Phylogenetic Analysis of Avidins and Expression of Novel Avidins from Lactrodectus hesperus and Hoeflea phototrophica

Avidins (Avds) are homotetrameric or homodimeric glycoproteins with typically less than 130 amino acid residues per monomer. They form a highly stable, non-covalent complex with biotin (vitamin H) with Kd = 10-15 M (for chicken Avd). The best-studied Avds are the chicken Avd from Gallus gallus and streptavidin from Streptomyces avidinii, although other Avd studies have also included Avds from various origins, e.g., from frogs, fishes, mushrooms and from many different bacteria. Several engineered Avds have been reported as well, e.g., dual-chain Avds (dcAvds) and single-chain Avds (scAvds), circular permutants with up to four simultaneously modifiable ligand-binding sites. These engineered Avds along with the many native Avds have potential to be used in various nanobiotechnological applications. In this study, we made a structure-based alignment representing all currently available sequences of Avds and studied the evolutionary relationship of Avds using phylogenetic analysis. First, we created an initial multiple sequence alignment of Avds using 42 closely related sequences, guided by the known Avd crystal structures. Next, we searched for non-redundant Avd sequences from various online databases, including National Centre for Biotechnology Information and the Universal Protein Resource; the identified sequences were added to the initial alignment to expand it to a final alignment of 242 Avd sequences. The MEGA software package was used to create distance matrices and a phylogenetic tree. Bootstrap reproducibility of the tree was poor at multiple nodes and may reflect on several possible issues with the data: the sequence length compared is relatively short and, whereas some positions are highly conserved and functional, others can vary without impinging on the structure or the function, so there are few informative sites; it may be that periods of rapid duplication have led to paralogs and that the differences among them are within the error limit of the data; and there may be other yet unknown reasons. Principle component analysis applied to alternative distance data did segregate the major groups, and success is likely due to the multivariate consideration of all the information. Furthermore, based on our extensive alignment and phylogenetic analysis, we expressed two novel Avds, lacavidin from Lactrodectus Hesperus, a western black widow spider, and hoefavidin from Hoeflea phototrophica, an aerobic marine bacterium, the ultimate aim being to determine their X-ray structures. These Avds were selected because of their unique sequences: lacavidin has an N-terminal Avd-like domain but a long C-terminal overhang, whereas hoefavidin was thought to be a dimeric Avd. Both these Avds could be used as novel scaffolds in biotechnological applications.

Disaster recovery of business critical 3-tiered ERP applications: Disaster Recovery of Nokia Groups SAP R/3

Nykyaikaisessa liiketoimintaympäristössä yritysten kriittisiksi resursseiksi ovat muodostuneet liiketoimintaa tukevat tietojärjestelmät. Mahdollisuus hyödyntää näitä resursseja riippuu ko. liiketoiminnalle kriittisten järjestelmien luotettavuudesta ja hyödynnettävien sovellusten saatavuudesta. Eräs tilanne jossa järjestelmien kyky tukea todellisia liiketoimintaprosesseja vaarantuu on katastrofi. Vaikutukseltaan katastrofi voi olla paikallinen tai kattaa laajojakin alueita. Eri tyyppisiin katastrofeihin on varauduttava niiden edellyttämin tavoin. Eräs kriittisten tietojärjestelmien arkkitehtuuriin vaikuttanut trendi 90-luvulla on ollut client/server lähestymistapa. Client/server paradigman mukaan sovellus jaetaan tasoihin siten että esitys-, sovellus- ja tietokantakerrokset voidaan erottaa fyysisesti toisistaan näiden silti muodostaessa loogisesti yhtenäisen kokonaisuuden. Liiketoiminnan näkökulmasta 90- luvun mullistavia IT-uutuuksia olivat toiminnanohjausjärjestelmät, joiden avulla oli mahdollista hallita koko tuotantoketjua ja muita prosessikokonaisuuksia lähes reaaliajassa. Monikerroksisten toiminnanohjausjärjestelmien luotettavuus on osoittautunut haastavavaksi sillä kaikkien kerrosten suojaaminen kaikilta mahdollisilta katastrofeilta täydellisesti on nykyisellä teknologialla mahdotonta. Kompromissien tekemiseksi on oltava selvillä kunkin menetetyn prosessin aiheuttamista taloudellisista ja liiketoiminnallisista vaikutuksista. Tämän vuoksi juuri toiminnanohjausjärjestelmät ovat mielenkiintoisia, vaikuttavathan ne liiketoimintaprosesseihin läpi koko yrityksen prosessiketjun. Monikerroksisten client/server arkkitehtuuriin pohjautuvien toiminnanohjausjärjestelmien suojaamisessa katastrofeilta onkin sovellettava useita tekniikoita ja teknologioita, ja yhdistettävä kokonaisuus prosessikehykseen. Näin voidaan luoda suunnitelmallinen osa IT strategiaa, joka ottaa kantaa liiketoiminnan jatkuvuuteen katastrofitilanteessa ja mahdollistaa nopean ja täydellisen palautumisen kaikissa olosuhteissa.

Computing the diameter of Coxeter groups

This thesis addresses the problem of computing the minimal and maximal diameter of the Cayley graph of Coxeter groups. We first present and assert relevant parts of polytope theory and related Coxeter theory. After this, a method of contracting the orthogonal projections of a polytope from Rd onto R2 and R3, d ¸ 3 is presented. This method is the Equality Set Projection algorithm that requires a constant number of linearprogramming problems per facet of the projection in the absence of degeneracy. The ESP algorithm allows us to compute also projected geometric diameters of high-dimensional polytopes. A representation set of projected polytopes is presented to illustrate the methods adopted in this thesis.

Strategic groups and performance: an empirical analysis of strategic groups in the wind energy industry in Europe

The strategic group theory provides an intermediate level of analysis between a single company and the whole industry for identifying issues about the company's competitive position and strategic choices. Strategic groups are companies within an industry with similar strategic characteristics or competing on similar bases. Strategic choices are aligned with the firms’ resources. The purpose of this study was to identify the strategic groups in the wind energy industry in Europe, and study, whether a certain group membership results in financial performance differences. Altogether 80 European wind energy companies were included in the study, which were clustered into four strategic groups according to their age and growth rate. Each group corresponds to a different strategy. The results show that the wind energy companies can be clustered according to the chosen strategic characteristics. Strategic decisions were investigated with characteristic variables. Performance variables were used in the analysis measuring profitability, liquidity and solvency of the groups. These strategic choices of the companies did not have a significant influence on the firms’ performance. The more mature and slower growing group proved to be the most successful. However, the differences between groups were generally not statistically significant. The only statistically significant difference found was in the solvency ratio between Mature Slow and Young Rapid groups. Measured with these variables, more mature and slower growing companies performed better. Therefore, a certain strategic group membership results in performance differences.

Considering Target Groups in the Creation of a Comprehensive City Branding Process

The aim of the research was to create a comprehensive city branding process. This was done by identifying the key target groups of the city and considering them in the city branding process. Also key stakeholders were identified and taken into consideration when creating the branding process. As an empirical study, three first stages of the city branding process were implemented for the city of Lappeenranta having "students" as the case target group. An interview with the city officials was conducted, as well as a student survey on the current city image of Lappeenranta. Quantitative research methods were used to analyze the results of the survey. A comprehensive city branding process with eight stages was created in the research. Target groups were considered in the process by identifying the target group dependent stages. The empirical study revealed that the current city image held by the students consists of six dimensions. These dimensions were analyzed from the viewpoint of Lappeenranta with the help of an importance performance analysis.

Collaborative information behaviour : a case study of two research groups

The aim of the licentiate thesis is to examine researchers' information practices in research groups. The researchers were involved with study communication and media related issues within Social Sciences and Humanities Faculties. The theoretical framework of the study comprises the new holistic models of information seeking (for example: Meho and Tibbo, 2003; Seldén, 1999) and the collective aspects of information behaviour (Prekop, 2002 ; Talja, 2002; Talja and Hansen, 2006). The research questions are: 1. How do scholars seek information in research groups? 2 What kind of collaborative information behaviour occurs in the research groups? The research data was gathered by interviews and observations. Three meetings of a research group at the University of Tampere were observed during the autumn of 2004. The group members and the group leader of the research group were interviewed in the spring of 2005. The research group members and the group leader of a research group at the University of Jyväskylä were interviewed in the autumn of 2005. Altogether, two research group leaders and eight researchers were interviewed. The significance of the research group for information seeking is more important in closeknit research groups than in rather loose research groups. The significance of the research group for information seeking can be at least threefold. First, research group members can inform the group about relevant information resources and potential library or other information services. Second, the research group can to some extent compensate for the information seeking systems of libraries by distributing material and information resources. Third, information seeking can be carried out in collaboration in research groups. The significance of the research group was found to be most important in informing about new information services and marketing library systems. Recommendations from colleagues were often needed to mobilize researchers into using new library services. The significance of colleagues in informing about library services is in line with earlier studies. The present study showed that sometimes information from colleagues was regarded as more important than information distributed directly by the local library. A culture of information sharing, including mutual trust, seemed mainly to be reflected in collaboration and collaborative information seeking in the research groups studied. The timing of the onset of individual research seemed to be related to the information sharing culture and social networks in research groups. The simultaneous onset of the research work by group members seemed to promote the growth of unbiased collaboration, also in information seeking.

Early Life Intestinal Microbiota in Health and in Atopic Eczema

Decrease in microbial contacts in affluent societies is considered to lie behind the rise in allergic and other chronic inflammatory diseases during the last decades. Indeed, deviations in the intestinal microbiota composition and diversity have been associated with several diseases, such as atopic eczema. However, there is no consensus yet on what would constitute a beneficial or harmful microbiota. The aim of this thesis was to study the microbiota development in healthy infants and to characterize intestinal microbiota signatures associated with disease status and severity in infants with atopic eczema. The methodological aim was to compare and optimize methods for DNA extraction from fecal samples to be used in high-throughput microbiota analyses. It was confirmed that the most critical step in successful microbial DNA extraction from fecal samples is the mechanical cell lysis procedure. Based on this finding, an efficient semi-automated extraction process was developed that can be scaled for use in high-throughput platforms such as phylogenetic microarray used in this series of studies. By analyzing a longitudinal motherchild cohort for 3 years it was observed that the microbiota development is a gradual process, where some bacterial groups reach the degree of adult-type pattern earlier than others. During the breast-feeding period, the microbiota appeared to be relatively simple, while major diversification was found to start during the weaning process. By the age of 3 years, the child’s microbiota composition started to resemble that of an adult, but the bacterial diversity has still not reached the full diversity, indicating that the microbiota maturation extends beyond this age. In addition, at three years of age, the child’s microbiota was more similar to mother’s microbiota than to microbiota of nonrelated women.In infants with atopic eczema, a high total microbiota diversity and abundance of butyrate-producing bacteria was found to correlate with mild symptoms at 6 months. At 18 months, infants with mild eczema had significantly higher microbiota diversity and aberrant microbiota composition when compared to healthy controls at the same age. In conclusion, the comprehensive phylogenetic microarray analysis of early life microbiota shows the synergetic effect of vertical transmission and shared environment on the intestinal microbiota development. By the age of three years, the compositional development of intestinal microbiota is close to adult level, but the microbiota diversification continues beyond this age. In addition, specific microbiota signatures are associated with the existence and severity of atopic eczema and intestinal microbiota seems to have a role in alleviating the symptoms of this disease.

Prodrug strategies of antiviral nucleotides: Studies on enzymatically and thermally removable phosphate protecting groups

Antiviral nucleosides are compounds that are used against viruses, such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV). To act as therapeutic agent, the antiviral nucleoside needs to be phosphorylated to nucleotide in the body in three consecutive phosphorylation steps by cellular or viral enzymes. The first phosphorylation to the nucleoside monophosphate is often inefficient and leads to poor antiviral activity. The antiviral efficacy can be improved by applying a prodrug strategy and delivering the antiviral nucleoside directly as its monophosphate. In prodrug strategies of antiviral nucleotides, the negative charges on the phosphate moiety are temporarily masked with protecting groups. Once inside the cell, the protecting groups are removed by enzymatic or chemical processes. Many prodrug strategies apply biodegradable protecting groups, the removal of which is triggered by esterase enzymes. Several studies have, however, demonstrated that the removal rate of the second and subsequent esterase labile protecting groups significantly slows down after the first protecting group is removed due to the negative charge on the phosphodiester intermediate, which disturbs the catalytic site of the enzyme. In this thesis, esterase labile protecting group strategies where the issue of retardation could be avoided were studied. Prodrug candidates of antiviral nucleotides were synthesized and kinetic studies on the chemical and enzymatic stability were carried out. In the synthesized compounds, the second protecting group is cleaved from the monophosphate some other mechanism than esterase triggered activation or the structure of prodrug requires only one protecting group. In addition, esterase labile protecting group which is additionally thermally removable was studied. This protecting group was cleaved from oligomeric phosphodiesters both enzymatically and thermally and seems most attractive of the studied phosphate protecting groups. However, the rate of the thermal removal still is too slow to allow efficient protection of longer oligonucleotides and needs optimization. Key words: antiviral, nucleotide, prodrug, protecting group, biodegradable