1
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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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2
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Perrett S, Fadini A, Hutchison CDM, Bhattacharya S, Morrison C, Turkot O, Jakobsen MB, Größler M, Licón-Saláiz J, Griese F, Flewett S, Valerio J, Schulz J, Biednov M, Jiang Y, Han H, Yousef H, Khakhulin D, Milne C, Barty A, van Thor JJ. Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE. Struct Dyn 2024; 11:024310. [PMID: 38638699 PMCID: PMC11026113 DOI: 10.1063/4.0000248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments. Here, we present a novel application of a droplet-on-demand injection method, which allowed operation at 47 kHz at the European XFEL (EuXFEL) by tailoring a multi-droplet injection scheme for each macro-pulse. We demonstrate a collection rate of 150 000 indexed patterns per hour. We show that the performance and effective data collection rate are comparable to GDVN, with a sample consumption reduction of two orders of magnitude. We present lysozyme crystallographic data using the Large Pixel Detector at the femtosecond x-ray experiment endstation. Significant improvement of the crystallographic statistics was made by correcting for a systematic drift of the photon energy in the EuXFEL macro-pulse train, which was characterized from indexing the individual frames in the pulse train. This is the highest resolution protein structure collected and reported at the EuXFEL at 1.38 Å resolution.
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Affiliation(s)
- Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Sayantan Bhattacharya
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Cade Morrison
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Mads Bregenholt Jakobsen
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - Michael Größler
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - José Licón-Saláiz
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | | | - Samuel Flewett
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Yifeng Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Anton Barty
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - Jasper J. van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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3
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Jacquemain V, Cheuleu C, Ranc N, Castelnau O, Michel V, Vinci D, Favier V, Mocuta C, Thiaudiere D. Investigation of the mechanical work during ultrasonic fatigue loading using pulsed time-resolved X-ray diffraction. J Synchrotron Radiat 2024; 31:17-27. [PMID: 37947304 PMCID: PMC10833421 DOI: 10.1107/s1600577523008767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
In the energy production and transportation industries, numerous metallic structures may be subjected to at least several billions of cycles, i.e. loaded in the very high cycle fatigue domain (VHCF). Therefore, to design structures in the VHCF domain, a reliable methodology is necessary. One useful quantity to characterize plastic activity at the microscopic scale and fatigue damage evolution is the mechanical work supplied to a material. However, the estimation of this mechanical work in a metal during ultrasonic fatigue tests remains challenging. This paper aims to present an innovative methodology to quantify this. An experimental procedure was developed to estimate the mechanical work from stress and total strain evolution measurements during one loading cycle with a time accuracy of about 50 ns. This was achieved by conducting time-resolved X-ray diffraction coupled to strain gauge measurements at a synchrotron facility working in pulsed mode (single-bunch mode).
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Affiliation(s)
- Vincent Jacquemain
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
| | - Christophe Cheuleu
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
| | - Nicolas Ranc
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
| | - Olivier Castelnau
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
| | - Vincent Michel
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
| | - Doriana Vinci
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Véronique Favier
- PIMM, Arts et Metiers Institute of Technology, CNRS, CNAM, HESAM University, 151 Boulevard de l’Hopital, Paris, France
| | - Cristian Mocuta
- Synchrotron SOLEIL, L’Orme des Merisiers, Départamentale 128, 91190 Saint-Aubin, France
| | - Dominique Thiaudiere
- Synchrotron SOLEIL, L’Orme des Merisiers, Départamentale 128, 91190 Saint-Aubin, France
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4
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Guest TW, Bean R, Kammering R, van Riessen G, Mancuso AP, Abbey B. A phenomenological model of the X-ray pulse statistics of a high-repetition-rate X-ray free-electron laser. IUCrJ 2023; 10:708-719. [PMID: 37782462 PMCID: PMC10619450 DOI: 10.1107/s2052252523008242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Many coherent imaging applications that utilize ultrafast X-ray free-electron laser (XFEL) radiation pulses are highly sensitive to fluctuations in the shot-to-shot statistical properties of the source. Understanding and modelling these fluctuations are key to successful experiment planning and necessary to maximize the potential of XFEL facilities. Current models of XFEL radiation and their shot-to-shot statistics are based on theoretical descriptions of the source and are limited in their ability to capture the shot-to-shot intensity fluctuations observed experimentally. The lack of accurate temporal statistics in simulations that utilize these models is a significant barrier to optimizing and interpreting data from XFEL coherent diffraction experiments. Presented here is a phenomenological model of XFEL radiation that is capable of capturing the shot-to-shot statistics observed experimentally using a simple time-dependent approximation of the pulse wavefront. The model is applied to reproduce non-stationary shot-to-shot intensity fluctuations observed at the European XFEL, whilst accurately representing the single-shot properties predicted by FEL theory. Compared with previous models, this approach provides a simple, robust and computationally inexpensive method of generating statistical representations of XFEL radiation.
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Affiliation(s)
- Trey W. Guest
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Raimund Kammering
- Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Grant van Riessen
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Adrian P. Mancuso
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Brian Abbey
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
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5
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Konold PE, You T, Bielecki J, Valerio J, Kloos M, Westphal D, Bellisario A, Varma Yenupuri T, Wollter A, Koliyadu JCP, Koua FH, Letrun R, Round A, Sato T, Mészáros P, Monrroy L, Mutisya J, Bódizs S, Larkiala T, Nimmrich A, Alvarez R, Adams P, Bean R, Ekeberg T, Kirian RA, Martin AV, Westenhoff S, Maia FRNC. 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers. IUCrJ 2023; 10:662-670. [PMID: 37721770 PMCID: PMC10619454 DOI: 10.1107/s2052252523007972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
X-ray free-electron lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit involves the delivery of samples to the X-ray interaction point in such a way that produces data of the highest possible quality and with maximal efficiency. This is hampered by intrinsic constraints posed by the light source and operation within a beamline environment. For liquid samples, the solution typically involves some form of high-speed liquid jet, capable of keeping up with the rate of X-ray pulses. However, conventional jets are not ideal because of radiation-induced explosions of the jet, as well as their cylindrical geometry combined with the X-ray pointing instability of many beamlines which causes the interaction volume to differ for every pulse. This complicates data analysis and contributes to measurement errors. An alternative geometry is a liquid sheet jet which, with its constant thickness over large areas, eliminates the problems related to X-ray pointing. Since liquid sheets can be made very thin, the radiation-induced explosion is reduced, boosting their stability. These are especially attractive for experiments which benefit from small interaction volumes such as fluctuation X-ray scattering and several types of spectroscopy. Although their use has increased for soft X-ray applications in recent years, there has not yet been wide-scale adoption at XFELs. Here, gas-accelerated liquid sheet jet sample injection is demonstrated at the European XFEL SPB/SFX nano focus beamline. Its performance relative to a conventional liquid jet is evaluated and superior performance across several key factors has been found. This includes a thickness profile ranging from hundreds of nanometres to 60 nm, a fourfold increase in background stability and favorable radiation-induced explosion dynamics at high repetition rates up to 1.13 MHz. Its minute thickness also suggests that ultrafast single-particle solution scattering is a possibility.
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Affiliation(s)
- Patrick E. Konold
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Tong You
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Alfredo Bellisario
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Tej Varma Yenupuri
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - August Wollter
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | | | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Petra Mészáros
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Szabolcs Bódizs
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Taru Larkiala
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Bagley Hall, Seattle, WA 98195, USA
| | - Roberto Alvarez
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Patrick Adams
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Richard A. Kirian
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Andrew V. Martin
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Sebastian Westenhoff
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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6
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Welke N, Majernik N, Ash R, Moro A, Agustsson R, Manwani P, Li K, Sakdinawat A, Aquila A, Benediktovitch A, Halavanau A, Rosenzweig J, Bergmann U, Pellegrini C. Development of spinning-disk solid sample delivery system for high-repetition rate x-ray free electron laser experiments. Rev Sci Instrum 2023; 94:103005. [PMID: 37801013 DOI: 10.1063/5.0168125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
X-ray free-electron lasers (XFELs) deliver intense x-ray pulses that destroy the sample in a single shot by a Coulomb explosion. Experiments using XFEL pulse trains or the new generation of high-repetition rate XFELs require rapid sample replacement beyond those provided by the systems now used at low repletion-rate XFELs. We describe the development and characterization of a system based on a spinning disk to continuously deliver a solid sample into an XFEL interaction point at very high speeds. We tested our system at the Linac Coherent Light Source and European XFEL hard x-ray nano-focus instruments, employing it to deliver a 25 μm copper foil sample, which can be used as a gain medium for stimulated x-ray emission for the proposed x-ray laser oscillator.
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Affiliation(s)
- N Welke
- Department of Physics, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - N Majernik
- Department of Physics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - R Ash
- Department of Physics, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - A Moro
- RadiaBeam Technologies, Santa Monica, California 90404, USA
| | - R Agustsson
- RadiaBeam Technologies, Santa Monica, California 90404, USA
| | - P Manwani
- Department of Physics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - K Li
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - A Sakdinawat
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - A Aquila
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - A Benediktovitch
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A Halavanau
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J Rosenzweig
- Department of Physics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - U Bergmann
- Department of Physics, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - C Pellegrini
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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