Papers by andreas schober
Cell Death & Disease, 2017
Current preclinical models in tumor biology are limited in their ability to recapitulate relevant... more Current preclinical models in tumor biology are limited in their ability to recapitulate relevant (patho-) physiological processes, including autophagy. Three-dimensional (3D) growth cultures have frequently been proposed to overcome the lack of correlation between two-dimensional (2D) monolayer cell cultures and human tumors in preclinical drug testing. Besides 3D growth, it is also advantageous to simulate shear stress, compound flux and removal of metabolites, e.g., via bioreactor systems, through which culture medium is constantly pumped at a flow rate reflecting physiological conditions. Here we show that both static 3D growth and 3D growth within a bioreactor system modulate key hallmarks of cancer cells, including proliferation and cell death as well as macroautophagy, a recycling pathway often activated by highly proliferative tumors to cope with metabolic stress. The autophagy-related gene expression profiles of 2D-grown cells are substantially different from those of 3D-gr...
The insertion of random sequences into protein-encoding genes in combination with biological sele... more The insertion of random sequences into protein-encoding genes in combination with biological selection techniques has become a valuable tool in the design of molecules that have useful and possibly novel properties. By employing highly effective screening protocols, a functional and unique structure that had not been anticipated can be distinguished among a huge collection of inactive molecules that together represent all possible amino acid combinations. This technique is severely limited by its restriction to a library of manageable size. One approach for limiting the size of a mutant library relies on 'doping schemes', where subsets of amino acids are generated that reveal only certain combinations of amino acids in a protein sequence. Three mononucleotide mixtures for each codon concerned must be designed, such that the resulting codons that are assembled during chemical gene synthesis represent the desired amino acid mixture on the level of the translated protein. In this paper we present a doping algorithm that 'reverse translates' a desired mixture of certain amino acids into three mixtures of mononucleotides. The algorithm is designed to optimally bias these mixtures towards the codons of choice. This approach combines a genetic algorithm with local optimization strategies based on the downhill simplex method. Disparate relative representations of all amino acids (and stop codons) within a target set can be generated. Optional weighing factors are employed to emphasize the frequencies of certain amino acids and their codon usage, and to compensate for reaction rates of different mononucleotide building blocks (synthons) during chemical DNA synthesis. The effect of statistical errors that accompany an experimental realization of calculated nucleotide mixtures on the generated mixtures of amino acids is simulated. These simulations show that the robustness of different optima with respect to small deviations from calculated values depends on their concomitant fitness. Furthermore, the calculations probe the fitness landscape locally and allow a preliminary assessment of its structure.
3D Multi Electrode Arrays
Neurobiological concepts derived from measurements provided by the current generation of MEA tech... more Neurobiological concepts derived from measurements provided by the current generation of MEA technology have so far lacked the complexity of actual high-level neurobiological systems. Two key advances are needed to improve our understanding of such systems: in vivo 3D-neuronal cell cultures (including multiple types of neural cells), and 3D MEA systems for measuring this 3D-cultures [1][2][3]. We have constructed an in vitro measurement system for exactly such 3D-neuronal cell cultures. The principal cultures to be investigated with this system will be neural cells derived from human stem cells.
Journal of Biochemical and Biophysical Methods, 1998
In this short note, we present the results of a case study for monitoring the whole polymerase ch... more In this short note, we present the results of a case study for monitoring the whole polymerase chain reaction (PCR) process (all steps) with a glass fiber fluorometer that was described in a former publication. To utilize this fluorometer, which was originally constructed for a PCR machine with three thermostatting devices, a new thermostatting device has been developed: the glass fiber matrix is integrated into the thermostatting device, while the PCR samples are heated and cooled. The device is able to monitor all samples throughout all stages of PCR with the help of an intercalating dye. This approach also permits one to choose arbitrarily different cooling and heating rates.
Journal of neuroscience methods, 2012
Experiments based on neuronal cell-transistor couplings were made from some groups during the las... more Experiments based on neuronal cell-transistor couplings were made from some groups during the last years. Pioneering work in this field was carried out by Fromherz and his group (Fromherz, 2003; Schmidtner and Fromherz, 2006). We were interested of the interaction of nerve cells to serine hydrolase inhibitor diisopropylfluorophosphate (DFP), monitored by using an aluminum-galliumnitride/galliumnitride (AlGaN/GaN) electrolyte gate field effect transistor (EGFET). The biocompatibility study of our sensor materials with nerve cells shows a proliferation rate of at least 95%. The inhibitors were added to the medium and the source-drain current of the EGFET was recorded as a function of time. The inhibitor was added to the NG108-15 nerve cells growing directly on the sensor surface, resulting in a fast decrease in the drain current, I(DS). Control measurements show that this response is associated with cationic fluxes pumped through ionic channels present in the cellular membrane. The se...
Uploads
Papers by andreas schober