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.

Across the Oceans : Development of Overseas Business Information Transmission, 1815-1875

Earlier studies have shown that the speed of information transmission developed radically during the 19th century. The fast development was mainly due to the change from sailing ships and horse-driven coaches to steamers and railways, as well as the telegraph. Speed of information transmission has normally been measured by calculating the duration between writing and receiving a letter, or between an important event and the time when the news was published elsewhere. As overseas mail was generally carried by ships, the history of communications and maritime history are closely related. This study also brings a postal historical aspect to the academic discussion. Additionally, there is another new aspect included. In business enterprises, information flows generally consisted of multiple transactions. Although fast one-way information was often crucial, e.g. news of a changing market situation, at least equally important was that there was a possibility to react rapidly. To examine the development of business information transmission, the duration of mail transport has been measured by a systematic and commensurable method, using consecutive information circles per year as the principal tool for measurement. The study covers a period of six decades, several of the world's most important trade routes and different mail-carrying systems operated by merchant ships, sailing packets and several nations' steamship services. The main sources have been the sailing data of mail-carrying ships and correspondence of several merchant houses in England. As the world's main trade routes had their specific historical backgrounds with different businesses, interests and needs, the systems for information transmission did not develop similarly or simultaneously. It was a process lasting several decades, initiated by the idea of organizing sailings in a regular line system. The evolution proceeded generally as follows: originally there was a more or less irregular system, then a regular system and finally a more frequent regular system of mail services. The trend was from sail to steam, but both these means of communication improved following the same scheme. Faster sailings alone did not radically improve the number of consecutive information circles per year, if the communication was not frequent enough. Neither did improved frequency advance the information circulation if the trip was very long or if the sailings were overlapping instead of complementing each other. The speed of information transmission could be improved by speeding up the voyage itself (technological improvements, minimizing the waiting time at ports of call, etc.) but especially by organizing sailings so that the recipients had the possibility to reply to arriving mails without unnecessary delay. It took two to three decades before the mail-carrying shipping companies were able to organize their sailings in an optimal way. Strategic shortcuts over isthmuses (e.g. Panama, Suez) together with the cooperation between steamships and railways enabled the most effective improvements in global communications before the introduction of the telegraph.