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  • Lehto, Anne-Mari (2019)
    Tiivistelmä gradun pdf-tiedostossa.
  • Larsson, Aron (2021)
    The science of fish stock assessment is one that is very resource and labor intensive, with stock assessment models historically being based on data that causes a model to overestimate the strength of a population, sometimes with drastic consequences. The need of cost-effective assessment models and approaches increases, which is why I looked into using Bayesian modeling and networks as an approach not often used in fisheries science. I wanted to determine if it could be used to predict both recruitment and spawning stock biomass of four fish species in the north Atlantic, cod, haddock, pollock and capelin, based on no other evidence other than the recruitment or biomass data of the other species and if these results could be used to lower the uncertanties of fish stock models. I used data available on the RAM legacy database to produce four different models with the statistical software R, based on four different Bayes algorithms found in the R-package bnlearn, two based on continuous data and two based on discrete data. What I found was that there is much potential in the Bayesian approach to stock prediction and forecasting, as our prediction error percentage ranged between 1 and 40 percent. The best predictions were made when the species used as evidence had a high correlation coefficient with the target species, which was the case with cod and haddock biomass, which had a unusually high correlation of 0.96. As such, this approach could be used to make preliminary models of interactions between a high amount of species in a specific area, where there is data abundantly available and these models could be used to lower the uncertanties of the stock assessments. However, more research into the applicability for this approach to other species and areas needs to be conducted.
  • Metso, Saana (2023)
    Lethal congenital contracture syndrome 1 (LCCS1) is a severe developmental disorder that is part of the Finnish disease heritage. The affected foetuses die in utero and show a lack of motor neurons accompanied by severe atrophy of the ventral spinal cord and muscles and severe contracture of joints, which result in a lack of involuntary movements. Other associated symptoms include hydrops, micrognatia (small jaw), pulmonary hypodysplasia and small size. The syndrome leads to prenatal death before 32nd gestational week, but the cause remains elusive. LCCS1 is caused by a homozygous mutation, FINmajor, in GLE1 RNA export mediator (GLE1) -gene. The mutation is a c.432- 10A > G substitution at the border of intron three and exon four, resulting in a new splice acceptor site 10 nucleotides upstream of the intron-exon junction. This results in aberrant splicing and nine extra nucleotides in the mRNA, corresponding to three extra amino acids in the GLE1 protein of the affected individuals. GLE1 is an important player in RNA biology in cells. In humans it has two isoforms, GLE1A and GLE1B, that have distinct roles. While GLE1A plays a role in cells’ stress response by mediating the formation and disassembly of stress granules in the cytoplasm, GLE1B is found at the nuclear envelope where it mediates mRNA transport from the nucleus to the cytoplasm. Earlier studies using HeLa cells and zebrafish have demonstrated that FINmajor in GLE1 knock-down background disrupts the mRNA export from nucleus to cytoplasm and leads to apoptosis in neural precursors and abnormal arborization of motor neurons, thus mimicking some of the phenotypic features observed in human patients. Kuure group has generated a mouse model with endogenous FINmajor, but it fails to morphologically phenocopy the human disorder (unpublished data). Importantly, human-origin non-cancerous models with endogenous FINmajor mutation have not yet been used in the studies of GLE1 and LCCS1. My aim in the thesis was to create a human embryonic stem (hES) cell line carrying homozygous FINmajor mutation in its genome. A relatively new tool, CRISPR/CAS -system allows for precise genetic engineering in a variety of model organisms. By optimizing the system to efficiently edit the GLE1 gene, I was able to introduce FINmajor mutation in hES cells, creating a new model system to study this disorder. While previous models had relied on temporary silencing of the gene with morpholinos or siRNAs, the hES cell line with GLE1 FINmajor mutation will for the first time give insights on how the mutation affects cellular functions, mRNA biology and cell differentiation in LCCS1. This way the hES cell line I have generated will yield new information on the development, progression and manifestation of the syndrome to better understand its mechanisms.
  • Rintamäki, Ella-Eevastiina (2024)
    In this thesis, the migration patterns of the legacy pesticide called atrazine were studied in the Laune aquifer in Lahti, Finland, using the MODFLOW groundwater modelling program connected to the MT3D tool. Three models were built for the thesis. In the first model, the migration of atrazine in the Laune aquifer was studied by simulating the steady release of 1.22 µg/L atrazine concentration from sediments in the Lahti railway area over 15 years. In the second model, the depletion of atrazine from soil deposits was studied over time in both sudden and gradual depletion scenarios for 10 and 30 years. In the third model, the effect of pumping contaminated groundwater from an extraction well and injecting remediated water back into the aquifer from another well was investigated on the atrazine concentration in groundwater in the study area for 15 years. Concentrations of atrazine in the aquifer either increased or decreased from the baseline concentrations in the first model. In certain areas in Laune, atrazine concentrations exceeded the EU safe limit values during the whole modelling period. In the second model, the dilution of atrazine was relatively slow, even in the scenario of sudden depletion. It can take decades for the groundwater concentrations to dilute to EU-safe limits once the limits have been exceeded. In the last model, the pumping and injection of remediated groundwater showed a decline in concentration of atrazine over time. However, the effects were only local. Regional effects would have required a higher number of injection wells covering a larger area. Modelling tools are an important part of ethical ecotoxicological research solving many logistical problems related to field studies. However, as the results are highly depend- ent on the parameters, the results should be critically evaluated and used as part of other research methods. In environmental restoration work, understanding and modelling the pa- rameters related to leaching risk can be used as part of risk management. Understanding the migration of stored pesticides into the environment, the development of environmental restoration methods, and preventive measures are crucial to securing clean drinking water quality and quantity in the future.
  • Riitakorpi, Johanna (2020)
    Ecosystem modelling gives us a tool to understand the complicated processes in an ecological system. When studying the changes in an ecosystem, the system health is one of the main characteristics to define. Healthy ecosystem can endure stress and is in stable state. Ecological network analysis and different ecological indices have been used as a basis for measuring the state of an ecosystem, characterizing the dynamics of marine environments, and quantifying the impacts of fishing. The Archipelago Sea, located in Northern Baltic Sea, is characterized by large gradients in salinity and numerous islands. The area is greatly affected by human impact and climate change. However, no broad research on ecosystem changes has been carried out, hence, there is a need for holistic models both scientifically and societally to understanding the changing ecosystem thoroughly and to provide contribution in the decision-making processes of environmental management actions. The aim of this study was to find out how the state of the Archipelago Sea food web has changed from 1990 to 2014. Three steady-state trophic models of the study area for three different years (1990, 2000 and 2014) were constructed using the Ecopath modelling software and approach. The changes in the study area were measured comparing the calculated ecological indices and fishing impact indicators. The models captured changes in the system such as before and after the invasion of non-indigenous species, increase of cormorants, increase of seals, and decrease of cod. The models consist of 23 (1990), 25 (2000) and 27 (2014) different functional groups from predators to producers and detritus. The quality of the models was tested and according to three different approaches, the models can be said to adequately represent the Archipelago Sea food web and ecosystem. The ecosystem indices calculated showed that there had been system wide changes. The state of the Archipelago Sea food web had changed during the study period to a less mature but more resilient condition. This was due to the increase in number of predator species and higher primary production and flow to detritus. The fishing impact on ecosystem changed as fishery practice experienced a change into a more industrialized direction. Changes in trophic levels and ecosystem composition were observed. The invasion of non-indigenous species and the increase in top predators such as seals and the great cormorant affected the structure of the food web. In Addition, the decrease of flounder and unsuccessful recovery of cod have had an impact on the ecosystem and its maturity. Further research on the Archipelago Sea food web is needed. The ecosystem is stressed and does not show recovery; hence, management actions may become necessary. Future simulations based on these Ecopath models would facilitate the selection of the most suitable ecosystem management application. Knowledge of the whole ecosystem and its health is required, and this can be achieved with the help of ecosystem modelling.
  • Johansson, Niko (2024)
    The taxonomy of the green macroalgal genus Monostroma is poorly known in the Baltic Sea region and worldwide.Two species of Monostroma are currently reported from the Baltic Sea: the cosmopolitan spring species Monostroma grevillei and a proposed endemic, free-floating summer species Monostroma balticum. However, previous work has highlighted the unclear taxonomic status of M. balticum, and some consider it a growth form of the cosmopolitan species M. grevillei or a monostromatic growth form of Ulva spp. No molecular data exists of M. balticum, and the morphological characteristics distinguishing this species from M. grevillei and similar species are unclear in the literature. The aim of this thesis is to explore the taxonomic status of M. balticum by firstly systematically reviewing the historical and contemporary literature, including the original description, to illuminate the current morphological circumscription of M. balticum and related species. Secondly, using DNA barcoding based on the tufA -marker, fresh collections of foliose monostromatic green algae from the Baltic Sea region are identified molecularly and put into an evolutionary context using phylogenetics. Thirdly, novel plastid genomes are produced from monostromatic green algae to explore the genomic features of these algae and to see if they aid in species delimitation or phylogenetic approaches. Based on the literature review, the morphological and ecological features used in specimen identification currently (micromorphology, free-floatingness and occurrence in summer) may not be enough for accurate identification, and especially the micromorphological features are quite vaguely described in contemporary literature making their use difficult in practise. All monostromatic specimens collected are identified using DNA barcoding as either M. grevillei, Kornmannia leptoderma or Ulva intestinalis, and those specimens mostly resembling the original description of M. balticum are recovered as U. intestinalis. Plastid genomes were produced from M. grevillei, K. leptoderma and U. intestinalis, from the latter species separate genomes were generated from a typical tubular-morphology specimen as well as a “M. balticum”-morphology specimen. M. grevillei and K. leptoderma plastids were unusual in being large, inflated by many introns and intrageneric regions and having many rearrangements. Produced U. intestinalis plastomes are similar and resemble previously published Ulva genomes. The accurate identification of M. balticum -like specimens is discussed, and for future work DNA barcoding is suggested to be the main tool for specimen identification. This thesis provides evidence towards a previous hypothesis that M. balticum is not a distinct species but a specific growth from of U. intestinalis. Investigating historical herbarium specimens, including original material, using molecular methods is proposed to verify if M. balticum should be synonymised formally with U. intestinalis. The potential drivers of the shift in growth form of U. intestinalis are discussed. Finally, the plastid genome landscape in these foliose green algae is discussed.
  • Sundaresh, Adithi (2022)
    Human induced pluripotent stem cells (iPSCs) are an important in vitro model of disease and development. iPSCs can be differentiated in culture into cell types which are difficult to access from patients, such as neurons. Applying iPSC-derived cellular models to disease studies requires a thorough characterization of the derived cell types, as well as assessing reproducibility across cell lines or differentiation batches. With the aim of providing such a comprehensive molecular characterization at an early stage of cortical neuronal differentiation in vitro, six iPSC lines from four donors were differentiated to cortical neural progenitors using a modification of an established protocol (Shi et al., 2012a). The protocol successfully produced neural progenitors, with over 75% of the differentiated cells aligning with a cortical identity, as confirmed via qPCR and immunocytochemistry of established markers such as PAX6, NES and SOX1. To further classify the cell types produced as well as identify potential differences between cell lines, gene expression of the obtained cells was profiled with single cell RNA sequencing of ~22,000 cells, which uncovered the heterogeneity of neural progenitors produced. Further, although two differentiation batches produced similar cell-type compositions on a whole, a fraction of the lines showed inter-individual differences in cell type composition, which correlated with expression variability of known marker genes. Additionally, the cell types produced in vitro were compared to those produced in vivo by mapping our dataset to a reference fetal brain dataset (Polioudakis et al., 2019). It was observed that the in vitro dataset represented a subset of the cell types present at mid-gestation. Overall, the single cell characterization of differentiated cells allowed greater resolution in understanding cell-type heterogeneity of cortical neurogenesis, which is of key relevance for future applications such as disease modeling.
  • March, Alexander (2016)
    This body of research focuses on establishing a drug screening pipeline for discovering drugs which increase the differentiation of pluripotent stem cells into cardiac myocytes, known as cardiogenic molecules. Cardiomyocytes can be utilized in regenerative medicine by offering a platform for testing molecules or drugs which may increase cardiomyocyte proliferation and for using cardiomyocytes produced outside of the body for clinical transplant, in order to heal the damage caused by heart attacks. Building on known models and developmental pathways three assays were designed and implemented for in vitro cardiogenic molecule screening. A pipeline comprised of three primary screening systems; an embryoid body (EB) model, a cardiomyocyte directed differentiation model, and a magnetic activated cell sort (MACS) model. The MACS model uses the cell surface receptors Fetal Liver Kinase 1 (FLK1) and/or Platelet Derived Growth Factor Receptor alpha (PDGFRα) as the most practical platform for screening drugs against an enriched mesodermal population of cells. The MACS system was confirmed with flow cytometry to ensure the enrichment of Myl2-eGFP+ (ventricular cardiomyocytes) cells in the FLK1+ cells. Furthermore unique known molecules help elucidate the molecular mechanisms governing cardiomyocyte differentiation, measured by cardiomyocyte purity in in vitro models. Also demonstrated are assay controls which decrease purity and acts as negative controls for the MACS assay such as a late stage GSK-3 Inhibitor treatment used to constitutively activate the canonical Wnt/β-catenin pathway and effectively reduce the cardiomyocyte proliferation. Additionally, an early stage Wnt Inhibitor compound IWP-4 was used as a potential positive control effectively blocking late stage activation of canonical Wnt/β-catenin pathway and increase the in vitro purity of cardiomyocytes. These controls provide two important reference points for the many molecules screened over the course of these experiments for the 3i Regeneration project. Additional molecular inhibitors are used to elucidate the mechanism of action within the MACS cells; including a Sonic Hedgehog inhibitor (cyclopamine), an NKX2.5 activator (ISX-9) and a novel small molecule (C1). These models act as an effective pipeline bringing a potential drug through first an EB model, followed by a cardiomyocyte enriched model, to finally a MACS model targeting FLK1. This pipeline tests the molecules against conditions of increasing resemblance to the native microenvironment of a cardiomyocyte.
  • Patrikainen, Linda (2023)
    Breast cancer is globally the leading cause of death in women. ER positive, HER2 negative breast cancer is the most common subgroup, covering two thirds of all breast cancer cases. The different isoforms of ERα, ERα66 and ERα36 are responsible of genomic and non-genomic ER signaling respectively. Tamoxifen is one of the most used drugs in ERα+ breast cancer. As a SERM tamoxifen blocks the activity of ERα66, but plays as an agonist for ERα36, which is associated with tamoxifen resistance. Tamoxifen resistance concerns more than 25% patients with ERα+ breast cancer but the molecular mechanisms that lead to development of resistant disease remain uncovered. Thus, the aim of this thesis was to reveal how two different ERα isoforms are used and regulated in tamoxifen resistance in two commonly used ERα+ breast cancer cell lines MCF7 and T47D. We studied the effect of hormones to tamoxifen sensitivity and to utilization of ERα isoforms. Additionally, we compared the transcriptomics of resistant and parental cells in both cell lines and tested how inhibition of key regulators affect the sensitivity against tamoxifen. In this thesis we report that MCF7 and T47D cell lines obtain different mechanisms of tamoxifen resistance, and that the development of tamoxifen resistance is a parallel process with the cell identity switch from luminal to basal. The EZH2 is involved in maintaining the luminal progenitor type of mammary cells, whereas c-Myc is highly expressed in the resistant cell lines. Hence, EZH2 and c-Myc are key players in development of tamoxifen resistance and could be considered as therapy targets in ERα+ breast cancers.
  • Schach, Julian (2024)
    Phylogenetics is the study of the evolutionary history of life on Earth, which has shifted from relying on morphological characteristics to molecular data with the advancements in sequencing technology. Understanding Earth's biodiversity is crucial, as it has important implications for conservation, ecology, and evolution. Speciation occurs when barriers restrict gene flow between previously interbreeding populations. One such barrier may be endosymbiotic bacteria, like Wolbachia, which can manipulate host reproduction and create incompatibilities between host lineages. Wolbachia is widely distributed among arthropods and is the most common endosymbiont of insects. The bacterium is known to alter its hosts' biology, serving as a master manipulator of reproduction. Wolbachia-induced phenotypes can lead to the divergence of host lineages and speciation events. The genus Cotesia (Hymenoptera: Braconidae: Microgastrinae) is a highly diverse group of parasitoid wasps, where several species parasitize Melitaeini butterflies, including two cryptic species complexes. The current phylogenies of these species are 20 years old and need an update, as they were built with few markers and contain unresolved nodes. Wolbachia has been observed in this system, but its role remains largely unexplored. In this study, I aim to reconstruct the phylogeny of Cotesia species parasitizing Melitaeini butterflies, using two mitochondrial markers and eight nuclear markers to update our understanding of the differentiation of the cryptic Cotesia species. Additionally, I screened the specimens for Wolbachia to determine its possible role in shaping the Cotesia host phylogeny. I expect different Cotesia lineages to carry divergent Wolbachia strains or have different infection statuses (infected vs. uninfected). With fresh Cotesia specimens collected from various locations in Europe, I amplified and sequenced two mitochondrial markers (16s, COI) and eight nuclear markers (18s, 28s, CfCN, CfEN, EF1A1, LwRh, SLD5, TCEB) for phylogenetic analysis. The phylogenetic analysis revealed two main clades: Clade A, where Cotesia acuminata forms a polyphyletic group, and Clade B, where Cotesia melitaearum forms a monophyletic group. Wolbachia was detected only in one species, Cotesia melitaearum Sp. G, where the strain has persisted for over 20 years. The strains infecting Cotesia belong to supergroup B and are all closely related. The close relationship and low infection rate suggest that Wolbachia is not responsible for the original divergence but may play an ongoing role in restricting gene flow between species. The updated phylogeny is in concordance with the previous works but also strengthens our understanding of the relationships within Clade B. Further work is required to resolve some relationships within Clade B and understand the cryptic species' divergence.
  • Varis, Saara (2022)
    Climate change and biodiversity loss are some of the most serious challenges the humanity is facing today. Current food systems are a major contributor to both global crises with massive negative impacts on climate and biodiversity, and thus, sustainable food system transition is inevitable in slowing down the further progress of climate change and biodiversity loss. One way to tackle the unsustainabilities of the food systems is through policy interventions, which can guide both food production and consumption to a more climate- and biodiversity-friendly direction. The aim of this thesis was to examine the popularity of different policy instruments in terms of reducing food’s climate and biodiversity impact among Finnish young adults. Moreover, this thesis aspired to find out which areas of food production and consumption Finnish young adults think policy interventions should target. Young adults were chosen as a target group, because they are in an important position in sustainability transitions. This research is based on survey data and the method applied was content analysis with characteristics from both qualitative and quantitative approaches. The data was analyzed in Atlas.ti program by using inductive and deductive content analysis methods. The results indicate that the most popular policy instruments for reducing food’s impact on climate and biodiversity among Finnish young adults were market-based, including taxes as the most popular and subsidies as the second most popular individual measure. This is in contrast to previous literature, where taxation and other market-based policies have been reported to be the least favored policies. Furthermore, information-based policies, of which especially raising awareness, regulatory instruments, of which particularly price regulation, as well as public procurement policies like a vegetarian day in public food services were among the most popular policy instruments. Although not directly examining acceptability, these results offer a glimpse on policy acceptability, which is found to be crucial in successful policy implementation. Further research is needed to study the acceptability of these policies comprehensively. Moreover, policy target areas related to food consumption rather than production were more popular among the respondents. Target areas such as favoring domestic food, reducing or ending animal product consumption and production, transitioning to vegetarian diets, making better (e.g. climate-friendly) choices easier, and converting meat into a luxury product were the most suggested. These results could be scaled up in future studies and then utilized in creating sustainable policies for food consumption and production, and that way reduce the climate and biodiversity impact they cause.
  • Kylliäinen, Mira (2019)
    Luonnon monimuotoisuus on vähentynyt viime vuosina globaalisti. Puhutaan jopa kuudennesta massasukupuutosta. Myös Suomessa erityisesti vanhojen metsien sekä niitty- ja perinneympäristöjen lajistot ovat heikentyneet. Suurin syy monimuotoisuuden vähenemiseen on elinympäristöjen katoaminen ihmistoiminnan ja maankäytönmuutosten vuoksi. Suomen uhanalaisia lajeja uhkaavat eniten metsä- ja maatalous ja niiden myötä vähenevät lahopuun ja niittyjen määrät. Luontotyypeistä erityisesti jalopuulehdot ovat katoamassa. Osansa maa-alasta vievät myös vapaa-ajan harrastukset, kuten esimerkiksi golf. Golfkenttien vaikutus monimuotoisuuteen on jakanut mielipiteitä. Golfkentän ekologiseen arvoon vaikuttaa se, millaiseen ympäristöön se on rakennettu. Urbaanissa ympäristössä golfkenttä voi merkittävästi lisätä monimuotoisuutta päinvastoin kuin metsäiseen ympäristöön rakennettuna. Golfkentät ovat kuitenkin usein laikuittaisia sisältäen useita erilaisia, pienialaisia kaistaleita alkuperäistä luontoa. Tässä työssä selvitin golfkentän rakentamisen aiheuttamia vaikutuksia metsäekosysteemin alkuperäiseen eliöyhteisöön sekä golfkentän monimuotoisuutta itsessään sekä verrattuna ympäröiviin alueisiin. Lisäksi pohdin, miten monimuotoisuutta kentällä voitaisiin parantaa. Tutkimuskohteena oli Hirsalan golfkenttä Kirkkonummella Etelä-Suomessa. Kesän 2018 aikana tein kentällä luontokartoituksen määrittämällä kentällä havaitut kasvit, nisäkkäät, linnut, matelijat ja sammakkoeläimet, perhoset sekä maakiitäjäiset (Coleoptera: Carabidae). Maakiitäjäisiä keräsin myös kentän reuna-alueelta sekä kentän ulkopuolelta. Perhosten keräämiseen käytin valorysää ja kolmea syöttirysää, keräys kesti toukokuusta elokuuhun. Maakiitäjäiset keräsin kuoppapyydyksillä (yht. 93) samalla aikataululla. Muut taksonit määritin näkö- ja kuulohavaintojen avulla. Mallinsin perhos- ja maakiitäjäisaineistoilla kentän ja vertailualueiden lajistojen runsausjakaumia. Maakiitäjäisaineistolla vertaisin kentän, kentän reuna-alueen ja kentän ulkopuolisen alueen monimuotoisuuksia Shannonin-Wienerin ja Simpsonin diversiteetti-indekseillä. Kasviaineiston avulla tein golfkentän alueesta luontotyyppikartan QGIS- paikkatieto-ohjelmalla. Muut aineistot täydensivät tilastomenetelmillä saatuja tuloksia. Golfkentän saamat diversiteetti-indeksit olivat pienempiä kuin kentän reunalla tai kentän ulkopuolella saadut arvot. Golfkentän lajistojen runsausjakauma oli epätasaisin muiden alueiden runsausjakaumiin verrattuna. Kentällä dominoi aitosysikiitäjäinen (Pterostichus melanarius, 65 % kentän lajistosta), joka on tunnettu häiriöekosysteemien generalistilaji. Perhosaineiston runsausjakauma ei kuitenkaan poikennut vertailuaineistosta. Golfkentällä havaittiin myös uhanalaisia ja suojeltuja lajeja, kuten liito-orava (Pteromys volans) sekä kartioakankaali (Ajuga pyramidalis). Kentällä ja sen läheisyydessä havaittiin myös useita metsäisiä lajeja, joista osa käytti kenttää esimerkiksi saalistamiseen tai laiduntamiseen. Kentältä löytyi luontotyyppejä niin karuista kalliometsistä tuoreisiin kankaisiin ja pähkinäpensaslehtoon. Kentältä löytyi myös joitain haitallisia vieraslajeja, kuten keltamajavankaali (Lysichiton americanus). Kentän rakentaminen on heikentänyt ja muuttanut alkuperäistä metsäekosysteemin eliöyhteisöä. Kenttää voidaan pitää häiriöekosysteeminä, jossa generalistilajit viihtyvät spesialistilajien kadotessa. Alueella voi myös olla vielä jäljellä rakentamisesta aiheutuvaa paikallista sukupuuttovelkaa esimerkiksi kasvi- ja hyönteislajien suhteen. Kenttä yhdessä ympäröivän luonnon kanssa muodostaa laikuittaisen elinympäristön, joka mahdollistaa monien lajien ravinnonhankinnan ja pesimisen kentällä ja sen läheisyydessä. Kentän monimuotoisuutta voitaisiin parantaa lisäämällä kentällä lahopuun sekä niittyjen määrää. Luonnonkasvien lisääminen ja niiden hallittu hoitamattomuus voi lisätä hyönteisten ja kasvinsyöjien määriä ja näin edelleen vaikuttaa kaskadiefektin kautta ylemmille ravintoketjun tasoille. Myös lampien ympärille olisi hyvä jättää suojavyöhykkeet. Alkuperäisiä luontokaistaleita tulisi vaalia, erityisesti kentällä sisällä olevaa pähkinäpensaslehtoa. Kentällä esiintyvät haitalliset vieraslajit ja puutarhakarkulaiset tulisi poistaa, etteivät ne vie elintilaa alkuperäislajeilta. Pöntötyksillä voidaan myös lisätä yksittäisten lajien tilaa lisäämällä niille mahdollisia pesimis- ja levähdyspaikkoja.
  • Holmström, Charlotta (2019)
    Tämän työn tutkimuskohteena on ihmisten ajattelu sekä ympäristö- ja kestävyyskysymysten kompleksisuus sekä Rittelin ja Webberin määrittelemä viheliäisyys. Tavoitteeni on kehittää sellaisia ajattelun välineitä, joilla kestävyysproblematiikkaa voisi ymmärtää mahdollisimman kokonaisvaltaisesti – monilla tasoilla sekä ilman liiallista osiin pilkkomista ja näkökulman tiukkaa rajaamista. Tämänkaltaisten työkalujen kehittämisen tarvetta on tuotu esiin varsin laajasti viime aikoina, kun huoli ilmastonmuutoksen, biodiversiteettikadon ja ilmastopakolaisuuden kaltaisista kompleksisista ongelmavyyhdeistä on kasvanut. Työn tarkempi tavoite on kehittää generalistis-holistis-holarkistinen viitekehys eli GHH-kehys jo olemassa olevan, Risto Willamon aiemmin esittelemän generalistis-holistisen GH-kehyksen pohjalta. GH-kehyksessä kokonaisvaltainen lähestymistapa tiivistetään kahteen ulottuvuuteen: tarkastelun näkökulmien ja kohteiden moninaisuutta korostavaan generalismiin sekä näiden näkökulmien ja kohteiden vuorovaikutusten merkitystä painottavaan holismiin. Lisään työssäni lähestymistapaan kolmannen ulottuvuuden: holarkismin, joka korostaa tarkasteluasetelman jäsentämistä monelle systeemiselle tasolle. Tarkemmalla tasolla tutkimustehtäviä on kolme: 1) GHH-kehyksen muodostaminen lisäämällä holarkismin idea GH-kehykseen, 2) heuristisen ja kehystä konkreettisemman GHH-mallin rakentaminen sekä 3) muodostetun kehyksen ja mallin pienimuotoinen soveltaminen kahden esimerkin avulla. Näistä ensimmäinen liittyy ihmisen luontosuhdekäsityksiin ja toinen YK:n kestävän kehityksen tavoitteiden (Agenda2030) jäsentämiseen. Jälkimmäinen sisältää lisäksi opettajien täydennyskoulutuksen yhteydessä kerätyn pienen empiirisen aineiston. Tuota havainnollistavaa aineiston käsittelyä lukuun ottamatta työ on metodologialtaan käsitteellis-teoreettinen ja työn painotus on voimakkaan epistemologinen ja näkökulmarelativistinen. GHH-kehyksen tärkein merkitys liittyy siihen, että se on eksplikoitu melko tarkasti sekä käsitejärjestelmänsä taustan että ymmärryksen edistämiseen liittyvän käyttönsä osalta. Kokonaisvaltaisessa metodologiassa on toistaiseksi tarkasti sanoitettuja työkaluja aika vähän, mikä vaikeuttaa kokonaisvaltaista työskentelyä. Empiirisen osan tulosten mukaan koulutukseen osallistuvista opettajista moni sai GHH-kehyksestä ja -mallista aidosti apua Agenda2030-tavoitteiden muodostaman kompleksisen kokonaisuuden jäsentämisessä. Nämä tulokset ovat kuitenkin vasta hyvin alustavia, ja työn lopussa esitetäänkin runsaasti ajatuksia sekä GHH-käsitejärjestelmän teoreettiseen että siitä johdettujen ajattelutyökalujen käytännölliseen jatkotutkimukseen.
  • Acosta Leinonen, Johanna Natalia (2019)
    Sleep is one of the most vital functions of newborns and infants, and it is essential for neuronal network development. Therefore, long-term sleep disturbances have been associated with growth delays and behavioral disorders. Commonly reported infant sleep disturbances, such as night awakenings and difficulties falling asleep, cause distress to parents. Yet, the development of infant sleep in the home environment has not been fully elucidated due to lack of objective measurement parameters. In the current study, we assessed the feasibility of a motion sensor, attached to wearable pants, and ECG textile electrodes to monitor sleep-related respiration and heart rate of newborns and infants. First, we compared signals recorded by the motion sensor’s measurement channels to the standard respiratory piezo effort belt’s signal during daytime EEG recordings. According to our results, the motion sensor’s gyroscope proved to measure respiratory rate most accurately, while the ECG signal transmitted by the sensor was reliable in interpretable sections. We then provided wearable garments and smartphones to families with infants to assess overnight home-use. Our results indicate that different sleep states could likely be identified based on respiration fluctuation visible in the gyroscope’s signals. Moreover, the wearable system was considered practical and easy to use by the parents. Future studies should focus on validating the sensor with clinically approved measures, in order to train the algorithms to automatically identify different sleep-wake states. By doing so, the wearable sensor could provide information on natural infant sleep structure development over long time periods. Additionally, clinical validation of the sensor may result in the development of a companion diagnostic tool for infant cardiorespiratory and movement disorders.
  • Koistinen, Ville V. T. (2008)
    Ligniini on heti selluloosan jälkeen puiden toiseksi yleisin rakenteellinen biomolekyyli. Ligniini on tärkeä biopolymeeri sekä biologisesti että taloudellisesti. Ligniini antaa kasville fysikaalista kestävyyttä, erityisesti vettä kuljettavissa solukoissa, se toimii kasvin puolustuksessa patogeeneja vastaan fysikokemiallisena suojana. Taloudellisesti ligniini on sekä haitallinen että hyödyllinen yhdiste. Paperiteollisuudessa ligniinistä pyritään pääsemään tarkasti eroon, koska hapettuessaan valon vaikutuksesta ligniinin absorbanssi muuttuu, ja kellastaa paperin. Energiatalouden kannalta ligniini on hyvin tärkeä molekyyli. Se sisältää paljon hiiltä ja sen polttaminen tuottaa näin ollen runsaasti energiaa. Ligniinin rakennetta kemiallisesti muokkaamalla siitä voidaan valmistaa monia hyödyllisiä yhdisteitä, kuten ravintolisiä, kuidunlähteitä, polttoainetta ja suoja-aineita. Ligniinin biosynteesin tunteminen on edellytys sen rakenteen muuttamiseen hyötykäyttöön. Paperiteollisuuden kannalta erityisen tärkeää olisi yrittää vähentää ligniinin määrää sellupuussa, näin säästettäisiin rahaa ja ympäristöä huomattavasti, koska kemiallinen ja fysikaalinen ligniinin poistaminen paperimassasta on kallista ja ympäristölle haitallista. Toisaalta energiapuun ligniinikoostumusta kannattaisi pikemminkin lisätä, näin puusta saatavaa energiamäärää voidaan tilavuuteen nähden kasvattaa. Ligniinin biosynteesi jakaantuu karkeasti ottaen kolmeen osaan: 1) ligniinin esiasteiden synteesiin 2) esiasteiden kuljetukseen solulimasta soluseinään 3) ligniinin polymerisaatioon soluseinässä. Ligniinin biosynteesin ensimmäinen ja kolmas vaihe tunnetaan yksityiskohdiltaankin jo sangen hyvin. Sen sijaan toinen vaihe esiasteiden kuljetus on lähes täysin tuntematon. Tämä ei suinkaan tarkoita, että kuljetusvaihe olisi biosynteesin kannalta merkityksetön. Päinvastoin, se on hyvin tärkeä osa synteesiä. Kuljetustapahtuma selvittäminen voi hyvinkin lisätä tietämystämme myös ligniinin biosynteesin säätelystä ja ajoituksesta. Kuljetusmekanismia ei tunneta, mutta sille on esitetty kolme hypoteesi: 1) monolignolien suora diffuusio solukalvon läpi soluseinään, 2) Golgin laite –välitteinen kuljetus 3) ABC-transportterivälitteinen kuljetus. Tämän työn tarkoituksena on tutkia Golgin laitteen ja ABC-transporttereiden osallisuutta monolignolien kuljetukseen. Tässä työssä koniferiinia, mahdollista monolignolin kuljetus- ja varastomuotoa vastaan on valmistettu ja karakterisoitu vasta-aine, anti-koniferiini. Anti-koniferiinia käyttämällä on yritetty selvittää koniferiinin paikallistumista kuusen erilaistumisvaiheessa olevissa putkisoluissa. Koniferiinin sijaintia on myös selvitetty lituruohon juuressa ja kuusen A3/85-solukkoviljelmän soluissa. ABC-transporttereiden osallisuutta monolignolien kuljetukseen on selvitetty inhiboimalla monolignolien kuljetusta kuusen solukkoviljelmän soluissa, jotka ovat saaneet radioaktiivista glukoosia ja seuraamalla kuinka inhibiittori vaikuttaa solujen erittämien radioaktiivisten monolignoleiden eritysnopeuksiin. Anti-koniferiinin havaittiin puhdistettuna tunnistavan sekä koniferiinin että koniferyylialkoholin. Jälkimmäisen tunnistus on kuitenkin heikompaa. Koniferiinin havaittiin paikallistuvan kolmevuotiaitten kuusten varressa puutuvien solujen soluseiniin. Lituruohossa koniferiini paikallistuu juuren huntuun. A3/85-soluissa koniferiini paikallistuu vakuolimaisiin rakenteisiin ja pistemäisiin rakenteisiin solukalvon läheisyydestä. Käytetyistä inhibiittoreista vanadaatin ei havaittu inhiboivan monolignoleiden kuljetusta, se päinvastoin kiihdyttää sitä. Reversin 121:stä saadut tulokset ovat tässä vaiheessa vielä ristiriitaisia.
  • Jutila, Suvi (2022)
    As a response to Arctic climate warming, Arctic vegetation is changing. Studies have shown a greening trend both in satellite-derived data (spectral greening) and in field measurements (vegetation greening). Some studies indicate that the increase in vegetation productivity in the Arctic is one of the drivers of the increase in organic carbon in lakes, lake brownification. The aim of this thesis is to bring more knowledge about this possible connection between vegetation change and lake brownification in a circumpolar context. My two main research questions are: 1) How has the summer terrestrial NDVI value, in short, the normalized vegetation index to estimate the amount of green vegetation, changed during the past 20 years in the study areas and is there variation between lake groups? and 2) How has the amount of organic carbon changed in the studied lakes? These questions are complemented by the following sub-questions: Have summer temperature or precipitation affected NDVI change? What is the relationship between summer NDVI and lake organic carbon, and between the change in temperature/precipitation and the change in lake organic carbon? I conducted a circumpolar study about multi-decadal greening and climate trends around 15 Arctic and subarctic lakes divided into five groups, using satellite-derived vegetation data (NDVI). I then compared these data with sediment data to study if potential greening has a connection to the lakes’ total organic carbon load. The study areas are located in South-Central Canada, Alaska, North Finland, Russia – Yakutia and Russia – Chukotka. I found that summer surface air temperature has increased significantly in all of the study areas during 1961-2018. Total summer precipitation has not significantly changed during the study period, but the trend has been positive in all study areas except for Russia, Chukotka. Winter precipitation has significantly decreased in Alaska, and in both of the Russian areas, and significantly increased in Jänkäjärvi, Finland during 1961-2018. NDVI has increased significantly in Jänkäjärvi (Finland), Rauchuagytgyn and Illerney (Russia, Chukotka) during 2000-2021. In these lakes the environmental variables were affecting NDVI. The connection between NDVI in the study areas and lake TOC was positive, but not statistically significant. The situation was the same for the comparison between temperature and TOC for most of the lakes. When comparing the change in summer and winter precipitation and the change in TOC, for most of the lakes, precipitation had decreased while TOC increased. In conclusion, the results indicate that environmental conditions are changing in the study areas and that in some areas that has led to an increase in summer terrestrial NDVI values. It may also be that catchment area greening can increase lake TOC. However, this connection needs more research, for instance with a larger sample size. This study with its varying results also supports the notion of heterogeneous Arctic environments.
  • Ahti, Ella (2023)
    Carnivores all around the world are struggling as a result of increased anthropogenic activity. In many areas, human-carnivore conflict is a main driver of this struggle, driven by environmental challenges and leading to negative results for both people and the wildlife. The natural habitat of most carnivore species is also disappearing fast, which can lead to population decreases and even local or global extinctions of some of the world’s most recognised carnivores. Carnivores have high ecological and cultural significance, and therefore it is vital to understand how these challenges are affecting the different species in various environments. Even though the struggle of carnivores is widely recognised, it has not been widely studied in all parts of the world. In my thesis I study how large carnivores in Sibiloi National Park, northern Kenya, are responding to a quickly increasing anthropogenic pressure in the area. Together with the Daasanach, camera traps were used near bomas for a timespan of three years to discover which species are still habiting this rapidly evolving landscape. I assumed that because of the different robustness at which different carnivore species are able to respond to environmental changes, the most commonly observed species would be the ones that have previously been often seen in the area by the Daasanach and researchers and exhibit a generalist behaviour towards prey and habitat preferences, such as the spotted hyena (Crocuta crocuta). In total I observed over 20 different mammal species out of which 6 were chosen as the focal carnivore species due to the higher amount of interactions they typically have with the people and their livestock. In addition I focus on the possible ecological and behavioural adaptations of the focal species, especially daily activity patterns near the bomas and seasonal variation of encounter rates. These results help us understand how carnivores have adapted to the changing landscape of Sibiloi where human-carnivore conflict has been increasing in recent years. My first hypothesis is that carnivores have become more nocturnal around the bomas than they would be in a completely natural habitat with little anthropogenic pressure to reduce the risk of being harmed by humans. I also hypothesise that there are more carnivores present during the dry seasons (June-September and January-February) due to the decrease in wild herbivores that forces the carnivores near the bomas. Through statistical analysis I will also study the probability of meeting a carnivore near the bomas. I predict that the frequency at which carnivores approach humans and their livestock will depend on the season and if there are either wild herbivores or livestock nearby. In the end I will discuss what implications the study results can have for the future conservation of Sibiloi National Park and why the discoveries of this study are important for mitigating the increasing conflict between the Daasanach and carnivores.
  • Valtonen, Saara (2020)
    Tiivistelmä – Referat – Abstract Sekajätteen koostumuksen tunteminen on tärkeää, kun kierrätystavoitteiden tiukentuessa suunnitellaan toimenpiteitä jätteen määrän vähentämiseksi ja kierrätyksen lisäämiseksi sekä kun arvioidaan toteutettujen toimenpiteiden vaikuttavuutta. Muovipakkausten erilliskeräys aloitettiin pääkaupunkiseudulla vuonna 2016 ja syksystä 2017 lähtien kaikki halukkaat asuinkiinteistöt ovat voineet tilata kiinteistölleen oman muovipakkausten keräysastian. Kiinteistökohtaisen keräyksen lisäksi kotitalouksien muovipakkauksia kerätään myös osalla pääkaupunkiseudun ekopisteistä, joihin muovipakkauksia voivat viedä kaikki alueen asukkaat, myös ne, joilla muovipakkausten erilliskeräystä ei ole järjestetty omalla kiinteistöllä. Tutkimuksen tavoitteena on selvittää, miten muovipakkauskeräyksen aloittaminen on vaikuttanut pääkaupunkiseudun kotitalouksien sekajätteen määrään ja koostumukseen sekä miten muovipakkausten määrä pääkaupunkiseudun kotitalouksien sekajätteessä on muuttunut muovipakkauskeräyksen aloituksen jälkeen. Tutkimuksessa selvitetään myös, miten muovipakkausten erilliskeräys omalla kiinteistöllä vaikuttaa muovipakkausten määrään sekajätteessä pääkaupunkiseudun isoilla yli 19 huoneiston kiinteistöillä. Tuloksia verrataan aiempiin pääkaupunkiseudun kotitalouksien sekajätteen koostumustutkimuksiin. Tutkimus toteutetaan keräämällä yli 15 000 pääkaupunkiseudun asukkaan sekajäte viikon ajalta ja lajittelemalla tutkimuskuormista otetut n. 100 kg:n kokoomanäytteet käsin. Otantamenetelmän käytetään ositettua otantaa. Kotitaloudet jaetaan viiteen eri tutkimusryhmään huoneistomäärien mukaan. Tutkimusryhmät ovat 1 huoneiston kiinteistöt, 2 - 4 huoneiston kiinteistöt, 5 - 9 huoneiston kiinteistöt, 10 - 19 huoneiston kiinteistöt ja yli 19 huoneiston kiinteistöt. Yli 19 huoneiston kiinteistöt jaetaan vielä kahteen ryhmään sen mukaan, onko niissä järjestetty kiinteistökohtainen muovipakkausten erilliskeräys vai ei. Tutkimuksen mukaan pääkaupunkiseudun kotitalouksissa tuotettiin vuonna 2018 keskimäärin 157 kg sekajätettä vuodessa, joka on noin 20 kg vähemmän kuin vuonna 2015. Muovipakkausten määrä kotitalouksien sekajätteessä oli vähentynyt keskimäärin yli 30 %, joka on n. 8 kg asukasta kohti vuodessa. Samaan aikaan markkinoille on laskettu yhä enemmän muovipakkauksia. Pääkaupunkiseudun isoissa, yli 19 huoneiston kiinteistöissä, joissa on muovipakkausten erilliskeräys omalla kiinteistöllä, laitettiin muovipakkauksia sekajätteeseen keskimäärin 14 kg asukasta kohti vuodessa. Yli 19 huoneiston kiinteistöillä, joissa muovipakkausten erilliskeräystä ei ole järjestetty, laitettiin muovipakkauksia sekajätteeseen kesimäärin 17 kg asukasta kohti vuodessa. Muovipakkauskeräyksen aloittaminen on vähentänyt muovipakkauksten määrää pääkaupunkiseudun kotitalouksien sekajätteessä. Pääkaupunkiseudun asukkaat ovat ottaneet muovipakkauskeräyksen hyvin vastaan ja yhä useammat asukkaat lajittelevat muovipakkauksena. Muovipakkauksia lajitelevat myös sellaisissa kiinteistöissä asuvat, joilla ei ole muovipakkauskeräystä omalla kiinteistöllään.
  • Heikkinen, Lea (2019)
    Tiivistelmä – Referat – Abstract Tunnistusmekanismit ovat tärkeä osa lisääntymisaltruismin ylläpitoa, ja isommassa mittakaavassa sosiaalisten järjestelmien olemassaoloa ylipäätään. Altruismia nimittäin mielellään hyödyntävät erilaiset huijarit, jotka vain hyötyvät toisten avusta tarjoamatta itse mitään vastineeksi. Tunnistusmekanismit ovat ase näitä huijareita vastaan. Tunnistusmekanismeja on tutkittu paljon sosiaalisilla hyönteisillä, varsinkin muurahaisilla, koska niiden pesät tarjoavat huijareille, kuten sosiaalisille loisille, houkuttelevan kohteen. Yksi keskeinen tutkimuskohde on jälkeläisten tunnistus – kuinka muurahaiset tunnistavat munia ja minkälaiset tekijät vaikuttavat niiden kykyyn tunnistaa omanlajisia munia. Tavoitteenani oli ensimmäisessä kokeessa selvittää, vaikuttaako loislajin munille altistuminen isäntätyöläisten kykyyn tunnistaa munia, ja miten isännän yhteiskuntarakenne vaikuttaa sen alttiudelle tehdä tunnistusvirheitä. Jatkokokeessa testasin myös, miten loiskuningattaren läsnäolo vaikuttaa isäntätyöläisten kykyyn tunnistaa munia. Tutkin areenakokein isäntälajin, mustamuurahaisen (Formica fusca), kykyä tunnistaa munia. Ensimmäisessä kokeessa käytin isäntälajin orpopesiä ja pesiä, joissa oli vaihteleva määrä kuningattaria. Käsittelynä altistin puolet isäntäpesistä loislajin (kantomuurahainen, Formica truncorum) munille, ennen kuin niiden oma kuningatar tai työläiset olivat alkaneet munia. Puolet pesistä toimi kontrollina. Toisessa kokeessa käytin vain isäntälajin orpokolonioita, jotka jaoin kolmeen käsittelyyn: ensimmäisessä käsittelyssä isäntäpesät altistettiin loislajin (tupsukekomuurhainen, Formica aquilonia) munille, toisessa käsittelyssä isäntäpesään laitettiin loismunien lisäksi loislajin kuningatar ja kolmas käsittely oli kontrolli, jolle ei siis tehty mitään manipulointia. Ensimmäisessä kokeessa havaittiin, että orpokolonioiden työläiset hyväksyivät enemmän loislajin munia, kun ne oli altistettu loisen munille varhain. Väliaikaisen loisen siis kannattaa, mikäli mahdollista, ajoittaa valtausyrityksensä varhaiseen kevääseen ja koettaa erityisesti vallata orpopesiä. Kuningattarellisilla isäntäpesillä nimittäin ei havaittu altistuksen lisäävän työläisten hyväksymien loismunien määrää. Isäntäkuningatarten määrällä ei myöskään ollut vaikutusta siihen, miten työläiset hyväksyvät loisen munia. Toisessa kokeessa ei kummallaan käsittelyllä (loismunien ja loismunien+loiskuningattaren läsnäolo) ollut vaikutusta siihen, miten paljon työläiset hyväksyivät loismunia. Tutkimukseni perusteella tiedämme, minkälaiset ekologiset tekijät voivat edesauttaa väliaikaisten sosiaalisten loisten pesänvaltausta. Ainakin isännän aikainen altistuminen loismunille ja se, että pesä on menettänyt kuningattarensa, lisäävät isäntien tekemiä tunnistusvirheitä siten, että ne hyväksyvät aikaisempaa enemmän loisten munia. Tutkimuksessa selvisi myös, että loislajien välillä oli eroja siinä, kuinka usein niiden munia hyväksyttiin, mikä tukee teoriaa loisten paikallisesta sopeutumisesta isäntälajin populaatioihin. Tulokset sopivat myös yhteen klassisen ekologisen kilpajuoksun periaatteen kanssa, jossa loinen ja isäntälaji pyrkivät jatkuvasti sopeutumalla tekemään tyhjäksi toistensa aikeet.
  • Vainio, Jere (2022)
    Anthocyanins are pigment molecules responsible for the majority of flower colors existing in nature. Emerging from the flavonoid biosynthetic pathway, anthocyanin biosynthetic pathway branches into orange pelargonidin derivates, red cyanidin derivates and blue delphinidin derivates. Dihydroflavonol 4-reductase (DFR), a NADPH-dependent oxidoreductase, catalyzes the first anthocyanin specific step after the branching point for all three branches. In some cases, DFR exhibits substrate specificity leading to some flowering plant species’ inability to produce certain colors; like petunias lacking orange colors. Ornamental plant industry thrives on breeding of novel colors and color patterns, and thus understanding of the capabilities of anthocyanin biosynthesis is of key importance. The aim of this study is to gain insight into the amino acid residues causing substrate specificities in Petunia hybrida. The study focused on an amino acid region that has been previously identified as affecting substrate specificities in Gerbera hybrida. To examine the effects of three different mutations in this region, enzyme activity was examined both in vitro and in vivo. Experiments consisted of kinetic assays with protein extracts from infiltrated Nicotiana benthamiana and determination of anthocyanin content from stable transformations of Petunia hybrida. Anthocyanin content was determined from transformed petunia flowers with high performance liquid chromatography. Kinetic assays show distinct substrate specificity profiles for all three mutations, indicating a correlation between the studied residues and substrate specificity. The transformed petunias also exhibited altered anthocyanin content, with two of the three mutant transformants exhibiting increased pelargonidin production. The observed effects of these mutations support the previous results indicating that this region has a role in determining substrate specificities of DFR enzymes.