PhD position (no. 2) in biological microED and single molecule electron diffraction

5 days left

University of Basel
Basel, Switzerland
Apr 18, 2021
May 16, 2021
Organization Type
University and College
Full Time
The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A PhD position funded by the NanED EU Marie Curie Innovative Training Network is available from September 2021 onwards in the group of Prof Jan Pieter Abrahams at the Biozentrum of the University of Basel. Applicants must have not resided or carried out their main activity (work, studies, etc.) in Switzerland for more than 12 months in the last 3 years preceding June 1, 2021. The applicant shall at the date of recruitment by the host organization, be in the first four years (full-time equivalent research experience) of their research career and have not been awarded a doctoral degree.

Cryo-electron microscopy can reveal the atomic structures of biological molecules by focusing the electrons that are scattered by the sample into an image. These electron images have low contrast and are very noisy, because electron beam damages the sample.

The Abrahams group has generated strong evidence that the signal-to-noise ratio of the electron image can be boosted significantly by measuring the scattered electrons directly. This resulted in the development of protein nano-crystallography (micro-ED) and we are extending the method to include non-crystalline samples and single molecule electron diffraction (simED). Novel, dedicated hardware will allow us to develop methods for automatically generating vast amounts of electron diffraction data short periods of time. We aim to develop novel tools based on Artificial Intelligence and Big Data technologies for interpreting these data. An important biological focus of our group is on molecular machines for protein degradation. (I. Mohammed, K. A. Schmitz, N. Schenck, T. Maier, J. P. Abrahams, Catalytic cycling of human mitochondrial Lon protease. Sci. Adv. 7, eabf0156 (2021).

Part of the work will be performed at, and will be supported by, the Paul Scherrer Institute .

Your position

Phasing protein microED data. Your project is part of an overall project of our group to establish novel technologies and methods for biomolecular structure determination. We will implement data collection strategies that allow experimental phasing of electron diffraction data by scanning crystals with a nano-beam (ptychography) and by measuring rotating crystals in imaging mode. We will develop algorithms and software to exploit the unique information provided by these modes of data collection for determining phase probabilities of nano-crystal electron diffraction data. Extending the nano-beam diffraction method to non-crystalline samples of macromolecules in close collaboration with a PhD student working on the phasing of simED data is foreseen.

Your profile
We are looking for a talented PhD student with the following research profiles:
  • Background in either structural biology, crystallography, software development / big data analysis, and/or electron microscopy.
  • A keen interest in developing break-through technologies.

We offer you
We offer an exciting and stimulating work environment with scientific collaborations within the institute and worldwide.
Basel is an international city with people from 150 nations. Located on the border where three countries meet - Switzerland-Germany- France -, it is Europe's most important life sciences hub. Basel provides a high standard of living and a rich and varied cultural atmosphere.

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