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PostDoc position available

Application time frame: 
The vacant PostDoc Position is to be filled in spring 2024. The application deadline is the 15th of January 2024. Shortlisting of candidates will start earlier.  

Topic:  
Cryo-electron tomography (cryo-ET) can provide unique ultrastructural insights into the molecular architecture of natively preserved cells. Combining it with subtomogram averaging (STA) allows for determining subnanometer resolution structures in situ. However, localizing proteins of interest (POIs) within cells during data acquisition and processing remains a bottleneck for this approach. Fluorescently tagged POIs for cryo-correlative light and electron microscopy (cryo-CLEM) can guide lamella preparation and data acquisition. However, fluorescence microscopy (FM) data will typically not support identifying POIs in cryo-electron tomograms for further processing.  
Thus, a tagging approach marking proteins in both imaging modalities would be highly desirable. At best, the resulting label should be able to recruit membrane-permeable synthetic fluorophores to allow for reliable detection of POIs at endogenous expression levels in FM, result in a uniquely shaped strong density in cryo-ET, and cause neglectable perturbations for cell physiology and protein function. This project aims to provide a genetically encoded two-component cryo-CLEM labeling system that can meet those challenging demands.  

Team:  
Our team is interested in how cells establish, maintain, and alter the shapes and orientations of their large-scale components, like organelles or the cytoskeleton. We are convinced that a holistic understanding of this cellular architecture can only be achieved by visualizing the machinery that organizes it. To do this under the most native conditions and at (sub-) nanometer resolutions, we rely on cryo-ET and STA performed on cellular specimens. In situ structural and ultrastructural insights obtained by this workflow can then serve as a framework for integrating results we gather from reverse genetics, light microscopy, biochemistry, and in vitro structural approaches.  

Available Technology:  
Department of Integrative Structural Biology (BSI) at the Institute of Genetics and Molecular and Cell Biology (IGBMC) has a strong focus on cryo-electron microscopy (cryo-EM) techniques and houses 2 Titan Krios, 1 Glacios, 1 cryo-Focused Ion Beam Scanning Electron Microscope (cryo-FIB/SEM), a cryo-light microscope, several vitrification devices (plunge freezing and high-pressure freezing) and a dedicated micromechanics workshop for developing and prototyping new instruments.  

Additional Motivation: 
IGBMC hosts many working with cellular model systems for a wide variety of developmental, homoeostatic, and pathologic processes, which are amenable to characterization by cryo-CLEM-guided cryo-ET but have yet to be explored by this methodology. This will provide the PostDoc with ample opportunities for in-house collaborations. 
We will support the postdoctoral fellow in the application for prestigious fellowship schemes (Marie Skłodowska-Curie, EMBO, HPSF) and scientific prices. 
The institute is located next to the beautiful city of Strasbourg (with a world-famous Christmas market) in the Alsace region of France, close to the German border and within a short distance to the Black Forrest and the Vosges mountain ranges boasting ample opportunities for recreational activities.   

Candidate:  
Essential requirements:  
-A Ph.D. in a field related to biology, chemistry, or physics  
-Experience in electron and/or fluorescence microscopy   
-Fluency in English (written and spoken)  

Preferential requirements:  
-Experience in cryo-ET, cryo-FM, and/or cryo-EM is considered a strong asset 
-Experience in mammalian cell culture and especially genome editing is a plus  
-Ability to communicate the acquired results by writing manuscripts and giving presentations  

Required personal skills:  
-Proactivity 
-Independence 
-Ability to work in a team  

Application Documents (in English) Compiled as a single PDF and sent to florian.faessler@igbmc.fr: 
-A motivation letter covering your education/scientific experiences and how they have 
prepared/motivated you to work on the development of cryo-CLEM labels (max 1 page)  
-Your CV  
-A description of how a perfectly functional cryo-CLEM label could have benefitted your PhD project or 
of a project in which you would like to employ such a label in the future (max 1 page) 
-The names and contacts of 2 referees  

 

 

 

 

Check out Florian's previous work

 

Cellular Architecture

 

 

Our team is interested in how cells establish, maintain, and alter the shapes and orientations of their large-scale components, like organelles or the cytoskeleton. We are convinced that a holistic understanding of this cellular architecture can only be achieved by visualizing the machinery that organizes it. To do this under the most native conditions and at (sub-) nanometer resolutions, we rely on cryo-electron tomography and subtomogram averaging performed on cellular specimen. In situ structural and ultrastructural insights obtained by this workflow can then serve as framework for the integration of results we gather from reverse genetics, light microscopy, biochemistry, and in vitro structural approaches.  

 

Current projects

Deciphering (ultra)structural mechanisms of Golgi organization (Delnia Nazari Banyarani, Ph.D. student)

Proper glycosylation of proteins in the endomembrane system is crucial for many biological processes, such as lysosomal sorting, extracellular matrix structuring, and signal transduction. Improper glycosylation, in turn, is associated with neurodegeneration, cancer, and autoimmune diseases. It is, thus, vital for cells to maintain the order of their central glycan modification hub, the Golgi apparatus.

In this context, the Golgi matrix, in concert with other players like the cytoskeleton, guides protein distribution amongst the individual Golgi cisternae, controls their shape, and keeps them stacked. Nevertheless, how the Golgi matrix itself is structured to achieve these functionalities remains largely unknown, as the usability of classical approaches based on fluorescence microscopy, room temperature electron microscopy, and in vitro reconstitution is limited by the small size and high complexity of the system. To overcome this, we will employ state-of-the-art in situ cryo-electron tomography to visualize the Golgi matrix and its interactors. Applying subtomogram averaging to selected players will further allow us to determine their structures at (sub-) nanometer resolution in their intracellular environment.

This will provide an (ultra-) structural framework for the integration of orthogonal data provided by reverse genetics, cell biology, and biochemistry techniques. Together, we will use these approaches to provide unprecedented insights into the structure-function relationship of the Golgi apparatus organization.

 

 

Cryo-CLEM labels for minimizing artifacts and background (Open PostDoc position)

Cryo-electron tomography (cryo-ET) can provide unique ultrastructural insights into the molecular architecture of natively preserved cells. Combining it with subtomogram averaging (STA) allows for determining subnanometer resolution structures in situ. However, localizing proteins of interest (POIs) within cells during data acquisition and processing remains a bottleneck for this approach. For solving structures of the Arp2/3 complex in its branch junction state, we recently employed its specific accumulation in lamellipodia and its characteristic integration into actin networks to select target sites for tilt-series and individual particle positions, respectively. For POIs, whose localization is less predictable from cell morphology alone, employing fluorescently tagged POIs for cryo-correlative light and electron microscopy (cryo-CLEM) can guide lamella preparation and data acquisition. However, fluorescence microscopy (FM) data will typically not support identifying POIs in cryo-electron tomograms for further processing.
Thus a tagging approach marking proteins in both imaging modalities would be highly desirable. At best, the resulting label should be able to recruit membrane-permeable synthetic fluorophores to allow for reliable detection of POIs at endogenous expression levels in FM, result in a uniquely shaped strong density in cryo-ET, and cause neglectable perturbations for cell physiology and protein function. This project aimes to provide a genetically encoded two-component cryo-CLEM labeling system that can meet those challenging demands.

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Fichier:Centre national de la recherche scientifique.svg — Wikipédia     IMCBio International PhD Program

 

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