In type 1 diabetes (T1D), an autoimmune disease, autoantibodies are preferentially directed against proteins associated with Golgi and post-Golgi secretory vesicles, including insulin secretory granules and synaptic-like microvesicles. Thus, the study of beta-cell autoantigens with yet unknown function may provide novel insight into the secretory machinery of beta-cells and led to the discovery of novel pathways. Islet cell autoantigen of 69 kDa (ICA69) is a T1D autoantigen. It is a cytosolic protein of still unknown function. An impairment in neurotransmitter release upon mutation of its homologue in C. elegans suggests, however, an involvement of ICA69 in neurosecretion. Interestingly, ICA69 contains a BAR domain, present in several proteins involved in intracellular transport. The BAR domain functions as a dimerization motif, provides a general binding interface for different types of GTPases, and is a membrane binding/bending module. Its presence in ICA69 is a further hint supporting the putative involvement of ICA69 in intracellular membrane trafficking. The first part of this thesis was concerned with the characterization of ICA69, and the elucidation of its role in membrane traffic in pancreatic beta-cells. ICA69 was shown to be enriched in the perinuclear region, where also markers of the Golgi region are found. ICA69 was shown to interact with several membrane lipids, preferentially with PI(4)P, enriched on the Golgi complex. During the course of this thesis a combination of biochemical and imaging techniques were applied to investigate the interaction between ICA69 and Rab2, a small GTPase associated with the intermediate compartment and involved in the trafficking between the ER and the Golgi complex. ICA69 was shown to co-immunoprecipitate with Rab2 from INS-1 cells extracts. GST-pull down assays demonstrated that this interaction is GTP-dependent. Furthermore, confocal microscopy indicated that ICA69 and Rab2 extensively colocalize in particulate structures throughout the cytoplasm. Immunocytochemistry and subcellular fractionation experiments suggested that Rab2 recruits ICA69 to membranes. Functional studies indicated that ICA69 over-expression in INS-1 cells has effects that resemble, and in some cases amplify those observed upon Rab2 over-expression. Specifically, it impairs the trafficking between ER and Golgi, measured through the appearance and the conversion of the pro-form of ICA512 in the mature form of the protein. Moreover, it correlates with a redistribution of the beta-COP subunit of the coatomer, participating in the early secretory pathway, between membrane-bound compartments and the cytosol and it reduces stimulated insulin secretion. The data reported in this thesis conclusively point to ICA69 as a novel Rab2 effector, and may therefore contribute to the elucidation the yet poorly understood mechanism of action of Rab2 in the secretory pathway. The second part of the thesis was devoted to the study of an ICA69 paralogue gene, called ICA69-RP. Similarly to ICA69, ICA69-RP mRNA was shown to be primarily present in tissues such as brain and pancreatic islets, showing the expression pattern of a gene preferentially expressed in neuroendocrine cells. Unlike ICA69, however, and similar to other genes associated with the secretory machinery of beta-cells, ICA69-RP appeared to be glucose regulated, as shown by a 1.55 fold increase in mRNA levels upon stimulation of the cells with 25 mM glucose for two hours.Glucose stimulation of beta-cells prompts the activation of post-transcripional mechanisms which quickly up-regulate the expression of secretory granule genes and consequently renew granule stores. The increased expression of ICA69-RP upon glucose stimulation of cells may be part of this process. Unfortunately, all attempts to elucidate the intracellular localization of endogenous ICA69-RP failed, and it was not possible to obtain significant insights about its localization by over-expressing a fusion protein between ICA69-RP and GFP. Unlike other paralogues containing the BAR domain, such as amphiphysin 1 and 2 or Rvs167p and Rvs161p, ICA69 and ICA69-RP were shown not to form heterodimers. Furthermore, ICA69-RP did not show any interaction with Rab2 or Rab1, involved in the anterograde transport between ER and Golgi. Thus, its physiological role remains to be investigated.

Les bones morphogenetic protein (Bmp) sont des morphogènes qui jouent des rôles sur la prolifération et la différenciation cellulaire. La perte de signalisation dans cette voie est associée à la polypose juvénile familiale et à un risque accru de cancer gastrique. Elle est aussi associée avec l’inflammation et la guérison des tissus. Il est montré qu’au niveau de l’estomac, les ligands et les récepteurs de la signalisation des Bmp sont exprimés dans les compartiments épithéliaux et mésenchymateux. Les différents modèles animaux développés ont confirmé l’importance de cette signalisation dans la carcinogenèse gastrique. Cependant, ces modèles causent une perte de signalisation dans l’ensemble de la muqueuse gastrique et ne réussissent pas à montrer un mécanisme. Parallèlement, notre laboratoire a montré qu’une perte de signalisation de la voie des Bmp, exclusivement dans le compartiment épithélial, ne développe pas les phénotypes associés à la progression du cancer gastrique. Ce résultat suggère que les cellules mésenchymateuses pourraient être la clé de l’importance de la signalisation des Bmp dans l’estomac. Afin de mettre en lumière le rôle de la signalisation des Bmp dans le compartiment mésenchymateux, des souris qui perdent de façon spécifique le récepteur de type 1a des Bmp dans ce compartiment ont été généré (Bmpr1aMES). Il semble que la perte de signalisation des Bmp induit au niveau du mésenchyme une modification du comportement et une activation des fibroblastes en myofibroblastes. Cette modification produit également un microenvironnement (matrices, facteurs de croissance, cytokines, interleukines) propice au développement du cancer et induire des modifications importantes de l’épithélium et un appel de cellules immunitaires. Cet environnement semble être suffisant pour réduire de façon importante le nombre de cellules endocriniennes et de cellules pariétales dans l’épithélium gastrique. Il semble que la perte mésenchymateuse de signalisation des Bmp au niveau gastrique entraîne le développement d’une métaplasie au niveau de l’estomac des souris, une hyperplasie atypique qui évolue jusqu'à une dysplasie accompagnée d’une desmoplasie importante. Mes travaux ont également démontré que, dans ce contexte, une mutation oncogénique, comme la perte de Trp53, pourrait devenir maligne. En conclusion, au sein du mésenchyme, la signalisation des Bmp est importante pour le maintien de celui-ci dans un état sain. Il est probable qu’elle joue un rôle important dans le retour à l’état normal suivant les gastrites. Sa perte rend l’estomac des souris fragile au développement d’adénomes. / Abstract : Bone morphogenetic proteins (Bmp) play roles in the proliferation and differentiation. It is also associated with inflammation and tissue repair. Disruption of signaling in this pathway is associated with familial juvenile polyposis and an increase risk of gastric cancer. It has been shown that in the stomach, Bmp signaling is bidirectional. Meaning that ligands and receptors are expressed in both the epithelial and stromal compartments. Gastric abrogation animal models of the Bmp signaling pathway have confirmed the importance of this signaling in gastric carcinogenesis. However these models cause a loss of signaling in both compartments of the gastric mucosa, and the mechanism of action for this has yet been undefined. Previous work by a student in our laboratory provided a model of loss of the Bmp signaling pathway exclusively in the epithelial compartment. This model does not develop phenotypes associated with the progression of gastric cancer, suggesting, that the stromal compartment is the key in tumorigenesis by Bmp signaling in the stomach. To further test this hypothesis, we generated mice with a stromal compartment-specific loss of type1a BMP receptor (Bmpr1aMES). It appears that this deletion in the stroma induced behavior alteration with activation of fibroblasts into myofibroblasts. This change also produces a microenvironment (matrix, growth factors, cytokines, and interleukins) that is conducive to the development of cancer and induces significant modifications of the epithelium as well as a recruitment of immune cells. This microenvironment seems to be sufficient to significantly reduce the number of endocrine cells and parietal cells in the gastric epithelium. It seems that the loss of stromal Bmp signaling in the mice’s stomachs causes development of metaplasia; atypical hyperplasia that progresses to dysplasia accompanied by a significant desmoplasia. My work also shows that in this environment an oncogenic mutation such as the loss of Trp53 may become malignant. In conclusion, in the stromal compartment, Bmp signaling is important for maintaining a healthy state. It is probably involved in the return to the normal state following gastritis, and its loss makes the mouse stomach susceptible to adenoma development.

Diese Arbeit präsentiert 9 Entwurfsmuster in einer Darstellung durch das Compartment Role Object Model(CROM). Dabei wird dessen graphische Notation für rollenbasierte Modelle mit verschiedenen Möglichkeiten zur Darstellung von Bedingungen des Entwurfsmusters benutzt. Über eine Evaluationsoll ermittelt werden, ob das CROM dazu geeignet ist, die Bedingungen von Entwurfsmustern verständlich und schnell erfassbar darzustellen. Dabei soll die graphische Dokumentation dieser helfen. Das kann positive E ekte auf die Entwicklung von Software haben, wie bessere Codequalität, verkürzte Entwicklungszeiten und die Vereinfachung der Kommunikation zwischen Entwicklern.:1 Einleitung 5 1.1 Motivation 5 1.2 Problemde nition 6 1.3 Zielstellung 6 2 Analyse der betrachteten Darstellungsformen 7 2.1 Beschreibungsform der Gang of Four 7 2.2 Beschreibungsform von Dirk Riehle 10 2.3 Darstellung mit dem Compartment Role Object Model 12 3 Aktualisierung der Entwurfsmuster 17 3.1 Strukturelle Entwurfsmuster 17 3.1.1 Composite Pattern 17 3.1.2 Bridge Pattern 22 3.2 Entwurfsmuster zur Kontextadaption 27 3.2.1 Object Adapter Pattern 27 3.2.2 Class Adapter Pattern 30 3.2.3 Decorator Pattern 33 3.3 Entwurfsmuster zur Zustandsverwaltung 38 3.3.1 State Pattern 38 3.3.2 Property Pattern 43 3.4 Verhaltensorientierte Entwurfsmuster 45 3.4.1 Iterator Pattern 45 3.4.2 Mediator Pattern 50 4 Schlussteil 54 4.1 Abschlieÿender Vergleich 54 4.2 Diskussion 57 4.2.1 Adapter Pattern 57 4.2.2 Klienten 57 4.2.3 Methoden und Attribute 58 4.2.4 Klassen 59 4.3 Zusammenfassung 59 4.3.1 Ergebnis 59 4.3.2 Ausblick 60

In type 1 diabetes (T1D), an autoimmune disease, autoantibodies are preferentially directed against proteins associated with Golgi and post-Golgi secretory vesicles, including insulin secretory granules and synaptic-like microvesicles. Thus, the study of beta-cell autoantigens with yet unknown function may provide novel insight into the secretory machinery of beta-cells and led to the discovery of novel pathways. Islet cell autoantigen of 69 kDa (ICA69) is a T1D autoantigen. It is a cytosolic protein of still unknown function. An impairment in neurotransmitter release upon mutation of its homologue in C. elegans suggests, however, an involvement of ICA69 in neurosecretion. Interestingly, ICA69 contains a BAR domain, present in several proteins involved in intracellular transport. The BAR domain functions as a dimerization motif, provides a general binding interface for different types of GTPases, and is a membrane binding/bending module. Its presence in ICA69 is a further hint supporting the putative involvement of ICA69 in intracellular membrane trafficking. The first part of this thesis was concerned with the characterization of ICA69, and the elucidation of its role in membrane traffic in pancreatic beta-cells. ICA69 was shown to be enriched in the perinuclear region, where also markers of the Golgi region are found. ICA69 was shown to interact with several membrane lipids, preferentially with PI(4)P, enriched on the Golgi complex. During the course of this thesis a combination of biochemical and imaging techniques were applied to investigate the interaction between ICA69 and Rab2, a small GTPase associated with the intermediate compartment and involved in the trafficking between the ER and the Golgi complex. ICA69 was shown to co-immunoprecipitate with Rab2 from INS-1 cells extracts. GST-pull down assays demonstrated that this interaction is GTP-dependent. Furthermore, confocal microscopy indicated that ICA69 and Rab2 extensively colocalize in particulate structures throughout the cytoplasm. Immunocytochemistry and subcellular fractionation experiments suggested that Rab2 recruits ICA69 to membranes. Functional studies indicated that ICA69 over-expression in INS-1 cells has effects that resemble, and in some cases amplify those observed upon Rab2 over-expression. Specifically, it impairs the trafficking between ER and Golgi, measured through the appearance and the conversion of the pro-form of ICA512 in the mature form of the protein. Moreover, it correlates with a redistribution of the beta-COP subunit of the coatomer, participating in the early secretory pathway, between membrane-bound compartments and the cytosol and it reduces stimulated insulin secretion. The data reported in this thesis conclusively point to ICA69 as a novel Rab2 effector, and may therefore contribute to the elucidation the yet poorly understood mechanism of action of Rab2 in the secretory pathway. The second part of the thesis was devoted to the study of an ICA69 paralogue gene, called ICA69-RP. Similarly to ICA69, ICA69-RP mRNA was shown to be primarily present in tissues such as brain and pancreatic islets, showing the expression pattern of a gene preferentially expressed in neuroendocrine cells. Unlike ICA69, however, and similar to other genes associated with the secretory machinery of beta-cells, ICA69-RP appeared to be glucose regulated, as shown by a 1.55 fold increase in mRNA levels upon stimulation of the cells with 25 mM glucose for two hours.Glucose stimulation of beta-cells prompts the activation of post-transcripional mechanisms which quickly up-regulate the expression of secretory granule genes and consequently renew granule stores. The increased expression of ICA69-RP upon glucose stimulation of cells may be part of this process. Unfortunately, all attempts to elucidate the intracellular localization of endogenous ICA69-RP failed, and it was not possible to obtain significant insights about its localization by over-expressing a fusion protein between ICA69-RP and GFP. Unlike other paralogues containing the BAR domain, such as amphiphysin 1 and 2 or Rvs167p and Rvs161p, ICA69 and ICA69-RP were shown not to form heterodimers. Furthermore, ICA69-RP did not show any interaction with Rab2 or Rab1, involved in the anterograde transport between ER and Golgi. Thus, its physiological role remains to be investigated.

The tibialis anterior (TA) muscle plays a vital role in human movement such as walking and running. Overuse of TA during these movements leads to an increased susceptibility of injuries e.g. chronic exertional compartment syndrome. TA activation has been shown to be affected by increases in exercise, age, and the external environment (i.e. incline and footwear). Because activation parameters of TA change with condition, it leads to the interpretation that force changes occur too. However,activation is only an approximate indicator of force output of a muscle. Therefore, the overall aim of this thesis was to investigate the parameters affecting accurate measure of TA force, leading to development of a subject-specific EMG-driven model, which takes into consideration specific methodological issues. The first study investigated the reasons why the tendon excursion and geometric method differ so vastly in terms of estimation of TA moment arm. Tendon length changes during the tendon excursion method, and location of the TA line of action and irregularities between talus and foot rotations during the geometric method, were found to affect the accuracy of TA moment arm measurement. A novel, more valid, method was proposed. The second study investigated the errors associated with methods used to account for plantar flexor antagonist co-contraction. A new approach was presented and shown to be, at worse, equivalent to current methods, but allows for accounting throughout the complete range of motion. The final study utilised the outputs from studies one and two to directly measure TA force in vivo. This was used to develop, and validate, an EMG-driven TA force model. Less error was found in the accuracy of estimating TA force when the contractile component length changes were modelled using the ankle, as opposed to the muscle. Overall, these findings increase our understanding of not only the mechanics associated with TA and the ankle, but also improves our ability to accurately monitor these.

There is always a need and drive to improve modern cancer care. Dynamic positron emission tomography (PET) offers the advantage of in vivo functional imaging, combined with the ability to follow the physiological processes over time. In addition, by applying tracer kinetic modeling to the dynamic PET data, thus estimating pharmacokinetic parameters associated to e.g. glucose metabolism, cell proliferation etc., more information about the tissue's underlying biology and physiology can be determined. This supplementary information can potentially be a considerable aid when it comes to the segmentation, diagnosis, staging, treatment planning, early treatment response monitoring and follow-up of cancerous tumors. We have found it feasible to use kinetic parameters for semi-automatic tumor segmentation, and found parametric images to have higher contrast compared to static PET uptake images. There are however many possible sources of errors and uncertainties in kinetic parameters obtained through compartment modeling of dynamic PET data. The variation in the number of detected photons caused by the random nature of radioactive decay, is of course always a major source. Other sources may include: the choice of an appropriate model that is suitable for the radiotracer in question, camera detectors and electronics, image acquisition protocol, image reconstruction algorithm with corrections (attenuation, random and scattered coincidences, detector uniformity, decay) and so on. We have found the early frame sampling scheme in dynamic PET to affect the bias and uncertainty in calculated kinetic parameters, and that scatter corrections are necessary for most but not all parameter estimates. Furthermore, analytical image reconstruction algorithms seem more suited for compartment modeling applications compared to iterative algorithms. This thesis and included papers show potential applications and tools for quantitative pharmacokinetic parameters in oncology, and help understand errors and uncertainties associated with them. The aim is to contribute to the long-term goal of enabling the use of dynamic PET and pharmacokinetic parameters for improvements of today's cancer care. / Det finns alltid ett behov och en strävan att förbättra dagens cancervård. Dynamisk positronemissionstomografi (PET) medför fördelen av in vivo funktionell avbilning, kombinerad med möjligheten att följa fysiologiska processer över tiden. Genom att därtill tillämpa kinetisk modellering på det dynamiska PET-datat, och därigenom skatta farmakokinetiska parametrar associerade till glukosmetabolism, cellproliferation etc., kan ytterligare information om vävnadens underliggande biologi och fysiologi bestämmas. Denna kompletterande information kan potentiellt vara till stor nytta för segmentering, diagnos, stadieindelning, behandlingsplanering, monitorering av tidig behandlingsrespons samt uppföljning av cancertumörer. Vi fann det möjligt att använda kinetiska parametrar för semi-automatisk tumörsegmentering, och fann även att parametriska bilder hade högre kontrast jämfört med upptagsbilder från statisk PET. Det finns dock många möjliga källor till osäkerheter och fel i kinetiska parametrar som beräknats genom compartment-modellering av dynamisk PET. En av de största källorna är det radioaktiva sönderfallets slumpmässiga natur som orsakar variationer i antalet detekterade fotoner. Andra källor inkluderar valet av compartment-modell som är lämplig för den aktuella radiotracern, PET-kamerans detektorer och elektronik, bildtagningsprotokoll, bildrekonstruktionsalgoritm med tillhörande korrektioner (attenuering, slumpmässig och spridd strålning, detektorernas likformighet, sönderfall) och så vidare. Vi fann att tidssamplingsschemat för tidiga bilder i dynamisk PET påverkar både fel och osäkerhet i beräknade kinetiska parametrar, och att bildkorrektioner för spridd strålning är nödvändigt för de flesta men inte alla parametrar. Utöver detta verkar analytiska bildrekonstruktionsalgoritmer vara bättre lämpade för tillämpningar som innefattar compartment-modellering i jämförelse med iterativa algoritmer. Denna avhandling med inkluderade artiklar visar möjliga tillämpningar och verktyg för kvantitativa kinetiska parametrar inom onkologiområdet. Den bidrar också till förståelsen av fel och osäkerheter associerade till dem. Syftet är att bidra till det långsiktiga målet att möjliggöra användandet av dynamisk PET och farmakokinetiska parametrar för att förbättra dagens cancervård.

<p>The mathematical modelling of the reaction and diffusion mechanism of lipophilic toxic compounds in the mammalian cell is a challenging task because of its considerable complexity and variation in the architecture of the cell. The heterogeneity of the cell regarding the enzyme distribution participating in the bio-transformation, makes the modelling even more difficult. In order to reduce the complexity of the model, and to make it less computationally expensive and numerically treatable, Homogenization techniques have been used. The resulting complex system of Partial Differential Equations (PDEs), generated from the model in 2-dimensional axi-symmetric setting is implemented in Comsol Multiphysics. The numerical results obtained from the model show a nice agreement with the in vitro cell experimental results. The model can be extended to more complex reaction systems and also to 3-dimensional space. For the reduction of complexity and computational cost, we have implemented a model of mixed PDEs and Ordinary Differential Equations (ODEs). We call this model as Non-Standard Compartment Model. Then the model is further reduced to a system of ODEs only, which is a Standard Compartment Model. The numerical results of the PDE Model have been qualitatively verified by using the Compartment Modeling approach. The quantitative analysis of the results of the Compartment Model shows that it cannot fully capture the features of metabolic system considered in general. Hence we need a more sophisticated model using PDEs for our homogenized cell model.</p> / Computational Modelling of the Mammalian Cell and Membrane Protein Enzymology

The activities of pairs of mammalian motor neurons (MNs) receiving varying degrees of common excitatory synaptic input were simulated to study the relationship between nearly-coincident spiking and common excitatory drive. The somatic membrane potential of each MN was modeled using a single compartment model. Each MN was modeled toreceive synaptic contacts from hundreds of pre-synaptic fibers. The percentage of pre-synaptic fibers that diverged to supply both MNs of a pair with common synaptic input could be varied from 0 (no common inputs) to 100% (all common inputs). Spikes trains on separate re-synaptic fibers were independent of one another and were modeled as realizations of renewal processes with mean firing rates (10 - 50Hz) resembling that associated with supra-spinal input. Maximum synaptic conductances and time constants were varied across synapsesto match experimentally observed somatic EPSPs. The number of active pre-synaptic fibers to each MN was adjusted in order that the firingrates of MNs were between 8 and 15 Hz. For each common input condition, 100 s of concurrent spiking activity of the MNs was usedto construct cross-correlation histograms. The sizes of the central peaks in the histograms were quantified using both the k' (Ellaway and Murthy 1985) and CIS (Nordstrom et al. 1992) indices ofsynchrony. Monotonically increasing linear relationships between the proportion of common synaptic input and the magnitude of synchronywere observed for both indices. For example, the model predicted that 10% common input would yield a CIS value of 0.27 whereas 100% commoninput would yield a CIS value of 1.5. These values are within the range of values observed experimentally. These results, therefore,provide a means to translate measures of nearly-coincident spiking into plausible renditions of synaptic connectivity.

Compartment syndrome is a rare but a well-documented complication in patients with trauma-induced group A streptococcus infection. Here, we present a case of a male who developed compartment syndrome on the left lower extremity after an injury inoculated by group A streptococcus on the right lower extremity. The patient was resuscitated with antibiotics, urgent fasciotomy, and immunoglobulin. The patient was eventually transferred to a burn center for further care.

The forced Oscillation Technique (FOT) can be used to measure lung impedance continuously during breathing. However, spectral overlap between the breathing waveform and the applied flow oscillation can be problematic if the frequency content of spontaneous breathing is unknown. This problem motivated us to develop a modification to the FOT system called the Tracked Breathing Trainer. The modification uses biofeedback to constrain subjects to breathe at a single predetermined frequency. This thesis investigates the engineering and physiological aspects of the modification we made. We studied 8 adult non-asthmatic and 8 adult asthmatic subjects. Three 16 s perturbatory flow oscillation signals ranging from 1-40 Hz were used on the subjects. Each subject received three trials per perturbation for both spontaneous and tracked breathing. We then fitted a resistance-elastance-inertance model of the lung to each data set. For non-asthmatic subjects, the average resistance (R) and elastance (E) values for the first spontaneous breathing trial were 2.5±0.15 cmH2O.s.ml-1 and 18.1±3.55 cmH2O.ml-1, and for the third spontaneous breathing trial were 2.4±0.12 cmH2O.s.ml-1 and 21.8±4 cmH2O.ml-1. R and E for the first tracked breathing trial were 2.3±0.21 cmH2O.s.ml-1 and 33.6±7.4 cmH2O.ml-1, and for the third tracked breathing trial were 2.4±0.14 cmH2O.s.ml-1 and 25.75±4.3 cmH2O.ml-1, respectively. For asthmatic subjects, the average R and E values for the first spontaneous breathing trial were 3.32±0.68 cmH2O.s.ml-1 and 39.13±9.8 cmH2O.ml-1, and for the third spontaneous breathing trial were 3.12±0.15 cmH2O.s.ml-1 and 39.91±6.2 cmH2O.ml-1. R and E for the first tracked breathing trial were 2.86±0.15 cmH2O.s.ml-1 and 32.47±4.1 cmH2O.ml-1, and for the third tracked breathing trial were 2.86±0.21 cmH2O.s.ml-1 and 33.89±10 cmH2O.ml-1, respectively. These results show that R was consistently lower during tracked breathing than spontaneous breathing in both non-asthmatic and asthmatic subjects. However, an increase in E was observed during tracked breathing. We suspect this effect may have resulted from dynamic hyperinflation. These results also show that R and E are reproducible with both spontaneous and tracked breathing, and that R and E were not noticeably different between both breathing maneuvers. We conclude that using biofeedback to control the breathing pattern during application of the FOT in normal subjects does not significantly affect impedance measurements, and thus may be useful for avoiding spectral overlap between FOT perturbations and the breathing pattern.