Real-time control of industrial robots for shape setting Nitinol rods

Most robots in industrial settings today rely on playback of precise pre-defined coordinates and do not adjust their motion using feedback from sensors. This thesis describes a system to implement real-time motion control of ABB Industrial robots through ROS (Robot Operating System), which enables general use for future experiments that control the robot arms using real-time feedback from force-torque sensors and/or computer vision. Additionally, these robots are used to bend a Nitinol rod into a desired shape and a hardware system has been built to shape-set Nitinol rods with Joule heating

Advanced Analytical Methods for Pharmaceutical and Diagnostic Applications

Driving forces for the development of novel analytical technologies in the life-science industry are described. Technologies which either were developed in Bio-Analytical Research or brought to a reliability required for routine applications will be elucidated and, on the basis of practical examples, the impact of modern analytical technologies on the industrial research and development will be discussed: Optical biosensors based on evanescent excitation of luminescence allow for real-time monitoring of the binding of active compounds to specific biomolecular recognition sites. Molecular imaging technologies have the potential to gain rapid access to physical maps of genomic materials. Capillary electrophoresis or affinity gel electrophoresis are well suited for the fast determination of oligonucleotide mixtures in nl amounts of samples. Integrated capillary electrophoresis on chips will allow to multiplex capillary systems at low costs and results in high separation efficiencies. MALDI-TOF MS is an easy to operate non-scanning mass spectrometric instrumentation for the analysis of high molecular weight biopolymers such as immunoglobulins

Electrostatic potential in a superconductor

The electrostatic potential in a superconductor is studied. To this end Bardeen's extension of the Ginzburg-Landau theory to low temperatures is used to derive three Ginzburg-Landau equations - the Maxwell equation for the vector potential, the Schroedinger equation for the wave function and the Poisson equation for the electrostatic potential. The electrostatic and the thermodynamic potential compensate each other to a great extent resulting into an effective potential acting on the superconducting condensate. For the Abrikosov vortex lattice in Niobium, numerical solutions are presented and the different contributions to the electrostatic potential and the related charge distribution are discussed.Comment: 19 pages, 11 figure

DNA and Protein Microarrays and their Contributions to Proteomics and Genomics

Knowledge in genomics and proteomics has exploded in the last two decades. This is in part due to key developments that have revolutionized the possibilities of bioanalytics such as the introduction of polymerase chain reaction (PCR) in the mid 80s that formed the base for the massively parallel sequencing of the genomes.A few years ago DNA and protein microarray analysis were added to the toolbox of life sciences analytics. These technologies already proved to be ideal tools for the identification of gene targets, the simultaneous measurement of the expression of a high number of genes or proteins, and the increase of the level of understanding of the biological functions of genes and proteins. A small number of experiments are now sufficient to obtain information on gene or protein expression which could not be obtained by using conventional bioanalytical technologies or which required an extremely high experimental effort. In the future applications, high sensitivity DNA and protein microarrays will allow low abundant genes and proteins to be monitored that so far have been inaccessible to current microarray technologies and thus will generate a new dimension of genomic and proteomic information

G-quadruplex recognition activities of <it>E. Coli</it> MutS

<p>Abstract</p> <p>Background</p> <p>Guanine quadruplex (G4 DNA) is a four-stranded structure that contributes to genome instability and site-specific recombination. G4 DNA folds from sequences containing tandemly repetitive guanines, sequence motifs that are found throughout prokaryote and eukaryote genomes. While some cellular activities have been identified with binding or processing G4 DNA, the factors and pathways governing G4 DNA metabolism are largely undefined. Highly conserved mismatch repair factors have emerged as potential G4-responding complexes because, in addition to initiating heteroduplex correction, the human homologs bind non-B form DNA with high affinity. Moreover, the MutS homologs across species have the capacity to recognize a diverse range of DNA pairing variations and damage, suggesting a conserved ability to bind non-B form DNA.</p> <p>Results</p> <p>Here, we asked if <it>E. coli</it> MutS and a heteroduplex recognition mutant, MutS F36A, were capable of recognizing and responding to G4 DNA structures. We find by mobility shift assay that <it>E. coli</it> MutS binds to G4 DNA with high affinity better than binding to G-T heteroduplexes. In the same assay, MutS F36A failed to recognize G-T mismatched oligonucleotides, as expected, but retained an ability to bind to G4 DNA. Association with G4 DNA by MutS is not likely to activate the mismatch repair pathway because nucleotide binding did not promote release of MutS or MutS F36A from G4 DNA as it does for heteroduplexes. G4 recognition activities occur under physiological conditions, and we find that M13 phage harboring G4-capable DNA poorly infected a MutS deficient strain of <it>E. coli</it> compared to M13mp18, suggesting functional roles for mismatch repair factors in the cellular response to unstable genomic elements.</p> <p>Conclusions</p> <p>Taken together, our findings demonstrate that <it>E. coli</it> MutS has a binding activity specific for non-B form G4 DNA, but such binding appears independent of canonical heteroduplex repair activation.</p

Preconcentration and separation of antisense oligonucleotides by on-column isotachophoresis and capillary electrophoresis in polymer-filled capillaries.

Small, single-stranded, chemically modified oligonucleotides, complementary to a specific gene section, commonly referred to as antisense compounds, are being investigated as potential therapeutic drugs. A number of modified oligonucleotides, in particular phosphorothioates, are in clinical development. Shorter fragments are found as metabolic products. Isotachophoresis (ITP) allows the introduction of large, diluted sample plugs into the separation capillary. In this work, ITP and capillary electrophoresis (CE) in polymer solutions were successfully coupled in a single capillary in a commercial instrument to increase sensitivity with UV detection and to shorten the time for sample pretreatment. It was shown that ITP-CE can be used as a preconcentration and clean-up method for phosphodiester- and phosphorothioate-containing samples. Up to 3 microL sample could be injected into the capillary without significantly disturbing the separation performance. ITP-CE of phosphodiesters directly out of salt- and protein-containing samples could be demonstrated. For phosphorothioates in serum samples an additional sample clean-up was necessary, due to oligonucleotide-protein binding. An optimized replaceable polymer solution was developed to increase the separation performance for heterogeneous phosphorothioates. A dextran-based sieving medium showed a good separation performance in ITP-CE of phosphorothioates. A concentration detection limit of 8.10(-9) mol/L for the 20-mer phosphorothioate ISIS5132, isolated from rat serum, was found

Integrated capillary electrophoresis on flexible silicone microdevices: analysis of DNA restriction fragments and detection of single DNA molecules on microchips.

Microchips for integrated capillary electrophoresis systems were produced by molding a poly(dimethylsiloxane) (PDMS) silicone elastomer against a microfabricated master. The good adhesion of the PDMS devices on clean planar surfaces allows for a simple and inexpensive generation of networks of sealed microchannels, thus removing the constraints of elaborate bonding procedures. The performance of the devices is demonstrated with both fast separations of φX-174/HaeIII DNA restriction fragments labeled with the intercalating dye YOYO-1 and fluorescently labeled peptides. Detection limits in the order of a few zeptomoles (10(-)(21) mol) have been achieved for each injected DNA fragment, corresponding to a mass detection limit of ∼2 fg for the 603 base pair fragment. Single λ-DNA molecules intercalated with YOYO-1 at a base pair-to-dye ratio of 10:1 could be detected with an uncomplicated laser-induced fluorescence detection setup. High single-molecule detection efficiency (>50%) was achieved under electrophoretically controlled mass transport conditions in PDMS microchannels

Functional immobilization of biomembrane fragments on planar waveguides for the investigation of side-directed ligand binding by surface-confined fluorescence

A method for the functional immobilization of Na,K-ATPase-rich membrane fragments on planar metal oxide waveguides has been developed. A novel optical technique based on the highly sensitive detection of surface-confined fluorescence in the evanescent field of the waveguide allowed us to investigate the interactions of the immobilized protein with cations and ligands. For specific binding studies, a FITC-Na,K-ATPase was used, which had been labelled covalently within the ATP-binding domain of the protein. Fluorophore labels of the surface-bound enzyme can be selectively excited in the evanescent field. A preserved functional activity of the immobilized enzyme was only found when a phospholipid monolayer was preassembled onto the hydrophobic chip surface to form a gentle, biocompatible interface. Insitu atomic force microscopy (AFM) was used to examine and optimize the conditions for the lipid and membrane fragment assembly and the quality of the formed layers. The enzyme's functional activity was tested by selective K+ cation binding, interaction with anti-fluorescein antibody 4-4-20, phosphorylation of the protein and binding of inhibitory ligand ouabain. The comparison with corresponding fluorescence intensity changes found in bulk solution provides information about the side-directed surface binding of the Na,K-ATPase membrane fragments. The affinity constants of K+ ions to the Na,K-ATPase was the same for the immobilized and the non-immobilized enzyme, providing evidence for the highly native environment on the surface. The method for the functional immobilization of membrane fragments on waveguide surfaces will be the basis for future applications in pharmaceutical research where advanced methods for exploring the molecular mechanisms of membrane receptor targets and drug screening are required

Na,K-ATPase on a waveguide sensor : supramolecular assembly and side directed binding studies by surface-confined fluorescence

The functional assembly of FITC-Na,K-ATPase membrane fragments on a surface-modified Ta205 waveguide allows to investigate the directed binding of ligands by surface-confined fluorescence studies. The results allow to draw conclusions about the sidedness of interactions. The fluorescence intensity decrease observed upon the selective binding of K+ is attributed to its coordination to a site ccessible from the former intracellular membrane side