Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Multicultural Belonging. Individuals across cultures, languages and places

The article-based doctoral dissertation deals with adult individuals in Western societies who were born into multilingual and multicultural families and have parents of different nationalities. The study’s participants grew up outside their parents’ countries of origin and relate to a multitude of bonds that link them across various cultures, languages and places. The study explores the social dimension of cultural belonging and examines diverse approaches that enable the participants to create notions of belonging and identification despite possessing at times contradictory transnational allegiances. The works offers new perspectives on transnational belonging and makes a timely contribution to discussions in the fields of cultural heritage studies, ethnology and transnational studies. The dissertation combines qualitative research methods with an insider perspective. The empirical material is based on semi-structured interviews with fifteen participants, among which are also the author’s siblings. The study addresses the relevance of the author’s personal situatedness and her multi-faceted roles as well as ethical concerns related to the methodological approach of insider research. The social dimension of cultural identities affect both the participants’ identification with their multiple attachments and language use in everyday life. The key research findings present interrelated discussions of the participants’ notion of being a mixture, the importance of family bonds and multilingualism, a specific mixed family lifestyle, the notion of non-belonging and the study participants’ sense of otherness as a means of creating communality with others. The study discusses the participants’ various life strategies of flexible relativising, juggling with multiple affiliations, the approach of “blending in” and their sense of ironic nation-ness for constructing a coherent sense of belonging. The author argues that multicultural belonging is inextricably connected to an association with multiple languages, cultures and places. Multicultural belonging is relational and depends on the context, social relationships and locations. The study proposes that multicultural belonging creates a tolerant understanding of membership and enables experiences of cosmopolitanism and selected notions of allegiance.

The Hybridity of Violence : Location, Dislocation, and Relocation in Contemporary Canadian Multicultural and Indigenous Writing

Cette thèse explore la relation entre les littératures autochtones et multiculturelles du Canada. Même si les critiques littéraires examinent les littératures dites mineures de plus en plus, ces dernières sont rarement étudiées sans la présence médiatrice de la littérature canadienne considérée comme étant dominante. Afin de produire une telle analyse, cette thèse mobilise le concept d’hybridité en tant que catégorie d’analyse de texte qui, en plus de son histoire raciale et coloniale, décrit convenablement les formes d’expérimentations stylistiques que les écrivains autochtones et multiculturels emploient afin de représenter et questionner leur marginalisation. Ne voulant pas reproduire les interprétations fétichistes qui réduisent les littératures autochtones et multiculturelles à leurs représentations de concepts d’altérité, j’examine ces textes dans leurs relations avec différents discours et débats ayant marqué les études littéraires canadiennes, notamment, le long poème canadien, l’écriture des prairies canadiennes, la littérature urbaine, le multiculturalisme, et les premières nations. Ma méthode d’analyse repose sur la façon dont chaque texte étudié alimente ces catégories d’analyse littéraire tout en les modifiant radicalement. De plus, je développe un cadre conceptuel et théorique permettant l’étude de la relation entre les textes autochtones et multiculturels sans toutefois confondre ou réduire les contextes d’où proviennent ces littératures. Ma thèse et ma méthode d’analyse se concrétise par l’interprétation des textes écrits par Armand Garnet Ruffo, Suzette Mayr, Rawi Hage, et Jeannette Armstrong. Le chapitre d’introduction détaille la façon dont la relation entre les textes autochtones et multiculturels a été appréhendée jusqu’à présent. J’y élabore mon cadre théorique qui joint et réinterprète de manière critique diverses théories, dont celle du postcolonialisme, de l’hybridité, et de la mondialisation, et la façon dont ces théories se rapportent aux études littéraires canadiennes. Dans mon deuxième chapitre, j’analyse le long poème d’Armand Garnet Ruffo, Grey Owl: The Mystery of Archie Belaney, en m’attardant particulièrement aux stratégies d’expérimentations stylistiques et génériques que Ruffo développe afin de rendre le genre du long poème canadien autochtone et de questionner l’identité de Grey Owl. Mon troisième chapitre examine Venous Hum, un roman de Suzette Mayr. Ce texte remet en question la tradition de « prairie writing », le multiculturalisme canadien, et le conservatisme albertain à travers son style expérimental, son usage des métaphores et du réalisme magique. Mon quatrième chapitre interprète le roman montréalais Cockroach, de Rawi Hage, en examinant la façon dont ses unités locales, nationales, et globales rencontrent le colonialisme et contestent les discours nationaux une fois que sa critique de la mondialisation se trouve réarticulée dans une approbation des discours d’interventions humanitaires de l’occident. Mon dernier chapitre explore le roman de Jeannette Armstrong, Whispering in Shadows, afin de démontrer les limites de ma méthode d’analyse. Puisque l’hybridité sous-entend inévitablement la notion d’assimilation, son application dans le contexte de l’œuvre d’Armstrong s’avèrerait réductrice. Pour cette raison, ce chapitre utilise des concepts autochtones définis par Armstrong afin de développer une méthode de lecture non-hégémonique. Ma thèse examine donc la façon dont chaque texte déploie le concept d’hybridité pour à la fois contester et enrichir les discours critiques qui tentent de contenir ces textes. Elle contribue aux études postcoloniales de la littérature canadienne en élargissant leur champ habituel pour inclure les complexités des théories de la mondialisation, et en examinant quelles stratégies littéraires les textes autochtones et multiculturels partagent, mais mobilisent à des fins différentes.

Analysis of applications and of conceptions for an application-oriented mathematics instruction

In connection with the (revived) demand for considering applications in the teaching of mathematics, various schemata or lists of criteria have been developed since the end of the sixties, which set up requirements about closeness to the real world or about the type of mathematics being used, and which have made it possible to analyze the available applications in their light. After having stated the problem (in section 1), we present (in section 2) a sketch of some of the best known of these and of some earlier schemata, although we are not aiming for a complete picture. Then (in section 3) we distinguish among different dimensions.in the analysis of applications. With this as a basis, we develop (in section 4) our own suggestion for categorizing types of applications and conceptions for an application-oriented mathematics instruction. Then (in section 5) we illustrate our schemata by some examples of performed evaluations. Finally (in section 6), we present some preliminary first results of the analysis of teaching conceptions.

Storm Tracking and eScience

A new 'storm-tracking approach' to analysing the prediction of storms by different forecast systems has recently been developed. This paper provides a brief illustration of the type of results/information that can be obtained using the approach. It also describes in detail how eScience methodologies have been used to help apply the storm-tracking approach to very large datasets

Jupiter's and Saturn's convectively driven banded jets in the laboratory

The banded patterns of cloud and wind are among the most striking features of the atmospheres of Jupiter and Saturn, but their dynamical origin remains poorly understood. Most approaches towards understanding zonation so far (also in the terrestrial oceans) have used highly idealized models to show that it might originate from dynamical anisotropy in a shallow turbulent fluid layer due to the planetary β-effect. Here we report the results of laboratory experiments, conducted on a 14-m diameter turntable, which quantitatively confirm that multiple zonal jets may indeed be generated and maintained by this mechanism in the presence of deep convection and a topographic β-effect. At the very small values of Ekman number (≤2 × 10−5) and large local Reynolds numbers (≥2000, based on jet scales) achieved, the kinetic energy spectra suggest the presence of both energy-cascading and enstrophy-cascading inertial ranges in addition to the zonation near twice the Rhines wave number.

Spontaneous generation and impact of inertia-gravity waves in a stratified, two-layer shear flow

Inertia-gravity waves exist ubiquitously throughout the stratified parts of the atmosphere and ocean. They are generated by local velocity shears, interactions with topography, and as geostrophic (or spontaneous) adjustment radiation. Relatively little is known about the details of their interaction with the large-scale flow, however. We report on a joint model/laboratory study of a flow in which inertia-gravity waves are generated as spontaneous adjustment radiation by an evolving large-scale mode. We show that their subsequent impact upon the large-scale dynamics is generally small. However, near a potential transition from one large-scale mode to another, in a flow which is simultaneously baroclinically-unstable to more than one mode, the inertia-gravity waves may strongly influence the selection of the mode which actually occurs.

A Bayesian approach to estimate sensible and latent heat over vegetated land surface

Sensible and latent heat fluxes are often calculated from bulk transfer equations combined with the energy balance. For spatial estimates of these fluxes, a combination of remotely sensed and standard meteorological data from weather stations is used. The success of this approach depends on the accuracy of the input data and on the accuracy of two variables in particular: aerodynamic and surface conductance. This paper presents a Bayesian approach to improve estimates of sensible and latent heat fluxes by using a priori estimates of aerodynamic and surface conductance alongside remote measurements of surface temperature. The method is validated for time series of half-hourly measurements in a fully grown maize field, a vineyard and a forest. It is shown that the Bayesian approach yields more accurate estimates of sensible and latent heat flux than traditional methods.

Inclusive approaches to teaching and learning mathematics

This chapter explores the role of mentors in supporting pre-service teachers to include all children in mathematics teaching, no matter what their individual needs.

Uncertainties In Future Projections Of Extreme Rainfall: The Role Of Climate Model, Emission Scenario And Randomness

Climate change has resulted in substantial variations in annual extreme rainfall quantiles in different durations and return periods. Predicting the future changes in extreme rainfall quantiles is essential for various water resources design, assessment, and decision making purposes. Current Predictions of future rainfall extremes, however, exhibit large uncertainties. According to extreme value theory, rainfall extremes are rather random variables, with changing distributions around different return periods; therefore there are uncertainties even under current climate conditions. Regarding future condition, our large-scale knowledge is obtained using global climate models, forced with certain emission scenarios. There are widely known deficiencies with climate models, particularly with respect to precipitation projections. There is also recognition of the limitations of emission scenarios in representing the future global change. Apart from these large-scale uncertainties, the downscaling methods also add uncertainty into estimates of future extreme rainfall when they convert the larger-scale projections into local scale. The aim of this research is to address these uncertainties in future projections of extreme rainfall of different durations and return periods. We plugged 3 emission scenarios with 2 global climate models and used LARS-WG, a well-known weather generator, to stochastically downscale daily climate models’ projections for the city of Saskatoon, Canada, by 2100. The downscaled projections were further disaggregated into hourly resolution using our new stochastic and non-parametric rainfall disaggregator. The extreme rainfall quantiles can be consequently identified for different durations (1-hour, 2-hour, 4-hour, 6-hour, 12-hour, 18-hour and 24-hour) and return periods (2-year, 10-year, 25-year, 50-year, 100-year) using Generalized Extreme Value (GEV) distribution. By providing multiple realizations of future rainfall, we attempt to measure the extent of total predictive uncertainty, which is contributed by climate models, emission scenarios, and downscaling/disaggregation procedures. The results show different proportions of these contributors in different durations and return periods.

Social sciences and social reality in Central America

Includes bibliography

Neuronal differentiation and epithelial integrity: the role of Drosophila Short stop

The nervous system is the most complex organ in animals and the ordered interconnection of neurons is an essential prerequisite for normal behaviour. Neuronal connectivity requires controlled neuronal growth and differentiation. Neuronal growth essentially depends on the actin and microtubule cytoskeleton, and it has become increasingly clear, that crosslinking of these cytoskeletal fractions is a crucial regulatory process. The Drosophila Spectraplakin family member Short stop (Shot) is such a crosslinker and is crucial for several aspects of neuronal growth. Shot comprises various domains: An actin binding domain, a plakin-like domain, a rod domain, calcium responsive EF-hand motifs, a microtubule binding Gas2 domain, a GSR motif and a C-terminal EB1aff domain. Amongst other phenotypes, shot mutant animals exhibit severely reduced dendrites and neuromuscular junctions, the subcellular compartmentalisation of the transmembrane protein Fasciclin2 is affected, but it is also crucially required in other tissues, for example for the integrity of tendon cells, specialised epidermal cells which anchor muscles to the body wall. Despite these striking phenotypes, Shot function is little understood, and especially we do not understand how it can carry out functions as diverse as those described above. To bridge this gap, I capitalised on the genetic possibilities of the model system Drosophila melanogaster and carried out a structure-function analysis in different neurodevelopmental contexts and in tendon cells. To this end, I used targeted gene expression of existing and newly generated Shot deletion constructs in Drosophila embryos and larvae, analyses of different shot mutant alleles, and transfection of Shot constructs into S2 cells or cultured fibroblasts. My analyses reveal that a part of the Shot C-terminus is not essential in the nervous system but in tendon cells where it stabilises microtubules. The precise molecular mechanism underlying this activity is not yet elucidated but, based on the findings presented here, I have developed three alternative testable hypothesis. Thus, either binding of the microtubule plus-end tracking molecule EB1 through an EB1aff domain, microtubulebundling through a GSR rich motif or a combination of both may explain a context-specific requirement of the Shot C-terminus for tendon cell integrity. Furthermore, I find that the calcium binding EF-hand motif in Shot is exclusively required for a subset of neuronal functions of Shot but not in the epidermal tendon cells. These findings pave the way for complementary studies studying the impact of [Ca2+] on Shot function. Besides these differential requirements of Shot domains I find, that most Shot domains are required in the nervous system and tendon cells alike. Thus the microtubule Gas2 domain shows no context specific requirements and is equally essential in all analysed cellular contexts. Furthermore, I could demonstrate a partial requirement of the large spectrin-repeat rod domain of Shot in neuronal and epidermal contexts. I demonstrate that this domain is partially required in processes involving growth and/or tissue stability but dispensable for cellular processes where no mechanical stress resistance is required. In addition, I demonstrate that the CH1 domain a part of the N-terminal actin binding domain of Shot is only partially required for all analysed contexts. Thus, I conclude that Shot domains are functioning different in various cellular environments. In addition my study lays the base for future projects, such as the elucidation of Shot function in growth cones. Given the high degree of conservation between Shot and its mammalian orthologues MACF1/ACF7 and BPAG1, I believe that the findings presented in this study will contribute to the general understanding of spectraplakins across species borders.

Nanoscale effects and applications of self-organized nanostructured thin films

A nanostructured thin film is a thin material layer, usually supported by a (solid) substrate, which possesses subdomains with characteristic nanoscale dimensions (10 ~ 100 nm) that are differentiated by their material properties. Such films have captured vast research interest because the dimensions and the morphology of the nanostructure introduce new possibilities to manipulating chemical and physical properties not found in bulk materials. Block copolymer (BCP) self-assembly, and anodization to form nanoporous anodic aluminium oxide (AAO), are two different methods for generating nanostructures by self-organization. Using poly(styrene-block-methyl methacrylate) (PS-b-PMMA) nanopatterned thin films, it is demonstrated that these polymer nanopatterns can be used to study the influence of nanoscale features on protein-surface interactions. Moreover, a method for the directed assembly of adsorbed protein nanoarrays, based on the nanoscale juxtaposition of the BCP surface domains, is also demonstrated. Studies on protein-nanopattern interactions may inform the design of biomaterials, biosensors, and relevant cell-surface experiments that make use of nanoscale structures. In addition, PS-b-PMMA and AAO thin films are also demonstrated for use as optical waveguides at visible wavelengths. Due to the sub-wavelength nature of the nanostructures, scattering losses are minimized, and the optical response is amenable to analysis with effective medium theory (EMT). Optical waveguide measurements and EMT analysis of the films’ optical anisotropy enabled the in situ characterization of the PS-b-PMMA nanostructure, and a variety of surface processes within the nanoporous AAO involving (bio)macromolecules at high sensitivity.

Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures

Membrane proteins play a major role in every living cell. They are the key factors in the cell’s metabolism and in other functions, for example in cell-cell interaction, signal transduction, and transport of ions and nutrients. Cytochrome c oxidase (CcO), as one of the membrane proteins of the respiratory chain, plays a significant role in the energy transformation of higher organisms. CcO is a multi centered heme protein, utilizing redox energy to actively transport protons across the mitochondrial membrane. One aim of this dissertation is to investigate single steps in the mechanism of the ion transfer process coupled to electron transfer, which are not fully understood. The protein-tethered bilayer lipid membrane is a general approach to immobilize membrane proteins in an oriented fashion on a planar electrode embedded in a biomimetic membrane. This system enables the combination of electrochemical techniques with surface enhanced resonance Raman (SERRS), surface enhanced reflection absorption infrared (SEIRAS), and surface plasmon spectroscopy to study protein mediated electron and ion transport processes. The orientation of the enzymes within the surface confined architecture can be controlled by specific site-mutations, i.e. the insertion of a poly-histidine tag to different subunits of the enzyme. CcO can, thus, be oriented uniformly with its natural electron pathway entry pointing either towards or away from the electrode surface. The first orientation allows an ultra-fast direct electron transfer(ET) into the protein, not provided by conventional systems, which can be leveraged to study intrinsic charge transfer processes. The second orientation permits to study the interaction with its natural electron donor cytochrome c. Electrochemical and SERR measurements show conclusively that the redox site structure and the activity of the surface confined enzyme are preserved. Therefore, this biomimetic system offers a unique platform to study the kinetics of the ET processes in order to clarify mechanistic properties of the enzyme. Highly sensitive and ultra fast electrochemical techniques allow the separation of ET steps between all four redox centres including the determination of ET rates. Furthermore, proton transfer coupled to ET could be directly measured and discriminated from other ion transfer processes, revealing novel mechanistic information of the proton transfer mechanism of cytochrome c oxidase. In order to study the kinetics of the ET inside the protein, including the catalytic center, time resolved SEIRAS and SERRS measurements were performed to gain more insight into the structural and coordination changes of the heme environment. The electrical behaviour of tethered membrane systems and membrane intrinsic proteins as well as related charge transfer processes were simulated by solving the respective sets of differential equations, utilizing a software package called SPICE. This helps to understand charge transfer processes across membranes and to develop models that can help to elucidate mechanisms of complex enzymatic processes.

Locating American Indian Sciences : a report on the development, use, and analysis of a survey of perceptions

All students in the United States of America are required to take science. But what if there is not a science, but in fact a number of sciences? Could every culture, perhaps every different grouping of people, create its own science? This report describes a preliminary survey, the goal of which is to improve the teaching of science at American Indian Opportunities and Industrialization Center in Minneapolis, Minnesota by beginning to understand the differences between Western and American Indian sciences.