39 resultados para MICROBIAL DIVERSITY


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Tutkimuksen tarkoituksena on selvittää kuinka moninaisuus ja sen johtaminen näkyvät voittoa tavoittelemattoman järjestön tiimityössä, kuinka moninaisuus ja tiimityö pystyvät selittämään motiiveja työskennellä voittoa tavoittelemattomassa järjestössä ja mitä tulisi huomioida tiimityön ja tiimin johtajuuden osalta, kun moninaisuus ja voittoa tavoittelemattoman järjestön luonne otetaan huomioon. Tämä tutkielma on laadullinen tutkimus, jossa tutkimusmenetelminä on käytetty yhdeksää teemahaastattelua, edellisen tutkimuksen tuloksia (Astikainen, 2005) sekä havainnointia. Tutkimuksen perusteellavoidaan todeta, että voittoa tavoittelemattoman järjestön luonne, tiimityö tai moninaisuus eivät sinällään merkitse paljoakaan tulosten kannalta, vaan niiden keskinäiset yhteydet. Nämä yhdessä, oikein hyödynnettynä, vaikuttavat työntekijöiden motivaatioon ja sitä kautta organisaation tuloksiin.

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Selostus: Pellavan ja kuituhampun mikrobiologinen laatu kasvukauden aikana

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Selostus: Maatalouspolitiikkauudistusten vaikutuksista pellonkäytön diversiteettiin

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Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

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Stable isotope fractionation analysis of contaminants is a promising method for assessing biodegradation of contaminants in natural systems. However, standard procedures to determine stable isotope fractionation factors, so far, neglect the influence of pollutant bioavailability on stable isotope fractionation. On a microscale, bioavailability may vary due to the spatio-temporal variability of local contaminant concentrations, limited effective diffusivities of the contaminants and cell densities, and thus, the pollutant supply might not meet the intrinsic degradation capacity of the microorganisms. The aim of this study was to demonstrate the effect of bioavailability on the apparent stable isotope fractionation, using a multiphase laboratory setup. The data gained show that the apparent isotope fractionation factors observed during biodegradation processes depend on the amount of biomass and/or the rate of toluene mass transfer from a second to the aqueous phase. They indicate that physico-chemical processes need to be taken into account when stable isotope fractionation analysis is used for the quantification of environmental contaminant degradation.

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This study addresses the role of EFL education, its potential and shortcomings, and the challenges the future of EFL education will bring. It is argued that new societal demands and the limited time we have at our disposal in the classroom make it necessary to rethink goals and content and move away from the transmissionof limited sets of facts and information to helping students develop awareness and competences that can be applied in many different situations, also in a perspective of lifelong learning. The overall aim of the current study is to problematize and increase understanding of the implementation of cultural aspects in the language classroom by addressing the interrelated what, why and how of the cultural dimension within EFL education. This has been conducted by means of theoretical explorations into the area, alongside an attempt at promoting intercultural competence (IC) in a more systematic and insightful manner within my own educational praxis. The focus of the intercultural work in the classroom was on the promotion of awareness of difference and diversity, as well as respect for such difference through the ability to decenter from cultural norms and behavior that previously have been taken for granted. These are two elements that have been suggested as fundamental for other work with IC in the classroom and for the realization of important aspects of the underlying values of basic education. In the context of this study, IC comprises several interconnected components supportingeach other in a variety of ways, with the further aim being interaction with and respect for difference in general, not only concerning e.g. representatives ofcertain English-speaking communities. The methodology was informed by action research, with myself in the role of the teacher-researcher or the reflective practitioner. For the purpose of the project I was authorized to take on the EFL education for the three years of upper comprehensive school of one random class of students originally assigned to one of the language teachers of the selected Finland-Swedish school. Thus, the class of 17 students was not specifically chosen for the project, and the aims and contents chosen for the development project were placed within the framework of the ordinary curriculum. By exploring the students¿ insights concerning different English-speaking cultural groups, mainly through a set of questionnaires, it was possible to outline the work with the cultural dimension in the classroom for the following three years. Work progress was evaluated at specific stages, and the final project evaluations were conducted through individual student interviews in grade 9. The interviews were focused on possible development of students¿ insights concerning different aspects of the cultural dimension. In particular this concerned awareness of difference and diversity, including modification of stereotypes, as well as the ability to decenterin order to be better able to respect such difference. I also explored students¿ awareness and views of the activities and approaches used in class, as well asaffordances both inside and outside the EFL classroom in relation to these intended insights. A further focus area was the perceived relevance to students of different aspects of the cultural dimension. The frameworks and approaches adopted for the work in the classroom all have in common that they are based on a constructivist framework, where knowledge is constructed and reconstructed through interaction with one¿s social and cultural environment, including interaction with others. Reflective processes precede or are simultaneous with the learning of basic factual knowledge. This entails a view of learning as a progression from simple to more complex models rather than as a progression from facts to understanding and analysis. Here, the development of intercultural competence is seen asa cyclical process, or along a spiral curriculum, from simple to more complex levels through a combination of cognitive, affective and behavioral elements within a framework of experiential learning. This project has shown one possible wayforward concerning the development of intercultural competence within EFL education through a more systematic and comprehensive approach regarding linguistic and cultural aspects. The evaluation of the educational process explored in the study suggests the possibilities for work with the promotion of awareness of difference and diversity concerning some specific context that, based on students¿ prior knowledge and preconceptions, would benefit from further work. In this case, the specific context primarily concerned different aspects of both cultural and linguistic conditions in the UK. It is also suggested that many students developed the ability to decenter, described in the study as integral to being able to respect otherness. What still remains to be explored are more individualized approaches considering students¿ different levels of departure. Further work alsoneeds to be put into how to apply insights gained in these specific situations to more general contexts. It is also necessary to explore the use of the suggested approaches in a wider range of different contexts.

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In my doctoral thesis I evaluate strategies designed to cope with the multicultural nature of four European nations: Great Britain, The Netherlands, Sweden, and Denmark. I also analyse and clarify the question of the place of religion in present-day Europe. The empirical material analysed in the study consists of politicians’ statements and policy documents dealing with immigration policy and religious and values education in the four countries. In addition, I analyse statements issued by the Council of Europe regarding religious education, along with all cases relevant to religious education brought before the United Nations Human Rights Committee or the European Court of Human Rights. The theoretical framework is formed by the scholarly debate – among philosophers, sociologists and scholars of religion in education – concerning the question of a just society. Special emphasis is given to philosophical theories that are in favour of granting special group rights to religious minorities in the name of equal treatment. With regard to the question of the appropriate place of religion, I apply Kim Knott’s methodological model for locating religion in secular contexts, and Émile Durkheim’s theory as to the significance of religion and collective sentiments in uniting adherents or members of a group into a single moral community. The study shows that even when the positive side of immigration, as a potential force for the enrichment of the public culture, is acknowledged, there is anxiety as to the successful integration of immigrants. The premises and goals of immigration policies have also been questioned. One central problem is the incommensurability between the values upheld by Western liberal democracies and certain religious traditions, above all those of Islam. Great Britain, The Netherlands, Sweden, and Denmark have tightened control over their citizens’ ethical attitudes and want to regulate these as well. In coping with cultural diversity, the significance of education, especially religious education, plays a significant role; as future citizens, pupils are expected to internalise the society’s core values as well as gaining an understanding of different cultures and ways of life. It is also worth noting that both the Council of Europe and the European Court of Human Rights have recently expressed the view that one important goal of religious education is to enable pupils to be critical and autonomous with regard to different religions and moral positions. The study shows that religion is not seen as purely a personal matter. Religion is closely linked to individual and national identity, and religious traditions thus have a place in the public domain. It should be noted, however, that a religious tradition – more precisely, an interpretation of religious tradition – qualifies as a legitimate partner in the democratic decision-making process only if it shares similar values with Western European nations.

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In nature, many animals use body coloration to communicate with each other. For example, colorations can be used as signals between individuals of the same species, but also to recognise individuals of other species, and if they may comprise a threat or not. Many animals use protective coloration to avoid predation. The two most common strategies of protective coloration are camouflage and aposematism. Camouflaged animals have coloration that minimises detection, usually by matching colours or structures in the background. Aposematic animals, on the other hand, signal to predators that they are defended. The defence can be physical structures, such as spikes and hairs, or chemical compounds that make the animal distasteful or even deadly toxic. In order for the warning signal to be effective, the predator has to recognise it as such. Studies have shown that birds for example, that are important visual predators on insects, learn to recognise and avoid unpalatable prey faster if they contrast the background or have large internal contrasts. Typical examples of aposematic species have conspicuous colours like yellow, orange or red, often in combination with black. My thesis focuses on the appearance and function of aposematic colour patterns. Even though researchers have studied aposematism for over a century, there is still a lot we do not know about the phenomenon. For example, as it is crucial that the predators recognise a warning signal, aposematic colorations should assumingly evolve homogeneously and be selected for maximal conspicuousness. Instead, there is an extensive variation of colours and patterns among warning colorations, and it is not uncommon to find typical cryptic colours, such as green and brown in aposematic colour patterns. One hypothesis to this variation is that an aposematic coloration does not have to be maximally signalling in order to be effective, instead it is sufficient to have distinct features that can be easily distinguished from edible prey. To be maximally conspicuous is one way to achieve this, but not the only way. Another hypothesis is that aposematic prey that do not exhibit maximal conspicuousness can exploit both camouflage and aposematism in a distance-dependent fashion, by being signalling when seen close up but camouflaged at a distance. Many prey animals also make use of both strategies by shifting colour at different ecological conditions such as seasonal variations, fluctuations in food resources or between life stages. Yet another explanation for the variation may be that prey animals are usually exposed to several predator species that vary in visual perception and tolerance towards various toxins. The aim with this thesis is, by studying their functions, to understand why aposematic warning signals vary in appearance, specifically in the level of conspicuousness, and if warning coloration can be combined with camouflage. In paper I, I investigated if the colour pattern of the aposematic larva of the Apollo butterfly (Parnassius apollo) can switch function with viewing distance, and be signalling at close range but camouflaged at a distance, by comparing detection time between different colour variants and distances. The results show that the natural coloration has a dual distance-dependent function. Moreover, the study shows that an aposematic coloration does not have to be selected for maximal conspicuousness. A prey animal can optimise its coloration primarily by avoiding detection, but also by investing in a secondary defence, which presence can be signalled if detected. In paper II, I studied how easily detected the coloration of the firebug (Pyrrhocoris apterus), a typical aposematic species, is at different distances against different natural backgrounds, by comparing detection time between different colour variants. Here, I found no distance-dependent switch in function. Instead, the results show that the coloration of the firebug is selected for maximal conspicuousness. One explanation for this is that the firebug is more mobile than the butterfly larva in study I, and movement is often incompatible with efficient camouflage. In paper III, I investigated if a seasonal related colour change in the chemically defended striated shieldbug (Graphosoma lineatum) is an adaptation to optimise a protective coloration by shifting from camouflage to aposematism between two seasons. The results confirm the hypothesis that the coloration expressed in the late summer has a camouflage function, blending in with the background. Further, I investigated if the internal pattern as such increased the effectiveness of the camouflage. Again, the results are in accordance with the hypothesis, as the patterned coloration was more difficult to detect than colorations lacking an internal pattern. This study shows how an aposematic species can optimise its defence by shifting from camouflage to aposematism, but in a different fashion than studied in paper I. The aim with study IV was to study the selection on aposematic signals by identifying characteristics that are common for colorations of aposematic species, and that distinguish them from colorations of other species. I compared contrast, pattern element size and colour proportion between a group of defended species and a group of undefended species. In contrast to my prediction, the results show no significant differences between the two groups in any of the analyses. One explanation for the non-significant results could be that there are no universal characteristics common for aposematic species. Instead, the selection pressures acting on defended species vary, and therefore affect their appearance differently. Another explanation is that all defended species may not have been selected for a conspicuous aposematic warning coloration. Taken together, my thesis shows that having a conspicuous warning coloration is not the only way to be aposematic. Also, aposematism and camouflage is not two mutually exclusive opposites, as there are prey species that exploit both strategies. It is also important to understand that prey animals are exposed to various selection pressures and trade-offs that affect their appearance, and determines what an optimal coloration is for each species or environment. In conclusion, I hold that the variation among warning colorations is larger and coloration properties that have been considered as archetypically aposematic may not be as widespread and representative as previously assumed.

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Biofilms are surface-attached multispecies microbial communities that are embedded by their self-produced extracellular polymeric substances. This lifestyle enhances the survival of the bacteria and plays a major role in many chronic bacterial infections. For instance, periodontitis is initiated by multispecies biofilms. The phases of active periodontal tissue destruction and notably increased levels of proinflammatory mediators, such as the key inflammatory mediator interleukin (IL)-1beta, are typical of the disease. The opportunistic periodontal pathogen Aggregatibacter actinomycetemcomitans is usually abundant at sites of aggressive periodontitis. Despite potent host immune system responses to subgingival invaders, A. actinomycetemcomitans is able to resist clearance attempts. Moreover, some strains of A. actinomycetemcomitans can generate genetic diversity through natural transformation, which may improve the species’ adjustment tothe subgingival environment in the long term. Some biofilm forming species are known to bind and sense human cytokines. As a response to cytokines, bacteria may increase biofilm formation and alter their expression of virulence genes. Specific outer membrane receptors for interferon-γ or IL-1β have been characterised in two Gram-negative pathogens. Because little is known about periodontal pathogens’ ability to sense cytokines, we used A. actinomycetemcomitans as a model organism to investigate how the species responds to IL-1beta. The main aims of this thesis were to explore cytokine binding on single-species A. actinomycetemcomitans biofilms and to determine the effects of cytokines on the biofilm formation and metabolic activity of the species. Additionally, the cytokine’s putative internalisation and interaction with A. actinomycetemcomitans proteins were studied. The possible impact of biofilm IL-1beta sequestering on the proliferation and apoptosis of gingival keratinocyte cells was evaluated in an organotypic mucosa co-culture model. Finally, the role of the extramembranous domain of the outer membrane protein HofQ (emHofQ) in DNA binding linked to DNA uptake in A. actinomycetemcomitans was examined. Our main finding revealed that viable A. actinomycetemcomitans biofilms can bind and take up the IL-1β produced by gingival cells. At the sites of pathogen-host interaction, the proliferation and apoptosis of gingival keratinocytes decreased slightly. Notably, the exposure of biofilms to IL-1beta caused their metabolic activity to drop, which may be linked to the observed interaction of IL-1beta with the conserved intracellular proteins DNA binding protein HU and the trimeric form of ATP synthase subunit beta. A Pasteurellaceaespecific lipoprotein, which had no previously determined function, was characterized as an IL-1beta interacting membrane protein that was expressed in the biofilm cultures of all tested A. actinomycetemcomitans strains. The use of a subcellular localisation tool combined with experimental analyses suggested that the identified lipoprotein, bacterial interleukin receptor I (BilRI), may be associated with the outer membrane with a portion of the protein oriented towards the external milieu. The results of the emHofQ study indicated that emHofQ has both the structural and functional capability to bind DNA. This result implies that emHofQ plays a role in DNA assimilation. The results from the current study also demonstrate that the Gram-negative oral species appears to sense the central proinflammatory mediator IL-1beta.

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Protein engineering aims to improve the properties of enzymes and affinity reagents by genetic changes. Typical engineered properties are affinity, specificity, stability, expression, and solubility. Because proteins are complex biomolecules, the effects of specific genetic changes are seldom predictable. Consequently, a popular strategy in protein engineering is to create a library of genetic variants of the target molecule, and render the population in a selection process to sort the variants by the desired property. This technique, called directed evolution, is a central tool for trimming protein-based products used in a wide range of applications from laundry detergents to anti-cancer drugs. New methods are continuously needed to generate larger gene repertoires and compatible selection platforms to shorten the development timeline for new biochemicals. In the first study of this thesis, primer extension mutagenesis was revisited to establish higher quality gene variant libraries in Escherichia coli cells. In the second study, recombination was explored as a method to expand the number of screenable enzyme variants. A selection platform was developed to improve antigen binding fragment (Fab) display on filamentous phages in the third article and, in the fourth study, novel design concepts were tested by two differentially randomized recombinant antibody libraries. Finally, in the last study, the performance of the same antibody repertoire was compared in phage display selections as a genetic fusion to different phage capsid proteins and in different antibody formats, Fab vs. single chain variable fragment (ScFv), in order to find out the most suitable display platform for the library at hand. As a result of the studies, a novel gene library construction method, termed selective rolling circle amplification (sRCA), was developed. The method increases mutagenesis frequency close to 100% in the final library and the number of transformants over 100-fold compared to traditional primer extension mutagenesis. In the second study, Cre/loxP recombination was found to be an appropriate tool to resolve the DNA concatemer resulting from error-prone RCA (epRCA) mutagenesis into monomeric circular DNA units for higher efficiency transformation into E. coli. Library selections against antigens of various size in the fourth study demonstrated that diversity placed closer to the antigen binding site of antibodies supports generation of antibodies against haptens and peptides, whereas diversity at more peripheral locations is better suited for targeting proteins. The conclusion from a comparison of the display formats was that truncated capsid protein three (p3Δ) of filamentous phage was superior to the full-length p3 and protein nine (p9) in obtaining a high number of uniquely specific clones. Especially for digoxigenin, a difficult hapten target, the antibody repertoire as ScFv-p3Δ provided the clones with the highest affinity for binding. This thesis on the construction, design, and selection of gene variant libraries contributes to the practical know-how in directed evolution and contains useful information for scientists in the field to support their undertakings.