Involvement of autophagy in the metabolism of Amyloid Precursor Protein and effects of familial Alzheimer’s disease-associated mutations of Presenilin-1

Alzheimer’s disease (AD) is the most common form of neurodegenerative diseases, which is associated with extracellular deposits of the amyloid β-peptide (Aβ) and intraneuronal aggregates of hyperphosphorylated tau protein in the brain. Aβ is generated by cleavage of APP C-terminal fragment β (APP-CTFβ) by γ-secretase. Thus, metabolism of APP-CTF is crucial for amyloid plaque deposition. Although many studies have been focused on understanding proteolytic cleavage of APP and amyloid plaque deposition, less is known about mechanisms that control the cellular metabolism of APP and its derivatives APP-CTFs. Autophagy plays an important role in intracellular protein quality control, especially of long-lived, misfolded and aggregated proteins (Nixon et al., 2008). Dysfunction of autophagy is implicated in the pathogenesis of AD-associated neurodegeneration (Kundu and Thompson, 2008). This study revealed an important role of autophagy in APP-CTF metabolism by using different autophagic modulations, such as nutrient starvation medium, lipid accumulation, and lysosomal inhibition. In the course of this study, the function of trehalose, which is well recognized as a stimulator of autophagy, has been revisited. Unexpectedly, this study demonstrated rather an inhibitory role of trehalose on lysosomal activity and thus, autophagic flux. The main project of this dissertation focused on the role of PS1 mutants on autophagy. Mutations in PS1 are the major cause of early-onset familial AD (EO-FAD). Recently, PS proteins have been shown to play role in lysosomal or autophagic capacity. However, these studies used non-neuronal models and the results were controversial. By using various cell models carrying different PS1 variants, ranging from human neurons derived from induced pluripotent or embryonic stem cells to mouse embryonic fibroblasts, the study indicated a decreased turn-over of long-lived proteins or autophagic capacity in FAD-linked PS1 mutant cells. Particularly, PS1 mutants or genetic deficiency reduced autophagic initiation via decreased phosphorylation of Bcl-2, which regulates the interaction with Beclin-1, and thereby decreased autophagosome formation. Additionally, PS1 mutant cells also revealed decreased autophagic flux by impairment of lysosomal function. Thus, the results support the hypothesis that autophagy is defective in AD brains, and elucidated two distinct effects of PS1 on induction and completion of autophagy. The findings further indicate that autophagy is an interesting targeted for therapeutic or preventive strategies in AD treatment

Fast numerical methods for mixed--integer nonlinear model--predictive control

This thesis aims at the investigation and development of fast numerical methods for nonlinear mixed--integer optimal control and model- predictive control problems. A new algorithm is developed based on the direct multiple shooting method for optimal control and on the idea of real--time iterations, and using a convex reformulation and relaxation of dynamics and constraints of the original predictive control problem. This algorithm relies on theoretical results and is based on a nonconvex SQP method and a new active set method for nonconvex parametric quadratic programming. It achieves real--time capable control feedback though block structured linear algebra for which we develop new matrix updates techniques. The applicability of the developed methods is demonstrated on several applications. This thesis presents novel results and advances over previously established techniques in a number of areas as follows: We develop a new algorithm for mixed--integer nonlinear model- predictive control by combining Bock's direct multiple shooting method, a reformulation based on outer convexification and relaxation of the integer controls, on rounding schemes, and on a real--time iteration scheme. For this new algorithm we establish an interpretation in the framework of inexact Newton-type methods and give a proof of local contractivity assuming an upper bound on the sampling time, implying nominal stability of this new algorithm. We propose a convexification of path constraints directly depending on integer controls that guarantees feasibility after rounding, and investigate the properties of the obtained nonlinear programs. We show that these programs can be treated favorably as MPVCs, a young and challenging class of nonconvex problems. We describe a SQP method and develop a new parametric active set method for the arising nonconvex quadratic subproblems. This method is based on strong stationarity conditions for MPVCs under certain regularity assumptions. We further present a heuristic for improving stationary points of the nonconvex quadratic subproblems to global optimality. The mixed--integer control feedback delay is determined by the computational demand of our active set method. We describe a block structured factorization that is tailored to Bock's direct multiple shooting method. It has favorable run time complexity for problems with long horizons or many controls unknowns, as is the case for mixed- integer optimal control problems after outer convexification. We develop new matrix update techniques for this factorization that reduce the run time complexity of all but the first active set iteration by one order. All developed algorithms are implemented in a software package that allows for the generic, efficient solution of nonlinear mixed-integer optimal control and model-predictive control problems using the developed methods

Economics and Business handbook

2004 handbook for the faculty of Economics and Busines

Development of a nanobody-based amperometric immunocapturing assay for sensitive and specific detection of Toxocara canis excretory-secretory antigen

Introduction Human Toxocariasis (HT) is a zoonosis that, despite of its wide distribution around the world, remains poorly diagnosed. The identification of specific IgG immunoglobulins against the Toxocara canis Excretory-Secretory antigen (TES), a mix of glycoproteins that the parasite releases during its migration to the target organs in infected patients, is currently the only laboratory tool to detect the disease. The main drawbacks of this test are the inability to distinguish past and active infections together with lack of specificity. These factors seriously hamper the diagnosis, follow-up and control of the disease. Aim To develop an amperometric immunocapturing diagnostic assay based on single domain immunoglobulins from camelids (nanobodies) for specific and sensitive detection of TES. Methods After immunization of an alpaca (Vicugna pacos) with TES, RNA from peripheral blood lymphocytes was used as template for cDNA amplification with oligo dT primers and library construction. Isolation and screening of TES-specific nanobodies were carried out by biopanning and the resulting nanobodies were expressed in Escherichia coli. Two-epitopes amperometric immunocapturing assay was designed using paramagnetic beads coated with streptavidin and bivalent nanobodies. Detection of the system was carried out with nanobodies chemically coupled to horseradish peroxidase. The reaction was measured by amperometry and the limit of detection (LOD) was compared to conventional sandwich ELISA. Results We obtained three nanobodies that specifically recognize TES with no-cross reactivity to antigens of Ascaris lumbricoides and A. suum. The LOD of the assay using PBST20 0.05% as diluent was 100 pg/ml, 10 times more sensitive than sandwich ELISA. Conclusion Sensitive and specific detection of TES for discrimination of active and past infections is one of the most difficult challenges of T. canis diagnosis. The main advantage of our system is the use of two different nanobodies that specifically recognize two different epitopes in TES with a highly sensitive and straightforward readout. Considering that the amounts of TES available for detection in clinical samples are in the range of picograms or a few nanograms maximum, the LOD found in our experiments suggests that the test is potentially useful for the detection of clinically relevant cases of HT

Economics and Business handbook

2004 handbook for the faculty of Economics and Busines

Economics and Business handbook

2003 handbook for the faculty of Economics and Busines

Modeling, Simulation and Visualization of Plant Growth

Pflanzenmodellierung ist ein interessantes und herausforderndes Thema für die wissenschaftlich interdisziplinäre Forschung im Bereich der Mathematik, Biologie, Botanik, Agrarwirtschaft und Informatik. Im Rahmen dieser Dissertation wird die auf Lindenmayer Systeme (L-Systeme) und Partikel Systeme (PT-Systeme) basierende Modellierung, Simulation und Visualisierung von Pflanzenwachstum präsentiert und anhand von zwei Methoden zur Erzeugung von Pflanzenstruktur vorgestellt. Die erste Methode basiert auf Geklammerten, Stochastischen und Parametrischen L-Systemen. Sie ist für eine präzise Modellierung von bereits bekannten Pflanzenstrukturen geeignet und bietet auch die Möglichkeit, die komplexe Struktur in kleine Bestandteile bezüglich der Produktionsregeln zu zerlegen. In der zweiten Methode wird das PT-System für die Simulation grober Struktur und schneller Produktionsvorgänge eingesetzt, die auf vordefinierter Form und Volumen von Spross und Wurzel der Pflanze basiert. Beide Methoden können für die Modellierung von Pflanzenspross, Wurzel und Blattader eingesetzt werden. Der Prototyp dieser beiden Methoden ist in einer Weise konstruiert, die die physiologischen Daten der Masse realer Pflanzen berücksichtigt wie beispielsweise Länge und Durchmesser des Internodiums, Länge und Durchmesser der Zweige, Länge und Breite des Blattes, Länge und Breite der Wurzel. Diese Daten werden durch Parameterschätzung mit der Anwendung der Levenberg-Marquardt Methode bestimmt, die auf einer N-Puls sigmoidalen Funktion basiert. Alle angepassten Parameter können im Prototyp für die Simulation von Wachstumsverhalten einer Pflanze verwendet werden. Beide vorgeschlagenen Methoden werden für die künstliche Erzeugung bestimmter Pflanzenarten eingesetzt, die mit L-Systemen vertraute Experten von der Natur ablesen und in ein künstliches Modell konvertieren. Auch schlagen wir hier eine Methode für das Umwandeln der erhobenen Daten in ein künstliches Verzweigungsnetzwerk vor, das sogenannte ,,inverse Problem vom L-System". Dieses inverse Problem vom L-System bietet die Möglichkeit, die Struktur eines Verzweigungsnetzwerks mithilfe von Eingabebildern oder Volumendaten der komplexen Struktur zu rekonstruieren. Die tatsächlich wachsende Wurzel im Bodenvolumen kann mit Computer Tomography (CT) gescannt und die Wurzelstruktur aus dem Volumen segmentiert werden. Die endgültige rekonstruierte Struktur wird in L-Systemen basierend auf Geklammerten und Parametrischen L-Systemen für die Weiterverwendung beschrieben. Die Struktur und das Wachstum der Wurzelsysteme sind stark von Umgebungsfaktoren im Boden abhängig. Die Diffusionsgleichung und Richardsgleichung werden verwendet, um die Diffusion der Nährstoffe und den Fluss des Wassers zu beschreiben. Das Wurzelstystem wächst gleichzeitig und abhängig davon, wie die Diffusion der Nährstoffe und der Fluss des Wassers verläuft. Nährstoff- und Wasseraufnahme werden zu jedem Zeitpunkt des Wachstumsprozesses berechnet. Diese Dissertation fördert letztendlich neue Methoden für die Modelierung und Simulierung von Pflanzenwachstum aufgrund von Klimafaktoren, die mit einem von uns neu entwickelten Software Tool durchgeführt werden kann. Ergebnisse, die in dieser Dissertation erreicht werden, können in vielen verwandten Gebieten angewendet werden wie zum Beispiel in der Landwirtschaft, Pflanzenmodellierung, Agrarmanagement, Ökonomie, etc. Die Visualisierung des virtuellen Pflanzenwachstums, das mit L-Systemen, PT-System, inversem Problem, Wasserfluss und Nährstoffdiffusion modelliert wird, kann durch die von uns entwickelte Software PlantVR (Plant Virtual Reality) dargestellt werden

Performance Models for Electronic Structure Methods on Modern Computer Architectures

Electronic structure codes are computationally intensive scientic applications used to probe and elucidate chemical processes at an atomic level. Maximizing the performance of these applications on any given hardware platform is vital in order to facilitate larger and more accurate computations. An important part of this endeavor is the development of protocols for measuring performance, and models to describe that performance as a function of system architecture. This thesis makes contributions in both areas, with a focus on shared memory parallel computer architectures and the Gaussian electronic structure code. Shared memory parallel computer systems are increasingly important as hardware man- ufacturers are unable to extract performance improvements by increasing clock frequencies. Instead the emphasis is on using multi-core processors to provide higher performance. These processor chips generally have complex cache hierarchies, and may be coupled together in multi-socket systems which exhibit highly non-uniform memory access (NUMA) characteristics. This work seeks to understand how cache characteristics and memory/thread placement affects the performance of electronic structure codes, and to develop performance models that can be used to describe and predict code performance by accounting for these effects. A protocol for performing memory and thread placement experiments on NUMA systems is presented and its implementation under both the Solaris and Linux operating systems is discussed. A placement distribution model is proposed and subsequently used to guide both memory/thread placement experiments and as an aid in the analysis of results obtained from experiments. In order to describe single threaded performance as a function of cache blocking a simple linear performance model is investigated for use when computing the electron repulsion integrals that lie at the heart of virtually all electronic structure methods. A parametric cache variation study is performed. This is achieved by combining parameters obtained for the linear performance model on existing hardware, with instruction and cache miss counts obtained by simulation, and predictions are made of performance as a function of cache architecture. Extension of the linear performance model to describe multi-threaded performance on complex NUMA architectures is discussed and investigated experimentally. Use of dynamic page migration to improve locality is also considered. Finally the use of large scale electronic structure calculations is demonstrated in a series of calculations aiming to study the charge distribution for a single positive ion solvated within a shell of water molecules of increasing size