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  • Virtanen, Pirjo Kristiina (Helsingin yliopisto, 2007)
    This thesis discusses the contemporary construction of the lived worlds of indigenous Amazonian youths. Today’s native peoples are considerably affected by the processes of globalization and urbanization, which have led to new ways of relating to their cultural traditions. This work presents a case study of Manchineri youngsters aged between 14 and 24 years old living in Acre state in Brazilian Amazonia. The Arawak-speaking Manchineri number some 1,000 people; their legally demarcated reserve is situated next to the River Yaco. The research is based on ethnographic material collected in the Mamoadate reserve and in the state capital, Rio Branco. By comparing the youth in different physical and social environments (the reserve and the city), my attempt has been to search for the most typical elements maintained, altered and created in the current lived worlds of Manchineri youths. Fieldwork methods included interviews, participant observation, photographs, video recordings, and drawings. The material was analyzed within the multidisciplinary framework of the social and cultural construction of knowledge. The study applies the concepts of social field, symbolic capital, and habitus as they have been used by Pierre Bourdieu; perspective as developed recently in Amazonian ethnology; the sacred as a cultural category as understood in the study of religion; and individual and person as concepts central to anthropology and sociology. Additionally, the study can be contextualized within youth studies, Latin American studies, and urban studies. The results of the study show that the everyday lives of young Amazonian native people are formed by a complex mixture of ‘modernity’ and ‘tradition’, fragmentation, and transitions between different conceptual frameworks. Part II discusses the ethnographic material in depth and shows that indigenous adolescents act from a variety of social perspectives: the native youth’s own ethnic group, divided into sub-groups, especially into urban residents and those living in the reserve; ancestors, super-human agents and spirits; other indigenous groups and non-natives. Consequently, besides the traditional initiation ritual, we find various contemporary rites of passage to adulthood: state-education, learning traditional practices, shamanism, matrimony, and transitions between the reserve and urban areas. According to these results, new social roles, political organization, responsibilities, and in general the desire to be respected, require both ‘modern’ and ‘traditional’ abilities. In Part III, the study shows that the current power relations constituted by new social contacts, ethnic recognition, and cooperation with different institutions have resulted in the formation of new social fields: youth cultures, the ethnic group, shamanic practices, the ethnopolitical movement, and indigenous students. The capacity of young Amazonian Indians to act in contemporary social fields produces them as full persons. The study also argues that the elements of the lived worlds can be divided into these social fields. When focusing on these fields, it became evident that these comprise the strategies adopted by young Indians to break through social and cultural barriers.
  • Aaltonen, Suvi (2006)
    Tämän työn aiheena on organisaation identiteetti ja mahdollisuus sen muutokseen muuttamalla organisaation nimeä. Tarkoitus on, eri tulkintojen kautta, tutkia mikä organisaation identiteetti on ja mitä se merkitsee organisaatiolle. Tätä selvennetään myöhemmin tapaustutkimuksella Varma-Sammon nimenmuutoksesta Eläkevakuutusyhtiö Varmaksi. Teoreettinen viitekehys on organisaatioista tehty tutkimus, joka selvittää miten identiteetti muodostuu ja vaikuttaa organisaatioon. Lisäksi tutkimus selvittää miten organisaation identiteettiä voidaan johtaa, sekä muutosviestinnän ja muutosjohtamisen tärkeyttä muutoksien aikana. Tutkimus jakautuu teoreettiseen ja empiriseen osaan. Teoreettinen osuus tarkastelee eri tutkijoiden näkemyksiä organisaation identiteettiin ja empiriinen osuus keskittyy tapaustutkimukseen yrityksen nimenmuutoksesta. Tutkimusmetodit ovat tietysti relevantti kirjallisuustutkimus, tutkimus Varman sisäisestä ilmapiiristä, kyselyt henkilökunnalle Varman Intranetissä sekä teemahaastattelut (strukturoimattomat). Tärkeimmät johtopäätökset liittyvät organisaation identiteetin joustavaan ja muuttuvaan luonteeseen, sekä muutosviestinnän tärkeään rooliin muutosten toteuttamisessa. Organisaation identiteetti muodostuu mm. imagosta, historiasta, organisaation tehtävästä ja luonteesta, joten se on altis muutoksille. Tutkimuksesta on myös pääteltävissä kuinka yrityksen nimenmuutoksen on mahdollista vaikuttaa ja vaikuttaakin organisaation identiteettiin. Empiirinen osuus osoittaa mitä johtajisto ja henkilökunta ajattelevat nimenmuutoksesta ja sen suhteesta yritykseen. Tärkeimmät lähteet ovat: Albert, S. & Whetten, D.A. (1985) 'Organizational Identity' in Cummings, L.L. & Staw, B.M. eds., Research in Organizational Behavior; An Annual Series of Analytical Essays and Critical Reviews, vol. 7 (1985), Jai Press, UK Balmer, J.M.T. & Greyser, S.A. (2003) Revealing the corporation, Routledge, UK Ind, N. (1992) The Corporate Image: Strategies for effective identity programmes, revised edition, Kogan Page, UK Markkanen, T.-R. (1999) Yrityksen identiteetin Johtaminen, WSOY, Finland
  • Aaltonen, Suvi (2006)
    The object of this study is organisational identity and the possibilities of changing it through changing the organisation's name. The purpose is, through different interpretations, to examine what organizational identity is and what it means to an organisation. This is farther examined in the case study of Varma-Sampo's name change to Mutual Pension Insurance Company Varma. Theoretical frame work is studies made of organisations, which examine how identity is formed and what is its impact on the organisation. The work examines how organisational identity can be influenced or managed, and the importance of change communication and change management within a company in times of change. The study is divided to theoretical and empirical sections. Theoretical part examines different researchers' views on organisational identity and the empirical part concentrates on case study on the name change of Mutual Pension Company Varma. Methods used are of course general literary study, examination of Varma's study of internal atmosphere, Intranet questionnaires to the personnel and theme (unformatted) interviews. The most important conclusions refer to the flexible and changeable nature of organisational identity and to the importance of change communication to a successful execution of organisational change. Organisational identity is formed by for example image, history, organisations mission and nature. Thus it is highly susceptible to change. The work also concludes that changing a company's name can and probably does have an influence on the organisational identity. The empirical part demonstrates how management and personnel view name change and its relationship with the company. Most significant sources are: Albert, S. & Whetten, D.A. (1985) 'Organizational Identity' in Cummings, L.L. & Staw, B.M. eds., Research in Organizational Behavior; An Annual Series of Analytical Essays and Critical Reviews, vol. 7 (1985), Jai Press, UK Balmer, J.M.T. & Greyser, S.A. (2003) Revealing the corporation, Routledge, UK Ind, N. (1992) The Corporate Image: Strategies for effective identity programmes, revised edition, Kogan Page, UK Markkanen, T.-R. (1999) Yrityksen identiteetin Johtaminen, WSOY, Finland
  • Tanska, Juha (2011)
    The subject and methodology of biblical scholarship has expanded immense-ly during the last few decades. The traditional text-, literary-, source- and form-critical approaches, labeled historical-critical scholarship , have faced the challenge of social sciences. Various new literary, synchronic readings, sometimes characterized with the vague term postmodernism, have in turn challenged historicalcritical, and social-scientific approaches. Widened limits and diverging methodologies have caused a sense of crisis in biblical criticism. This metatheoretical thesis attempts to bridge the gap between philosophical discussion about the basis of biblical criticism and practical academic biblical scholarship. The study attempts to trace those epistemological changes that have produced the wealth of methods and results within biblical criticism. The account of the cult reform of King Josiah of Judah as reported in 2 Kings 22:1 23:30 serves as the case study because of its importance for critical study of the Hebrew Bible. Various scholarly approaches embracing 2 Kings 22:1 23:30 are experimentally arranged around four methodological positions: text, author, reader, and context. The heuristic model is a tentative application of Oliver Jahraus s model of four paradigms in literary theory. The study argues for six theses: 1) Our knowledge of the world is con-structed, fallible and theory-laden. 2) Methodological plurality is the neces-sary result of changes in epistemology and culture in general. 3) Oliver Jahraus s four methodological positions in regard to literature are also an applicable model within biblical criticism to comprehend the methodological plurality embracing the study of the Hebrew Bible. 4) Underlying the methodological discourse embracing biblical criticism is the epistemological ten-sion between the natural sciences and the humanities. 5) Biblical scholars should reconsider and analyze in detail concepts such as author and editor to overcome the dichotomy between the Göttingen and Cross schools. 6) To say something about the historicity of 2 Kings 22:1 23:30 one must bring together disparate elements from various disciplines and, finally, admit that though it may be possible to draw some permanent results, our conclusions often remain provisional.
  • Kapanen, Heini (2002)
    The research goal was to find out how regional needs result in projects funded by the structural fund. The scope was in Finland’s Objective 2 programs and the projects based on them in 1995-1999. Objective 2 areas are regions affected by industrial decline. In 1995-1999 there were Objective 2 programs in eight regions in Finland. The research analysed Objective 2 programs, regional development programs, project lists from Fimos database, TEKES and Ministry of Trade, and evaluation reports of the Objective programs. The persons responsible for Objective 2 programs answered a questionnaire about the groundwork for program process, the regional emphasis and the participation of citizens in the program preparation work. Two implemented projects (Hamina bastion and Lahti harbour) were studied by interviewing actors related to the project financing. Hoppe´s (1993) model was used when anaysing the interviews. The needs end up as financed projects by a combined effect of two processes: Needs affect strategy programs and the project selection criteria. Needs also arouse applications to finance projects. A project is financed if there is a match between the objectives of the strategy program, the needs of the project owner, and the criteria valued by the financing authority. This is especially influenced by the ability of the regional strategy program to reflect true regional needs. The nature of the strategy formation process affects the strategy that in turn guides the project funding through the project selection criteria. It was essential how the decision-making authorities interpreted the implementation of programs and EU principles in their own region. The Objective Programs might have implemented sectoral objectives of the ministries rather than regional needs. Getting the regional needs on the agenda depends on the national competence in the program work. Proceeding with a projects demands interest consolidation between the EU objectives, the national goals of the regional policy, and the regional needs, both vertically trough these levels and horizontally within them. The success of the case projects to get EU funding was a result of a practical model where local, regional needs where combined with central government's targets.
  • Hoppu, Pekka (Helsingin yliopisto, 2008)
    The number of drug substances in formulation development in the pharmaceutical industry is increasing. Some of these are amorphous drugs and have glass transition below ambient temperature, and thus they are usually difficult to formulate and handle. One reason for this is the reduced viscosity, related to the stickiness of the drug, that makes them complicated to handle in unit operations. Thus, the aim in this thesis was to develop a new processing method for a sticky amorphous model material. Furthermore, model materials were characterised before and after formulation, using several characterisation methods, to understand more precisely the prerequisites for physical stability of amorphous state against crystallisation. The model materials used were monoclinic paracetamol and citric acid anhydrate. Amorphous materials were prepared by melt quenching or by ethanol evaporation methods. The melt blends were found to have slightly higher viscosity than the ethanol evaporated materials. However, melt produced materials crystallised more easily upon consecutive shearing than ethanol evaporated materials. The only material that did not crystallise during shearing was a 50/50 (w/w, %) blend regardless of the preparation method and it was physically stable at least two years in dry conditions. Shearing at varying temperatures was established to measure the physical stability of amorphous materials in processing and storage conditions. The actual physical stability of the blends was better than the pure amorphous materials at ambient temperature. Molecular mobility was not related to the physical stability of the amorphous blends, observed as crystallisation. Molecular mobility of the 50/50 blend derived from a spectral linewidth as a function of temperature using solid state NMR correlated better with the molecular mobility derived from a rheometer than that of differential scanning calorimetry data. Based on the results obtained, the effect of molecular interactions, thermodynamic driving force and miscibility of the blends are discussed as the key factors to stabilise the blends. The stickiness was found to be affected glass transition and viscosity. Ultrasound extrusion and cutting were successfully tested to increase the processability of sticky material. Furthermore, it was found to be possible to process the physically stable 50/50 blend in a supercooled liquid state instead of a glassy state. The method was not found to accelerate the crystallisation. This may open up new possibilities to process amorphous materials that are otherwise impossible to manufacture into solid dosage forms.
  • Niemi, Jarkko (Helsingin yliopisto, 2007)
    Aerosol particles can cause detrimental environmental and health effects. The particles and their precursor gases are emitted from various anthropogenic and natural sources. It is important to know the origin and properties of aerosols to efficiently reduce their harmful effects. The diameter of aerosol particles (Dp) varies between ~0.001 and ~100 μm. Fine particles (PM2.5: Dp < 2.5 μm) are especially interesting because they are the most harmful and can be transported over long distances. The aim of this thesis is to study the impact on air quality by pollution episodes of long-range transported aerosols affecting the composition of the boundary-layer atmosphere in remote and relatively unpolluted regions of the world. The sources and physicochemical properties of aerosols were investigated in detail, based on various measurements (1) in southern Finland during selected long-range transport (LRT) pollution episodes and unpolluted periods and (2) over the Atlantic Ocean between Europe and Antarctica during a voyage. Furthermore, the frequency of LRT pollution episodes of fine particles in southern Finland was investigated over a period of 8 years, using long-term air quality monitoring data. In southern Finland, the annual mean PM2.5 mass concentrations were low but LRT caused high peaks of daily mean concentrations every year. At an urban background site in Helsinki, the updated WHO guideline value (24-h PM2.5 mean 25 μg/m3) was exceeded during 1-7 LRT episodes each year during 1999-2006. The daily mean concentrations varied between 25 and 49 μg/m3 during the episodes, which was 3-6 times higher than the mean concentration in the long term. The in-depth studies of selected LRT episodes in southern Finland revealed that biomass burning in agricultural fields and wildfires, occurring mainly in Eastern Europe, deteriorated air quality on a continental scale. The strongest LRT episodes of fine particles resulted from open biomass-burning fires but the emissions from other anthropogenic sources in Eastern Europe also caused significant LRT episodes. Particle mass and number concentrations increased strongly in the accumulation mode (Dp ~ 0.09-1 μm) during the LRT episodes. However, the concentrations of smaller particles (Dp < 0.09 μm) remained low or even decreased due to the uptake of vapours and molecular clusters by LRT particles. The chemical analysis of individual particles showed that the proportions of several anthropogenic particle types increased (e.g. tar balls, metal oxides/hydroxides, spherical silicate fly ash particles and various calcium-rich particles) in southern Finland during an LRT episode, when aerosols originated from the polluted regions of Eastern Europe and some open biomass-burning smoke was also brought in by LRT. During unpolluted periods when air masses arrived from the north, the proportions of marine aerosols increased. In unpolluted rural regions of southern Finland, both accumulation mode particles and small-sized (Dp ~ 1-3 μm) coarse mode particles originated mostly from LRT. However, the composition of particles was totally different in these size fractions. In both size fractions, strong internal mixing of chemical components was typical for LRT particles. Thus, the aging of particles has significant impacts on their chemical, hygroscopic and optical properties, which can largely alter the environmental and health effects of LRT aerosols. Over the Atlantic Ocean, the individual particle composition of small-sized (Dp ~ 1-3 μm) coarse mode particles was affected by continental aerosol plumes to distances of at least 100-1000 km from the coast (e.g. pollutants from industrialized Europe, desert dust from the Sahara and biomass-burning aerosols near the Gulf of Guinea). The rate of chloride depletion from sea-salt particles was high near the coasts of Europe and Africa when air masses arrived from polluted continental regions. Thus, the LRT of continental aerosols had significant impacts on the composition of the marine boundary-layer atmosphere and seawater. In conclusion, integration of the results obtained using different measurement techniques captured the large spatial and temporal variability of aerosols as observed at terrestrial and marine sites, and assisted in establishing the causal link between land-bound emissions, LRT and air quality.
  • Salusjärvi, Tuomas (Helsingin yliopisto, 2006)
    The work covered in this thesis is focused on the development of technology for bioconversion of glucose into D-erythorbic acid (D-EA) and 5-ketogluconic acid (5-KGA). The task was to show on proof-of-concept level the functionality of the enzymatic conversion or one-step bioconversion of glucose to these acids. The feasibility of both studies to be further developed for production processes was also evaluated. The glucose - D-EA bioconversion study was based on the use of a cloned gene encoding a D-EA forming soluble flavoprotein, D-gluconolactone oxidase (GLO). GLO was purified from Penicillium cyaneo-fulvum and partially sequenced. The peptide sequences obtained were used to isolate a cDNA clone encoding the enzyme. The cloned gene (GenBank accession no. AY576053) is homologous to the other known eukaryotic lactone oxidases and also to some putative prokaryotic lactone oxidases. Analysis of the deduced protein sequence of GLO indicated the presence of a typical secretion signal sequence at the N-terminus of the enzyme. No other targeting/anchoring signals were found, suggesting that GLO is the first known lactone oxidase that is secreted rather than targeted to the membranes of the endoplasmic reticulum or mitochondria. Experimental evidence supports this analysis, as near complete secretion of GLO was observed in two different yeast expression systems. Highest expression levels of GLO were obtained using Pichia pastoris as an expression host. Recombinant GLO was characterised and the suitability of purified GLO for the production of D-EA was studied. Immobilised GLO was found to be rapidly inactivated during D-EA production. The feasibility of in vivo glucose - D-EA conversion using a P. pastoris strain co-expressing the genes of GLO and glucose oxidase (GOD, E.C. of A. niger was demonstrated. The glucose - 5-KGA bioconversion study followed a similar strategy to that used in the D-EA production research. The rationale was based on the use of a cloned gene encoding a membrane-bound pyrroloquinoline quinone (PQQ)-dependent gluconate 5-dehydrogenase (GA 5-DH). GA 5-DH was purified to homogeneity from the only source of this enzyme known in literature, Gluconobacter suboxydans, and partially sequenced. Using the amino acid sequence information, the GA 5-DH gene was cloned from a genomic library of G. suboxydans. The cloned gene was sequenced (GenBank accession no. AJ577472) and found to be an operon of two adjacent genes encoding two subunits of GA 5-DH. It turned out that GA 5-DH is a rather close homologue of a sorbitol dehydrogenase from another G. suboxydans strain. It was also found that GA 5-DH has significant polyol dehydrogenase activity. The G. suboxydans GA 5-DH gene was poorly expressed in E. coli. Under optimised conditions maximum expression levels of GA 5-DH did not exceed the levels found in wild-type G. suboxydans. Attempts to increase expression levels resulted in repression of growth and extensive cell lysis. However, the expression levels were sufficient to demonstrate the possibility of bioconversion of glucose and gluconate into 5-KGA using recombinant strains of E. coli. An uncharacterised homologue of GA 5-DH was identified in Xanthomonas campestris using in silico screening. This enzyme encoded by chromosomal locus NP_636946 was found by a sequencing project of X. campestris and named as a hypothetical glucose dehydrogenase. The gene encoding this uncharacterised enzyme was cloned, expressed in E. coli and found to encode a gluconate/polyol dehydrogenase without glucose dehydrogenase activity. Moreover, the X. campestris GA 5-DH gene was expressed in E. coli at nearly 30 times higher levels than the G. suboxydans GA 5-DH gene. Good expressability of the X. campestris GA-5DH gene makes it a valuable tool not only for 5-KGA production in the tartaric acid (TA) bioprocess, but possibly also for other bioprocesses (e.g. oxidation of sorbitol into L-sorbose). In addition to glucose - 5-KGA bioconversion, a preliminary study of the feasibility of enzymatic conversion of 5-KGA into TA was carried out. Here, the efficacy of the first step of a prospective two-step conversion route including a transketolase and a dehydrogenase was confirmed. It was found that transketolase convert 5-KGA into TA semialdehyde. A candidate for the second step was suggested to be succinic dehydrogenase, but this was not tested. The analysis of the two subprojects indicated that bioconversion of glucose to TA using X. campestris GA 5-DH should be prioritised first and the process development efforts in future should be focused on development of more efficient GA 5-DH production strains by screening a more suitable production host and by protein engineering.
  • Chamlagain, Bhawani Shankar (2011)
    Dynamics of raw milk associated bacteria during cold storage of raw milk and their antibiotic resistance was reviewed, with focus on psychrotrophic bacteria. This study aimed to investigate the significance of cold storage of raw milk on antibiotic-resistant bacterial population and analyse the antibiotic resistance of the Gram-negative antibiotic-resistant psychrotrophic bacteria isolated from the cold-stored raw milk samples. Twenty-four raw milk samples, six at a time, were obtained from lorries that collected milk from Finnish farms and were stored at 4°C/4 d, 6°C/3 d and 6°C/4 d. Antibiotics representing four classes of antibiotics (gentamicin, ceftazidime, levofloxacin and trimethoprim-sulfamethoxazole) were used to determine the antibiotic resistance of mesophilic and psychrotrophic bacteria during the storage period. A representative number of antibiotic-resistant Gram-negative isolates retrieved from the cold-stored raw milk samples were identified by the phenotypic API 20 NE system and a few isolates by the 16S rDNA gene sequencing. Some of the isolates were further evaluated for their antibiotic resistance by the ATB PSE 5 and HiComb system. The initial average mesophilic counts were found below 105 CFU/mL, suggesting that the raw milk samples were of good quality. However, the mesophilic and psychrotrophic population increased when stored at 4°C/4 d, 6°C/3 d and 6°C/4 d. Gentamicin- and levofloxacin-resistant bacteria increased moderately (P < 0.05) while there was a considerable rise (P < 0.05) of ceftazidime- and trimethoprim-sulfamethoxazole-resistant population during the cold storage. Of the 50.9 % (28) of resistant isolates (total 55) identified by API 20 NE, the majority were Sphingomonas paucimobilis (8), Pseudomonas putida (5), Sphingobacterium spiritivorum (3) and Acinetobacter baumanii (2). The analysis by ATB PSE 5 system suggested that 57.1% of the isolates (total 49) were multiresistant. This study showed that the dairy environment harbours multidrug-resistant Gramnegative psychrotrophic bacteria and the cold chain of raw milk storage amplifies the antibioticresistant psychrotrophic bacterial population.
  • Blom, Titta S. (Helsingin yliopisto, 2003)
  • Vainio, Ulla (Helsingin yliopisto, 2007)
    Wood is an important material for the construction and pulping industries. Using x-ray diffraction the microfibril angle of Sitka spruce wood was studied in the first part of this thesis. Sitka spruce (Picea sitchensis [Bong.] Carr.) is native to the west coast of North America, but due to its fast growth rate, it has also been imported to Europe. So far, its nanometre scale properties have not been systematically characterised. In this thesis the microfibril angle of Sitka spruce was shown to depend significantly on the origin of the tree in the first annual rings near the pith. Wood can be further processed to separate lignin from cellulose and hemicelluloses. Solid cellulose can act as a reducer for metal ions and it is also a porous support for nanoparticles. By chemically reducing nickel or copper in the solid cellulose support it is possible to get small nanoparticles on the surfaces of the cellulose fibres. Cellulose supported metal nanoparticles can potentially be used as environmentally friendly catalysts in organic chemistry reactions. In this thesis the size of the nickel and copper containing nanoparticles were studied using anomalous small-angle x-ray scattering and wide-angle x-ray scattering. The anomalous small-angle x-ray scattering experiments showed that the crystallite size of the copper oxide nanoparticles was the same as the size of the nanoparticles, so the nanoparticles were single crystals. The nickel containing nanoparticles were amorphous, but crystallised upon heating. The size of the nanoparticles was observed to be smaller when the reduction of nickel was done in aqueous ammonium hydrate medium compared to reduction made in aqueous solution. Lignin is typically seen as the side-product of wood industries. Lignin is the second most abundant natural polymer on Earth, and it possesses potential to be a useful material for many purposes in addition to being an energy source for the pulp mills. In this thesis, the morphology of several lignins, which were produced by different separation methods from wood, was studied using small-angle and ultra small-angle x-ray scattering. It was shown that the fractal model previously proposed for the lignin structure does not apply to most of the extracted lignin types. The only lignin to which the fractal model could be applied was kraft lignin. In aqueous solutions the average shape of the low molar mass kraft lignin particles was observed to be elongated and flat. The average shape does not necessarily correspond to the shape of the individual particles because of the polydispersity of the fraction and due to selfassociation of the particles. Lignins, and especially lignosulfonate, have many uses as dispersants, binders and emulsion stabilisers. In this thesis work the selfassociation of low molar mass lignosulfonate macromolecules was observed using small-angle x-ray scattering. By taking into account the polydispersity of the studied lignosulfonate fraction, the shape of the lignosulfonate particles was determined to be flat by fitting an oblate ellipsoidal model to the scattering intensity.
  • Koskinen, Kaisa (Helsingin yliopisto, 2013)
    Microbes are essential for all life on Earth. They are found in all viable habitats from deep sea sediments and bedrock to high up in the atmosphere with a variety that exceeds by far the eukaryotic diversity. Ecosystem services provided by microorganisms, such as degradation of organic material and mediation of biogeochemical cycles are fundamentally important for the whole biosphere and its inhabitants. Microbes also form symbiotic relationships with multicellular organisms, and play important roles in nutrition and disease. Recent developments in molecular techniques, especially the next generation sequencing technologies and microarray applications, have opened new possibilities in studying diverse microbial communities. In this thesis, the aim was to determine the diversity and community structure of environmental samples collected from the northern Baltic Sea water column and anaerobic digestion reactor, and to assess how the prevailing abiotic factors affect the microbial community structure. We applied 16S rRNA and ITS gene amplicon sequencing method with 454 sequencing technology to form a detailed taxonomic description of studied communities. The produced sequence data was further utilised in designing probes for a new padlock probe based ligation detection reaction (LDR) microarray that could be employed for specific and sensitive taxonomic identification of microbial groups in diverse communities. The functionality, specificity and sensitivity of the microarray were assessed using artificial and real environmental samples. Additionally, selected amplicon sequencing data analysis methods were compared in order to discover which algorithms work most reliably. In this subproject, we aimed to clarify how significantly the selected analysis methods, specifically denoising and clustering algorithms, affect the results and how comparable the results derived from different analysis pipelines are. Amplicon sequencing revealed diverse microbial communities in the northern Baltic Sea water column and anaerobic digestion reactor. The pelagic bacterial communities in the northern Baltic Sea were strongly stratified, with aerobic Bacteria such as Pseudomonas and Flavobacterium dominating in the surface layer and Oleispira and sulfate-reducing bacteria in the anoxic deep waters. Based on the sequence data the diversity was assessed one order of magnitude less diverse compared to Atlantic and Pacific ocean bacterial communities. The anaerobic digestion reactor communities were dominated by Bacteria belonging to phyla Bacteroidetes, Firmicutes and Thermotogae and methanogenic Archaea, all essential and typical degraders in anaerobic digestion. The process also supported a diverse fungal community of phyla Ascomycota and Basidiomycota, including several taxa capable of degrading organic material in anaerobic conditions. The LDR microarray technology proved sensitive, specific and semiquantitative method for identifying microbes in diverse communities. The proof of principle tests and experiments with real environmental samples showed that if the probes are designed carefully, the detection is comparable to qPCR and amplicon sequencing. The detection limit was 0.01 fmol/µl/template. Data analysis method comparisons revealed prominent differences in observed operational taxonomic units and relative abundance of identified taxa. The majority of tested methods assessed the species richness too high. Using a functioning denoising method evened out the differences in the number of observed OTUs caused by various clustering algorithms. The ability to filter out the spurious taxa produced by amplification and sequencing, but still retain all the real diversity varied between methods. This study shows both the potential and the challenges in the use of amplicon sequencing and microarray technologies in studying diverse microbial communities. The results indicate that the padlock based LDR microarray can be designed for very accurate and sensitive identification of microbial groups of interest. The data suggest that amplicon sequencing is a powerful tool in identifying microbes and assessing the diversity but distinguishing between spurious and true community members remain a challenge. There is still work to be done in the development and application of data analysis tools.
  • Sarén, Matti-Paavo (Helsingin yliopisto, 2006)
    In recent years there has been growing interest in selecting suitable wood raw material to increase end product quality and to increase the efficiency of industrial processes. Genetic background and growing conditions are known to affect properties of growing trees, but only a few parameters reflecting wood quality, such as volume and density can be measured on an industrial scale. Therefore research on cellular level structures of trees grown in different conditions is needed to increase understanding of the growth process of trees leading to desired wood properties. In this work the cellular and cell wall structures of wood were studied. Parameters, such as the mean microfibril angle (MFA), the spiral grain angles, the fibre length, the tracheid cell wall thickness and the cross-sectional shape of the tracheid, were determined as a function of distance from the pith towards the bark and mutual dependencies of these parameters were discussed. Samples from fast-grown trees, which belong to a same clone, grown in fertile soil and also from fertilised trees were measured. It was found that in fast-grown trees the mean MFA decreased more gradually from the pith to the bark than in reference stems. In fast-grown samples cells were shorter, more thin-walled and their cross-sections were rounder than in slower-grown reference trees. Increased growth rate was found to cause an increase in spiral grain variation both within and between annual rings. Furthermore, methods for determination of the mean MFA using x-ray diffraction were evaluated. Several experimental arrangements including the synchrotron radiation based microdiffraction were compared. For evaluation of the data analysis procedures a general form for diffraction conditions in terms of angles describing the fibre orientation and the shape of the cell was derived. The effects of these parameters on the obtained microfibril angles were discussed. The use of symmetrical transmission geometry and tangentially cut samples gave the most reliable MFA values.
  • Rantakari, Anssi (Helsingin yliopisto, 2005)
  • Holvikari, Kira (2015)
    MRP2 on ABC-kuljetinproteiineihin kuuluva effluxi-kuljetinproteiini, joka esiintyy solukalvojen apikaalipuolella pääasiassa maksassa, maha-suolikanavan enterosyyteissä, munuaisissa ja keuhkoissa. Tämä kuljetinproteiini on yhdistetty ilmiöön (lääkeresistenssi, multidrug resistance), jossa lääkkeen imeytyminen vähenee kuljetinproteiinin ansiosta tämän kuljettaessa lääkeainetta ulos solusta. Tämän ilmiön estämiseksi etsitään voimakkaita kuljetinproteiinin estäjiä ja substraatteja. On esitetty, että lukuisat flavonoidit ovat inhibiittoreita MRP2-kuljetinproteiiniille, mutta tutkimus flavonoideihin liittyen jatkuu. Toinen ryhmä aineita, joista on esitetty estäjiä MRP2 kuljetinproteiinille, on farmaseuttiset apuaineet. Molemmat, sekä flavonoidit että apuaineet, ovat aineita, joita tutkitaan jatkuvasti lääke-yhteisvaikutuksiin liittyen. Nykyään voidaankin arvioida, että apuaineet eivät ole täysin reagoimattomia aineita elimistössä, kuten aiemmin on ajateltu. Tällä hetkellä MRP2-kuljetinproteiinin tieteellinen tutkimus keskittyy in vitro tutkimuksiin. Tämän erikoistyön kokeellisessa osuudessa tutkitaan luonnonaineiden ja farmaseuttisten apuaineiden vaikutuksia MRP2-kuljetinproteiiniin vesikkelikuljetusanalyysillä (VT-analyysi), käyttäen MRP2-Spodoptera frugiperda 9 (Sf9)- membraanivesikkeleitä ja 5(6)-karboksi-2,′7′-diklorofluoresiini (CDCF)-yhdistettä koettimena. Ajatuksena on löytää MRP2 kuljetinproteiinin estäjiä ja substraatteja. Yhteensä 157 ainetta seulotaan käyttäen tätä in vitro metodia ja näistä löytyvät potentiaaliset aineet tutkitaan tarkemmin suorittamalla IC50- ja Ki-määrityksiä. Potentiaalisia aineita tutkitaan myös kahdella eri metodilla, dynaamisella valo sironnalla (Dynamic light scattering, DLS) ja nefelometrillä, jotta voidaan varmistua täydellisestä aineiden liukenemisesta ja siitä että kuljetinproteiinin esto ei aiheudu mikrokeräytymien johdosta. Lopuksi potentiaaliset MRP2 substraatit tutkitaan käyttäen VTanalyysiä, jossa on detektorina nestekromatografi-massa spetrometri (LC-MS). 157 yhdisteestä löytyi 19 (12%) ainetta, jotka osoittivat muutoksia CDCF:n kuljetuksessa. 6 ainetta stimuloi (CDCF:n kuljetus kasvoi ≥ 150%) ja 13 ainetta inhibioi MRP2 kuljetusta (CDCF kuljetus laski ≦ 50%). IC50 määritys tehtiin 12 aineelle, joille saattiin seuraavat tulokset: Ellaghappo 10.4 μM, gossypiini 17.4 μM, moriinidihydraatti 19.4 μM, myrisetiini 27.1 μM, nordihydroguaiareettihappo (NDGA) 36.2 μM, oktyyligallaatti 20.3 μM, silybiini 52.3 μM, pluronic ®F98 6.9 μM, lutrol F127 ∼ 8.2 μM and tanniinihappo 1.99 μM. Ki määritys tehtiin kolmelle aineelle, joista tuloksiksi saatiin seuraavaa: Myrisetiini 42.9 ± 47.4 μM, gossypiini 19.4 ± 12.5 μM and tanniinihappo 0.0538 ± 0.0398 μM. Ki määrityksen yhteydessä myös inhibition tyyppi määritettiin: Kilpaileva inhibitio; tanniinihappo ja gossypiini sekä kilpailematon inhibitio; myrisetiini. Mikrokeräytymien ja liukoisuuden mittauksissa ei esiintynyt merkittäviä keräytymiä ja inhibitio tällä mekanismilla voidaan sulkea pois. Mikrokertymien ja liukoisuuden mittaaminen tulisi kuitenkin optimoida, luotettavien tulosten saamiseksi. Stimulaattorit baikaleiini, baikaliini, digitoksigeniini sekä inhibiittorit myrisetiini, gossypiini ja tanniinihappo tutkittiin lopuksi LC-MS metodilla. Tuloksista käy ilmi, että gossypiini, jonka +ATP tulos oli suurempi kuin -ATP tulos 50μM:n konsentraatiossa, voisi olla MRP2-substraatti. Yhteenvetona, gossypiinilla on kilpailevaa inhibitiota MRP2-kuljetinproteiinia kohtaan ja näyttää siltä, että se olisi myös MRP2-substraatti. Nämä tulokset on kuitenkin varmistettava jatkotutkimuksin.
  • Hukkinen, Maria (2010)
    Tupakointitutkimukset keskittyvät perinteisesti säännöllisesti tai runsaasti tupakoiviin. Koska ei ole osoitettu mitään terveyden kannalta haitattoman tupakoinnin rajaa, määrältään vähäisenkin tupakoinnin tutkiminen on tärkeää. Tutkielman tavoitteina oli analysoida päivittäin 1-4 savuketta polttavien ominaispiirteitä, tupakointitottumusten pysyvyyttä sekä tupakointitavan muutosta ennustavia tekijöitä. Tutkimuksessa käytettiin vuosina 1975, 1981 ja 1990 kerätyn suomalaisen kaksoskohorttitutkimuksen kyselyaineistoa. Vuoden 1975 aineistossa oli 9 940 päivittäistupakoitsijaa, joista 8% poltti alle 5 ja 20% vähintään 20 savuketta päivässä. Tutkimuksessa verrattiin päivittäin vähän ja paljon polttavien ominaispiirteitä. Vähän tupakoivat olivat todennäköisemmin naisia, yksin eläviä, liikunnallisia, korkeammin koulutettuja, elämäänsä tyytyväisiä ja vähemmän stressaantuneita kuin runsaasti polttavat. Pienempi osuus vähemmän tupakoivista käytti runsaasti kahvia ja alkoholia tai tupakoidessaan hengitti savua keuhkoihin. Pitkittäistarkastelussa ikä, koulutusaste, siviilisäädyn muutos ja alkoholin käyttö ennustivat tupakointitapojen muuttumista. Yksilötasolla vähäinen tupakointi oli usein väliaikaista: seuranta-aikana valtaosa lopetti tupakoinnin tai lisäsi savukemäärää. Väestötasolla vähän tupakoivien osuus pysytteli samana: tupakoinnin aloittajia, vähentäjiä sekä aiemmin lopettaneita mutta uudelleen aloittaneita siirtyi tähän ryhmään.