Graduate Students Mini Symposium V - 2023

Program

13:15 h Imre Banlaki - ENG Niederholtmeyer
A cell-free trigger wave in two dimensional cell-mimic arrays

Intercellular communication is a fundamental function in biology to organize cooperation. Diffusive signals are used by unicellular and multicellular organisms to synchronize behavior or even govern differentiation. The latter case is of particular interest as it requires complex systems, generally including multiple diffusing signals. Cell-free synthetic biology allows to build such model systems and investigate their functionality in a well-controlled environment. In vitro transcription and translation (TXTL) was used to investigate communication in two dimensions, in batch reactions, and one dimension at steady state. My work expands on previous systems, combining the two-dimensionality of the batch experiments with the continuous perfusion of the one-dimensional system. The presented microfluidic device vertically perfuses a 2D array of DNA loaded cell-mimics through a diffusive hydrogel barrier. This barrier protects the cell-mimics from flow perturbations which allows for the expression of a trigger wave, activated by reaction diffusion, expanding against the perfusion flow.

13:45 h Stijn Tobias de Vries - DNA Foundry - Schindler

Towards assembly of synthetic chromosomes and novel induction systems to study chromosomal stability in Saccharomyces cerevisiae.

Building synthetic chromosomes has traditionally focused on reconstructing existing chromosomes rather than creating them from scratch. In this seminar, we present an innovative and high-throughput molecular assembly method for constructing synthetic chromosomes in S. cerevisiae. Our method incorporates scarless cloning methods, enabling the construction of mostly scarless synthetic chromosomes. Furthermore, we introduce a precise molecular tool designed to induce structural rearrangements in the synthetic chromosomes. This tool will provide a valuable means to investigate the fundamental principles governing chromosomal stability in S. cerevisiae in the future. Our research holds the potential to significantly advance the field of synthetic chromosome construction and provide insights into the complex nature of chromosomal stability. We anticipate that the outcomes of this study will contribute to a deeper understanding of genome stability mechanisms and pave the way for the development of more stable synthetic chromosomes with enhanced applications in various domains.

14:15 h Paulo Alexandrino - AG Erb

Exploring the potential of non-model organisms as sources of enzyme candidates for novel metabolic pathways

Bioretrosynthetic analysis is a powerful tool for designing innovative metabolic pathways, as evidenced by the development of the CETCH cycle. Despite the success in automating this process, computer-assisted bioretrosynthesis often generates a surplus of impractical pathways due to a scarcity of enzyme candidates for hypothetical reactions. To tackle this issue, the forthcoming Mini-Symposium will concentrate on a cheminformatics method that facilitates the screening of promiscuous enzyme activities for alternative applications.