Research and Thesis Projects

• Master Thesis: Developing Functional Inclusion Body Tags

Location: Bioprocess Laboratory (Prof. Sven Panke), D-BSSE, ETH Zurich, Basel, Switzerland
Start: March 2025
Duration: 6 months
Contact: Berk Kocar ()

Inclusion bodies are dense protein aggregates formed in the cytoplasm of bacteria like E. coli. While often regarded as problematic, proteins that are sequestered in such inclusion bodies continue to be active and are simple to purify. By tagging proteins of interest with specific “inclusion body tags”, even proteins that would remain soluble can be sequestered into inclusion bodies upon expression.
This project aims to design and evaluate novel inclusion body tags with tailored properties for diverse applications. Of special interest are tags that are detectable in electrospray ionization mass spectrometry (ESI-MS).

Project Description
The successful candidate will design and screen tag libraries in E. coli to identify and characterize functional inclusion body tags compatible with high-throughput mass spectrometry (MS) analysis. This involves advanced molecular biological techniques and opportunities to learn cutting-edge analytical methods such as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) MS. Additionally, the project offers exposure to droplet microfluidics for high-throughput analysis and potential training in computational peptide design and structural biology.

Requirements
A background in molecular biology or bioengineering particularly in bacterial cultures and genetic manipulation as well as enthusiasm for interdisciplinary research and willingness to learn new analytical and computational techniques is helpful. This project is ideal for a motivated student passionate about protein engineering and innovative biotechnological methods. The starting date is flexible.

What we offer:
We provide exceptional infrastructure, advanced facilities, mentorship from experienced researchers, and a supportive work environment within an international setting. If you are interested, please submit your CV, university transcripts, and a brief letter outlining your motivation.

• Master thesis project: 
  Effect of in vivo RNA circularization on the production of Antimicrobial Peptides (AMPs)

Location: Bioprocess Laboratory (Prof. Sven Panke), D-BSSE, ETH Zurich, Basel, Switzerland
Start: January/February 2025
Duration: 6 months
Contact: Aurellia Galliot ()

In vivo circularization of short recombinant RNA expressed from a plasmid has proved to be effective in Escherichia coli (Daròs JA, et al., Sci Rep. 2018). Ligation of RNA extremities, or circularization, protects from intracellular degradation by endonucleases, thus significantly increasing the RNA stability in cells, enabling their accumulation at ribosomal RNA levels (~80 % of total RNA).
While we have previously worked on the recombinant expression of small non-coding RNAs, we propose here to study the translation of small coding circular mRNAs or circ(m)RNA. To investigate the translation of these circ(m)RNA, we will test known AMPs, such as Bac7 and assess whether increasing the stability of their RNAs results in a proportional increase in the strength and duration of their antimicrobial effect.
The corresponding circ(m)RNA of identified AMPs would then be purified with the ultimate goal of developing an RNA-based antimicrobial drug, bioproduced in E. coli.

We are looking for a motivated student with a background in molecular/synthetic biology. In the course of this project, the applicant will obtain hands-on experience in RNA biology, RNA therapeutics.
We offer excellent infrastructure and state-of-the-art facilities, supervision and guidance by experienced researchers and pleasant working environment in an international setting.
If interested, please send your CV, university transcripts and a short letter describing your

• We have no other available projects at this time.

Please consult the research section on general topics and come by to discuss projects in detail or contact us via e-mail: