Structural studies on enzymes of biotechnological and biomedical interest

Structural studies of proteins aim at elucidating the atomic details of molecular interactions in biological processes of living organisms. These studies are particularly important in understanding structure, function and evolution of proteins and in defining their roles in complex biological settings. Furthermore, structural studies can be used for the development of novel properties in biomolecules of environmental, industrial and medical importance. X-ray crystallography is an invaluable tool to obtain accurate and precise information about the structure of proteins at the atomic level. Glutathione transferases (GSTs) are amongst the most versatile enzymes in nature. They are able to catalyze a wide variety of conjugation reactions between glutathione (GSH) and non-polar components containing an electrophilic carbon, nitrogen or sulphur atom. Plant GSTs from the Tau class (a poorly characterized class) play an important role in the detoxification of xenobiotics and stress tolerance. Structural studies were performed on a Tau class fluorodifen-inducible glutathione transferase from Glycine max (GmGSTU4-4) complexed with GSH (2.7 Å) and a product analogue Nb-GSH (1.7 Å). The three-dimensional structure of the GmGSTU4-4-GSH complex revealed that GSH binds in different conformations in the two subunits of the dimer: in an ionized form in one subunit and a non-ionized form in the second subunit. Only the ionized form of the substrate may lead to the formation of a catalytically competent complex. Structural comparison between the GSH and Nb-GSH bound complexes revealed significant differences with respect to the hydrogen-bonding, electrostatic interaction pattern, the upper part of -helix H4 and the C-terminus of the enzyme. These differences indicate an intrasubunit modulation between the G-and Hsites suggesting an induced-fit mechanism of xenobiotic substrate binding. A novel binding site on the surface of the enzyme was also revealed. Bacterial type-II L-asparaginases are used in the treatment of haematopoietic diseases such as acute lymphoblastic leukaemia (ALL) and lymphomas due to their ability to catalyze the conversion of L-asparagine to L-aspartate and ammonia. Escherichia coli and Erwinia chrysanthemi asparaginases are employed for the treatment of ALL for over 30 years. However, serious side-effects affecting the liver and pancreas have been observed due to the intrinsic glutaminase activity of the administered enzymes. Structural studies on Helicobacter pylori L-asparaginase (HpA) were carried out in an effort to discover novel L-asparaginases with potential chemotherapeutic utility in ALL treatment. Detailed analysis of the active site geometry revealed structurally significant differences between HpA and other Lasparaginases that may be important for the biological activities of the enzyme and could be further exploited in protein engineering efforts.

Wood-derived biomaterials for biomedical applications

Driven by the global trend in the sustainable economy development and environmental concerns, the exploring of plant-derived biomaterials or biocomposites for potential biomedical and/or pharmaceutical applications has received tremendous attention. Therefore, the work of this thesis is dedicated to high-value and high-efficiency utilization of plant-derived materials, with the focus on cellulose and hemicelluloses in the field of biomedical applications in a novel biorefinery concept. The residual cellulose of wood processing waste, sawdust, was converted into cellulose nanofibrils (CNFs) with tunable surface charge density and geometric size through 2,2,6,6-tetramethylpiperidinyloxy (TEMPO)-mediated oxidation and mechanical defibrillation. The sawdust-based CNFs and its resultant free-standing films showed comparable or even better mechanical properties than those from a commercial bleached kraft pulp at the same condition, demonstrating the feasibility of producing CNFs and films thereof with outstanding mechanical properties from birch sawdust by a process incorporated into a novel biorefinery platform recovering also polymeric hemicelluloses for other applications. Thus, it is providing an efficient route to upgrade sawdust waste to valuable products. The surface charge density and geometric size of the CNFs were found to play key roles in the stability of the CNF suspension, as well as the gelling properties, swelling behavior, mechanical stiffness, morphology and microscopic structural properties, and biocompatibility of CNF-based materials (i.e. films, hydrogels, and aerogels). The CNFs with tunable surface chemistry and geometric size was found promising applications as transparent and tough barrier materials or as reinforcing additive for production of biocomposites. The CNFs was also applied as structural matrices for the preparation of biocomposites possessing electrical conductivity and antimicrobial activity by in situ polymerization and coating of polypyrrole, and incorporation of silver nanoparticles, which make the material possible for potential wound healing application. The CNF-based matrices (films, hydrogels, and aerogels) with tunable structural and mechanical properties and biocompatibility were further prepared towards an application as 3D scaffolds in tissue engineering. The structural and mechanical strength of the CNF matrices could be tuned by controlling the charge density of the nanocellulose, as well as the pH and temperature values of the hydrogel formation conditions. Biological tests revealed that the CNF scaffolds could promote the survival and proliferation of tumor cells, and enhance the transfection of exogenous DNA into the cells, suggesting the usefulness of the CNF-based 3D matrices in supporting crucial cellular processes during cell growth and proliferation. The CNFs was applied as host materials to incorporate biomolecules for further biomedical application. For example, to investigate how the biocompatibility of a scaffold is influenced by its mechanical and structural properties, these properties of CNF-based composite matrices were controlled by incorporation of different hemicelluloses (O-acetyl galactoglucomanan (GGM), xyloglucan (XG), and xylan) into CNF hydrogel networks in different ratios and using two different approaches. The charge density of the CNFs, the incorporated hemicellulose type and amount, and the swelling time of the hydrogels were found to affect the pore structure, the mechanical strength, and thus the cells growth in the composite hydrogel scaffolds. The mechanical properties of the composite hydrogels were found to have an influence on the cell viability during the wound healing relevant 3T3 fibroblast cell culture. The thusprepared CNF composite hydrogels may work as promising scaffolds in wound healing application to provide supporting networks and to promote cells adhesion, growth, and proliferation.

Benchmarking project of the Department of Electrical Engineering of Lappeenranta University of Technology

Lappeenrannan teknillisen korkeakoulun sähkötekniikan osasto muutti 1.8.2005 sähkötekniikan tutkinnon kaksiportaiseksi ja vastaamaan näin Bologna-prosessia ja Suomen yliopistolainsäädäntöä. Tutkinnonuudistuksen myötä osasto haluaa varmistaa sähkötekniikan tutkintojen laadun ja vertailtavuuden sekä parantaa opiskelijoidensekä henkilökunnan liikkuvuutta. Tutkintojen laatu ja vertailtavuus osoitetaan sähkötekniikan osaston benchmark-projektilla, jossa kerätään tietoja maisteri- ja tohtorintutkintoa tarjoavista eurooppalaisista yliopistoista. Diplomityö käsittää BM-projektin kolmannen vaiheen suunnittelun ja toteutuksen sisältäen teoriaa benchmark-projekteille tyypillisistä toimintatavoista. Hyväksi havaitut menetelmiä, kuten kyselyt ja matriisit, on tässä työssä otettu soveltuvin osin sähkötekniikan osaston BM-projektin työkaluiksi. Diplomityössä analysoidaan työkalujen avulla BM-kumppaneilta kerättyjä tietoja sekä esitetään ratkaisuja, miten sähkötekniikan osastolla voidaan jatkaa parhaiden toimintatapojen löytämistä.

Project controlling and risk management in German machine and plant engineering industry

Tutkielman tavoitteena on määritellä projektikontrolloinnin ja - riskijohtamisen roolit ja toiminnot saksalaisissa kone- ja tehdassuunnitteluteollisuusyrityksissä. Tämä on kvalitatiivinen tutkielma, jossa käytetään voimakkaasti kuvailevia metodeita. Materiaali tutkimuksen empiiriseen osaan kerättiin kyselykaavakkeen avulla. Kyselykaavakkeiden tulokset käsiteltiin Microsoft Office Access- ohjelmalla ja analysoitiin Microsoft Office Excel- ohjelmalla ja Pivot table- työkalun avulla. Tutkimustulokset osoittavat, että asianmukaisessa projektikontrollointi- ja riskijohtamismetodien käytössä ja käyttötiheydessä esiintyy puutteita saksalaisissa kone- ja tehdassuunnitteluteollisuusyrityksissä. Tehostamalla ja keskittymällä enemmän projektikontrollointi- ja riskijohtamismetodeihin ja prosesseihin sekä projektien että yritysten suorituskyky paranisi.

Finding the Fit Between Engineering Design and Cost Information

This paper analyzes the possibilities of integrating cost information and engineering design. Special emphasis is put on finding the potential of using the activity-based costing (ABC) method. Today, the problem of cost estimation in engineering design is that there are two separate extremes of knowledge. On the one extreme, the engineers model the technical parametres behindcosts in great detail but do not get appropriate cost information to their elegant models. On the other extreme, the accounting professionals are stuck with traditional cost accounting methods driven by the procedures and cycles of financial accounting. Therefore, in many cases, the cost information needs of various decision making groups, for example design engineers, are not served satisfactorily. This paper studies if the activity-based costing (ABC) method could offer a compromise between the two extremes. Recognizing activities and activity chains as well as activity and cost drivers could be specially beneficial for design engineers. Also, recognizing the accurate and reliable product costs of existing products helps when doing variant design. However, ABC is not at its best if the cost system becomes too complicated. This is why a comprehensive ABC-cost information system with detailed cost information for the use of design engineers should be examined critically. ABC is at its best when considering such issues as which activities drive costs, the cost of product complexity, allocating indirect costs on the products, the relationships between processes and costs, and the cost of excess capacity.

On the innovation capacity of technologyrelated knowledge-intensive business services. A case study of the technology and engineering consulting (TEC) sector in Singapore

Even though the research on innovation in services has expanded remarkably especially during the past two decades, there is still a need to increase understanding on the special characteristics of service innovation. In addition to studying innovation in service companies and industries, research has also recently focused more on services in innovation, as especially the significance of so-called knowledge intensive business services (KIBS) for the competitive edge of their clients, othercompanies, regions and even nations has been proved in several previous studies. This study focuses on studying technology-based KIBS firms, and technology andengineering consulting (TEC) sector in particular. These firms have multiple roles in innovation systems, and thus, there is also a need for in-depth studies that increase knowledge about the types and dimensions of service innovations as well as underlying mechanisms and procedures which make the innovations successful. The main aim of this study is to generate new knowledge in the fragmented research field of service innovation management by recognizing the different typesof innovations in TEC services and some of the enablers of and barriers to innovation capacity in the field, especially from the knowledge management perspective. The study also aims to shed light on some of the existing routines and new constructions needed for enhancing service innovation and knowledge processing activities in KIBS companies of the TEC sector. The main samples of data in this research include literature reviews and public data sources, and a qualitative research approach with exploratory case studies conducted with the help of the interviews at technology consulting companies in Singapore in 2006. These complement the qualitative interview data gathered previously in Finland during a larger research project in the years 2004-2005. The data is also supplemented by a survey conducted in Singapore. The respondents for the survey by Tan (2007) were technology consulting companies who operate in the Singapore region. The purpose ofthe quantitative part of the study was to validate and further examine specificaspects such as the influence of knowledge management activities on innovativeness and different types of service innovations, in which the technology consultancies are involved. Singapore is known as a South-east Asian knowledge hub and is thus a significant research area where several multinational knowledge-intensive service firms operate. Typically, the service innovations identified in the studied TEC firms were formed by several dimensions of innovations. In addition to technological aspects, innovations were, for instance, related to new client interfaces and service delivery processes. The main enablers of and barriers to innovation seem to be partly similar in Singaporean firms as compared to the earlier study of Finnish TEC firms. Empirical studies also brought forth the significance of various sources of knowledge and knowledge processing activities as themain driving forces of service innovation in technology-related KIBS firms. A framework was also developed to study the effect of knowledge processing capabilities as well as some moderators on the innovativeness of TEC firms. Especially efficient knowledge acquisition and environmental dynamism seem to influence the innovativeness of TEC firms positively. The results of the study also contributeto the present service innovation literature by focusing more on 'innovation within KIBs' rather than 'innovation through KIBS', which has been the typical viewpoint stressed in the previous literature. Additionally, the study provides several possibilities for further research.

Aspects on Process Engineering in the Finnish Pulp and Paper Industry : Thesis for the Degree of Licentiate in Science of Technology

Process development will be largely driven by the main equipment suppliers. The reason for this development is their ambition to supply complete plants or process systems instead of single pieces of equipment. The pulp and paper companies' interest lies in product development, as their main goal is to create winning brands and effective brand management. Design engineering companies will find their niche in detail engineering based on approved process solutions. Their development work will focus on increasing the efficiency of engineering work. Process design is a content-producing profession, which requires certain special characteristics: creativity, carefulness, the ability to work as a member of a design team according to time schedules and fluency in oral as well as written presentation. In the future, process engineers will increasingly need knowledge of chemistry as well as information and automation technology. Process engineering tools are developing rapidly. At the moment, these tools are good enough for static sizing and balancing, but dynamic simulation tools are not yet good enough for the complicated chemical reactions of pulp and paper chemistry. Dynamic simulation and virtual mill models are used as tools for training the operators. Computational fluid dynamics will certainlygain ground in process design.

Introducing Basic Systematic Requirements Engineering Practices in Small Organizations with an Easy to Adopt Method

Requirements-relatedissues have been found the third most important risk factor in software projects and as the biggest reason for software project failures. This is not a surprise since; requirements engineering (RE) practices have been reported deficient inmore than 75% of all; enterprises. A problem analysis on small and low maturitysoftware organizations revealed two; central reasons for not starting process improvement efforts: lack of resources and uncertainty; about process improvementeffort paybacks.; In the constructive part of the study a basic RE method, BaRE, was developed to provide an; easy to adopt way to introduce basic systematic RE practices in small and low maturity; organizations. Based on diffusion of innovations literature, thirteen desirable characteristics; were identified for the solution and the method was implemented in five key components:; requirements document template, requirements development practices, requirements; management practices, tool support for requirements management, and training.; The empirical evaluation of the BaRE method was conducted in three industrial case studies. In; this evaluation, two companies established a completely new RE infrastructure following the; suggested practices while the third company conducted continued requirements document; template development based on the provided template and used it extensively in practice. The; real benefits of the adoption of the method were visible in the companies in four to six months; from the start of the evaluation project, and the two small companies in the project completed; their improvement efforts with an input equal to about one person month. The collected dataon; the case studies indicates that the companies implemented new practices with little adaptations; and little effort. Thus it can be concluded that the constructed BaRE method is indeed easy to; adopt and it can help introduce basic systematic RE practices in small organizations.

Cost information in engineering design -Potentials and limitations of activity-based costing

The purpose of this thesis is to analyse activity-based costing (ABC) and possible modified versions ofit in engineering design context. The design engineers need cost information attheir decision-making level and the cost information should also have a strong future orientation. These demands are high because traditional management accounting has concentrated on the direct actual costs of the products. However, cost accounting has progressed as ABC was introduced late 1980s and adopted widely bycompanies in the 1990s. The ABC has been a success, but it has gained also criticism. In some cases the ambitious ABC systems have become too complex to build,use and update. This study can be called an action-oriented case study with some normative features. In this thesis theoretical concepts are assessed and allowed to unfold gradually through interaction with data from three cases. The theoretical starting points are ABC and theory of engineering design process (chapter2). Concepts and research results from these theoretical approaches are summarized in two hypotheses (chapter 2.3). The hypotheses are analysed with two cases (chapter 3). After the two case analyses, the ABC part is extended to cover alsoother modern cost accounting methods, e.g. process costing and feature costing (chapter 4.1). The ideas from this second theoretical part are operationalized with the third case (chapter 4.2). The knowledge from the theory and three cases is summarized in the created framework (chapter 4.3). With the created frameworkit is possible to analyse ABC and its modifications in the engineering design context. The framework collects the factors that guide the choice of the costing method to be used in engineering design. It also illuminates the contents of various ABC-related costing methods. However, the framework needs to be further tested. On the basis of the three cases it can be said that ABC should be used cautiously when formulating cost information for engineering design. It is suitable when the manufacturing can be considered simple, or when the design engineers are not cost conscious, and in the beginning of the design process when doing adaptive or variant design. If the design engineers need cost information for the embodiment or detailed design, or if manufacturing can be considered complex, or when design engineers are cost conscious, the ABC has to be always evaluated critically.