Bio- ja ympäristötieteellinen tiedekunta

 

Recent Submissions

  • 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.
  • Oikkonen, Jaana (Helsingin yliopisto, 2012)
    Genome wide linkage and association methods are used to map genes affecting traits with genetic predisposition. In this thesis, I compare the methods suitable for quantitative trait mapping in complex, extended pedigrees. As a case study, gene-mapping study of musical aptitude is performed with these methods. Linkage analysis methods are developed for family studies. However, only a few methods are suitable for extended families with a quantitative trait. Three linkage programs were successfully applied for such data in this study. These programs are the SOLAR, JPSGCS and KELVIN. All of these three programs are based on different methods and thus, the same calculations are not repeated. SOLAR is based on the variance components method, JPSGCS on a graphical method and KELVIN on the Bayesian method. Association analysis is also difficult to implement for large pedigrees, because it is best suited for case- control data. Fortunately, methods are extended also for family-based studies. Here, a genomic control method was used to correct for the familial relationships. The method evaluates the relatedness from the whole genome data and the association tests are corrected for the relatedness rates. This method was implemented from the GenAbel program. As a case study, these methods were applied to a musical aptitude study. The musical aptitude is here understood as an ability to perceive the melody, harmony and rhythm of music, and to recognize structures in set of sounds. These abilities were tested with Carl Seashore s tests for pitch and time and Kai Karma's test for auditory structuring. The data consists of 107 pedigrees and 93 sporadic subjects, comprising in total of 915 individuals. Each family includes 2 50 individuals. These individuals were genotyped with a SNP chip for over 700,00 SNPs. The linkage analyses revealed several promising loci for the musical aptitude. The best result was located in 4q12 and it was found with all of the three linkage programs. Most of the other results could also be identified with multiple programs, but some differences also occurred. However, none of the findings could be discovered with association analysis, probably due to a too small sample size.
  • Östman, Sanna (Helsingin yliopisto, 2015)
    This interdisciplinary study seeks to raise awareness of and generate interest in projects that combine science and art. A number of such projects are discussed and analyzed with the help of the concept Ecovention . The concept is operationalized to include works of art that ecologically restore, reclaim, and remediate damaged ecosystems by physical actions and inventions. They transform the ecosystem and often slowly disappear into the environment, contributing to the overall wellbeing of the ecosystem. These works of art are long-lasting and site-specific. They are built outdoors by using material that is already available in the ecosystem or by bringing in environmental-friendly material into the ecosystem. The central research question for the study is as follows: How significantly does environmental art affect the local ecosystem when the starting point is ecological restoration? This is a qualitative study. The data for the study consist of interviews with experts together with analyses of the historical, cultural, and ecological background material for two Finnish environmental artworks. The two artworks are Agnes Denes's Puuvuori (Tree Mountain - A Living Time Capsule, 1996) and Jackie Brookner's Veden taika (The Magic of Water, 2007- 2010). These works of art were chosen because of the availability of historical and natural scientific research data about how they were planned and how they were constructed. The availability of this kind of data related to environmental art is rare in Finland. The Magic of Water consists of three floating islands in Salo. They are situated in a lagoon that was formerly used as a clarification pool at the Salo Municipal Sewage Treatment Facility. The artwork has succeeded in supplying a peaceful nesting habitat for the birdlife in the area. It has been shown that a colony of black-headed gulls (Larus ridibundus) is a new species nesting in the islands. The Magic of Water did not provide a significant improvement of the water quality by phytoremediation since the islands are relatively small in relation to the area of the lagoon. Tree Mountain - A Living Time Capsule is to be found in Pinsiönkangas, at the most important groundwater area in Ylöjärvi. The artwork reclaims a former gravel pit. Tree Mountain is a 28 meter tall hill in an area of elliptical shape that spans nine hectares. 10,600 pine tree saplings (Pinus sylvestris) and about 40,000 cubic meters of soil from the area was used to build the artwork. Tree Mountain is nowadays owned by the town of Ylöjärvi and Pinsiönkangas is principally a conservation area. The Tree Mountain - A Living Time Capsule is argued to fit well in the regionally precious ridgescenary since the work of art has enough of biological values. Most likely the building of the artwork has had a preventive effect on possible ecological harm and it has made the community take responsibility for taking care of the reclaimed environment in the long term. In the face of high-quality ecological restoration plans it is important to approach the restoration of ecosystems from a holistic perspective. The artist s vision of how an ecosystem can be restored adds a surplus value to ecological restoration work since also the aesthetic and ideological dimensions are reconstructed. The probable positive view of the community towards the restored ecosystem can promote not only the attendance by the community to that particular area in the future, but it can also promote the attendance of a community to other areas as well.
  • Mutanen, Justus (Helsingin yliopisto, 2015)
    The International Biology Olympiad is a yearly science competition; hundreds of high school students from over 60 countries take part in it. In Finland, the students are chosen by the national biology competition and the national Olympiad training camp. The research subject of this study is Finnish training for International Biology Olympiad (IBO). About ten high school students who are interested in biology take part at each training camp. Science competitions, such as IBO and training camps, are classified as non-formal or out-of-school science education. Since there is very little scientific knowledge about non-formal biology education, especially about science competitions, the theoretical framework of this study consists of non-formal science education, the relevance of science education and the development of interest. In this study, design research methodology with three research cycles was applied to develop the course. In the study, both theoretical and empirical problem analyses were used. There were two main research questions: 1) What are the needs for the development of the training camp? 2) What kind of training is relevant for the participants? The first research question was elaborated by examining a) what kind of topics of interest the participants have, b) how the participants expect the training to be relevant for them, c) what kind of relevance the previous participants experienced, and d) what kind of effects the previous training camps had on the participants interest in biology and career choice. The features of relevant biology Olympiad training were searched in the second research question. The data was collected from pre-camp and post-camp questionnaires, post-camp interviews and a questionnaire sent for the previous camp participants. The qualitative data was analyzed by content analysis and quantitative data from the questionnaires was analyzed by statistical methods. The main results were following: 1) The biggest needs for development were diversifying the contents and balancing the workload of the camp. The participants of the training camps were interested mostly about medicine and human biology -related topics and cell and molecular biology. In addition, it was found out that the previous participants considered biology education to be individually, vocationally and societally relevant for them. According to them, the training camps were especially individually relevant and had some effects on the career choice. 2) The new training camp for biology Olympiad is especially individually relevant for the participants but it has also some vocational relevance. In the science Olympiad training, special attention should be directed towards developing vocational and societal relevance. A new model for Biology Olympiad training camps was developed based on the collected research data. The individual dimension can be improved by i) diversifying the contents of the camps, ii) including inquiry-based learning modules and by iii) taking a student-centered approach to the development process. The vocational and societal dimensions of relevance can be targeted by iv) allowing the teachers of the participants to take part at camps. The vocational dimension of relevance can be enhanced v) by organizing visits to research laboratories and companies and vi) by enabling the participants to meet university students. The results of this study can be applied to not only to Science Olympiad training but also to non-formal biology education. This research provides models for developing out-of-school biology education and its relevance. This is the first design research study about Biology Olympiad training and it opens up discussion about the relevance of science competitions and Science Olympiad training.
  • Autio, Mirka (Helsingin yliopisto, 2015)
    Phosphorus is traditionally considered to be the primary nutrient limiting primary production in lakes. More recent studies show that sometimes nitrogen can be the limiting nutrient for phytoplankton production in temperate lakes. This study investigated whether the nitrogen has a major role along with phosphorus in the primary production of lakes. In addition, it was studied if the limiting nutrient changes during the growing season and does the residence time of the lake affect the level of nutrient limitation. The subject lakes were Ormajärvi, Suolijärvi, Lehee, Pyhäjärvi and Iso-Roine, which are the headwater lakes of the Kokemäenjoki in Kanta-Häme. The lakes were sampled for bioassays once a month from June to September in 2004 and in May 2005, a total of five times. There were four treatments: control, lake water + P, lake water + N, lake water + P + N. For each treatment there were five replicates. There was one concentration level for each nutrient treatment. The nutrient concentration of treatments depended on the nutrient content of the lakes. To determine the combined effect of nutrients both of them were added at the same time. Nitrogen treatment solution was prepared from potassium nitrate and phosphorus treatment solution from potassium dihydrogen phosphate. Bioassays were conducted as a pure culture of Pseudokirchneriella subcapitata Prinz- algae. Zooplankton was removed from the lake water samples, which were then sampled for nutrient analysis. The water samples were autoclaved and filtered prior to the bioassays. Bioassays were carried out in Erlenmeyer flasks containing 60 ml of lake water, the nutrient solutions and 0.5 ml pure culture of P. subcapitata. Algae were grown in continuous illumination until the exponential growth stopped. Algal growth was monitored by taking samples of a few ml from the flasks roughly every other day. Algae in samples were counted by a microscope in Lund chambers. The actual variables were the maximum number of cells or yield and the growth rate. The limiting nutrient was found out by comparing the yield and the growth rate of different nutrient treatments to the control. The results of the bioassays were tested statistically with non-parametric Kruskal-Wallis H-test. Algal bioassays expressed only phosphorus limitation. Phosphorus limited the yield in the bioassays of Suolijärvi in August 2004 and May 2005. In Lehee and Pyhäjärvi phosphorus limited growth rate in May 2005. There was neither nitrogen limitation nor co-limitation in any of the bioassays. So the limiting nutrient didn t change during the growing season. Phosphorus treatments inhibited the growth of algae from time to time in 2004 in Ormajärvi, Suolijärvi, Pyhäjärvi and Lehee. In May 2005 there was no inhibition. Nutrient limitation was stronger in lakes with a long retention time. These bioassays indicate that reducing phosphorus loading would control eutrophication of this chain of lakes. The phosphorus treatments couldn t cause the inhibition. The cause of inhibition originated most likely from the drainage area due to heavy rains in summer 2004. It could be, for example, zinc or arsenic.
  • Raulo, Aura (Helsingin yliopisto, 2015)
    Abstract Microbiota, the microbial communities living in the gut, skin and glands of vertebrates, is the functional link between a physiological individual and it s surrounding ecosystem. Mutualistic microbes play a role in social systems as well, since they are transmitted through social behaviors and claimed to affect host sociality and behavior. Furthermore, individual stress physiology can affect both behavior and microbiota. I took first steps to reveal the role of gut microbiota in the social dynamics of a group-living cooperative primate, the red-bellied lemur (Eulemur rubriventer). Gut microbiota was affected by seasonal change, stress hormonal profile and pregnancy, and individuals were found to have a strongly group-specific gut microbial composition, highlighting the role of social environment in determining gut microbial composition. Unlike expected, individual sociality was negatively associated with gut microbial diversity. Gut microbiota seems to be largely determined by social factors in this species, indicating that social transmission of beneficial microbiota might have played a role in the evolution of sociality.