Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • Lindholm, Sara (Helsingin yliopisto, 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 girsl 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.
  • Tuomaala, Emilia (Helsingin yliopisto, 2014)
    Taita Hills are situated in southeastern Kenya (03°20’S 38°15’E), only 350 km from the equator. Ecology and biodiversity of the area is one of a kind and has been subject to multiple studies of natural sciences during the last decades. Taita Hills belong to the Eastern Arc Mountains, an ancient chain of mountains in Eastern Africa and one of the 25 biodiversity hotspots of the world. To qualify as a biodiversity hotspot an area must have lost significant amounts of its original vegetation and inhabit a number of endemic plant species. Both of these criteria are met in Taita Hills where the favorable climate enables endemic species to thrive. Large areas of forest has been cut down in order get more room for agriculture, the main source of livelihood in Kenyan countryside, making the environment threatened. The diverse environment of Taita Hills produces a multitude of ecosystem services. Ecosystem services can be defined as all benefits people obtain from nature. They are often divided into four categories: provisioning services, regulating services, cultural services and supporting services. Ecosystem services link ecological knowledge and economics together by enabling monetary valuation of abstract aspects of nature (e. g. water retention). This link helps decision makers to take environmental issues into consideration by providing a possibility to compare concrete and abstract aspects of nature with each other through tangible monetary values. Research on ecosystem services has grown exponentially in the recent years and decades. However, most of this research has been conducted in developed countries and only little research has been completed in developing countries such as Kenya. It has been established that provisioning services are considered the most important services in developing countries, though. This was the case in Taita Hills, too; the majority of ecosystem services recognized by the local people were provisioning services. Services like firewood, medicinal usage of local plants and scenery were familiar to local people and the role of water was also emphasized in their perceptions of ecosystem services and biodiversity as a whole. Phoenix reclinata was one of the keystone species of ecosystem services. People’s perceptions of biodiversity can vary a lot. Like ecosystem services, biodiversity is a subjective concept that can be understood differently by different people. Understanding how people see nature that surrounds them and biodiversity it beholds can help e. g. in planning nature conservation areas. When people agree on decisions made about their environment and recognize their own basic values in the decisions made they are more eager to support them. Even so, research on people’s perceptions of biodiversity is currently lacking. Results that have been obtained have suggested that plants’ role in people’s perceptions is emphasized and people respond better to beautiful and imposing species than modest or ugly species. This was true also in Taita Hills where people linked plants and forest directly to biodiversity. They also recognized local plant species well, regardless of their nativeness, and had a close relationship with nature overall.
  • Kallio, Jarkko (Helsingin yliopisto, 2017)
    The spreading of non-indigenous species by human activities is a growing problem globally. Invasive species are generally assumed to have negative impacts on ecosystems, because they threaten biodiversity and the balance of ecological systems. Other simultaneous changes in the ecosystem can impact, or intensify the effects of, the invasion. The invasive rock shrimp Palaemon elegans, is an invasive species that has spread to the Baltic sea via human introduction in the early 2000’s. There have also been drastic changes in the ecology of Baltic sea, particularly the increase of primary production. A common mesopredator, the three-spined stickleback Gasterosteus aculeatus, has greatly increased in number in the Baltic sea in recent years. It is presumed to influence the primary production by predation of zooplankton grazers. P. elegans is an omnivore that both grazes filamentous green algae, as well as preys upon the invertebrate grazers that live amongst the algae. If the invasion of P. elegans influences the populations of stickleback, it might also influence the accumulation of primary production. Recent studies have shown, that P. elegans can potentially influence the reproductive behavior of stickleback, but the effect on the success of reproduction has not been proven. This study was composed of two parts: field monitoring and a mesocosm experiment. In the monitoring, individuals of stickleback and P. elegans were caught, counted and measured in three shallow bays and two depths from May to August of 2015. The differences in number of caught individuals were analyzed using Kruskal-Wallis analysis of variance and differences in lengths were analyzed with Mann-Whitney U-test. The effect of P. elegans on sticklebacks was analyzed using covariance analysis. The hypothesis was, that the amount of P. elegans and stickleback or their lengths would show negative correlation, which could be a sign of interaction through predation or resource competition. In the mesocosm experiment stickleback fry were exposed to P. elegans or a non-parent stickleback in tanks with filamentous algae Cladophora glomerata and associated fauna. The resulting differences in in fry number, fry size and the amount of algae between treatments in the tanks were analyzed with Kruskal-Wallis analysis of variance. Correlations between variables were analyzed using Spearman’s rank-order correlation. The hypothesis was that P. elegans would have a negative effect on the amount of fry through predation, or the size of the fry through perceived predation risk. In the field study, no significant correlations were found between P. elegans and sticklebacks, and therefore the results do not suggest a causal link between the two species. Differences between the areas were found, which were attributed to physical differences between the areas. In the mesocosm experiment not enough repetitions were accumulated to provide reliable results. The increase of P. elegans in the Baltic sea is most likely not going to affect the three-spined stickleback via direct predation. P. elegans appears in the shallow bays where sticklebacks reproduce later in the year and it consumes mainly algae and invertebrates. Even though P. elegans will feed on fish eggs if there is an opportunity, stickleback males defend their nests fiercely. The invasion of P. elegans in the Baltic sea is very recent, but it can affect the accumulation of filamentous algae due to their great number. It feeds on invertebrates, but can itself be a potential food item in the diet of ie. cod.
  • Toivio, Viivi (Helsingin yliopisto, 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.
  • Sartamo, Laura (Helsingin yliopisto, 2017)
    Baltic Sea has undergone major changes in the last few decades and its ecological condition has changed. Paleolimnology provides methods to detect changes in the past, mostly from the times when no surveillance was conducted. This Master’s thesis is about the response of a common Cladocera, Eubosmina maritima to the past environmental change in Sandöfjärden, Gulf of Finland. I studied past isotopes, δ13C and δ15N to detect past changes in the eutrophic changes from sedimented subfossil remains to detect how the E. maritima population abundance and morphology have changed due to eutrophication and increased predation pressure. I analyzed a 30 cm sediment core of which I counted E. maritima remains. I also measured the lengths of carapaces, mucros and antennules in order to detect changes in their morphology. I used carbon nitrogen ratio, total carbon, total nitrogen, and their stable status of the sea area. To indicate predation pressure on E. maritima, I used the resting egg data of a predatory cladocera Cercopagis pengoi, that was introduced to the area at the beginning of the 1990’s. The sediment core is stratigraphic, meaning that the layers are connected to each other and therefore cannot be treated as independent samples. The data was first viewed graphically to reveal correlations. I applied redundancy analysis (RDA) to find out if changes in the Eubosmina-populations are explained by the environmental changes. Associated is Monte Carlo permutation test to check which explanatory variables are the most important. Finally I performed variance partitioning to separate the effects of the environment caused by time in the sediment time series. My results show that E. maritima population has increased in number since the 1950’s and a positive correlation with δ15N suggests that this has a connection to increased nutrient levels. It also seems that big E. maritima individuals became more common in eutrophic conditions. Increased predation pressure affected E. maritima populations the strongest right after C. pengoi was introduced to the area when also the longest mucros were found. There also was a slight decrease in the E. maritima abundance at that time. The changes of the lengths of the appendages seem to be more connected to predation pressure, whereas the abundance and the overall body size seem to have a connection with eutrophication. Along with the eutrophication increased the number of E. maritima in the Gulf of Finland. The effect of predation pressure was the clearest right after the introduction and then later smoothened.
  • Collins, Steven (Helsingin yliopisto, 2016)
    Cities of the 21st century consume massive amounts of energy, and indoor climate control within the built environment is responsible for a large fraction of the total demand. With pressures to make buildings more environmentally friendly, new energy efficient technologies and designs are continually sought after. A green roof, or a living roof, is a structural design approach that can provide a variety of ecosystem services along with the reduction of building energy demands. It has been shown that green roofs are effective tools for reducing cooling energy demands in warm and sunny climates; however, in cold climates, where heat energy demands dominate, there is a lack of research and general uncertainty about how beneficial a green roof may be. This thesis, conducted during the winter of 2013-2014, focused on the thermal performance of green roofs in cold weather (winter) conditions. The aim of the study was to quantify the reduction in energy loss that a green roof achieves and to examine the thermal behaviour of each of the green roof layers. Extensive green roofs with hot boxes underneath were constructed in Lahti (southern Finland). Heat sensors were placed vertically through the bare and green roofs to measure linear heat transfer from the interior to the exterior. Heat transfer by conduction was assessed, and a steady state analysis was used to quantify heat flux values. Furthermore, a green roof thermal conductivity model was developed to estimate the thermal conductivity of each of the layers under various environmental conditions (changing moisture contents, frost depths, and during freezing and thawing periods). Monthly comparisons of the energy lost through the two roofing structures were quantified. My results showed that green roofs reduced the amount of energy loss through the surface compared to bare roofs throughout the winter season. The overall reduction in energy loss, due to the presence of green roofs, was on average, 32.6%. Layer analysis showed that thermal conductivity of each of the layers decreased when penetrated by frost. A frost depth that extended through the whole green roof yielded the highest thermal resistance for the green roof at 3.96 m2KW-1. Comparatively, the bare roof had a thermal resistance of 0.27 m2KW-1. During times of snow coverage, the snow acted as a good thermal insulator, reducing the relative benefits achieved from green roofs. During refreezing and thawing, the green roof experienced the lowest values of thermal resistance at 1.83 m2KW-1. These results can be used for quantifying possible heat loss reductions in similar climates using a similar green roof, and the layer analysis provides information of how to best design green roof components for thermal resistance.
  • Helenius, Leena (Helsingin yliopisto, 2016)
    The purpose of this Master’s thesis is to examine and analyse contradictions typical to many environmental questions and to bring forth the thinking underlying them. The thesis explores how the contradictions are perceived and examines them with the concept of paradigm. Paradigm is defined as a mental model through which the world is seen. Two specific paradigms, exclusive and inclusive paradigm, are identified and conceptualised in environmental thinking and analysed via two case-studies. The aim is to improve understanding of environmental contradictions and conflicts and to find ways to tackle them with paradigmatic level of thinking. The objectives of the thesis are first, to develop theoretical tools to ease comprehensive understanding of contradictions, and second, to enable examination of dichotomies and polarized juxtapositions. The research approach is holistic, and the analytical process applies philosophical methods of problematization, explication and argumentation. Other methodological tools utilized include hermeneutic thinking and abductive reasoning. The case-studies in focus are the human perception of inclusion with nature and the human-wolf conflict in Finland. In the human-wolf conflict case-study content analysis is also applied. The thesis first presents the concepts of opposite and contradiction and examines how they are approached in the Western philosophical tradition. The special focus is on the differences between the logics and the dialectics traditions regarding exclusive and inclusive thinking. The logical laws of non-contradiction and excluded middle and dialectical thinking are the key elements of the theoretical framework. Based on these elements two cognitive models are built: a) a seven-point model that describes the process of neutral opposites turning to problematic contradictions, and b) a four-field sub-paradigm model, which enables examination of contradictions via four different sub-paradigms (atomistic dualism, atomistic pluralism, holistic dualism and holistic pluralism). The models are applied to the two case-studies. The first case-study of human perception of inclusion with nature deals with the human-nature relationship, i.e. to what extent human is perceived to be a part of nature or separate of it. The seven-point model shows how human and nature are separated from each other and perceived as polar opposites at conceptual level in Western thinking. The sub-paradigm model illustrates four alternative ways, exclusive and inclusive, to see the human-nature relationship. In conclusion, juxtaposition of human and nature is shown to result from logical misconception combined with exclusive thinking. Instead of being detached from nature, human is fully dependent on it. The second case-study of the human-wolf conflict in Finland is a classic wicked problem: a complex, multi-stakeholder issue, solving of which requires holistic understanding. The human-wolf conflict is examined utilising both previous academic literature and news and magazine articles on the case. The purpose of this case-study is to offer an illustrative example and to show in a more concrete way the significance of inclusive and exclusive paradigm to the understanding of such environmental conflicts. It is suggested that the polarized situation of the human-wolf conflict could be unraveled by applying the models built in this thesis. Specifically, the inclusive paradigm could have a central role in resolving the conflict. The last section of the thesis discusses why it is important to distinguish what kind of contradiction is at hand and what kind of paradigms they are seen through: paradigms always shape the way the contradictions are seen. It’s important to recognise the situations where the two different paradigms should be used. Inclusive paradigm suits to seeking comprehensive understanding to complex problems. Exclusive paradigm on the other hand can help with concrete solutions and decisions. Inclusive and exclusive paradigms themselves form contrary opposites, and should therefore be understood dialectically. The thesis introduces a concept of meta-dialectics emphasising balanced application of the two paradigms in a case- and context-specific manner. Further research could include applications of the models built in this thesis to different environmental cases, investigating in further detail what kind of issues and conflicts would need more inclusive or exclusive thinking. Finally, further development of comprehensive and holistic research methodologies would be highly needed in our increasingly complex world.
  • Duru, Ilhan Cem (Helsingin yliopisto, 2017)
    Lactobacilli are gram-positive lactic acid bacteria with wide beneficial properties for human health and food production. Today most of the fermented products and probiotic foods are produced by lactobacilli species. One of the most using area of lactobacilli species is fermented products especially dairy products. Lactobacilli species can be used as starter or adjunct cultures in dairy products and play important role for preservation and quality, texture and flavor formation. Additionally, probiotic properties of lactobacilli species provide several health effect for human by stimulation of immune system and protection against pathogens. Lactobacillus rhamnosus LC705 is a facultatively heterofermentative type lactobacilli which is used in production of dairy products as adjunct starter and protective culture. The complete and annotated genome sequence of L. rhamnosus strain LC705 published on 2009. Known characteristics of L. rhamnosus strain LC705 are food preservation, toxin removal and health benefits when combined with other probiotic strains. However, molecular mechanism behind these characteristics are not known or not clearly understood. To get further insight on these properties and roles in cheese ripening of strain LC705, we re-annotated genome of the LC705 with updated methods and databases, analyzed metabolic pathways of LC705, and performed RNA-seq experiment to determine gene expression changes of LC705 during warm room (25 °C) and cold room (5 °C) cheese ripening process. Several un-characterized proteins of LC705 were annotated (77) and 1197 enzyme commission (EC) numbers are added to annotation file with re-annotation of genes of LC705. More importantly, re-annotation provided us 72 new pathways of LC705 which is 35% of the entire collection of 201 pathways. Analyzes of pathways showed that genome of LC705 has responsible genes for production of flavor compounds such as acetoin and diacetyl which are provide buttery flavor to dairy products, and hydrogen sulfide which is a volatile sulfur compound that cause unlikeable odor. Additionally to flavor compounds, we defined genes that produce anti-fungus compounds and bacteriocin which provide food preservation characteristic to LC705. Determination of gene expression respond of LC705 during warm room and cold room cheese ripening process with RNA-Seq showed that central metabolism genes that responsible for lyase activity, degradation activity, disaccharides and monosaccharides metabolism are warm induced genes. The genes play role in citrate metabolism pathways were significantly down-regulated during cold room, citrate degradation pathways are critical for buttery flavor products, therefore buttery flavor compounds are produced by LC705 during warm room. Finally, during cold room ripening, the genes of LC705 that produces ethanol and acetyl-CoA from pyruvate was up-regulated, so we may say that LC705 uses pyruvate to produce ethanol and acetyl-CoA instead of lactic acid.
  • Liao, Wenfei (Helsingin yliopisto, 2017)
    Urbanisation has caused many environmental problems, such as air pollution and the loss of biodiversity. One way to mitigate these problems is to expand green spaces. Roofs, as the last frontier, could be made full use of. Green roofs have become a hot topic in recent years. In this study, I investigated the ability of green roofs to support urban biodiversity by conducting a literature review, and then I sought the criteria for biodiversity roofs under Finnish conditions by interviewing ecologists. My research questions in this study were 1) What kinds of habitats could be ideal ecosystems to be mimicked on biodiversity roofs in Finland; 2) which plant species could exist on roofs and whether they contribute to biodiversity; 3) what kinds of substrates support the biodiversity on roofs; 4) whether green roofs support faunal diversity and what faunal taxa could exist on roofs; 5) if and how roof structural characteristics influence roof biodiversity; 6) what kinds of management are practiced on biodiversity roofs; 7) what are people s attitudes towards or perceptions of biodiversity roofs in general. In this study, I conduct that 1) Sunny dry habitats, such as meadows and tundra, can be regarded as model ecosystems for biodiversity roofs in the Finnish context. 2) Substrate heterogeneity is a key to biodiversity on green roofs. Different materials and different combinations of materials could be applied on the same roof to mimic diverse types of soil types in the most biodiverse Finnish ecosystems. 3) Native species from the model ecosystems are ideal plants for biodiversity roofs. Combining multiple greening methods on the same roof can be a solution to achieve instant greening effects with only native species. 4) An ideal biodiversity roof in the Finnish context could support birds, bats, and invertebrates, such as spiders. To attract and support fauna, a roof needs a diverse plant community, as well as extra elements, such as deadwood. 5) Roof structural characteristics (i.e. roof height, size, slope, direction, location, and age) impact biodiversity by determining the accessibility to and the dispersal of flora and fauna, as well as microclimates on roofs. 6) Management, such as irrigation, might help biodiversity at least for newly established biodiversity roofs, but biodiversity roofs aim at being self-sustaining eventually. 7) People have generally positive attitudes towards green roofs, but their willingness to actually install a biodiversity roof is influenced by other issues, such as the financial cost and roof safety.
  • Porkka, Kaija (Helsingin yliopisto, 2017)
    Tiivistelmä Referat Abstract Chitinolytic enzymes belong to a group of pathogenesis-related proteins, which are induced in plants by a pathogenic attack. They have also been shown to function in abiotic stresses and related to signalling. Chitinases catalyze the degradation of β-1,4-N-acetyl glucosamine units of chitin. Chitin is not found in plants, but for example the shells of invertebrates, cell walls of certain fungi, algae and bacteria contain it abundantly. Lately chitinases have gathered attention because of their potential utilization possibilities in medicine, agriculture, food industry and biofuels. Strong chitinase gene expression and also chitinolytic activity has been found in a spruce (Picea abies L. Karst.) cell culture, which produces apoplastic lignin into the medium. Plant chitinases are known to be induced also in developmental processes. Chitinase-like genes have been shown to be essential in cellulose synthesis and in development of cell walls and tracheary elements and also affected the localisation of lignin in tissues. Therefore, the secretion of chitinases into the culture medium has not necessarily been caused by stress and chitinases might use also some endogenic substrate in addition to chitin. Because chitin is a structural component of plant pathogens but not present in plants and the growing circumstances of the studied aceptic spruce cell culture were stable, the research hypothesis was, that the secreted chitinases in the culture medium were not a stress reaction but related to development and besides chitin of the pathogens they utilize some own polysaccharide substrate of spruce. Additional hypothesis was connection of the strong expression of chitinases and chitinase-like genes in the culture medium and the production of apoplastic lignin by the spruce cell line. The aim of the study was to characterize the chitinases and chitinase-like enzymes of the spruce cell suspension culture medium and developing xylem by isolating, purifying and cloning them and by producing them heterologously. The aim was also to identify the putative endogenous substrates for the chitinases and chitinase-like proteins to reach better understanding about the meaning of the chitinases in the development of the spruce tissues. Two chitinases of the spruce cell suspension culture were isolated and purified by chromatographic methods. One chitinase gene in spruce cell culture and one chitinase-like gene in spruce xylem were cloned, after which the chitinases and chitinase-like proteins were produced in Pichia pastoris yeast. The total proteins of the culture medium, the purified chitinases isolated from the medium and the chitinases and chitinase-like proteins produced in P. pastoris were used to examine their substrate alternatives with the carbohydrate microarray method. The connection between apoplastic lignin and the chitinolytic enzymes in culture medium was not found and obvious candidates for the endogenous substrates were not detected. However, the mannan degradation in the presence of the chitinases was strong enough to give reason to further analyses.
  • Korppoo, Annakarin (Helsingin yliopisto, 2017)
    Trichoderma reesei, an anamorph of Hypocrea jecorina, is a filamentous fungus widely used for producing industrial enzymes. T. reesei is used for both endogenous and heterogenous protein production. The optimization of the production conditions and the effects of extracellular agents to T. reesei s production and secretion capacity are crucial for economically sustainable biotechnical production. The available carbon sources, most commonly different types of sugars, have a significant effect on the production and secretion of enzymes by T. reesei. Genetic modification of the pathways through which the fungi recognizes extracellular signals could bring advancements to industrial enzyme production. Because of T. reesei s potential and use as a production strain, the species is an interesting platform for genetic modifications that would enhance the production capacities. With the current methods the genome editing of T. reesei is however slow, and introducing multiple mutations to a single strain can take years. The aim of this study is to optimize the fairly new CRISPR/Cas9 genome editing system for use in T. reesei. In the CRISPR/Cas9 method, a catalytically active Cas9 enzyme is bound to a specific locus of the genome, guided by a guide RNA and the Watson-Crick base pairing principle. Once in the RNA-guided locus, Cas9 introduces a double stranded break in the DNA, which can be repaired by the cells endogenous non-homologous end joining pathways. This repair is error prone and produces mutations to site of the double stranded break. A donor DNA is often introduced together with the Cas9 and guide RNA. This donor DNA includes sequence homology to the site of interest and allows for the use of the cells homologous repair pathways. In this case, the mutation can be better controlled, and for example the risk of chromosomal mutations is reduced. Currently the CRISPR/Cas9 system is widely used in mammalian cell studies and up to 100% mutation frequencies have been reported in yeast cells. In this study the method is optimized for use in T. reesei. To our best knowledge, the research community has not found an organism in which CRISPR/Cas9 would not function. The question mainly lies on what type of set up and component introduction is suitable for each cell type and research purpose. In this thesis, three putative and one already published genes believed to be involved in hexose sugar sensing will be deleted from a T. reesei production strain with the help of CRISPR/Cas9. The effect of these deletions will be assessed through studying the secretion and activity of endogenous cellulases with enzymatic assays. One sugar transporter that may play a part in glucose sensing was identified in this study. The deletion of this transporter caused a decrease in cellulase production and/or secretion. The three other transporters or sensors did not have a significant effect on cellulase production in spent grain extract and lactose or glucose media. It s possible that these genes are involved in the uptake and use of other carbon sources. The continuous expression of the CRISPR/Cas9 system in T. reesei proved difficult. In the continuous expression method at least one of the CRISPR/Cas9 components, the Cas9 protein or the guide RNA, is produced in the cells in vivo. Neither was achieved in this study. Instead, a fully synthetic method in which the Cas9 is transformed into the cells as a protein along with an in vitro produced guide RNA was set up and produced up to 1000 × higher mutation frequencies when compared to the traditional transformation method used for T. reesei. This study also demonstrates a simultaneous deletion of two genes in T. reesei. To the best of our knowledge, multiple simultaneous gene modifications have never been achieved in T. reesei.
  • Jalkanen, Joel (Helsingin yliopisto, 2016)
    Biotopes and biodiversity within the Metropolitan Area of Helsinki (cities of Helsinki, Espoo, Vantaa and Kauniainen) were prioritized with a spatial conservation prioritization software called Zonation. The aim of the thesis was to examine how different, largely urban or semi-urban, areas supported biodiversity and thus, indirectly, ecosystem services provisioning. Furthermore, the effects of the new City of Helsinki Strategic Plan 2050 on the prioritization were examined. The analyses were based on expert elicitations, in which different urban biotopes were evaluated in terms of how well they supported species richness and the occurrence of specialist species of 8 taxonomic groups. Following the biotope classification, an urban biotope map was compiled from various GIS sources. Based on the expert answers, these biotope maps were then converted to suitability maps for each of the eight taxonomic groups. The urban biotope map, as well as the suitability maps, were made according to two land-use versions: current land-use in the research area, and a scenario describing the actual City of Helsinki Strategic Plan 2050. Separate Zonation prioritizations were then made for both scenarios. Urban biotopes a-priori evaluated as important for biodiversity, such as lakes and their shores, ruderal areas, dry meadows, manor yards, shoreline meadows and herb-rich forests, became emphasized in Zonation prioritizations as well, whereas the currently heavily built areas received lowest conservation priority in the analysis. Thus, according to this study, densification of the current residential and built-up areas does not threaten the urban biodiversity or ecosystem services of the Metropolitan Area of Helsinki. According to the present analysis, the new Helsinki Strategic Plan would have some relatively small effects on biodiversity in the research area. While the plan proposes development in some top-value biodiversity areas, the estimated effects of the plan were on average only a 3.3% loss of biotopes across taxonomic groups. Nevertheless, the plans of Helsinki could influence biodiversity priority areas in neighboring cities, and I recommend that the broader Metropolitan Area should be treated as a whole from the perspective of urban biodiversity. Rather than preserving sets of defined species, multi-functionality and ecosystem services provided by urban biodiversity should be emphasized when planning for urban nature conservation. As biodiversity ultimately underlies and supports both of these objectives, it should be central in the urban planning as well. Spatial conservation prioritization can well be used for ecologically sustainable urban planning, as long as the quality of the input data is taken care of and different uncertainties and limitations of the analyses are recognized in interpretation.
  • Tiusanen, Mikko (Helsingin yliopisto, 2015)
    Ihmistoiminta muuttaa elinympäristöjä maailmanlaajuisesti. Vaikutukset näkyvät niin yksittäisten lajien populaatioissa, lajien välisissä vuorovaikutuksissa kuin kokonaisten ekosysteemien toiminnassakin. Monimutkaisuutensa ja vaikean havainnoitavuutensa takia lajien väliset vuorovaikutukset ja erityisesti niiden yhteys ekosysteemien toimintaan tunnetaan osin huonosti. Ympäristömuutoksista ilmaston lämpeneminen vaikuttaa erityisen voimakkaasti arktisella alueella. Muuttuva ja yksinkertainen arktinen eliöyhteisö tarjoaakin loistavan malliekosysteemin lajien välisten vuorovaikutusten havainnoimiselle ja niiden rakenteen mallintamiselle. Tässä tutkielmassa selvitän pölyttäjäyhteisön rakennetta ja toimintaa yhden kasvilajin, lapinvuokon Dryas octopetala × integrifolia, pöly-tyksessä. Lapinvuokko on runsain kukkakasvi monilla pohjoisilla alueilla, ja sitä voidaankin pitää avainlajina paikallisissa pölytysyhteisöissä. Liittääkseni pölyttäjäyhteisön rakenteen lapinvuokon siementuotannon onnistumiseen havainnoin lapinvuokon pölyttäjäyhteisön vaihtelua tilassa ja ajassa. Tähän käytin kukanmuotoisia liimapahvista valmistettuja pyydyksiä. Tein liimakukkapyyntejä 21 koealalla Zackenbergin laaksossa Grönlannissa. Tutkin koealoilla lisäksi lapinvuokon siementuotantoa. Tutkimuksessani havaitsin, että lapinvuokon kukinnan ajoittumisessa on suurta alueellista vaihtelua. Ensimmäiset kukat puhkeavat heti pälvien ilmestyessä ja viimeisten yksilöiden kukinta alkaa vasta juuri ennen ensilumia. Myös lapinvuokon siementuotannon onnistuminen vaihtelee paljon (12,7 52,7 % kukista) alueellisesti. Alueellinen vaihtelu siementuotannon onnistumisessa johtuu osittain ympäristöolosuhteista, mutta myös pölyttäjäyhteisöllä on selvä vaikutuksensa. Lapinvuokolla tapahtuu itse- ja tuulipölytystä (8,6 % onnistuneesta siementuotannosta), mutta pölyttäjien läsnä ollessa siementuotanto on moninkertainen (33,7 %). Tutkimusalueellani Zackenbergissa maailmanlaajuisesti tärkeimmät pölyttäjät, mesipistiäiset, puuttuvat lähes tyystin. Runsaimpien pölyttäjien paikan ovat vallanneet kärpäset erityisen runsaslukuisten sukaskärpästen johdolla. Havaintojeni perusteella sukaskärpästen runsaus selittääkin parhaiten lapinvuokon siementuotannon onnistumista. Kesän edetessä havaitsin pölyttäjäyhteisön kasvavan huomattavasti sekä yksilö- että lajimäärältään. Pölyttäjäyhteisön runsastuminen kasvukauden edetessä antaa olettaa, että lapinvuokon pölytys voi parantua ainakin lyhyellä aikavälillä. Ilmaston lämmetessä pölyttäjien esiintymisen on havaittu liukuvan aikaisemmaksi kasvien kukintaa nopeammin. Näin ollen aikaisin kukkivat kasvit kohtaavat yhä enemmän pölyttäjiä ja myöhäisimmätkin kasvit onnistuvat tuottamaan siemeniä ennen syksyä, kun niiden kukinta siirtyy absoluuttisesti aikaisemmaksi. Toisaalta sukaskärpästen määrän on havaittu vähenevän ilmaston lämmetessä. Tutkimukseni pohjalta sukaskärpäset ovat lapinvuokon tärkeimpiä pölyttäjiä, ja jos niiden väheneminen jatkuu, on lapinvuokon pölytys Zackenbergissa uhattuna. Kaiken kaikkiaan tutkimukseni viittaa siihen, että lapinvuokon pölytys voi lyhyellä aikavälillä parantua, mutta pitkällä aikavälillä muutokset pölyttäjäyhteisössä uhkaavat lapinvuokon pölytyksen onnistumista. Lapinvuokko on arktisen alueen tärkeimpiä kasveja niin pölyttäjien kuin monien muidenkin hyönteisten ravintona. Siten muutokset sen menestyksessä heijastunevat koko pölyttäjien ja kukkakasvien muodostamaan yhteisöön.