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(2022)Master's thesis project includes the backbone assignment of the human activity-regulated cytoskeleton-associated protein C-lobe (hArc, Uniprot ID: Q7LC44), 7-fluoroindole-based tryptophan-labeling method, and comparing that with the 100% double-labeled and 20%(13C) fractionally labeled samples. The project focuses on the effects of 7-fluoroindole-based fluorotryptophan-labeling. hArc C-lobe has only one tryptophan, which makes the analysis easier. Typically fluorotryptophan-labeling is a costly method – fluorotryptophan itself is very expensive and attaching the fluorine to the tryptophan while expressing is expensive and complicated. Fluoroindolebased labeling circles around the problem, as indole and serine are used in procaryotic systems for tryptophan biosynthesis – meaning that fluoroindole, which is cheap, could be used as an alternative for previous methods. Fluoro-labeled tryptophan is used in protein NMR; for example, in binding studies – fluorine-probes are sensitive, and binding of ligand or protein would move these peaks, indicating binding. This project aims to get an insight into the application of this labeling method. The goal is to see if one could utilize one sample with both (1H, 15N, 13C) labeling and 7-fluorotryptophan labeling for binding and structural studies. However, fluorine is very electronegative, affecting surrounding structures and possibly sequentially nearby amino acids. This possible effect will be observed and determined by comparing the 1H15N-chemical shifts between well-established labeling methods and fluoroindolebased labeling. To determine what amino acids in the protein are affected, if they are affected, will be determined by using the backbone assignment results and the results from the sample comparisons.
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(2015)Sound travels faster and further in water than in air while electromagnetic radiation, among it visible light, attenuates fast. Marine animals have adapted to use sound in foraging, predator avoidance, orientation and communication with conspecifics. The underwater soundscape of the Baltic Sea remains largely undiscovered. The area is a unique acoustic environment due to its variant hydrography, broken coastline, shallowness, low salinity and the resulting strong stratifications. The harbor porpoise (Phocoena phocoena) is the only cetacean inhabiting the area, and its Baltic Sea subpopulation is critically endangered. This work is based on first sound pressure measurements of BIAS (Baltic Sea Information on the Acoustic Soundscape) -project by Finnish Environment Institute and other project participants. Measured sound pressure levels are compared to weather and shipping observations to collect information about the contributions of natural and anthropogenic sound sources to underwater sound pressure levels in the Baltic Sea. In addition porpoise observations collected at the Universities of Southern Denmark and Århus are compared to measured sound pressure levels and shipping data to examine if increased noise levels or increased shipping activity have an impact on harbor porpoise echolocation activity. The results show that at the Gulf of Finland both weather and shipping drive the levels of ambient noise at low frequencies (63 and 125 Hz third-octave bands). However the sound pressure levels caused by ships near the stations (up to 5 km) always exceeded all natural variation. Increased sound pressure levels and ship proximity seemed to have an impact on porpoise activity at the area. When a ship was very close (2 km), the registrations of porpoise echolocation clicks decreased with decreasing proximity to ship. On the other hand during spring months an increase in porpoise echolocation was recorded in relation to increased sound pressure levels, which might indicate the porpoises compensating to increased background noise by echolocating more frequently or loudly.
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(2023)Ecosystem accounting is a new framework for integrating the value of nature into decision-making. Previous measures of natural capital accounting have not been able to achieve policy relevancy and have only limited use cases. It is important to look into the usability of ecosystem accounting, to ensure that it is implemented in a way that supports decision-making. The goal of my research is to provide a categorization of barriers and enablers of use, as well as provide some insight into how to make ecosystem accounting usable for decision-making. There is only limited literature on ecosystem accounting, so I conducted a scoping literature review on barriers and enablers of use of natural capital accounting to look into the issues and opportunities in making ecosystem accounting usable. I complemented this literature review with interviews of ecosystem accounting experts from Norway and Germany. Both countries have started the implementation journey and thus provide a view into the active development phase. My main results are the categorization of barriers and enablers of use of ecosystem accounting, as well as main messages for creating usable accounts. I categorized the barriers and enablers into 12 categories under three themes of political, structural and relevancy related barriers and enablers. The categories can be used when planning implementation to identify potential issues and to plan accounts to be as usable as possible. I have three main messages for compiling usable ecosystem accounts. First, sufficient resources are essential in gathering comprehensive accounts. Second, compiling the accounts rely on cooperation of multiple institutions, thus there is a need to agree on forms of coordination. Third, the categories of barriers and enablers are interconnected, and thus there are positive feedback loops that can support making ecosystem accounts usable for policymaking.
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(2022)My master’s thesis aims to determine the effect of salinity on phytoplankton traits related to nutrient acquisition, and particularly how this interacts with resource availability. Salinity is an important driver structuring phytoplankton communities in the Baltic Sea. Salinity can also influence nutrient uptake by increasing metabolic rates required for osmotic adjustment. Thus, interaction between salinity and nutrient availability is expected to change community structure by altering phytoplankton traits determining resource competition. This is a particularly relevant area of study for the Baltic Sea due to predicted future freshening of the sea’s upper layer. We performed a microcosm experiment using artificial communities of 10 diverse phytoplankton species grown under different combinations of salinity (0, 5, 12 and 24), Nitrogen to Phosphorus molar ratio (N:P ratio = 2, 10, 16 and 80) and light (10 and 130 µmol photon m-2 s-1) conditions. A three-way interaction among these environmental parameters influenced phytoplankton traits associated with resource competition, as well as the presence and proportions of phytoplankton taxa. Light limitation inhibited community growth under all salinity conditions, but allowed diatom Phaeodactylum tricornutum to dominate. Community growth rate was higher under high light, but also more variable between salinity conditions. The strongest negative effects of nutrient limitation (N, P, and both nutrients together), both on growth rate and taxonomic diversity, were observed in the highest salinity treatment. In the freshwater treatment with the highest proportion of green algae Monoraphidium sp., N-limitation did not inhibit phytoplankton community growth and P-limitation had a more profound negative effect on community performance. Decreasing salinity appeared to decrease community C:N and C:P ratios. This shift is in opposition to the increasing C:N and C:P predicted as a consequence of other climate change-related drivers. Our results emphasise the importance of a trade-off between salinity and resource limitation in functioning of phytoplankton communities and suggest that future freshening of the Baltic Sea is likely to modify phytoplankton community composition and performance.
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(2021)Oil spills in aquatic environments are devastating disasters with both biological and economic impacts. Fish populations are among the many subjects of these impacts. In literature, there are numerous assessments of oil spill impacts on fish populations. From all applied research methods, the focus of this thesis is on Bayesian methods. In prior research, several Bayesian models have been developed for assessing oil spill impacts on fish populations. These models, however, have focused on the assessment of impacts from past spills. They have not been used for predicting impacts of possible future oil spills. Furthermore, the models have not utilized data from laboratory studies. Some examples can be found of models assessing economic impacts of oil spills on fish populations however, none of them assess the economic impacts that follow from decreases in biomass. The aim of this thesis is to develop a Bayesian bioeconomic prediction model, which would be able to predict oil spill impacts on Baltic Sea main basin herring population, and the consequential economic impacts on fishermen. The idea is to predict the impacts of several hypothetical oil spill scenarios. As a result of this thesis, a bioeconomic prediction model was developed, which can predict both biological and economic impacts of oil spills on Baltic Sea main basin herring through additional oil induced mortality of herring eggs. The model can be applied to other fish populations in other regions as well. The model utilizes laboratory studies for assessing population level impacts. The model can be used for both assessing risks of the impacts of possible future oil spills, and for decision analysis after a spill has already occurred. Furthermore, the model can be used for assessing unknown aspects of past oil spills. The economic predictions can be used, for example, to estimate the compensations that could possibly be paid to fishermen. In the future, the prediction model should be developed further, especially regarding its stock-recruitment relationship assumptions. In addition, the model’s assumptions regarding the calculation of oil induced additional mortality and the economic impacts, should be expanded.
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(2014)Urbanization is occurring at rapid rates worldwide. While the effects of urbanization are numerous, those on wildlife are of utmost concern in the continued fight for biodiversity conservation. Specifically, the focus on global pollinator declines is of interest due to the interconnectedness between pollinators and plant communities. It is feared that urban areas could become dead zones to these species, specifically bumblebees. Bumblebees are one of the native pollinators of Finland, and therefore were the focus of this study, which was conducted in Helsinki (southern Finland). This project's focus was on the influence of both local (i.e. flowering resources) and landscape (i.e. levels of urbanization) features on bumblebee communities. More specifically, I was interested in the effects of urbanization on bumblebee abundance and species richness. To study this question, community gardens (allotment gardens) were used as study sites along a gradient of urbanization from low to high (chosen by GIS mapping of the levels of impervious surfaces within 500 m of the sites). It is thought that these greenspaces could function as habitat for bumblebees in cities. This study was conducted during the summer of 2013 in 12 community gardens across the city of Helsinki. Two methods to survey bee populations were utilized, pan traps as well as sweep netting. Furthermore, a vegetation analysis was conducted to assess the level of resources present within the gardens, while GIS was used to measure a set of landscape variables in and around each garden. At the end of the season (June to September) the bees were identified and Generalized Linear Mixed Effects models were used to analyze the data. This study found that local variables more strongly predicted both bee abundance and species richness. Even though landscape variables were not strong predictors, this does not make them irrelevant in future conservation strategies. However, it is thought that as long as community gardens are planted appropriately (i.e. native flowers) the bees will be present in these gardens despite the surrounding matrix of inhospitable land (sealed surfaces). In conjunction with the investigation into the effects of local versus landscape determinants, this study also aimed to investigate the perception of gardeners towards bees. A questionnaire was utilized in order to gauge gardeners' opinions towards the bees in their plot and the garden as a whole. These results helped to evaluate the overall attitude towards bees, and in short, were very favorable. This extrapolates to a possibility of working in conjunction with gardeners to conserve habitat for pollinators in the continued effort for interconnected greenspaces in urban areas.
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(2023)Urbanisation threatens species and biodiversity globally. Consequent habitat loss and habitat fragmentation force species upon one another, inevitably also increasing human-wildlife conflicts. Despite the situation growing dire for many organisms, studies also show species from a variety of taxa being able to adapt to urban environments. Most studies of primates’ ability to adapt to urban environments have been done on diurnal species. To my knowledge, the African lesser bushbaby (Galago moholi) is the only nocturnal primate in which this has been studied. To assess urban adaptability in another nocturnal primate, I present transect and recording data on the abundance of the white-tailed small-eared greater galago (Otolemur garnettii lasiotis) in an urban and rural environment in the biodiversity hotspot Taita Hills, Kenya. Sampling was done in Wundanyi town and Ngangao forest and the two locations were then compared by fitting a negative binomial as well as a Poisson model for recording and transect count data. Additionally, preliminary observations are made regarding behavioural and spectral acoustic adaptation, increased sociality, and colouration coupled traits. My results indicate O. g. lasiotis to be significantly more abundant in the town than in the forest. In the town, I observed a two-fold increase in total number of vocalizations and mean vocalization rate, and a seven-fold increase in total number of sightings and mean encounter rate, as indicated by recordings and transects respectively. This discrepancy in estimated abundance differences in location from transect and recording data (two-fold versus seven-fold) suggest that urban individuals vocalize less than rural individuals. The spectral profile of three vocalization types were studied and urban individuals exhibited significantly higher high frequencies in the clustered squawk vocalization. I found town dwelling individuals to be a part of a larger group or pair considerably more often than forest dwelling individuals. A dark morph, as opposed to a light morph, was significantly more frequently encountered in the urban location, whereas both morphs were encountered almost equally often in the rural location. In summary, O. g. lasiotis seems to be capable of adapting to an urban environment, as indicated by its’ greater abundance in the town than in the forest. My data suggest decreased vocalization rate, increased sociality, and colouration coupled traits being possible adaptations affecting O. g. lasiotis’ capability to inhabit an urban environment. Further research is required to draw conclusions on what factors and adaptations might allow for the high abundance of O. g. lasiotis in the town.
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(2023)The shallow bays and inlets of the coastal Baltic Sea consist of a patchy seafloor with different sediment types that are affected by anthropogenic pressure, such as organic matter loading. Benthic macrofauna affects the carbon and nutrient stock capacity of such coastal areas by storing these elements in their body tissues and thus working as a temporary carbon and nutrient pool. These nutrient stocks are especially stable when the animals are large and long-lived. Fluctuations in organic input have been suggested to modify the diversity, abundance, and biomass of the benthic communities and therefore affect the nutrient reserves bound within the fauna. However, there is little information on how stress, in form of increasing sediment organic matter content, change the stocks and stoichiometric ratios of benthic macrofaunal communities. This thesis investigates if the changes in sediment organic matter affect benthic community composition and organism size and its ability to function as a carbon (C), nitrogen (N) and phosphorous (P) pool by measuring: 1) how the benthic faunal diversity, abundance, and biomass composition and 2) the C:N:P content and ratios of the benthic fauna change between three different sediment categories. A significant difference was found between sandy and muddy sediments in terms of benthic biomass and abundance, as well as the carbon and phosphorus stocks. Large long-living bivalves were found in sandy sediments, but overall organism size was not significantly different between the sediment categories. In general, the results show that higher sediment organic matter content resulted in fewer individuals, biomass, and thus a smaller storage capacity of carbon and nutrients. No statistical differences were found between the C:N and N:P and C:P ratios along the three sediment types. However, somewhat more P was bound within the fauna at sites with more organic matter, compared to the sandy and mixed sediments. The results highlight the importance of macrofauna in the functional performance of the ecosystem function and their potential for shifts with increasing disturbance. In conclusion, the increase in sediment organic matter can significantly change the capacity of macrofaunal communities to bind carbon and nutrients and this might have implications for the coastal nutrient filter. More research regarding the fauna's ability to adapt to the changing environment is needed.
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(2020)Innovation in food packaging interlinks many sustainability challenges ranging from food loss and waste through the value chains, to resource extraction and growing amounts of plastic waste globally. Food packaging innovations arising from regulation often focus on material waste and ignore other facets of sustainability such as food loss and waste. Simultaneously, conventional notions of innovations are focused on firm growth and competitiveness. This study investigates the perceptions of sustainability in food packaging among expert actors in Finland. Moreover, it examines how notions of Responsible Research and Innovation (RRI) are reflected in the research and development processes in the field. Here, RRI is understood as a framework for examining the role of socio-ethical considerations in research and development. The study aimed to find out which packaging attributes are considered sustainable, what motivations actors in the field have, what type of obstacles exist to innovation in the field, and which actor groups are perceived to be responsible for accelerating the food packaging transition towards sustainability. Semi-structured expert interviews were conducted with 14 participants, and the interview data were analyzed using qualitative content analysis (QCA). The results show that perceptions of sustainability in food packaging vary across the field. However, reducing food waste and loss was considered the most important facet of sustainability in food packaging. Actors in the field are motivated by personal reasons and the anticipated profitability of sustainable innovations. However, innovations in the field are slowed down because of regulatory issues, food safety requirements, unpredictable future changes, and technological lock-ins. Finally, the results of this study indicate that actors in the sector believe the Finnish government and brand owners in the food and beverage industries should be responsible for driving innovation towards improved sustainability. However, the qualitative approach taken here limits the generalizability of the results. The results suggest an ongoing narrative shift in innovation towards greater inclusion of social and ethical considerations in the research and development process.
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(2006)The goal of this study has been to compile and to further develop a collection of biodiversity indicators for Finland. Biodiversity indicators aim at bringing forth information related to biodiversity change and the factors causing it in a condensed and easy to understand manner. The factual information which indicators provide is supposed to appeal to the reader's intellect and thus to have an influence on her opinions and behavior. Biodiversity indicators also aim at influencing biodiversity related politics. Being successful at this, biodiversity indicators can make a strong contribution towards reaching the most important goal of nature conservation - the perpetuation of natural variety. The study is divided into two parts. The first part presents a preliminary collection of 75 biodiversity indicators. These indicators are based on the biodiversity monitoring and research data as well as other statistical data which were readily available at the time of their composition. In addition to the statistics and literature reviewed the study is based on interviews of numerous experts. The collection of 75 biodiversity indicators enables a reasonably comprehensive assessment of the major factors effecting biodiversity as well as of the state and development of some components of biodiversity (e.g. endangered species). It, however, contains too few indicators on the state and development of common species and on many important characteristics of ecosystems. The data for such indicators were not available. The second part of the study consists of a review of some European national biodiversity monitoring schemes, international biodiversity indicator development projects as well as Finnish national biodiversity monitoring field programs. Based on the review, recommendations for the further development of the indicator based biodiversity information system are made. The second part of the study concludes with a proposal for an expanded biodiversity indicator collection which contains 31 new indicators. The expanded biodiversity indicator collection could provide a sound factual foundation on which comprehensive assessments of state and development of biodiversity could be based. Such assessments are needed when the effects of biodiversity related politics are evaluated and decisions concerning where to focus conservation efforts are made. At the end of this study possible applications of the expanded biodiversity indicator collection are examined in the light of four different conservation objectives
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(2022)The need to develop and expand urban areas is increasing in most countries, but urbanization also increases the threat for global biodiversity. Some cities have acknowledged this challenge and formed strategies and action plans for biodiversity preservation. How can we ensure that such strategies are realized in city planning? Negotiations are a crucial part of urban planning, and therefore can be a leverage point of intervention to effectively implement strategies to pro-tect biodiversity. However, little is known about the dynamics of the actual negotiation process in city planning. I applied a game theoretic approach to study how information availability influences the suc-cess and efficiency of negotiations. A role-playing game was used to simulate a negotiation on specific measures to preserve biodiversity in a residential building project. Eleven urban devel-opment specialists played the game with different sets of information. In addition to the direct outcomes of the negotiation, I analysed the post hoc discussion and arguments used to gain in-sights into perceptions of biodiversity-related negotiations in urban planning. Results indicate that information availability can increase the efficiency of negotiations. Partici-pants favour principled and integrative negotiation, but incomplete information seems to push them to take a more positional stance. The post hoc discussion also reveals some issues rele-vant to the design of urban planning process for biodiversity. The overall results suggest that a simple game-theoretic framework, implemented in (a) game-like simulation with quasi-experimental control and (b) qualitative analysis of discussions, holds potential for both under-standing (i) how decision makers frame and resolve the negotiation with conflicting interests and (ii) how to design efficient administrative processes taking into account not only the partic-ipants’ preferences but also wider public interests, such as biodiversity preservation.
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(2022)Biodiversity is essential for human wellbeing and activities as it supports a diverse set of ecosystem services. Currently, biodiversity is rapidly declining. Biodiversity loss is the second significant global risk after climate change. To reduce environmental stress, there is a need to find sustainable alternatives to unsustainable raw materials and consumables. The chemical industry has an important role in developing environmentally friendly solutions such as bio- based products and solutions, which require utilization of biomass. However, extraction of bio- based raw materials creates more pressure on biodiversity and contributes to biodiversity loss. It is essential that companies who extract natural resources are transparent about their actions concerning biodiversity. By adequately sharing information in corporate reports, companies can enhance their legitimacy. This thesis contributes to scientific discussion on biodiversity reporting which is researched to a limited extent. Material of the thesis was collected from corporate reports and interviews with globally operating chemical companies. By using qualitative content analysis, this thesis describes how chemical companies report on biodiversity as part of their corporate reporting to maintain their legitimacy and how biodiversity is perceived within the chemical industry. Biodiversity is a complex concept and intangible system, which cannot be sufficiently measured yet. This may help to explain why biodiversity reporting within the chemical industry is varying and inconsistent. There is a need to improve companies’ understanding on biodiversity to enhance biodiversity reporting. Adequate reporting can help to understand complex natural processes, enhance environmental protection, and reduce the problem of greenwashing.
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(2016)Pohjoismaissa syntypaikkalajitellun biojätteen kompostointi suurissa kompostointilaitoksissa on yleistynyt merkittävästi 2000-luvun aikana. Viime vuosina biojätteiden ja muiden orgaanisten jätteiden käsittelyssä on alettu suosimaan yhä enemmän mädätysprosessia sekä mädätyksen ja kompostoinnin yhdistävää osavirtamädätysprosessia. Mädätysprosessin avulla orgaanisten jätteiden sisältämästä energiasta pystytään tuottamaan biokaasua ja siitä edelleen uusiutuvaa energiaa. Tämän tutkimuksen lähtökohtana oli tarkastella biohiilen lisäyksen vaikutuksia kompostointiprosessiin, jossa yhdistyvät mädätys ja kompostointi. Aiempien tutkimusten perusteella biohiilen lisäyksellä on todettu olevan positiivisia vaikutuksia erilaisten orgaanisten jätteiden kompostointiprosessiin. Aiemmat tutkimukset on suurimmaksi osaksi tehty pienemmässä mittakaavassa ja ne ovat keskittyneet enemmän maatalousjätteiden kompostointiin. Tämän tutkimuksen tarkoituksena oli selvittää, voidaanko verrattain pienellä biohiilen lisäyksellä nopeuttaa orgaanisen aineksen hajoamista sekä parantaa typen pidättymistä kompostimassassa erilliskerätyn biojätteen osavirtamädätysprosessin kompostointivaiheessa. Tutkimuksen kokeellinen osuus koostui laboratoriomittakaavan kompostointikokeesta sekä laitosmittakaavan kompostointikokeesta Ämmässuon jätteenkäsittelykeskuksessa. Laboratoriomittakaavan kokeiden tarkoituksena oli saada tietoa eri biohiilipitoisuuksien vaikutuksesta kompostointiprosessiin ja toistomäärien kautta saada tuloksille tieteellistä pätevyyttä. Laboratoriokokeissa saatuja tuloksia sovellettiin laitosmittakaavan kokeissa. Tuloksia pyritään tarkastelemaan mikrobiologisen prosessin lisäksi osana jätehuoltoa ja sen kehittämistä. Tulosten perusteella biohiilen lisäyksellä oli myönteinen vaikutus kompostointiprosessiin osavirtamädätysprosessin kompostointivaiheessa. Laboratoriokokeissa biohiilen lisäyksellä oli merkitsevä vaikutus orgaanisen aineksen hajoamiseen ja siten kompostimassan mikrobiaktiivisuuteen. Vaikka laitosmittakaavan kokeessa biohiilen lisäys ei vaikuttanut orgaanisen aineksen hajoamiseen tilastollisesti merkitsevästi, voidaan kokonaisuutena arvioida, että biohiililisäsi kompostien mikrobiaktiivisuutta. Biohiilellä havaittiin merkitsevä vaikutus kompostien stabiloitumisnopeuteen ja ammoniumtypen pidättymiseen kokeen lopputilanteessa. Verrattain pienet biohiilipitoisuudet eivät vaikuttaneet haihtuneen ammoniakin määrään eivätkä kokonaistyppihäviöön kompostoinnin alkuvaiheessa. Biohiilikompostien stabiloitumisnopeudella ja mikrobiaktiivisuuden lisääntymisellä on kompostoinnin ympäristövaikutusten vähentämisen lisäksi kompostointilaitoksille myös taloudellinen merkitys, koska niiden avulla pystytään mahdollisesti säästämään tuotantokustannuksissa sekä säästämään kompostien jälkikypsytykseen tarvittavaa tilaa tai vastaavasti lisäämään kompostointilaitosten kapasiteettia. Tulevaisuudessa biohiili on teoriassa mahdollista saada osaksi orgaanisten jätteiden käsittelykokonaisuutta. Jäteperäisten biohiilten käytöllä voi tulevaisuudessa olla mahdollista parantaa resurssien kestävää käyttöä ja alueellisia kierrätysmääriä.
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(2022)Formation of template switching mutation has previously been proposed as a mechanism of RNA evolution. TSM mechanism may contribute to the creation, maintenance, and modification of the RNA Hairpin. The finding of de novo TSM in RNA sequences will provide evidence for this hypothesis. Ribosomal RNAs (rRNAs) appear in multicopy clusters on different chromosomes and evolve through concerted evolution. To study the properties of de novo TSM and the dynamics of the concerted evolution of rRNA, we developed a computational tool to analyze pairwise differences and the phylogenetic relationship of rRNA genes on different chromosomes. The genome assemblies that are based on traditional short-read sequencing methods have limitations on studying long tandem repeat rDNA, because the reading length is shorter than on the rRNA gene. To overcome this limitation. PacBio Hifi long-read sequencing data for human rRNA 18S and 28S genes were studied. By analyzing the diversity of rRNA genes between individuals and families, single nucleotide mutations, multiple nucleotide insertions, and deletions were identified. As expected, genetic variations in ribosomal genes were detected both within and between individuals. A larger sample size may be required for TSM identification. The finding of this research that related to the dynamics and concerted evolution of human rRNA may contribute to a better understanding of rRNA mutation-related genetic disorders.
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(2020)Tiivistelmä – Referat – Abstract Proteins differ from one another on the basis of their amino acid sequences, display a different spatial shape and structure, and have different functions. The linear order of amino acid residues are chained to one another by peptide bond. The ß-strands and α-helices can be considered as the key components present in the three-dimensional structure of a protein. There are several bioinformatic methods involved to predict structure and function of protein such as searching sequencing similarities, multiple sequence alignment, characterisation of domains, solvent accessibility, and modelling three-dimensional structures at atomic level. The main focus of this study was to build the three-dimensional structure models and then compare the homologues regions in different models. 36 reviewed capsid L1 and L2 protein sequences of human papilloma virus subtypes were selected based on 65% sequences similarity from Universal Protein database. We utilised several computational algorithms in this study for the analysis of protein sequences for the evolutionary relationship and modelled the three-dimensional structures of capsid L1 and L2 proteins of oncogenic human papilloma virus subtypes. For domains analysis in the protein sequences, we used Simple Modular Architecture Research Tool algorithms and predicted secondary structure of protein using Protein Prediction Protein 4.0 tool. I-TASSER Iterative threading assembly refinement algorithms were utilised for three-dimensional structure modelling of capsid L1 and L2 proteins. We found out a different evolutionary relationship and conserved residues in capsid L1 protein of human papilloma virus and L2 protein of human papilloma virus, and their different level of effect on the protein structure. We also predicted three-dimensional structure models for capsid L2 protein of human papilloma virus subtypes 41 and 13 which are folded completely differently from the rest L2 proteins. X-ray crystallography study is suggested for the determination of three-dimensional structure of L2 protein for understanding their contribution in viral assembly process.
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(2023)Tässä työssä tutkin, minkälaiset käyttäytymistä määrittävät tekijät koetaan esteiksi biojätteen lajittelulle sekä mitkä ihmisryhmät lajittelevat biojätteensä passiivisemmin kuin toiset HSY:n alueella. Analysoin tutkielmassani kyselytutkimusaineistoa klusterianalyysin avulla, jonka perusteella etsin mahdollisia lajittelua estäviä tekijöitä ja tarkastelen vastaajien demografisten tekijöiden jakaumaa passiivisten ja aktiivisten lajittelijoiden joukoissa. Lisäksi hyödynnän ympäristöpsykologian teorioita ja tutkimusta ympäristömyönteiseen käyttäytymiseen kannustamisesta. Tätä teoriataustaa ja tuloksiani soveltamalla ehdotan mahdollisia interventioita, joiden avulla voidaan tehostaa kotitalouksien biojätteen lajittelua pääkaupunkiseudulla ja Kirkkonummella. Biojätteen lajittelu kotitalouksissa on tärkeää, sillä lajitellulla voidaan lisätä jätteiden hyötykäyttöä, mikä edistää kiertotaloutta Suomessa. Biojäte on erityisen tärkeä jätelaji kierrättää, koska kompostoinnin ja mädätyksen avulla siitä saadaan lopputuotteina uusiutuvaa biokaasua, josta tuotetaan energiaa sähkönä yhteiskunnan tarpeeseen, sekä ravinnerikasta multaa, jota voidaan hyödyntää maanviljelyssä ja viherrakentamisessa keinolannoitteiden korvaajana. Kotitalouksissa syntyvä orgaaninen jäte sisältää runsaasti typpeä, joten biojätteen lajittelu edistää myös ekologisesti kestävää typen kiertoa. Analysoin työssäni HSY:n kuluttajakäyttäytymiskyselyn vastauksia monimenetelmällisesti hyödyntämällä kvantitatiivista klusterianalyysia sekä kvalitatiivista teema-analyysia. Tulosteni perusteella havaitaan, että passiivisten lajittelijoiden vastauksissa korostuu lajittelun vaivalloisuus, tiedonpuute sekä paikalliset deklaratiiviset normit käyttäytymistä rajoittavina tekijöinä. Lajitteluesteiden tunnistaminen ja kuvaileminen auttaa arvioimaan mahdollisia käyttäytymismuutostekniikoita, joilla kannustaa asukkaita lajittelemaan biojätteensä paremmin. Tuloksistani voidaan päätellä, että proseduraalisen tiedon saaminen, lajittelun ympäristövaikutuksista oppiminen sekä lajittelun helpottaminen voivat kannustaa asukkaita lajittelemaan biojätteensä huolellisemmin. Löydösten perusteella voidaan kohdentaa viestinnässä ja kampanjoinnissa käytettäviä tekniikoita, jolloin niillä voidaan tehokkaammin kannustaa ympäristömyönteiseen käyttäytymiseen ja saadaan HSY:n alueen lajitteluaste nousemaan biojätteen osalta.
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(2015)Viime vuosikymmeninä tiedonalakohtaista oppimista on tutkittu paljon käsitteellisen muutoksen näkökulmasta. Käsitteellinen muutos tarkoittaa oppijan tietorakenteiden muuttumista tai jäsentymistä virheellisistä kohti tieteellistä mallia. Käsitteellisen muutoksen teorioiden mukaan oppijoiden aikaisempien virhekäsitysten tunteminen ja huomioiminen on keskeistä oppimisen ja opetuksen onnistumisen kannalta. Tässä tutkimuksessa selvitettiin biologian yliopisto-opiskelijoiden fotosynteesiin liittyviä virhekäsityksiä, niiden muuttumista opetustekstin lukemisen seurauksena sekä biologian pääaineopiskelijoiden ja sivuaineopiskelijoiden virhekäsitysten eroja. Suomalaisten opiskelijoiden virhekäsityksiä on aiemmin tutkittu niukasti. Tämän tutkimuksen tavoitteena oli selvittää virhekäsityksiä suomalaisten opetussuunnitelmien mukaan opiskelleilta opiskelijoilta sekä selvittää virhekäsitysten yksityiskohtaista muuttumista käsitteellisen muutoksen näkökulmasta. Tutkimuksen aineistona oli yliopiston biologian peruskurssin opiskelijoiden (n=171) vastaukset fotosynteesiä ja sen ekologista merkitystä koskeviin avoimiin kysymyksiin. Opiskelijat vastasivat kysymyksiin ennen opetustekstin lukemista, heti opetustekstin lukemisen jälkeen sekä kaksi viikkoa lukemisen jälkeen. Aineisto analysoitiin laadullisin menetelmin kuvaamalla, tyypittelemällä ja tulkitsemalla havaittuja virhekäsityksiä. Virhekäsitysten tulkinnassa hyödynnettiin tiedon ja ajattelutaitojen tasojen luokittelua. Opiskelijoilla havaittiin yhteensä 58 fotosynteesiä koskevaa selkeästi virheellistä käsitystä ja 14 puutteellista tai epämääräistä käsitystä. Virhekäsitykset liittyivät fotosynteesireaktioon, kasvien rakenteisiin, kasvin energiatalouteen ja fotosynteesin ekologiseen merkitykseen. Lähes kaikki virhekäsitykset ja puutteelliset käsitykset olivat yleisempiä biologian sivuaineopiskelijoilla kuin pääaineopiskelijoilla. Virhekäsitykset vähenivät opetustekstin lukemisen seurauksena, ja monimutkaisempia tiedon ja ajattelutaitojen tasoja ilmentävät virhekäsitykset vähenivät vähintään yhtä paljon kuin muutkin. Lukuisia virhekäsityksiä kuitenkin säilyi oikeat vastaukset antaneesta opetustekstistä huolimatta. Kaksi viikkoa opetustekstin lukemisen jälkeen osa jo virhekäsityksensä korjanneista opiskelijoista vastasi jälleen virheellisesti. Tutkimus osoittaa, että suomalaisen peruskoulun ja lukion fotosynteesin oppimista koskevat tavoitteet eivät täyty edes monen biologian yliopisto-opiskelijan kohdalla. Suomalaisilla opiskelijoilla on pitkälti samoja virhekäsityksiä kuin kansainvälisesti tehdyssä tutkimuksessa on havaittu. Fotosynteesin oppimisen kannalta keskeisin tutkimuksessa havaittu ymmärryksen puute on vaikeus ymmärtää fotosynteesin merkitys Auringon valoenergian ja ravintoketjujen energian välisenä linkkinä. Opiskelijoiden vaikeudet korjata virhekäsityksiään selittyvät käsitteellisen muutoksen prosessin haastavuudella ja hitaudella. Fotosynteesiä koskevan oppimisen edistämiseksi opetuksessa tulisi aiempaa paremmin huomioida käsitteellisen muutoksen haasteet kognitiivisesta, sosiaalisesta ja motivaatioon liittyvistä näkökulmista. Tämä tutkimus tarjoaa tietoa niistä fotosynteesin oppimista koskevista erityispiirteistä, joita ilmiön tehokkaaseen oppimiseen pyrkivän opetuksen tulee huomioida.
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(2021)There are no comprehensive research data on Finnish matriculation examinations in biology. This type of data is needed, because evaluation guides what and how students learn and what they consider important. Genetics is one the most challenging topics in biology, and in the opinion of teachers it will continue to be an important discipline in the future. The importance of studying genetics can also be justified with philosophical, social and health reasons. This is why the present study focused on the genetics component of the matriculation exam in biology. The aim of the study was to provide information on the challenges and contents of past matriculation examinations in biology and how they have aligned with high school curricula. The results of the study could be used to evaluate this alignment in relation to genetics questions in the biology exam, and could help in designing new matriculation examinations that align better with the existing high or new high school curricula and their aims. The research questions were: 1. What knowledge and cognitive dimensions are measured with the genetics-related questions in matriculation examinations in biology? 2. How do knowledge and cognitive dimensions in genetics-related questions in biology matriculation examinations relate to high school curriculum aims? The data comprised matriculation examination papers in biology from spring 2011 to autumn 2020 (20 exams) and the aims of the Finnish national High School Curriculum in 2003 and in 2015. Qualitative content analysis was performed on the knowledge dimensions (factual, conceptual or procedural knowledge) and the cognitive process dimensions (remembering, understanding, applying, analyzing, evaluating or creating). The basis of this qualitative content analysis was Bloom’s revised taxonomy. The analysis was conducted on genetics-related matriculation examination questions and on the aims of the high school curriculum. The test questions and the aims were compared to determine whether they aligned. Classified questions were divided into two subcategories depending on which high school curricula they corresponded to. Genetics-related questions from spring 2011 to autumn 2017 corresponded to the High School Curriculum in 2003 and questions from spring 2018 to autumn 2020 corresponded to the High School Curriculum in 2015. Questions from the previous period were divided into all knowledge dimensions. All questions, except one, incorporated lower cognitive dimensions (remembering, understanding and applying). The main combined class was understanding conceptual knowledge. Questions from the later time period were also divided into all knowledge dimensions. Mostly lower cognitive dimensions were incorporated into the questions, but a few subquestions addressed higher cognitive dimensions (analyzing, evaluating and creating). The main combined class was understanding conceptual knowledge. All the aims were classified into conceptual or procedural knowledge classes. The aims were also divided between all cognitive dimensions, except remembering. Using constructive alignment as the basis for matching aims with questions, two aims in the High School Curriculum of 2003 and six aims in the High School Curriculum of 2015 had no questions that matched them. These aims mostly measured the cognitive dimension of creating. Several aims appeared to incorporate higher cognitive dimensions, but the questions were less well aligned with the aims than with those incorporating lower cognitive dimensions. The results concerning knowledge and cognitive dimensions were mostly as expected. Lower cognitive dimensions were highlighted in genetics-related matriculation examination questions in biology. The challenge of interpretation brought ambiguity to the aims and cumulative levels of cognitive dimensions when aligning questions with aims, as some of the questions aligned with aims did not assess such high cognitive dimensions as would be expected based on the aims, but were nonetheless aligned with them. Furthermore, there may be several reasons behind the absence of the creating dimension in matriculation examination questions. The alignment of questions and aims would be important to consider in the future, because evaluation has a considerable impact on studying.
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(2017)No comprehensive research has been conducted on matriculation examinations in biology. This kind of data are needed, however, as evaluation (e.g. challenges and contents of test assignments) direct the way students study and learn and what they consider important in the taught matter. Thus, it is impossible to say, if the tests really measure core knowledge of biology, or just fragmentary facts. The aim of this study was to provide information on the challenges and contents of matriculation examination in biology and to provide, for the first time, comprehensive information on the factors affecting competence. The results of the study can be used to evaluate the impact of the new curriculum of upper secondary school and to support the development of the new electronic matriculation examination assignments. The research questions were: 1. How do the test tasks of biology matriculation examination measure the core content and the levels of both knowledge and cognitive dimensions? 2. Are the types of test assignments, knowledge and cognitive dimensions distributed equally between all core contents? 3. Do the results vary among a) the examinations, b) the type of tasks, c) the core contents or d) the knowledge and cognitive dimensions? 4. Is the competence of a) task type or b) knowledge or cognitive dimension levels, subject to the different types of core contents? 5. How does gender explain the choice and competence of different tasks? The qualitative content analysis was used to identify the different aspects; the task types (selected response, brief constructed response or performance-based assessment), the knowledge dimensions (factual, conceptual or procedural knowledge) and the cognitive process dimensions (remember, understand, apply, analyze, evaluate or create). The content variation of matriculation exam was examined and classified using the biological core contents. The data comprised matriculation examinations in biology from spring 2011 to spring 2015 (9 exams, 108 tasks). Additionally, statistical analyses were used to examine how the test subjects (n = 28,777) succeeded in these different assignments and whether girls and boys were equally successful. The task type "selected response" was considered only in four (out of 108) tasks. All levels of knowledge dimensions were found but higher level cognitive processes, such as "analyse" or "create" were not required; the main emphasis in the tasks was in the understanding of conceptual knowledge. The majority of the tasks dealt with the core content "From the molecules to the organisms", i.e. the focus was on biological structures and processes. The analysis of scores obtained in the tests showed that the total scores were higher in the autumn examinations than in the spring examinations and that the scores had been steadily declining. The achievement in the task was most influenced by the type of task and the required level of cognitive process. The interest and knowledge varied between different core contents. Biological evolution appeared to be the most interesting topic to students and had also the highest scores. The girls mastered biology generally better than the boys, but the difference between the sexes was minimal in tasks requiring some form of applied aspect. In particular, the boys excelled the girls in tasks related to ecosystems which mostly required applications. The study also showed other factors affecting student achievement, one of the most significant being the impact of the use or non-use of verbs in the assignment. If the assignment lacked a verb describing what the task requires (e.g. distinguish, subtract, describe), the candidates managed the task poorly. Structural aspects of the task seem to have a great impact especially on the boys' level of knowledge. Future research should classify assignments, for example through assignment instruction guidance or visual interaction on knowledge.
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(2021)Effective population coding is dependent on connectivity, active and passive postsynaptic membrane parameters but how it relates to information transfer and information representation in the brain is still poorly understood. Recently, Brendel et al. (2020) showed how spiking neuronal networks can efficiently represent a noise input signal. This "D_Model” successfully showed that spiking neural networks can recreate input signal representations and how these networks can be resilient to the loss of neurons. However, this model has multiple unphysiological characteristics, such as instantaneous firing and the lack of units related to physical values. The aim of the present study is to build upon the D_Model to add biological accuracy to it and study how information transfer is affected by biophysical parameters. We first modified the D_Model in the MATLAB environment to allow for the simultaneous firing of the neurons. Using our CxSystem2 simulator in a Python environment (Andalibi et al. 2019), we built a network replicating the one used in the D_Model. We quantified the information transfer of Leaky Integrate-and-Fire units that had identical physiological values for both inhibitory and excitatory units (Comrade class) as well as more biologically accurate physiological values (Bacon class). We used various information transfer metrics such as granger causality, transfer entropy, and reconstruction error to quantify the information transfer of the network. We examined the behaviour of the network while altering the values of the capacitance, synaptic delay, equilibrium potential, leak conductance, reset potential, and voltage threshold. Broad parameter searches showed that no single set of biophysical parameters maximised all information transfer metrics, but some ranges fully blocked information transfer by either saturating or stopping neuronal firing. This suggests theoretical boundaries on the possible electrophysiological values neurons can have. From narrow searches within electrophysiological ranges, we conclude that there is no single optimal set of physiological values for information transfer. We hypothesise that different neuronal types may specialise in transferring different aspects of information such as accuracy, efficiency, or to act as frequency filters.
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