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  • Aulio, Mikko (2023)
    Supplementary bird feeding is a popular pastime, as well as one of the most important types of human–wildlife interaction, in Western countries. Bird-feeder sites are visited by birds, mammals, as well as other animals; some of these species are wanted visitors, some unwanted. Supplementary food at feeding sites offers visitors benefits, at least during winter. However, effects at the species, population and community level can be complex, and none of these levels necessarily benefit automatically from supplementary feeding. On the other hand, bird feeding generally increases human wellbeing. Animal attitudes affect the way we think about non-human animals. It has been discovered that how we view animals visiting feeding sites affects the ways in which people feasibly change the supplementary feeding they provide. Research on the subject has mostly been Anglo-American in context to date. Animal attitudes also affect official rules and regulations that govern the supplementary feeding or control measures of wildlife, for example. In this thesis, I have investigated the responses from a 2021 survey by the Finnish Museum of Natural History (Luomus) and BirdLife Finland. The survey was concerned with supplementary bird feeding and recent changes thereof. The survey got over 14,000 responses, over 9,000 of which included answers to open-ended questions. I sifted through the open-ended responses to find out which animal species and other organisms affect supplementary bird feeding provided by the respondents, and why. I utilised both quantitative and qualitative research methods to uncover such organisms and their effects. I used qualitative content analysis as my main method. I discovered that there are many types of primarily animal-/organism-related reasons behind changes in bird-feeding behaviour. I categorised these 28 reasons under seven subcategories within three main categories. Many of the reasons can have both negative (stop/decrease/shorten) and positive (start/increase/extend) effects on supplementary feeding. A discernible portion of the reasons are propped by one animal attitude or another. The category-based assortment of reasons acts as the main finding of this study, and it reflects the complexity of animal attitudes. I have additionally listed all taxons (species/groups of organisms) found in the survey responses along with their effects on supplementary feeding. I have produced novel information on which animal-related factors affect supplementary bird feeding in Finland, and why. Were we to better understand the inherent complexity of animal attitudes, authorities’ facts-based decision-making and a favourable general attitude towards endangered-species conservation could be enhanced. Zoonosis control could also gain new perspectives from novel information.
  • Moog, Maia (2022)
    Catastrophic childhood epilepsies are characterized by persistent seizures and are frequently associated with cognitive and developmental impairments. Many, approximately 30%, of these epilepsies are rare genetic disorders that do not have effective therapeutic options. The bench to drug process is lengthy and expensive, and thus it is critical to find more affordable drug screening options. Zebrafish are an ideal model organism for screening studies as they share considerable (70%) genetic similarities with humans and are cheap to maintain with efficient breeding capabilities. In the present study, 37 zebrafish lines were screened for epileptic brain activity to identify high priority genes for future pharmacology studies. Each zebrafish line, generated by CRISPR-Cas9 represents a single gene loss of function mutation associated with 3 epilepsy based on genome wide association studies. Larval zebrafish were screened for spontaneous seizure activity using electrophysiological assays. The following 8 genes were significantly associated with spontaneous seizure activity in zebrafish: EEF1A, ARX, GRIN1, GABRB3, PNPO, STRADA, SCN1A, and STXBP1. There is now an open-source database for all 37 zebrafish lines, which contains sequencing information, survival curves, behavioral profiles, and electrophysiological data. The findings reveal novel target genes for future drug development and discovery. Future work is needed to explore whether zebrafish also model co-morbidities commonly seen in human patients with epilepsy.
  • Toivio, Viivi (2017)
    Lämpenevä ilmasto muuttaa boreaalisten metsien lajikoostumusta. Uudet lajit levittäytyvät yhä pohjoisemmaksi lämpenemisen siirtäessä kullekin lajille luontaisia elinympäristöjä. Lisäksi perustuotannon, karikkeen hajoamisen ja ravinteiden saatavuuden on ennustettu muuttuvan, mikä asettaa uusia sopeutumistarpeita kasvien typpitaloudelle. Erityisesti pitkäikäiset puut kohtaavat merkittävän haasteen suotuisten elinympäristöjen siirtyessä nopeammin kuin puut kykenevät itse leviämään uusiin kasvuympäristöihin. Tässä pro gradu- työssä tarkastelen elinympäristön muutoksen vaikutuksia neljän rauduskoivupopulaation (Betula pendula) puiden elinvoimaisuutta ilmentäviin ominaisuuksiin sekä niiden tuottaman karikkeen laatuun ja hajoamiseen. Hyödynsin tutkimuksessani olemassa olevaa koeasetelmaa, jossa pohjois-eteläsuuntaista gradienttia edustavista populaatioista (alkuperistä) kloonattuja rauduskoivun taimia on istutettu yhteisille "common garden" -kasvupaikoille Tuusulaan, Joensuuhun ja Kolariin. Erityisesti etelään päin siirron on tarkoitus simuloida ilmaston lämpenemistä. Tutkimusaineistoni koostuu 233 taimesta, joista määritin pituuskasvun, lehtien hiili- (C), typpi- (N) ja vesipitoisuuden sekä typen takaisinottotehokkuuden, lehtialaindeksin ja herbivorivioituksen. Lisäksi määritin maatuvan lehtikarikkeen massahäviön ja lehtikarikkeesta vapautuvan typen määrän 3 kk kestäneessä maatumiskokeessa. Aineiston keräsin puiden neljäntenä kasvukautena aikavälillä 27.6.2014 – 6.3.2015. Tulosten tilastolliseen analysoimiseen käytin varianssi- ja korrelaatioanalyysejä. Vihreiden lehtien N-pitoisuus (%) pieneni lineaarisesti pohjois-eteläsuuntaisesti, kun taas typen takaisinottotehokkuus heikkeni ja muodostuvan lehtikarikkeen N % kasvoi, kun populaatioita siirrettiin pohjoiseen tai etelään alkuperäiseltä kasvupaikaltaan. Siirto vähensi myös pituuskasvua ja lehtien vesipitoisuutta. Herbivorivioitus ja lehtialaindeksi eivät reagoineet siirtoon. Vihreiden lehtien N % korreloi positiivisesti typen takaisinottotehokkuuden kanssa. Mitä suurempi takaisinottotehokkuus, sitä pienempi oli typpipitoisuus lehtikarikkeessa. Maatuvan karikkeen massahäviö kasvoi, mitä suurempi oli maatuvan karikkeen N-pitoisuus. Erityisesti Joensuun ja Tuusulan kasvupaikoilta kerätyn karikkeen massahäviö oli sitä suurempaa, mitä pohjoisemmasta alkuperästä oli kyse. Typpeä ei vapautunut maatumiskokeen aikana, eikä typen vapautuminen korreloinut lehdistä mitattujen ominaisuuksien kanssa. Tulokseni osoittavat, että rauduskoivun pituuskasvu, lehtien vesipitoisuus ja sisäinen typpitalous ovat parhaimmillaan alkuperäisellä kasvupaikalla, ts. populaatiot ovat paikallisesti sopeutuneita. Muutokset typen takaisinottotehokkuudessa näyttävät liittyvän rauduskoivun kasvuun, joka heikkeni elinympäristön muuttuessa. Populaatioiden pohjois-etelä-siirto heikensi typen takaisinottotehokkuutta ja lisäsi maatuvan karikkeen massahäviötä. Tulokseni osoittavat, että tulevaisuuden muuttuvat ilmasto- ja ympäristöolosuhteet voivat heikentää puiden elinvoimaisuutta pohjoisissa ekosysteemeissä, mutta toisaalta samanaikaisesti kiihdyttää karikkeen maatumista parantamalla muodostuvan kasvikarikkeen laatua.
  • Norontaus, Maija (2022)
    Mercury is a toxic heavy metal that ends up in aquatic ecosystems both as atmospheric deposition as well as from the catchment area surrounding the water body. Under the right circumstances, inorganic mercury can be methylated into methylmercury, which accumulates in organisms and food webs and is harmful to humans and animals. Humans are exposed to methylmercury mainly through consumed fish as almost all the total mercury content in fish muscle consist of methylmercury. Mercury content of fish is affected by numerous different factors, such as the food consumed by the fish, the characteristics of the fish species and fish individual, level of lake eutrophication, mercury concentration in water and catchment area. Thesis studies total mercury content and mercury bioaccumulation in cyprinid fish. The species included in the study are roach (Rutilus rutilus), bream (Abramis brama), bleak (Alburnus alburnus), white bream (Blicca bjoerkna), blue bream (Ballerus ballerus), ide (Leuciscus idus), tench (Tinca tinca), rudd (Scardinius erythrophthalmus) and crucian carp (Carassius carassius). Three main research questions were: (1) Can diet of different cyprinid fish explain the mercury content? (2) Is mercury content consistent between fish species in different lake types, or does lake type affect mercury content? (3) Is mercury bioaccumulation consistently similar between fish species between lake types? The fish samples for this study were gathered prior to MSc during July-August in 2020 and 2021 from Kukkia, Hauhonselkä and Pääjärvi, which are classified as mesotrophic lakes, and from eutrophic Vesijärvi, Tuusulanjärvi and Hulausjärvi. Total length, weight, sex, sexual maturity, condition factor (K), fish diet and muscle total mercury content were determined from each fish. The diet of the fish and the differences in the total mercury content were tested with analysis of variance. Mercury bioaccumulation was tested with using linear regression analysis and the slope coefficient obtained from the regression equation was tested for bleak and roach with t-test. From the abundant species of the study the highest length corrected (to length 16.6 cm) mercury contents were measured in bleak and roach, while the contents were lower in white bream and bream. The mercury content differed most clearly in species whose feeding behaviour was very specialized. For example, the differences in mercury contents between bleak, which mainly consumes surface insects and zooplankton, and bream, which prefers benthic food, were clear in every lake studied. Mercury contents were mainly higher in mesotrophic lakes compared to eutrophic lakes, but results varied by species. In addition to fish diet and lake type, fish’s metabolism, growth rate and life cycle length probably influenced the species-specific mercury contents. When comparing the abundant species, the bioaccumulation of mercury was steepest in bleak and roach. Compared to these species’ bioaccumulation was slower in white bream and bream. When comparing mercury bioaccumulation within species between different lake types, the differences were species-specific. For example, the bioaccumulation of bleak was consistently steeper in mesotrophic lakes compared to eutrophic lakes, but the bioaccumulation of white bream was steeper in eutrophic lakes. Based on this study, it can be concluded that mercury content and bioaccumulation in cyprinid fish were influenced by e.g., species-specific characteristics, fish diet and level of the lake productivity. In addition to these factors, mercury content and bioaccumulation of fish may have been affected by the land use of the lake catchment area, as well as the anoxic areas of the lakes, which are propitious places for methylation. This study provided valid information on which factors may be relevant for cyprinid fish when observing their mercury content and bioaccumulation.
  • Jokinen, Maija (2019)
    Parvoviruses are among the smallest known viruses. The parvovirus genome is a single stranded DNA, approximately 5 kb in size. The virion has a small (20 to 30 nm), rugged, non-enveloped icosahedral capsid. Parvoviruses can cause a number of diseases. Possibly the most recognized human parvovirus is parvovirus B19 (B19V), which can cause the so-called fifth disease, anemias and fetal death. Another relatively well characterised parvovirus is human bocavirus 1 (HBoV1), which causes respiratory tract infections in young children. Bufavirus (BuV) tusavirus (TuV) and cutavirus (CuV) are emerging parvoviruses, discovered during the years 2012-2016 using next generation sequencing methods. All three viruses were originally discovered in feces of patients suffering from diarrhea. BuV was originally found in Burkina Faso and has since been detected in fecal samples with polymerase chain reaction (PCR)-based methods from Europe, Asia and Africa. The seroprevalence of BuV differs between countries. TuV was found in a single stool sample from Tunisia, but no further reports of it have since emerged. CuV was found in 2016 and it has been linked to cutaneous T-cell lymphoma, but it is not known if the virus is the cause of the cancer or if the virus simply prefers quickly dividing cancer cells for its replication. BuV, TuV and CuV belong to the Protoparvovirus genus, but it is still unclear whether TuV is a human pathogen. More research is needed to study the epidemiology of these viruses and their role in illnesses. There were two main aims in this thesis: to set up an IgM µ-capture enzyme immunoassay (EIA) for human protoparvoviruses using BuV1 as an example and to screen three stool sample cohorts for BuV, TuV and CuV using an in-house multiplex quantitative PCR (qPCR). The IgM EIAs developed for B19V and HBoV1 was used as the base for developing human protoparvovirus IgM EIA, using Virus-like particles (VLP) as antigens. Setting up the EIA required a great amount of optimization and finally troubleshooting, since the assay did not work as expected. The troubleshooting revealed that the ambiguous results in the IgM µ-capture EIA were possibly due to degraded VLPs or that the sensitive µ-capture format requires extremely carefully purified VLPs. More optimizing is needed for this assay, however, the work done in this thesis offers a good base for further development of protoparvovirus IgM EIA. All three viruses were found in the stool samples during multiplex qPCR screening. Based on the qPCR and sequencing results one sample was positive for BuV DNA, one sample for TuV DNA and a total of 12 samples for CuV DNA. This is the first time TuV DNA has been found since its discovery. In addition to that, CuV DNA was identified in fecal samples for the first time since the discovery, previously CuV DNA had been found mostly in skin biopsies. As for TuV, based on the parvovirus phylogenetic analyses, its sequence is more closely related to rodent parvoviruses than CuV or BuV. More research is needed, possibly with animal and human samples, to establish the role of TuV as a human virus.
  • Arima, Tai (2022)
    Clathrin-mediated endocytosis is the most common pathway by which cells internalize cargoes from the membrane. It is a critical process in cell communication, development, and homeostasis. In order to study endocytic dynamics, it is critical that one can clearly distinguish receptors that have entered the cell from those which remain on the cell membrane. Current techniques for investigating endocytosis rely on removing membrane-bound components with harsh treatments which may interfere with cell physiology, and often depend on antibodies which are not widely available and - even when they are - may give unreliable signals and may affect receptor behavior and internalization rates. Additionally, a large portion of studies on clathrin-mediated endocytosis have been done on a single receptor, the transferrin receptor. Here we have developed a new assay which resolves the above issues through use of a novel protein probe. This fusion protein will allow us to resolve the issues with current endocytic assays mentioned above, and in theory can be used to study any membrane receptor which is endocytosed. Our preliminary results show that we can use our protein to effectively track endocytosed receptors without interference from signal of receptors remaining on the cell membrane. This shows that our protein may be a powerful tool for studying endocytosis across a wide variety of membrane-bound receptors.
  • Lähteenmäki, Lauri (2020)
    Russia’s energy security is considered to rest on hydrocarbon exports, as the country’s economy and political regime depends on revenue generated in energy trade. Today, Russia faces a problem, as interests toward climate change mitigation and renewable energy have increased globally. Particularly the EU, Russia’s primary gas trade partner, seeks to reduce fossil fuel consumption due to its climate policy targets and concerns over energy security. Via the Yamal LNG project, Russia begun to diversify its markets toward East Asia in 2017. The project is expected to spur energy infrastructure development in the Arctic region, as it ships liquefied natural gas (LNG) along the Northern Sea Route. This study finds out how the stakeholders of the Yamal LNG project consider it to connect with the energy security of Russia, to which climate change mitigation poses a potential threat. Since securitization of energy is the result of a social process where political actors contest over the meanings of energy, the study also looks at whose interests the Yamal LNG project actually secures as “energy security”, and how that concept becomes projected as a general national interest, instead of having energy transition among the top objectives of energy policy. Neo-Gramscian analytical approach and frame analysis are used to deliver results from a data consisting of 11 research interviews and 40 archival sources. The stakeholders make sense of Yamal LNG’s relation to energy security and energy transition through four frames, which reflect distinct interest groups. The stakeholders appeal on others by utilizing the frames discursively, as they strategically contest over the meanings of energy. Ultimately, a hegemonic group consisting of the Russian state, JSC Yamal LNG shareholders, industrial organizations, and fossil energy lobbies determines the meanings of Yamal LNG’s production as general interests. Subordinate groups, including environmental NGOs and local indigenous residents, consent as they face combinations of discursive, organizational and material power. With the concession of others, the hegemonic group is able to project a “reality” that presents natural gas production as compatible with energy transition and climate change mitigation as an inferior interest to energy security. The Yamal LNG case shows that incumbent fossil energy regimes can effectively counter attempts to direct energy policy on low-carbon paths by pleading to security, which is a topic that research often neglects.
  • Kaya, Meryem Ecem (2019)
    Synthetic biology is an emerging interdisciplinary field of biology that aims to system-atically design artificial biological systems. As synthetic biologists seek increasingly complex control over cellular processes to achieve robust and predictable systems. A new frontier in synthetic biology is engineering synthetic microbial consortia. This ap-proach employs the concept of division of labor, instead of introducing large genetic cir-cuitry to homogenous cell populations. In this approach, different cell types are assigned to execute a portion of the overall circuit. Each cell type communicates with their co-worker subpopulations to complete the circuit. The main advantage of this strategy is the reduced metabolic burden on each cell type. Thus, leading to more reliable and stable overall performance. In this work, to simplify cellular communication between the mem-bers of the consortium, we used the simple architecture of quorum sensing machinery. We constructed a toolbox that contains promoter, receptor and quorum sensing signal synthase genes along with fluorescent reporters. Using this toolbox, we constructed dif-ferent cell types that can be used in synthetic consortia forming various communication topologies. We characterized the constructed cell types individually and in co-cultures.
  • Alander, Sari (2012)
    The Arctic region is experiencing significant environmental, social and geopolitical changes as climate change impacts the region and thaws the Arctic sea-ice. The notable amount of emerging hydrocarbon and other resources as well as new navigation routes have attracted a lot of interest by a variety of Arctic and non-Arctic actors. The European Union (EU) has been one of these actors. The Arctic affairs have gained increasing attention within its institutions since the launching of the EU s Arctic policy in 2008. The purpose of this study is to find out how the Arctic is perceived in the eyes of the EU as well as how and to what extent the environmental dimension emerge in relation to other topics. A secondary purpose is to examine how these perceptions have changed since 2008. A comprehensive material is used, covering all relevant EU documents. The material is analyzed using a three-staged coding method within Grounded theory. The EU documents discuss several important topics relating to the Arctic region. This study identifies six categories of these topics. These relate to the changes that the Arctic region is facing, the emerging resources, the geopolitical situation and the governance of the region, the EU s role in the Arctic as well as the protection of the Arctic environment. The qualitative approach is mixed with quantitative aspect to find out how much attention each of these concepts get in the documents and how significant the environmental dimension is compared to the other concepts. The EU is globally recognized as an ambitious environmental actor. This study shows that the environmental aspects are well represented also in the EU s Arctic policy documents. The focus of the documents has changed over the years from Arctic resources and a range of problems towards the importance of cooperation and environmental protection in the region. Environmental protection has been motivated by the responsibilities that the EU feels towards the region. However, a goal has simultaneously been to be acknowledged as a legitimate Arctic actor, which would highly benefit the EU in a number of ways. There is nonetheless reason to presume that the EU is serious in pursuing protection of the Arctic environment and this cannot be seen merely as a means to achieve other ends.
  • Pazos Boubeta, Yago (2019)
    Neurotrophin, Brain-derived neurotrophic factor (BDNF) and its cognate receptor Tropomyosin receptor kinase B (TrkB), have been concomitantly linked with neuronal plasticity as well as antidepressant mechanism of action. Adult hippocampal neurogenesis involves proliferation and survival of new-born neurons and has been related to antidepressant mechanisms and cognitive improvement. Environmental enrichment (EE) enhances adult hippocampal neurogenesis (AHN) and induces anxiolytic-like effects. This study postulates that EE-living conditions could restore the abnormal serotonergic modulation on AHN of our transgenic mice. In this study, a transgenic mouse line wherein TrkB receptor is compromised from serotonergic neurons and AHN found to be impaired was used. To assess the behavioural effects and the changes in learning and memory tasks produced by 10-weeks of EE, a behavioural battery test was performed. Our results suggested anxiolytic-like effects from EE in the transgenic mice. Likewise, cognitive improvements were also observed in both control and transgenic mice promoted by EE. Moreover, hyperactivity observed in transgenic mice in standard conditions could be rescued, and no phenotypical differences were observed between control and transgenic mice subjected to EE. To further study the effects of EE on AHN, cellular proliferation and survival were studied through the incorporation of BrdU. The results indicate that the abnormal serotonergic regulation of AHN was rescued upon EE-living conditions. Moreover, molecular methods used to measure the alteration of gene expression revealed significant upregulation of genes related to neuronal plasticity and epigenetic modifications. Altogether, these results suggest EE promotes the neuronal plasticity, rescues the impaired regulation of AHN and modulates the genetic expression of the transgenic mice. Findings from this study could provide new insights regarding novel targets that could modulate adult brain plasticity.
  • Syrjälä, Sami (2021)
    Electronic waste is the fastest growing type of waste stream in the world, and this development results from the rapidly accelerating digitalization. Electronic devices become obsolete on an accelerating speed, as there are constantly more powerful devices coming to the market. The most significant environmental impacts of this development are greenhouse gas emissions and natural resource consumption. Circular economy has been proposed as a solution to these environmental challenges, and the goal of this approach is to preserve the value of the materials in the circulation as efficiently as possible. One way of implementing the principles of circular economy is the product-as-a-service-based business model. This research examines the differences between the product-as-a-service-based model and ownership-based model in terms of the environmental impacts that are related to the laptop and tablet procurements. The results of this thesis will be utilized in implementing the actions of the City of Helsinki’s Roadmap for Circular and Sharing Economy. This research was conducted as streamlined life cycle assessment, in which the systematic literature review was used for tracking the environmental impacts of the products’ life cycle stages and components. In addition, expert interviews were carried out in order to collect information about the reuse and recycling practices of the supplier companies that follow these previously mentioned business models. Finally, based on the results of the systematic literature review and the interviews, the company specific differences were assessed in terms of the greenhouse gas emissions and material waste that result from the procurements. The City of Helsinki’s annual procurement volumes were used in this assessment. Based on the results of this research, production and use are the most significant life cycle stages in terms of the devices’ greenhouse gas emissions. Printed circuit boards/printed wiring boards, integrated circuits, displays, and casings are the components with the most significant impact. The results suggest that increasing the lifespan of the devices provides opportunities for significantly lowering impacts in both impact categories, if the devices are efficiently recycled after this.
  • Kivisaari, Kiira (2022)
    Environmental sustainability and environmentally responsible management have found their way as discussion topics in the Finnish contemporary art field. The contemporary art event Helsinki Biennial chose to make environmental sustainability as one of their corner stones of producing the event (Taskinen et al 2021). In this master’s thesis I assess the environmental responsibility of Helsinki Biennial and how its environmental actions reflect on the expectations of the contemporary art field in Finland from a managerial perspective. The research was conducted through autoethnographic and content analysis methods. This research will try to answer three questions 1. What environmental actions were taken and how were they selected? (R1) 2. How do the environmental action taken compare to the current expectations of environmentally responsible management in the Finnish contemporary art field? (R2) I am also interested in finding out 3. What types of hopes and concerns about future work are identified by Helsinki Biennial organizers and other experts in the Finnish contemporary art field? (R3) The results show that Helsinki Biennial compared well on the expectations of the field. Based on the answers of the interviewees, there is a lot of potential and moti-vation within the field which waits to be unleashed, for example through new financ-ing and travel policies and by increasing the knowledge and time resource of em-ployees. This study also found out about the future visions regarding environmental matters within the contemporary art field.
  • Joensuu, Laura (2010)
    Carbon dioxide (CO2) is the most significant greenhouse gas produced by mankind. The oceans play a significant role in the global carbon cycle. Due to its restricted size the Baltic Sea doesn't play an important role as a global reservoir. However, due to its large annual fluctuations, alternations in salinity in the different basins, and a wide drainage-basin with varying soil, it is an excellent study system. The aim of this research was to examine both the vertical and the horizontal distributions of the components of the inorganic carbon in the Baltic Sea, their interactions and annual fluctuations. In addition, the long-term alterations of the surface water pH were reviewed. The study was performed at the Finnish Meteorological Institute as a part of an international research programme regarding the Baltic Sea (BONUS: Baltic-C). The total alkalinity in the Baltic Sea was found to be determined mainly by salinity. Surface water alkalinity is controlled by mixing of highly saline waters originating in the North Sea and waters of low salinity from the rivers draining into the Baltic Sea. The amount of total alkalinity entering the Baltic Sea through the rivers is dependent on the soil quality in the catchment area. According to the alkalinity-salinity-relation, the Baltic Sea can be divided into four distinguishable basins. The alkalinity is lowest in the Bothnian Bay and grows towards the Kattegat as a function of salinity. Salinity controls alkalinity, which together with biological activity controls the concentration of total inorganic carbon. The distribution of total inorganic carbon is very similar to that of total alkalinity. The results in this study support earlier findings on total inorganic carbon and total alkalinity in the Baltic Sea. As the atmospheric partial pressure of carbon dioxide (pCO2) rises, the partial pressure in the surface waters rises as well. In addition to the concentration of total inorganic carbon, the biological activity has a great impact on the annual fluctuations of pCO2. The primary production forms the basis of the biological uptake of carbon dioxide in the surface waters. The results indicate that the Baltic Sea fluctuates from being a source to being a sink for atmospheric CO2 according to the annual fluctuations in primary production. However, simultaneous measurements on the atmospheric pCO2 are needed to ascertain the assumptions on the direction of CO2 flux between the sea and the atmosphere. The rise of the pCO2 in water leads to descending pH levels, because of a relative shift in the components of total inorganic carbon. The results indicate a slight decreasing trend in pH levels In the Baltic Sea during the 30-year observation period, however more research on the subject is needed. The reliability of pCO2-values calculated from known parameters was estimated by comparing them to the measured values. The study shows that pCO2 results for the Baltic Sea derived from the program developed for the oceans, should be used with caution.
  • Niskanen, Julia (2016)
    Epidermolysis bullosa (EB) is a group of hereditary skin disorders caused by mutations in the genes that code for adhesion molecules in keratinocytes. The symptoms of the disease include blisters and erosions in the skin as well as abnormalities in the mucosal membranes, nails and tooth enamel. Depending on the causative mutation the severity of the disease ranges from mild to lethal. This master s thesis was carried out in professor Hannes Lohi s canine genetics research group. It is a case study aiming to identify the genetic cause of EB present in Central Asian shepherd dogs. Furthermore, the mode of inheritance, frequency of the mutation in the breed and the effect of the mutation on the tissue were also examined. Primary research material included blood and tissue samples from a family of Central Asian shepherd dogs. Additional samples were obtained from other Central Asian shepherd dogs as well as from dogs of closely related breeds. All dogs included in this study are owned by private persons, and participation in this study was voluntary. The research methods used in this study included both wet laboratory experiments and bioinformatic in silico procedures. The genome of one affected dog was sequenced in order to identify the gene causing EB, and data from the sequencing was filtered with multiple programs according to recessive model. The model was decided after analyzing the pedigree of the affected dogs. After finding the likely causative gene the mutation was validated in a larger cohort with Sanger sequencing. Protein expression in the tissue of affected dogs was also studied using immunofluorescence staining. As a result of this study, a new mutation causing recessive dystrophic EB was identified. The mutation is specific to Central Asian shepherd dogs. Affected dogs have a homozygous mutation in the COL7A1 gene, which codes for collagen VII α1 protein. The mutation causes a premature stop codon in the mRNA sequence, which results in abnormal protein production and separation of skin layers. The frequency of the mutation allele in the sample is approximately 18 % and more than a fourth of the dogs in the sample are carriers. Based on the pedigree analysis, the mutation is relatively new and it is only found in a small population. The disease can be prevented from becoming more common in the breed with the help of a gene test, and the test will be available in the commercial MyDogDNA gene test panel.
  • elDandashi, Rahaf (2021)
    Epigenetics is the study of changes in gene function without affecting the DNA sequence. Epigenetics studies the effects of the environment and behavior on the genome. Researchers have been able to detect several epigenetic modifications such as –DNA methylation, histone acetylation, and microRNA-associated gene silencing. Changes in the epigenome are essential for proper cell function and normal development and can also be induced by environmental factors. Stress is defined as a biological response to physiological and psychological demands which can affect cellular homeostasis. Factors such as prenatal life stress can affect gene function without directly altering the DNA nucleotide sequence. Elevated levels of stress can immobilize with the ability to impair cognitive function. There is evidence that suggests the involvement of epigenetic regulation in disorders such as addiction, depression, schizophrenia, and cognitive dysfunction. Therefore, this systematic review discusses recent findings of the role of epigenetics in prenatal exposure to stress. To achieve this, the thesis will cover different subtopics from genetics, neurobiology, and diseases, neuroscience, biological psychiatry, life sciences, medicine, behavioral brain research, biochemistry & molecular biology, as well as neuroendocrinology. Research questions are 1) Is there an association between epigenetics and prenatal stress? 2) What kind of mechanisms have been found? 3) What kind of techniques have been used in the identification of potential epigenetic mechanisms? What genes are associated with these epigenetic changes?. This study followed the "The Preferred Reporting Items for Systematic Reviews and Meta-Analyses" (PRISMA) guideline checklist. Eligibility criteria and search terms where be selected and documented to offer the widest range of articles covering the subjects of this study. A literature search was done using PubMed/Medline, Google scholar, and gray literature. The last sample comprised 59 articles. Data were extracted so that the participants, intervention, comparisons, and outcomes were included. The literature search conducted in this systematic review identified a few findings. First is that the majority of animal and human studies found a significant or moderate association between epigenetics and prenatal stress. Second, DNA methylation is the most studied epigenetic mechanism in maternal exposure to stress Third, genome-wide studies were more common in human studies than in animals and the most widely used method used is Infinium HumanMethylation450 Bead Chip. However, the common methods used in human and animal studies are most likely because of the small sample size and causation cannot be determined. Finally, NR3C1 and FKBP5 genes were the most studied in human studies where they showed the strongest association between prenatal stress and epigenetic modifications. While in animal studies, the most studied genes were Bdnf and Dnmt1 as they showed a significant methylation level after maternal prenatal stress exposure. In conclusion, maternal prenatal stress could trigger epigenetic alterations in neonates in both animals and humans. This holistic review detailed and evaluated locus-specific and studies exploring current knowledge about associations between maternal prenatal stress and epigenetic changes.
  • Heino, Olivia (2023)
    The intestinal stem cells (ISCs) adapt in response to environmental factors and continually proliferate to renew the mammalian intestinal epithelium due to its rapid turnover. Overall, intestinal homeostasis is maintained by the differentiation and self-renewal of ISCs, which are regulated by different mechanisms, including epigenetic histone modifications. Earlier studies in the host laboratory have shown that the histone methyltransferase Su(var)3-9 is essential in the nutrient-induced activation of intestinal stem cells. Su(var)3-9 specifically trimethylates histone H3 on lysine 9 (H3K9me3), which is a repressive histone mark, responsible for transcriptional silencing at heterochromatin regions. It influences stem cell maturation, lineage specification, and many other cellular processes. However, the precise mechanisms behind its function in ISCs remain unknown – that knowledge is important for understanding the development of many diseases, including cancer and metabolic disorders. This thesis aimed to investigate the distribution of the heterochromatin mark H3K9me3 in the intestine with an emphasis on ISCs, using the Drosophila midgut and mouse intestinal organoids as models. Confocal microscopy was used together with cell-type-specific fluorescent staining, to obtain the expression of the H3K9me3 specific histone methyltransferase Su(var)3-9, in the midgut. An antibody was used for the detection of H3K9me3 distribution along the anterior/posterior axis in Su(var)3-9 overexpressed flies. Additionally, DNA adenine methyltransferase identification (DamID) was applied in order to find target genes of the H3K9me3 regulation in the genome with the specific chromo domain of M-phase phosphoprotein 8 (MPHOSPH8) that binds to H3K9me3. The number of lineage-labeled differentiated enterocytes was shown to be locally higher in the Su(var)3-9 overexpressed flies compared with the control, although the flies were on starvation without nutrient-induced activation. Moreover, the number of lineage-labeled progenitor cells was not remarkably altered between the samples. However, the intensity of H3K9me3 was significantly higher throughout the whole midguts in the Su(var)3-9 overexpressed flies in comparison to the control. According to one replicate, the DamID in mouse intestinal organoids revealed that the peaks of H3K9me3 were divergent between the samples grown in different conditions. The first sample was assumed to contain more ISCs, whereas the other one was assumed to contain more differentiated intestinal cells. According to my results, the Su(var)3-9 overexpression drives the stem cells against the differentiation of enterocytes. Furthermore, the MPHOSPH8 chromo domain in the organoids was successfully applied in DamID; thus, more replicates should be prepared for additional analysis, because I found several potential target genes of H3K9me3. In the future, it is important to further study the epigenetic regulation of ISCs, for applying the epigenetic marks as targets for the treatment of many human pathophysiological conditions, such as cancer, obesity, and metabolic disorders.
  • Matikainen, Riikka (2019)
    In this master’s theses, Finnish biology teachers’ needs for material for continuing education and educational material for upper secondary school in epigenetics were studied. Two sets of educational materials, continuing educational material for teachers and educational material for upper secondary school teaching was produced accordant with the results. Epigenetics is used to describe stable alterations in gene expression which do not consider mutations in DNA sequence. DNA methylation, histone modifications and chromatin remodelling are the main epigenetic mechanisms to affect gene expression. Epigenetic modification patterns can alter de novo, or they can be originated by some environmental factor. Epigenetic regulation was introduced as a new subject matter in National Core Curriculum for General Upper Secondary Schools 2015 in Finland. Epigenetics is a relatively new branch in biology, and as a result many teachers have not studied the subject matter at the university. Continuing educational material is needed to update their knowledge. Biology teachers’ needs for material in epigenetics were studied with a survey which was distributed to the Biology and Geography Teachers’ Union’s e-mail list subscribers. Data was analysed qualitatively and quantitatively. In order to produce continuing educational material for teachers, literature regarding teacher competence, adult education and Finnish biology teachers’ subject expertise was examined. The concept of constructivist learning, and conceptual change were applied in the production of educational material for upper secondary school teaching. Relevant scientific literature in epigenetics was gathered and used to produce both sets of materials. In the study survey, the teachers reported specific individual educational needs which were acknowledged in the production of both sets of materials, alongside literature listed earlier. The survey showed that one of 33 biology teachers had studied epigenetics at the university, 20 of 33 teachers independently and 13 of 33 hadn’t studied epigenetics at all. The extent of the teachers’ studies in epigenetics was most often elementary and the main motivation to study epigenetics independently was a desire to handle the basics. The most common resource teachers used to study epigenetics was non-scientific magazines. Among the teachers who had not studied epigenetics at all, lack of time was the most common reason mentioned. However, 14 teachers described epigenetics as an important subject matter. Three teachers reported that they lack the expertise in teaching epigenetics and three felt that textbooks don’t offer support in teaching epigenetics. Online material and expert lectures were the most common continuing education material forms requested. Regarding the content of the continuing educational material for teachers, the most common requests were that the material should include the basics of epigenetics and practical examples. The form of educational material for upper secondary school teaching was most commonly requested to be online text or educational video. Regarding the content of the educational material for upper secondary school teaching, the most common requests among teachers were a summary of the theory of epigenetics and practical examples. The continuing educational material for teachers produced in this thesis consists of an introduction part and four parts about different subjects in epigenetics. The titles of the parts are: 1) What is epigenetics? 2) Molecular mechanisms of epigenetic gene regulation 3) Epigenetic gene regulation and 4) Epigenetic inheritance. The material was designed in a way that texts 3) and 4) are possible to comprehend without studying text 2) about molecular mechanisms of epigenetic regulation. The educational material for upper secondary school teaching consists of seven parts. At the beginning there is an introduction to teachers which is followed by six separate parts for students. Each part has a “Rehearse before reading”-box which introduces students to the subject and encourages rehearsal of biological concepts and vocabulary which are necessary for comprehending each part. After each part there are questions which test students’ learning as well as encourage to apply freshly acquired knowledge about epigenetics to other biological contexts. Titles for different parts are: 1) What is epigenetics? 2) Epigenetics and nutrition 3) Epigenetics and exercise 4) Epigenetics and mental health 5) Epigenetics and tortoiseshell cats and 6) Epigenetic inheritance. The material has been designed in such a way that the parts can be taught and learned separately. References are provided at the end of both material sets. Both materials produced in this thesis meet the teachers’ requests revealed in the survey. The form of the continuing educational material for teachers is online material, which was one of the most common requests among the teachers who answered the survey. The contents of the material correspond to the teachers requests as well, since most requested contents were the basics of epigenetics and practical examples. The educational material for upper secondary school teaching was requested as online material with a summary of the theory of epigenetics and practical examples, and all these requests were met. Both materials were produced considering relevant theories on pedagogy and adult education. Results of this study cannot be applied nationally in Finland since the sample size was small. Therefore, national relevance of the materials cannot be predicted. Predictions about the impact of the materials on teachers’ and students’ understanding about epigenetics cannot be made either, since learning is an active process which requires effort from the learner. However, a strong case can be made for the produced material, because materials include relevant information and their pedagogic choices can be justified by the literature. This thesis uncovered many questions for future research. For example, the efficacy of the materials could be studied in a practical classroom situation. Other possible questions for research or study designs could be about biology teachers’ expertise and continuing education in Finland.
  • Kuru, Saarajohanna (2023)
    Lichens are sensitive organisms widely used for environmental biomonitoring. Urban environments have been under heavy pollution, especially sulphur dioxide and nitrogen oxides, due to human activity which has led to the disappearance of lichens in city centres. Regulations and technological changes have led to cleaner air and less deposition of pollutants, especially sulphur dioxide on the vegetation in both rural and urban areas. This in turn has led to recolonization of lichens in former lichen deserted areas. In this study epiphytic macrolichens on park maples were surveyed using simple tree-based random sampling in three parks in Helsinki, and in one park in Loviisa, Siuntio and Raasepori each. The sampling and surveying methods were selected based on the SFS standard “Ambient air. Biomonitoring with lichens. Assessing epiphytic lichen diversity”. Species identification took place on site and in Botanical museum (Finnish Museum of Natural History). The results from parks in Helsinki were used to estimate if lichens have recolonized the trees. In addition, the results from the other Uusimaa municipalities were used to assess how different is the lichen species assemblage when comparing the relatively more polluted region of Helsinki to the less polluted regions in Uusimaa. The study found that pollution levels in Helsinki have declined enough to enable recolonization, of which there have been signs already in 1990s and 2000. The study used lichen diversity value of defined functional groups as one of the statistical methods which gave new information about how the species tolerance or sensitivity to pollutants shapes the recolonization. Comparison between the study areas in Uusimaa region revealed that concentrations of nitrogen oxides steer lichen species assemblage in Helsinki. Lichen surveys in Helsinki are scarce. This study brings topical information about the lichen situation in Helsinki, and it uses an as yet relatively unknown method to extract information from lichen assemblage. Regular, comparable lichen surveys are needed to further research the pressure that human activities cause on urban nature. Such time series would help to monitor both the urban nature loss and the impact of climate change on the urban nature.
  • Nieminen, Martta (2013)
    The trend of energy policy in European Union as well as in international context has lately been to increase the share of renewable biofuels. The causes for this are global warming, shrinking reserves of fossil fuels and governments' aspiration for energy independence. Microalgae have shown to be a potential source of biofuels. Though cultivation of microalgae has a long history, has production for fuel yet been unprofitable. Production has become more effective as cultivation has shifted from open ponds to controlled photobioreactors but to achieve effective cultivation methods substantially more understanding on the ecophysiology of microalgae is needed. The aim of my thesis was to research the optimal light intensity and temperature of photosynthesis for three microalgae (Chlorella pyrenoidosa, Euglena gracilis and Selenastrum sp.), which are the main parameters limiting the level of photosynthesis in nutrient rich environments such as photobioreactor. The research strains were incubated in eight light intensities (0,15-250 µmol m-2 s-2) and in 5-6 temperatures (10-35 °C). Photosynthetic activity was determined with radiocarbon method which is based on the stoichiometry of photosynthesis. The purpose of radiocarbon method is to estimate how much dissolved carbon dioxide do the algae assimilate when photosynthesizing. In the method the algae are incubated in light and dark bottles where certain amount of radiocarbon (14C) has been added as a tracer. The algae fix 14C in the proportion to available 12C. 14C method has become the most common way to measure the photosynthesis of microalgae. All of the algal strains grew in 10-30 °C but C. pyrenoidosa was the only one which grew also in 35 °C. The data was analyzed by fitting them with two photosynthesis-light intensity relationship models and one photosynthesis-temperature relationship model and as a result values of essential parameters, i.e. optimal light intensity (Iopt) and temperature (Topt) for photosynthesis, could be estimated. The model which gave the best fit was chosen to describe the photosynthesis-light intensity relationship. The optimal light intensity for C. pyrenoidosa ranged between 121–242 µmol m-2 s-2 and optimal temperature was 15 °C. Corresponding values for E. gracilis were 117-161 µmol m-2 s-2 and 24,1 °C, and for Selenastrum sp. 126-175 µmol m-2 s-2 and 16,7 °C. Q10-values were also determined. With all research strains, the level of photosynthesis increased as light intensity and temperature grew until optimal values were reached. The strains tolerated higher light intensities in warmer temperatures but after reaching the optimal temperature, the level of photosynthesis did not increase any more with elevating temperature. Robust algal strains, i.e. strains, that are most adaptable in terms of light intensity and temperature, are the most prominent ones for biofuel production. From these research strains the most adaptable strain in terms of light intensity was C. pyrenoidosa and in terms of temperature Selenastrum sp. C. pyrenoidosa had superior carbon fixation rate in relation to cell size. Therefore it can be concluded that C. pyrenoidosa is the most suitable algal strains for biofuel applications of the strains assessed here.
  • Saarinen, Eeva (2014)
    Mikrolevien käyttöä biodieselin raaka-aineena on viime vuosina tutkittu paljon niiden ollessa hiilineutraali vaihtoehto fossiilista alkuperää oleville uusiutumattomille polttoaineille. Tämän lisäksi ne ovat myös ekologisesti ja eettisesti kannattava uusiutuvan energianlähde ja tukevat pyrkimystä kohti energiaomavaraisuuden saavuttamista. Mikrolevien todellista mikso- ja heterotrofiaa on tutkittu toistaiseksi vähän eikä niiden hyödyntämän hiilen määrästä ole tarjolla tutkimustietoa. Mikroleväkantojen todellisen mikso- ja heterotrofiakyvyn selvittäminen mahdollistaa kantojen kustannustehokkaamman kasvatuksen, koska mikso- ja heterotrofiaan kykenevät kannat voivat hyödyntää kasvussaan heikompia valaistusolosuhteita korvaamalla ne osittain tai täysin orgaanisilla hiilen lähteillä. Miksotrofisten leväkantojen käytöllä voidaan myös saavuttaa kasvatuksissa korkeampi solusaanto sekä solujen korkeampi lipidipitoisuus. Heterotrofisten kantojen käytöllä voidaan taas kiertää monia mikrolevien kasvatukseen liittyviä ongelmia. Toteutin tutkimukseni kolmella mikroleväkannalla: Selenastrum sp., Chlorella pyrenoidosa ja Euglena gracilis. Tein aluksi kasvatuskokeita, joissa kasvatin kaikkia leväkantoja auto-, mikso- ja heterotrofisissa olosuhteissa. Selenastrum sp. – ja Chlorella pyrenoidosa – kannan kasvatuksissa käytin epäorgaanista COMBO – kasvatusliuosta. Euglena gracilis – kannalla käytin epäorgaanista AF6 – kasvatusliuosta. Tutkin leväkantojen potentiaalista kykyä mikso- ja heterotrofiaan glukoosin ja asetaatin lisäyksen avulla. Seurasin leväkantojen kasvua solumäärän kehityksen kautta. Kasvatuskokeiden perusteella tein päätöksen ottaa kaikki käyttämäni leväkannat mukaan varsinaisiin mikso- ja heterotrofiakyvyn mittauksiin sekä käyttää ainoastaan glukoosia orgaanisen hiilen lähteenä, sillä leväkannat menestyivät heikosti asetaattikasvatuksissa. Mikso- ja heterotrofiakyvyn mittaamiseen käytin 14C-menetelmää. Kaikkien leväkantojen kyky hyödyntää asetaattia (pitoisuus 5 g l-1) oli yleisesti heikompi verrattuna niiden kykyyn hyödyntää glukoosia (pitoisuus 5 g l-1). Kasvatuskokeissa Selenastrum sp. – kannalla vaihtelu oli eri käsittelyiden välillä solumäärän kehityksen ja kasvunopeuden suhteen suurinta. Euglena gracilis – kannalla vaihtelu solusaannon kehityksen ja kasvunopeuden välillä oli pienintä kasvatusten välillä. Selenastrum sp. – kannan miksotrofisesti ottama hiilen määrä oli suurin muihin miksotrofisesti kasvatettuihin leväkantoihin verrattuna. Heterotrofisesti otetun hiilen määrä oli suurin Euglena gracilis – kannalla. Tutkimukseni merkittävin tulos on käyttämieni leväkantojen todellisen mikso- ja heterotrofiakyvyn todistaminen. Laajemmat lisätutkimukset leväkantojen todellisesta mikso- ja heterotrofiasta ovat kuitenkin tarpeen muun muassa mikroleväbiomassan käyttösovellusten kehittämisen ja käyttöönoton sekä vesiekosysteemien hiilenkierron tuntemisen kannalta.