Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

Kohti ulkorajoja : Lukion toimintakulttuurikuvaus ohjauksen ja johtamisen näkökulmasta

The aim of this qualitative study is to chart the operational context of the upper-secondary school principals and the historical, cultural and structural factors that steer their day-to-day work. The concepts regarding the study environment and operational culture are defined and analysed in terms of how they are interrelated. Furthermore it is explained why the upper-secondary schools must describe their operational culture within the curriculum. The study also aims to connect the description of the operational culture with the operational system of the upper-secondary school and to analyse the descriptions of the five upper-secondary schools in relation to the commitment to developing a study environment conducive to learning and participation, as well as conducive to supporting interaction. Interview data is used to provide the background for the description of the operational culture and to particularise the results of the analysis. According to the theory used in this study, the steering sources of the day-to-day work of the upper-secondary school are the rules system of the state, the municipality, the curriculum, and on the level of the upper-secondary school administration. The research data consist of the literature concerning the steering, steering forms and the principals professional picture in general terms, from 1950 to the present, and the steering texts concerning the educational environment and operational culture. Furthermore the research data include five descriptions of the operational culture concerning the upper-secondary school, the action reports and student guides. The methods of analysis include the level model and content analysis. The first is a part of the theory used in this study. For the purpose of content analysis, moreover, classifying grounds are established on the basis of theoretical and empirical research data. A result of this study is that, from the perspective of steering, the function of describing the operational culture is clearly linked to the evaluation supporting the goals and the vision of a learning organization. From an administrative point of view, a description is a problem-solving strategy and an instrument of evaluation. The study environment is a structural context in and through which the actors of the school create, change and renew the elements of the structure rooted in the context; this structure is their historically and culturally mediated way of thinking and acting. The initial situation and orientation of the students affect the emphasis of the operational culture descriptions; principals also have their own personal style of leadership. Key words: source of steering, educational environment, operational culture, self-evaluation, learning organisation

Venäjän politiikka ja perustuslaki : Tutkimus Venäjän perustuslakikäsitteistön kehityksestä 1900-luvulla

Constitutional politics in Russia, a conceptual history study of the constitutional rhetoric in the 20th century In April 2006 the Russian Constitution had its 100th anniversary. Following its late start, five constitutions have been adopted. The great number of constitutions is partly explained in my work by the fact that Russia s political system has changed many times, from one state system to another. From a monarchical state power, it changed first, with the October revolution, into the Russian Socialist Federal Soviet Republic, and after that, in 1924, into the Union of Soviet Socialist Republics. In 1991, the Russian Federation was established. The great number of constitutions can also be explained by the fact that in a one-party system, constitutional concepts became one of the most important instruments for introducing political programmes. When the political unity of the state was not only restricted by the Constitution, but also by the party ideology, the political debates concerning constitutional concepts were the key discussions for all the reformative pursuits of Soviet politics. It can be said that, in the Soviet Union, almost all political discourses dealt with constitutional concepts. In the context of restricted unity, the constitutional concepts were the most important tools to argue and create a basis for a new presentation and new political programmes. Thus, the basic feature of the Soviet political discourses has been a continuous competition regarding the constitutional concepts. By defining the constitutional concepts, a new, the political elites wanted especially to redefine, their own way, the traditional meanings of the October 1917 Revolution, and to differentiate them from those of the preceding period of power. From a methodological point of view, I argue that the Russian constitutional concepts make a conceptual historical approach very suitable, and change the focus on history. This approach studies history in contemporary contexts which follow after each other, and whose texts are the main research target. The picture of history is created through the interpretation of the original sources of contemporary contexts. Focusing on the dynamic and traditional characteristic of Russian constitutional concepts, I refer to a certain kind of value and the task of these concepts to justify and define the political and societal unity in every situation. This is done by combining the pursued future orientation of constitutional unity with the new acts of preservation of the traditional principles of the revolution. The different time layers of the constitutional concepts, the past, the present and the future, are the key aspects of storytelling in justifying the continuity and redefining the constitutional unity for the sake of reform. These aspects of constitutional concepts, in addition to all the other functions, have been the main elements of the argumentative structure of acting against opponents.

Elements of Volatility at High Frequency

Volatility is central in options pricing and risk management. It reflects the uncertainty of investors and the inherent instability of the economy. Time series methods are among the most widely applied scientific methods to analyze and predict volatility. Very frequently sampled data contain much valuable information about the different elements of volatility and may ultimately reveal the reasons for time varying volatility. The use of such ultra-high-frequency data is common to all three essays of the dissertation. The dissertation belongs to the field of financial econometrics. The first essay uses wavelet methods to study the time-varying behavior of scaling laws and long-memory in the five-minute volatility series of Nokia on the Helsinki Stock Exchange around the burst of the IT-bubble. The essay is motivated by earlier findings which suggest that different scaling laws may apply to intraday time-scales and to larger time-scales, implying that the so-called annualized volatility depends on the data sampling frequency. The empirical results confirm the appearance of time varying long-memory and different scaling laws that, for a significant part, can be attributed to investor irrationality and to an intraday volatility periodicity called the New York effect. The findings have potentially important consequences for options pricing and risk management that commonly assume constant memory and scaling. The second essay investigates modelling the duration between trades in stock markets. Durations convoy information about investor intentions and provide an alternative view at volatility. Generalizations of standard autoregressive conditional duration (ACD) models are developed to meet needs observed in previous applications of the standard models. According to the empirical results based on data of actively traded stocks on the New York Stock Exchange and the Helsinki Stock Exchange the proposed generalization clearly outperforms the standard models and also performs well in comparison to another recently proposed alternative to the standard models. The distribution used to derive the generalization may also prove valuable in other areas of risk management. The third essay studies empirically the effect of decimalization on volatility and market microstructure noise. Decimalization refers to the change from fractional pricing to decimal pricing and it was carried out on the New York Stock Exchange in January, 2001. The methods used here are more accurate than in the earlier studies and put more weight on market microstructure. The main result is that decimalization decreased observed volatility by reducing noise variance especially for the highly active stocks. The results help risk management and market mechanism designing.

Functional Analysis of MrpL55, Vig and Mat1 Acting at the Crossroad of Cell Cycle, Transcription and Metabolism Regulation

Cell proliferation, transcription and metabolism are regulated by complex partly overlapping signaling networks involving proteins in various subcellular compartments. The objective of this study was to increase our knowledge on such regulatory networks and their interrelationships through analysis of MrpL55, Vig, and Mat1 representing three gene products implicated in regulation of cell cycle, transcription, and metabolism. Genome-wide and biochemical in vitro studies have previously revealed MrpL55 as a component of the large subunit of the mitochondrial ribosome and demonstrated a possible role for the protein in cell cycle regulation. Vig has been implicated in heterochromatin formation and identified as a constituent of the RNAi-induced silencing complex (RISC) involved in cell cycle regulation and RNAi-directed transcriptional gene silencing (TGS) coupled to RNA polymerase II (RNAPII) transcription. Mat1 has been characterized as a regulatory subunit of cyclin-dependent kinase 7 (Cdk7) complex phosphorylating and regulating critical targets involved in cell cycle progression, energy metabolism and transcription by RNAPII. The first part of the study explored whether mRpL55 is required for cell viability or involved in a regulation of energy metabolism and cell proliferation. The results revealed a dynamic requirement of the essential Drosophila mRpL55 gene during development and suggested a function of MrpL55 in cell cycle control either at the G1/S or G2/M transition prior to cell differentiation. This first in vivo characterization of a metazoan-specific constituent of the large subunit of mitochondrial ribosome also demonstrated forth compelling evidence of the interconnection of nuclear and mitochondrial genomes as well as complex functions of the evolutionarily young metazoan-specific mitochondrial ribosomal proteins. In studies on the Drosophila RISC complex regulation, it was noted that Vig, a protein involved in heterochromatin formation, unlike other analyzed RISC associated proteins Argonaute2 and R2D2, is dynamically phosphorylated in a dsRNA-independent manner. Vig displays similarity with a known in vivo substrate for protein kinase C (PKC), human chromatin remodeling factor Ki-1/57, and is efficiently phosphorylated by PKC on multiple sites in vitro. These results suggest that function of the RISC complex protein Vig in RNAi-directed TGS and chromatin modification may be regulated through dsRNA-independent phosphorylation by PKC. In the third part of this study the role of Mat1 in regulating RNAPII transcription was investigated using cultured murine immortal fibroblasts with a conditional allele of Mat1. The results demonstrated that phosphorylation of the carboxy-terminal domain (CTD) of the large subunit of RNAPII in the heptapeptide YSPTSPS repeat in Mat-/- cells was over 10-fold reduced on Serine-5 and subsequently on Serine-2. Occupancy of the hypophosphorylated RNAPII in gene bodies was detectably decreased, whereas capping, splicing, histone methylation and mRNA levels were generally not affected. However, a subset of transcripts in absence of Mat1 was repressed and associated with decreased occupancy of RNAPII at promoters as well as defective capping. The results identify the Cdk7-CycH-Mat1 kinase submodule of TFIIH as a stimulatory non-essential regulator of transcriptional elongation and a genespecific essential factor for stable binding of RNAPII at the promoter region and capping. The results of these studies suggest important roles for both MrpL55 and Mat1 in cell cycle progression and their possible interplay at the G2/M stage in undifferentiated cells. The identified function of Mat1 and of TFIIH kinase complex in gene-specific transcriptional repression is challenging for further studies in regard to a possible link to Vig and RISC-mediated transcriptional gene silencing.

"Onko yhteisöllisyydellä väliä?" : identiteettiprosessi ja sosiaalinen pääoma epävarmuuden sietämisen merkityksellisinä elementteinä

”Does the community really count? – identity process and social capital as elements in surviving in insecurity and uncertainty” is a combination of five articles. The aim of this study is to answer the question: how or in which ways is it possible to find the role of identity process and social capital in surviving in insecurity and uncertainty? In the introduction part the concepts of community and social capital are examined. Then I will study the articles and try to find out what kinds of elements of identity process and social capital in them can be found in order to survive in the societal change. The study consists of the introduction part and the articles. The articles are: 1. “Is Becoming a Researcher Some Kind of Role-playing” - Roles of the Researcher in the Process of Forming the Identity 2. What Composes Collective Identity in the Polytechnic Community? 3. Opportunities to Succeed or Fear of Failure? -Entrepreneurship from the Youngsters` Point of View 4. Learning Risk-taking Competences 5. “Bricolage”, or Just Putting Things Together? The starting point for the study is the feeling of insecurity that surrounds a person living in the present society: you cannot be sure with whom you are going to co-operate tomorrow. In the “Good Old Days” the harmonious communities “protected” their members and worked strongly toward common aims. Nowadays, partly because of urbanisation, we are so busy that we only have time to take care of ourselves, or rather to say: just of myself. As Bauman (2001) puts it: people turn to communities in which they feel like home. They still long for communality. For Mead (1962) the group and the communality plays a big role: a person needs others to become the whole ”Self.” In acting with others a person can gain much more than working alone (Field 2003). But, as Day (2006) puts it, the reality of community as discovered by empirical reserach is a great deal messier than the abstract and idealized versions used by theorists. Keywords: uncertainty, insecurity, communality, identity process, social capital, significant groups, survival.

Transposable elements in a marginal plant population

Background
How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation.

Results
Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen.

Conclusions
We hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.