disappearance of lichens in city centres. Regulations and technological changes have led to cleaner air and less deposition of pollutants, especially sulphur dioxide on the vegetation in both rural and urban areas. This in turn has led to recolonization of lichens in former lichen deserted areas. In this study epiphytic macrolichens on park maples were surveyed using simple tree-based random sampling in three parks in Helsinki, and in one park in Loviisa, Siuntio and Raasepori each. The sampling and surveying methods were selected based on the SFS standard “Ambient air. Biomonitoring with lichens. Assessing epiphytic lichen diversity”. Species identification took place on site and in Botanical museum (Finnish Museum of Natural History). The results from parks in Helsinki were used to estimate if lichens have recolonized the trees. In addition, the results from the other Uusimaa municipalities were used to assess how different is the lichen species assemblage when comparing the relatively more polluted region of Helsinki to the less polluted regions in Uusimaa. The study found that pollution levels in Helsinki have declined enough to enable recolonization, of which there have been signs already in 1990s and 2000. The study used lichen diversity value of defined functional groups as one of the statistical methods which gave new information about how the species tolerance or sensitivity to pollutants shapes the recolonization. Comparison between the study areas in Uusimaa region revealed that concentrations of nitrogen oxides steer lichen species assemblage in Helsinki. Lichen surveys in Helsinki are scarce. This study brings topical information about the lichen situation in Helsinki, and it uses an as yet relatively unknown method to extract information from lichen assemblage. Regular, comparable lichen surveys are needed to further research the pressure that human activities cause on urban nature. Such time series would help to monitor both the urban nature loss and the impact of climate change on the urban nature.
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(2013)The trend of energy policy in European Union as well as in international context has lately been to increase the share of renewable biofuels. The causes for this are global warming, shrinking reserves of fossil fuels and governments' aspiration for energy independence. Microalgae have shown to be a potential source of biofuels. Though cultivation of microalgae has a long history, has production for fuel yet been unprofitable. Production has become more effective as cultivation has shifted from open ponds to controlled photobioreactors but to achieve effective cultivation methods substantially more understanding on the ecophysiology of microalgae is needed. The aim of my thesis was to research the optimal light intensity and temperature of photosynthesis for three microalgae (Chlorella pyrenoidosa, Euglena gracilis and Selenastrum sp.), which are the main parameters limiting the level of photosynthesis in nutrient rich environments such as photobioreactor. The research strains were incubated in eight light intensities (0,15-250 µmol m-2 s-2) and in 5-6 temperatures (10-35 °C). Photosynthetic activity was determined with radiocarbon method which is based on the stoichiometry of photosynthesis. The purpose of radiocarbon method is to estimate how much dissolved carbon dioxide do the algae assimilate when photosynthesizing. In the method the algae are incubated in light and dark bottles where certain amount of radiocarbon (14C) has been added as a tracer. The algae fix 14C in the proportion to available 12C. 14C method has become the most common way to measure the photosynthesis of microalgae. All of the algal strains grew in 10-30 °C but C. pyrenoidosa was the only one which grew also in 35 °C. The data was analyzed by fitting them with two photosynthesis-light intensity relationship models and one photosynthesis-temperature relationship model and as a result values of essential parameters, i.e. optimal light intensity (Iopt) and temperature (Topt) for photosynthesis, could be estimated. The model which gave the best fit was chosen to describe the photosynthesis-light intensity relationship. The optimal light intensity for C. pyrenoidosa ranged between 121–242 µmol m-2 s-2 and optimal temperature was 15 °C. Corresponding values for E. gracilis were 117-161 µmol m-2 s-2 and 24,1 °C, and for Selenastrum sp. 126-175 µmol m-2 s-2 and 16,7 °C. Q10-values were also determined. With all research strains, the level of photosynthesis increased as light intensity and temperature grew until optimal values were reached. The strains tolerated higher light intensities in warmer temperatures but after reaching the optimal temperature, the level of photosynthesis did not increase any more with elevating temperature. Robust algal strains, i.e. strains, that are most adaptable in terms of light intensity and temperature, are the most prominent ones for biofuel production. From these research strains the most adaptable strain in terms of light intensity was C. pyrenoidosa and in terms of temperature Selenastrum sp. C. pyrenoidosa had superior carbon fixation rate in relation to cell size. Therefore it can be concluded that C. pyrenoidosa is the most suitable algal strains for biofuel applications of the strains assessed here.
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(2014)Mikrolevien käyttöä biodieselin raaka-aineena on viime vuosina tutkittu paljon niiden ollessa hiilineutraali vaihtoehto fossiilista alkuperää oleville uusiutumattomille polttoaineille. Tämän lisäksi ne ovat myös ekologisesti ja eettisesti kannattava uusiutuvan energianlähde ja tukevat pyrkimystä kohti energiaomavaraisuuden saavuttamista. Mikrolevien todellista mikso- ja heterotrofiaa on tutkittu toistaiseksi vähän eikä niiden hyödyntämän hiilen määrästä ole tarjolla tutkimustietoa. Mikroleväkantojen todellisen mikso- ja heterotrofiakyvyn selvittäminen mahdollistaa kantojen kustannustehokkaamman kasvatuksen, koska mikso- ja heterotrofiaan kykenevät kannat voivat hyödyntää kasvussaan heikompia valaistusolosuhteita korvaamalla ne osittain tai täysin orgaanisilla hiilen lähteillä. Miksotrofisten leväkantojen käytöllä voidaan myös saavuttaa kasvatuksissa korkeampi solusaanto sekä solujen korkeampi lipidipitoisuus. Heterotrofisten kantojen käytöllä voidaan taas kiertää monia mikrolevien kasvatukseen liittyviä ongelmia. Toteutin tutkimukseni kolmella mikroleväkannalla: Selenastrum sp., Chlorella pyrenoidosa ja Euglena gracilis. Tein aluksi kasvatuskokeita, joissa kasvatin kaikkia leväkantoja auto-, mikso- ja heterotrofisissa olosuhteissa. Selenastrum sp. – ja Chlorella pyrenoidosa – kannan kasvatuksissa käytin epäorgaanista COMBO – kasvatusliuosta. Euglena gracilis – kannalla käytin epäorgaanista AF6 – kasvatusliuosta. Tutkin leväkantojen potentiaalista kykyä mikso- ja heterotrofiaan glukoosin ja asetaatin lisäyksen avulla. Seurasin leväkantojen kasvua solumäärän kehityksen kautta. Kasvatuskokeiden perusteella tein päätöksen ottaa kaikki käyttämäni leväkannat mukaan varsinaisiin mikso- ja heterotrofiakyvyn mittauksiin sekä käyttää ainoastaan glukoosia orgaanisen hiilen lähteenä, sillä leväkannat menestyivät heikosti asetaattikasvatuksissa. Mikso- ja heterotrofiakyvyn mittaamiseen käytin 14C-menetelmää. Kaikkien leväkantojen kyky hyödyntää asetaattia (pitoisuus 5 g l-1) oli yleisesti heikompi verrattuna niiden kykyyn hyödyntää glukoosia (pitoisuus 5 g l-1). Kasvatuskokeissa Selenastrum sp. – kannalla vaihtelu oli eri käsittelyiden välillä solumäärän kehityksen ja kasvunopeuden suhteen suurinta. Euglena gracilis – kannalla vaihtelu solusaannon kehityksen ja kasvunopeuden välillä oli pienintä kasvatusten välillä. Selenastrum sp. – kannan miksotrofisesti ottama hiilen määrä oli suurin muihin miksotrofisesti kasvatettuihin leväkantoihin verrattuna. Heterotrofisesti otetun hiilen määrä oli suurin Euglena gracilis – kannalla. Tutkimukseni merkittävin tulos on käyttämieni leväkantojen todellisen mikso- ja heterotrofiakyvyn todistaminen. Laajemmat lisätutkimukset leväkantojen todellisesta mikso- ja heterotrofiasta ovat kuitenkin tarpeen muun muassa mikroleväbiomassan käyttösovellusten kehittämisen ja käyttöönoton sekä vesiekosysteemien hiilenkierron tuntemisen kannalta.
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(2019)Diesel, which belong to the fossil fuels, have been exposed recently because of global warming and because of decrease of known fossil fuel reserves. It has been estimated that reserves of fossil fuels will last next 40-50 years. Burning of fossil diesels will cause not only carbon dioxide emissions but also particle and metal emissions. There have been attempt to develop alternative energy sources. Growing alternative, which have came to the market, is renewable diesels, which can be produced from many sources such as reeds and biowaste. Biodiesels differ from fossil diesels by their chemical structure. Contrary to fossil diesel, completely renewable diesels do not contain aromatic compounds and they burn more purely. Diesel might end up in soil in accidents. Behaviour of fossil diesels in a ground is well known, however, the behaviour of renewable diesels is not known so well. Even though solubility of renewable diesels is similar with fossil diesels, renewable diesels may have different behavior due to different chemical structure compared with fossil diesels. Soil removal and taking the soil to be cleaned up is the most popular way to clean diesel contaminated soil resulted from diesel leaking. Alternative way to clean diesel contaminated soil is to use bioremediation where the microbes are used. In bioremediation microbes are added to the soil or activity of the microbes is boosted by improving living conditions of microbes by adding nutrients and oxygen. In this master thesis spreading of three different diesels qualities in soil and with water in laboratory were viewed. Results of the laboratory experiment were compared to the result of Katariina Lahti-Leikas’ lysimeter experiment in Jokimaa. Diesel qualities used in experiment were completely fossil EN590, partly renewable ProDiesel and completely renewable NEXBTL. Experiment were executed in soil columns in laboratory conditions where pure lysimeter sand were exposed to diesel. Biostimulation were made to half of the soil columns using urea that every diesel had natural decomposition and biostimulation. Soil columns were watered and hydrocarbons C10-C40 from collected water below the column were analysed. In addition, soil samples were collected and hydrocarbons C10-C40 were analysed. The pH of the soil and water samples were followed throught the experiment. Biostimulation decreased concentration of hydrocarbons in the water in every diesel quality. Biggest concentration were in water from NEXBTL columns which move in soil mostly in NAPL. In soil samples there was not the same kind of decrease in hydrocarbon concentration as in water samples. Diesel moved from the upper part of the soil columns to the lower part of soil columns during the experiment. The reason why biostimulation did not decreased the hydrocarbon concentration in soil is probably because the experiment period was too short. Other things to affect the result are probably wrong comparison of nutrients or lack of oxygen, which have slowed down decomposition of hydrocarbons. The results of this study are consistent with the results of Katariina Lahti-Leikas’ lysimeter experiment in Jokimaa.
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(2020)Haitalliset vieraslajit aiheuttavat muutoksia luonnon monimuotoisuuteen, ekosysteemien toimintaan sekä niiden tarjoamiin ekosysteemipalveluihin vaikuttamalla esimerkiksi elinympäristöihin, ravintoketjuihin ja kilpailuasetelmiin. Haitalliset vieraskasvit voivat syrjäyttää alkuperäisiä kasveja kilpaillessaan niiden kanssa tilasta ja resursseista. Lisäksi vieraskasvit voivat heikentää paikallisten lajien elinmahdollisuuksia muokkaamalla ekosysteemejä niille sopimattomiksi. Komealupiini (Lupinus polyphyllus) on yksi yleisimmistä vieraskasveista Suomessa. Tämä kansallisesti haitalliseksi vieraslajiksi luokiteltu kasvi on levinnyt jo vuosikymmenien ajan erityisesti tienpientareilla ja joutomailla. Kasvustojen ikääntyminen voi muuttaa vieraskasvin vaikutuksia elinympäristönsä alkuperäiseen kasvillisuuteen, mutta komealupiinin kohdalla ikääntymisen vaikutuksista ei ole tietoa. Tämän pro gradu -tutkielman tavoitteena oli selvittää eri-ikäisten komealupiinikasvustojen vaikutuksia alkuperäiseen kasvillisuuteen sekä yhteisötasolla että eri lajiryhmissä. Tutkin myös kasvuston ikääntymisen vaikutusta komealupiinin peittävyyteen. Kartoitin putkilokasvilajistoa Päijät-Hämeen alueella 19 tutkimuskohteessa, jotka olivat maaperältään hiekkaisia tai soraisia. Tutkimuskohteet jaettiin komealupiinikasvuston iän mukaan kolmeen luokkaan: 1) nuoret (alle 6 v vanhat), 2) keski-ikäiset (noin 10 v) ja 3) vanhat (yli 13 v). Eri-ikäisten kohteiden kasviyhteisöjä vertaamalla tutkittiin komealupiinikasvuston ikääntymistä ja sen vaikutuksia muuhun kasviyhteisöön. Komealupiinin vaikutusten yleistämiseksi esiintyneet putkilokasvilajit luokiteltiin kymmeneen ryhmään suotuisten elinympäristöjen sekä elinympäristöjen ravinteikkuuden ja kosteuden mukaan. Aineiston analysointiin käytettiin ei-metristä moniulotteista skaalausta (NMDS) sekä yleistettyjä lineaarisia sekamalleja (GLMM). Komealupiinilla ei ollut huomattavaa vaikutusta kasviyhteisöjen rakenteeseen tai lajimääriin. Komealupiini vähensi kuitenkin kuivien elinympäristöjen lajien sekä generalistien peittävyyksiä. Komealupiinin peittävyys ei vähentynyt kasvuston ikääntyessä. Komealupiini ei vaikuttanut kovin voimakkaasti elinympäristöönsä, mikä johtui todennäköisesti siitä, että komealupiinin peittävyydet olivat melko vähäisiä (keskimäärin 35 % ± SD 12). Tämän tutkimuksen perusteella komealupiinin vaikutukset tälläisessä kuivassa elinympäristössä eivät ole kovin voimakkaat, mikäli sen peittävyys on vähäinen. Luultavasti komealupiinin haitallisuus liittyykin juuri sen kykyyn muodostaa tiheitä kasvustoja. Komealupiinin torjunnassa olisikin tehokkainta keskittyä niihin alueisiin, joissa komealupiini muodostaa tiheitä kasvustoja. Toisaalta huomiota tulisi kiinnittää myös paikkoihin, joissa kasvaa etenkin uhanalaisia kuivien elinympäristöjen lajeja sekä lajeja, jotka pärjäävät heikosti lajienvälisessä kilpailussa.
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(2022)Finnish matriculation examination in biology transitioned into a digital examination from traditional pen-and-paper examination in spring of 2018 as a part of larger process aiming to digitalize the entire matriculation examination. Tthe requirements for the exam have also changed: in addition to subject knowledge, the digital examination also requires the candidate to also be master the digital skills outlined in the Finnish high school curriculum, for example the use of image- and data processing programs. It has been suggested hat candidates from higher socioeconomic background benefit more from digital skill teaching. It has also been shown that some teachers overestimate the digital skills of the students, omitting parts of the teaching process that are integral for learning. Tthis study examines whether the matriculation examination answers requiring digital skills differ from questions that can be answered without advanced digital skills. Statistically significantly worse performance in questions requiring digital skills might indicate digital skill teaching that is insufficient compared to the skill level required in matriculation examination. Insufficient teaching may disproportionately affect those from lower socioeconomic background. The data of this study consists of 30 full-length answers from matriculation examinations of spring 2018, autumn 2018 and spring 2019, for a total of 90 full-length answers. The data was a randomized sample provided by Ylioppilastutkintolautakunta (Finnish Matriculation Examination Board). The differences were analysed with Mann-Whitney U-test and Fisher’s z-transformation. The study found that questions requiring digital skills were statistically significantly more popular than questions that didn’t require digital skills. Although the level of cognitive processing outlined by Bloom’s Taxonomy was lower in questions requiring digital skills, there was no statistically significant difference in the success (measured by attained score) between the answers. According to results, the digital proficiency of the candidates was at a sufficient level to answer to the questions.. The study also speculates on factors that could explain the observed differences in answer popularity, cognitive depth and difficulty level of the questions.
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(2021)Rapid environmental changes over the last 100 years have led to substantial range shifts across taxonomic groups. Understanding what facilitates successful shifts is important for predicting ecological consequences and planning efficient conservation actions. Interestingly, the very process of range expansion can affect the success of the shift by causing genetic changes in the expanding populations. Theory predicts that without sufficient gene flow, repeated founder events and strong genetic drift can result in allele frequency gradients and loss of genetic diversity along the expansion axis. Empirical studies testing these expectations in environment-driven range shifts are still relatively scarce, and how range expansions affect genetics in highly mobile species remains unclear. In this study, I investigated the genetic consequences of a recent range expansion in a long-distance migratory passerine, the reed warbler (Acrocephalus scirpaceus). Utilizing genome-wide data from restriction site-associated DNA sequencing (RAD-seq), I studied whether the expansion was reflected in either population structure or genetic diversity of the recently established Finnish range edge population. Despite philopatry and genetic differentiation to the range core populations, principal component analysis (PCA) and a model-based Bayesian clustering approach (fineRADstructure) revealed a lack of spatial population structure along a putative colonization route. Levels of genetic diversity, based on expected heterozygosity, nucleotide diversity, and private allele count, were found to be very similar between range edge (Finland) and range core (Central Europe). The results likely indicate high levels of gene flow both within the new population and across greater spatial distances during or after the range expansion. Due to a detected sequencing batch effect, however, the exact diversity estimates must be considered preliminary. These findings suggest that species with high enough dispersal propensity may escape the predicted genetic costs of range expansions, retaining high levels of genetic variation at range margins. This study provides valuable insights for understanding range shifts in mobile taxa, and highlights the need to investigate further the traits of species that enable the preservation of evolutionary potential during range shifts.
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(2022)Schizophrenia is a debilitating psychiatric disorder associated with reduced life expectancy. The biological mechanism of schizophrenia is nebulous; however, many findings point to the central nervous system and neurons, where a reduction in dendritic spines has been indicated by previous research. The genetic findings support the involvement of synapses in the pathogenesis of schizophrenia. To study the biological properties stemming from genetics, relevant model systems and efficient methods are needed. Induced pluripotent stem cell (iPSC) technology offers a robust method for modeling the biological processes underlying schizophrenia. Somatic cells, e.g. fibroblasts, can be reprogrammed back to a pluripotent state resembling embryonic stem cells, and further differentiated into any cell type of the body, which might not be otherwise accessible. This allows establishing and characterizing neuronal cultures from patient and control cell lines, potentially revealing biological differences associated to the disease phenotype. The field of schizophrenia research has adopted iPSC technology and multiple studies have been conducted. These include assessments of synaptic density in the produced neuronal cultures, many of which reported decreased density associated with schizophrenia. In this thesis, a modified version of Nehme et al. (2018) protocol was used to differentiate iPSCs into neurons in co-cultures with human iPSC-derived astrocytes. The overarching aim was to construct an immunocytochemistry (ICC) -based assay to measure synaptic density in the produced co-cultures. First, suitable markers for characterization by ICC were tested and selected. The markers were selected to inform about neuronal identity, maturity, and synapses of the differentiated neurons. Next, the culturing conditions were optimized regarding the cell density and coating of the culturing wells. Finally, to estimate the utility of the assay, a pilot study was performed with three cell lines derived from a healthy control and a monozygotic twin pair discordant for schizophrenia. iPSCs from these cell lines were differentiated into neurons in co-cultures with astrocytes, and then characterized with ICC using selected markers and image analysis software. The synaptic density was quantified for each cell line. The performance of the assay was evaluated with analysis of variance (ANOVA) and restricted maximum likelihood model (RELM). An assay to quantify synaptic structures in mature neurons was established. The average synaptic density for all cell lines was approximately 1 synapse per 100μm of neurite. Analysis of the data produced with the assay revealed a notable batch effect and technical variation. This suggests that further optimization is needed to reduce variance from undesired sources. The pilot data suggests that the differences in synaptic density between cases and controls may be modest, further highlighting the need for minimizing noise in the assay to improve signal to noise ratio. However, indicated by power analysis, large sample sizes are needed to identify meaningful differences between cases and controls. In light of these results, more attention should be drawn to the methodology in the field of iPSC-based studies, as the principals of the assay constructed here were similar to other synaptic assays used in previous publications.
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(2023)The group has identified two rare, previously uncharacterized missense variants in the YBX3 gene in a Finnish patient presenting with an unusual form of nemaline myopathy. The patient also inherited two biallelic TPM3 variants, one RYR1 variant from the father and one SRPK3 variant from the mother. TPM3 and RYR1 are known nemaline myopathy causing genes and the other variants identified in the patients, including the YBX3 variants, are thought to have a modifying effect on the phenotype. YBX3 encodes Y-box binding protein 3 (YB-3) and, YB-3 is a member of the Y-box binding (YB) protein family, that in addition to YB-3 consists of YB-1 and YB-2. The YB-proteins have mainly been studied in the context of cancer, with most studies focusing on YB-1. Studies indicate the ability of YB-proteins to compensate for the loss of one homolog suggesting functional redundancy between YB-3 and YB-1, and YB-3 and YB-2. Compared to its homologs, YB-3 is highly expressed in skeletal muscle. The aim of this thesis was to try out a new cell culturing method when investigating the role of YB-3 in the differentiation of myoblasts into myotubes. MSY-3 is the murine orthologue of YB-3. MSY3-knockdown mouse C2C12 myoblast lines were established using GIPZ lentiviral short hairpin constructs and by selection with puromycin. The success of transfection was determined using qPCR. The myoblasts were differentiated for 20 days on a gelatin hydrogel surface to support long-term culture and to provide phenotypes of higher physiological relevance with improved contractile maturity. Myoblasts cultured on coverslips were immunofluorescently stained for MSY-3. HeLa cells were transfected with a construct encoding N-terminally FLAG-tagged human YB-3 in a pcDNA-vector. YB-3-FLAG was purified using anti-FLAG magnetic beads. The eluated immunoprecipitation sample was sent to N-terminal sequencing to obtain information on post-translational modifications, to support further experiments regarding the post-translational cleavage of YB-3. N-terminal sequencing revealed an enrichment of YB-3 and YB-1 in the immunoprecipitation sample but not of YB-2, and previously undescribed post-translational modifications were identified. The MSY3-knockdown myotubes exhibited no spontaneous twitching on the hydrogel, while the control C2C12 myotubes twitched frequently. Misalignment of the MSY3-knockdown myotubes and changes in morphology was also observed in one of the MSY3-knockdown cell lines. This suggests that differentiating myoblasts on gelatin hydrogel is a potential strategy for studying the functions of YB-3 in myoblast differentiation and to elucidate its role in skeletal muscle.
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(2018)As a genome editing tool, CRISPR-Cas9 has provided a robust way to generate mutations in the gene of interest, at a certain time point, and in selected cell populations. The impairment of dopaminergic neurons in the substantia nigra is addressed to be one of the main pathologies of Parkinson’s disease. The histopathology of Lewy Bodies, with an undetermined role, accompanies the demise of DA neurons. Development of strategies for the prevention the neurodegeneration has a potential to slow down the progression of Parkinson’s disease. In this study, a novel, neuron-specific CRISPR-Cas9 system was developed for the purpose of dissecting neuroprotective pathways in primary dopaminergic neurons. The optimization of the tool was done by targeting EGFP at TH-positive neurons obtained from transgenic animals expressing EGFP in dopaminergic neurons. Complete loss of EGFP was achieved at day 6 after the introduction of the CRISPR-Cas9 via lentiviral vectors. There were no survival or transduction efficiency differences. Two significant pathways for the survival of dopaminergic neurons, the microRNA biogenesis and GDNF/RET signaling were selected to collect the preliminary data. Dicer, Trbp, Translin, Ago-2 and Ret were targeted with single sgRNAs, which were specifically designed to create indel mutations in these genes, and specific lentivirus vectors were produced with each guide. After transduction with the lentivirus vectors, survival of the TH-positive neurons was unaffected. Data obtained from the quantitative PCR suggested that there was 50-70% decline in transcript levels of Trbp. However, the unchanged transcript levels of the other miRNA-related targets suggest the need for further optimization of the specific guides. Knockdown of Ret was validated by inhibition of pharmacological benefits of GDNF. Overall, this research has shown the further development of this CRISPR-Cas9 tool would be useful to dissect neuroprotective signaling pathways in dopaminergic neurons.
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(2021)Ovarian cancers (OCs) are gynecological malignancies that cause the most gynecological cancer related deaths due to asymptomatic early-stage development and late diagnosis. The treatment of OC has not improved significantly during the last decades, and challenges are often caused by chemoresistance and the heterogeneity of cancer cell populations. Therefore, there is an urgent need to improve OC treatment outcome and implement new targeted therapies that could address the subtype specific characteristics. The most common type of OC is epithelial ovarian cancer (EOC), that can be further divided into five subtypes with distinct molecular and histological characteristics. High-grade serous subtype represents majority of cases with up to 75% of EOC patients, while other subtypes such as low-grade serous, mucinous, clear cell and endometrioid OC being less common. Considerable progress has been made in cancer treatment via precision oncology, in which individual cancer biology and tumor molecular features are investigated and used to improve treatment decisions. For this purpose, the development of patient-derived cancer cells (PDCs) offers a good opportunity to study cancer biology in vitro and to build models for preclinical molecular profiling and functional testing. PDCs can be used to establish 2D and 3D models, and most recently, wide interest has been focused on patient-derived organoids (PDOs), that offer a better model of tumor and its microenvironment, while allowing long-term culture, cryopreservation, modification and high-throughput opportunities. In this study, the aim was to establish PDO cultures using tumor cells from low-grade serous OC patients for molecular profiling and functional drug testing. PDOs were generated from both fresh and frozen tumor tissue or ascitic samples resulting to successful development of long-term PDOs from three of the five models. In order to identify optimal culturing conditions for low-grade serous OC PDOs, two previously unpublished growth mediums were tested in parallel. The more complex of the mediums showed slightly better PDO growth in general. The immunohistochemistry staining with pan-cytokeratin and PAX8 was used to confirm the epithelial and ovarian origin of PDOs. In addition, cancer panel sequencing was performed to identify mutation profiles. Importantly, the small-scale drug testing, which was performed using conventional chemotherapeutics cisplatin and paclitaxel and targeted drugs gedatolisib and trametinib, showed sample-specific responses. In conclusion, the results from this project show that PDOs are good models for ex vivo precision medicine functional studies. Importantly, we managed to establish PDOs from frozen tumor cells, suggesting that PDOs could be initiated from living biobank samples. However, the challenges related to culturing of PDOs for functional assays included slower growth rate compared to 2D cancer cell cultures and technical challenges related to Matrigel, limiting the possibilities of high-throughput drug testing. By improving these factors, PDOs will offer an efficient 3D model for preclinical use.
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(2023)This thesis explores the relationship between energy justice and demand response electricity pricing schemes in the residential market. As energy retailers make the transition towards demand response contracts, many opportunities arise for justice and injustice. It is vital that consumers are protected from arising injustices, and that the benefits of demand response schemes are distributed across the population. I use a popular energy justice framework to evaluate the demand response schemes of three European electricity retailers for their adherence to the principles of energy justice. The eight evaluative criteria are availability, affordability, due process, good governance, sustainability, intragenerational equity, intergenerational equity and responsibility. The three retailers are Tibber, E.ON Next, and Helen. Through this evaluation, I demonstrate that novel developments in energy systems by some energy retailers can positively inform the policies and practices of conventional retailers. There is room for growth in customer communication, stakeholder involvement, and smart home integration. My evaluation shows that retailers are yet to meet the aspirations of energy justice with their demand response schemes, but the potential for promoting justice clearly exists. I conclude with a set of recommendations Helen can take to meet the goals of energy justice in their electricity contracts.
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(2020)It is widely acknowledged that previous efforts to communicate the severity and rate of climate change have failed. Science communication has for decades relied on the presumption that more information leads to more informed decisions, thus so far, the scientific consensus about human-caused climate change has not resulted in required changes in behaviour. Previous communication efforts have, for the most part, attributed inaction to the lack of information, but in doing so, have excluded many social and psychological elements of communication. Although raising the level of awareness about climate change has been successful, climate change remains to be perceived to be a distal threat. Recently, more sophisticated approaches have been developed to meaningfully communicate climate change, drawing attention to the framing of the communication. In this study, a new approach to science-based environmental communication is evaluated. The case study seeks to address how immersive Virtual Reality (VR) can be used as a tool in science-based environmental communication for policymakers in a locally relevant context. Via immersive VR, information about forests’ role in climate change is mediated to forest policymakers. In the science communication, climate change is framed as an experiential, local, and present risk, promoting a problem definition that focuses on the climate effects of forest utilisation. I evaluate the success of the science-based environmental communication by measuring participants’ personal responses. I focus on measuring enjoyment, interest, trust, and usability. The study participants are members of the Parliament of Finland and governmental officials from the Ministry of Agriculture and Forestry; and the Ministry of the Environment. The study material consists of feedback forms from participants (N=65) and interviews of the key actors (N=7). To consider the historical background and many conflicting interests in Finnish forest and climate politics, I focus on the comparison between the natural resource position and the environmental position. The results of this study offer compelling evidence for how differently policymakers representing these two positions perceive the usage of immersive VR in science-based environmental communication. The environmental position indicated significantly higher levels of success on all measured components. Considering that the science communication framed forest utilisation as an environmental issue, it is not surprising that participants holding the environmental position perceived the science communication to be more enjoyable, interesting, trustworthy, and usable. Accordingly, the study results provide additional support for the idea of Finnish forest policy as a polarised field of policy with two main positions. With the means of immersive VR, I was able to induce strong personal responses to the science communication. Participants holding the natural resource position were more likely to challenge the legitimacy of the information and the use of VR in science communication than participants holding the environmental position. The results point to the likelihood that communicating climate change via immersive VR can induce strong negative emotions in the participants, but when the communication is comparable with the policymaker's policy preferences, they respond more positively. The study results also suggest, that to communicate climate change more meaningfully, immersive VR should be further explored as a supplementary tool in science communication.
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(2006)The Seychelles magpie robin Copsychus sechellarum is among the most threatened of the twelve avian species endemic to Seychelles. Originally relatively abundant and widespread in Seychelles, its population has severely diminished, mainly on account of introduced predators and habitat destruction. The lowest count was recorded in 1965, when the number of birds was between eight and fifteen, all confined to just one island. In 1990 a successful recovery program was implemented, and the population has now recovered to approximately 150 birds on four islands. Translocations to new islands are a major part of the recovery program. So far Seychelles magpie robins have been translocated to three islands, and three more target islands still need to be chosen if the long-term goals of the project are to be reached. Determining habitat suitability at the translocation target area is essential before attempting a translocation. Cockroaches are a major part of the bird's diet. Cockroach abundance has been shown to be a good indicator of magpie robin habitat quality, but it is very laborious and time consuming to measure. The objective of this study is to build a model that can be used to predict cockroach abundance, and thereby Seychelles magpie robin habitat quality, with relatively simple and inexpensive measurements. The data for this project was collected on Cousin, Cousine and Aride islands in Seychelles during October and November 2004. Several potential predictors of cockroach abundance were measured using simple and low-cost methods. The measured variables were Seychelles skink Mabuya sechellensis abundance, altitude from sea level, slope gradient, rock type, canopy cover, shrub cover, litter depth, soil depth, the relative canopy cover of different tree species, and percentage of ground covered by litter, rock, grass, woody vegetation and bare ground. These variables were measured in several 25 × 25 m plots on each island. Cockroach abundance had been measured in the same plots previously. Several multiple linear regression models were built using these variables, with cockroach abundance as the dependent variable. The Akaike Information Criterion was used to rank the models and to find the most important explanatory variables. Stepwise regression was used as a secondary method in order to see if two different methods point to the same result. Both methods indicated that slope gradient and granitic rock type are the two most important predictors of those tested. These are features that are invariably associated with granitic terrain, and both are positively correlated with cockroach abundance. A simple comparison of average cockroach abundance between granitic and coralline rock types also showed a significant difference, with granitic terrain providing higher cockroach abundance. The islands in Seychelles can be divided into two main categories: granitic and coralline islands. Steep slopes and granitic rock are both features associated with granitic terrain and granitic islands only. Therefore, based on the results of this study, granitic islands are likely to provide higher cockroach abundance and thus better Seychelles magpie robin habitat quality. Hence it is recommended that Seychelles magpie robin translocation efforts are focused preferentially on granitic islands.
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(2022)Each year many new-borns are at risk for long-term developmental deficits due to adverse perinatal events. Early gross motor abilities have been shown to link with cognitive development and studying infant motor behaviour may provide means to assess global neurodevelopment. This thesis aims to explore a potential association between early gross motor abilities recorded at infancy with a multi-sensor wearable jumpsuit MAIJU and later neurocognitive development assessed at two years of age. The study sample (N=26) consisted of healthy full-term infants and those with prematurity or perinatal asphyxia. Spontaneous motor activity was recorded at home with the jumpsuit. Machine learning methods were used to quantitate the time infants spent in different postures and estimate the maturity of their motor abilities, which were compared to cognitive development at two years of age with correlational- and regression analyses. There was a positive trend between early motor abilities and later cognitive development. Specifically, standing posture explained the association, such that infants who spent more time standing had better cognitive abilities at two years of age. Standing may support cognitive development by increasing opportunities for visual and manual exploration and learning. Shared neuronal circuitries for motor and cognitive functions and faster neuronal maturation may also underlie the association. The current study supports the creation of future studies with larger sample sizes to establish the potential for the use of postural and movement information obtained from wearable jumpsuit MAIJU to assess the variability of neurocognitive development of at risk and typical infants with potential goal to identify future cognitive deficits at early stage.
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(2019)Not much attention is paid on the conservation of invertebrates despite their importance to the ecosystems in general and their benefits and ecosystem services to us, humans. This study is part of a project aiming to start the Sampled Red List Index (SRLI) for spiders. The IUCN Red List Index (RLI) is used for measuring the overall extinction risk of groups of species and the sampled approach is a way to evaluate the trajectory towards extinction of megadiverse groups without the need to assess every species of the whole group of interest. A random sample of 200 spider species were selected from the global checklist and assessed according to IUCN Red List Categories and Criteria. Given the availability of data, I was able to calculate the extent of occurrence and area of occupancy for 80 species, of which 70 species had an EOO above 20000 km² and 75 species an AOO above 2000 km², the thresholds below which species can be considered threatened. The trends in EOO and AOO were assumed to be stable for most species (49 species) given the inexistence of monitoring data for any taxon. Evidence of decline was found for only 10 species, usually inferred from habitat loss. Habitat data was collected for 118 species. The most common habitat type was forest (73 species), followed by grasslands (24 species) and artificial habitats (22 species). For 44 species the habitat trend was inferred to be stable, only declining, according to available knowledge, for 14 species and increasing for one species. For the remaining 141 species the habitat trend could not be inferred and was thus assumed to be unknown. The most commonly mentioned threat types were agriculture (11 species), fires (7 species) and logging (6 species). For 39 species there were no known threats and for the rest of the 132 species the threats were unknown. Conservation actions in place were observed for 104 species, most commonly site and area protection (100 species) and resource and habitat protection (88 species). Conservation actions such as education and awareness (8 species), resource and habitat protection (7 species) and site and area management (6 species) were to take into consideration. All the 200 species were estimated to be in need of further basic research especially on threats (143 species and distribution (140 species), but also on life history and ecology (135 species). Due to several knowledge shortfalls, including the Wallacean (distribution of species), Prestonian (population trends) and Hutchinsonian (response to environmental change), no threat category could be reached for the vast majority of the species. The results show that an IUCN category could be reached for only 59 species, of which 55 were assessed as Least Concern and a threatened category was reached for only 4 species (t as Critically Endangered and one as Vulnerable). The baseline SRLI at this first point in time was 0.95 (in a 0-1 scale, where 0 means all species are extinct and 1 for all species are Least Concern). We hypothesize however that among the 141 Data Deficient species there should be a higher proportion of threatened species than among the 59 evaluated. This would be due to two reasons. First, the scarcity of information on many species might in part be due to their rarity. Second, widespread species were often the only for which an assessment could be reached, creating a bias in the dataset towards a large base SRLI value. The strategy currently imposed by IUCN is therefore clearly inadequate for taxa with scarce information, which represent the vast majority of species. I propose the future use of a different, non-random, approach to the selection of species in the SRLI and its adoption for other taxa which represent in fact most extant and threatened species.
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