The Centre for Integrative Biology in Strasbourg, France have a position available for an enthusiastic scientist in super-resolution microscopy to join their team
They have recently done a series of developments in super-resolution fluorescence microscopy to facilitate single molecule localization microscopy (SMLM) analysis. This includes a pipeline for image reconstruction, drift correction, chromatic aberration correction for dual-color analysis and resolution estimation (Andronov et al., Bioinformatics 2016), Voronoi-diagram based tools for 2D clustering and segmentation analysis (Andronov et al., Sci Rep 2016) and most recently 3D clustering and segmentation analysis based on Voronoi diagrams (Andronov et al., Bioinformatics 2018). These have had several important applications for the analysis of macromolecular complexes in the cell. Our latest development comprises a spectral demixing method which facilitates co-localization of proteins in SMLM.
The person to be recruited should have a strong interest in conducting such developments, which aim at performing (i) developments in correlative light and electron microscopy (CLEM) at the interface between imaging, FIB/SEM, cryo electron tomography and single particle cryo-EM, (ii) routine implementation of SMLM for various projects at the institute and for external users as part of the National and European Infrastructures FRISBI and Instruct-ERIC. The long-term aim is to interface SMLM and cryo-EM to observe and reconstruct in 3D macromolecular complexes at higher resolution once they have been localized and imaged in the cellular context.
The mission will be to design, develop and conduct specialized super-resolution microscopy to locate individual protein molecules in the cellular context, including fluorescence microscopy under cryo conditions to preserve samples for correlative imaging and cryo-EM analysis, and hence participate in the development and implementation of the necessary instrumentation, technology and image processing.
The person to be recruited (Engineer or PhD) should have a master or a PhD and have a strong background in imaging, optics, physics or informatics & software developments and ideally have experience in super-resolution microscopy (e.g. dSTORM or PALM etc.).
Furthermore, there is an opportunity in our team for a master internship, for example at the master M2 level with the possibility of conducting a PhD thesis afterwards.
For more details please see below.
Some recent publications:
- L. Andronov, R. Genthial, D. Hentsch, B. P. Klaholz. A spectral demixing method for high-precision multi-color localization microscopy applied to nuclear pore complexes. 2022. https://doi.org/10.1101/2021.12.23.473862
- L. Andronov, J.-L. Vonesch & B. P. Klaholz. Practical aspects of super-resolution imaging and segmentation of macromolecular complexes by dSTORM. Methods Mol Biol. 2021, 2247, 271-286. https://doi.org/10.1007/978-1-0716-1126-5_15. Book chapter.
- L. Andronov, K. Ouararhni, I. Stoll, B. P. Klaholz & A. Hamiche. CENP-A nucleosome clusters form rosette-like structures around HJURP during G1. Nat Commun., 2019, 10, 4436. https://doi.org/10.1038/s41467-019-12383-3.
- L. Andronov, J. Michalon, K. Ouararhni, I. Orlov, A. Hamiche, J.-L. Vonesch & B. P. Klaholz.3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. Bioinformatics, 2018. http://dx.doi.org/10.1093/bioinformatics/bty200.
- I. Orlov, A. G. Myasnikov, L. Andronov, S. K. Natchiar, H. Khatter, B. Beinsteiner, J-F. Ménétret, I. Hazemann, K. Mohideen, K. Tazibt, R. Tabaroni, H. Kratzat, N. Djabeur, T. Bruxelles, F. Raivoniaina, L. di Pompeo, M. Torchy, I. Billas, A. Urzhumtsev & B. P. Klaholz. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell., 2017, 109, 81. http://dx.doi.org/10.1111/boc.201600042.
- S. K. Natchiar, A. G. Myasnikov, H. Kratzat, I. Hazemann & B. P. Klaholz. Visualization of chemical modifications in the human 80S ribosome structure. Nature, 2017, 551, 472-477. http://dx.doi.org/10.1038/nature24482.
- L. Andronov, I. Orlov, Y. Lutz, J-L. Vonesch & B. P. Klaholz. ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy. Sci. Rep. 2016, 6, 24084. http://dx.doi.org/10.1038/srep24084.
- L. Andronov, Y. Lutz, J-L. Vonesch & B. P. Klaholz. SharpViSu: integrated analysis and segmentation of super-resolution microscopy data. Bioinformatics, 2016, 32, 2239-2241. http://dx.doi.org/10.1093/bioinformatics/btw123.
For ongoing projects and full publication list of the associated team and the infrastructures see:
http://www.igbmc.fr/grandesstructures/cbi
The platform and associated research groups are located at the Centre for Integrative Biology (CBI) at IGBMC, Illkirch/Strasbourg, France, which comprises cutting-edge imaging and cryo-EM facilities:
The CBI provides a leading-edge scientific and technological environment in integrated structural biology to address the structure and function of biological systems, notably on gene expression, from the atomic, molecular to the cellular scales. The CBI http://www.igbmc.fr/grandesstructures/cbi/, hosts the French and European Infrastructures for Integrated Structural Biology, FRISBI https://frisbi.eu/ Instruct-ERIC https://www.structuralbiology.eu/ and iNEXT-Discovery https://inext-discovery.eu, which comprises super-resolution fluorescence microscopy (dSTORM/GSDIM Leica Microsystems SRGSD, equipped with adaptive optics for 3D SMLM image acquisition and an image splitter for co-localization studies), advanced electron microscopy facilities equipped with cutting-edge instrumentation such as Titan Krios and Glacios cryo electron microscopes for cryo-EM and tomography, and cryo Focused Ion Beam Scanning Electron Microscope (cryo-FIB/SEM) including for cryo FIB milling / lamella production. The Titan Krios microscope is equipped with phase plate and Cs corrector, Falcon 3 camera, GIF energy filter and K3 camera, the Glacios with a K2 camera. In addition, the EM facility has a suite of associated equipments for sample preparation and dedicated computing resources for image analysis, processing and 3D reconstruction by fluorescence microscopy, single particle cryo-EM and cryo electron tomography (cryo-ET), and a dedicated opto-meca micromechanics workshop for developing and prototyping new instruments.
Applications should be sent via email to klaholz@igbmc.fr including CV, list of publications, names of 3 referees and motivation letter. The position remains open until filled, with an initial deadline for first applications April 22nd 2022.
