The Pseudomonas syringae-derived HrpA pilins - molecular characterization and biotechnological application of the transcripts

Many Gram-negative bacteria pathogenic to plants and animals possess type III secretion systems that are used to cause disease. Effector proteins are injected into host cells using the type III secretion machineries. Despite vigorous studies, the nature of the secretion signal for type III secreted proteins still remains elusive. Both mRNA and proteinaceous signals have been proposed. Findings on coupling of translation to secretion by the type III secretion systems are also still contradictory. This study dealt with the secretion signal of HrpA from Pseudomonas syringae pathovar tomato. HrpA is the major component of the type III secretion system-associated Hrp pilus and a substrate for the type III secretion systems. The secretion signal was shown to reside in the first 15 codons or amino acids, a location typical for type III secretion signals. Translation of HrpA in the absence of a functional type III secretion system was established, but it does not exclude the possibility of coupling of translation to secretion when the secretion apparatus is present. The hrpA transcripts from various unrelated plant pathogenic bacteria were shown to be extremely stable. The biological relevance of this observation is unknown, but possible explanations include the high prevalence of HrpA protein, an mRNA secretion signal or timing of secretion. The hrpA mRNAs are stable over a wide range of temperatures, in the absence of translating ribosomes and even in the heterologous host Escherichia coli. The untranslated regions (UTRs) of hrpA transcripts from at least 20 pathovars of Pseudomonas syringae are highly homologous, whilst their coding regions exhibit low similarity. The stable nature of hrpA messenger RNAs is likely to be due to the folding of their 5 and 3 UTRs. In silico the UTRs seem to form stem-loop structures, the hairpin structures in the 3 UTRs being rich in guanidine and cytosine residues. The stable nature of the hrpA transcript redirected the studies to the stabilization of heterologous transcripts and to the use of stable messenger RNAs in recombinant protein production. Fragments of the hrpA transcript can be used to confer stability on heterologous transcripts from several sources of bacterial and eukaryotic origin, and to elevate the levels of production of the corresponding recombinant proteins several folds. hrpA transcript stabilizing elements can be used for improving the yields of recombinant proteins even in Escherichia coli, one of the most commonly used industrial protein production hosts.

Bioavailability and toxicity of chemicals in inland waters : the importance of prevailing water chemistry and implications for risk assessment

Physicochemical characterization of freshwater samples from Finland, Sweden, the Netherlands, and Spain revealed that water hardness and pH decreased and the quantity and quality of humic substances changed considerably in this geographical series from south to north. Since the ambient water chemistry may affect the availability of chemicals, the total aqueous concentration of a chemical may be insufficient to predict the bioconcentration, subsequent biological response, and thus risk. In addition, organisms could be affected directly by water quality characteristics. In this context the main objective of this thesis was to investigate the bioavailability of selected ecotoxicologically relevant chemicals (cadmium, benzo(a)pyrene, and pyrene) in various European surface waters and to show the importance of certain water chemistry characteristics in interpreting the bioavailability and toxicity results. The bioavailability of cadmium to Daphnia magna was examined in very soft humic lake water. Humic substances as natural ligands decreased the free and bioavailable proportion of cadmium in soft lake water. As a consequence the uptake rate and the acute toxicity decreased compared with the humic-free reference. When the hardness of humic lake water was artificially elevated, the acute toxicity of cadmium decreased, although the proportion of free cadmium increased. The decreased bioavailability of cadmium in hard water was a result of effective competition for uptake by the hardness cations, especially calcium ions. The protective role of humic substances and water hardness against cadmium toxicity was also observed in Lumbriculus variegatus, although D. magna was more sensitive to cadmium. The bioavailability of two polycyclic aromatic hydrocarbons (PAHs), pyrene and benzo(a)pyrene, was studied in European surface waters of varying water chemistry. Humic substances acted as complexing ligands with both PAHs, but the bioavailability of the more lipophilic benzo(a)pyrene to D. magna was affected more by humic substances than that of pyrene. In addition, not only the quantity of humic substances, but also their quality affected the bioavailability of benzo(a)pyrene. Nevertheless, the humic substances played a protective role in the photo-enhanced toxicity of pyrene under UV-B radiation. Water hardness had no effect on pyrene toxicity. Results indicate that the typical physicochemical characteristics of boreal freshwaters should be considered carefully in local and regional risk assessment of chemicals concerning the Fennoscandian region.

Ecological communities in variable environments : dynamics and diversity under coloured environmental stochasticity

While environmental variation is an ubiquitous phenomenon in the natural world which has for long been appreciated by the scientific community recent changes in global climatic conditions have begun to raise consciousness about the economical, political and sociological ramifications of global climate change. Climate warming has already resulted in documented changes in ecosystem functioning, with direct repercussions on ecosystem services. While predicting the influence of ecosystem changes on vital ecosystem services can be extremely difficult, knowledge of the organisation of ecological interactions within natural communities can help us better understand climate driven changes in ecosystems. The role of environmental variation as an agent mediating population extinctions is likely to become increasingly important in the future. In previous studies population extinction risk in stochastic environmental conditions has been tied to an interaction between population density dependence and the temporal autocorrelation of environmental fluctuations. When populations interact with each other, forming ecological communities, the response of such species assemblages to environmental stochasticity can depend, e.g., on trophic structure in the food web and the similarity in species-specific responses to environmental conditions. The results presented in this thesis indicate that variation in the correlation structure between species-specific environmental responses (environmental correlation) can have important qualitative and quantitative effects on community persistence and biomass stability in autocorrelated (coloured) environments. In addition, reddened environmental stochasticity and ecological drift processes (such as demographic stochasticity and dispersal limitation) have important implications for patterns in species relative abundances and community dynamics over time and space. Our understanding of patterns in biodiversity at local and global scale can be enhanced by considering the relevance of different drift processes for community organisation and dynamics. Although the results laid out in this thesis are based on mathematical simulation models, they can be valuable in planning effective empirical studies as well as in interpreting existing empirical results. Most of the metrics considered here are directly applicable to empirical data.

Two views on interstellar dust: near-infrared scattering and polarized thermal dust emission

Interstellar clouds are not featureless, but show quite complex internal structures of filaments and clumps when observed with high enough resolution. These structures have been generated by 1) turbulent motions driven mainly by supernovae, 2) magnetic fields working on the ions and, through neutral-ion collisions, on neutral gas as well, and 3) self-gravity pulling a dense clump together to form a new star. The study of the cloud structure gives us information on the relative importance of each of these mechanisms, and helps us to gain a better understanding of the details of the star formation process. Interstellar dust is often used as a tracer for the interstellar gas which forms the bulk of the interstellar matter. Some of the methods that are used to derive the column density are summarized in this thesis. A new method, which uses the scattered light to map the column density in large fields with high spatial resolution, is introduced. This thesis also takes a look at the grain alignment with respect to the magnetic fields. The aligned grains give rise to the polarization of starlight and dust emission, thus revealing the magnetic field. The alignment mechanisms have been debated for the last half century. The strongest candidate at present is the radiative torques mechanism. In the first four papers included in this thesis, the scattered light method of column density estimation is formulated, tested in simulations, and finally used to obtain a column density map from observations. They demonstrate that the scattered light method is a very useful and reliable tool in column density estimation, and is able to provide higher resolution than the near-infrared color excess method. These two methods are complementary. The derived column density maps are also used to gain information on the dust emissivity within the observed cloud. The two final papers present simulations of polarized thermal dust emission assuming that the alignment happens by the radiative torques mechanism. We show that the radiative torques can explain the observed decline of the polarization degree towards dense cores. Furthermore, the results indicate that the dense cores themselves might not contribute significantly to the polarized signal, and hence one needs to be careful when interpreting the observations and deriving the magnetic field.

Det översättande jaget: homo significans – homo interpres

Abstract (The translating subject: Homo significans – homo interpres): A whole discipline, translation studies, is built around the translator’s acts and the translating event. What is the translating subject? How is (s)he working and why? I discuss some aspects of the translating subject, analyzed from literary translators’ descriptions of themselves in anthologies. Within the theoretical framework of semiotics and hermeneutics, I comment on the creative processes of literary translators, where they act as a medium in the translator’s space: an encounter of the author, the translator, and the reader. With respect to reading, interpreting, and translating a text, the translating subject is a homo interpres, i.e. a homo significans producing meaning. The goal of the translating subject is the chiasm of semiosis, the dynamic process when meaning is manifested in the semiosphere. The mission for the translating subject is to deal with the paradox: to create the same but other text. For the complexity of the act of reading, interpreting, and translating texts, I use the concept of palimpsest.

Beyond Words : The European Court of Justice and Legal Certainty in Multilingual EU Law

This study addresses the issue of multilingualism in EU law. More specifically, it explores the implications of multilingualism for conceptualising legal certainty, a central principle of law both in domestic and EU legal systems. The main question addressed is how multilingualism and legal certainty may be reconciled in the EU legal system. The study begins with a discussion on the role of translation in drafting EU legislation and its implications for interpreting EU law at the European Court of Justice (ECJ). Uncertainty regarding the meaning of multilingual EU law and the interrelationship between multilingualism and ECJ methods of interpretation are explored. This analysis leads to questioning the importance of linguistic-semantic methods of interpretation, especially the role of comparing language versions for clarifying meaning and the ordinary meaning thesis, and to placing emphasis on other, especially the teleological, purpose-oriented method of interpretation. As regards the principle of legal certainty, the starting-point is a two-dimensional concept consisting of both formal and substantive elements; of predictability and acceptability. Formal legal certainty implies that laws and adjudication, in particular, must be predictable. Substantive legal certainty is related to rational acceptability of judicial decision-making placing emphasis on its acceptability to the legal community in question. Contrary to predictability that one might intuitively relate to linguistic-semantic methods of interpretation, the study suggests a new conception of legal certainty where purpose, telos, and other dynamic methods of interpretation are of particular significance for meaning construction in multilingual EU law. Accordingly, the importance of purposive, teleological interpretation as the standard doctrine of interpretation in a multilingual legal system is highlighted. The focus on rational, substantive acceptability results in emphasising discourse among legal actors among the EU legal community and stressing the need to give reasons in favour of proposed meaning in accordance with dynamic methods of interpretation including considerations related to purposes, aims, objectives and consequences. In this context, the role of ideal discourse situations and communicative action taking the form of interaction among the EU legal community in an ongoing dialogue especially in the preliminary ruling procedure is brought into focus. In order for this dialogue to function, it requires that the ECJ gives persuasive, convincing and acceptable reasons in justifying its decisions. This necessitates transparency, sincerity, and dialogue with the relevant audience.

Light scattering in random media with wavelength-scale structures : astronomical and industrial applications

Light scattering, or scattering and absorption of electromagnetic waves, is an important tool in all remote-sensing observations. In astronomy, the light scattered or absorbed by a distant object can be the only source of information. In Solar-system studies, the light-scattering methods are employed when interpreting observations of atmosphereless bodies such as asteroids, atmospheres of planets, and cometary or interplanetary dust. Our Earth is constantly monitored from artificial satellites at different wavelengths. With remote sensing of Earth the light-scattering methods are not the only source of information: there is always the possibility to make in situ measurements. The satellite-based remote sensing is, however, superior in the sense of speed and coverage if only the scattered signal can be reliably interpreted. The optical properties of many industrial products play a key role in their quality. Especially for products such as paint and paper, the ability to obscure the background and to reflect light is of utmost importance. High-grade papers are evaluated based on their brightness, opacity, color, and gloss. In product development, there is a need for computer-based simulation methods that could predict the optical properties and, therefore, could be used in optimizing the quality while reducing the material costs. With paper, for instance, pilot experiments with an actual paper machine can be very time- and resource-consuming. The light-scattering methods presented in this thesis solve rigorously the interaction of light and material with wavelength-scale structures. These methods are computationally demanding, thus the speed and accuracy of the methods play a key role. Different implementations of the discrete-dipole approximation are compared in the thesis and the results provide practical guidelines in choosing a suitable code. In addition, a novel method is presented for the numerical computations of orientation-averaged light-scattering properties of a particle, and the method is compared against existing techniques. Simulation of light scattering for various targets and the possible problems arising from the finite size of the model target are discussed in the thesis. Scattering by single particles and small clusters is considered, as well as scattering in particulate media, and scattering in continuous media with porosity or surface roughness. Various techniques for modeling the scattering media are presented and the results are applied to optimizing the structure of paper. However, the same methods can be applied in light-scattering studies of Solar-system regoliths or cometary dust, or in any remote-sensing problem involving light scattering in random media with wavelength-scale structures.

Looking-Glass Reflections : Norms in translating Lewis Carroll

This thesis in the field of translation studies focusses on the role of norms in the work of a literary translator. Norms are seen as guidelines for the translator; they also reflect the way the target audience either accepts or rejects the translation. Thus they are of an intersubjective nature. The theoretical background of the study is based on the views on norms of Andrew Chesterman and Gideon Toury. The writer makes use of her own editing and publishing experience, as well as her experience in translating Lewis Carroll, considering these in respect to theoretical views of norms and vice versa. The aim is also to bring to light some of the tacit knowledge related to translating, editing and publishing in Finland. The study has three angles. First, the writer introduces the norms of Finnish literary translation as gathered from her own working experience. The sources from which these norms arise and which affect them are briefly described. Six central translation norms emerge; they are described and exemplified through cases of Carroll translation. Secondly, a small-scale questionnaire study is presented. This was carried out in order to sound the normative views of other translators and to limit the role of subjectivity. The views of the informants largely support the set of norms presented by the writer, although the norms of quotability and harmony between translation and illustration do not arise. Instead, the answers give rise to a seventh, ethical norm, which is labelled the norm of integrity. Thirdly, there is a brief presentation of Lewis Carroll, his Alice books and their translation history in Finland. The retranslation hypothesis and the motives of retranslation are considered in the light of the work of Outi Paloposki and Kaisa Koskinen. The final part of the thesis plunges into actual translation work. It includes one and a half chapters of Through the Looking-Glass (Alicen seikkailut peilintakamaassa) as translated into Finnish by the writer. The translation commentary first discusses a number of recurring and general translation points; the running commentary then analyses 77 individual translation solutions and their justifications. The writer uses introspection as a way of reflecting on her own translation process, its decisive points and the role of norms therein. Keywords: Translation studies, Carroll, norms