Computational Studies on Bimetallic Clusters

The chemical and physical properties of bimetallic clusters have attracted considerable attention due to the potential technological applications of mixed-metal systems. It is of fundamental interests to study clusters because they are the link between atomic surface and bulk properties. More information of metal-metal bond in small clusters can be hence released. The studies in my thesis mainly focus on the two different kinds of bimetallic clusters: the clusters consisting of extraordinary shaped all metal four-membered rings and a series of sodium auride clusters. As described in most general organic chemistry books nowadays, a group of compounds are classified as aromatic compounds because of their remarkable stabilities, particular geometrical and energetic properties and so on. The notation of aromaticity is essentially qualitative. More recently, the connection has been made between aromaticity and energetic and magnetic properties. Also, the discussions of the aromatic nature of molecular rings are no longer limited to organic compounds obeying the Hückel’s rule. In our research, we mainly applied the GIMIC method to several bimetallic clusters at the CCSD level, and compared the results with those obtained by using chemical shift based methods. The magnetically induced ring currents can be generated easily by employing GIMIC method, and the nature of aromaticity for each system can be therefore clarified. We performed intensive quantum chemical calculations to explore the characters of the anionic sodium auride clusters and the corresponding neutral clusters since it has been fascinating in investigating molecules with gold atom involved due to its distinctive physical and chemical properties. As small gold clusters, the sodium auride clusters seem to form planar structures. With the addition of a negative charge, the gold atom in anionic clusters prefers to carry the charge and orients itself away from other gold atoms. As a result, the energetically lowest isomer for an anionic cluster is distinguished from the one for the corresponding neutral cluster. Mostly importantly, we presented a comprehensive strategy of ab initio applications to computationally implement the experimental photoelectron spectra.

Methods in general model localization

The aim of this study was to evaluate and test methods which could improve local estimates of a general model fitted to a large area. In the first three studies, the intention was to divide the study area into sub-areas that were as homogeneous as possible according to the residuals of the general model, and in the fourth study, the localization was based on the local neighbourhood. According to spatial autocorrelation (SA), points closer together in space are more likely to be similar than those that are farther apart. Local indicators of SA (LISAs) test the similarity of data clusters. A LISA was calculated for every observation in the dataset, and together with the spatial position and residual of the global model, the data were segmented using two different methods: classification and regression trees (CART) and the multiresolution segmentation algorithm (MS) of the eCognition software. The general model was then re-fitted (localized) to the formed sub-areas. In kriging, the SA is modelled with a variogram, and the spatial correlation is a function of the distance (and direction) between the observation and the point of calculation. A general trend is corrected with the residual information of the neighbourhood, whose size is controlled by the number of the nearest neighbours. Nearness is measured as Euclidian distance. With all methods, the root mean square errors (RMSEs) were lower, but with the methods that segmented the study area, the deviance in single localized RMSEs was wide. Therefore, an element capable of controlling the division or localization should be included in the segmentation-localization process. Kriging, on the other hand, provided stable estimates when the number of neighbours was sufficient (over 30), thus offering the best potential for further studies. Even CART could be combined with kriging or non-parametric methods, such as most similar neighbours (MSN).

Designing Creativity Through Clusters - A periodisation of cluster discourse

The thesis focuses on one of the most dominant articulations of the relation between geographical place and development, clusters - internationally competing place-bound economic system of production in related industries. The dominant articulation of cluster discourse represents the subnational region as a system of production, and as a means for competitiveness for Western countries. Its reproduction in theories has become one of the most prolific exports of economic geography to other disciplines and for policymaking. By analysing cluster discourse the thesis traces how the languages and processes of globalization have over time altered the understandings of the relation between geographical place and the economy. It shows how in its latest incarnation of the cluster discourse, the language of mainstream economics is combined with ‘softer’ elements (e.g. community, learning, creativity) in the economic geographic discourse. This is typical for the idea of soft capitalism, wherein it is assumed that economic success emanates from soft characteristics, such as knowledge, learning and creativity, rather than straightforward technological or cost advantages. A reoccurring critique against the dominant understanding of the relationship between competitiveness and regions, as articulated in cluster discourse, has pinpointed the perspective’s inability to reconcile the respective and reciprocal roles of local standard of living with firm competitiveness. The thesis traces how such critique is increasingly appropriated through the fusion of the economic, social and cultural landscape into the language of capitalism. It shows how cluster discourse has appropriated its critique, by focusing on creativity, with its strong associations to arts, individual artists and the cultural sphere in general, while predominantly creating its meaning in relation to competitiveness. The thesis consists of six essays that each outlines the development of the cluster discourse. The essays show how meaning systems and strategies are created, accepted and naturalized in cluster discourse, how this affects individuals, the economic landscape and society at large, as well as showing which understandings are marginalized in the process. The thesis argues that clusters are a) inseparable from ideology and politics and b) they are the result of purposeful social practice. It calls for increased reflexivity within corporate and economic geographic research on clusters, and underlines the importance of placing issues of power at the centre of analysis.

Preliminary phonological analysis of the Limi dialect of Humla Bhotia

The purpose of this research was to analyse the phonological system of the Limi dialect of Humla Bhotia. Humla Bhotia is a Tibeto-Burman language that is spoken by approximately 4000 5000 people in the far northwestern Humla province of the Kingdom of Nepal. The language has not previously been the subject of analysis. The data base for this thesis was collected on two different dialects of Humla Bhotia in Kathmandu, the capital of Nepal, from February to May 2000. I had three language informants who speak Humla Bhotia as their mother tongue. One of the informants speaks the Upper Humla dialect and the other two informants speak the Limi dialect. In this thesis I have concentrated on the phonology of the dialect of Limi but occasionally I also make reference to the Upper Humla dialect. The Limi data base consists of 600 words elicited in isolation, sentences where words have been checked for consonantal and pitch variation, and five texts comprising 117 sentences. Firstly, I have studied the geographical location, population and dialects of Humla Bhotia. Five dialects were identified: Limi, Upper Humla, La Yakba, Nyinba and Humli Khyampa. Information on the dialect areas is based on the accounts of seven mother tongue speakers of the language and on Nancy Levine s (1988) anthropological research of the ethnic group Nyinba. Secondly, I have analysed the phonological system of Limi from the viewpoint of American stucturalism much along the lines followed by Pike 1966 [1947] ja 1967 [1948]. In defining the prosodic elements I have also used acoustic analysis. In the Limi dialect there are 7 vowel phonemes. No vowel clusters occur within the same syllable. In this preliminary analysis 29 contrastive plosives, 8 affricates and 5 6 fricatives were found. The data also revealed 4 nasal phonemes, two rhotic phonemes, one lateral phoneme and two central approximants. Further research is however called for to check the phonemic status of these segments. Four contrastive prosodic elements were encountered: nasalisation, length, phonation type and pitch movement. There are two contrastive types of phonation: tense and lax. Many words were found with a third type of phonation, modal phonation. How modal phonation relates to the prosodic system is unclear at this stage and is therefore left for further research to determine. There are two contrastive pitch movement tonemes: a rising toneme and falling toneme. The falling toneme occurs in free variation with a level pitch contour. Rising appears to be linked with lax phonation and falling with tense phonation.

Representing the epistemic nature of teachers’ practical knowledge : The case of class teachers’ general pedagogy

The present study addressed the epistemology of teachers’ practical knowledge. Drawing from the literature, teachers’ practical knowledge is defined as all teachers’ cognitions (e.g., beliefs, values, motives, procedural knowing, and declarative knowledge) that guide their practice of teaching. The teachers’ reasoning that lies behind their practical knowledge is addressed to gain insight into its epistemic nature. I studied six class teachers’ practical knowledge; they teach in the metropolitan region of Helsinki. Relying on the assumptions of the phenomenographic inquiry, I collected and analyzed the data. I analyzed the data in two stages where the first stage involved an abductive procedure, and the second stage an inductive procedure for interpretation, and thus developed the system of categories. In the end, a quantitative analysis nested into the qualitative findings to study the patterns of the teachers’’ reasoning. The results indicated that teachers justified their practical knowledge based on morality and efficiency of action; efficiency of action was found to be presented in two different ways: authentic efficiency and naïve efficiency. The epistemic weight of morality was embedded in what I call “moral care”. The core intention of teachers in the moral care was the commitment that they felt about the “whole character” of students. From this perspective the “dignity” and the moral character of the students should not replaced for any other “instrumental price”. “Caring pedagogy” was the epistemic value of teachers’ reasoning in the authentic efficiency. The central idea in the caring pedagogy was teachers’ intentions to improve the “intellectual properties” of “all or most” of the students using “flexible” and “diverse” pedagogies. However, “regulating pedagogy” was the epistemic condition of practice in the cases corresponding to naïve efficiency. Teachers argued that an effective practical knowledge should regulate and manage the classroom activities, but the targets of the practical knowledge were mainly other “issues “or a certain percentage of the students. In these cases, the teachers’ arguments were mainly based on the notion of “what worked” regardless of reflecting on “what did not work”. Drawing from the theoretical background and the data, teachers’ practical knowledge calls for “praxial knowledge” when they used the epistemic conditions of “caring pedagogy” and “moral care”. It however calls for “practicable” epistemic status when teachers use the epistemic condition of regulating pedagogy. As such, praxial knowledge with the dimensions of caring pedagogy and moral care represents the “normative” perspective on teachers’ practical knowledge, and thus reflects a higher epistemic status in comparison to “practicable” knowledge, which represents a “descriptive” perception toward teachers’ practical knowledge and teaching.

Is a Majority Enough? Psychological Well-being and Its Relation to Academic and Prosocial Motivation, Self-regulation and Achievement at school

This cross-sectional study analyzed psychological well-being at school using the Self-Determination theory as a theoretical frame-work. The study explored basic psychological needs fulfillment (BPNS), academic (SRQ-A), prosocial self-regulation (SRQ-P) and motivation, and their relationship with achievement in general, special and selective education (N=786, 444 boys, 345 girls, mean age 12 yrs 8 mths). Motivation starts behavior which becomes guided by self-regulation. The perceived locus of control (PLOC) affects how self-determined this behavior will be; in other words, to what extent it is autonomously regulated. In order learn and thus to be able to accept external goals, a student has to feel emotionally safe and have sufficient ego-flexibility—all of which builds on satisfied psychological needs. In this study those conditions were explored. In addition to traditional methods Self-organizing maps (SOM), was used in order to cluster the students according to their well-being, self-regulation, motivation and achievement scores. The main impacts of this research were: a presentation of the theory based alternative of studying psychological well-being at school and usage of both the variable and person-oriented approach. In this Finnish sample the results showed that the majority of students felt well, but the well-being varied by group. Overall about for 11–15% the basic needs were deprived depending on the educational group. Age and educational group were the most effective factors; gender was important in relation to prosocial identified behavior. Although the person-oriented SOM-approach, was in a large extent confirming what was no-ticed by using comparison of the variables: the SEN groups had lower levels of basic needs fulfillment and less autonomous self-regulation, interesting deviations of that rule appeared. Some of the SEL- and GEN-group members ended up in the more unfavorable SOM-clusters, and not all SEN-group members belonged to the poorest clusters (although not to the best either). This evidence refines the well-being and self-regulation picture, and may re-direct intervention plans, and turn our focus also on students who might otherwise remain unnoticed. On the other hand, these results imply simultaneously that in special education groups the average is not the whole truth. On the basis of theoretical and empirical considerations an intervention model was sug-gested. The aim of the model was to shift amotivation or external motivation in a more intrinsic direction. According to the theoretical and empirical evidence this can be achieved first by studying the self-concept a student has, and then trying to affect both inner and environmental factors—including a consideration of the basic psychological needs. Keywords: academic self-regulation, prosocial self-regulation, basic psychological needs, moti-vation, achievement

Terveyteen liittyvä elämänlaatu laitoskuntoutuksen vaikuttavuuden arvioinnissa : RAND-36-mittarin soveltuvuus työikäisten laitoskuntoutuksen ongelmaprofiilin määrittämiseen ja kuntoutuksen vaikutusten arvioimiseen

The aim of the present research was to examine the validity of the RAND-36 measure of health-related quality of life among the working age rehabilitation clients. The research included two cross-sectional studies and one follow-up study. The subjects of the first study (n = 794) participated in the first period of the five following types of rehabilitation: occupationally oriented medical rehabilitation, musculoskeletal rehabilitation, medical rehabilitation for job burnout, rehabilitation for supporting the work ability and capacity of disabled subjects (vocational rehabilitation) and individualized rehabilitation between October 2000 and October 2001. The subjects of the second study (n = 990) participated in the same rehabilitation during their first rehabilitation period between May 2007 and May 2008. The first subjects participated in a follow-up period no later than May 2003 with the exception of the individual rehabilitation clients (n = 588). Based on the ICF classification, the RAND-36 provides a diverse measure of the health-related quality of life and of the capacity for subjective, perceived physical and psycho-social functioning. The construct properties of the RAND-36 measure proved to be very consistent on the basis of both the cluster and confirmatory factor analyses. At the group level, the RAND-36 measure was shown to be illustrative and sensitive in differentiating the clients’ rehabilitation needs. The results of cluster analyses with the two cross-sectional data indicated a consistent five-cluster solution of rehabilitation groups on the basis of the eight subscales of health-related quality of life. Each of these clusters represented a clear difference in their need for rehabilitation. The RAND-36 measure proved to be sensitive to change. The changes observed in the pre- and post-conditions in relation to all the subscales of quality of life were statistically significant. Depending on the rehabilitation type, different changes in the subscales of the measure were observed, and these changes corresponded to the different emphasis and goals of the specific type of rehabilitation intervention. Similarly, changes in the subscales of the measure were observed in relation to the RAND groups formed by cluster analysis, which were logical and corresponded to the problem profiles of these groups. The confirmatory factor analysis indicated a two-factor solution: an index of the capacity for physical functioning (self-rated general health, bodily pain, physical functioning, physical role functioning) and an index of the capacity for psycho-social functioning (psychological well-being, social functioning, psychological role functioning and energy). These two indices describing functional capacity proved also to be sensitive to change. This two-factor solution seems to be usable for group level analyses when assessing the effects of rehabilitation. The moderately strong correlation between the RAND-36 and work ability index suggests that they partly measure the same phenomenon: perceived health-related quality of life, subjective capacity for activity and perceived work ability have strong links. As expected, the capacity for physical functioning had a stronger correlation with work ability index than with the capacity for psycho-social functioning. According to the present research, the RAND-36 measure can be considered as a screening method for rehabilitation orientation in relation to rehabilitation needs and as a follow-up measure for the health-related quality of life among the working age clients. The RAND-36 measure is also shown to be a useful instrument in estimating the benefits of rehabilitation as well as in effectiveness research.

The epidemiology of severe Streptococcus pyogenes disease in Europe

Diseases caused by the Lancefield group A streptococcus, Streptococcus pyogenes, are amongst the most challenging to clinicians and public health specialists alike. Although severe infections caused by S. pyogenes are relatively uncommon, affecting around 3 per 100,000 of the population per annum in developed countries, the case fatality is high relative to many other infections. Despite a long scientific tradition of studying their occurrence and characteristics, many aspects of their epidemiology remain poorly understood, and potential control measures undefined. Epidemiological studies can play an important role in identifying host, pathogen and environmental factors associated with risk of disease, manifestation of particular syndromes or poor survival. This can be of value in targeting prevention activities, as well directing further basic research, potentially paving the way for the identification of novel therapeutic targets. The formation of a European network, Strep-EURO, provided an opportunity to explore epidemiological patterns across Europe. Funded by the Fifth Framework Programme of the European Commission s Directorate-General for Research (QLK2.CT.2002.01398), the Strep-EURO network was launched in September 2002. Twelve participants across eleven countries took part, led by the University of Lund in Sweden. Cases were defined as patients with S. pyogenes isolated from a normally sterile site, or non-sterile site in combination with clinical signs of streptococcal toxic shock syndrome (STSS). All participating countries undertook prospective enhanced surveillance between 1st January 2003 and 31st December 2004 to identify cases diagnosed during this period. A standardised surveillance dataset was defined, comprising demographic, clinical and risk factor information collected through a questionnaire. Isolates were collected by the national reference laboratories and characterised according to their M protein using conventional serological and emm gene typing. Descriptive statistics and multivariable analyses were undertaken to compare characteristics of cases between countries and identify factors associated with increased risk of death or development of STSS. Crude and age-adjusted rates of infection were calculated for each country where a catchment population could be defined. The project succeeded in establishing the first European surveillance network for severe S. pyogenes infections, with 5522 cases identified over the two years. Analysis of data gathered in the eleven countries yielded important new information on the epidemiology of severe S. pyogenes infections in Europe during the 2000s. Comprehensive epidemiological data on these infections were obtained for the first time from France, Greece and Romania. Incidence estimates identified a general north-south gradient, from high to low. Remarkably similar age-standardised rates were observed among the three Nordic participants, between 2.2 and 2.3 per 100,000 population. Rates in the UK were higher still, 2.9/100,000, elevated by an upsurge in drug injectors. Rates from these northern countries were reasonably close to those observed in the USA and Australia during this period. In contrast, rates of reports in the more central and southern countries (Czech Republic, Romania, Cyprus and Italy) were substantially lower, 0.3 to 1.5 per 100,000 population, a likely reflection of poorer uptake of microbiological diagnostic methods within these countries. Analysis of project data brought some new insights into risk factors for severe S. pyogenes infection, especially the importance of injecting drug users in the UK, with infections in this group fundamentally reshaping the epidemiology of these infections during this period. Several novel findings arose through this work, including the high degree of congruence in seasonal patterns between countries and the seasonal changes in case fatality rates. Elderly patients, those with compromised immune systems, those who developed STSS and those infected with an emm/M78, emm/M5, emm/M3 or emm/M1 were found to be most likely to die as a result of their infection, whereas those diagnosed with cellulitis, septic arthritis, puerperal sepsis or with non-focal infection were associated with low risk of death, as were infections occurring during October. Analysis of augmented data from the UK found use of NSAIDs to be significantly associated with development of STSS, adding further fuel to the debate surrounding the role of NSAIDs in the development of severe disease. As a largely community-acquired infection, occurring sporadically and diffusely throughout the population, opportunities for control of severe infections caused by S. pyogenes remain limited, primarily involving contact chemoprophylaxis where clusters arise. Analysis of UK Strep-EURO data were used to quantify the risk to household contacts of cases, forming the basis of national guidance on the management of infection. Vaccines currently under development could offer a more effective control programme in future. Surveillance of invasive infections caused by S. pyogenes is of considerable public health importance as a means of identifying long and short-term trends in incidence, allowing the need for, or impact of, public health measures to be evaluated. As a dynamic pathogen co-existing among a dynamic population, new opportunities for exploitation of its human host are likely to arise periodically, and as such continued monitoring remains essential.

Molecular pathogenesis of human parechovirus 1 infection

The Parechoviruses (HPEV) belong to the family Picornaviridae of positive-stranded RNA viruses. Although the parechovirus genome shares the general properties of other picornaviruses, the genus has several unique features when compared to other family members. We found that HPEV1 attaches to αv integrins on the cell surface and is internalized through the clathrin-mediated endocytic pathway. During he course of the infection, the Golgi was found to disintegrate and the ER membranes to swell and loose their ribosomes. The replication of HPEV1 was found to take place on small clusters of vesicles which contained the trans-Golgi marker GalT as well as the viral non-structural 2C protein. 2C was additionally found on stretches of modified ER-membranes, seemingly not involved in RNA replication. The viral non-structural 2A and 2C proteins were studied in further detail and were found to display several interesting features. The 2A protein was found to be a RNA-binding protein that preferably binds to positive sense 3 UTR RNA. It was found to bind also duplex RNA containing 3 UTR(+)-3 UTR(-), but not other dsRNA molecules studied. Mutagenesis revealed that the N-terminal basic-rich region as well as the C-terminus, are important for RNA-binding. The 2C protein on the other hand, was found to have both ATP-diphosphohydrolase and AMP kinase activities. Neither dATP nor other NTP:s were suitable substrates. Furthermore, we found that as a result of theses activities the protein is autophosphorylated. The intracellular changes brought about by the individual HPEV1 non-structural proteins were studied through the expression of fusion proteins. None of the proteins expressed were able to induce membrane changes similar to those seen during HPEV1 infection. However, the 2C protein, which could be found on the surface of lipid droplets but also on diverse intracellular membranes, was partly relocated to viral replication complexes in transfected, superinfected cells. Although Golgi to ER traffic was arrested in HPEV1-infected cells, none of the individually expressed non-structural proteins had any visible effect on the anterograde membrane traffic. Our results suggest that the HPEV1 replication strategy is different from that of many other picornaviruses. Furthermore, this study shows how relatively small differences in genome sequence result in very different intracellular pathology.

Evolution and detection of cyanobacterial hepatotoxin synthetase genes

Mass occurrences (blooms) of cyanobacteria are common in aquatic environments worldwide. These blooms are often toxic, due to the presence of hepatotoxins or neurotoxins. The most common cyanobacterial toxins are hepatotoxins: microcystins and nodularins. In freshwaters, the main producers of microcystins are Microcystis, Anabaena, and Planktothrix. Nodularins are produced by strains of Nodularia spumigena in brackish waters. Toxic and nontoxic strains of cyanobacteria co-occur and cannot be differentiated by conventional microscopy. Molecular biological methods based on microcystin and nodularin synthetase genes enable detection of potentially hepatotoxic cyanobacteria. In the present study, molecular detection methods for hepatotoxin-producing cyanobacteria were developed, based on microcystin synthetase gene E (mcyE) and the orthologous nodularin synthetase gene F (ndaF) sequences. General primers were designed to amplify the mcyE/ndaF gene region from microcystin-producing Anabaena, Microcystis, Planktothrix, and Nostoc, and nodularin-producing Nodularia strains. The sequences were used for phylogenetic analyses to study how cyanobacterial mcy genes have evolved. The results showed that mcy genes and microcystin are very old and were already present in the ancestor of many modern cyanobacterial genera. The results also suggested that the sporadic distribution of biosynthetic genes in modern cyanobacteria is caused by repeated gene losses in the more derived lineages of cyanobacteria and not by horizontal gene transfer. Phylogenetic analysis also proposed that nda genes evolved from mcy genes. The frequency and composition of the microcystin producers in 70 lakes in Finland were studied by conventional polymerase chain reaction (PCR). Potential microcystin producers were detected in 84% of the lakes, using general mcyE primers, and in 91% of the lakes with the three genus-specific mcyE primers. Potential microcystin-producing Microcystis were detected in 70%, Planktothrix in 63%, and Anabaena in 37% of the lakes. The presence and co-occurrence of potential microcystin producers were more frequent in eutrophic lakes, where the total phosphorus concentration was high. The PCR results could also be associated with various environmental factors by correlation and regression analyses. In these analyses, the total nitrogen concentration and pH were both associated with the presence of multiple microcystin-producing genera and partly explained the probability of occurrence of mcyE genes. In general, the results showed that higher nutrient concentrations increased the occurrence of potential microcystin producers and the risk for toxic bloom formation. Genus-specific probe pairs for microcystin-producing Anabaena, Microcystis, Planktothrix, and Nostoc, and nodularin-producing Nodularia were designed to be used in a DNA-chip assay. The DNA-chip can be used to simultaneously detect all these potential microcystin/nodularin producers in environmental water samples. The probe pairs detected the mcyE/ndaF genes specifically and sensitively when tested with cyanobacterial strains. In addition, potential microcystin/nodularin producers were identified in lake and Baltic Sea samples by the DNA-chip almost as sensitively as by quantitative real-time PCR (qPCR), which was used to validate the DNA-chip results. Further improvement of the DNA-chip assay was achieved by optimization of the PCR, the first step in the assay. Analysis of the mcy and nda gene clusters from various hepatotoxin-producing cyanobacteria was rewarding; it revealed that the genes were ancient. In addition, new methods detecting all the main producers of hepatotoxins could be developed. Interestingly, potential microcystin-producing cyanobacterial strains of Microcystis, Planktothrix, and Anabaena, co-occurred especially in eutrophic and hypertrophic lakes. Protecting waters from eutrophication and restoration of lakes may thus decrease the prevalence of toxic cyanobacteria and the frequency of toxic blooms.

Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.

Spirometric studies on the adult general population of Helsinki : bronchodilation responses, determinants, and intrasession repeatability of FEV1, FEV6, FVC, and forced expiratory time

Spirometry is the most widely used lung function test in the world. It is fundamental in diagnostic and functional evaluation of various pulmonary diseases. In the studies described in this thesis, the spirometric assessment of reversibility of bronchial obstruction, its determinants, and variation features are described in a general population sample from Helsinki, Finland. This study is a part of the FinEsS study, which is a collaborative study of clinical epidemiology of respiratory health between Finland (Fin), Estonia (Es), and Sweden (S). Asthma and chronic obstructive pulmonary disease (COPD) constitute the two major obstructive airways diseases. The prevalence of asthma has increased, with around 6% of the population in Helsinki reporting physician-diagnosed asthma. The main cause of COPD is smoking with changes in smoking habits in the population affecting its prevalence with a delay. Whereas airway obstruction in asthma is by definition reversible, COPD is characterized by fixed obstruction. Cough and sputum production, the first symptoms of COPD, are often misinterpreted for smokers cough and not recognized as first signs of a chronic illness. Therefore COPD is widely underdiagnosed. More extensive use of spirometry in primary care is advocated to focus smoking cessation interventions on populations at risk. The use of forced expiratory volume in six seconds (FEV6) instead of forced vital capacity (FVC) has been suggested to enable office spirometry to be used in earlier detection of airflow limitation. Despite being a widely accepted standard method of assessment of lung function, the methodology and interpretation of spirometry are constantly developing. In 2005, the ATS/ERS Task Force issued a joint statement which endorsed the 12% and 200 ml thresholds for significant change in forced expiratory volume in one second (FEV1) or FVC during bronchodilation testing, but included the notion that in cases where only FVC improves it should be verified that this is not caused by a longer exhalation time in post-bronchodilator spirometry. This elicited new interest in the assessment of forced expiratory time (FET), a spirometric variable not usually reported or used in assessment. In this population sample, we examined FET and found it to be on average 10.7 (SD 4.3) s and to increase with ageing and airflow limitation in spirometry. The intrasession repeatability of FET was the poorest of the spirometric variables assessed. Based on the intrasession repeatability, a limit for significant change of 3 s was suggested for FET during bronchodilation testing. FEV6 was found to perform equally well as FVC in the population and in a subgroup of subjects with airways obstruction. In the bronchodilation test, decreases were frequently observed in FEV1 and particularly in FVC. The limit of significant increase based on the 95th percentile of the population sample was 9% for FEV1 and 6% for FEV6 and FVC; these are slightly lower than the current limits for single bronchodilation tests (ATS/ERS guidelines). FEV6 was proven as a valid alternative to FVC also in the bronchodilation test and would remove the need to control duration of exhalation during the spirometric bronchodilation test.