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Now showing items 194-213 of 974
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(2020)As biodiversity is being lost worldwide at an accelerating rate due to anthropogenic activities, the frequency and severity of many infectious diseases has been observed to increase. Together these patterns have brought forth an urgent need to understand the possible linkages between biodiversity and disease risk. Two contradicting hypotheses have been proposed to explain the diversity-disease relationship. The dilution effect hypothesis suggests that increasing host community species diversity ‘dilutes’ disease risk, whereas the amplification effect hypothesis predicts disease risk to increase with increasing diversity. Even though most of the studies support the dilution effect, there remains an intensive debate regarding the generality of this effect. As most of the research efforts to understand the relationship between diversity and disease have focused on animals and crop plants or have been carried out experimentally, one of the research gaps is how relevant the dilution effect is in wild plant communities. In nature, plants and their diseases are affected simultaneously by multiple abiotic and biotic environmental factors that might confound or supersede the effects of diversity. It is also poorly understood, whether we might expect dilution effects to occur not only on diversity gradients driven by anthropogenic diversity loss, but also on natural diversity gradients. To study the possible association between host community species diversity and disease risk in the wild and to test whether this association could be detected after accounting for the effects of abiotic factors, I surveyed grassland vascular plant communities for their species diversity and foliar disease symptoms along a natural diversity gradient driven by elevation. I also recorded data on the mean soil surface temperature in the surveyed plant communities and used structural equation modelling to differentiate and compare the effects of biotic and abiotic variables on disease risk. The data were collected on Mount Calanda in the Swiss Alps during summer 2019. In this thesis I show that host community species diversity and disease risk are negatively associated with each other along a natural diversity gradient driven by elevation. Furthermore, this negative effect can be detected even after accounting for the effects of elevation and mean soil surface temperature on disease. Together the results support the occurrence and the ecological relevance of the dilution effect in wild plant communities along natural diversity gradients and suggest that diversity might protect wild plant communities from increased disease risk. Future studies should aim to identify the exact mechanisms of the association to help us better understand when and where we might expect dilution effects to occur in the wild. This knowledge can be used to predict how epidemics, that affect the well-being of ecosystems, humans and wildlife, are born in the changing world.
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(2023)Macrozooplankton is an understudied size class of plankton in the Arctic, but even though species composition is similar around the Svalbard archipelago, the relative composition can act as a proxy for climate change. This study investigated if the fjords around Svalbard are similar in species composition and if any differences could be explained. 11 fjords were sampled with a focus on common and indicator species in terms of abundance, relative composition and length distribution. I found low presence of T.libellula and high abundances of T.abyssorum and T.inermis. T.abyssorum was the only species whos abundance was significantly correlated to water mass (Atlantic water), but T.libellula, T.abyssorum, T.inermis, T.longicaudata and A.digitale all showed significant differences in length distribution. This study provides further understanding of species composition in the different high Arctic fjords around Svalbard.
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(2023)Morphological features are considered as markers of microglial functionality, and they show regional heterogeneity in the brain. Recently the sleep-wake cycle was shown to affect microglial morphology in mice and correlate with cortical sleep slow wave activity (SWA). Microglial sizes and ramification increased during the dark period and decreased during the light period in cerebral areas associated with SWA, suggesting that neuronal activation could be affecting microglial morphology through SWA. I studied microglia in the hindbrain areas with and without functional connection to SWA to further investigate the association between SWA and alterations in morphology, and to investigate if there are differences in microglial morphology and their diurnal alterations in brain regions other than those commonly investigated. I examined three hindbrain areas (cerebellar cortex (CC), deep cerebellar nucleus (DCN) and medial vestibular nucleus (MVN)) and somatosensory cortex (SC) of mice (n=15) at two timepoints: 6 hours after the light onset (high SWA) and offset (low SWA). My aims were to answer if there are morphological differences in microglia between 1) the four brain areas at both timepoints and 2) between the two timepoints in each brain area. My hypotheses were that CC and DCN which have functional connections to cortical SWA, would show similar diurnal morphology alterations as demonstrated in the cerebral areas, and MVN that has no known cortical SWA connection, would lack significant alterations. As microglia are heterogenous throughout brain, I expected microglia to differ between different brain areas, especially the hindbrain and the SC. I found that microglial morphologies significantly differed between the hindbrain and the cortex, while the hindbrain areas were more similar in morphology. Moreover, the brain areas demonstrated diurnal morphology alterations of microglia with varying extent: CC and DCN microglial morphology did not correlate with SWA as clearly as SC did, and interestingly, morphological features of MVN microglia showed a pattern opposite to other areas, microglia being larger during the light period than the dark period. These results highlight the importance of the diurnal time to microglial morphology and the heterogeneity of microglia between different brain regions.
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(2020)The diversity of different neuronal types lays the foundation for different functions in the brain. The development of different subpopulations and special features of neurons in the central nervous system are still partly unknown. Finding answers to these developmental issues could help in the process of characterisation of cell types and mapping of neuronal networks between the brainstem nuclei in the brain. Previous studies have shown that a ventrolateral neuroepithelial domain in the anterior hindbrain, rV2, produces excitatory (glutamatergic) and inhibitory (GABAergic) neurons, which are related to monoaminergic nuclei in the brainstem (Lahti et al., 2016). In this master’s thesis project, the development of a subpopulation of neurons expressing Gsc2 transcription factor in the interpeduncular nucleus was studied. This project was based on single-cell RNA sequencing results conducted in E13.5 mice. Predicted by single-cell RNA sequencing results, Gsc2 expressing cells are GABAergic interneurons and originate from the rV2 domain of the rhombomere 1 region in the hindbrain. Co-expression pattern with another transcription factor Sall3 with Gsc2 during development was also addressed in the study. Furthermore, the role of Notch signalling in the binary cell fate decision between GABAergic and the glutamatergic fate of rV2 neurons was investigated. Validation of single-cell RNA sequencing results was performed using in situ hybridisation and immunohistochemistry methods with mice embryos at the age of E12.5 and E15.5. This study verified previously shown origin of Gsc2 expressing cells to the rhombomere 1 region and in addition, showed that Gsc2 expressing cells are GABAergic. Co-expression pattern of Gsc2 with Sall3 neither in the rV2 domain nor in the interpeduncular nucleus was seen in our results. In the rV2 domain, the depletion of Notch signalling decreased the expression of differentiating GABAergic neurons. This indicates that Notch has a role in GABAergic neurotransmitter identity during the development of brainstem neurons in mice. Based on our results, Gsc2 could be used as a lineage marker for GABAergic interneurons originating from the rhombomere 1 region and as a marker for a subpopulation of the interpeduncular nucleus. Furthermore, results from the role of Notch signalling could help in discovering the mechanisms related to the determination of neurotransmitter identity in rV2 neurons. Further investigations, in different developmental time points and with additional markers, are needed to verify these results.
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(2019)Background- Colorectal cancer (CRC) is the third most common epithelial carcinoma. There is an increased risk of colorectal cancer in people with longstanding inflammation in the large intestine, including individuals with ulcerative colitis (UC). Epigenetic changes in CRC such as aberrant DNA methylation alterations are common changes in human cancer. The aim of this study is to identify the DNA methylation alterations of selected inflammation related genes in UC-CRC vs. Lynch syndrome (LS). Method- DNA was extracted from archival tissue specimens from normal and tumor samples from UC-CRC (n= 31), and LS-CRC (n=29). Methylation-specific multiple ligation-dependent probe amplification (MS-MLPA) assays were used to detect CIMP status and CpG promoter methylation status of seven inflammation related genes. Microsatellite instability analysis was carried out using two mononucleotide repeat markers BAT25 and BAT26. Results- Increased hypermethylation frequencies in carcinoma vs. normal colonic mucosa were detected for all the inflammatory marker genes in specimens of UC-CRC patients. Statistically significant differences for methylation frequencies were observed in the NTSR1 gene (p value =0.008) and SOCS2 gene (p value =0.04) in specimens of UC-CRC patients. NTSR1 gene showed significantly increased methylation of normal colonic mucosae from UC-CRC vs. LS patients (p value=0.01). Conclusion- UC-CRC and LS tumor specimens revealed varying frequencies of hypermethylation in all the inflammatory genes. Methylation of the NTSR1 in the normal colonic mucosa suggests a possible field defect in UC-CRC, and could thus be used as an early biomarker to detect increased UC-CRC risk in non-neoplastic epithelium.
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(2011)Pro gradu tutkielmani aiheena oli tutkia koirien (Canis familiaris) saalistushalukkuutta ja persoonallisuutta sekä näiden mahdollista yhteyttä dopamiinireseptori D4 –geeniin (myöh. DRD4-geeni). DRD4-geeni ilmenee lähinnä hermosoluissa ja se vaikuttaa erityisesti aivojen limbisen järjestelmän toimintaan. Limbinen järjestelmä säätelee tunnetiloja ja tunteisiin liittyviä autonomisia toimintoja sekä motivaatiota eli samoja asioita, joihin dopamiinin tiedetään vaikuttavan. Dopamiini vaikuttaa elimistöön sitoutumalla esimerkiksi aivojen limbisen alueen dopamiinireseptoreihin. Dopamiinin on havaittu liittyvän assosiatiiviseen oppimiseen ja DRD4-geenin puolestaan mm. aktiivisuuteen ja impulsiivisuuteen sekä uteliaisuuteen mistä syystä se valittiinkin kandidaattigeeniksemme tutkimukseen. Koira puolestaan sopii erityisen hyvin mallilajiksi kandidaattigeenitutkimukseen, koska koirarodut ovat geneettisiä isolaatteja ja eroavat toisistaan niin rakenteensa kuin käyttäytymisensäkin puolesta. Kytkentäepätasapaino eli alleeliassosiaatio on koirissa huomattavasti voimakkaampaa kuin ihmisissä ja siten koiralta on merkittävästi helpompaa löytää mm. tautigeenejä. Koirilla kytkentäepätasapaino yltää noin 2 Mb laajuudelle, kun vastaava luku ihmisellä on vain noin 0,28 Mb. Tutkimuksen 405 suursnautserin ja saksanpaimenkoiran saalistushalukkuus testattiin koiran luonteenkuvauksesta eli MH-testistä tutulla viehetestillä. Viehetestissä koiran edestä yllättäen "pakenee" saalista muistuttava mutkittelevasti kulkeva kankainen viehe. Koirien suoritukset viehetestissä videoitiin ja suoritukset luokiteltiin neljään luokkaan äärimmäisen saalistushalukkaasta saalistushaluttomaan. Muita persoonallisuuspiirteitä tutkittiin koirien omistajien täyttämien luonnelomakkeiden avulla. Kaikista viehetestillä testatuista koirista otettiin verinäytteet, joista eristettiin DNA. Saalistustestissä äärimmäisen saalistushalukkaat ja täysin saalistushaluttomat saksanpaimenkoirat (N=44) valittiin DRD4-geenin alleeliassosiaatiotutkimukseen. Tutkittavaa geenialuetta monistettiin käyttämällä alleelispesifejä alukkeita PCR-reaktiossa. Tutkimuksen koirista löydettiin DRD4-geenin alleeleja 2 ja 3a. Luonnelomakeaineiston taustalta paljastui faktorianalyysin avulla neljä faktoria: sosiaalisuus ihmisiä kohtaan, leikkisyys ja aktiivisuus, aggressiivisuus koiria kohtaan sekä rohkeus. Näistä ensimmäinen assosioitui merkittävästi alleelin 3a kanssa. Koirat jotka kantoivat tätä alleelia olivat vähemmän aggressiivisia ihmisiä kohtaan kuin koirat, joilla 3a-alleelia ei ollut. Saalistushalukkuuteen kumpikaan alleeleista eikä mikään genotyypeistä assosioitunut. Saalistushalukkuutta kokonaisaineistossa selitti parhaiten leikkisyys ja aktiivisuus. Rodut erosivat toisistaan ihmisiin ja koiriin suuntautuvalta aggressiivisuudeltaan siten, että saksanpaimenkoirat olivat suursnautsereita aggressiivisempia.
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(2005)1-Bentsyylipiperatsiini (BZP) on viime vuosina laittomille markkinoille ilmaantunut ns. design-huume, jonka on todettu muistuttavan vaikutuksiltaan amfetamiinia. Sen myynti tapahtuu tyypillisesti tanssiklubeilla ja Internetin välityksellä. Esimerkiksi Yhdysvalloissa BZP on luokiteltu laittomaksi, mutta suurimmassa osassa maailmaa aine on huumausainelainsäädännön ulkopuolella. Suomesta ainetta takavarikoitiin neljästi vuosina 2002-04. Tässä tutkimuksessa selvitetään ehdollistetun paikkahakuisuuskokeen avulla, onko BZP:lla palkitsevia ominaisuuksia. Kokeessa koe-eläimet opetetaan yhdistämään tutkittavan aineen vaikutukset tiettyyn ympäristöön, ja mikäli eläin alkaa tämän jälkeen suosia ympäristöä, eli aine aiheuttaa paikkahakuisuutta, tulkitaan aineella olevan palkitsevia ominaisuuksia. Palkitsevien ominaisuuksien katsotaan heijastavan aineen riippuvuuspotentiaalia, sillä useimpien ihmisten väärinkäyttämien aineiden on todettu aiheuttavan ehdollistettua paikkahakuisuutta. BZP:n todettiin aiheuttavan rotille ehdollistettua paikkahakuisuutta annosriippuvaisesti, minkä jälkeen selvitettiin reseptorisalpaajien avulla dopamiinireseptorien merkitystä paikkahakuisuuden synnylle. Dopamiini-1-, eli D1-reseptorisalpaus esti paikkahakuisuuden, kun taas D2-salpauksella ei ollut siihen vaikutusta. Kokeiden perusteella BZP:lla on palkitsevia vaikutuksia, jotka välittyvät D1-, mutteivät D2-reseptorien kautta. Tulokset viittaavat BZP:lla olevan väärinkäyttö- ja riippuvuuspotentiaalia, minkä vuoksi olisi perusteltua, että se kuuluisi lainsäädännöllisesti samaan kategoriaan mm. amfetamiinin kanssa.
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Drone-kuvien käyttö haurujen (Fucus spp.) kartoitukseen ja monitorointiin itäisellä Suomenlahdella (2023)Tämä opinnäytetyö käsittelee uuden ympäristöseurantamenetelmän kehitystyötä. Hauruja (Fucus spp.) on seurattu Suomen rannikolla jo pitkään, mutta nykyisiin kartoitus- ja seurantamenetelmiin liittyy haasteita ja epätarkkuutta. Hauruvaltaiset elinympäristöt ovat uudessa uhanalaisuusarvioinnissa määritelty erittäin uhanalaisiksi. Tarvetta uusille seurantamenetelmille siis on. Drone-teknologia on kehittynyt ja halventunut viime vuosina, mikä on avannut uusia mahdollisuuksia hyödyntää kaukokartoitusta. Edulliset valokuvaamiseen tarkoitetut dronet mahdollistavat sekä ajallisesti että paikallisesti erittäin tarkkojen ilmakuvien tuottamisen. Näitä on maailmalla käytetty menestyksellisesti myös rannikon kartoituksessa ja seurannassa. Suomessa drone-kuvia ei kirjallisuuden perusteella ole käytetty makrolevien kartoitukseen tai seurantaan. Tämän tutkimuksen tarkoitus on selvittää, sopivatko tällaiset drone-kuvat hauruyhteisöjen kartoitukseen ja monitorointiin itäisellä Suomenlahdella sekä tuottaa tietoa menetelmän jatkokehitystä ajatellen. Kuvasin 22 merenranta-alueen reunaympäristön alkukesällä 2020. Kuvatuista alueista valitsin kahdeksan jatkotutkimuksiin, jotka kuvattiin uudelleen syksyllä 2020. Tällöin niiden alueelta kerättiin kuvatulkinnan tueksi 263 tukipistettä, joilta mitattiin veden syvyys ja arvioitiin haurujen esiintyvyys Drop-kuvausmenetelmällä. Rajasin ilmakuvilta näkyvät haurualueet ja vertasin niitä tukipisteaineistoon. Havaitsin, että 80 % havainnoista tieto luokittui oikein. Cohenin kappa -testin perusteella kohteiden välillä sekä eri syvyyksillä olevilla kasvustoilla oli suuria eroja havaintojen luotettavuudessa. Syvemmällä kuin 2,5 metrissä olevien haurukasvustojen erottaminen onnistui huomattavasti huonommin. Myös matalimman kasvuston (0 – 0,5 m) erottaminen oli hankalaa. Tulokset ovat lupaavat, mutta niiden perusteella menetelmää ei kuitenkaan vielä voi todeta toimivaksi, vaan lisätutkimuksia tarvitaan. Tämän tutkimuksen perusteella kehitystyötä kannattaa jatkaa käyttämällä tarkkaa paikkatietoa ilmakuvien ja tukipisteaineiston tuottamiseen sekä uusia kuvantamismenetelmiä, jotka kykenevät tuottamaan tavanomaista RGB-kameraa paremman erottelukyvyn. Drone- ja meritöiden turvallisuuden parantamiseksi tehtiin riskienhallintaprosessi, jossa tunnistin, analysoin sekä raportoin töihin liittyvät merkittävimmät riskit.
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(2020)Multiple myeloma (MM) is a heterogeneous plasma cell cancer that results from the excessive proliferation of mutated B cells in the bone marrow and the accumulation of ineffective antibodies, monoclonal proteins, in the blood. Despite recent advances in research and novel therapeutics, MM remains incurable, mainly due to the mechanisms underlying disease progression and drug resistance. Therefore, novel biomarkers and therapeutics for the treatment of relapsed and refractory MM are urgently needed. MicroRNAs (miRNAs), short non-coding RNA molecules that play a key role in post-transcriptional gene regulation, have been found to be associated with different hallmarks of MM. Previous studies have indicated that abnormally functioning miRNA-mediated gene regulation followed by oncogene activation and tumor suppressor gene silencing results in drastic alterations in cell proliferation, apoptosis, growth, and metabolism. These changes in cellular functions have been indicated to be associated with the pathogenesis, progression, and formation of drug resistance in MM. Therefore, the role and potential of miRNAs to act as biomarkers to predict MM progression and drug sensitivity should be further investigated to ultimately improve the survival rates of patients. The aim of this master’s thesis was to investigate the relationships between drug sensitivity, disease progression and miRNA regulation in MM patients. Bioinformatically predicted miRNAs identified to be associated with sensitivity to panobinostat, a novel histone deacetylase inhibitor, and MM progression were validated in MM patient samples by using real-time quantitative reverse transcription PCR (RT-qPCR). In addition, the specific gene targets of miRNAs involved in the regulation of drug responses and MM progression were predicted by identifying statistically significant, negatively correlated interactions between the miRNA and RNA sequencing data of 45 MM patients in pairwise comparative correlation analysis. Finally, the predicted miRNA targets genes were validated in MM patient samples using RT-qPCR. Based on the bioinformatic analyses and RT-qPCR validation, mir-424 expression was significantly increased in relapsed MM patients as compared to respective patient samples taken at diagnosis, suggesting a potential role of mir-424 in MM progression. Similarly, mir-4433b expression was significantly elevated in panobinostat-resistant patients compared to sensitive patients, suggesting a potential effect of mir-4433b on the regulation of panobinostat drug response in MM patients. In addition, the RT-qPCR validation demonstrated that the disease progression and drug sensitivity associated mir-92b, mir-363 and mir-221, would potentially regulate the expression of FGF2, MFF, and TMEM248, respectively, providing novel insights into the functional roles of miRNAs in MM pathways.
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(2020)Upregulation of specific helpful proteins represents a possible method for preventing or treating human diseases. Endogenous upregulation (knockup) is the increase of a gene's expression only in cells in which it is already expressed, thus avoiding physiologically abnormal spatiotemporal patterning. A gene's three prime untranslated region (3′UTR) affects protein expression through stability regulation of RNA already transcribed, which suggests 3′UTR modification as a viable route for endogenous upregulation. Mammalian model organisms can be generated in order to test the effects of different 3′UTR modifications, but at great cost of time, effort, and money. If able to predict in advance with an in vitro assay whether an in vivo modification would cause a desirable or undesirable change, these costs could be substantially reduced. In this thesis project, an in vitro assay was used to compare the protein expression influence of twenty neurodegeneration-relevant mouse genes' 3′UTRs to that of a flip-excision cassette (flex-cassette) previously used for in vivo conditional knockup. The assay used was the Promega Dual-Luciferase Reporter Assay, in which plasmids expressing Renilla and Firefly luciferase as reporter and internal control are co-transfected into in vitro cells, then each luciferase's expression measured with its respective substrate and a luminometer. Transfections were carried out in three-well replicates and on multiple days. The aims of the project were the evaluation of the assay's ability to predict in vivo results, the suggestion of 3′UTRs which could be upregulated in vivo by the conditional knockup flex-cassette, and the identification of any trends in 3′UTR-based protein expression influence according to gene function. A number of gene 3′UTRs were identified which were either candidates for flex-cassette upregulation or candidates for use in the flex-cassette to upregulate other genes. However, the flex-cassette's in vitro results were only partially consistent with its previous in vivo results. Specifically, the lox sites in the flex-cassette was observed to lower expression level to a degree not observed in vivo. Additionally, in the course of the project a number of possible workflow improvements were identified, for which suggestions have been made in the text. As such, this in vitro approach requires further study in order to determine suitability for prediction of in vivo 3′UTR behaviour.
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(2014)The purpose of this thesis was to examine the diversity and species composition of dung beetle (Scarabaeinae) communities in degraded rainforest landscapes in southeastern Madagascar. Several studies elsewhere in the world have revealed that forest-dwelling dung beetle communities and especially large species suffer from forest degradation and fragmentation by decreased species diversity. The most important factors affecting community structure of forest-dwelling dung beetles are habitat area, connectivity and vegetation quality i.e. microclimate. The hypothesis of this study was that the situation is the same in Madagascar. As dung beetles provide several important ecosystem services, like nutrient cycling and bioturbation, loss of dung beetle diversity imposes a secondary threat to the extraordinary nature of Madagascar by decreasing the regeneration ability of vegetation. Material for the study was collected in forest fragments of different size and quality between two areas of primary tropical rainforest – Ranomafana National Park and Vatovavy mountain – in November and December 2011 and January 2012. The sampling was conducted by transects of 30–60 fish- or carrion-baited pitfall traps which were set up in 55 localities in the study area. In each locality, several variables were measured to describe the vegetation and microclimatic conditions. The variables included temperature, humidity, estimate of vegetation quality by 6 observation-based classes, vegetation density, hights of three clearly visible vegetation layers, altitude and slope steepness. In addition, connectivities were measured for the localities using GIS and a satellite image –based vegetation classification. In order to demonstrate the differences between certain localities the study sites were divided into seven zones in terms of their distance from the Ranomafana National Park, average connectivity of the transects and elevation. Altogether 4,199 individuals belonging to 24 species were collected. Six of the species are currently under identification process in the Paris Museum of Natural History. According to the preliminary results they include two species new to science. Largest numbers of species were collected from good quality fragments between Ranomafana and Vatovavy. Also, a clear transition zone in species composition was detected a few kilometers west from Vatovavy, where altitude changes sharply. The study reveals that the species assemblages in the forest fragments and degraded forest areas are surprisingly species rich. This may, however, be partly because of extinction debt, and many of the still surviving species may soon die out due to restricted dispersal possibilities. Connectivity and vegetation quality were shown to have an effect on Canthonini species richness, with less species in less connected areas and lower vegetation quality. Vegetation quality was also shown to have an impact on the proportions of species with different body length: more small and medium-sized (< 8 mm) species were found in fragments where vegetation was more degraded. In addition to revealing how rainforest fragmentation and degradation affect local communities, the study gives interesting information about the distribution of certain species of Epilissus (Scarabaeinae: Canthonini). It has been known before that four species of Epilissus show elevational differentiation in their occurrence in Ranomafana. In this study, two more species of the same genus, E. prasinus and E. emmae obscurpennis, were shown to continue this pattern in lower elevations near Vatovavy mountain, about 50 kilometers east of Ranomafana.
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(2020)Finland är ett skogsrikt land, men de existerande skogarna utgör dock kvalitativt enformiga habitat och det råder brist på varierade habitat i form av till exempel blandskog, skogar i naturligt tillstånd och äldre skog. Enligt tidigare studier utgör äldre skogar viktiga habitat för många skogslevande arter och mångfalden i skogarna minskar som en följd av habitatförstörelse. Vidare påvisar forskning att skogarna i Finland är ojämnt skyddade och merparten av skogsskyddet förekommer i norra Finland på statlig mark. Forskning påvisar att dagens moderna skogsbruksmetoder bidrar till att våra skogar är artfattiga och till de största hoten mot mångfalden i våra skogar klassas skogsbruket samt klimatförändringen. Att skogslandskapet i Finland utarmas är ett stort problem i och med att mångfald ökar ett ekosystems beständighet mot yttre störningar. För att åtgärda förlusten av biologisk mångfald har genvägar eller verktyg, med vars hjälp större arealer och flera arter samtidigt kan skyddas tagits fram. Till de här verktygen hör konceptet paraplyarter och en paraplyart är kortfattat en art med vars hjälp flera andra arter kan skyddas och vars förekomst indikerar på att ett lokalt habitat i närheten av paraplyarten är av hög kvalitet. Paraplyarter används explicit för att skydda habitat av hög kvalitet till exempel på områden där biodiversiteten är hög. Tidigare studier har visat att stora dagrovfåglar vanligen är effektiva paraplyarter i och med att deras boplatser kan associeras med en hög biodiversitet. Syftet med den här undersökningen är att klargöra huruvida skogslandskap i närheten av duvhökens (Accipiter gentilis) boplatser uppvisar en högre förekomst av vissa arter jämfört med kontrollområden. Kontrollområdena med vilka boplatserna jämfördes var av två slag: (a) äkta skogskontroller och (b) slumpmässigt utvalda skogskontroller. De äkta skogskontrollerna utgjordes av områden som kvalitativt motsvarade skogen intill duvhöksbon, medan de slumpmässigt utvalda skogskontrollerna utgjordes av skog av vilken typ som helst. För vart och ett av de här områdena undersöktes förekomsten av flygekorre (Pteromys volans) och blåbär (Vaccinium myrtillus). Förekomst av flygekorre karterades på basen av spillningsfynd och blåbärsrisets riklighet uppskattades via analyser av fotografier tagna över fältskiktet. Det insamlade materialet för båda arterna analyserades statistiskt med hjälp av LME - modeller. Resultaten påvisade att flygekorre förekom rikligare vid duvhökens boplatser än i de två kontrollskogarna. Flygekorrens habitatpreferenser överlappar till stor del med duvhökens och mina resultat överensstämmer med tidigare forskning som har påvisat att flygekorren har en nytta av duvhökens närvaro i form av skydd mot predation från nattaktiva rovfåglar. Flygekorren prefererar således samma skogstyper som duvhöken och intressant nog verkar duvhökens närvaro i sig vara viktigare för flygekorren än själva skogstypen. Enligt resultaten från avhandlingen är det dock inte heller uteslutet att en annan art/egenskap tillsammans med duvhöken fungerade som en paraplyart för flygekorren. Blåbärsris däremot uppvisade en rikligare förekomst vid äkta skogskontroller och duvhöksskogarna var troligen överlag för lummiga för blåbärets trivsel, men blåbärsris förekom dock rikligt vid 50 m från boplatserna. Således kan slutsatsen dras att flygekorren kan skyddas i fall av att skogslandskap med duvhöksbon skyddas. Duvhöken kan även ses som ett verktyg för naturskydd eller som en indikator för skogslandskap med hög mångfald, i vilka flygekorre samt en del blåbärsris förekommer. Om vi i framtiden vill ha flygekorre och blåbär i våra skogar bör därmed äldre skogar bevaras i och med resultaten påvisar att nämnda arter inte verkar trivas i moderna ekonomiskogar. En tillämpning av resultaten kunde vara att bruka paraplyarter och förekomst av nyckelbiotoper för naturskydd simultant.
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(2017)Tausta ja tavoitteet: D-vitamiinia sitova proteiini (DBP) kuljettaa D-vitamiinia ja sen aineenvaihduntatuotteita, esim. 25-hydroksi-D-vitamiinia (25(OH)D), verenkierrossa. Geneettinen muuntelu GC-geenissä, joka koodaa DBP:tä, on yhdistetty 25(OH)D-konsentraatioiden vaihteluun. Tavoitteena olikin tutkia GC:n geneettisten tekijöiden vaikutusta 25(OH)D-konsentraatioon suomalaisilla vastasyntyneillä. Lisäksi tutkittiin GC:ssä esiintyvän muuntelun aiheuttamia eroja lapsen kasvussa raskauden aikana. Menetelmät: GC:n SNP:ssä, eli yksittäisen nukleotidin vaihdoksissa, esiintyvää polymorfiaa ja raskauden aikaisen 25(OH)D-konsentraation ja napaveren 25(OH)D-konsentraation suhdetta arvioitiin 933 valkoihoisella vastasyntyneellä pojalla (468) ja tytöllä (465). 25(OH)D-konsentraatio määritettiin raskausviikoilta 6-13 ja napaverestä. Äidin D-vitamiinin saanti ravintolisistä määritettiin ruuankäytön frekvenssikyselylomakkeen avulla kahdelta viimeiseltä raskauskuukaudelta. GC:n kolme SNP:tä genotyypitettiin Taq-polymeraasin aktiivisuuteen perustuvan qPCR:n avulla (Bio-Rad, CFX384 C1000 Touch™ Real-Time PCR Detection System, USA): rs4588, rs7041 ja rs705124. Genotyyppien rs4588 ja rs7041 yhdistelmästä muodostettiin kuusi tunnettua diplotyyppiä ja kaikista kolmesta genotyypistä edelleen haplotyypit. Eroja geno-, diplo- ja haplotyyppien välillä 25(OH)D-konsentraatioissa ja kasvussa testattiin kovarianssianalyysin (ANCOVA) avulla käyttämällä relevantteja kovariaatteja. Tulokset: SNP rs4588 ja rs7041 geno- ja diplotyyppien välillä löydettiin tilastollisesti merkitsevä ero 25(OH)D-konsentraatioissa (keskiarvo (nmol/l) ± keskivirhe). Napaveren 25(OH)D-konsentraatio oli alhaisin geno- ja diplotyypillä GC 2/2 (77.8 ± 4.3, p=0.010, p=0.028, ANCOVA) ja korkein diplotyypillä GC 1F/1S (93.8 ± 2.0). Haplotyypillä ATG oli alhaisin napaveren 25(OH)D-konsentraatio (77.9 ± 3.8, p=0.016, ANCOVA). Raskauden ajan 25(OH)D-konsentraatiossa ei löytynyt eroja geno-, diplo- tai haplotyyppien välillä (ANCOVA). Genotyypin rs7041 sekä diplotyyppien ja päänympäryksen välilllä havaittiin ero (p=0.005, p=0.002, ANOVA), mutta geneettisen muuntelun ja syntymäpainon ja –pituuden välillä ei löytynyt eroja. Kun valittiin relevantit kovariaatit, niin genotyyppien rs7041 sekä diplotyyppien ja päänympäryksen välillä ei löytynyt enää tilastollisesti merkitseviä eroja. Yhteenveto: Tulokset osoittavat, että DBP:tä koodaavan geenin geneettisellä muuntelulla ja napaveren 25(OH)D-konsentraatiolla olisi vaikutusta jo vastasyntyneiden D-vitamiinitilaan ja aineenvaihduntaan. Saatujen tulosten perusteella GC:n geneettinen muuntelu ei kuitenkaan ollut yhteydessä lapsen kasvuun. Tulevaisuudessa GC:n SNP:n vaikutusta 25(OH)D-konsentraatioon voisi tarkastella syntymän jälkeisten vuosien aikana.
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(2021)Post-transcriptional modifications (PTMs) in RNA are present in all known RNA species and conserved in all kingdoms of life. Transfer RNA (tRNA) has been shown to have numerous conserved modifications, which exemplifies the importance of modifications having impact on the structure of the tRNA and its function as carrier of the amino acids. Ribosomal RNAs (rRNA) are universally modified as well, and modifications are situated at functionally important spots of the ribosome. Given the fact that types and sites of modifications are conserved, it is likely that these modifications have been selected for and that they optimize the ribosomal structure and functions. Stress, such as temperature or infection by a pathogen, is known to change the presence or abundance of modifications in RNA molecules and thereby affect translation efficacy. In line with that, this master’s thesis project sought to gain insight into the dynamics of PTMs in tRNA and rRNA upon oxidative stress, with the goal of utilizing recently optimized UPLC/MS method for identifying modified ribonucleosides. As the specific aim of the thesis was to estimate the change in PTMs in tRNA and rRNA in response to oxidative stress with 0.5 mM and 2 mM hydrogen peroxide H2O2, 3 immediate goals were: (i) to isolate total tRNA from yeast grown in stress conditions, (ii) to isolate rRNA from yeast 80S ribosomes, and (iii) to identify present modifications using mass spectrometry. Yeast was cultured in presence of H2O2 as a stressor in mentioned concentrations, and both treatments considered showed a difference in survival when compared to the control. Rough cell concentration estimates (OD600) did not show the effect of the stressor on cell survival clearly, but when number of viable cells per mL was estimated, it was clear that growth of the stressed yeast cultures was hindered 2 hours after exposure to H2O2 but recovered during the 24 hours. Firstly, using UPLC/MS analysis, 29 modifications were identified in tRNA from control and H2O2 treated yeast. Most identified modifications showed no change in abundance in treatments, which is to be verified with additional replicates. However, distinct dynamics of stress-related change was found for several modifications, revealing additional modifications that may play a role in stress related modificome reprogramming to the previously known signature modifications of oxidative stress. It was expected that recovery of culture growth after 24 hours may be accompanied with modification level recovery. However, that was not demonstrated here as downregulation at 2 hours followed by upregulation at 24 hours was seen for 2-methylthio-N6-methyladenosine, N4-acetylcytidine and 5-methoxycarbonylmethyl-2-thiouridine, and the reverse was shown for N4-methylcytidine. Upregulation in both time points was also shown here for some modifications. Taken together, these results confirm a complex and dynamic control of tRNA modifications in cellular survival responses. Modifications found to be affected by oxidative stress are most frequently located on the wobble position 34 and anticodon loop position 37, so it is expected that changes in their modification levels could directly affect the tRNA function in translation, making them a specific target for future research. Secondly, modifications in rRNA from control yeast cultures were identified, such as expected methylations of all 4 canonical nucleosides. However, further analysis will be needed to confirm the other identified modifications, due to the potential mRNA and tRNA contamination. Optimizing the method for rRNA modifications identifications by acquiring more modified nucleosides specific for the rRNA to use as standards in the analysis, analyzing rRNA types separately and using tandem mass spectrometry would enable getting a deeper understanding of which modifications are present and where they are positioned. Finally, it would enable reliable identification of the signals of novel modifications present in rRNA, such as the tRNA modification 5-carbamoylmethyluridine signal found here. In conclusion, this thesis work lays the foundation to study the evolutionary conserved function of PTM changes during stress as modulators of translation, using the methodological approaches discussed in-depth within the thesis, primarily to confirm the intriguing results found here.
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(2022)Biochar is a porous, carbon-rich material, made from organic material by pyrolysis in low oxygen conditions, and it can be used to sequester carbon into the soil. This review aspires to give an overview of the economic dimensions of using biochar in Finnish (Boreal and sub-boreal) forests. A literature review was conducted to collect and summarize the information about studies and applications elsewhere, and how we could possibly apply them into Finnish forest ecosystems. This thesis is done as part of Helsus Co-Creation Lab -project, where our group was tasked with looking into how biochar could enhance biodiversity in soil and accelerate transformation to low carbon economy. From this larger topic, this paper is looking into the economic side, and whether it is economically viable to use biochar to enhance and uphold biodiversity. This is evaluated by reviewing and categorizing 164 papers and conducting a literature review. My conclusions are that the current biochar applications show lower economic efficiency than other carbon dioxide abatement technologies. The stability of biochar in soil is a key factor, as the half-lives of biochars may not be as long as commonly suggested. Furthermore, competition for biomass resource use can restrict the availability of feedstock, and make it more expensive. Subsidies for biochar application are required if biochar is to be- come a significant part of the national or global climate mitigation policy. The results in different articles are quite variable and there is currently no standard approach to them. There is a need for specific research on what kind of biochar benefits what soil and vegetation, which is expensive. A primary goal is to incorporate a consistent and standardized testing or analysis method for biochar stability into the certification programs run and administered by the International and the European Biochar Initiatives. In the foreseeable future, biochar by itself is unlikely to play a significant role in climate mitigation strategies. Biochar might be just one of several alternatives in a bundle strategy to re- duce carbon emissions. However, its potential use must still be researched more.
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(2021)Abstract: The EEG measurement protocol is standardized and in use globally. The skull is measured to ensure that the electrodes are placed in the correct position. Measurements are necessary because skull sizes and shapes are different. Studies for placing electroencephalograph (EEG) electrodes on a human head are typically introduced theoretically before students are granted the opportunity to practice. Due to the limited availability of EEG equipment and supervisory staff, students encounter shortened practical training sessions and lengthy waiting periods transitioning from theory to practical components. The main aim of this project was to create a learning environment with game technologies to help students study electrode placement during the idle time between theory lessons and practical training. We set out to determine whether students experienced some learning gain and if they had a positive experience with the learning environment. We simultaneously assessed if fuzzy feedback is preferred over exact feedback. Additionally, the aim was to make use of a design-based approach with the information from a User Experience Questionnaire (UEQ) the EEG-simulator. Our group developed and tested a digital learning application that provides a 3D model of a human head, on which learners can practice placing EEG electrodes. We followed a user-centric design science approach to ensure our application appeals to our target audience. We used an observational post-test only design with two experimental groups and a control group. We applied a widely accepted user experience questionnaire to ascertain which of our two feedback systems elicited the best user experience. We also qualitatively analyzed diaries the students kept, as they worked with the learning environment, to better understand future development options for further maximizing the environment’s learning benefit. The overall application was well-received, and students opined that the application significantly enhanced their practical session experience. Although the post-test evaluation showed no difference between the two experimental groups, the user experience questionnaire showed that the fuzzy feedback system was preferred over the exact feedback. Furthermore, it was evident that students who had not used the learning environment struggled more to come to terms with the practical session. The personal experience recording by the students revealed several suggested improvements to the learning environment. We conclude that, with further development, this EEG placement learning application could address the idle period between demonstration lessons and practical training. We also venture to state that fuzzy feedback is preferred because of the high-fidelity mimicry of real teacher feedback. The last part of the research was to develop the EEG simulator so that it will increase theory learning with a simulator, that works, and this is ongoing. We have developed the last EEG simulator version with AR (augmented reality) mobile version that can be used with any smart devices. The future work is to test EEG application and does application influence student's theory learning process.
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(2023)Climate change is one of the biggest challenges our planet and humanity are experiencing. The time window for finding ways to miti-gate carbon emissions is getting smaller and there is an urgent need to find solutions that aim not only to reduce greenhouse gas (GHG) emissions, but to address the complex problems of land use change, deforestation, loss of biodiversity, and inequality. REDD+ is a multi-objective initiative under UNFCCC designed to reduce GHG emissions through deforestation and forest degradation togeth-er with non-carbon co-benefits of livelihoods, poverty, biodiversity, and local peoples and indigenous peoples rights. By applying a Qualitative comparative analysis (QCA) this thesis compares 12 various REDD+ countries national political contexts and particularly REDD+ policies and measures over time in order to identify conditions that enable or hinder the countries from achieving results in reversing forest cover trajectories. All the countries analyzed here are tropical, developing, or emerging countries with a political commitment to REDD+ with characteristics that hinder carbon-effective, cost-efficient, and equitable (3E) implementation of REDD+. The thesis builds on three previous REDD+ qualitative comparative analyses of various REDD+ countries' progress in developing and implementing national REDD+ policies and measures. The analysis follows an underlining theoretical assumption that both insti-tutions and agencies affect the REDD+ policy outcome. The longitudinal data used in the analysis is based on expert assessments conducted in three various data collection rounds in 2012, 2014, and 2016. The results show a set of enabling conditions under which countries can achieve a positive outcome. The findings from the previous studies have highlighted the importance of already initiated policy change and effective forest legislation from the institutional context, and from the actor-centered policy arena, the presence of powerful coalitions and the availability of performance-based payments. Here, two enabling remote conditions are identified (1) pressure from the forest resources and (2) the presence of effective forest legislation. The pressure from the forest resources leads to a positive outcome together with (3) strong national ownership and politi-cal will combined with (4) performance-based payments or (5) REDD+ policies and measures. The effective forest legislation.leads away from business-as-usual practices towards a broader transformational change when combined with (6) powerful transformation-al coalitions and (7) inclusive policy processes. Policy relevance: Well over a decade has passed since REDD+ was launched in 2007 but the progress has been much slower than it was initially expected. The evidence on what works and what does not is essential to achieve the GHG reductions needed to keep the global warming below 2C. The findings from this study can guide towards more effective, efficient, and equitable REDD+ policy design formulation and implementation.
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(2020)There is a naturally reproducing Atlantic salmon population in the River Teno in northern Norway and Finland. The Teno population has a strong population structure and up to 28 subpopulations have been recognized. Estimation of effective population size is important in conservation of the subpopulations. Effective population size tells about genetic variation of a population and is among the most important concepts in conservation genetics. In this study, current and past effective population sizes of 28 subpopulations were estimated from high density SNP-data for 1137 individuals in total. The estimation was done with the linkage disequilibrium method and the effects of using different assumptions were studied. Current estimated effective population sizes in subpopulations were generally low and ranged from around nine to 272 individuals. Only four populations had a current effective population size bigger than 50 individuals. Past effective population sizes showed a clear declining trend from the most distant generations in all populations. The choice between physical and linkage map as well as female, male or average linkage map had an effect to estimates. Also, different sample size corrections resulted in different estimates. Furthermore, effective population size was estimated with temporal method in three populations. It was detected that the estimates from temporal and linkage disequilibrium method were different from each other. The results of this study suggest that Teno Atlantic salmon subpopulations have declined over the past 150 generations and are in risk of losing genetic variation due to current low effective population size. This should be taken into account in conservation plans.
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(2010)Genetic variation is vital for both contemporary and long-term wellbeing of populations. Whereas heterozygosity (Ho) and allelic richness (A) are commonly used to measure the level of genetic diversity in a population, effective population size (Ne) describes the speed of loss of genetic variation. Various effective population sizes are proposed as standards for safe retention of genetic variation in a Minimum Viable Population (MVP). Since the 1940s, several types of effective population size estimators have been developed. Earlier estimators relied on demographic parameters, whereas genetic estimators are based on the analysis of either one or two genetic samples from a population. All Ne estimators have their unique sensitivities and limiting assumptions, which complicate the choice of estimator, comparison of results of different studies and the assessment of the reliability of the results. Ne estimators have recently been used e.g. in the monitoring of many aquatic populations, but their reliability and comparability has not often been tested with extensive ecological and genetic data, and it is not well established how much added value they bring to the conservation of easily observable species. I tested this with an extensive dataset on the Siberian jays (Perisoreus infaustus) living in Suupohja, Finland (62°22'N, 21°30'E). The Suupohja Siberian jays form one of the few isolates of Siberian jays in Southern Finland. I utilised three demographic and three genetic Ne estimators to estimate the Ne and the Ne/N ratio in the Suupohja Siberian jays, and compared the findings to the Ho and A estimates calculated with the same data, and to various suggested MVP standards. The results showed that the ratio of effective and census population sizes (Ne/N) is close to 0.6 in the Suupohja Siberian jays. Uneven survival of offspring and population size fluctuations are the main factors in the formation of this ratio. The average genetic Ne estimate would, then, suggest a census population size of 44 % higher than the average N in the Suupohja study area. This result is probably connected to the high proportion of breeding immigrants in the data, which would cause the Ne estimates to reflect a larger genetic neighbourhood than the study area. The genetic Ne estimates also suggest that the Suupohja Siberian jays might not be able to maintain their genetic diversity in the long term if gene flow would cease due to further isolation, especially if isolation would also cause a faster demographic decline. Conservation attempts should aim at ensuring gene flow to the remaining Siberian jay isolates in Southern Finland, in order to protect them from increasing genetic uniformity and inbreeding. It is possible that while the average dispersal distances in the Siberian jay are short, occasional long-distance dispersal events have an important role in the pretention of genetic structuring in a Siberian jay population. Ne estimation based on demographic data was laborious in the case of the Suupohja Siberian jays, whereas the genetic Ne estimates showed large variation depending on year and estimation method used. Reliable estimation of Ne with genetic methods would have required information on the large-scale genetic structure of the population. In any case, Ne estimates gave a clearer picture on the genetic viability of the Suupohja Siberian jays than the Ho and A estimates, which did not indicate any decrease of genetic diversity during the study period.
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(2019)SH3 domains are relatively short and most common of modular protein binding domain in eukaryotes. They are present in proteins that play critical role in various cell signaling and regulatory pathway. Human genome encoded 296 types of SH3 domains have been successfully displayed in phagemid using classical PelB signal sequence and used for finding novel binding partners. However, given its shorter length and tendency to fold rapidly it is useful to understand if signal sequence that directs SH3 translocation through Co translational pathway is much more efficient in displaying these domains than the one that translocate protein post translationally. For the study, PelB signal sequence of phagemid displayed human SH3 library was replaced with DsbA signal sequence using round the horn PCR method (Site directed mutagenesis) and verified with agarose gel electrophoresis. Subsequently, infective phages were prepared. The infective titer of newly generated DsbAss based library was found to be higher than that of PelBss based library. Both libraries normalized at 1 x1012cfu/ml were panned against known protein targets MC159(Molluscum contagiosum 159), NCF2(Neutrophil cytosolic factor 2) and NS1(Nonstructural protein 1). Enrichment with DsbAss library was moderately higher for each antigen. However sequencing results showed that results for proteins panned with PelBss library were congruent with previous finding whereas DsbAss library selected some potential weak binders and nonspecific ones along with strong binders. Panning results of DsbAss with NCF2 was striking as all clones selected were NCF1 SH3 domains. Although further functional study was not performed. Based on the study, we concluded that both libraries have its own advantage. PelBss based library can be used for finding strong binders while DsbAss based library can be used for studying weaker interaction and functional role of NCF2-NCF1 SH3 domain interaction is still an open question.
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