Biosynthesis of Yersinia enterocolitica serotype O:3 lipopolysaccharide outer core

Lipopolysacharide (LPS) present on the outer leaflet of Gram-negative bacteria is important for the adaptation of the bacteria to the environment. Structurally, LPS can be divided into three parts: lipid A, core and O-polysaccharide (OPS). OPS is the outermost and also the most diverse moiety. When OPS is composed of identical sugar residues it is called homopolymeric and when it is composed of repeating units of oligosaccharides it is called heteropolymeric. Bacteria synthesize LPS at the inner membrane via two separate pathways, Lipid A-core via one and OPS via the other. These are ligated together in the periplasmic space and the completed LPS molecule is translocated to the surface of the bacteria. The genes directing the OPS biosynthesis are often clustered and the clusters directing the biosynthesis of heteropolymeric OPS often contain genes for i) the biosynthesis of required NDP-sugar precursors, ii) glycosyltransferases needed to build up the repeating unit, iii) translocation of the completed O-unit to the periplasmic side of the inner membrane (flippase) and iv) polymerization of the repeating units to complete OPS. The aim of this thesis was to characterize the biosynthesis of the outer core (OC) of Yersinia enterocolitica serotype O:3 (YeO3). Y. enterocolitica is a member of the Gram-negative Yersinia genus and it causes diarrhea followed sometimes by reactive arthritis. The chemical structure of the OC and the nucleotide sequence of the gene cluster directing its biosynthesis were already known; however, no experimental evidence had been provided for the predicted functions of the gene products. The hypothesis was that the OC biosynthesis would follow the pathway described for heteropolymeric OPS, i.e. a Wzy-dependent pathway. In this work the biochemical activities of two enzymes involved in the NDP-sugar biosynthesis was established. Gne was determined to be a UDP-N-acetylglucosamine-4-epimerase catalyzing the conversion of UDP-GlcNAc to UDP-GalNAc and WbcP was shown to be a UDP-GlcNAc- 4,6-dehydratase catalyzing the reaction that converts UDP-GlcNAc to a rare UDP-2-acetamido- 2,6-dideoxy-d-xylo-hex-4-ulopyranose (UDP-Sugp). In this work, the linkage specificities and the order in which the different glycosyltransferases build up the OC onto the lipid carrier were also investigated. In addition, by using a site-directed mutagenesis approach the catalytically important amino acids of Gne and two of the characterized glycosyltranferases were identified. Also evidence to show the enzymes involved in the ligations of OC and OPS to the lipid A inner core was provided. The importance of the OC to the physiology of Y. enterocolitica O:3 was defined by determining the minimum requirements for the OC to be recognized by a bacteriophage, bacteriocin and monoclonal antibody. The biological importance of the rare keto sugar (Sugp) was also shown. As a conclusion this work provides an extensive overview of the biosynthesis of YeO3 OC as it provides a substantial amount of information of the stepwise and coordinated synthesis of the Ye O:3 OC hexasaccharide and detailed information of its properties as a receptor.

Determination of the critical activities of a public-private intermediary organization with the help of value chain analysis

Tämän diplomityön tavoitteena oli selvittää arvoketjuanalyysin avulla toiminnot, joilla voittoatavoittelemattoman, julkisen osakeyhtiön toimintaa voitaisiin kuvata. Tarkoituksena oli selvittää mainitut toiminnot yleisesti ja luoda malli kohdeyrityksen arvoketjusta ja sen toiminnoista. Tutkielma jakautuu teoreettiseen ja empiiriseen osaan. Ensimmäinen pohjautuu aikaisempaan tutkimukseen ja kirjallisuuteen sidosryhmistä, arvon muodostumisesta ja arvoketjuanalyysistä. Jälkimmäinen on laadullista tapaustutkimusta. Empiriassa mallinnettiin Lappeenranta Innovation Oy:nsisäisiä toimintoja ja sidosryhmien odotuksia. Empiirinen tutkimus perustui kohdeyrityksen omistajille ja henkilöstölle tehtyihin haastatteluihin sekä yrityksen toiminnan päivittäiseen seurantaan. Johtopäätöksenätodettiin, että julkisen, voittoa tavoittelemattoman yrityksen toiminnot on mahdollista kuvata arvoketjuanalyysin avulla. Alan ja yrityksen asettamat erityispiirteet toivat haasteita määrittelylle, mutta silti arvoketju antoi selkeän tavan kohdeyrityksen toimintojen mallintamiselle.

Biochemical treatment of brown grade rejects in recycling process

Ruskeisiin kierrätysmassoihin kuuluu kulutuksen kannalta tärkeimpänä laatuna OCC (old corrugated containers). OCC sisältää noin 70-100% aaltopahvia eli pääasiassa se koostuu valkaisemattomasta kemiallisesta massasta. OCC uusiomassan ensisijainen käyttökohde on aaltopahvin valmistus. OCC:n kierrätyskuituprosessissa syntyy merkittäviä määriä rejektiä. Rejektin määrä riippuu paljolti kierrätettävän materiaalin laadusta ja puhtaudesta, mutta myös tulevan massan käyttötarkoituksesta sekä prosessiolosuhteista. OCC-prosessissa rejektoituvan aineksen määrä voi nousta korkeaksi, mikäli kierrätettävä materiaali sisältää märkälujaliimoja tai muuten raskaasti liimattuja komponentteja sekä runsaasti kontaminantteja, kuten muoveja, teippejä ja metalleja. Keskimäärin OCC-rejekti sisältää 30-60% kiinteää ainesta, 30-90% (kuivapaino) kuituja, 5-70% (kuivapaino) muoveja ja 1-10% (kuivapaino) tuhkaa. Syntynyt rejekti voidaan polttaa energiaksi tai käyttää maantäyttöaineena. Harvinaisempia sovelluksia rejektin käsittelyssä ovat rejektin kuitujen talteenotto uudelleenprosessointia varten tai alkoholin ja levuliinihapon tuottamiseen. Rejektin asianmukaisella käsittelyllä voidaan vähentää kaatopaikkakustannuksia, sekä parantaa kierrätysprosessin tuottavuutta. Tämän työn tarkoituksena oli tutkia biokemiallisen käsittelyn mahdollisuudet OCC-rejektin hajotuksessa. Alustavissa laboratoriomittakaavan kokeissa etsittiin sopiva käsittelytapa, joka toteutettiin sitten pilot plant -mittakaavassa. Tulokset osoittavat, että biokemiallisen käsittelyn avulla rejekti voidaan hajottaa jolloin jätteenkäsittelykustannukset pienenevät ja kierrätyskuituprosessin taloudellisuus paranee.

Challenges and Means for the Front End Activities of Software Development

The front end of innovation is regarded as one of the most important steps in building new software products or services, and the most significant benefits in software development can be achieved through improvements in the front end activities. Problems in the front end phase have an impact on customer dissatisfaction with delivered software, and on the effectiveness of the entire software development process. When these processes are improved, the likelihood of delivering high quality software and business success increases. This thesis highlights the challenges and problems related to the early phases of software development, and provides new methods and tools for improving performance in the front end activities of software development. The theoretical framework of this study comprises two fields of research. The first section belongs to the field of innovation management, and especially to the management of the early phases of the innovation process, i.e. the front end of innovation. The second section of the framework is closely linked to the processes of software engineering, especially to the early phases of the software development process, i.e. the practice of requirements engineering. Thus, this study extends the theoretical knowledge and discloses the differences and similarities in these two fields of research. In addition, this study opens up a new strand for academic discussion by connecting these research directions. Several qualitative business research methodologies have been utilized in the individual publications to solve the research questions. The theoretical and managerial contribution of the study can be divided into three areas: 1) processes and concepts, 2) challenges and development needs, and 3) means and methods for the front end activities of software development. First, the study discloses the difference and similarities between the concepts of the front end of innovation and requirements engineering, and proposes a new framework for managing the front end of the software innovation process, bringing business and innovation perspectives into software development. Furthermore, the study discloses managerial perceptions of the similarities and differences in the concept of the front end of innovation between the software industry and the traditional industrial sector. Second, the study highlights the challenges and development needs in the front end phase of software development, especially challenges in communication, such as linguistic problems, ineffective communication channels, a communication gap between users/customers and software developers, and participation of multiple persons in software development. Third, the study proposes new group methods for improving the front end activities of software development, especially customer need assessment, and the elicitation of software requirements.

Biochemical Modification of Thermomechanical Pulp Fibers

The first objective of this study was to find out reliable laboratory methods to predict the effect of enzymes on specific energy consumption and fiber properties of TMP pulp. The second one was to find with interactive software called “Knowledge discovery in databases” enzymes or other additives that can be used in finding a solution to reduce energy consumption of TMP pulp. The chemical composition of wood and enzymes, which have activity on main wood components were presented in the literature part of the work. The results of previous research in energy reduction of TMP process with enzymes were also highlighted. The main principles of knowledge discovery have been included in literature part too. The experimental part of the work contains the methods description in which the standard size chip, crushed chip and fiberized spruce chip (fiberized pulp) were used. Different types of enzymatic treatment with different dosages and time were tested during the experiments and showed. Pectinase, endoglucanase and mixture of enzymes were used for evaluation of method reliability. The fines content and fiber length of pulp was measured and used as evidence of enzymes' effect. The refining method with “Bauer” laboratory disc refiner was evaluated as not highly reliable. It was not able to provide high repeatability of results, because of uncontrolled feeding capacity and refining consistency. The refining method with Valley refiner did not have a lot of variables and showed stable and repeatable results in energy saving. The results of experiments showed that efficient enzymes impregnation is probably the main target with enzymes application for energy saving. During the work the fiberized pulp showed high accessibility to enzymatic treatment and liquid penetration without special impregnating equipment. The reason was that fiberized pulp has larger wood surface area and thereby the contact area between the enzymatic solution and wood is also larger. Standard size chip and crushed chip treatment without special impregnator of enzymatic solution was evaluated as not efficient and did not show visible, repeatable results in energy consumption decrease. Thereby it was concluded that using of fiberized pulp and Valley refiner for measurements of enzymes' effectiveness in SEC decrease is more suitable than normal size chip and crushed chip with “Bauer” refiner. Endoglucanase with 5 kg/t dosage showed about 20% energy consumption decrease. Mixture of enzymes with 1.5 kg/t dosage showed about 15% decrease of energy consumption during the refining. Pectinase at different dosages and treatment times did not show significant effect on energy consumption. Results of knowledge discovery in databases showed the xylanase, cellulase and pectinase blend as most promising for energy reduction in TMP process. Surfactants were determined as effective additives for energy saving with enzymes.

Assessment of endocrine disrupting activities in the aquatic environment

Hormonstörande ämnen är syntetiska eller naturliga ämnen som stör organismers hormonsystem och bidrar till könsförvirring och sterilitet. Sådana ämnen kommer i ökande takt ut i vattenmiljön genom rester av läkemedel, bekämpningsmedel och industriprodukter. Eftersom det finns många likheter mellan hormonsystemen hos människan och övriga ryggradsdjur kan till exempel fiskar användas som modellsystem för att underöka detta problem. I tidigare undersökningar har man funnit hormonella störningar, bl.a. feminisering och maskulinisering hos fiskar som utsatts för avfallsvatten från kommunala reningsverk eller avfallsvatten från pappersindustrin. Målet med denna avhandling var att undersöka om renat avfallsvatten från kommunala reningsverk längs Finlands kust innehåller hormonstörande ämnen i sådana mängder att de kan försorsaka hormonstörande effekter på fisk. Målet i denna avhandling var också att utveckla cellulära testsystem baserade på fiskceller, eftersom behovet av tillförlitliga och kostnadseffektiva cellbaserade tester för att underlätta riskbedömningen av hormonstörande ämnen är mycket stort för tillfället. Som testsystem har storspiggen använts, som besitter flera användbara biomarkörer för att mäta hormonstörande ämnens påverkan. Resultaten tyder på att problemen med hormonstörande påverkan på fisk inte är lika utbredda i Finland som i många andra europeiska länder. Detta beror troligtvis på att finska reningsverk har effektiva reningstekniker som reducerar mängden hormonstörande ämnen, eller på att utspädningen av avloppen i recipienterna är större än i många andra länder. Dock kan problemen inte helt uteslutas eftersom vissa feminiserande (estrogena) effekter kunde observeras hos fisken i de undersökta recipienterna utanför kommunala reningsverk. I kontrollerade laboratorieförsök där storpsiggar exponerades för kommunalt avloppsvatten uppmättes även här effekter som tyder på förekomst av estrogener i avloppsvattnet. De cell-baserade testsystemen klarade av att förutspå hormonella effekter hos hel fisk och kan därför vara mycket användbara i fortsatta studier av hormonstörande ämnens verkningsmekanismer i preliminära toxicitetsbedömningar.

Thinking Outside the Box: Enhancing Science Teaching by Combining (Instead of Contrasting) Laboratory and Simulation Activities

The focus of the present work was on 10- to 12-year-old elementary school students’ conceptual learning outcomes in science in two specific inquiry-learning environments, laboratory and simulation. The main aim was to examine if it would be more beneficial to combine than contrast simulation and laboratory activities in science teaching. It was argued that the status quo where laboratories and simulations are seen as alternative or competing methods in science teaching is hardly an optimal solution to promote students’ learning and understanding in various science domains. It was hypothesized that it would make more sense and be more productive to combine laboratories and simulations. Several explanations and examples were provided to back up the hypothesis. In order to test whether learning with the combination of laboratory and simulation activities can result in better conceptual understanding in science than learning with laboratory or simulation activities alone, two experiments were conducted in the domain of electricity. In these experiments students constructed and studied electrical circuits in three different learning environments: laboratory (real circuits), simulation (virtual circuits), and simulation-laboratory combination (real and virtual circuits were used simultaneously). In order to measure and compare how these environments affected students’ conceptual understanding of circuits, a subject knowledge assessment questionnaire was administered before and after the experimentation. The results of the experiments were presented in four empirical studies. Three of the studies focused on learning outcomes between the conditions and one on learning processes. Study I analyzed learning outcomes from experiment I. The aim of the study was to investigate if it would be more beneficial to combine simulation and laboratory activities than to use them separately in teaching the concepts of simple electricity. Matched-trios were created based on the pre-test results of 66 elementary school students and divided randomly into a laboratory (real circuits), simulation (virtual circuits) and simulation-laboratory combination (real and virtual circuits simultaneously) conditions. In each condition students had 90 minutes to construct and study various circuits. The results showed that studying electrical circuits in the simulation–laboratory combination environment improved students’ conceptual understanding more than studying circuits in simulation and laboratory environments alone. Although there were no statistical differences between simulation and laboratory environments, the learning effect was more pronounced in the simulation condition where the students made clear progress during the intervention, whereas in the laboratory condition students’ conceptual understanding remained at an elementary level after the intervention. Study II analyzed learning outcomes from experiment II. The aim of the study was to investigate if and how learning outcomes in simulation and simulation-laboratory combination environments are mediated by implicit (only procedural guidance) and explicit (more structure and guidance for the discovery process) instruction in the context of simple DC circuits. Matched-quartets were created based on the pre-test results of 50 elementary school students and divided randomly into a simulation implicit (SI), simulation explicit (SE), combination implicit (CI) and combination explicit (CE) conditions. The results showed that when the students were working with the simulation alone, they were able to gain significantly greater amount of subject knowledge when they received metacognitive support (explicit instruction; SE) for the discovery process than when they received only procedural guidance (implicit instruction: SI). However, this additional scaffolding was not enough to reach the level of the students in the combination environment (CI and CE). A surprising finding in Study II was that instructional support had a different effect in the combination environment than in the simulation environment. In the combination environment explicit instruction (CE) did not seem to elicit much additional gain for students’ understanding of electric circuits compared to implicit instruction (CI). Instead, explicit instruction slowed down the inquiry process substantially in the combination environment. Study III analyzed from video data learning processes of those 50 students that participated in experiment II (cf. Study II above). The focus was on three specific learning processes: cognitive conflicts, self-explanations, and analogical encodings. The aim of the study was to find out possible explanations for the success of the combination condition in Experiments I and II. The video data provided clear evidence about the benefits of studying with the real and virtual circuits simultaneously (the combination conditions). Mostly the representations complemented each other, that is, one representation helped students to interpret and understand the outcomes they received from the other representation. However, there were also instances in which analogical encoding took place, that is, situations in which the slightly discrepant results between the representations ‘forced’ students to focus on those features that could be generalised across the two representations. No statistical differences were found in the amount of experienced cognitive conflicts and self-explanations between simulation and combination conditions, though in self-explanations there was a nascent trend in favour of the combination. There was also a clear tendency suggesting that explicit guidance increased the amount of self-explanations. Overall, the amount of cognitive conflicts and self-explanations was very low. The aim of the Study IV was twofold: the main aim was to provide an aggregated overview of the learning outcomes of experiments I and II; the secondary aim was to explore the relationship between the learning environments and students’ prior domain knowledge (low and high) in the experiments. Aggregated results of experiments I & II showed that on average, 91% of the students in the combination environment scored above the average of the laboratory environment, and 76% of them scored also above the average of the simulation environment. Seventy percent of the students in the simulation environment scored above the average of the laboratory environment. The results further showed that overall students seemed to benefit from combining simulations and laboratories regardless of their level of prior knowledge, that is, students with either low or high prior knowledge who studied circuits in the combination environment outperformed their counterparts who studied in the laboratory or simulation environment alone. The effect seemed to be slightly bigger among the students with low prior knowledge. However, more detailed inspection of the results showed that there were considerable differences between the experiments regarding how students with low and high prior knowledge benefitted from the combination: in Experiment I, especially students with low prior knowledge benefitted from the combination as compared to those students that used only the simulation, whereas in Experiment II, only students with high prior knowledge seemed to benefit from the combination relative to the simulation group. Regarding the differences between simulation and laboratory groups, the benefits of using a simulation seemed to be slightly higher among students with high prior knowledge. The results of the four empirical studies support the hypothesis concerning the benefits of using simulation along with laboratory activities to promote students’ conceptual understanding of electricity. It can be concluded that when teaching students about electricity, the students can gain better understanding when they have an opportunity to use the simulation and the real circuits in parallel than if they have only the real circuits or only a computer simulation available, even when the use of the simulation is supported with the explicit instruction. The outcomes of the empirical studies can be considered as the first unambiguous evidence on the (additional) benefits of combining laboratory and simulation activities in science education as compared to learning with laboratories and simulations alone.

Proactive and Preventive Student Welfare Activities in Finnish Preschool and Elementary School: Handling of Transition to Formal Schooling and a National Anti-Bullying Program as Examples

Prerequisites and effects of proactive and preventive psycho-social student welfare activities in Finnish preschool and elementary school were of interest in the present thesis. So far, Finnish student welfare work has mainly focused on interventions and individuals, and the voluminous possibilities to enhance well-being of all students as a part of everyday school work have not been fully exploited. Consequently, in this thesis three goals were set: (1) To present concrete examples of proactive and preventive psycho-social student welfare activities in Finnish basic education; (2) To investigate measurable positive effects of proactive and preventive activities; and (3) To investigate implementation of proactive and preventive activities in ecological contexts. Two prominent phenomena in preschool and elementary school years—transition to formal schooling and school bullying—were chosen as examples of critical situations that are appropriate targets for proactive and preventive psycho-social student welfare activities. Until lately, the procedures concerning both school transitions and school bullying have been rather problem-focused and reactive in nature. Theoretically, we lean on the bioecological model of development by Bronfenbrenner and Morris with concentric micro-, meso-, exo- and macrosystems. Data were drawn from two large-scale research projects, the longitudinal First Steps Study: Interactive Learning in the Child–Parent– Teacher Triangle, and the Evaluation Study of the National Antibullying Program KiVa. In Study I, we found that the academic skills of children from preschool–elementary school pairs that implemented several supportive activities during the preschool year developed more quickly from preschool to Grade 1 compared with the skills of children from pairs that used fewer practices. In Study II, we focused on possible effects of proactive and preventive actions on teachers and found that participation in the KiVa antibullying program influenced teachers‘ self-evaluated competence to tackle bullying. In Studies III and IV, we investigated factors that affect implementation rate of these proactive and preventive actions. In Study III, we found that principal‘s commitment and support for antibullying work has a clear-cut positive effect on implementation adherence of student lessons of the KiVa antibullying program. The more teachers experience support for and commitment to anti-bullying work from their principal, the more they report having covered KiVa student lessons and topics. In Study IV, we wanted to find out why some schools implement several useful and inexpensive transition practices, whereas other schools use only a few of them. We were interested in broadening the scope and looking at local-level (exosystem) qualities, and, in fact, the local-level activities and guidelines, along with teacherreported importance of the transition practices, were the only factors significantly associated with the implementation rate of transition practices between elementary schools and partner preschools. Teacher- and school-level factors available in this study turned out to be mostly not significant. To summarize, the results confirm that school-based promotion and prevention activities may have beneficial effects not only on students but also on teachers. Second, various top-down processes, such as engagement at the level of elementary school principals or local administration may enhance implementation of these beneficial activities. The main message is that when aiming to support the lives of children the primary focus should be on adults. In future, promotion of psychosocial well-being and the intrinsic value of inter- and intrapersonal skills need to be strengthened in the Finnish educational systems. Future research efforts in student welfare and school psychology, as well as focused training for psychologists in educational contexts, should be encouraged in the departments of psychology and education in Finnish universities. Moreover, a specific research centre for school health and well-being should be established.

Reflexive model of research-based theatre – processing innovation at the crossroads of theatre, reflection and practice-based innovation activities

Contemporary organisations have to embrace the notion of doing ‘more with less’. This challenges knowledge production within companies and public organisations, forcing them to reorganise their structures and rethink what knowledge production actually means in the context of innovation and how knowledge is actually produced among various professional groups within the organisation in their everyday actions. Innovations are vital for organisational survival, and ‘ordinary’ employees and customers are central but too-often ignored producers of knowledge for contemporary organisations. Broader levels of participation and reflexive practices are needed. This dissertation discusses the missing links between innovation research conducted in the context of industrial management, arts, and culture; applied drama and theatre practices (specifically post-Boalian approaches); and learning – especially organising reflection – in organisational settings. This dissertation (1) explores and extends the role of research-based theatre to organising reflection and reflexive practices in the context of practice-based innovation, (2) develops a reflexive model of RBT for investigating and developing practice-based organisational process innovations in order to contribute to the development of a tool for innovation management and analysis, and (3) operationalises this model within private- and publicsector organisations. The proposed novel reflexive model of research-based theatre for investigating and developing practice-based organisational process innovations extends existing methods and offers a different way of organising reflection and reflexive practices in the context of general innovation management. The model was developed through five participatory action research processes conducted in four different organisations. The results provide learning steps – a reflection path – for understanding complex organisational life, people, and relations amid renewal and change actions. The proposed model provides a new approach to organising and cultivating reflexivity in practice-based innovation activities via research-based theatre. The results can be utilised as a guideline when processing practice-based innovation within private or public organisations. The model helps innovation managers to construct, together with their employees, temporary communities where they can learn together through reflecting on their own and each others’ experiences and to break down assumptions related to their own perspectives. The results include recommendations for practical development steps applicable in various organisations with regard to (i) application of research-based theatre and (ii) related general innovation management. The dissertation thus contributes to the development of novel learning approaches in knowledge production. Keywords: practice-based innovation, research-based theatre, learning, reflection, mode 2b knowledge production