Alueellinen imago ja identiteetti liikkeessä

Regions are considered to be in competition for investments, industries, inhabitants and skilled labour nationally as well as internationally. In the context of tightening competition, more and more attention has been paid to regional attractors. A positive image is an important attractor in regional competition. In Finland, many towns and regions have either implemented or are planning to implement various image-enhancing campaigns or other measures aimed at improving their image. The role of identity is very important in developing a regional image. Good regional image should be based on a strong regional identity and awareness. Related to this is the perception of one's own region as separate from others and the familiarity of the region. If a region has no place in the awareness of its residents or if the inhabitants do not identify with it, its very existence as a social construct can be questioned. This means that building the regional image, which in this context is seen as social constructivism, is extremely difficult if the degree of regional awareness and identification is low. On the other hand, regional identity is being built also by developing the regional image. In a way, regional discourses have become more marketing-oriented in that instead of trying to create a regional esprit de corps there is now more image-oriented speech aimed at striving to improve the attractivity to outsiders of the region. Even though the goal is to bring the region to the attention of non-residents, a measure of construction of regional identity for the local population is automatically effected at the same time. Regional image and identity are consequences of linguistic producing and understanding of a region. It means that both image and identity are seen as language-created social constructions. The regional image is created through various discourses, but also the construction of a regional identity as regional consciousness and identification is largely a linguistic process. Essential in this context is perceiving the region as a discursive project characterized by its representation as texts, images and symbols. The linguistic production of a region is not a neutral description of "reality", but a representation based on interpretations, experiences and different motivations. Production and perceiving vary in time, so regional image and identity are on the move. This research is driven by the ongoing change of the regional system. The municipal and service structure reform is in progress and the number of municipalities seems to be on the decrease. At the same time, European Union s regional policy and regionalism on the whole are changing the status of sub-regions. At municipal level the crucial question is how the municipal structure reform will affect regional identity. This study points out that strong sense of municipal identity is a source of opposition to changes in municipal structure, but on the other hand the deinstitutionalization of the old municipality in municipal merger does not in itself mean the weakening of municipal identity.

Gene flow from transgenic plant populations: models and applications for risk assessment

The future use of genetically modified (GM) plants in food, feed and biomass production requires a careful consideration of possible risks related to the unintended spread of trangenes into new habitats. This may occur via introgression of the transgene to conventional genotypes, due to cross-pollination, and via the invasion of GM plants to new habitats. Assessment of possible environmental impacts of GM plants requires estimation of the level of gene flow from a GM population. Furthermore, management measures for reducing gene flow from GM populations are needed in order to prevent possible unwanted effects of transgenes on ecosystems. This work develops modeling tools for estimating gene flow from GM plant populations in boreal environments and for investigating the mechanisms of the gene flow process. To describe spatial dimensions of the gene flow, dispersal models are developed for the local and regional scale spread of pollen grains and seeds, with special emphasis on wind dispersal. This study provides tools for describing cross-pollination between GM and conventional populations and for estimating the levels of transgenic contamination of the conventional crops. For perennial populations, a modeling framework describing the dynamics of plants and genotypes is developed, in order to estimate the gene flow process over a sequence of years. The dispersal of airborne pollen and seeds cannot be easily controlled, and small amounts of these particles are likely to disperse over long distances. Wind dispersal processes are highly stochastic due to variation in atmospheric conditions, so that there may be considerable variation between individual dispersal patterns. This, in turn, is reflected to the large amount of variation in annual levels of cross-pollination between GM and conventional populations. Even though land-use practices have effects on the average levels of cross-pollination between GM and conventional fields, the level of transgenic contamination of a conventional crop remains highly stochastic. The demographic effects of a transgene have impacts on the establishment of trangenic plants amongst conventional genotypes of the same species. If the transgene gives a plant a considerable fitness advantage in comparison to conventional genotypes, the spread of transgenes to conventional population can be strongly increased. In such cases, dominance of the transgene considerably increases gene flow from GM to conventional populations, due to the enhanced fitness of heterozygous hybrids. The fitness of GM plants in conventional populations can be reduced by linking the selectively favoured primary transgene to a disfavoured mitigation transgene. Recombination between these transgenes is a major risk related to this technique, especially because it tends to take place amongst the conventional genotypes and thus promotes the establishment of invasive transgenic plants in conventional populations.

Data mining for telecommunications network log analysis

Telecommunications network management is based on huge amounts of data that are continuously collected from elements and devices from all around the network. The data is monitored and analysed to provide information for decision making in all operation functions. Knowledge discovery and data mining methods can support fast-pace decision making in network operations. In this thesis, I analyse decision making on different levels of network operations. I identify the requirements decision-making sets for knowledge discovery and data mining tools and methods, and I study resources that are available to them. I then propose two methods for augmenting and applying frequent sets to support everyday decision making. The proposed methods are Comprehensive Log Compression for log data summarisation and Queryable Log Compression for semantic compression of log data. Finally I suggest a model for a continuous knowledge discovery process and outline how it can be implemented and integrated to the existing network operations infrastructure.

Tuomarin rooli siviili- ja hallintoprosessissa

Tutkielmassa on vertailtu tuomarin roolia siviiliprosessin dispositiivisissa asioissa ja hallintoprosessissa. Vertailussa käytetään apuna kahta ratkaisumallia, jotka ovat peräisin Carol Gilliganin kehittelemästä sukupuolten moraalikehityspsykologiasta. Siten naisen moraalisissa ratkaisuissa käytetään arvoja, jotka ovat muotoutuneet samaistumisen kokemuksena hoivaajaan ja joissa ihmissuhteiden ja vastuun merkitys on korostunut. Naisen eettisenä ratkaisumallina on vastuun etiikka, jossa painottuvat tilannekohtaisen oikeudenmukaisuuden arvot, vastuu, kohtuus ja joustavuus. Vastuun oikeuden heikko kohta on se, että heikompi ei vaadi oikeuksiaan ja hänen asemansa voi heikentyä edelleen. Vastuun etiikka liitetään tutkielmassa hallintoprosessin tuomarin rooliin, koska hallintoprosessin tuomari toimii virallisperiaatteen alaisena ja on selvitysvastuussa joustavassa prosessissa. Miehen moraalikehitys kumpuaa erillisyyden tunteesta hoivaajaansa ja siinä korostuu yksilöllisyys ja oikeuksien painottuminen. Eettinen ratkaisumalli on oikeuden etiikka, jolle on tyypillistä reilun pelin säännöt, tasapuolisuus, ongelmien abstrahoituminen ja muodollisuus. Oikeuden etiikan heikko kohta on tilannekohtainen kohtuuttomuus oikeuksien korostamisen vuoksi. Tämä ratkaisumalli liitetään siviiliprosessin dispositiiviseen menettelyyn. Tutkielman näkökulmana on yksityisen asianosaisen asema ja kokemus prosessissa. Asianosainen on eri asemassa prosesseissa siinä suhteessa, että siviiliprosessiin osallistuminen edellyttää käytännössä asianajajan apuun turvautumista. Hallintoprosessissa on pyrkimys siihen, että yksityinen pärjää ilman avustajaa. Syynä on pidetty heikkoa kaksiasianosaissuhdetta ja sitä, että yksityisen asemaa on tasapainotettava suhteessa viranomaistahoon. Silti siviiliprosessissa asetelma saattaa yhtä hyvin olla epätasapainossa siten, että yksityinen on tiedollisesti ja taidollisesti heikommassa asemassa kuin vastapuolensa. Tuomarin roolia vertaillaan prosesseissa menettelyperiaatteiden ja vastuun jakautumisen sääntöjen avulla. Asianosaiset ovat siviiliprosessissa vastuussa asian oikeudellistamisesta. Myös totuuden käsite muodostuu erilaiseksi, koska selvitysvastuullinen hallintotuomari on lopulta vastuussa selvityksen riittävyydestä, kun taas siviiliprosessissa asianosaisen oikeussuojapyyntö rajaa totuuden. Siviiliprosessia on moitittu liiasta muodollisuudesta varsinkin sovittelukeskustelussa. Muodollisuus vaikeuttaa asianosaisen osallistumismahdollisuuksia ja etäännyttää häntä oikeusjutun käsittelystä. Muodollisuus edistää kuitenkin oikeusvarmuutta. Tuomioistuinsovittelussa on sanouduttu irti muodollisuudesta ja siinä sivussa myös aineellisesta oikeudesta. Sovittelussa on olemassa vaara siitä, että heikomman asema heikkenee entisestään. Joustava prosessi nähdään asianosaisen osallistumisen kannalta suotavampana menettelynä. Joustavuuden syynä on hallintoprosessissa käsiteltävien asioiden monimuotoisuus. Joustavuus ilmenee käytännössä virallisperiaatteen noudattamisena. Tuomarin toiminnan on oltava puolueetonta, mutta heikko asianosaissuhde ja yksityisen heikompi asema vaikuttavat siten, että tuomarin toiminta on tasapainottavaa paitsi yksityisen suuntaan, mutta myös yleisen edun suuntaan. Joustavuuden vuoksi asianosaisen luottamus saattaa vaarantua sen vuoksi, että prosessi ei ole ennakoitavaa ja prosessiasetelmaa on vaikea hahmottaa. Siten hallintoprosessissa onkin paineita oikeudellistamisen suuntaa. Joustavuuden rajana on puolueettomuuden vaatimus. Siviiliprosessissa puolueettomuus on kaksiasianosaissuhteen vuoksi korostuneempi kuin hallintoprosessissa. Puolueettomuuden vaatimus saattaa kuitenkin vaikuttaa siten, että tuomari ei voi auttaa heikompaa osapuolta riidan oikeudellistamisessa. Siten puolueettomuudella legitimoidaan vahvemman prosessiosapuolen asemaa. Olisiko virallisperiaatteesta apua siviiliprosessin muodollisuuden ongelmaan ja tasapainottamaan epätasapainoista suhdetta prosessiosapuolten välillä? Siviiliprosessi ja hallintoprosessi ovat lähentyneet toisiaan ja oikeuskirjallisuudessa on ennustettu tämän kehityksen jatkuvan. Myös oikeuden ja vastuun etiikka lähentyvät aikuisiässä toisiaan siten, että vastuun etiikka vahvistuu oikeuksien tärkeyden hahmottamisella ja oikeuden etiikassa kehittyy käsitys kohtuudesta. Prosessien kehityksessä olisi toivottavaa, että otettaisiin oppia toisen prosessilajin kehityksestä ja kokemuksista.

Geenipankkitutkimuksen eettiset kysymykset ja Ulrich Beckin riskiyhteiskuntateoria

Geenipankki on yleistä lääketieteellistä tutkimusta varten kerätty kokoelma geenitietoa sisältäviä näytteitä sekä muita potilasta koskevia tietoja. Geenipankkeja voidaan käyttää esimerkiksi populaatiogeneettiseen tutkimukseen, tietylle taudille altistavien geenien löytämiseen, kliiniseen tutkimukseen ja farmako­geneettiseen tutkimukseen, jossa tutkitaan geneettisten tekijöiden merkitystä lääkkeen vaikutuksissa. Monet sairaudet johtuvat perimän (geenien), elämäntapojen ja ympäristötekijöiden yhteisvaikutuksesta. Kun samassa tietokannassa olisi tiedot sekä henkilön perimästä (DNA-näyte), potilastiedoista sekä elämäntavoista, voitaisiin tietoja yhdistelemällä eri tekijöiden osuutta sairauksien ilmentymisessä. Geenipankeissa on kyse ihmisillä tehtävästä lääketieteellisestä tutkimuksesta, jota koskevat eettiset lähtökohdat ovat 1) ihmisarvon kunnioittaminen, 2) yhdenvertaisuus, 3) henkilökohtainen koskemattomuus, 4) yksilön edun ensisijaisuus tieteeseen tai yhteiskuntaan nähden, 5) itsemääräämisoikeus, 6) suojeluperiaate, 7) vapaaehtoisuus, 8) yksityiselämän suoja, 9) tieteellisen tutkimuksen vapaus ja 10) elämän suojelun periaate. Tärkeitä käsitteellisiä erotteluja ovat tutkimus- ja hoitosuhteen ero sekä hoidollisen ja ei-hoidollisen tutkimuksen ero. Lähtökohdista seuraavia tärkeitä periaatteita ovat tutkittavan ensisijaisuus ja vapaaehtoinen tietoon perustuva suostumus. Geenipankkitutkimuksessa nämä periaatteet ovat ongelmallisia. Kun geenipankkeihin näytteitä kerätään yleiseen lääketieteelliseen tutkimukseen, luovuttajille ei voida antaa tarkkoja tietoja näytteiden käytöstä, kuten tutkimuksen tavoitteista, odotettavista hyödyistä, tulosten käyttötavoista, rahoituksesta, eturistiriidoista tai muista sellaisista asioista, jotka saattaisivat vaikuttaa päätökseen näytteen antamisesta. Valta päättää siitä, millaisiin tutkimuksiin ja tarkoituksiin näytteitä saadaan käyttää, saatetaan näytteen ottamisen jälkeen antaa eettiselle komitealle tai muulle asiantuntijaelimelle. Yksiselitteistä ratkaisua siihen, mitä tietoja, kenelle ja miten geenipankista voidaan luovuttaa, ei ole löydetty. Nämä vaikeudet geenipankkitutkimuksessa johtuvat osittain geenitiedon erityisluonteesta muuhun lääketieteelliseen tietoon verrattuna. Geenitieto asettaa lääketieteellisen etiikan periaatteet keskenään ristiriitaan tavalla, johon ei ole yksiselitteistä ratkaisua. Esitetyissä ratkaisumalleissa keskeistä tuntuu olevan pikemminkin periaatteiden kiertäminen kuin tasapainon löytäminen niiden välillä. Tästä huolimatta geenipankkitutkimusta ei ole kyseenalaistettu. Havainto sopii yhteen sosiologi Ulrich Beckin riskiyhteiskuntateorian kanssa. Beckin mukaan länsimaiset yhteiskunnat ovat muuttumassa riskiyhteiskunniksi. Tämä prosessi johtuu siirtymisestä yksinkertaisesta modernisaatiosta refleksiiviseen modernisaatioon. Tässä siirtymässä tieteen ja teknologian kehitys ovat keskeisiä. Geenipankit ovat Beckin käsitteiden mukaan yksinkertaisen modernisaation ilmiö. Geenipankkitutkimuksessa asiantuntijat käyttävät merkittävää valtaa ja tutkimuksen poliittinen säätely on epätäydellistä. Ongelmista huolimatta tutkimusta on silti yritettävä tehdä ja skeptikot nähdään irrationaalisina edistyksen vastustajina tai atavististen pelkojen vaalijoina. Geenipankkien puolesta käytetyt perustelut sopivat yhteen Beckin teorian edistysuskon kanssa.

Mammapalstat : Voimaantuminen vanhoillislestadiolaisten äitien internetyhteisöissä

Tutkimuksen tarkoituksena oli selvittää, millaisia voimaantumisen kokemuksia äideillä on vanhoillislestadiolaisten äitien suljetuissa internetyhteisöissä. Lisäksi tutkimuksessa tarkasteltiin sitoutumista voimaantumisen tuloksena. Tutkimuksen kohteena oli kolme vanhoillislestadiolaisten äitien internetyhteisöä, joita kutsutaan mammapalstoiksi. Tutkimusote oli kvalitatiivinen. Aineisto kerättiin keväällä 2007. Tutkimusaineistona oli kymmenen vanhoillislestadiolaisen äidin haastattelut eri puolilla Suomea. Haastattelujen tarkoituksena oli saada äitien kokemuksia voimaantumisesta tietyillä osa-alueilla ja siitä syystä haastattelut suoritettiin teemahaastatteluina. Tutkimuksen teoreettinen viitekehys pohjautui Siitosen voimaantumisen teoriaan, jonka ytimenä on voimaantuminen yksilön henkilökohtaisena prosessina. Tutkimuksessa käytetiin soveltavasti apuna myös Siitosen katalyytti-ideaa, jonka mukaan vahva voimaantuminen johtaa vahvaan sitoutumiseen. Teoreettinen viitekehys toimi suuntaa antavana, mutta analyysissa jätettiin tilaa myös tutkittavan ilmiön aineistolähtöisille ominaispiirteille. Sisällönanalyysissa aineistosta kerättiin kaikki voimaantumiseen liittyvät ilmaukset ja ne jaettiin sisällön mukaisiin ryhmiin. Jaottelun tuloksena muodostui neljä voimaantumisen ulottuvuutta, jotka kuvaavat kukin voimaantumisen kokemuksia mammapalstoilla eri näkökulmasta. Näitä ulottuvuuksia olivat virtuaalisuus, identifikaatio, yhteisöllisyys ja itsetietoisuus.Virtuaalinen ulottuvuus kuvaa niitä tekijöitä, jotka internetin ja tekniikan puolesta vaikuttavat voimaantumiseen. Internetissä toimivat mammapalstat toivat etäisyyttä niin taustayhteisöön kuin muihin äiteihinkin, mikä helpotti vaikeista asioista keskustelua. Identifikaation eli samastumisen ulottuvuus luo näkökulman äitien yhteiseen taustaan vanhoillislestadiolaiseen liikkeeseen kuuluvina. Voimaantumiseen vaikuttivat positiivisesti äitien samankaltainen arvomaailma ja elämäntilanne, kun voitiin jakaa asioita ymmärtävässä seurassa.Yhteisöllinen ulottuvuus valottaa voimaantumiseen vaikuttavia tekijöitä yhteisön toiminnan kautta. Toimiva ja tasa-arvoiseksi koettu yhteisö toi hyväksytyksi tulemisen kokemuksia, mikä lisäsi äitien uskoa omiin kykyihin selvitä elämässä.Itsetietoisuuden ulottuvuus kuvaa vertaistuen merkitystä yksilön itseluottamuksen kasvulle ja siten voimaantumiselle. Analyysin tuloksena mammapalstat päädyttiin näkemään äitien itsensä määrittäminä henkisinä tiloina äidiksi kasvamisessa ja uuteen rooliin sopeutumisessa. Voimaantumisen prosessi toimi haastateltujen kohdalla kahdella tasolla: Voimaantuminen johti taustayhteisön normistoon sopeutumiseen. Äidit myös sitoutuivat oman hyvinvointinsa hoitamiseen ja kehittämiseen. Tutkimuksen päätuloksena oli, että mammapalstat toimivat osana vanhoillislestadiolaisten äitien elämänhallintaa. Mammapalstat auttoivat äitejä luottamaan tulevaisuuteen ja selviytymään yhteiskunnan ja taustayhteisön normistoon sopeutumisen ristipaineessa. Äitiys nähtiin vanhoillislestadiolaisen liikkeen kantavaksi rakenteeksi ja siten äitiydessä tapahtuvat muutokset koskettavat koko liikettä.

Essays on Illegal Activities, Institutions and Economic Growth

In public economics, two extremist views on the functions of a government compete: one emphasizes government working for the public interest to provide value for the citizens, while another regards government mainly as a workhorse for private interests. Moreover, as the sole legitimate authority, the government has the right to define the rules and laws as well as to enforce them. With respect to regulation, two extremes arise: from too little regulation to too much of it. If the government does not function or ceases to exist, the state falls into anarchy or chaos (Somalia). If it regulates too much, it will completely suffocate private activities, which might be considered extralegal (the former Soviet Union). In this thesis I scrutinize the government s interventionist policies and evaluate the question of how to best promote economic well-being. The first two essays assume that the government s policies promote illegal activity. The first paper evaluates the interaction between the government and the mafia, and pays attention to the law enforcement of underground production. We show that the revenue-maximizing government will always monitor the shadow economy, as monitoring contributes to the government s revenue. In general, both legal and illegal firms are hurt by the entry of the mafia. It is, however, plausible that legal firms might benefit by the entry of the mafia if it competes with the government. The second paper tackles the issue of the measurement of the size of the shadow economy. To formulate policies it is essential to know what drives illegal economic activity; is it the tax burden, excess regulation, corruption or a weak legal environment? In this paper we propose an additional explanation for tax evasion and shadow production, namely cultural factors as manifested by religion as determinants of tax morality. According to our findings, Catholic and Protestant countries do not differ in their tax morale. The third paper contributes to the literature discussing the role of the government in promoting economic and productivity growth. Our main result is that, given the complex relationship between economic growth and economic freedom, marketization has not necessarily been beneficial in terms of growth. The last paper builds on traditional growth literature and revisits the debate on convergence clubs arising from demographic transition. We provide new evidence against the idea that countries within a club would converge over time. Instead, we propose that since the demographic transition is a dynamic process, one can expect countries to enter the last regime of stable, modern growth in stages.

ORP1L, a new Rab7 effector and regulator of late endosome functions

Oxysterol binding protein (OSBP) homologues have been found in eukaryotic organisms ranging from yeast to humans. These evolutionary conserved proteins have in common the presence of an OSBP-related domain (ORD) which contains the fully conserved EQVSHHPP sequence motif. The ORD forms a barrel structure that binds sterols in its interior. Other domains and sequence elements found in OSBP-homologues include pleckstrin homology domains, ankyrin repeats and two phenylalanines in an acidic tract (FFAT) motifs, which target the proteins to distinct subcellular compartments. OSBP homologues have been implicated in a wide range of intracellular processes, including vesicle trafficking, lipid metabolism and cell signaling, but little is known about the functional mechanisms of these proteins. The human family of OSBP homologues consists of twelve OSBP-related proteins (ORP). This thesis work is focused on one of the family members, ORP1, of which two variants were found to be expressed tissue-specifically in humans. The shorter variant, ORP1S contains an ORD only. The N-terminally extended variant, ORP1L, comprises a pleckstrin homology domain and three ankyrin repeats in addition to the ORD. The two ORP1 variants differ in intracellular localization. ORP1S is cytosolic, while the ankyrin repeat region of ORP1L targets the protein to late endosomes/lysosomes. This part of ORP1L also has profound effects on late endosomal morphology, inducing perinuclear clustering of late endosomes. A central aim of this study was to identify molecular interactions of ORP1L on late endosomes. The morphological changes of late endosomes induced by overexpressed ORP1L implies involvement of small Rab GTPases, regulators of organelle motility, tethering, docking and/or fusion, in generation of the phenotype. A direct interaction was demonstrated between ORP1L and active Rab7. ORP1L prolongs the active state of Rab7 by stabilizing its GTP-bound form. The clustering of late endosomes/lysosomes was also shown to be linked to the minus end-directed microtubule-based dynein-dynactin motor complex through the ankyrin repeat region of ORP1L. ORP1L, Rab7 and the Rab7-interacting lysosomal protein (RILP) were found to be part of the same effector complex recruiting the dynein-dynactin complex to late endosomes, thereby promoting minus end-directed movement. The proteins were found to be physically close to each other on late endosomes and RILP was found to stabilize the ORP1L-Rab7 interaction. It is possible that ORP1L and RILP bind to each other through their C-terminal and N-terminal regions, respectively, when they are bridged by Rab7. With the results of this study we have been able to place a member of the uncharacterized OSBP-family, ORP1L, in the endocytic pathway, where it regulates motility and possibly fusion of late endosomes through interaction with the small GTPase Rab7.

DNA Packaging and Host Cell Lysis: Late Events in Bacteriophage PRD1 Infection

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.

The Gerbera cDNA Microarray: A Tool for Large-Scale Identification of Genes Involved in Flower Development

During the past ten years, large-scale transcript analysis using microarrays has become a powerful tool to identify and predict functions for new genes. It allows simultaneous monitoring of the expression of thousands of genes and has become a routinely used tool in laboratories worldwide. Microarray analysis will, together with other functional genomics tools, take us closer to understanding the functions of all genes in genomes of living organisms. Flower development is a genetically regulated process which has mostly been studied in the traditional model species Arabidopsis thaliana, Antirrhinum majus and Petunia hybrida. The molecular mechanisms behind flower development in them are partly applicable in other plant systems. However, not all biological phenomena can be approached with just a few model systems. In order to understand and apply the knowledge to ecologically and economically important plants, other species also need to be studied. Sequencing of 17 000 ESTs from nine different cDNA libraries of the ornamental plant Gerbera hybrida made it possible to construct a cDNA microarray with 9000 probes. The probes of the microarray represent all different ESTs in the database. From the gerbera ESTs 20% were unique to gerbera while 373 were specific to the Asteraceae family of flowering plants. Gerbera has composite inflorescences with three different types of flowers that vary from each other morphologically. The marginal ray flowers are large, often pigmented and female, while the central disc flowers are smaller and more radially symmetrical perfect flowers. Intermediate trans flowers are similar to ray flowers but smaller in size. This feature together with the molecular tools applied to gerbera, make gerbera a unique system in comparison to the common model plants with only a single kind of flowers in their inflorescence. In the first part of this thesis, conditions for gerbera microarray analysis were optimised including experimental design, sample preparation and hybridization, as well as data analysis and verification. Moreover, in the first study, the flower and flower organ-specific genes were identified. After the reliability and reproducibility of the method were confirmed, the microarrays were utilized to investigate transcriptional differences between ray and disc flowers. This study revealed novel information about the morphological development as well as the transcriptional regulation of early stages of development in various flower types of gerbera. The most interesting finding was differential expression of MADS-box genes, suggesting the existence of flower type-specific regulatory complexes in the specification of different types of flowers. The gerbera microarray was further used to profile changes in expression during petal development. Gerbera ray flower petals are large, which makes them an ideal model to study organogenesis. Six different stages were compared and specifically analysed. Expression profiles of genes related to cell structure and growth implied that during stage two, cells divide, a process which is marked by expression of histones, cyclins and tubulins. Stage 4 was found to be a transition stage between cell division and expansion and by stage 6 cells had stopped division and instead underwent expansion. Interestingly, at the last analysed stage, stage 9, when cells did not grow any more, the highest number of upregulated genes was detected. The gerbera microarray is a fully-functioning tool for large-scale studies of flower development and correlation with real-time RT-PCR results show that it is also highly sensitive and reliable. Gene expression data presented here will be a source for gene expression mining or marker gene discovery in the future studies that will be performed in the Gerbera Laboratory. The publicly available data will also serve the plant research community world-wide.

Characterisation, cloning and production of industrially interesting enzymes: gluconolactone oxidase of Penicillium cyaneo-fulvum and gluconate 5-dehydrogenase of Gluconobacter suboxydans

The work covered in this thesis is focused on the development of technology for bioconversion of glucose into D-erythorbic acid (D-EA) and 5-ketogluconic acid (5-KGA). The task was to show on proof-of-concept level the functionality of the enzymatic conversion or one-step bioconversion of glucose to these acids. The feasibility of both studies to be further developed for production processes was also evaluated. The glucose - D-EA bioconversion study was based on the use of a cloned gene encoding a D-EA forming soluble flavoprotein, D-gluconolactone oxidase (GLO). GLO was purified from Penicillium cyaneo-fulvum and partially sequenced. The peptide sequences obtained were used to isolate a cDNA clone encoding the enzyme. The cloned gene (GenBank accession no. AY576053) is homologous to the other known eukaryotic lactone oxidases and also to some putative prokaryotic lactone oxidases. Analysis of the deduced protein sequence of GLO indicated the presence of a typical secretion signal sequence at the N-terminus of the enzyme. No other targeting/anchoring signals were found, suggesting that GLO is the first known lactone oxidase that is secreted rather than targeted to the membranes of the endoplasmic reticulum or mitochondria. Experimental evidence supports this analysis, as near complete secretion of GLO was observed in two different yeast expression systems. Highest expression levels of GLO were obtained using Pichia pastoris as an expression host. Recombinant GLO was characterised and the suitability of purified GLO for the production of D-EA was studied. Immobilised GLO was found to be rapidly inactivated during D-EA production. The feasibility of in vivo glucose - D-EA conversion using a P. pastoris strain co-expressing the genes of GLO and glucose oxidase (GOD, E.C. 1.1.3.4) of A. niger was demonstrated. The glucose - 5-KGA bioconversion study followed a similar strategy to that used in the D-EA production research. The rationale was based on the use of a cloned gene encoding a membrane-bound pyrroloquinoline quinone (PQQ)-dependent gluconate 5-dehydrogenase (GA 5-DH). GA 5-DH was purified to homogeneity from the only source of this enzyme known in literature, Gluconobacter suboxydans, and partially sequenced. Using the amino acid sequence information, the GA 5-DH gene was cloned from a genomic library of G. suboxydans. The cloned gene was sequenced (GenBank accession no. AJ577472) and found to be an operon of two adjacent genes encoding two subunits of GA 5-DH. It turned out that GA 5-DH is a rather close homologue of a sorbitol dehydrogenase from another G. suboxydans strain. It was also found that GA 5-DH has significant polyol dehydrogenase activity. The G. suboxydans GA 5-DH gene was poorly expressed in E. coli. Under optimised conditions maximum expression levels of GA 5-DH did not exceed the levels found in wild-type G. suboxydans. Attempts to increase expression levels resulted in repression of growth and extensive cell lysis. However, the expression levels were sufficient to demonstrate the possibility of bioconversion of glucose and gluconate into 5-KGA using recombinant strains of E. coli. An uncharacterised homologue of GA 5-DH was identified in Xanthomonas campestris using in silico screening. This enzyme encoded by chromosomal locus NP_636946 was found by a sequencing project of X. campestris and named as a hypothetical glucose dehydrogenase. The gene encoding this uncharacterised enzyme was cloned, expressed in E. coli and found to encode a gluconate/polyol dehydrogenase without glucose dehydrogenase activity. Moreover, the X. campestris GA 5-DH gene was expressed in E. coli at nearly 30 times higher levels than the G. suboxydans GA 5-DH gene. Good expressability of the X. campestris GA-5DH gene makes it a valuable tool not only for 5-KGA production in the tartaric acid (TA) bioprocess, but possibly also for other bioprocesses (e.g. oxidation of sorbitol into L-sorbose). In addition to glucose - 5-KGA bioconversion, a preliminary study of the feasibility of enzymatic conversion of 5-KGA into TA was carried out. Here, the efficacy of the first step of a prospective two-step conversion route including a transketolase and a dehydrogenase was confirmed. It was found that transketolase convert 5-KGA into TA semialdehyde. A candidate for the second step was suggested to be succinic dehydrogenase, but this was not tested. The analysis of the two subprojects indicated that bioconversion of glucose to TA using X. campestris GA 5-DH should be prioritised first and the process development efforts in future should be focused on development of more efficient GA 5-DH production strains by screening a more suitable production host and by protein engineering.

Flight metabolic rate in the Glanville fritillary butterfly

Dispersal is a highly important life history trait. In fragmented landscapes the long-term persistence of populations depends on dispersal. Evolution of dispersal is affected by costs and benefits and these may differ between different landscapes. This results in differences in the strength and direction of natural selection on dispersal in fragmented landscapes. Dispersal has been shown to be a nonrandom process that is associated with traits such as flight ability in insects. This thesis examines genetic and physiological traits affecting dispersal in the Glanville fritillary butterfly (Melitaea cinxia). Flight metabolic rate is a repeatable trait representing flight ability. Unlike in many vertebrates, resting metabolic rate cannot be used as a surrogate of maximum metabolic rate as no strong correlation between the two was found in the Glanville fritillary. Resting and flight metabolic rate are affected by environmental variables, most notably temperature. However, only flight metabolic rate has a strong genetic component. Molecular variation in the much-studied candidate locus phosphoglucose isomerase (Pgi), which encodes the glycolytic enzyme PGI, has an effect on carbohydrate metabolism in flight. This effect is temperature dependent: in low to moderate temperatures individuals with the heterozygous genotype at the single nucleotide polymorphism (SNP) AA111 have higher flight metabolic rate than the common homozygous genotype. At high temperatures the situation is reversed. This finding suggests that variation in enzyme properties is indeed translated to organismal performance. High-resolution data on individual female Glanville fritillaries moving freely in the field were recorded using harmonic radar. There was a strong positive correlation between flight metabolic rate and dispersal rate. Flight metabolic rate explained one third of the observed variation in the one-hour movement distance. A fine-scaled analysis of mobility showed that mobility peaked at intermediate ambient temperatures but the two common Pgi genotypes differed in their reaction norms to temperature. As with flight metabolic rate, heterozygotes at SNP AA111 were the most active genotype in low to moderate temperatures. The results show that molecular variation is associated with variation in dispersal rate through the link of flight physiology under the influence of environmental conditions. The evolutionary pressures for dispersal differ between males and females. The effect of flight metabolic rate on dispersal was examined in both sexes in field and laboratory conditions. The relationship between flight metabolic rate and dispersal rate in the field and flight duration in the laboratory were found to differ between the two sexes. In females the relationship was positive, but in males the longest distances and flight durations were recorded for individuals with low flight metabolic rate. These findings may reflect male investment in mate locating. Instead of dispersing, males with high flight metabolic rate may establish territories and follow a perching strategy when locating females and hence move less on the landscape level. Males with low metabolic rate may be forced to disperse due to low competitive success or may show adaptations to an alternative strategy: patrolling. In the light of life history trade-offs and the rate of living theory having high metabolic rate may carry a cost in the form of shortened lifespan. Experiments relating flight metabolic rate to longevity showed a clear correlation in the opposite direction: high flight metabolic rate was associated with long lifespan. This suggests that individuals with high metabolic rate do not pay an extra physiological cost for their high flight capacity, rather there are positive correlations between different measures of fitness. These results highlight the importance of condition.

Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.

Pathobiological Aspects of Nonreheumatic Aortic Valve Stenosis

Aortic valve stenosis (AS) is an active disease process akin to atherosclerosis, with chronic inflammation, lipid accumulation, extracellular matrix remodeling, fibrosis, and extensive calcification of the valves being characteristic features of the disease. The detailed mechanisms and pathogenesis of AS are still incompletely understood, however, and pharmacological treatments targeted toward components of the disease are not currently available. In this thesis project, my coworkers and I studied stenotic aortic valves obtained from 86 patients undergoing valve replacement for clinically significant AS. Non-stenotic control valves (n=17) were obtained from patients undergoing cardiac transplantation or from organ donors without cardiac disease. We identified a novel inflammatory factor, namely mast cell, in stenotic aortic valves and present evidence showing that this multipotent inflammatory cell may participate in the pathogenesis of AS. Using immunohistochemistry and double immunofluorescence stainings, we found that a considerable number of mast cells accumulate in stenotic valves and, in contrast to normal valves, the mast cells in diseased valves were in an activated state. Moreover, valvular mast cells contained two effective proteases, chymase and cathepsin G, which may participate in adverse remodeling of the valves either by inducing fibrosis (chymase and cathepsin G) or by degrading elastin fibers in the valves (cathepsin G). As chymase and cathepsin G are both capable of generating the profibrotic peptide angiotensin II, we also studied the expression and activity of angiotensin-converting enzyme (ACE) in the valves. Using RT-PCR, imunohistochemistry, and autoradiography, we observed a significant increase in the expression and activity of ACE in stenotic valves. Besides mast cell-derived cathepsin G, aortic valves contained other elastolytic cathepsins (S, K, and V). Using immunohistochemistry, RT-PCR, and fluorometric microassay, we showed that the expression and activity of these cathepsins were augmented in stenotic valves. Furthermore, in stenotic but not in normal valves, we observed a distinctive pattern of elastin fiber degradation and disorganization. Importantly, this characteristic elastin degradation observed in diseased valves could be mimicked by adding exogenous cathepsins to control valves, which initially contained intact elastin fibers. In stenotic leaflets, the collagen/elastin ratio was increased and correlated positively with smoking, a potent AS-accelerating factor. Indeed, cigarette smoke could also directly activate cultured mast cells and fibroblasts. Next, we analyzed the expression and activity of neutral endopeptidase (NEP), which parallels the actions of ACE in degrading bradykinin (BK) and thus inactivates antifibrotic mechanisms in tissues. Real-time RT-PCR and autoradiography revealed NEP expression and activity to be enhanced in stenotic valves compared to controls. Furthermore, both BK receptors (1 and 2) were present in aortic valves and upregulated in stenotic leaflets. Isolated valve myofibroblasts expressed NEP and BK receptors, and their upregulation occurred in response to inflammation. Finally, we observed that the complement system, a source of several proinflammatory mediators and also a potential activator of valvular mast cells, was activated in stenotic valves. Moreover, receptors for the complement-derived effectors C3a and C5a were expressed in aortic valves and in cultured aortic valve myofibroblasts, in which their expression was induced by inflammation as well as by cigarette smoke. In conclusion, our findings revealed several novel mechanisms of inflammation (mast cells and mast cell-derived mediators, complement activation), fibrosis (ACE, chymase, cathepsin G, NEP), and elastin fiber degradation (cathepsins) in stenotic aortic valves and highlighted these effectors as possible pathogenic contributors to AS. These results support the notion of AS as an active process with inflammation and extracellular matrix remodeling as its key features and identify possible new targets for medical therapy in AS.

Growth factor induction in intervertebral disc tissue: Observations in basic mechanisms of disc degeneration and rearrangement

The intervertebral disc is composed of concentrically arranged components: annulus fibrosus, the transition zone, and central nucleus pulposus. The major disc cell type differs in various parts of the intervertebral disc. In annulus fibrosus a spindle shaped fibroblast-like cell mainly dominates, whereas in central nucleus pulposus the more rounded chondrocyte-like disc cell is the major cell type. At birth the intervertebral disc is well vascularized, but during childhood and adolescence blood vessels become smaller and less numerous. The adult intervertebral disc is avascular and is nourished via the cartilage endplates. On the other hand, degenerated and prolapsed intervertebral discs are again vascularized, and show many changes compared to normal discs, including: nerve ingrowth, change in collagen turnover, and change in water content. Furthermore, the prolapsed intervertebral disc tissue has a tendency to decrease in size over time. Growth factors are polypeptides which regulate cell growth, extracellular matrix protease activity, and vascularization. Oncoproteins c-Fos and c-Jun heterodimerize, forming the AP-1 transcription factor which is expressed in activated cells. In this thesis the differences of growth factor expression in normal intervertebral disc, the degenerated intervertebral disc and herniated intervertebral disc were analyzed. Growth factors of particular interest were basic fibroblast growth factor (bFGF or FGF-2), platelet-derived growth factor (PDGF), vascular endothelial growth factor (VEGF), and transforming growth factor beta (TGFβ). Cell activation was visualized by the expression of the AP-1 transcription promoters c-Fos and c-Jun. The expression was shown with either mono- or polyclonal antibodies by indirect avidin-biotin-peroxidase immunohistochemical staining method. The normal control material was collected from a tissue bank of five organ donors. The degenerated disc material was from twelve patients operated on for painful degenerative disc disease, and herniated disc tissue material was obtained from 115 patients operated on for sciatica. Normal control discs showed only TGFβ immunopositivity. All other factors studied were immunonegative in the control material. Prolapsed disc material was immunopositive for all factors studied, and this positivity was located either in the disc cells or in blood vessels. Furthermore, neovascularization was noted. Disc cell immunoreaction was shown in chondrocyte-like disc cells or in fibroblast-like disc cells, the former being expressed especially in conglomerates (clusters of disc cells). TGFβ receptor induction was prominent in prolapsed intervertebral disc tissue. In degenerated disc material, the expression of growth factors was analyzed in greater detail in various parts of the disc: nucleus pulposus, anterior annulus fibrosus and posterior annulus fibrosus. PDGF did not show any immunoreactivity, whereas all other studied growth factors were localized either in chondrocyte-like disc cells, often forming clusters, in fibroblast-like disc cells, or in small capillaries. Many of the studied degenerated discs showed tears in the posterior region of annulus fibrosus, but expression of immunopositive growth factors was detected throughout the entire disc. Furthermore, there was a difference in immunopositive cell types for different growth factors. The main conclusion of the thesis, supported by all substudies, is the occurrence of growth factors in disc cells. They may be actively participating in a network regulating disc cell growth, proliferation, extracellular matrix turnover, and neovascularization. Chondrocyte-like disc cells, in particular, expressed growth factors and oncoproteins, highlighting the importance of this cell type in the basic pathophysiologic events involved in disc degeneration and disc rearrangement. The thesis proposes a hypothesis for cellular remodelling in intervertebral disc tissue. In summary, the model presents an activation pattern of different growth factors at different intervertebral disc stages, mechanisms leading to neovascularization of the intervertebral disc in pathological conditions, and alteration of disc cell shape, especially in annulus fibrosus. Chondrocyte-like disc cells become more numerous, and these cells are capable of forming clusters, which appear to be regionally active within the disc. The alteration of the phenotype of disc cells expressing growth factors from fibroblast-like disc cells to chondrocyte-like cells in annulus fibrosus, and the numerous expression of growth factor expressing disc cells in nucleus pulposus, may be a key element both during pathological degeneration of the intervertebral disc, and during the healing process after trauma.