Isotropic reconstruction for electron tomography with deep learning

Liu, Yuntao; Zhang, Heng; Wang, Hui; Tao, Chang-Lu; Bi, Guo-Qiang; Zh, Zhou

doi:10.1038/s41467-022-33957-8

Cited by 175 publications

(121 citation statements)

References 66 publications

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“…Tomograms from resulting image stacks were reconstructed in IMOD 54 using weighted back projection after patch track alignment. The missing wedge was corrected in IsoNet 55 . Particles were visualized in these 3D volumes in ChimeraX.…”

Section: Cryo-electron Tomography Data Collection and Processingmentioning

confidence: 99%

Structural consequences of turnover-induced homocitrate loss in nitrogenase

et al. 2023

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Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein – a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA – that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.

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Section: Cryo-electron Tomography Data Collection and Processingmentioning

confidence: 99%

Structural consequences of turnover-induced homocitrate loss in nitrogenase

et al. 2023

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“…Tilt series were drift-corrected using alignframes in IMOD 105 and 4×-binned tomograms were reconstructed by weighted-back projection in IMOD. To enhance the contrast for visualization and particle picking, tomograms were CTF-deconvolved and filtered using isonet 106 . 2D projection images were lowpass-filtered using mtffilter in IMOD.…”

Section: Tomogram Reconstruction Data Processing and Segmentationmentioning

confidence: 99%

Actin cytoskeleton and complex cell architecture in an Asgard archaeon

Rodrigues-Oliveira

Wollweber

Ponce‐Toledo

et al. 2022

Nature

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Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1–3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4–6, but never visualized. Here we describe a highly enriched culture of ‘Candidatus Lokiarchaeum ossiferum’, a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7–14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying ‘Ca. L. ossiferum’ cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin—one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.

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“…Another common attempt is to couple a reconstruction technique, e.g., backprojection reconstruction, with a deep learning denoising approach. Here, denoising is applied either on the tilt-series before reconstruction [15], [16], [17], or after the reconstruction on tomograms created with traditional techniques [18], [19]. Alternatively, reconstruction methods including regularization terms have been proposed to handle this ill-posed problem, but only for 2D synthetic limited angle data [39], [40].…”

Section: Related Workmentioning

confidence: 99%

“…This is in accordance with what we found when running more than a hundred iterations with only SART in our ablation studies. We used IMOD's tomograms (bin-4 and bin-8) for training IsoNet (3 tomograms were used for training) for 20 iterations with the recommended configuration [19]. Finally, we created reconstructions with our framework, using LADMM for 2×80 iterations with and without NLM in the final two iterations.…”

Section: Influenza Tilt-seriesmentioning

confidence: 99%

“…back-projection reconstruction) coupled with a deep learning denoising approach. Here, denoising is applied either on the tiltseries before the reconstruction [15], [16], [17], or after the reconstruction on tomograms created with traditional techniques [18], [19]. One difficulty with such complex image processing pipelines is that the final reconstructions cannot easily be traced back to the individual raw input data to obtain an estimate of the reconstruction error or uncertainty.…”

Section: Introductionmentioning

confidence: 99%

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GPU Accelerated 3D Tomographic Reconstruction and Visualization From Noisy Electron Microscopy Tilt-Series

Ramirez

Rautek

Bohak

et al. 2024

IEEE Trans. Visual. Comput. Graphics

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We present a novel framework for 3D tomographic reconstruction and visualization of tomograms from noisy electron microscopy tilt-series. Our technique takes as an input aligned tilt-series from cryogenic electron microscopy and creates denoised 3D tomograms using a proximal jointly-optimized approach that iteratively performs reconstruction and denoising, relieving the users of the need to select appropriate denoising algorithms in the pre-reconstruction or post-reconstruction steps. The whole process is accelerated by exploiting parallelism on modern GPUs, and the results can be visualized immediately after the reconstruction using volume rendering tools incorporated in the framework. We show that our technique can be used with multiple combinations of reconstruction algorithms and regularizers, thanks to the flexibility provided by proximal algorithms. Additionally, the reconstruction framework is open-source and can be easily extended with additional reconstruction and denoising methods. Furthermore, our approach enables visualization of reconstruction error throughout the iterative process within the reconstructed tomogram and on projection planes of the input tilt-series. We evaluate our approach in comparison with state-of-the-art approaches and additionally show how our error visualization can be used for reconstruction evaluation.

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Isotropic reconstruction for electron tomography with deep learning

Cited by 175 publications

References 66 publications

Structural consequences of turnover-induced homocitrate loss in nitrogenase

Structural consequences of turnover-induced homocitrate loss in nitrogenase

Actin cytoskeleton and complex cell architecture in an Asgard archaeon

GPU Accelerated 3D Tomographic Reconstruction and Visualization From Noisy Electron Microscopy Tilt-Series

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