Alexander Nesterov-Müller

Quality analysis of selective microparticle deposition on electrically programmable surfaces

Image processing and pattern analysis can evaluate the deposition quality of triboelectrically charged microparticles on charged surfaces. The image processing method presented in this paper aims at controlling the quality of peptide arrays generated by particle based solid phase Merrifield combinatorial peptide synthesis. Incorrectly deposited particles are detected before the amino acids therein are coupled to the growing peptide. The calibration of the image acquisition is performed in a supervised training step in which all parameters of the quality analyzing algorithm are learnt given one representative image. Then, the correct deposition pattern is determined by a linear support vector machine. Knowing the pattern, contaminated areas can be detected by comparing the pattern with the actual deposition. Taking into account the resolution of the image acquisition system and its magnification factor, the number and size of contaminating particles can be calculated out of the number of connected foreground pixels.

Identification of a Tetanus Toxin Specific Epitope in Single Amino Acid Resolution

Vaccinations are among the most potent tools to fight infectious diseases. However, cross‐reactions are an ongoing problem and there is an urgent need to fully understand the mechanisms of the immune response. For the development of a methodological workflow, the linear epitopes in the immune response to the tetanus toxin is investigated in sera of 19 vaccinated Europeans applying epitope mapping with peptide arrays. The most prominent epitope, appearing in nine different sera (923IHLVNNESSEVIVHK937), is investigated in a substitution analysis to identify the amino acids that are crucial for the binding of the corresponding antibody species − the antibody fingerprint. The antibody fingerprints of different individuals are compared and found to be strongly conserved (929ExxEVIVxK937), which is astonishing considering the randomness of their development. Additionally, the corresponding antibody species is isolated from one serum with batch chromatography using the amino acid sequence of the identified epitope and the tetanus specificity of the isolated antibody is verified by ELISA. Studying antibody fingerprints with peptide arrays should be transferable to any kind of humoral immune response toward protein antigens. Furthermore, antibody fingerprints have shown to be highly disease‐specific and, therefore, can be employed as reliable biomarkers enabling the study of cross‐reacting antigens.

Kombinatorische Chemie im hochdichten Arrayformat

We synthesize peptide arrays by using laser pulses to transfer amino acids onto a synthesis slide that are embedded in a polymer. After patterning these razor-thin spots, the coupling starts by heating the polymer that now serves as a solvent to couple monomers to the surface. The main advantages of this nanolayer solid phase chemistry are the high degree of automation, the very high spot density, and the in situ activation of monomers due to mixing different reagents in the stacked nanolayers.

Image Processing Quality Analysis for Particle Based Peptide Array Production on a Microchip

Highly complex microarray systems based on combinatorial synthesis techniques are in wide-spread use in biological, medical and pharmaceutical research Chee et al. (1996); Cretich et al. (2006); Debouck & Goodfellow (1999). Two prominent examples are micro arrays for the artificial synthesis of arbitrary DNA sequences out of nucleic acids Heller (2002) and peptide synthesis out of amino acids Beyer et al. (2007); Templin et al. (2003). In the case of DNA arrays, these experiments mostly focus on gene identification or gene expression profiling to determine the effects of single genes on cellular evolution. Peptide arrays aim at understanding interactions of peptides with other molecules. As sequences in proteins, peptides are involved in the regularisation of biological activity.