Stress impacts upon all organisms and a robust stress response is required for adaptive interactions of the organism with the environment. In most higher organisms, an individual’s response to stress is mediated by the hypothalamic pituitary adrenal (HPA) axis. Inappropriate regulation of this axis can cause debilitating mental health disorders including depression and anxiety. These disorders can affect an individual’s ability to interact and respond appropriately as different situations arise. An important component of this axis is the vasopressin V1b receptor (V1bR), which mediates adrenocorticotropin (ACTH) secretion from the anterior pituitary in response to stimulation by arginine vasopressin (AVP). AVP also potentiates the ACTH secretion mediated by corticotropin-releasing hormone type 1 receptor (CRH-R1) in response to corticotropin- releasing hormone (CRH) stimulation. Both the V1bR and CRH-R1 are G protein coupled receptors (GPCRs). A common feature of GPCR signalling is desensitisation of the response following prolonged or repeated exposure to an agonist. Phosphorylation of the receptor is one of the mechanisms of desensitisation. This directly, or indirectly, results in rapid and reversible uncoupling of the receptor from its heterotrimeric guanine nucleotide binding protein (G-protein). Previous research has shown that G protein coupled receptor kinases (GRKs) are key phosphorylators involved in the molecular mechanism of GPCR desensitisation. One of the mains goals of the research carried out in the Mason laboratory is to examine the molecular mechanisms of V1bR desensitisation. The current short term aim is to examine the potential role for GRKs in this mechanism. It is difficult to study a single receptor type and the molecular mechanisms involved in its regulation in a system larger than a cell based assay. As the proposed method of assessing the involvement of GRKs in desensitisation of the V1bR is to use RNA interference (RNAi) to knock down the expression of the GRKs, primary cell cultures of pituitary corticotrophs are an inappropriate choice. This is due to a number of factors, including the difficulty involved in transfecting primary cells, and the difficulty involved in interpreting the results from primary cell culture experiments as these cultures are composed heterogenous population of cells. Therefore, the main aim of this research was to develop a model cell system from an immortalised cell line, stably-transfected with the V1bR, in which the involvement of GRKs in the molecular mechanism of V1bR desensitisation could be studied. Development of stably-transfected cell lines requires substantial preliminary work and planning in order to produce a successful outcome. Once developed, characterisation of the clonal cell lines is required. The preliminary work involved determining the cell proliferation rate of the parental cell line, plasmid sub-cloning and production of a large quantity of plasmid DNA, optimisation of the antibiotic selection conditions, and optimisation of the transfection protocol, as well as modification of the inositol phosphate (IP) assay protocol. The V1bR activates the phospholipase Cβ (PLCβ) second messenger signalling pathway in response to stimulation with AVP. This results in the production of IPs and therefore, measurement of IPs in response to AVP stimulation of cells labelled with myo-[³H]inositol can be used as an indicator of functional V1bR expression. In this research a total of nine clonal cell lines resistant to the antibiotic G418 were generated. Initial testing of these lines indicated that four probably expressed the V1bR and these were selected for characterisation in greater detail. All of these four lines showed significantly increased IP production in response to AVP stimulation (P<0.05; t-test). A significant decrease in IP production in response to AVP stimulation following an AVP pre-treatment was also seen with all four lines (P<0.05; t-test). Current evidence therefore suggests that the V1bR in these clonal cell lines signals and desensitises in the normal way. Although further characterisation of the clonal cell line is desirable, the data to date indicate that these lines should be considered to provide an appropriate model system for examining the molecular mechanisms involved in the regulation of the V1bR. It appears that there are some minor differences in signalling between the clonal cell lines and therefore this should be a consideration when deciding which line is most appropriate to use for investigating a particular question.

This work describes the results of experimental study of the flow of soft objects (microgels) through microchannels. This work was carried with the intention of building a fundamental biophysical model for the flow of neutrophil cells in microcirculatory system. In Chapter 1 we give a summary of the literature describing the flow of cells and “model cells” in microchannels. Paramount to this we developed methods to modify microchannels fabricated in poly(dimethyl siloxane) (PDMS). Originally, these microchannels could not be used to mimic biological microenvironments because they are hydrophobic and have rectangular cross-sections. We designed a method to create durable protein coatings in PDMS microchannels, as outlined in Chapter 3. Surface modification of the channels was accomplished by a two-step approach which included (i) the site-specific photografting of a layer of poly(acrylamide) (PAAm) to the PDMS surface and (ii) the bioconjugation of PAAm with the desired protein. This method is compatible with different channel geometries and it exhibits excellent longevity under shear stresses up to 1 dyn/cm. The modification was proven to be successful for various proteins of various molecular weights and does not affect protein activity. The microchannels were further modified by modifying the cross-sections in order to replicate cardiovascular flow conditions. In our work, we transformed the rectangular cross-sections into circular corss-sections. Microchannels were modified by polymerizing a liquid silicone oligomer around a gas stream coaxially introduced into the channel, as outlined in Chapter 3. We demonstrated the ability to control the diameter of circular cross-sections of microchannels. The flow behaviour of microgels in microchannels was studied in a series of experiments aimed at studying microgel flow (i) under electrostatic interactions (Chapter 4), (ii) binding of proteins attached to the microgel and the microchannel (Chapter 5) and (iii) under the conditions of varying channel geometry (Chapter 6). This work overall present’s new methods to study the flow of soft objects such as cells, in the confined geometries of microchannels. Using these methods, variables can be independently probed and analyzed.

This work describes the results of experimental study of the flow of soft objects (microgels) through microchannels. This work was carried with the intention of building a fundamental biophysical model for the flow of neutrophil cells in microcirculatory system. In Chapter 1 we give a summary of the literature describing the flow of cells and “model cells” in microchannels. Paramount to this we developed methods to modify microchannels fabricated in poly(dimethyl siloxane) (PDMS). Originally, these microchannels could not be used to mimic biological microenvironments because they are hydrophobic and have rectangular cross-sections. We designed a method to create durable protein coatings in PDMS microchannels, as outlined in Chapter 3. Surface modification of the channels was accomplished by a two-step approach which included (i) the site-specific photografting of a layer of poly(acrylamide) (PAAm) to the PDMS surface and (ii) the bioconjugation of PAAm with the desired protein. This method is compatible with different channel geometries and it exhibits excellent longevity under shear stresses up to 1 dyn/cm. The modification was proven to be successful for various proteins of various molecular weights and does not affect protein activity. The microchannels were further modified by modifying the cross-sections in order to replicate cardiovascular flow conditions. In our work, we transformed the rectangular cross-sections into circular corss-sections. Microchannels were modified by polymerizing a liquid silicone oligomer around a gas stream coaxially introduced into the channel, as outlined in Chapter 3. We demonstrated the ability to control the diameter of circular cross-sections of microchannels. The flow behaviour of microgels in microchannels was studied in a series of experiments aimed at studying microgel flow (i) under electrostatic interactions (Chapter 4), (ii) binding of proteins attached to the microgel and the microchannel (Chapter 5) and (iii) under the conditions of varying channel geometry (Chapter 6). This work overall present’s new methods to study the flow of soft objects such as cells, in the confined geometries of microchannels. Using these methods, variables can be independently probed and analyzed.

Tato práce se zabývá buněčným cyklem kvasinky Saccgaromyces cerevisiae. Oblastí našeho zájmu je přechod mezi G1 a S fází, kde je naším cílem identifikovat velikosti buňky v době počátku DNA replikace. Nejprve se věnujeme nedávno publikovanému matematickému modelu, který popisuje mechanismy vedoucí k S fázi. Práce poskytuje detailní popis tohoto modelu, stejně jako časový průběh některých důležitých proteinů či jejich sloučenin. Dále se zabýváme pravděpodobnostním modelem aktivace replikačních počátků DNA. Nově uvažujeme vliv šíření DNA replikace mezi sousedícími počátky a analyzujeme jeho důsledky. Poskytujeme také senzitivní analýzu kritické velikosti buňky vzhledem ke konstantám popisujícím dynamiku reakcí v modelu G1/S přechodu.

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Temporal lobe epilepsy is the most common form of epilepsy and hippocampal sclerosis represents the main underlying structural abnormity. Approximately 20% of TLE cases are non- lesional due to absence of any obvious epileptogenic lesion and tetanus toxin model is traditionally considered as a model of non-lesional temporal lobe epilepsy. The main aim of this study was to evaluate the presence of the cell damage and to determine its spatiotemporal profile. Tetanus toxin was stereotaxically injected into CA3 subregion of dorsal hippocampus in adult male Wistar rats. Brain tissue was extracted 4, 8 and 16 days following the surgery. Postfixed brains were sectioned to 50 µm slices and labeled using Nissl's and FluoroJade B staining (FJB). Hippocampal sclerosis was present only in animals from D16 group, however, it was localized mainly in contralateral CA1 area. Additional finding was decreased Nissl's staining in contralateral hippocampus which corresponded with the presence of FJB positive neurons. In animals from group D8, we have identified presence of FJB positive neurons predominantly in ipsilateral hippocampus. In D4 animals, cellular degeneration was absent. To examine the non- lesional nature of tetanus toxin model, we have performed blind study, when Nissl's staining were reviewed...

During development, organs with different shape and functionality form from a single fertilized egg cell. Mechanisms that control shape, size and morphology of tissues pose challenges for developmental biology. These mechanisms are tightly controlled by an underlying signaling system by which cells communicate to each other. However, these signaling networks can affect tissue size and morphology through limited processes such as cell proliferation, cell death and cell shape changes,which are controlled by cell mechanics and cell adhesion. One example of such a signaling system is the network of interacting proteins that control planar polarization of cells. These proteins distribute asymmetrically within cells and their distribution in each cell determines of the polarity of the neighboring cells. These proteins control the pattern of hairs in the adult Drosophila wing as well as hexagonal repacking of wing cells during development. Planar polarity proteins also control developmental processes such as convergent-extension. We present a theoretical study of cell packing geometry in developing epithelia. We use a vertex model to describe the packing geometry of tissues, for which forces are balanced throughout the tissue. We introduce a cell division algorithm and show that repeated cell division results in the formation of a distinct pattern of cells, which is controlled by cell mechanics and cell-cell interactions. We compare the vertex model with experimental measurements in the wing disc of Drosophila and quantify for the first time cell adhesion and perimeter contractility of cells. We also present a simple model for the dynamics of polarity order in tissues. We identify a basic mechanism by which long-range polarity order throughout the tissue can be established. In particular we study the role of shear deformations on polarity pattern and show that the polarity of the tissue reorients during shear flow. Our simple mechanisms for ordering can account for the processes observed during development of the Drosophila wing.

Despite spectacular progress in biophysics, molecular biology and biochemistry our ability to predict the dynamic behavior of multicellular systems under different conditions is very limited. An important reason for this is that still not enough is known about how cells change their physical and biological properties by genetic or metabolic regulation, and which of these changes affect the cell behavior. For this reason, it is difficult to predict the system behavior of multicellular systems in case the cell behavior changes, for example, as a consequence of regulation or differentiation. The rules that underlie the regulation processes have been determined on the time scale of evolution, by selection on the phenotypic level of cells or cell populations. We illustrate by detailed computer simulations in a multi-scale approach how cell behavior controlled by regulatory networks may emerge as a consequence of an evolutionary process, if either the cells, or populations of cells are subject to selection on particular features. We consider two examples, migration strategies of single cells searching a signal source, or aggregation of two or more cells within minimal multiscale models of biological evolution. Both can be found for example in the life cycle of the slime mold Dictyostelium discoideum. However, phenotypic changes that can lead to completely different modes of migration have also been observed in cells of multi-cellular organisms, for example, as a consequence of a specialization in stem cells or the de-differentiation in tumor cells. The regulatory networks are represented by Boolean networks and encoded by binary strings. The latter may be considered as encoding the genetic information (the genotype) and are subject to mutations and crossovers. The cell behavior reflects the phenotype. We find that cells adopt naturally observed migration strategies, controlled by networks that show robustness and redundancy. The model simplicity allow us to unambiguously analyze the regulatory networks and the resulting phenotypes by different measures and by knockouts of regulatory elements. We illustrate that in order to maintain a cells' phenotype in case of a knockout, the cell may have to be able to deal with contradictory information. In summary, both the cell phenotype as well as the emerged regulatory network behave as their biological counterparts observed in nature.

The process of cell-sorting is essential for development and maintenance of tissues. With the Differential Adhesion Hypothesis, Steinberg proposed that cellsorting is determined by quantitative differences in cell-type-specific intercellular adhesion strengths. An implementation of the Differential Adhesion Hypothesis is the Differential Migration Model by Voss-Böhme and Deutsch. There, an effective adhesion parameter was derived analytically for systems with two cell types, which predicts the asymptotic sorting pattern. However, the existence and form of such a parameter for more than two cell types is unclear. Here, we generalize analytically the concept of an effective adhesion parameter to three and more cell types and demonstrate its existence numerically for three cell types based on in silico time-series data that is produced by a cellular-automaton implementation of the Differential Migration Model. Additionally, we classify the segregation behavior using statistical learning methods and show that the estimated effective adhesion parameter for three cell types matches our analytical prediction. Finally, we demonstrate that the effective adhesion parameter can resolve a recent dispute about the impact of interfacial adhesion, cortical tension and heterotypic repulsion on cell segregation. / Der Prozess der Zellsortierung ist für die Entwicklung und Erhaltung von Geweben unerlässlich. Mit der Differentiellen Adhäsionshypothese schlug Steinberg vor, dass die Zellsortierung durch quantitative Unterschiede in den zelltypspezifischen interzellulären Adhäsionsstärken bestimmt wird. Eine Umsetzung der Differentiellen Adhäsionshypothese ist das Differentielle Migrationsmodell von Voss-Böhme und Deutsch. In diesem wurde für Systeme mit zwei Zelltypen ein effektiver Adhäsionsparameter analytisch hergeleitet, der das asymptotische Sortiermuster vorhersagt. Die Existenz und Form eines solchen Parameters für mehr als zwei Zelltypen ist jedoch unklar. Hier verallgemeinern wir analytisch das Konzept eines effektiven Adhäsionsparameters für drei und mehr Zelltypen und zeigen numerisch seine Existenz für drei Zelltypen auf der Basis von in silico Zeitreihendaten, die von einem zellulären Automaten des Differentiellen Migrationsmodells erzeugt werden. Darüber hinaus klassifizieren wir das Segregationsverhalten mithilfe statistischer Lernverfahren und zeigen, dass der geschätzte effektive Adhäsionsparameter für drei Zelltypen mit unserer analytischen Vorhersage übereinstimmt. Schließlich zeigen wir, dass der effektive Adhäsionsparameter eine kürzlich aufgekommene Diskussion über den Einfluss von Grenzflächenadhäsion, Kortikalspannung und heterotypischer Abstoßung auf die Zellsegregation lösen kann.