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| Title | Convolutional networks for supervised mining of molecular patterns within cellular context. |
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| Journal, issue, pages | Nat Methods, Vol. 20, Issue 2, Page 284-294, Year 2023 |
| Publish date | Jan 23, 2023 |
 Authors | Irene de Teresa-Trueba / Sara K Goetz / Alexander Mattausch / Frosina Stojanovska / Christian E Zimmerli / Mauricio Toro-Nahuelpan / Dorothy W C Cheng / Fergus Tollervey / Constantin Pape / Martin Beck / Alba Diz-Muñoz / Anna Kreshuk / Julia Mahamid / Judith B Zaugg /   |
| PubMed Abstract | Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning ...Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community. |
 External links | Nat Methods / PubMed:36690741 / PubMed Central |
| Methods | EM (subtomogram averaging) / EM (tomography) |
| Resolution | 9.3 - 34.0 Å |
| Structure data |  EMDB-14404: Subtomogram average of S. pombe fatty acid synthase complex from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14405: Subtomogram average of S. pombe 80S ribosomes close to mitochondria from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14406: Subtomogram average of S. pombe 80S ribosomes associated to the ER from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14408: Subtomogram average of S. pombe 80S ribosomes from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14409: Subtomogram average of S. pombe 60S large ribosomal subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14410: Subtomogram average of S. pombe 80S ribosomes with an additional density close to the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14411: Subtomogram average of S. pombe 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae  EMDB-14412: Subtomogram average of S. pombe fatty acid synthase complex from cryo-tomograms acquired on cryo-FIB-lamellae  EMDB-14413: Subtomogram average of S. pombe 80S ribosomes close to mitochondria from tomograms acquired on cryo-FIB-lamellae  EMDB-14415: Subtomogram average of S. pombe 80S ribosomes associated to the ER from tomograms acquired on cryo-FIB-lamellae  EMDB-14417: Subtomogram average of S. pombe 80S ribosomes from tomograms acquired on cryo-FIB-lamellae  EMDB-14418: Subtomogram average of well-aligned 80S ribosomes from tomograms acquired on cryo-FIB-lamellae of S. pombe  EMDB-14419: Subtomogram average of S. pombe 80S ribosomes with an additional density close to the head of the small subunit from tomograms acquired on cryo-FIB-lamellae  EMDB-14420: Subtomogram average of 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired on cryo-FIB-lamellae of S. pombe  EMDB-14422: Subtomogram average of S. pombe fatty acid synthase complex predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae  EMDB-14423: Subtomogram average of 80S ribosomes close to mitochondria predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae of S. pombe  EMDB-14424: Subtomogram average of 80S ribosomes associated to the ER predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae of S. pombe  EMDB-14425: Subtomogram average of 80S ribosomes predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae of S. pombe  EMDB-14426: Subtomogram average of well-aligned 80S ribosomes from tomograms acquired on cryo-FIB-lamellae of S. pombe  EMDB-16136: Cryo-electron tomogram acquired on a cryo-FIB lamella of a retinal pigment epithelial (RPE1) cell |
| Source |
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Schizosaccharomyces pombe (fission yeast)
