Seminar Series

CompuGene Seminar Series – Upcoming Talks

All guests are very welcome!

 

May 23, 2018 – B2|03-109 (4 p.m.)

Dr. Dora Tang (MPI Dresden)

Prof. Yolanda Schaerli (Lausanne)

Dr. Dora Tang (MPI Dresden),

Tang Group

Dynamic Protocellular systems

Biology is well equipped in exploiting a large number of out of equilibrium processes to support life. A complete understanding of these mechanisms is still in its infancy due to the complexity and number of the individual components involved in the reactions. However, a bottom up approach allows us to replicate key biological processes using a small number of basic building blocks. This methodology has the added advantage that properties and characteristics of the artificial cell can be readily tuned and adapted. Working between biophysics, materials science and synthetic biology we reimagine and translate the physical phenemona which drive out of equilibrium processes in cells into novel, robust and dynamic systems for synthetic biology applications.

Compartmentalisation

A key property of the cell is its ability to compartmentalize chemical reactions. This allows the cell to control different chemical and physical environments, utilize the membrane as a reaction surface and protect enzymes and proteins from degradation. Membrane delineated compartments based on lipids have been extensively used to fulfill this criteria, however they lack an internal heterogeneity that is characteristic of natural cells. Therefore, membrane free droplets based on coacervation or liquid-liquid phase separation have not only been associated with mechanisms within the natural cell but have offered an alternative model to compartmentalization.

We use a range of techniques to understand the chemical and physical processes which drive molecular organization in lipids, polymers and proteins to rationally control self-assembly for the construction of novel proto-cellular platforms. This methodology is applied to protein-lipid and protein-polymer interactions as well as in-vitro compartmentalized transcription-translation processes which enables us to activate our compartments in a highly controlled manner. In addition, understanding these interactions can give insights to key questions in the origin of life i.e. what were the conditions required to drive molecular organization from disorder? and how did a biological world derive from chemistry?

Methodological and technical expertise:

  • Artificial cell synthesis (coacervates, lipid vesicles, hybrid protocells)
  • High pressure SAXS and CD for soft matter
  • Cell free expression
  • Analytical techniques (spectroscopy, DLS, DSC, ITC)
  • Lipid Membrane curvature (inverse bicontinuous cubic phases)

Prof. Yolanda Schaerli (Lausanne)

Schaerli Group

Synthetic gene regulatory networks for pattern formation

During embryonic development, cells acquire different identities, depending on their spatial positions. This developmental process is called pattern formation. The molecular details of pattern formation are complicated, but are thought to be governed by general principles such as the use of morphogen gradients to provide positional information. We build, study and model synthetic gene regulatory networks to improve our understanding of such general principles.

Evolution of gene regulatory networks

What constrains the evolution of gene regulatory networks? What makes a gene regulatory network robust to mutations and/or evolvable? How does the regulatory mechanism of a network influence its evolution? How can gene regulatory networks change extensively, while maintaining overall circuit output? How do mutations in gene regulatory networks interact to produce novel phenotypes? What happens after a gene has been duplicated?

Robustness, cryptic genetic variation and innovation in transcription factor binding

In collaboration with Prof. Payne, ETH Zurich and Prof. Wagner, University of Zurich.

Mutational robustness is a striking and widespread property of biological systems. One consequence of this robustness is that genetic diversity may accumulate in transcription factor binding sites. Such diversity is often referred to as cryptic because it does not manifest as phenotypic diversity unless an environmental or genetic perturbation disrupts the function of the cognate transcription factor. What is the mutational robustness of transcriptional binding sites? How is cryptic genetic diversity accumulated? Does cryptic genetic variation in transcription factor binding sites facilitate evolutionary innovation?

We are using a synthetic gene regulatory circuit in E. coli, molecular evolution experiments and computational modelling to address these questions.

May 23 2018

Dr. Dora Tang (MPI Dresden),

Prof. Yolanda Schaerli (Lausanne)

September 5 2018

Prof. Ilka Axmann (Düsseldorf)

October 18 2018

Prof. Francois Kepes (Paris)

Prof. Torsten Waldminghaus (Marburg, Synmikro)

November 7 2018

Prof. Ulrich Gerland (TU München)