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  • Hautala, Harri (Helsingin yliopisto, 2008)
    The immediate effects of two human-related vegetation disturbances, (1) green tree retention (GTR) patch felling and scarification by harrowing and (2) experimental understorey vegetation layer removal, were examined in boreal forest stands in Finland. Effects of GTR patch felling and scarification on tree uprootings, on coarse woody debris (CWD) and on epixylic plant community were followed in upland and in paludified forest types. Uprootings increased considerably during 2-3 years after the fellings and were more frequent (47%) in the paludified than in the upland forest (13%). Scarification reduced 68% of the CWD in the felling area. Cover and especially species richness of epixylics declined in the both areas during 1-2 years after the felling. The increasing size of GTR patch correlated positively with the species richness. Regeneration of understorey vegetation community and Vaccinium myrtillus and Vaccinium vitis-idaea after different removals of vegetation layers in an old-growth forest took four years. The regeneration occurred mainly by vegetative means and it was faster in the terms of species richness than in the cover. In the most severe treatment, recovery occurred merely by sexual reproduction. V. myrtillus recovered mainly by producing new shoots. V. vitis-idaea recovered faster than V. myrtillus, mainly by increasing length growth. For ecological reasons, use of larger GTR patches on paludified biotope would be recommendable. In felling areas, scarification by harrowing could be replaced with some other spot-wise method. After moderate intensity level disturbance, recovery occurs rapidly by vegetative regrowth of the dominating species. High level of intensity may prevent the recovery of vegetation community for years, while enabling also the genetic regeneration of the initial species. Local anthropogenic-related disturbances are currently increasing and they can interact during temporally short times, which should be taken in to account in the future forest management plans.
  • Rauramo, Suvi (2000)
    Tutkielmassa tarkastellaan, millaisia kerronnallisia konventioita tietokonepelit käyttävät temmatakseen pelaajan "sisään" tarinamaailmaan. Komparatiivista lähestymistapaa soveltaen tutkielma pyrkii kartoittamaan yhteneväisyyksiä ja eroavaisuuksia tietokonepelien ja aikaisempien audiovisuaalisten medioiden välillä. Tutkimuksen empiirisenä aineistona on 36 PlayStation- ja PC-peliä vuosilta 1996-2000. Elokuvan kerronnan teoriaa hyväksi käyttäen eritellään, miten tietokonepeleissä käytetään audiovisuaalisen kerronnan elementtejä. Pelin maailmarakenne nousee keskeiseksi jäsentäväksi tekijäksi. Maailman taustalla oleva looginen rakenne viime kädessä säätelee pelaamista. Maailma rajoittaa pelaajan toimintaa huomattavasti, vaikka peli pyrkiikin usein kätkemään rajoitukset diegeettisesti. Maailman yhtenäisyys ja jatkuvuus ovat elintärkeitä spatiaalisen immersion luomisen kannalta. Tutkielma vahvistaa, että navigointi maailmassa on keskeinen kerronnallinen voima. Fokalisoijahahmon liikuttaminen tai nondiegeettisen näkymän kontrollointi vaikuttaa tarinan purkautumiseen, kameran liikkeeseen, otosten siirtymiin sekä joskus myös kerronnallisen näkökulman vaihteluun. Kerronnallisten peruselementtien - maailman, sen rajauksen ja sen sisäisten siirtymien - analysoinnin perusteella tutkielmassa muodostetaan tietokonepeleille tyypilliset kerronnalliset näkökulmat. Tietokonepelit käyttävät useita kerronnallisia näkökulmia: ensimmäisen persoonan näkökulmaa, seuraajanäkökulmaa, neljännen seinän näkökulmaa, lintunäkökulmaa tai jumalnäkökulmaa. Kuitenkin yleensä vain yhtä tai kahta näkökulmaa käytetään kussakin pelissä. Hahmo on alisteisessa asemassa maailmaan nähden silloinkin, kun hahmo on fokalisoija. Tätä korostaa kuvan rajaaminen kaukaa: hahmo on (hyvin) pieni, kun taas ympäröivä maailma nousee pääosaan. Lisäksi kerronta on usein nondiegeettistä, jolloin näkymä ei ole lainkaan sidoksissa hahmoon. Maailma, eikä hahmo, on pelaajan huomion keskipiste. Pelien kerronta näyttää kehittyvän kohti lyhyempiä otospituuksia ja entistä monipuolisempaa kameran sijoittelua ja liikettä. Suuntaus vie entistä moninaisempiin kerronnallisiin näkökulmiin ja kerronnan tasoihin, mikä on perustavanlaatuinen edellytys kehittyneelle tarinankerronnalle. Keskeiset lähteet ovat Edward Braniganin Narrative comprehension and film (1992) ja Lev Manovichin The language of new media (ilmestyy 2000).
  • Hacklin, Saara (Helsingin yliopisto, 2012)
    Maurice Merleau-Ponty (1908-1961) has been known as the philosopher of painting. His interest in the theory of perception intertwined with the questions concerning the artist s perception, the experience of an artwork and the possible interpretations of the artwork. For him, aesthetics was not a sub-field of philosophy, and art was not simply a subject matter for the aesthetic experience, but a form of thinking. This study proposes an opening for a dialogue between Merleau-Pontian phenomenology and contemporary art. The thesis examines his phenomenology through certain works of contemporary art and presents readings of these artworks through his phenomenology. The thesis both shows the potentiality of a method, but also engages in the critical task of finding the possible limitations of his approach. The first part lays out the methodological and conceptual points of departure of Merleau-Ponty s phenomenological approach to perception as well as the features that determined his discussion on encountering art. Merleau-Ponty referred to the experience of perceiving art using the notion of seeing with (voir selon). He stressed a correlative reciprocity described in Eye and Mind (1961) as the switching of the roles of the visible and the painter. The choice of artworks is motivated by certain restrictions in the phenomenological readings of visual arts. The examined works include paintings by Tiina Mielonen, a photographic work by Christian Mayer, a film by Douglas Gordon and Philippe Parreno, and an installation by Monika Sosnowska. These works resonate with, and challenge, his phenomenological approach. The chapters with case studies take up different themes that are central to Merleau-Ponty s phenomenology: space, movement, time, and touch. All of the themes are interlinked with the examined artworks. There are also topics that reappear in the thesis, such as the notion of écart and the question of encountering the other. As Merleau-Ponty argued, the sphere of art has a particular capability to address our being in the world. The thesis presents an interpretation that emphasises the notion of écart, which refers to an experience of divergence or dispossession. The sudden dissociation, surprise or rupture that is needed in order for a meeting between the spectator and the artwork, or between two persons, to be possible. Further, the thesis suggests that through artworks it is possible to take into consideration the écart, the divergence, that defines our subjectivity.
  • Torsti, Pilvi (2003)
    Tutkimuksen tavoite oli kaksiosainen: historian käytön analysointi sodanjälkeisessä Bosnia ja Hertsegovinassa erityisesti nuorten näkökulmasta sekä Bosnian serbi-, kroaatti-, ja bosniakkinuorten historiallisen ajattelun tarkastelu. Tutkimustavoite konkretisoitui seuraavaan kolmeen pääanalyysiin: Analyyseista ensimmäinen käsitteli yleistä historian läsnäoloa sodanjälkeisessä Bosniassa. Jäsentelin analyysin historiallisten ilmiöiden, kuten historiakulttuurin, historiatietoisuuden ja historiapolitiikan ympärille. Toinen pääanalyysi keskittyi kolmeen erilliseen 8. luokan historian oppikirjaan (8. luokka on peruskoulun viimeinen luokka), joita Bosnian kolme kansallista ryhmää ovat käyttäneet sotavuosista lähtien. Koulukirjakäsittely rakentui sodan, rauhan ja kansakunnan käsitteiden ympärille. Keskuskäsitteiden katsotaan olevan keskeisiä yhteiskuntahistoriallisia käsitteitä sodanjälkeisessä Bosniassa. Kolmas pääanalyysi käsitteli kansainvälistä Nuoret ja Historia -tutkimusta, jonka keräsin kahdeksasluokkalaisilta bosnialaisilta 1999–2000. Nuorten historiallista ajattelua ja käsityksiä kuvannut tilastollinen analyysi perustui 907 oppilaan vastauksiin ja keskittyi samojen kolmen pääkäsitteen representaatioihin kuin oppikirja-analyysi. Bosnian kansallisten ryhmien vastauksia verrattiin muiden maiden tuloksiin sekä keskenään. Analyysi historian läsnäolosta kuvasti historiakulttuurin jakautumista kolmeen erilliseen ja osin jopa vastakkaiseen kulttuuriin sodanjälkeisessä Bosniassa. Historian oppikirjat havainnollistivat, kuinka kolmen kansanryhmän esitykset menneestä luovat viholliskuvia muista kansanryhmistä maan sisällä. Kirjat rakentavat kolmea erilaista historiantulkintaa neljän miljoonan asukkaan yhteiskunnan sisällä ja rinnastavat usein menneen ja nykyisen. Samaan aikaan Nuoret ja Historia –tutkimus osoitti, että valtaosassa kysymyksiä Bosnian kansalliset ryhmät erottuivat toisistaan vain marginaalisesti. Eurooppalaisessa vertailussa Bosnian nuoret muodostivat oman yksittäisen ryhmänsä: he uskoivat vahvasti rauhaan tulevaisuudessa eivätkä pitäneet sotia tärkeinä historian muutosvoimina.
  • Torsti, Pilvi (2003)
    The task of the research was binary: to determine the use of history in the post-war Bosnia and Herzegovina from the perspective of young people, and to define the historical thinking of youth among Bosnian Serbs, Croats and Bosniacs. The task coalesced into three main analyses. The first analysis discussed the general presence of history in post-war Bosnian society. The analysis was organised around history-related phenomena: history culture, historical consciousness and history politics. Three separate 8th-grade (the 8th grade is the last year of obligatory schooling) history textbooks used by the three Bosnian national communities were the subject of the second analysis, which focused on the representations of three socio-historical concepts central in post-war Bosnian society: war, peace and nation. The third analysis of the historical thinking of the youth was based on the international Youth and History survey which I conducted among 8th-grade pupils in Bosnia in 1999-2000. The descriptive statistic analysis of the answers of 907 pupils concentrated on the representations of the same three concepts as in the textbooks analysis. The answers of the Bosnian national groups were compared to each other and to other European country samples. The description of the presence of history illustrated the division of history culture into three separate – and even opposing – cultures in post-war Bosnia and Herzegovina. History textbooks further demonstrated how presentations of the past among the three communities create hostile images of the country’s other national groups. They construct three different interpretations of the past within a society of four million people often equating the past with the present. Finally, the Youth and History survey analysis showed that in most questions, the national groups differed only marginally in their thinking. In the European comparison, Bosnians formed a single group and demonstrated great belief in future peace and did not consider wars important factors of change in history.
  • Klingenberg, Daniela (2011)
    Bakteriesläktet Stenotrophomonas består av 12 arter. De existerar överallt i naturen, men speciellt S. maltophilia, S. rhizophila och S. pavanii är associerade med växter. Stammar av den mest förekommande arten, S. maltophilia, har konstaterats ha fördelaktiga effekter på växters tillväxt och hälsa, förmåga att bryta ner svårnerbrytbara föreningar samt producera biomolekyler av bioteknologiskt och ekonomiskt värde. Många S. maltophilia -stammar är även multiresistenta mot antibiotika och kan fungera som opportunistiska människopatogener. Under ett INCO-projekt (1998-2002) isolerades rhizobiestammar från det tropiska baljväxtträdet Calliandra calothyrsus Meisn. rotknölar från länder i Centralamerika, Afrika och Nya Kaledonien. Rhizobiekollektionen identifierades vid Kvävegruppen (Helsingfors universitet), där det framkom att en del stammar tillhörde släktet Stenotrophomonas. Många av Stenotrophomonas-stammarna inducerade i växtförsök vita, tumör- eller rotknölsliknande strukturer på Calliandra-plantors rötter. Bakterierna kunde förutom rotknölar även isoleras från ytsteriliserade rötter och stammar. Syftet med mitt arbete var att undersöka i) stammarnas arttillhörighet, ii) om stammarna har samma ursprung, iii) om det finns andra skillnader än koloniutseende mellan fasvariationer av samma stam, iv) har tillväxtfrämjande (eng. plant growth promoting, PGP) egenskaper eller annan fördelaktig inverkan på växter, och v) likt rhizobier har förmåga att inducera uppkomsten av rotknölar. För att kunna dra slutsatser om Stenotrophomonas-stammarnas geografiska ursprung undersöktes stammarnas genetiska diversitet och gruppering med AFLP-fingerprinting. Med hjälp av kommersiella API-test för bakterieidentifikation undersöktes skillnader mellan faserna vad beträffar enzymatiska egenskaper samt förmåga att använda olika kol- och energikällor. Stammarnas förmåga att infektera rothår och inducera rotknölar undersöktes både genom växtförsök med värdväxten Calliandra och genom PCR-amplifiering av stammarnas nodA- och nodC-gener för rotknölsbildning. Stammarnas PGP-aktivitet utreddes in vitro främst genom odlingsmetoder. Stenotrophomonas-bakteriernas inverkan in vivo på växternas tillväxt, kväveinnehåll och uppkomsten av rotknölar undersöktes genom växthusförsök med baljväxterna Phaseolus vulgaris och Galega orientalis. Både den genetiska och fenotypiska diversiteten hos Stenotrophomonas-stammarna var mycket liten, vilket indikerar att de har ett gemensamt ursprung. Stenotrophomonas-bakterierna fick till stånd förändringar i rothåren hos Calliandra-plantornas rötter och de ökade även mängden rothår. Däremot uppkom det inga rotknölar hos Calliandra-plantorna. Av de testade PGP-egenskaperna kunde stammarna producera IAA, proteas och lipas. De uppvisade även tillväxtfrämjande effekt på G. orientalis, både enskilt och vid saminokulering med R. galegae HAMBI 540 samt aktiverade effektiva rhizobiers rotknölsbildning hos P. vulgaris i växthus. Det krävs vidareforskning för att utreda vilka mekanismer de uppkomna positiva effekterna grundar sig på. Resultaten i detta arbete bekräftar dock tidigare forskningsresultat angående Stenotrophomonas-bakteriers positiva inverkan på växter.
  • Kautto, Mikko (2001)
    The thesis explores patterns of welfare state adjustment in Nordic welfare states in a Western European context, with a focus on changes in the 1990s. Its theoretical starting points are in the contemporary controversy between the power resource theory and the welfare regime approach that have underlined the role of ideology and politics as explanatory factors for the character of welfare states and their enduring divergence; and the new convergence thesis that sees 'external' factors, such as globalisation and EU, push for declining differences among welfare states. For both strands of thinking a crucial empirical question concerns how policy reforms affect diversity among welfare states, i.e. the patterning of differences and similarities that differentiate types of welfare states. To consider this problematic two research questions are formulated: Are there systematic patterns of differences among welfare states? Do welfare states converge over time? Empirically the study addresses variation and trends in statutory fiscal and welfare policies with the help of statistics, especially with Eurostat's social protection expenditure data. The study outlines an ideal typical picture of the Nordic welfare model for gauging change, and employs basic statistical parameters, tables, graphical methods and clustering techniques that suit the case-oriented approach in general, but the aim of examining types in particular. Three studies are included in the thesis. Financing of welfare states and redistribution strategies are examined in two broader studies including fifteen Western European countries. The third study is a more focused case study on welfare state adjustment in Finland and Sweden between 1990-98. The study concludes with four generalisations: Firstly, over the period examined the Nordic countries as a group had moved further away from the ideal typical picture of the Nordic welfare model. Secondly, in a relative comparison and in most of the areas examined the Nordic countries still clustered together and showed family resemblance. Thirdly, there were signs for convergence in several instances, although not to the extent to abolish diversity. Fourthly, these convergence processes meant that the distinctiveness of the Nordic countries by late-1990s was less evident than earlier.
  • Kautto, Mikko (2001)
    Tutkimus tarkastelee pohjoismaisten hyvinvointivaltioiden muutoksia länsi-eurooppalaisessa vertailussa keskittyen 1990-luvun tapahtumiin. Tutkimuksen teoreettinen tausta liittyy viimeaikaista vertailevaa hyvinvointivaltiotutkimusta ohjanneeseen vastakkainasetteluun. Valtaresurssiteorian ja siitä ammentavan hyvinvointiregiimi-näkökulman mukaan etenkin ideologiset ja poliittiset eroavuudet selittävät hyvinvointivaltioiden kehitystä ja hyvinvointivaltioiden välisiä 'laadullisia' eroja. Regiimiajattelun mukaan maiden kehitys on malli- tai polkuriippuvaa, ja siksi se näkee erojen säilyvän. Uusi konvergenssiteesi puolestaan haastaa tämän näkemyksen esittäessään, että 1990-luvun muuttuneissa oloissa ulkoiset syyt, ennen kaikkea globalisaatio ja Euroopan unionin toiminta, selittävät kehitystä ja johtavat hyvinvointivaltioiden välisten erojen supistumiseen. Molempien näkökulmien kannalta keskeinen empiirinen kysymys on missä määrin kansalliset sosiaali- ja yhteiskuntapolitiikan muutokset hämärtävät ns. hyvinvointivaltiomalleja erottavia rajoja. Typologioiden osuvuus ja pysyvyys ovat siten paitsi empiirisisesti myös teoreettisesti perusteltavissa olevia kysymyksiä. Tältä pohjalta tutkimuksessa asetetaan kaksi tutkimuskysymystä. Onko hyvinvointivaltioiden välillä systemaattisia eroja? Konvergoituvatko hyvinvointivaltiot? Tutkimuksen lähtökohtana käytetään ideaalityyppistä pohjoismaista mallia, jonka perusteella valitaan tarkasteltavat ulottuvuudet ja jota vasten arvioidaan muutosta. Pohjoismaisten hyvinvointivaltioiden muutosta tarkastellaan sekä yksittäisten piirteiden että piirteiden kokonaisuuden näkökulmasta. Tutkimuksen empiirisissä osissa tarkastellaan sosiaaliturvan rahoituksen ja sosiaalipolitiikan kehittymistä vertailukelpoisen tilastoaineiston, ennen kaikkea Eurostatin sosiaalimenotilastojen valossa. Menetelminä käytetään tilastollisia tunnuslukuja, taulukoita, graafisia menetelmiä sekä ryhmittelyanalyysiä, jotka soveltuvat tapauksien erojen ja yhtäläisyyksien sekä tyyppien arvioimiseen. Tutkimus sisältää kolme artikkelia. Ensimmäisessä vertaillaan sosiaaliturvan rahoitusta, toisessa uudelleenjaon strategioita (tulonsiirrot/palvelut). Molempiin vertailuihin on otettu 15 läntisen Euroopan maata (14 EU-maata ja Norja). Kolmas tutkimus tarkastelee lähemmässä vertailussa hyvinvointivaltion sopeuttamista Suomessa ja Ruotsissa vuosien 1990 ja 1998 välisenä aikana. Tutkimusten tulosten perusteella tehdään neljä loppupäätelmää. Ensinnäkin, tarkastelluilla ulottuvuuksilla ja ajanjaksolla pohjoismaat olivat ryhmänä siirtyneet kauemmaksi ideaalityyppisestä pohjoismaisesta mallista. Toiseksi, suhteellisessa vertailussa pohjoismaat erottuivat edelleenkin yhtenäisenä ryhmä. Kolmanneksi, tutkimus paikansi konvergenssikehitystä useilla ulottuvuuksilla, joskaan tämä kehitys ei poistanut maaryhmien välisiä eroja. Neljänneksi, konvergenssiprosessien seurauksena pohjoismaiden erilaisuus suhteessa muihin läntisen Euroopan maihin oli tarkastelluilla ulottuvuuksilla vähemmän selkeä kuin aikaisemmin.
  • Aserse, Aregu Amsalu (Helsingin yliopisto, 2013)
    Nitrogen is one of the major essential nutrients for plant growth along with phosphorus and potassium. Some specialized bacterial and archaeal species are able to fix atmospheric N2 into NH3, and that is subsequently converted into plant usable form of nitrogen, NH4+ or NO3-. The biological nitrogen fixation (BNF) process that occurs by the symbiotic interaction of leguminous plants and certain bacterial species (commonly known as rhizobia) is the main source of biological nitrogen input into the soil and therefore plays an important role in maintaining the sustainability of ecosystem services. Due to the fixed N they get from symbiosis, legume species grow better than other plants in nutrient poor, degraded soils. Thereby leguminous trees and shrubs restore degraded farmland and soil fertility by increasing the content of nitrogen and organic carbon in the soil. The versatile leguminous trees and shrubs, such as Erythrina brucei, Crotalaria spp., and Indigofera spp., can be used as forage for cattle and applied as intercrops or fallow crops in low-input agriculture. The usefulness of these legumes can be boosted by inoculating them with effective symbiotic nitrogen-fixing rhizobia. The yield of food legumes such as common bean and soybean can also partly be increased through the use of efficient rhizobial inoculants. Thus, detailed information about the indigenous rhizobia nodulating local food and woody legumes is essential for selecting good inoculant strains. Therefore, this thesis deals with diversity and phylogeny of 143 bacterial isolates obtained from root nodules of E. brucei, Crotalaria spp., Indigofera spp., common bean and soybean growing in different sites in Ethiopia. Taxonomy of the root nodule bacteria was studied using multilocus sequence analyses (MLSA) of the core genes 16S rRNA, recA, rpoB, and glnII. Phylogeny of nodulation (nodA, nodC, nodK/Y) and nitrogen-fixation (nifH) genes of the rhizobia were also studied. The whole genome based AFLP fingerprinting technique was used to study the diversity of the strains within the species. Based on MLSA and AFLP fingerprinting analyses combined with nodulation test result, twenty-five strains belonging to the Rhizobium leguminosarum complex (Rhizobium phaseoli, Rhizobium etli, Rhizobium leguminosarum and a novel Rhizobium taxa) were found to be true common bean nodulating rhizobia in Ethiopia (Paper I). Fifty-six strains isolated from root nodules of E. brucei, Crotalaria spp., Indigofera spp., and soybean (Glycine max) were mainly identified as genetically very diverse slow-growing Bradyrhizobium species, being distributed into fifteen phylogenetic groups under Bradyrhizobium japonicum and Bradyrhizobium elkanii super clades. The majority of these strains represented undescribed Bradyrhizobium genospecies. Two unique lineages which most likely represent novel Ethiopian Bradyrhizobium species were discovered among the collections (Paper II). In addition to Bradyrhizobium species, a few Rhizobium species (six strains) were found to sporadically nodulate E. brucei, Indigofera spp., and common bean. Fifty-six non-symbiotic endophytic bacterial strains representing diverse Gram-negative and Gram-positive bacterial genera were also isolated from nodules of E. brucei, Crotalaria spp., Indigofera spp., soybean and common bean (Paper I, III). Among the non-symbiotic bacteria, five strains obtained from nodules of Crotalaria spp. and E. brucei represented a putative novel Rhizobium species (Paper III). Phylogenetically the nodA genes of all Ethiopian Bradyrhizobium species belonged to the cosmopolitan nodA clade III.3, which includes nodA genes from Bradyrhizobium species nodulating diverse legume hosts in sub-Saharan Africa. The nifH and nodY/K gene phylogenies of the Ethiopian Bradyrhizobium strains were generally consistent with the nodA gene phylogeny, supporting the monophyletic origin of the symbiotic genes in Bradyrhizobium (Paper II). The symbiotic gene phylogenies of Bradyrhizobium species were somewhat consistent to their housekeeping gene phylogenies. Nevertheless, the symbiotic gene phylogenies of different Rhizobium species (Paper I and III) were fairly similar regardless of their taxonomic background, suggesting that, in contrast to the core genome of the species, the symbiotic genes required for nodulation and nitrogen fixation might have a common origin in Rhizobium, indicative of horizontal gene transfer among these rhizobia. The nodulation test results showed that most rhizobial species were effective in nitrogen fixation on their respective host plants. Non-nodulating, endophytic bacterial strains representing seven genera, namely Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium and Serratia, were found to colonize nodules of Crotalaria incana and common bean when co-inoculated with symbiotic rhizobia. In addition, the majority of nodule endophytic bacterial strains and the sporadic symbionts showed several plant growth promoting activities, which indicate their potential role in improving plant growth.
  • Audzijonyte, Asta (Helsingin yliopisto, 2006)
  • Juvonen, Riikka (Helsingin yliopisto, 2009)
    Megasphaera cerevisiae, Pectinatus cerevisiiphilus, Pectinatus frisingensis, Selenomonas lacticifex, Zymophilus paucivorans and Zymophilus raffinosivorans are strictly anaerobic Gram-stain-negative bacteria that are able to spoil beer by producing off-flavours and turbidity. They have only been isolated from the beer production chain. The species are phylogenetically affiliated to the Sporomusa sub-branch in the class "Clostridia". Routine cultivation methods for detection of strictly anaerobic bacteria in breweries are time-consuming and do not allow species identification. The main aim of this study was to utilise DNA-based techniques in order to improve detection and identification of the Sporomusa sub-branch beer-spoilage bacteria and to increase understanding of their biodiversity, evolution and natural sources. Practical PCR-based assays were developed for monitoring of M. cerevisiae, Pectinatus species and the group of Sporomusa sub-branch beer spoilers throughout the beer production process. The developed assays reliably differentiated the target bacteria from other brewery-related microbes. The contaminant detection in process samples (10 1,000 cfu/ml) could be accomplished in 2 8 h. Low levels of viable cells in finished beer (≤10 cfu/100 ml) were usually detected after 1 3 d culture enrichment. Time saving compared to cultivation methods was up to 6 d. Based on a polyphasic approach, this study revealed the existence of three new anaerobic spoilage species in the beer production chain, i.e. Megasphaera paucivorans, Megasphaera sueciensis and Pectinatus haikarae. The description of these species enabled establishment of phenotypic and DNA-based methods for their detection and identification. The 16S rRNA gene based phylogenetic analysis of the Sporomusa sub-branch showed that the genus Selenomonas originates from several ancestors and will require reclassification. Moreover, Z. paucivorans and Z. raffinosivorans were found to be in fact members of the genus Propionispira. This relationship implies that they were carried to breweries along with plant material. The brewery-related Megasphaera species formed a distinct sub-group that did not include any sequences from other sources, suggesting that M. cerevisiae, M. paucivorans and M. sueciensis may be uniquely adapted to the brewery ecosystem. M. cerevisiae was also shown to exhibit remarkable resistance against many brewery-related stress conditions. This may partly explain why it is a brewery contaminant. This study showed that DNA-based techniques provide useful tools for obtaining more rapid and specific information about the presence and identity of the strictly anaerobic spoilage bacteria in the beer production chain than is possible using cultivation methods. This should ensure financial benefits to the industry and better product quality to customers. In addition, DNA-based analyses provided new insight into the biodiversity as well as natural sources and relations of the Sporomusa sub-branch bacteria. The data can be exploited for taxonomic classification of these bacteria and for surveillance and control of contaminations.
  • Jäämaa, Sari (Helsingin yliopisto, 2011)
    Prostate cancer is one of the most prevalent cancer types in men. The development of prostate tumors is known to require androgen exposure, and several pathways governing cell growth are deregulated in prostate tumorigenesis. Recent genetic studies have revealed that complex gene fusions and copy - number alterations are frequent in prostate cancer, a unique feature among solid tumors. These chromosomal aberrations are though to arise as a consequence of faulty repair of DNA double strand breaks (DSB). Most repair mechanisms have been studied in detail in cancer cell lines, but how DNA damage is detected and repaired in normal differentiated human cells has not been widely addressed. The events leading to the gene fusions in prostate cancer are under rigorous studies, as they not only shed light on the basic pathobiologic mechanisms but may also produce molecular targets for prostate cancer treatment and prevention. Prostate and seminal vesicles are part of the male reproductive system. They share similar structure and function but differ dramatically in their cancer incidence. Approximately fifty primary seminal vesicle carcinomas have been reported worldwide. Surprisingly, only little is known on why seminal vesicles are resistant to neoplastic changes. As both tissues are androgen dependent, it is a mystery that androgen signaling would only lead to tumors in prostate tissue. In this work, we set up novel ex vivo human tissue culture models of prostate and seminal vesicles, and used them to study how DNA damage is recognized in normal epithelium. One of the major DNA - damage inducible pathways, mediated by the ATM kinase, was robustly activated in all main cell types of both tissues. Interestingly, we discovered that secretory epithelial cells had less histone variant H2A.X and after DNA damage lower levels of H2AX were phosphorylated on serine 139 (γH2AX) than in basal or stromal cells. γH2AX has been considered essential for efficient DSB repair, but as there were no significant differences in the γH2AX levels between the two tissues, it seems more likely that the role of γH2AX is less important in postmitotic cells. We also gained insight into the regulation of p53, an important transcription factor that protects genomic integrity via multiple mechanisms, in human tissues. DSBs did not lead to a pronounced activation of p53, but treatments causing transcriptional stress, on the other hand, were able to launch a notable p53 response in both tissue types. In general, ex vivo culturing of human tissues provided unique means to study differentiated cells in their relevant tissue context, and is suited for testing novel therapeutic drugs before clinical trials. In order to study how prostate and seminal vesicle epithelial cells are able to activate DNA damage induced cell cycle checkpoints, we used primary cultures of prostate and seminal vesicle epithelial cells. To our knowledge, we are the first to report isolation of human primary seminal vesicle cells. Surprisingly, human prostate epithelial cells did not activate cell cycle checkpoints after DSBs in part due to low levels of Wee1A, a kinase regulating CDK activity, while primary seminal vesicle epithelial cells possessed proficient cell cycle checkpoints and expressed high levels of Wee1A. Similarly, seminal vesicle cells showed a distinct activation of the p53 - pathway after DSBs that did not occur in prostate epithelial cells. This indicates that p53 protein function is under different control mechanisms in the two cell types, which together with proficient cell cycle checkpoints may be crucial in protecting seminal vesicles from endogenous and exogenous DNA damaging factors and, as a consequence, from carcinogenesis. These data indicate that two very similar organs of male reproductive system do not respond to DNA damage similarly. The differentiated, non - replicating cells of both tissues were able to recognize DSBs, but under proliferation human prostate epithelial cells had deficient activation of the DNA damage response. This suggests that prostate epithelium is most vulnerable to accumulating genomic aberrations under conditions where it needs to proliferate, for example after inflammatory cellular damage.
  • Lee, Elina (2005)
    Vuonna 1995 kehitettiin DNA-mikrosiruihin perustuva menetelmä tutkia yhtäaikaisesti tuhansia geenejä. Menetelmää on siitä lähtien sovellettu monilla tieteenaloilla mm. syöpätutkimuksessa, lääkkeiden kehittämisessä ja genomiikan tutkimuksessa. Viimeisen kymmenen vuoden aikana on ilmestynyt lukuisia julkaisuja, jotka käsittelevät DNA-mikrosirutekniikan sovelluksia eri biotieteen aloihin. Tässä työssä luodaan yleiskatsaus DNA-mikrosirutekniikan perusperiaatteisiin sekä esitellään sen käyttöä elintarvikepatogeenien tutkimuksessa. Elintarvikepatogeenitutkimuksissa DNA-mikrosirutekniikkaa on käytetty lähinnä viiteen tarkoitukseen: diagnostiikkaan, genotyypitykseen, evolutiivisen genomiikan tutkimuksiin, geeniekspressiotutkimuksiin ja isäntä-patogeeni-vuorovaikutuksen tutkimiseen. DNA-mikrosirutekniikalla on nykyään useita variaatioita, mutta periaate on kaikissa sama: lastumaiselle tukimateriaalille, esimerkiksi mikroskooppilasille, on erittäin tiheään asetettu tutkittavia geenejä edustavat koettimet. Näytteen DNA-juosteet kiinnittyvät emäspariperiaatteen mukaisesti (A-T ja G-C) kukin omalle koettimelleen. Tämän pariutumistapahtuman tuloksia luetaan mikrosirulta ja analysoidaan. Näyte-DNA saadaan eristämällä tutkimuskohteesta DNA:ta tai RNA:ta, joka käännetään käänteistranskriptiolla komplementaariseksi DNA:ksi. DNA-mikrosirukokeeseen liittyy monia eri vaiheita: 1. Mikrosirun valmistus 2. Näytteen valmistus ja leimaus 3. Hybridisaatio 4. Tulosten lukeminen mikrosirulta 5. Tulosten käsittely ja analyysi 6. Koetulosten tulkinta DNA-mikrosirutekniikan suurimmat edut ovat sen tarkkuus ja nopeus. Geenit pystytään tunnistamaan ja erottamaan toisistaan tarkasti niiden spesifisen emäsjärjestyksen perusteella ja yhdellä kokeella saadaan tietoa koko genomista. Tekniikan ongelmat liittyvät toisaalta juuri valtavaan tietomäärään, jota on vaikea käsitellä ja tulkita sekä kokeen monivaiheisuuteen, mikä lisää virhemahdollisuutta. Lisäksi menetelmä on monilta osin vielä hyvin kallis.
  • Ziedaite, Gabija (Helsingin yliopisto, 2008)
    The object of this study is a tailless internal membrane-containing bacteriophage PRD1. It has a dsDNA genome with covalently bound terminal proteins required for replication. The uniqueness of the structure makes this phage a desirable object of research. PRD1 has been studied for some 30 years during which time a lot of information has accumulated on its structure and life-cycle. The two least characterised steps of the PRD1 life-cycle, the genome packaging and virus release are investigated here. PRD1 shares the main principles of virion assembly (DNA packaging in particular) and host cell lysis with other dsDNA bacteriophages. However, this phage has some fascinating individual peculiarities, such as DNA packaging into a membrane vesicle inside the capsid, absence of apparent portal protein, holin inhibitor and procapsid expansion. In the course of this study we have identified the components of the DNA packaging vertex of the capsid, and determined the function of protein P6 in packaging. We managed to purify the procapsids for an in vitro packaging system, optimise the reaction and significantly increase its efficiency. We developed a new method to determine DNA translocation and were able to quantify the efficiency and the rate of packaging. A model for PRD1 DNA packaging was also proposed. Another part of this study covers the lysis of the host cell. As other dsDNA bacteriophages PRD1 has been proposed to utilise a two-component lysis system. The existence of this lysis system in PRD1 has been proven by experiments using recombinant proteins and the multi-step nature of the lysis process has been established.