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Open Positions

 

Outstanding postdoc applicants and students interested in doing a PhD, Master's or Bachelor's project in my group are welcome to get in touch with me at berenike.maier(at)uni-koeln.de. 

Currently, we offer a PhD position in Experimental Evolution and a Master/Bachelor thesis in Experimental Imaging of Biofilms.

 

Open Position - PhD position in Experimental Evolution

Our research: Horizontal gene transfer can speed up adaptive evolution of bacteria; in particular, it is involved in acquisition of antibiotic resistance. At the molecular scale, our lab focuses both on the molecular mechanism of bacterial transformation (a form of horizontal gene transfer). At the population level, we develop methods for quantifying its costs and benefits during adaptive evolution. To this end, biologists and physicists work in close collaboration.

The project: The recently funded CRC 1310 of the German Science Foundation (DFG), will address Predictability in Evolution. The specific project will focus on the question how horizontal gene transfer affects the fitness of bacteria during adaptation to novel environments. In close collaboration with theorists (Lässig group), we aim at predicting effects of gene transfer on the rate of evolution. To this end, a massively parallel laboratory evolution setup will be developed.

Research techniques applied in this project will include, but are not limited to:

  • experimental evolution
  • molecular biology, in particular design and generation of bacterial mutant strains
  • high-throughput techniques for laboratory evolution (liquid-handling platform, FACS)
  • whole genome sequencing, RNSseq, and analysis in collaboration with bioinformatics facility
  • single cell analysis and fluorescence microscopy
  • developing and planning research projects

The position: The PhD students will have the opportunity to join the Graduate School for Biological Science at the University of Cologne (http:// http://www.gs-biosciences.uni-koeln.de).

Your profile: Required criteria are: M.Sc. in biology or comparable; skills in molecular cloning and strong interest in genomics are mandatory. Experience in molecular microbiology, evolutionary biology, or biophysics or are beneficial but not essential. Applicants should be highly motivated, creative and independent individuals and have an excellent acade­mic record.

Applications from disabled persons are welcome. Disabled persons with equal qualifications will be given priority. Applications from women are specifically encouraged. Women with comparable qualifications will receive particular consideration, unless another applicant displays compelling reasons to prefer this person.

Please send your application (cover letter, CV, list of publications, certificates, and two references) as a single PDF file by email to berenike.maier@uni-koeln.de. It is mandatory that you visit Cologne for an interview.

 

 

Spinning Disk Confocal Microscopy image of stained Neisseria gonorrhoeae bacteria aggregated in a spherical micro-colony (focal plane at half height).

Open Position - Master and Bachelor Thesis in Experimental Biophysics - Cell dynamics of aggregated bacteria

Many bacterial species self- organize into biofilms. Biofilms are often associated with persistent diseases owing to the fact that they are resilient to immune surveillance and antibiotic treatment. We aim at better understanding the physical principles that underlie this resilience. How do molecular interaction forces govern biofilm structure and dynamics? Recent experiments revealed that early biofilms have many properties of fluids. How do bacteria tune structure and dynamics to increase their chance of survival in the presence of external stress?

A current challenge in the field is to track the dynamics of each single cell within biofilms consisting of thousands or even millions of cells. We employ an interdisciplinary approach combining methods from biophysics (advance image analysis, advanced light microscopy) with methods from microbiology and biochemistry. In this specific project, you will employ spinning disc confocal microscopy to image early biofilms. For a Master thesis, you will first create an image processing pipeline which will allow to determine the trajectories of the cells (for spherical and rod-shaped bacteria) within the colony starting from the recorded images. From these trajectories, the main dynamical parameter (e.g. their velocity) will be extracted. Furthermore, you will address questions like: How does the colony dynamic change under different stress conditions including antibiotic treatment?. What are the possible benefits for the bacteria when they change their interaction forces? Which physical models can be used and adjusted to explain these dynamics? For a Bachelor thesis, we are especially interested in tracking and analyzing dead cells (stained separately) within the aggregate. Here, you might adress questions like: How does the dynamic of inactive (dead) cells differ from the dynamic of living ones? Does the relative position of dead cells differ from the position of actively retracting cells?

Supervisors: Prof. Dr. Berenike Maier / Dr. Marc Hennes

Contact: berenike.maier@uni-koeln.de