No description available.

Computational and mathematical models of cellular processes promise great benets in important elds such as molecular biology and medicine. Increasingly, researchers are incorporating the fundamentally discrete and stochastic nature of biochemical processes into the mathematical models that are intended to represent them. This has led to the formulation of models for genetic networks as continuous-time, discrete state, Markov processes, giving rise to the so-called Chemical Master Equation (CME), which is a discrete, partial dierential equation, that governs the evolution of the associated probability distribution function (PDF). While promising many insights, the CME is computationally challenging, especially as the dimension of the model grows. In this thesis, novel methods are developed for computing the PDF of the Master Equation. The problems associated with the high-dimensional nature of the Chemical Master Equation are addressed by adapting Krylov methods, in combination with Finite State Projection methods, to derive algorithms well-suited to the Master Equation. Variations of the approach that incorporate the Strang splitting and a stochastic analogue of the total quasi-steady-state approximation are also derived for chemical systems with disparate rates. Monte Carlo approaches, such as the Stochastic Simulation Algorithm, that simulate trajectories of the process governed by the CME have been a very popular approach and we compare these with the PDF approaches developed in this thesis. The thesis concludes with a discussion of various implementation issues along with numerical results for important applications in systems biology, including the gene toggle, the Goldbeter-Koshland switch and the Mitogen-Activated Protein Kinase Cascade.

Computational and mathematical models of cellular processes promise great benets in important elds such as molecular biology and medicine. Increasingly, researchers are incorporating the fundamentally discrete and stochastic nature of biochemical processes into the mathematical models that are intended to represent them. This has led to the formulation of models for genetic networks as continuous-time, discrete state, Markov processes, giving rise to the so-called Chemical Master Equation (CME), which is a discrete, partial dierential equation, that governs the evolution of the associated probability distribution function (PDF). While promising many insights, the CME is computationally challenging, especially as the dimension of the model grows. In this thesis, novel methods are developed for computing the PDF of the Master Equation. The problems associated with the high-dimensional nature of the Chemical Master Equation are addressed by adapting Krylov methods, in combination with Finite State Projection methods, to derive algorithms well-suited to the Master Equation. Variations of the approach that incorporate the Strang splitting and a stochastic analogue of the total quasi-steady-state approximation are also derived for chemical systems with disparate rates. Monte Carlo approaches, such as the Stochastic Simulation Algorithm, that simulate trajectories of the process governed by the CME have been a very popular approach and we compare these with the PDF approaches developed in this thesis. The thesis concludes with a discussion of various implementation issues along with numerical results for important applications in systems biology, including the gene toggle, the Goldbeter-Koshland switch and the Mitogen-Activated Protein Kinase Cascade.

No description available.

The longitudinal muscle layer in gut is the functional opponent to the circular muscle layer during the peristalsis reflex. Differences in innervation of the layers allow for the contraction of one layer that corresponds with the simultaneous relaxation of the other, enabling the passage of gut contents in a controlled fashion. Differences in development have given the cells of the two layers differences in receptor populations, membrane lipid handling, and calcium handling profiles/behaviors. The kinase signaling differences between the two layers is not as well characterized. Upon activation of cells from the circular muscle layer, it is known that Rho kinase and ERK1/2 promote contraction, while CaMKK/AMPK and CaMKII perform inhibitory/self-inhibitory roles. Such behaviors are poorly understood in the longitudinal muscle layer. In longitudinal muscle strips, we measured muscarinic receptor-mediated contraction following incubation with kinase inhibitors. Upon comparison to control, contributions of Rho Kinase and ERK1/2 were similar to those seen in circular muscle. Inhibition of both of these enzymes leads to diminished contraction. However, CaMKK/AMPK and CaMKII have effects in longitudinal muscle opposite to their regulation in circular muscle – their inhibition also diminishes the contractile response. These contractile data from strips were supported by immunokinase assay measurements of MLCK activity from strip homogenates with and without kinase inhibition. Therefore, we suggest that the activities of CaMKK/AMPK and CaMKII in longitudinal muscle are indeed different from their regulatory roles in circular muscle, perhaps a consequence of the different calcium handling modalities of the two muscle types.

No description available.

Für den Zusammenbau des HBV-Partikels ist die Interaktion zwischen Oberflächenproteinen und dem Nukleokapsid notwendig. Sich überlappende synthetische Peptide aus dem Bereich der HBcAg-Bindungsdomäne im C-Terminus der PreS1-Region und dem TLM, sind nach Internalisierung vor allem im Kern lokalisiert. Die Aminosäuren 101-115 der PreS1-Region interagieren mit dem Nukleokapsid, während die PreS2-Domäne keine Interaktion mit dem Nukleokapsid eingeht. Mit den synthetischen Peptiden konnte Einfluss auf die Sekretion viraler Partikel genommen werden. Die Lokalisation von HBcAg als Interaktionspartner in HBV-produzierenden Zellen verändert sich bei Inkubation mit den synthetischen Peptiden, es tritt vermehrt im Kern auf. Rekombinante Proteine ähnlich den synthetischen Peptiden aber mit der vollständigen PreS2-Region, sind nach Internalisierung im Zytosol nachweisbar. Die Sekretion viraler Partikel wurde partiell inhibiert. Das HBV-Genom kodiert zwei virale Aktivatoren, das HBx und die PreS2-Region im LHBs. Beide aktivieren den c-Raf-1/MEK-Signalweg. Durch die selektive Inhibierung der Effektoren (Ras oder Proteinkinase C) von HBx oder PreS2 im LHBs konnte kein Effekt auf die Genexpression/ Sekretion nachgewiesen werden. Durch simultane Inhibierung der Signalkaskade so kommt die Virussekretion fast vollständig zum Erliegen. Die Ursache hierfür ist in einer reduzierten Neusynthese von viralen Proteinen zu finden und nicht in der Akkumulation der Proteine in der Zelle. Zur Untersuchung des Einflusses der Funktionalität der beiden Aktivatoren wurden HBx- bzw. PreS2- und HBx/PreS2-defiziente HBV-Expressionsplasmide generiert. Die Einzelmutanten zeigten nur einen geringen reduzierenden Einfluss auf die Genexpression/Virussekretion. Beim Einsatz der Doppelmutante wurde die Genexpression/Virussekretion fast vollständig inhibiert. HBx und PreS2 im LHBs sind für die Virusreplikation von Bedeutung aber sie können einander ersetzen. / Assembly of HBV particles and subsequent secretion of mature virus requires the interaction of the nucleocapsid with defined domains of the surface proteins. Overlapping synthetic peptides covering the C-terminal part of the PreS1 domain and the cell permeable domain of PreS2 (TLM) were shown to localize most of all in the nucleus. Based on these peptides aa 101-115 of PreS1 were found to be essential for the interaction with the nucleocapsid, while the PreS2 domain does not interact with the nucleus. Presence of the peptides that compete the nucleocapsid surface protein interaction a block of HBV and antigen secretion was achieved. HBcAg as natural interaction partner of the surface proteins then arises increased in the nucleus. Recombinant proteins similar to the synthetic peptides but with the whole PreS2 domain localize in the cytoplasm and block HBV and antigen secretion. The genome of HBV encodes two transcriptional activators: the HBx protein and the PreS2 activator LHBs. Both trigger activation of c-Raf-1/MEK kinase cascade. To evaluate the importance of both activators for viral replication selective inhibitions of signal transduction cascades were performed and do not result in a decrease of viral replication. Simultaneous inhibition of both activators abolished viral secretion. It is due to a reduced de novo synthesis and not to an accumulation of viral proteins in cells. The relevance of activator function was tested by mutated HBV genome defective for HBx and / or PreS2 activator function. After transfection single mutants show no significant reduced HBV expression whereas at the double mutated HBV genome a strong reduced virus expression could be observed. The HBx protein and the PreS2 activator LHBs are important for viral replication but they can replace each other.