Bio- ja ympäristötieteellinen tiedekunta

 

Recent Submissions

  • 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.
  • Österblad, Ika (Helsingin yliopisto, 2016)
    Parasitoid host interactions are intimately associated with food web dynamics as well as with evolutionary change. The parasitoid s possibility to expand its host range or switch to different hosts is affected by parasitic strategy. Strong specialization to a narrow host repertoire can arise e.g. if the larva spends considerable time in close contact with an active, developing host (koinobiosis). In contrast, an ectoparasitic larva, growing rapidly on a sessile host, does not have to be equally tightly adapted to host physiology. This may permit a wider host range. However, there are other restricting factors, such as egg production capacity. Extant parasitoids show a staggering species diversity, most notably among the Hymenoptera. Theories concerning speciation in association with host range have been developed, but draw from knowledge of merely a small part of this diversity. This study adds information by showing a number of radical host shifts in the evolutionary history of the ichneumonid wasp genus Gelis. Species of this genus exploit either insect prepupae or spider eggs. These are similar in being rather defenceless, aside from a protective silk covering. Nonetheless, differences are large enough to restrict Gelis species to each utilise only one of the two groups. In order to trace ancient host group shifts, host data was mapped onto a phylogeny constructed through bayesian analysis of sequence data. Sequences from the COI (mitochondrial) and ITS2 (nuclear, noncoding) regions were used. The results suggested at least four host group shifts within the genus. In addition, wing reduction was found to have occurred in two different lineages. Through COI barcode sequence clustering supported by morphological traits, a previously undescribed species from the G. bicolor-species complex was detected. The phylogenetic analyses also indicated the existence of further cryptic species, and the genus Thaumatogelis Schwarz was found to be nested within Gelis.
  • Tsui, Ka Man (Helsingin yliopisto, 2015)
    Forest certification has been used as a tool to promote forestry responsibility towards sustainable forest management. Forest Stewardship Council (FSC) is one of the certification systems that is well recognised in Europe. Nevertheless, compared to other European countries, the number of FSC chain of custody (CoC) certifications in Finland is relatively low. Semi-structured interviews were conducted with six FSC CoC certified companies to explore their experiences towards implementing and maintaining the system in their companies. The sample group was comprised of wood and paper product industries in manufacturing and trading sectors. Thematic analysis of the interviews revealed the challenges companies encountered. The results indicated that there were eight types of challenges, including three internal and five external ones, hindering the development of FSC CoC certification in Finland. Internal challenges included competence, financial resources, and a lack of motivation to change. External challenges included insufficient marketing and demand, uncertain cost benefit, keen competitor programmes, limited supply, and long trademark approval time. Meanwhile, the relevant solutions these companies adopted to deal with the challenges were discussed. Since external challenges out-numbered internal ones, it seemed that certified companies are not able to tackle the existing challenges alone. Joint-effort among other actors in the forestry sector, for instance, the national authority, FSC national office, certification bodies are essential to influence the rate of certification uptake. Furthermore, participants discussed about the future development of FSC CoC certification system in Finland. Interviewees believed that the enactment of the EU Timber Regulation (EUTR) and the introduction of forest certification into national public procurement policy could positively impact the development of the system. The results of this study could be used as a reference for potential certificate users to prepare themselves for implementing FSC CoC certification system. In addition, the study could shed a light on the development of FSC in Finland in the future.
  • Hänninen, Emmi (Helsingin yliopisto, 2016)
    Meriympäristöihin kohdistuvat ihmistoiminnan paineet kasvavat koko ajan. Merialueita uhkaavat esimerkiksi luonnonvarojen liikakulutus sekä meriekosysteemin vahingoittaminen ja elinympäristöjen tuhoaminen. Tietoisuus vedenalaisten elinympäristöjen tilasta on luonut tarpeen tutkia ja lisätä vedenalaista tietämystä. Vesiympäristöjä inventoidaan erilaisin mittauksin, kaukokartoituksin ja kenttäkartoitusmenetelmin. Merenpohjaa kartoitetaan esimerkiksi sukeltamalla ja videoimalla sekä erilaisilla kaikuluotaus- ja kaukokartoitusmenetelmillä. Itämeren vedenalaisen meriluonnon monimuotoisuuden inventointiohjelman VELMUn tavoitteena on lisätä vedenalaisen meriluonnon tietämystä kartoittamalla Suomen rannikkoalueita ja vedenalaisia elinympäristöjä. Tutkimuksessani vertailin sukellus-, videointi- ja haramenetelmien vahvuuksia ja heikkouksia ja arvioin niiden tarkkuutta ja todenmukaisuutta. Kovilta pohjilta otettiin lisäksi Kautsky-näytteitä lajien tunnistamisen vertailua varten. Halusin selvittää 1) Vaihteleeko lajintunnistuksen tarkkuus eri luokkatasojen välillä, ja mitkä ovat ne luokkatasot, jotka pystytään luotettavasti arvioimaan videometodein erilaisissa ympäristöissä? 2) Vaihteleeko lajintunnistuksen tarkkuus habitaattien sisällä ja välillä? 3) Onko videomateriaalin perusteella tehtävän lajintunnistuksen tarkkuuden ja pohjaorganismien peittävyyden välillä yhteyttä? 4) Onko linja-arvioinnin ja pistearvioinnin antamien tulosten välillä eroja? Verifiointityö toteutettiin Hangon ja Tammisaaren vesialueilla läntisellä Suomenlahdella heinä-syyskuussa 2007. Tutkimuksessa videoitiin ja arvioitiin sukeltamalla yhteensä 99 kasvillisuuslinjaa lieju-, hiekka- ja kovilta pohjilta. 10 metrin pituiset linjat sijoitettiin maksimissaan 8 metrin syvyydelle. Lisäksi jokaisen linjan lähettyviltä tehtiin 2−3 ruutuarviointia alaltaan 0,25 m2. Vertailun kohteena olivat eri menetelmät (sukellus, videointi ja hara) sekä eri peittävyysalat (linjat ja ruudut). Tulokset osoittivat, että videomenetelmä on karkeampi menetelmä kuin sukellus. Videoanalysoinneissa lajimäärä jäi vähäisemmäksi kuin sukeltajan arvioinneissa. Sukeltaja tunnisti kaikilla luokkatasoilla enemmän makrofyyttejä kuin videoarviointi. Parhaiten videolta erottuivat suuret ja dominoivat lajit ja pienet, matalat ja harvinaiset yksilöt jäivät herkästi videolta huomaamatta. Videotulkinnoissa tuli virheitä niin lajitason (Potamogeton perfoliatus --> P. praelongus) kuin heimotason tarkastelussa samankaltaisten lajien osalta (Potamogeton vrt. Zannichellia). Luhter-haralla saatiin lajimääristä ja peittävyyssuhteista samankaltaisia tuloksia kuin sukeltamalla. Linja-arvioiden lajimäärät olivat suurempia kuin ruutuarvioiden. Myös peittävyydet arvioitiin suuremmiksi linjoilla kuin ruuduilla. Pohjatyypillä ei ollut vaikutusta eri arviointimenetelmien toimivuuteen lajimääriä arvioitaessa. Sen sijaan peittävyysarviot vaihtelivat niin menetelmien kuin pohjatyyppien välillä. Sukeltajan ja videomenetelmän peittävyysarviot poikkesivat toisistaan hiekkapohjalla, muilla pohjatyypeillä arviot olivat samankaltaisia. Menetelmien erot peittävyyksien arvioinnissa poikkesivat toisistaan hiekkapohjan linjojen ja ruutujen välillä, kun muilla pohjatyypeillä ja peittävyysaloilla menetelmät toimivat yhtäläisesti. Sinisimpukkaa havaittiin harvemmin videolla kuin sukeltajan arvioissa. Toisaalta videoarviointien peittävyydet olivat sukeltajan arvioita suuremmat siellä, missä sinisimpukkaa havaittiin. Lajin runsaus vähensi makrofyyttimääriä ja lisäsi niiden tunnistusvirheitä videoarvioinneissa. Sinisimpukka voi olla vaikeasti havaittavissa pohjamosaiikista ja varsinkin sen peittävyyttä on hankala arvioida videokuvasta. Turbiditeetti ei vaikuttanut lajihavaintojen määrään videoarvioinneissa, mutta sukeltajan arvioissa liejupohjalla turbiditeetin voimakkuus vähensi lajimäärää, kun taas kovalla pohjalla vaikutus oli päinvastainen. On tärkeää, että lajinmääritys osuu oikeaan, eikä vain sinnepäin . Väärä lajinmääritys voi johtaa vääriin päätelmiin ja tätä kautta esimerkiksi vääriin suojelutoimenpiteisiin. Videoarvioinneilla on tarkoitus tehdä yhteisötason kartoitusta, jota täydennetään muilla menetelmillä, kuten sukelluksin ja näytteenotoin. Videoarvioissa ylletään harvoin lajitason tunnistuksiin eikä niitä ole tarkoituskaan tehdä. Siksi on aina parempi jättää tunnistus karkeammalle tasolle kuin tehdä väärä tunnistus. Koska kansallinen päätöksenteko Itämeren käyttöön liittyen perustuu pitkälti VELMUn tuottamiin luontotyyppimäärityksiin, on tärkeää, että sen tuottama informaatio on luotettavaa. Tämän tutkimuksen tuloksista on hyötyä VELMU-projektille, koska ulkopuolista tarkastusta ei käytetyille kartoitusmenetelmille ole aiemmin tehty. Tulosten avulla voidaan suunnitella parannuksia kartoituksen luotettavuuteen ja tarkkuuteen.
  • Lautala, Katri (Helsingin yliopisto, 2016)
    Liito-oravaa (Pteromys volans) esiintyy EU:n alueella ainoastaan Virossa ja Suomessa. Lajin kanta heikkenee jatkuvasti metsätaloustoimien vuoksi. Liito-orava kuuluu EU:n luontodirektiivin suojaamiin lajeihin ja sen lisääntymis- ja levähdyspaikkojen hävittäminen on kielletty luonnonsuojelulailla. Liito-oravaa on suojeltu vuosina 2004 2016 Elinkeino-, liikenne- ja ympäristökeskuksen (ELY) toteuttamin rajausmenettelyin, jotka vuonna 2016 poistettiin käytöstä. Metsätoimijoiden vastuu liito-oravan suojelusta on kasvanut. Tässä työssä tutkin metsänomistajien asenteita liito-oravaa, sen suojelua sekä suojeluviranomaisia kohtaan. Olin kiinnostunut lainsäädännöllisen velvoittavan suojelun vaikutuksesta metsänomistajien asenteisiin suojeltavaa lajia kohtaan. Lisäksi halusin selvittää, millaiset taustatekijät voivat vaikuttaa asenteisiin. Taustateorioina käytin sosiaalipsykologian asenneteorioita, joiden pohjalta uskoin vastaajien asenteissa näkyvän joko kielteistä tai myönteistä suhtautumista liito-oravan suojeluun. Kielteinen suhtautuminen osoittaisi reaktanssia eli psykologista ilmiötä, jossa käskeminen aiheuttaa halun rikkoa annettua käskyä, jotta oma valinnanvapaus säilytetään. Myönteinen suhtautuminen kertoisi dissonanssi-ilmiöstä eli psykologisesta ilmiöstä, jossa käyttäytymistä ei voi lainsäädännön takia muuttaa ja siksi muutetaan asenne lakia myötäileväksi. Aiempien sääntöjen noudattamista käsitelleiden asennetutkimusten perusteella molempia ilmiöitä tulisi esiintyä vastaajien joukossa. Toteutin tutkimuksen puhelimitse tapahtuvan haastattelun avulla. Metsänomistajat oli jaettu kolmeen ryhmään heidän liito-oravakokemuksensa perusteella. Kontrolliryhmällä ei ollut ollenkaan omakohtaisia liito-oravakokemuksia. Kahdella muulla ryhmällä oli joko ELY-keskuksen antama liito-oravapäätös ilman hakkuurajoituksia, tai ELY-keskuksen määrittämä liito-oravapäätös hakkuurajoituksineen. Kokemuksen merkitystä analysoin mm. lineaarisen regressioanalyysin avulla. Tulokset osoittivat, että noin puolet metsänomistajista suhtautuivat liito-oravaan ja sen suojeluun kielteisesti ja heidän vastauksissaan oli havaittavissa selkeää reaktanssia. Taustatekijöistä asenteisiin vaikutti eniten vastaajan omistaman metsän pinta-ala. Kielteiset metsänomistajat vastustivat heidän metsätaloustoimiaan rajoittavaa lainsäädäntöä, eivätkä uskoneet liito-oravan olevan kovin uhanalainen. Metsänomistajat, joille oli määrätty rajauksia, suhtautuivat kaikista kielteisemmin liito-oravaan liittyviin väittämiin. Ryhmittelyanalyysin perusteella kuitenkin noin puolet vastaajista suhtautuivat melko myönteisesti liito-oravaan ja 70 % metsänomistajista olivat tyytyväisiä saamiinsa liito-oravapäätöksiin. Vuoden 2016 muutokset tulevat varmasti heikentämään entisestään liito-oravan suojelua, kun muutokset antavat käsityksen, ettei lajinsuojelu ole tärkeää. Liito-oravan suojelun jatkosuunnitteluun kannattaisi tämän tutkimuksen tulosten perusteella ottaa metsänomistajat mukaan. Iso lajinsuojelullinen ongelma on se, ettei suuri osa metsänomistajista usko liito-oravan olevan uhanalainen. Tätä epäkohtaa voitaisiin korjata esimerkiksi osallistamalla metsänomistajia liito-oravakannan koon arviointiin.
  • Lappalainen, Juho (Helsingin yliopisto, 2016)
    The productivity and biodiversity of coastal areas, one of the most productive ecosystems on earth, are threatened by eutrophication and habitat loss which also drive deterioration of the macroalgal communities of shallow rocky bottoms and their perennial key species. The underwater light, being one of the most important factors determining the zonation and distribution of macroalgae, alternates in space and time. The water quality at the study area, Gulf of Finland, has deteriorated during the past hundred years which has lowered the amount of light at the bottom. Comprehensive studies on spatio-temporal changes at euphotic bottom and the their effects on macroalgae are yet to be done. This study investigates how the area of euphotic bottom at the Gulf of Finland has fluctuated during 2003 2011, and how the amount of light on the bottom determinates the zonation and distribution of macroalgae. Furthermore, the changes in the areas of euphotic bottom when the euphotic depth is altered and the effects on macroalgae are surveyed. One hypothesis is that in many areas macroalgae are not affected by too low light levels but the unsuitable bottom substrate that limits their distribution. The study material consists of euphotic depth GIS (Geographic Information System) layers derived from MERIS (MEdium Resolution Imaging Spectrometer) satellite images from May to September from 2003 2011, inventory data of the Finnish Inventory Programme for the Underwater Marine Environment (VELMU), water quality measurements and HIRLAM (High Resolution Limited Area Model) weather model. The distribution of euphotic bottom and its area were calculated for four parts of the Gulf of Finland. Changes in euphotic bottoms were evaluated in scenarios where euphotic depth changed -100 87,5 %. The effect of light on the zonation and distribution patterns of macroalgae were surveyed using distribution models. Boosted Regression Tree (BRT), Generalized Additive Model (GAM) and Climate Envelope Model (CEM) were utilized on bladderwrack (Fucus vesiculosus L.). In addition, scenarios of euphotic depth changing -50 50 % were modelled. The area of euphotic bottom varied seasonally and changed slightly between the study years. The area was larger in the inner archipelago compared to the outer arhcipelago and the difference was greater when the areas were normalized with local sea area. Always and occasionally euphotic bottoms were located near the shoreline and reefs. The altered euphotic depth affects euphotic bottoms the most in the outer archipelago. There were local differences in the performance of the distribution models. The change in euphotic depth affects the distribution of bladderwrack considerably: a deterioration of 25 % narrows off the distribution widely and a decline of 50 % suggests that the species is going to disappear from the Gulf of Finland. A decline in euphotic depth shifts the inner distribution limit towards the outer archipelago and narrows the macroalgae zone locally while even a small improvement expands the area significantly. However, the substrate of the newly exposed zone is only partially suitable for macroalgae and the portion of rocky substrate decreases as a function of euphotic depth. Changes in the optical properties of the sea affect the penetrance of light at the bottom and the area of euphotic bottom. Increasing turbidity of the sea is a remarkable threat to macroalgae. Vice versa, clarification of the water expands light-limited distribution and enlarges the macroalgal zones even though the growing amount of unsuitable soft substrate inhibits the distribution and zonation of macroalgae.
  • Niskanen, Julia (Helsingin yliopisto, 2016)
    Epidermolysis bullosa (EB) is a group of hereditary skin disorders caused by mutations in the genes that code for adhesion molecules in keratinocytes. The symptoms of the disease include blisters and erosions in the skin as well as abnormalities in the mucosal membranes, nails and tooth enamel. Depending on the causative mutation the severity of the disease ranges from mild to lethal. This master s thesis was carried out in professor Hannes Lohi s canine genetics research group. It is a case study aiming to identify the genetic cause of EB present in Central Asian shepherd dogs. Furthermore, the mode of inheritance, frequency of the mutation in the breed and the effect of the mutation on the tissue were also examined. Primary research material included blood and tissue samples from a family of Central Asian shepherd dogs. Additional samples were obtained from other Central Asian shepherd dogs as well as from dogs of closely related breeds. All dogs included in this study are owned by private persons, and participation in this study was voluntary. The research methods used in this study included both wet laboratory experiments and bioinformatic in silico procedures. The genome of one affected dog was sequenced in order to identify the gene causing EB, and data from the sequencing was filtered with multiple programs according to recessive model. The model was decided after analyzing the pedigree of the affected dogs. After finding the likely causative gene the mutation was validated in a larger cohort with Sanger sequencing. Protein expression in the tissue of affected dogs was also studied using immunofluorescence staining. As a result of this study, a new mutation causing recessive dystrophic EB was identified. The mutation is specific to Central Asian shepherd dogs. Affected dogs have a homozygous mutation in the COL7A1 gene, which codes for collagen VII α1 protein. The mutation causes a premature stop codon in the mRNA sequence, which results in abnormal protein production and separation of skin layers. The frequency of the mutation allele in the sample is approximately 18 % and more than a fourth of the dogs in the sample are carriers. Based on the pedigree analysis, the mutation is relatively new and it is only found in a small population. The disease can be prevented from becoming more common in the breed with the help of a gene test, and the test will be available in the commercial MyDogDNA gene test panel.