Time-Resolved Visualization of the Yeast Ribosome-Biogenesis by Cryo-Electron Tomography
Final Report Abstract
This project built on our earlier work that used electron tomography and image processing to visualize pre-ribosomal particles in the context of the so-called Miller trees in yeast. The in-situ analysis of the crowded cellular environment requires dedicated denoising techniques to depict individual complexes. At the same time, since the cryo-electron tomograms represent snapshots taken during ongoing cellular processes (co-transcriptional formation of pre-ribosomal particles), classification of subtomograms was used to improve the resolution of the subtomogram averaging. Subsequently, placing back the structures in the natural context and annotation of the cryo-tomograms is indispensable to decipher the biological mechanism. Within the project time frame, we developed a dedicated software (ArtiaX) for the interactive handing, the display, selection, and editing of particles within tomograms. This opensource software already proofed to be extremely successful in diverse cryo-electron tomography projects world-wide. Driven by the demand of the scientific community, further tools, e.g. to implement correlative fluorescent-superresolution light microscopy, are presently implemented. Furthermore, since the resolution obtained on data which had been acquired on samples prepared according to the previously established protocols did limit the scopes of the project, we developed a genetic engineering strategy that significantly enhanced the amount of preribosomal particles per cryo-electron tomogram. The analysis of the cryo-electron tomography data based on the improved image processing and sample preparation work achieved in the project, that shall ultimately lead to a time-resolved analysis of ribosome biogenesis in-situ, is still ongoing.
Publications
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Enhancing Patch-Based Methods with Inter-Frame Connectivity for Denoising Multi-Frame Images. 2019 IEEE International Conference on Image Processing (ICIP), 2414-2418. IEEE.
Bodduna, Kireeti & Weickert, Joachim
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Hough Based Evolutions for Enhancing Structures in 3D Electron Microscopy. Lecture Notes in Computer Science, 102-112. Springer International Publishing.
Bodduna, Kireeti; Weickert, Joachim & Frangakis, Achilleas S.
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Image denoising with less artefacts: novel nonlinear filtering on fast patch reorderings.
Bodduna, K. & Weickert, J.
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Ex vivo visualization of RNA polymerase III-specific gene activity with electron microscopy. Communications Biology, 4(1).
Manger, Sina; Ermel, Utz H. & Frangakis, Achilleas S.
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It’s noisy out there! A review of denoising techniques in cryo-electron tomography. Journal of Structural Biology, 213(4), 107804.
Frangakis, Achilleas S.
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ArtiaX: An electron tomography toolbox for the interactive handling of sub‐tomograms in UCSF ChimeraX. Protein Science, 31(12).
Ermel, Utz H.; Arghittu, Serena M. & Frangakis, Achilleas S.
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Mean curvature motion facilitates the segmentation and surface visualization of electron tomograms. Journal of Structural Biology, 214(1), 107833.
Frangakis, Achilleas S.
