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Low-dose phase retrieval of biological specimens using cryo-electron ptychography

Author

Listed:
  • Liqi Zhou

    (Nanjing University)

  • Jingdong Song

    (Chinese Center for Disease Control and Prevention)

  • Judy S. Kim

    (University of Oxford, Parks Road
    Diamond Light Source Ltd., Harwell Science and Innovation Campus
    Harwell Campus)

  • Xudong Pei

    (Nanjing University)

  • Chen Huang

    (University of Oxford, Parks Road
    Diamond Light Source Ltd., Harwell Science and Innovation Campus)

  • Mark Boyce

    (University of Oxford)

  • Luiza Mendonça

    (University of Oxford)

  • Daniel Clare

    (Harwell Science and Innovation Campus)

  • Alistair Siebert

    (Harwell Science and Innovation Campus)

  • Christopher S. Allen

    (University of Oxford, Parks Road
    Diamond Light Source Ltd., Harwell Science and Innovation Campus)

  • Emanuela Liberti

    (University of Oxford, Parks Road
    Diamond Light Source Ltd., Harwell Science and Innovation Campus)

  • David Stuart

    (University of Oxford
    Harwell Science and Innovation Campus)

  • Xiaoqing Pan

    (University of California)

  • Peter D. Nellist

    (University of Oxford, Parks Road)

  • Peijun Zhang

    (University of Oxford
    Harwell Science and Innovation Campus)

  • Angus I. Kirkland

    (University of Oxford, Parks Road
    Diamond Light Source Ltd., Harwell Science and Innovation Campus
    Harwell Campus)

  • Peng Wang

    (Nanjing University)

Abstract

Cryo-electron microscopy is an essential tool for high-resolution structural studies of biological systems. This method relies on the use of phase contrast imaging at high defocus to improve information transfer at low spatial frequencies at the expense of higher spatial frequencies. Here we demonstrate that electron ptychography can recover the phase of the specimen with continuous information transfer across a wide range of the spatial frequency spectrum, with improved transfer at lower spatial frequencies, and as such is more efficient for phase recovery than conventional phase contrast imaging. We further show that the method can be used to study frozen-hydrated specimens of rotavirus double-layered particles and HIV-1 virus-like particles under low-dose conditions (5.7 e/Å2) and heterogeneous objects in an Adenovirus-infected cell over large fields of view (1.14 × 1.14 μm), thus making it suitable for studies of many biologically important structures.

Suggested Citation

  • Liqi Zhou & Jingdong Song & Judy S. Kim & Xudong Pei & Chen Huang & Mark Boyce & Luiza Mendonça & Daniel Clare & Alistair Siebert & Christopher S. Allen & Emanuela Liberti & David Stuart & Xiaoqing Pa, 2020. "Low-dose phase retrieval of biological specimens using cryo-electron ptychography," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16391-6
    DOI: 10.1038/s41467-020-16391-6
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    Citations

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    Cited by:

    1. Philipp M. Pelz & Sinéad M. Griffin & Scott Stonemeyer & Derek Popple & Hannah DeVyldere & Peter Ercius & Alex Zettl & Mary C. Scott & Colin Ophus, 2023. "Solving complex nanostructures with ptychographic atomic electron tomography," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    2. Zhiyuan Ding & Si Gao & Weina Fang & Chen Huang & Liqi Zhou & Xudong Pei & Xiaoguo Liu & Xiaoqing Pan & Chunhai Fan & Angus I. Kirkland & Peng Wang, 2022. "Three-dimensional electron ptychography of organic–inorganic hybrid nanostructures," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Berk Küçükoğlu & Inayathulla Mohammed & Ricardo C. Guerrero-Ferreira & Stephanie M. Ribet & Georgios Varnavides & Max Leo Leidl & Kelvin Lau & Sergey Nazarov & Alexander Myasnikov & Massimo Kube & Jul, 2024. "Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    4. Xudong Pei & Liqi Zhou & Chen Huang & Mark Boyce & Judy S. Kim & Emanuela Liberti & Yiming Hu & Takeo Sasaki & Peter D. Nellist & Peijun Zhang & David I. Stuart & Angus I. Kirkland & Peng Wang, 2023. "Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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