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Baba N, Kaneko K, Baba M. Novel nonlinear reconstruction method with grey-level quantisation units for electron tomography. Sci Rep 2020; 10:20146. [PMID: 33214577 PMCID: PMC7678869 DOI: 10.1038/s41598-020-77156-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/05/2020] [Indexed: 11/22/2022] Open
Abstract
We report a new computed tomography reconstruction method, named quantisation units reconstruction technique (QURT), applicable to electron and other fields of tomography. Conventional electron tomography methods such as filtered back projection, weighted back projection, simultaneous iterative reconstructed technique, etc. suffer from the 'missing wedge' problem due to the limited tilt-angle range. QURT demonstrates improvements to solve this problem by recovering a structural image blurred due to the missing wedge and substantially reconstructs the structure even if the number of projection images is small. QURT reconstructs a cross-section image by arranging grey-level quantisation units (QU pieces) in three-dimensional image space via unique discrete processing. Its viability is confirmed by model simulations and experimental results. An important difference from recently developed methods such as discrete algebraic reconstruction technique (DART), total variation regularisation-DART, and compressed sensing is that prior knowledge of the conditions regarding the specimen or the expected cross-section image is not necessary.
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Affiliation(s)
- Norio Baba
- Major of Informatics, Graduate School, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo, 192-0015, Japan.
| | - Kenji Kaneko
- Department of Materials Science and Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Misuzu Baba
- Research Institute for Science and Technology, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo, 192-0015, Japan
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Baba M, Tomonaga S, Suzuki M, Gen M, Takeda E, Matsuura A, Kamada Y, Baba N. A nuclear membrane-derived structure associated with Atg8 is involved in the sequestration of selective cargo, the Cvt complex, during autophagosome formation in yeast. Autophagy 2018; 15:423-437. [PMID: 30238844 DOI: 10.1080/15548627.2018.1525475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy (hereafter autophagy) is a conserved intracellular degradation mechanism required for cell survival. A double-membrane structure, the phagophore, is generated to sequester cytosolic cargos destined for degradation in the vacuole. The mechanism involved in the biogenesis of the phagophore is still an open question. We focused on 4 autophagy-related (Atg) proteins (Atg2, Atg9, Atg14, and Atg18), which are involved in the formation of the phagophore in order to gain a more complete understanding of the membrane dynamics that occur during formation of the autophagosome. The corresponding mutants, while defective in autophagy, nonetheless generate the membrane-bound form of Atg8, allowing us to use this protein as a marker for the nascent autophagosome precursor membrane. Using electron microscopy (EM), we discovered in these atg mutants a novel single-membrane structure (~120 to 150 nm in size). Electron tomography revealed that this structure originates from a part of the nuclear membrane, and we have named it the alphasome. Our data suggest that the alphasome is associated with Atg8, and sequesters selective cargo, the Cvt complex, during autophagy. Abbreviations: 3D: three-dimensional; AB: autophagic body; AP: autophagosome; Atg: autophagy-related; Cvt: cytoplasm-to-vacuole targeting; EM: electron microscopy; IEM: immunoelectron microscopy; L: lipid droplet; N: nucleus; NM: nuclear membrane; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor aminopeptidase I; rER: rough endoplasmic reticulum; TEM: transmission electron microscopy; V: vacuole; VLP: virus-like particle.
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Affiliation(s)
- Misuzu Baba
- a Research Institute for Science and Technology , Kogakuin University , Hachioji, Tokyo , Japan
| | - Sachihiko Tomonaga
- b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
| | - Masato Suzuki
- b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
| | - Maeda Gen
- b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
| | - Eigo Takeda
- c Department of Nanobiology , Graduate School of Advanced Integration Science, Chiba University , Inage-ku, Chiba , Japan
| | - Akira Matsuura
- c Department of Nanobiology , Graduate School of Advanced Integration Science, Chiba University , Inage-ku, Chiba , Japan.,d Department of Biology , Graduate School of Science, Chiba University , Inage-ku, Chiba , Japan
| | - Yoshiaki Kamada
- e Laboratory of Biological Diversity , National Institute for Basic Biology, and School of Life Science, Graduate School of Advanced Studies , Myodaiji Okazaki, Aichi , Japan
| | - Norio Baba
- a Research Institute for Science and Technology , Kogakuin University , Hachioji, Tokyo , Japan.,b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
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Sakamoto S, Masumoto T, Tezuka S, Baba M, Baba N. PM-06A spot auto-focus method with high definition ACF and applications to electron tomography. Microscopy (Oxf) 2016. [DOI: 10.1093/jmicro/dfw069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tomonaga S, Baba M, Baba N. A new field-of-view autotracking method based on back-projected ray image cross-correlation for online tomography reconstruction. Microscopy (Oxf) 2016; 63 Suppl 1:i23-i24. [PMID: 25359820 DOI: 10.1093/jmicro/dfu058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In general, a tomogram cannot be observed immediately after the acquisition of a series of specimen tilt images, but is instead observed after the post-processing of the tilt series alignment, which often requires a substantial amount of time. Moreover, for general specimens, the automatic acquisition of the tilt series is difficult because field-of-view tracking frequently fails as the tilt angle or specimen thickness increases.In this study, we focus on the improvement of the field-of-view autotracking technique for the purpose of online tomography reconstruction and propose a new alternative technique [1,2]. The method we proposed uses a so-called 'back-projected ray image' instead of a specimen tilt image. The back-projected ray image is a cross-section image calculated from each projection image only during reconstruction. As a result of a study on 'ray images', the quality and accuracy of the cross-correlation between a pair of neighboring ray images among the tilt series were observed to be very high compared with those between a pair of projection images. We observed that a back projected ray image reliably cross-correlates with other neighboring ray images at the position of an existing three-dimensional object. The proposed method can therefore consistently track the field-of-view, overcoming the weakness of a conventional image-matching-based method. In addition, the present method is simple, and high speed processing is expected to be achieved because fast Fourier transform (FFT) and inverse fast Fourier transform (IFFT) algorithms can be used.We applied this method to real specimens in online experiments using a TEM and thereby demonstrated its successful performance. Online autotracking experiments with thin-section samples were used to demonstrate the effectiveness of the proposed method. The field-of-view was automatically tracked with high accuracy through a tilt angle range. Furthermore, online tomograms were obtained immediately after the last specimen tilting. With increases in the tracking speed, in situ tomographic observations for analyzing the dynamic behavior might become feasible in the future.jmicro;63/suppl_1/i23-a/DFU058F1F1DFU058F1Fig. 1.Comparison of the proposed autotracking method with the conventional PCF based alignment method using the yeast cell thin-section. a and b: Reconstructed X-Y cross-section images from tracking results at 8° increment angle with the PCF method and with the proposed method. N, nucleus; V, vacuole; NVJ, nucleus-vacuole junction. c: A reconstructed cross-section image from autotracking result at 1° increment angle with the proposed method. (scale bar: 100 nm).
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Affiliation(s)
- Sachihiko Tomonaga
- Major of Informatics, Graduate School, Kogakuin University, 2665-1 Nakano, Hachioji, Japan
| | - Misuzu Baba
- Major of Informatics, Graduate School, Kogakuin University, 2665-1 Nakano, Hachioji, Japan Research Institute for Science and Technology, Kogakuin University, 2665-1 Nakano, Hachioji,Japan
| | - Norio Baba
- Major of Informatics, Graduate School, Kogakuin University, 2665-1 Nakano, Hachioji, Japan
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