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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization

Author

Listed:
  • Elias Amselem

    (Uppsala University)

  • Bo Broadwater

    (Uppsala University)

  • Tora Hävermark

    (Uppsala University)

  • Magnus Johansson

    (Uppsala University)

  • Johan Elf

    (Uppsala University)

Abstract

Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.

Suggested Citation

  • Elias Amselem & Bo Broadwater & Tora Hävermark & Magnus Johansson & Johan Elf, 2023. "Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36879-1
    DOI: 10.1038/s41467-023-36879-1
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    References listed on IDEAS

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    1. Mikhail Metelev & Erik Lundin & Ivan L. Volkov & Arvid H. Gynnå & Johan Elf & Magnus Johansson, 2022. "Direct measurements of mRNA translation kinetics in living cells," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Günter Kramer & Thomas Rauch & Wolfgang Rist & Sonja Vorderwülbecke & Holger Patzelt & Agnes Schulze-Specking & Nenad Ban & Elke Deuerling & Bernd Bukau, 2002. "L23 protein functions as a chaperone docking site on the ribosome," Nature, Nature, vol. 419(6903), pages 171-174, September.
    3. Roman Schmidt & Tobias Weihs & Christian A. Wurm & Isabelle Jansen & Jasmin Rehman & Steffen J. Sahl & Stefan W. Hell, 2021. "MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Emil Marklund & Brad Oosten & Guanzhong Mao & Elias Amselem & Kalle Kipper & Anton Sabantsev & Andrew Emmerich & Daniel Globisch & Xuan Zheng & Laura C. Lehmann & Otto G. Berg & Magnus Johansson & Joh, 2020. "DNA surface exploration and operator bypassing during target search," Nature, Nature, vol. 583(7818), pages 858-861, July.
    5. Evan P. Perillo & Yen-Liang Liu & Khang Huynh & Cong Liu & Chao-Kai Chou & Mien-Chie Hung & Hsin-Chih Yeh & Andrew K. Dunn, 2015. "Deep and high-resolution three-dimensional tracking of single particles using nonlinear and multiplexed illumination," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
    6. Shangguo Hou & Jack Exell & Kevin Welsher, 2020. "Real-time 3D single molecule tracking," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
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