Comparative and functional genome analysis of fungi for development of the protein production host Trichoderma reesei

Filamentous fungi of the subphylum Pezizomycotina are well known as protein and secondary metabolite producers. Various industries take advantage of these capabilities. However, the molecular biology of yeasts, i.e. Saccharomycotina and especially that of Saccharomyces cerevisiae, the baker's yeast, is much better known. In an effort to explain fungal phenotypes through their genotypes we have compared protein coding gene contents of Pezizomycotina and Saccharomycotina. Only biomass degradation and secondary metabolism related protein families seem to have expanded recently in Pezizomycotina. Of the protein families clearly diverged between Pezizomycotina and Saccharomycotina, those related to mitochondrial functions emerge as the most prominent. However, the primary metabolism as described in S. cerevisiae is largely conserved in all fungi. Apart from the known secondary metabolism, Pezizomycotina have pathways that could link secondary metabolism to primary metabolism and a wealth of undescribed enzymes. Previous studies of individual Pezizomycotina genomes have shown that regardless of the difference in production efficiency and diversity of secreted proteins, the content of the known secretion machinery genes in Pezizomycotina and Saccharomycotina appears very similar. Genome wide analysis of gene products is therefore needed to better understand the efficient secretion of Pezizomycotina. We have developed methods applicable to transcriptome analysis of non-sequenced organisms. TRAC (Transcriptional profiling with the aid of affinity capture) has been previously developed at VTT for fast, focused transcription analysis. We introduce a version of TRAC that allows more powerful signal amplification and multiplexing. We also present computational optimisations of transcriptome analysis of non-sequenced organism and TRAC analysis in general. Trichoderma reesei is one of the most commonly used Pezizomycotina in the protein production industry. In order to understand its secretion system better and find clues for improvement of its industrial performance, we have analysed its transcriptomic response to protein secretion stress conditions. In comparison to S. cerevisiae, the response of T. reesei appears different, but still impacts on the same cellular functions. We also discovered in T. reesei interesting similarities to mammalian protein secretion stress response. Together these findings highlight targets for more detailed studies.

Matti Laurila : Jääkäriupseeri, suojeluskuntapäällikkö, rintamakomentaja

Matti Laurila (1895 1983) This is a biographical research of a Jaeger officer, a Civil Guard Chief, a Field Commander Matti Laurila. A broader practice of qualitative methods was utilized in the research. The main aim is a permanent reconstruction and reinterpretation of past events through the experiences of the study object. The life and times of Laurila are intertwined with the crucial events that led to the Finnish Declaration of Independence. Afterwards he helped to ensure that the young republic also stayed independent. As a Jaeger in the winter of 1917 Laurila witnessed an incident he would never forget. After disobeying a direct order, Sven Saarikoski from Lapua was shot dead by his commanding officer, K. A. Ståhlberg, on the ice of the river Aa. Laurila faced the horrors of war at closer quarters, for he lost his father and his brother in the battle of Länkipohja on 16th March 1918. This battle was a major turning point for Laurila and profoundly influenced the rest of his life. The relationship between Laurila and his superiors was problematic almost throughout his military career, haunted as he was by the memory of Sven Saarikoski's execution and the losses in Länkipohja The position of Laurila as an authority in South Ostrobothnia was a key factor in preventing the extreme right from rallying enough Civil Guard troops to escalate the embryonic Mäntsälä rebellion of 1932. After the rebellion Laurila routinely opposed anything he saw as a threat to the independence of the Civil Guard. He would flatly refuse to even consider the integration of the Civil Guard into the national defence force. His uncompromising stand in this matter annoyed some among the higher ranking officers. After the Winter War Laurila got himself into a dispute with Jaeger Colonel H. E. Hannuksela that would have long-lasting consequences. The conflicts between them became widely known in the attack phase of the Continuation War in 1941 at the latest. Laurila had to give up his military career at the end of 1944. In the years that followed he did what he could to ensure that the South Ostrobothnia Civil Guard patrimony remained in the province. Laurila's position as a respected authority in South Ostrobothnia remained unchanged until his death.

Patient exposure monitoring and radiation qualities in two-dimensional digital x-ray imaging

The methods for estimating patient exposure in x-ray imaging are based on the measurement of radiation incident on the patient. In digital imaging, the useful dose range of the detector is large and excessive doses may remain undetected. Therefore, real-time monitoring of radiation exposure is important. According to international recommendations, the measurement uncertainty should be lower than 7% (confidence level 95%). The kerma-area product (KAP) is a measurement quantity used for monitoring patient exposure to radiation. A field KAP meter is typically attached to an x-ray device, and it is important to recognize the effect of this measurement geometry on the response of the meter. In a tandem calibration method, introduced in this study, a field KAP meter is used in its clinical position and calibration is performed with a reference KAP meter. This method provides a practical way to calibrate field KAP meters. However, the reference KAP meters require comprehensive calibration. In the calibration laboratory it is recommended to use standard radiation qualities. These qualities do not entirely correspond to the large range of clinical radiation qualities. In this work, the energy dependence of the response of different KAP meter types was examined. According to our findings, the recommended accuracy in KAP measurements is difficult to achieve with conventional KAP meters because of their strong energy dependence. The energy dependence of the response of a novel large KAP meter was found out to be much lower than with a conventional KAP meter. The accuracy of the tandem method can be improved by using this meter type as a reference meter. A KAP meter cannot be used to determine the radiation exposure of patients in mammography, in which part of the radiation beam is always aimed directly at the detector without attenuation produced by the tissue. This work assessed whether pixel values from this detector area could be used to monitor the radiation beam incident on the patient. The results were congruent with the tube output calculation, which is the method generally used for this purpose. The recommended accuracy can be achieved with the studied method. New optimization of radiation qualities and dose level is needed when other detector types are introduced. In this work, the optimal selections were examined with one direct digital detector type. For this device, the use of radiation qualities with higher energies was recommended and appropriate image quality was achieved by increasing the low dose level of the system.

Hyvän hallinnon muunnelmat : Julkisoikeudellinen tutkimus

This doctoral thesis analyses the concepts of good governance and good administration. The hypothesis is that the concepts are radically indeterminate and over-inclusive. In the study the mechanisms of this indeterminacy are examined: why are the concepts indeterminate; how does the indeterminacy work and, indeed, is it by any means plausible to try to define the concepts in a closed way? Therefore, the study focuses on various current perspectives, from which the concepts of good governance and good administration are relevant and what kind of discursive contents they may include. The approach is both legal (a right to good administration) and one of moral philosophy and discourse analysis. It appears that under the meta-discourse of good governance and good administration there are different sub-discourses: at least a legal sub-discourse, a moral/ethical sub-discourse and sub-discourses concerning economic effectiveness and the promotion of societal and economic development. The main claim is that the various sub-discourses do not necessarily identify each other s value premises and conceptual underpinnings: for which value could the attribute good be substituted in different discourses (for example, good as legal, good as ethical and so on)? The underlying presumption is, of course, that values are ultimately subjective and incommensurable. One possible way of trying to resolve the dynamics of possible discourse collisions is to employ the systems theory approach. Can the different discourses be interpreted as autopoietic systems, which create and change themselves according to their own criteria and are formed around a binary code? Can the different discourses be reconciled or are they indifferent or hostile towards each other? Is there a hegemonic super discourse or is the construction of a correct meaning purely contextual? The questions come back to the notions of administration and governance themselves the terms the good in its polymorphic ways is attempting to define. Do they engage different political rationalities? It can be suggested that administration is labelled by instrumental reason, governance by teleological reason. In the final analysis, the most crucial factor is that of power. It is about a Schmittian battle of concepts; how meanings are constructed in the interplay between conceptual ambiguity and social power. Thus, the study deals with administrative law, legal theory and the limits of law from the perspective of revealing critique.

Hyvinvointivaltion läpimurto : Pienviljelyhegemonian rapautumisen, kansalaisliikehdinnän ja poliittisen murroksen keskinäiset suhteet suomalaisessa yhteiskunnassa 1950-luvun loppuvuosina

A Breakthrough of Welfare State. The inter-relationships of the civic movement, political transformation, and eroding of a hegemony based on small scale farming in the Finnish society in the late 1950's. The unusually rapid and powerful structural change; the non-parliamentary civic movements of 1956 - 1963; and the left majority in the Finnish parliament between 1958 - 1962 all took place as the Finnish welfare state started to develop. The aim of my research is to analyse the inter-relationships of these processes. The research describes the way the former semi self-sufficient, semi-proletarian and labour-intensive form of production - a simple and discriminatory system in itself - made it possible for the majority of the population to survive through hard work. For some it even provided a possibility to prosper. The waning vitality of semi self-sufficiency and small scale agriculture triggered a political ferment and started a period of searching for something new. The process was so intense that it broke up most of the parties and tore down the old consensus that was based on the power of economic and political elite. The most crucial battle of the great transformation was waged over the nature of the state: Should we build a welfare state and construct social security systems, or should we revert to the old night watchman state and, for example, cancel the modest forms of redistribution of income carried out in the 1950's? The people joining the civic movements were either cottagers of the impoverishing countryside or, quite often, people who had come from the countryside and thus had grown up under conditions of some form of solidarity that included taking care of one's own family. The Finnish social insurance developed in the midst of a change in the structure of production of the society, and it became a compromise to satisfy the needs of both the waning society of small scale agriculture and the rising proletarian society based on wage labour. The hodgepodge of political schemes and use of power became a battle between different notions of the economy and the state; the distribution of national income; and the position of Finland in the international context. This battle created a shape of an interregnum - a period of transformation including two notions of society, two alternative paths for the future and the logic of a correctional move. The transformation of Finland from a poor developing country into a prosperous society has been praised as a success story. In 1956 - 1959, when the old form of governance based on the interests of small scale agriculture and wood processing industry was in decay, and when the future seemed uncertain, the projects to reduce social benefits and efforts to distribute national income even more unequally than before led to a powerful counter-movement by citizens and started an hegemonic change and a equal socia development.

Power and Authority. Birgitta of Sweden and her Revelations

In the High Middle Ages female saints were customarily noble virgins. Thus, as a wife and a mother of eight children, the Swedish noble lady Birgitta (1302/3 1373) was an atypical candidate for sanctity. However, in 1391 she was canonized only 18 years after her death and became a role model for many late medieval women, who were mothers and widows. The dissertation Power and Authority Birgitta of Sweden and Her Revelations investigates how Birgitta went about establishing her power and authority during the first ten years of her career as a living saint, in 1340 1349. It is written from the perspectives of gender, authority, and power. The sources consist of approximately seven hundred revelations, hagiographical texts and other medieval documents. This work concentrates on the interaction between Birgitta and her audience. During her lifetime Birgitta was already regarded as a holy woman, as a living saint. A living saint could be given no formal papal or other recognition, for one could never be certain about his or her future activities. Thus, the living saint needed an audience for whom to perform signs of sanctity. In this study particular attention is paid to situations within which the power relations between the living saint and her audience can be traced and are open to critical analysis. Situations of conflict that arose in Birgitta s life are especially fruitful for this purpose. During the Middle Ages, institutional power and authority were exclusively in the hands of secular male leaders and churchmen. In this work it is argued, however, that Birgitta used different kinds of power than men. It is evident that she exercized influence on lay people as well as on secular and clerical authorities. The second, third, and fourth chapter of this study examine the beginning of Birgitta s career as a visionary, what factors and influences lay behind it, and what kind of roles they played in establishing her religious authority. The fifth, sixth, and seventh chapter concentrate on Birgitta s exercising of power in specific situations during her time in Sweden until she left on a pilgrimage to Rome in 1349. The central question is how she exercised power with different people. As a result, this book will offer a narrative of Birgitta s social interactions in Sweden seen from the perspectives of power and authority. Along with the concept of power, authority is a key issue. By definition, one who has power also has authority but a person who does not have official power can, nevertheless, have authority. Authority in action is defined here as meaning that a person was listened to. Birgitta acted both in situations of open conflict and where no conflict was evident. Her strategies included, for example, inducement, encouragement and flattery. In order to make people do as she felt was right she also threatened them openly with divine wrath. Sometimes she even used both positive persuasion and threats. Birgitta s power seems very similar to that of priests and ascetics. Common to all of them was that their power demanded interaction with other people and audiences. Because Birgitta did not have power and authority ex officio she had to persuade people to believe in her powers. She did this because she was convinced of her mission and sought to make people change their lives. In so doing, she moved from the domestic field to the public fields of religion and politics.

Molecular characterization of mitochondrial ataxias : with emphasis on MIRAS and IOSCA

Uusi hermoston rappeumasairaus MIRAS: Suomessa kantajia joka 125. väestöstä Tässä väitöskirjatyössä on kuvattu uusi peittyvästi periytyvä hermoston rappeumasairaus, MIRAS (mitochondrial recessive ataxia syndrome), ja sen geenitausta. Tauti osoittautui tutkimuksessamme Suomen yleisimmäksi perinnölliseksi ataksiasairaudeksi. Tutkimuksessa on tutkittu perinnöllisiä aivosairauksia, joissa yhtenä oireena on ataksia (kävelyn epävarmuus, tasapainovaikeus ja liikkeiden haparointi), sekä lukuisia muita aivojen toimintahäiriöstä johtuvia oireita. Seuloessamme suomalaisilta ataksiapotilailta MIRAS-geenivirhettä, 27 potilasta sai diagnoosin aikaisemmin tuntemattomalle, etenevälle ataksiasairaudelleen. Tutkimuksen tuloksena kyseisen geenivirheen DNA-diagnostiikka on otettu käyttöön suomalaisissa ja eurooppalaisissa laboratorioissa, ja toista sataa potilasta ympäri maailman on saanut diagnoosin. Suomen väestössä joka 125. kantaa MIRAS geenivirhettä, mutta taudin saa vain, jos perii geenivirheen molemmilta vanhemmiltaan. MIRAS on taudinkuvaltaan vaihteleva, mutta vaikea etenevä neurologinen sairaus. Useilla potilailla esiintyvät oireet ovat ataksia, puheen puuromaisuus (dysartria), ääreishermorappeuma (neuropatia), pakkoliikkeet, psykiatriset oireet sekä vaikea epilepsia. Erityisen tärkeää MIRAS-taudin tunnistaminen on siihen liittyvän epilepsian hoitopäätöksessä: valproaatti-lääkitys voi aiheuttaa MIRAS-potilaille vaikean maksavaurion. Väitöskirjatyön tuloksena selvisi, että kaikki suomalaiset, norjalaiset, belgialaiset, englantilaiset, australialaiset ja uusi-seelantilaiset MIRAS potilaat olivat kaukaista sukua samalle, tuhansia vuosia sitten eläneelle eurooppalaiselle esivanhemmalle. Ataksiasairauksien tautimekanismeja selvitimme tutkimalla MIRAS-ataksiaa ja sitä muistuttavaa IOSCA sairautta (infantile onset spinocerebellar ataxia), jonka aiheuttaa peittyvästi periytyvä geenivirhe Twinkle-geenissä. Tutkimuksessa löydettiin myös uusi, Twinkle-geenin geenivirheestä johtuva taudinkuva: vaikea-asteinen, varhaisella iällä alkava aivosairaus, jossa on lisäksi viitteitä maksasairaudesta. Löysimme potilaiden aivoista muutoksia mitokondrioiden eli solun voimalaitosten perimän määrässä. Nämä tulokset antavat arvokasta lisätietoa ataksiasairauksien taustalla olevista muutoksista, joiden ymmärtäminen on välttämätön edellytys hoitomahdollisuuksien tutkimiselle tulevaisuudessa.

The Art of Adaptation : A study on the Europeanization of Finland's foreign and security policy

This study examines how Finnish foreign and security policy has been influenced by the European Union and its Common Foreign and Security Policy. It points to a growing interplay and misfit between the external expectations originating from the European level and the domestic expectations and traditional ways-of-doing-things. It is concluded that the deepening European integration in the sphere of foreign, security and defence policy has played a significant role in a number of transformations in the Finnish policies since 1995. New, more European, meanings have been attached to the key concepts of Finnish foreign and security policy. Neutrality and traditional peacekeeping have been replaced by a minimalist reading of military non-alignment and participation in crisis management operations and EU battle groups. Traditional small state identity has been recast more and more as small member stateness . At the same time Finland has entered an era of post-consensus in national foreign and security policy. A key theoretical argument in the background of the study is that collective understandings attached to European policies, when not resonating well with domestic understandings, cause adaptation pressures on domestic-level processes and may lead to changes in the way interests and identities are constructed. This means that Europeanization is principally seen as identity reconstruction. Consequently, the theoretical framework of the study builds on the Europeanization research literature and constructivist IR theory on state identity. Foreign and security policy is defined as the practice in which state identity is reproduced, and the key foreign and security policy concepts are seen as the vehicles of identity production. It is concluded that for Finland, participation in the EU s foreign, security and defence policies represents not only a tool for responding to the changes in the international security environment but also a new means of self-identification. Concerning the Finnish attempts of projecting national interests on the European security policy agenda, it is concluded that they mainly relate to the compatibility of the potential development of EU s defence dimension with the Finnish military non-alignment. Although neutrality was cast aside in the official security policy when Finland joined the EU, the analysis shows that its impact has continued in the domestic political debate and in the mind-set of the decision-makers. The primary research material includes official Finnish foreign and security policy documentation and the related parliamentary debates from 1994 to 2007. This study serves also as a comprehensive empirical overview on Finland s reactions and contributions to the EU Common Foreign and Security Policy.

Publishing in the Networked World: Transforming the Nature of Communication, 14th International Conference on Electronic Publishing 16-18 June 2010, Helsinki, Finland

The title of the 14th International Conference on Electronic Publishing (ELPUB), “Publishing in the networked world: Transforming the nature of communication”, is a timely one. Scholarly communication and scientific publishing has recently been undergoing subtle changes. Published papers are no longer fixed physical objects, as they once were. The “convergence” of information, communication, publishing and web technologies along with the emergence of Web 2.0 and social networks has completely transformed scholarly communication and scientific papers turned to living and changing entities in the online world. The themes (electronic publishing and social networks; scholarly publishing models; and technological convergence) selected for the conference are meant to address the issues involved in this transformation process. We are pleased to present the proceedings book with more than 30 papers and short communications addressing these issues. What you hold in your hands is a by-product and the culmination of almost a Year long work of many people including conference organizers, authors, reviewers, editors and print and online publishers. The ELPUB 2010 conference was organized and hosted by the Hanken School of Economics in Helsinki, Finland. Professors Turid Hedlund of Hanken School of Economics and Yaşar Tonta of Hacettepe University Department of Information Management (Ankara, Turkey) served as General Chair and Program Chair, respectively. We received more than 50 submissions from several countries. All submissions were peer-reviewed by members of an international Program Committee whose contributions proved most valuable and appreciated. The 14th ELPUB conference carries on the tradition of previous conferences held in the United Kingdom (1997 and 2001), Hungary (1998), Sweden (1999), Russia (2000), the Czech Republic (2002), Portugal (2003), Brazil (2004), Belgium (2005), Bulgaria (2006), Austria (2007), Canada (2008) and Italy (2009). The ELPUB Digital Library, http://elpub.scix.net serves as archive for the papers presented at the ELPUB conferences through the years. The 15th ELPUB conference will be organized by the Department of Information Management of Hacettepe University and will take place in Ankara, Turkey, from 14-16 June 2011. (Details can be found at the ELPUB web site as the conference date nears by.) We thank Marcus Sandberg and Hannu Sääskilahti for copyediting, Library Director Tua Hindersson – Söderholm for accepting to publish the online as well as the print version of the proceedings. Thanks also to Patrik Welling for maintaining the conference web site and Tanja Dahlgren for administrative support. We warmly acknowledge the support in organizing the conference to colleagues at Hanken School of Economics and our sponsors.

Studies on Stone Age Housepits in Fennoscandia (4000 - 2000 cal BC) : Changes in ground plan, site location and degree of sedentism

Housepits have a remarkably short research history as compared to Fennoscandian archaeological research on the Stone Age in general. The current understanding of the numbers and the distribution of Stone Age housepits in the Nordic countries has, for the most part, been shaped by archaeological studies carried out over the last twenty to thirty years. The main subjects of this research are Neolithic housepits, which are archaeological remains of semi-subterranean pithouses. This dissertation consists of five peer-reviewed articles and a synthesis paper. The articles deal with the development of housepits as seen in the data gathered from Finland (the Lake Saimaa area and south-eastern Finland) and Russia (the Karelian Isthmus). This synthesis expands the discussion of the changes observed in the Papers to include Fennoscandian housepit research as a whole. Certain changes in the size, shape, environmental location, and clustering of housepits extended into various cultures and ecological zones in northern Fennoscandia. Previously, the evolution of housepits has been interpreted to have been caused by the adaptation of Neolithic societies to prevailing environmental circumstances or to re-organization following contacts with the agrarian Corded Ware/Battle Axe Cultures spreading to North. This dissertation argues for two waves of change in the pithouse building tradition. Both waves brought with them certain changes in the pithouses themselves and in the practices of locating the dwellings in the environment/landscape. The changes in housepits do not go hand in hand with other changes in material culture, nor are the changes restricted to certain ecological environments. Based on current information, it appears that the changes relate primarily to the spread of new concepts of housing and possibly to new technology, as opposed to representing merely a local response to environmental factors. This development commenced already before the birth of the Corded Ware/Battle Axe Cultures. Therefore, the changes are argued to have resulted from the spreading of new ideas through the same networks that actively distributed commodities, exotic goods, and raw materials over vast areas between the southern Baltic Sea, the north-west Russian forest zone, and Fennoscandia.