High quality reagents are preconditions for high performance protein analyses. But despite progress in some techniques, e.g. mass spectrometry, there is still a lack of affinity-based detection techniques with enhanced precision, specificity, and sensitivity. Building on the concept of multiple affinity recognition reactions and signal amplification, a proximity ligation assay (PLA) was developed as a molecular tool for analyzing proteins and their post-translational modification and interactions. PLA enhanced the analysis of protein expression levels and post-translational modifications in western blotting (Paper I), which had elevated sensitivity and specificity, and an ability to investigate protein phosphorylation. A general and straightforward method was established for the functionalization of affinity reagents through adding DNA strands to protein domains for protein analysis in medicine (Paper II). A method for protein domain-mediated conjugation was developed to simplify the use of recombinant affinity reagents, such as designed ankyrin repeat protein (DARPin), in DNA-mediated protein analyses. Alzheimer’s disease (AD) is characterized by progressive cognitive decline and memory impairment, and amyloid-beta plaques and neurofibrillary tangles (NFT) in the brain are clinical hallmarks of the disease. In order to understand the mechanisms underlying the formation of NFT, in situ PLA was used to explore the role of microtubule affinity related kinase 2 (MARK2) in phosphorylating tau protein during the pathological progress of AD (Paper III). The analyses of roles of MARK proteins 1-4 in phosphorylating tau protein in cells and in post-mortem human brains were performed in Paper IV. The focus of this thesis was the study of post-translational modifications and interactions of proteins in medicine. Procedures for high performance protein analysis in western blotting via proximity ligation were developed, and a functionalization method for recombinant affinity reagents in DNA-mediated protein analysis was established. These and other techniques were used to investigate the roles of tau-phosphorylating MARK family proteins in AD.

One of the main advantages of the Gantry-Tau machine is a large accessible workspace\footprint ratio compared to many other parallel machines. The Gantry-Tau improves this ratio further by allowing a change of assembly mode without internal link collisions or collisions between the links and the moving TCP platform. In this Thesis some of the features of the Gantry-Tau structure are described and results are presented from the analysis of the kinematic, elastostatic and elastodynamic properties of the PKM. However, the optimal kinematic, elastostatic and elastodynamic design parameters of the machine are still difficult to calculate and this thesis introduces a multi-objective optimisation scheme based on the geometric approach for the workspace area, unreachable area, joint angle limitations and link collisions as well as the functional dependencies of the elements of the static matrix and the Laplace transform to define the first resonance frequency and Cartesian and torsional stiffness. The method to calculate the first resonance frequency assumes that each link and universal joint can be described by a mass-springdamper model and calculates the transfer function from a Cartesian (TCP) force or torque to Cartesian position or orientation. The geometric methods involve the simple geometric shapes (spheres, circles, segments, etc) and vectors. The functional dependencies are based on the properties between the kinematic parameters. These approaches are significantly faster than analytical methods based on the inverse kinematics or the general Finite Elements Method (FEM). The reconfigurable Gantry-Tau kinematic design obtained by multi-objective optimisation gives the following features: • Workspace/footprint ratio more than 3.19. • First resonance frequency greater than 48 Hz. • Lowest Cartesian stiffness in the workspace 5N/μm. • The unreachable space in the middle of the workspace is not detected. • No link collisions. The results show that by careful design of the PKM, a collision free workspace without the unreachable area in the middle can be achieved. High stiffness and high first resonance frequency are important parameters for the the Gantry-Tau when used in industrial applications, such as cutting, milling and drilling of steel or aluminium and pick-and-place operations. These applications require high static and dynamic accuracy in combination with high speed and acceleration. The optimisation parameters are the support frame lengths, actuator positions,endeffector kinematics and the robot’s arm lengths. Because of the fast computational speed of the geometric approaches and computational time saving of the methods based on the functional dependency, they are ideal for inclusion in a design optimisation framework, normally a nonlinear optimisation routine. In this Thesis the evolutionary algorithm based on the complex search method is used to optimise the 3-DOF Gantry-Tau. The existing lab prototype of this machine was assembled and completed at the University of Agder

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2002. / Härtill 5 uppsatser.

Ulm, Univ., Diss., 2009.

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2005. / Includes bibliographical references (leaves 372-384). Also available in electronic version.

Parkinson's disease (PD) primarily manifests as loss of motor control through the degeneration of nigrostriatal dopaminergic neurons. The microtubule-associated protein tau (MAPT) locus is highly genetically associated with PD, wherein the H1 haplotype confers disease risk and the H2 haplotype is protective. As this haplotype variation does not alter the amino acid sequence, disease risk may be conferred by altered gene expression, either of total MAPT or of specific isoforms, of which there are six in adult human brain. To investigate haplotype-specific control of MAPT expression in the neurons that die in PD, induced pluripotent stem cells (iPSCs) from H1/H2 heterozygous individuals were differentiated into dopaminergic neuronal cultures that expressed all six mature isoforms of MAPT after six months' maturation. A reporter construct using the human tyrosine hydroxylase locus was also generated to identify human dopaminergic neurons in mixed cultures. Haplotype-specific differences in the inclusion of exon 3 and total MAPT were observed in iPSC-derived dopaminergic neuronal cultures and a novel variant in MAPT intron 10 increased the inclusion of exon 10 by two-fold. RNA interference tools were generated to knockdown total MAPT or specific isoforms, wherein knockdown of the 4-repeat isoform of tau protein increased the velocity of axonal transport in iPSC-derived neurons. MAPT knockdown also reduced p62 levels, suggesting an impact of tau on macroautophagy, likely through altered axonal transport. These results demonstrate how variation at a disease susceptibility locus can alter gene expression, thereby impacting on neuronal function.

This thesis outlines the search for neutral Higgs bosons in a mass range of m_H/A = 200 GeV − 1.2 TeV, decaying to a pair of hadronically decaying tau leptons. The search is performed using √s = 13 TeV proton-proton collision data, corresponding to an integrated luminosity of 3.21 fb^-1, recorded by the ATLAS detector. No excess over the predicted Standard Model background is observed and upper limits are placed on the production cross section times branching fraction as a function of the mass of the scalar resonance. When combined with the results of the analysis where one of the tau leptons decays to either a muon or electron, the 95% confidence level upper limit on the cross section times branching fraction ranges from 1.4 pb at m_H/A = 200 GeV to 0.025 pb at m_H/A = 1.2 TeV for a scalar boson produced via gluon-gluon fusion, and 1.6 pb at m_H/A = 200 GeV to 0.028 pb at m_H/A = 1.2 TeV for a scalar boson produced via b-associated production. The results are interpreted in the Minimal Supersymmetric extension to the Standard Model (MSSM) as a limit on the value of tanβ, as a function of the mass of the neutral CP-odd MSSM Higgs boson. In the mmod+ scenario, the 95% confidence level upper limit is tanβ < 7.6 for m_A = 200 GeV, and tanβ < 47 for m_A = 1 TeV. For the mass range m_A > 500 GeV, the upper limit on tanβ is improved in comparison to previous ATLAS searches.

An electron-positron linear collider is an option for future large particle accelerator projects. Such a collider would focus on precision tests of the Higgs boson properties. This thesis describes three studies related to the optimisation of highly granular calorimeters and one study on the sensitivity of Higgs couplings at CLIC. Photon reconstruction algorithms were developed for highly granular calorimeters of a future linear collider detector. A sophisticated pattern recognition algorithm was implemented, which uses the topological properties of electromagnetic showers to identify photon candidates and separate them from nearby particles. It performs clustering of the energy deposits in the detector, followed by topological characterisation of the clusters, with the results being considered by a multivariate likelihood analysis. This algorithm leads to a significant improvement in the reconstruction of both single photons and multiple photons in high energy jets compared to previous reconstruction software. The reconstruction and classification of tau lepton decay products was studied. Utilising highly granular calorimeters, the high resolution of energy and invariant mass of the tau decay products enabled a high classification rate. A hypothesis test was performed for expected decay final states. A multivariate analysis was trained to classify decay final states with a machine learning method. The performance of tau decay classification is used for the electromagnetic calorimeter optimisation at the ILC or CLIC. A proof-of-principle analysis using the correlation between the polarisations of the tau pair from a boson decay as a signature to differentiate the Higgs boson from the Z boson is presented. Sensitivity of Higgs couplings at CLIC was studied using the double Higgs production process. Algorithms were developed for signal event selection. The event selection relies on the jet reconstruction and the flavour tagging. A multivariate analysis is performed to select signal events. An attempt at extracting Higgs trilinear self-coupling and quartic coupling was conducted.