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Berberich TB, Molodtsov SL, Kurta RP. A workflow for single-particle structure determination via iterative phasing of rotational invariants in fluctuation X-ray scattering. J Appl Crystallogr 2024; 57:324-343. [PMID: 38596737 PMCID: PMC11001396 DOI: 10.1107/s1600576724000992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/29/2024] [Indexed: 04/11/2024] Open
Abstract
Fluctuation X-ray scattering (FXS) offers a complementary approach for nano- and bioparticle imaging with an X-ray free-electron laser (XFEL), by extracting structural information from correlations in scattered XFEL pulses. Here a workflow is presented for single-particle structure determination using FXS. The workflow includes procedures for extracting the rotational invariants from FXS patterns, performing structure reconstructions via iterative phasing of the invariants, and aligning and averaging multiple reconstructions. The reconstruction pipeline is implemented in the open-source software xFrame and its functionality is demonstrated on several simulated structures.
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Affiliation(s)
- Tim B. Berberich
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- I. Institute of Theoretical Physics, University of Hamburg, Notkestraße 9-11, 22607 Hamburg, Germany
| | - Serguei L. Molodtsov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger Straße 23, 09599 Freiberg, Germany
- Center for Efficient High Temperature Processes and Materials Conversion (ZeHS), TU Bergakademie Freiberg, Winklerstrasse 5, 09599 Freiberg, Germany
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2
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Das D, Deka P, Bhattacharjee H, Deshmukh S, Gupta P, Deka A, Sultana S. Fluorescein dye as a novel cost-effective approach for staining raw specimens in ophthalmic pathology. Indian J Ophthalmol 2021; 68:2175-2178. [PMID: 32971634 PMCID: PMC7728015 DOI: 10.4103/ijo.ijo_2153_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Purpose: To study the usefulness of sodium fluorescein dye for staining raw specimens in ophthalmic pathology. Methods: Laboratory-based observational study. Eye specimens received in the ocular pathology department of a tertiary eye care center in northeast India were included in the study after obtaining the informed consent. The study period was from 2016 to 2019. Specimens received were a corneal button, lid, orbital tissues, enucleated eyeballs, eviscerated eye, explanted intraocular lens (IOLs), optic nerve and ocular parasites. Sections of the gross specimens were stained with sodium fluorescein (C20H12O5NA) dye. The average duration of tissue-stain contact time was 45 s. The sections were analyzed under the compound microscope. The intensity of illumination of the microscope was modulated to obtain high contrast digital photographs. Results: 26 corneal buttons with or without limbal tissue specimens were analyzed with fluorescein staining procedure; limbus with its pigmented cells were seen in the enucleated eyeballs. 33 enucleated eyes (retinoblastoma [RB] (n = 24), phthisical eyes (n = 4), choroidal melanomas (n = 2), and others (n = 3) were included in the study cohort. In these 33 enucleated eyes, vitreous were also examined for the presence of hyalocytes and other pathological cells. Retinal pigment epithelial cells were also seen (n = 11). RB seeds were seen with fluorescein stain and documented in 14 specimens. The RB seeds were mostly in vitreous (n = 9) and subretinal space (n = 5). Fat cells (n = 8) from orbital tissues and sebaceous cells (n = 5) from frozen section specimens were also observed and documented. Conclusion: This study highlights a novel method of rapid staining of gross ophthalmic pathology specimens.
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Affiliation(s)
- Dipankar Das
- Department of Ocular Pathology, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | - Panna Deka
- Department of Ocular Pathology, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | | | - Saurabh Deshmukh
- Department of Ophthalmology, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | - Pooja Gupta
- Department of Ophthalmology, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | - Apurba Deka
- Department of Ocular Pathology, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | - Sabrin Sultana
- Department of Ophthalmology, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
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3
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Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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4
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Arai G, Hara H, Hatano T, Ejima T, Jiang W, Ohashi H, Namba S, Sunahara A, Sasaki A, Nishikino M, O'Sullivan G, Higashiguchi T. Intense water-window soft x-ray emission by spectral control using dual laser pulses. OPTICS EXPRESS 2018; 26:27748-27756. [PMID: 30469835 DOI: 10.1364/oe.26.027748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/07/2018] [Indexed: 06/09/2023]
Abstract
We demonstrate intense emission in the water-window soft x-ray spectral region by controlling the spectral behavior through changing the balance between emissivity and self-absorption in an expanding plasma. The number of photons obtained from a dual laser irradiated target with a 150-ps pre-pulse was maximized at 3.8 × 1014 photons/sr in λ = 2.34 - 4.38 nm at a pulse separation time of 7 - 10 ns. Enhancement of the number of photons is attributed to efficient coupling with the main laser pulse while maintaining a tiny source size.
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5
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Du M, Jacobsen C. Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials. Ultramicroscopy 2018; 184:293-309. [PMID: 29073575 PMCID: PMC5696083 DOI: 10.1016/j.ultramic.2017.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 12/01/2022]
Abstract
Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 µm (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.
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Affiliation(s)
- Ming Du
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne IL 60439, USA; Department of Physics & Astronomy, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston IL 60208, USA.
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6
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Kurta RP, Donatelli JJ, Yoon CH, Berntsen P, Bielecki J, Daurer BJ, DeMirci H, Fromme P, Hantke MF, Maia FRNC, Munke A, Nettelblad C, Pande K, Reddy HKN, Sellberg JA, Sierra RG, Svenda M, van der Schot G, Vartanyants IA, Williams GJ, Xavier PL, Aquila A, Zwart PH, Mancuso AP. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses. PHYSICAL REVIEW LETTERS 2017; 119:158102. [PMID: 29077445 PMCID: PMC5757528 DOI: 10.1103/physrevlett.119.158102] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 05/19/2023]
Abstract
We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.
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Affiliation(s)
- Ruslan P Kurta
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Jeffrey J Donatelli
- Mathematics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Peter Berntsen
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Hasan DeMirci
- Biosciences Division, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Max Felix Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, SE-751 05 Uppsala, Sweden
| | - Kanupriya Pande
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Jonas A Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Ivan A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, 115409 Moscow, Russia
| | - Garth J Williams
- NSLS-II, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973, USA
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, 22607 Hamburg, Germany
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Peter H Zwart
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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7
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Hosseinizadeh A, Mashayekhi G, Copperman J, Schwander P, Dashti A, Sepehr R, Fung R, Schmidt M, Yoon CH, Hogue BG, Williams GJ, Aquila A, Ourmazd A. Conformational landscape of a virus by single-particle X-ray scattering. Nat Methods 2017; 14:877-881. [PMID: 28805793 DOI: 10.1038/nmeth.4395] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/05/2017] [Indexed: 11/09/2022]
Abstract
Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.
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Affiliation(s)
- Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeremy Copperman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ali Dashti
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Reyhaneh Sepehr
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Russell Fung
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Brenda G Hogue
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona, USA.,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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8
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Shi Y, Qin H, Fisch NJ. Laser-pulse compression using magnetized plasmas. Phys Rev E 2017; 95:023211. [PMID: 28297990 DOI: 10.1103/physreve.95.023211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Proposals to reach the next generation of laser intensities through Raman or Brillouin backscattering have centered on optical frequencies. Higher frequencies are beyond the range of such methods mainly due to the wave damping that accompanies the higher-density plasmas necessary for compressing higher frequency lasers. However, we find that an external magnetic field transverse to the direction of laser propagation can reduce the required plasma density. Using parametric interactions in magnetized plasmas to mediate pulse compression, both reduces the wave damping and alleviates instabilities, thereby enabling higher frequency or lower intensity pumps to produce pulses at higher intensities and longer durations. In addition to these theoretical advantages, our method in which strong uniform magnetic fields lessen the need for high-density uniform plasmas also lessens key engineering challenges or at least exchanges them for different challenges.
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Affiliation(s)
- Yuan Shi
- Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543, USA
| | - Hong Qin
- Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543, USA
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Nathaniel J Fisch
- Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543, USA
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9
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Schmidt M. Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/08940886.2015.1101324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Marius Schmidt
- University of Wisconsin-Milwaukee, Physics Department, Milwaukee, Wisconsin, USA
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10
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Hosseinizadeh A, Dashti A, Schwander P, Fung R, Ourmazd A. Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041601. [PMID: 26798800 PMCID: PMC4711626 DOI: 10.1063/1.4919740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/21/2015] [Indexed: 05/22/2023]
Abstract
Single-particle structure recovery without crystals or radiation damage is a revolutionary possibility offered by X-ray free-electron lasers, but it involves formidable experimental and data-analytical challenges. Many of these difficulties were encountered during the development of cryogenic electron microscopy of biological systems. Electron microscopy of biological entities has now reached a spatial resolution of about 0.3 nm, with a rapidly emerging capability to map discrete and continuous conformational changes and the energy landscapes of biomolecular machines. Nonetheless, single-particle imaging by X-ray free-electron lasers remains important for a range of applications, including the study of large "electron-opaque" objects and time-resolved examination of key biological processes at physiological temperatures. After summarizing the state of the art in the study of structure and conformations by cryogenic electron microscopy, we identify the primary opportunities and challenges facing X-ray-based single-particle approaches, and possible means for circumventing them.
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Affiliation(s)
- A Hosseinizadeh
- Department of Physics, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
| | - A Dashti
- Department of Physics, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
| | - P Schwander
- Department of Physics, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
| | - R Fung
- Department of Physics, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
| | - A Ourmazd
- Department of Physics, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
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11
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Ourmazd A. Preface for Special Issue on Biology with X-ray Lasers 2. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041501. [PMID: 26798799 PMCID: PMC4711608 DOI: 10.1063/1.4928768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 05/29/2023]
Affiliation(s)
- Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee , 3135 N. Maryland Ave., Milwaukee, W isconsin 53211, USA
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12
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Schwander P, Fung R, Ourmazd A. Conformations of macromolecules and their complexes from heterogeneous datasets. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130567. [PMID: 24914167 PMCID: PMC4052876 DOI: 10.1098/rstb.2013.0567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.
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Affiliation(s)
- P Schwander
- Department of Physics, University of Wisconsin Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211, USA
| | - R Fung
- Department of Physics, University of Wisconsin Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211, USA
| | - A Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211, USA
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13
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Abstract
X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.
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Affiliation(s)
- Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
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14
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Neutze R. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130318. [PMID: 24914150 PMCID: PMC4052859 DOI: 10.1098/rstb.2013.0318] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 1012 X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.
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Affiliation(s)
- Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, 40530 Gothenburg, Sweden
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15
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Abstract
The opening of hard X-ray free-electron laser facilities, such as the Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory in the United States, has ushered in a new era in structural determination. With X-ray pulse durations down to 10 fs or shorter, and up to 10(13) transversely coherent photons per pulse in a narrow spectral bandwidth, focused irradiances of 10(18) to 10(21) W cm(-2) or higher can be produced at X-ray energies ranging from 500 eV to 10 keV. New techniques for determining the structure of systems that cannot be crystallized and for studying the time-resolved behavior of irreversible reactions at femtosecond timescales are now available.
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Affiliation(s)
- Anton Barty
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany.
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16
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Fromme P, Spence JCH. Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination. Curr Opin Struct Biol 2011; 21:509-16. [PMID: 21752635 DOI: 10.1016/j.sbi.2011.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 06/08/2011] [Indexed: 10/18/2022]
Abstract
The invention of free electron X-ray lasers has opened a new era for membrane protein structure determination with the recent first proof-of-principle of the new concept of femtosecond nanocrystallography. Structure determination is based on thousands of diffraction snapshots that are collected on a fully hydrated stream of nanocrystals. This review provides a summary of the method and describes how femtosecond X-ray crystallography overcomes the radiation-damage problem in X-ray crystallography, avoids the need for growth and freezing of large single crystals while offering a new method for direct digital phase determination by making use of the fully coherent nature of the X-ray beam. We briefly review the possibilities for time-resolved crystallography, and the potential for making 'molecular movies' of membrane proteins at work.
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Affiliation(s)
- Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.
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17
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Moths B, Ourmazd A. Bayesian algorithms for recovering structure from single-particle diffraction snapshots of unknown orientation: a comparison. Acta Crystallogr A 2011; 67:481-6. [PMID: 21844653 PMCID: PMC3171899 DOI: 10.1107/s0108767311019611] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 05/24/2011] [Indexed: 11/21/2022] Open
Abstract
The advent of X-ray free-electron lasers promises the possibility to determine the structure of individual particles such as microcrystallites, viruses and biomolecules from single-shot diffraction snapshots obtained before the particle is destroyed by the intense femtosecond pulse. This program requires the ability to determine the orientation of the particle giving rise to each snapshot at signal levels as low as ~10(-2) photons per pixel. Two apparently different approaches have recently demonstrated this capability. Here we show they represent different implementations of the same fundamental approach, and identify the primary factors limiting their performance.
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Affiliation(s)
- Brian Moths
- Department of Physics, University of Wisconsin–Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin–Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211, USA
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18
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Huang X, Nelson J, Kirz J, Lima E, Marchesini S, Miao H, Neiman AM, Shapiro D, Steinbrener J, Stewart A, Turner JJ, Jacobsen C. Soft X-ray diffraction microscopy of a frozen hydrated yeast cell. PHYSICAL REVIEW LETTERS 2009; 103:198101. [PMID: 20365955 PMCID: PMC2866741 DOI: 10.1103/physrevlett.103.198101] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 07/29/2009] [Indexed: 05/07/2023]
Abstract
We report the first image of an intact, frozen hydrated eukaryotic cell using x-ray diffraction microscopy, or coherent x-ray diffraction imaging. By plunge freezing the specimen in liquid ethane and maintaining it below -170 degrees C, artifacts due to dehydration, ice crystallization, and radiation damage are greatly reduced. In this example, coherent diffraction data using 520 eV x rays were recorded and reconstructed to reveal a budding yeast cell at a resolution better than 25 nm. This demonstration represents an important step towards high resolution imaging of cells in their natural, hydrated state, without limitations imposed by x-ray optics.
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Affiliation(s)
- Xiaojing Huang
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Johanna Nelson
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Janos Kirz
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Enju Lima
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Huijie Miao
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Aaron M. Neiman
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - David Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Steinbrener
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Andrew Stewart
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Joshua J. Turner
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Chris Jacobsen
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
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19
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Xiong H, Xu H, Fu Y, Yao J, Zeng B, Chu W, Cheng Y, Xu Z, Takahashi EJ, Midorikawa K, Liu X, Chen J. Generation of a coherent x ray in the water window region at 1 kHz repetition rate using a mid-infrared pump source. OPTICS LETTERS 2009; 34:1747-1749. [PMID: 19488169 DOI: 10.1364/ol.34.001747] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We demonstrate the generation of a coherent x ray in the water window region in a gas cell filled with neon gas using a wavelength-tunable mid-IR femtosecond laser operating at 1 kHz repetition rate. The cutoff energy and conversion efficiency of the water window x ray can be optimized by tuning gas pressure as well as the focal position.
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Affiliation(s)
- Hui Xiong
- State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800, China
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20
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Abstract
The intense, brief pulses of X-rays from upcoming free-electron lasers will greatly extend X-ray microscopy to the femtosecond time domain and to interatomic length scales. From recent experiments and simulations one can envisage imaging macromolecules with X-rays without the need for crystallization.
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Affiliation(s)
- Henry N Chapman
- Centre for Free-Electron Laser Science, University of Hamburg, and DESY, Notkestrasse 85, 22607 Hamburg, Germany.
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21
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Feasibility of imaging living cells at subnanometer resolutions by ultrafast X-ray diffraction. Q Rev Biophys 2008; 41:181-204. [DOI: 10.1017/s003358350800471x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractDetailed structural investigations on living cells are problematic because existing structural methods cannot reach high resolutions on non-reproducible objects. Illumination with an ultrashort and extremely bright X-ray pulse can outrun key damage processes over a very short period. This can be exploited to extend the diffraction signal to the highest possible resolution in flash diffraction experiments. Here we present an analysis of the interaction of a very intense and very short X-ray pulse with a living cell, using a non-equilibrium population kinetics plasma code with radiation transfer. Each element in the evolving plasma is modeled by numerous states to monitor changes in the atomic populations as a function of pulse length, wavelength, and fluence. The model treats photoionization, impact ionization, Auger decay, recombination, and inverse bremsstrahlung by solving rate equations in a self-consistent manner and describes hydrodynamic expansion through the ion sound speed. The results show that subnanometer resolutions could be reached on micron-sized cells in a diffraction-limited geometry at wavelengths between 0·75 and 1·5 nm and at fluences of 1011–1012 photons μm−2in less than 10 fs. Subnanometer resolutions could also be achieved with harder X-rays at higher fluences. We discuss experimental and computational strategies to obtain depth information about the object in flash diffraction experiments.
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22
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Chapman HN, Hau-Riege SP, Bogan MJ, Bajt S, Barty A, Boutet S, Marchesini S, Frank M, Woods BW, Benner WH, London RA, Rohner U, Szöke A, Spiller E, Möller T, Bostedt C, Shapiro DA, Kuhlmann M, Treusch R, Plönjes E, Burmeister F, Bergh M, Caleman C, Huldt G, Seibert MM, Hajdu J. Femtosecond time-delay X-ray holography. Nature 2007; 448:676-9. [PMID: 17687320 DOI: 10.1038/nature06049] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 06/22/2007] [Indexed: 11/08/2022]
Abstract
Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging can be used to achieve high resolution, beyond radiation damage limits for biological samples. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.
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Affiliation(s)
- Henry N Chapman
- University of California, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
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23
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Gaffney KJ, Chapman HN. Imaging Atomic Structure and Dynamics with Ultrafast X-ray Scattering. Science 2007; 316:1444-8. [PMID: 17556577 DOI: 10.1126/science.1135923] [Citation(s) in RCA: 298] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Measuring atomic-resolution images of materials with x-ray photons during chemical reactions or physical transformations resides at the technological forefront of x-ray science. New x-ray-based experimental capabilities have been closely linked with advances in x-ray sources, a trend that will continue with the impending arrival of x-ray-free electron lasers driven by electron accelerators. We discuss recent advances in ultrafast x-ray science and coherent imaging made possible by linear-accelerator-based light sources. These studies highlight the promise of ultrafast x-ray lasers, as well as the technical challenges and potential range of applications that will accompany these transformative x-ray light sources.
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Affiliation(s)
- K J Gaffney
- PULSE Center, Stanford Linear Accelerator Center, Stanford University, Stanford, CA 94305, USA.
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24
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Hau-Riege SP, London RA, Chapman HN, Szoke A, Timneanu N. Encapsulation and diffraction-pattern-correction methods to reduce the effect of damage in x-ray diffraction imaging of single biological molecules. PHYSICAL REVIEW LETTERS 2007; 98:198302. [PMID: 17677667 DOI: 10.1103/physrevlett.98.198302] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Indexed: 05/16/2023]
Abstract
Short and intense x-ray pulses may be used for atomic-resolution diffraction imaging of single biological molecules. Radiation damage and a low signal-to-noise ratio impose stringent pulse requirements. In this Letter, we describe methods for decreasing the damage and improving the signal by encapsulating the molecule in a sacrificial layer (tamper) that reduces atomic motion and by postprocessing the pulse-averaged diffraction pattern to correct for ionization damage. Simulations show that these methods greatly improve the image quality.
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25
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Hau-Riege SP, Chapman HN, Krzywinski J, Sobierajski R, Bajt S, London RA, Bergh M, Caleman C, Nietubyc R, Juha L, Kuba J, Spiller E, Baker S, Bionta R, Sokolowski Tinten K, Stojanovic N, Kjornrattanawanich B, Gullikson E, Plönjes E, Toleikis S, Tschentscher T. Subnanometer-scale measurements of the interaction of ultrafast soft x-ray free-electron-laser pulses with matter. PHYSICAL REVIEW LETTERS 2007; 98:145502. [PMID: 17501285 DOI: 10.1103/physrevlett.98.145502] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Indexed: 05/15/2023]
Abstract
At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multilayers with fluxes up to 3 x 10(14) W/cm2. Even though the nanostructures were ultimately completely destroyed, we found that they maintained their integrity and reflectance characteristics during the 25-fs-long pulse, with no evidence for any structural changes over lengths greater than 3 A. This experiment demonstrates that with intense ultrafast pulses, structural damage does not occur during the pulse, giving credence to the concept of diffraction imaging of single macromolecules.
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Affiliation(s)
- Stefan P Hau-Riege
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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26
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Bortel G, Faigel G. Classification of continuous diffraction patterns: A numerical study. J Struct Biol 2007; 158:10-8. [PMID: 17126564 DOI: 10.1016/j.jsb.2006.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 09/28/2006] [Accepted: 10/05/2006] [Indexed: 10/24/2022]
Abstract
The very intense and short pulses of future X-ray free electron lasers may allow the atomic resolution imaging of small, non-periodic objects. Preliminary estimates show that images obtained from single pulses do not contain statistically enough photons to allow successful reconstruction. Therefore multiple exposures of randomly oriented identical replicas have to be taken and the individual images have to be classified according to the object's orientation. The classification has been analytically treated by Huldt et al. [Huldt, G., Szoke, A., Hajdu, J., 2003. J. Struct. Biol. 144, 219.]. In this paper we extend the analytical results with numerical model calculations. This allows us to simulate realistic situations, which we will face in real experiments. We find significant deviations from the analytical expectations, even in the ideal case of spherical particles with random atomic distributions. We introduce a new norm for the individual scattering patterns and describe a criterion to select images belonging to similar orientation, which makes the classification more reliable in practice. We also discuss the effects of particle shape and size, partial orientational ordering, the measurement's resolution and the charge error caused by the Coulomb explosion.
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Affiliation(s)
- G Bortel
- Research Institute for Solid State Physics and Optics, H-1525 Budapest, P.O. Box 49, Hungary.
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27
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Marchesini S. Invited article: a [corrected] unified evaluation of iterative projection algorithms for phase retrieval. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2007; 78:011301. [PMID: 17503899 DOI: 10.1063/1.2403783] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free diffraction-limited imaging and the possibility of using radiation for which no lenses exist. The challenge of this imaging technique is transferred from the lenses to the algorithms. We evaluate these new computational "instruments" developed for the phase-retrieval problem, and discuss acceleration strategies.
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Affiliation(s)
- S Marchesini
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550-9234, USA.
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28
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Smith RF, Dunn J, Filevich J, Moon S, Nilsen J, Keenan R, Shlyaptsev VN, Rocca JJ, Hunter JR, Marconi MC. Plasma conditions for improved energy coupling into the gain region of the Ni-like Pd transient collisional x-ray laser. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:036404. [PMID: 16241576 DOI: 10.1103/physreve.72.036404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Indexed: 05/05/2023]
Abstract
We have directly probed the conditions in which the Ni-like Pd transient collisional x-ray laser is generated and propagates by measuring the near-field image and by utilizing picosecond resolution soft x-ray laser interferometry of the preformed Pd plasma gain medium. The electron density and gain region of the plasma have been determined experimentally and are found to be in good agreement with simulations. We observe a strong dependence of the laser pump-gain medium coupling on the laser pump parameters. The most efficient coupling occurs with the formation of lower density gradients in the preformed plasma and when the duration of the main heating pulse is comparable to the gain lifetime (approximately 10 ps for mid- Z Ni-like schemes). This increases the output intensity by more than an order of magnitude relative to the commonly utilized case where the same pumping energy is delivered within a shorter heating pulse duration (<3 ps) . In contrast, the higher intensity heating pulses are observed to be absorbed at higher electron densities and in regions where steep density gradients limit the effective length of the gain medium.
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Affiliation(s)
- R F Smith
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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29
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Miao J, Chapman HN, Kirz J, Sayre D, Hodgson KO. Taking X-ray diffraction to the limit: macromolecular structures from femtosecond X-ray pulses and diffraction microscopy of cells with synchrotron radiation. ACTA ACUST UNITED AC 2004; 33:157-76. [PMID: 15139809 DOI: 10.1146/annurev.biophys.33.110502.140405] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent work is extending the methodology of X-ray crystallography to the structure determination of noncrystalline specimens. The phase problem is solved using the oversampling method, which takes advantage of "continuous" diffraction patterns from noncrystalline specimens. Here we review the principle of this newly developed technique and discuss the ongoing experiments of imaging nonperiodic objects, such as cells and cellular structures, using coherent and bright X rays produced by third-generation synchrotron sources. In the longer run, the technique may be applicable to image single biomolecules using anticipated X-ray free electron lasers. Here, computer simulations have so far demonstrated two important steps: (a) by using an extremely intense femtosecond X-ray pulse, a diffraction pattern can be recorded from a macromolecule before radiation damage manifests itself; and (b) the phase information can be retrieved in an ab initio fashion from a set of calculated noisy diffraction patterns of single protein molecules.
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Affiliation(s)
- Jianwei Miao
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Stanford University, Stanford, California 94309-0210, USA.
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30
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Hau-Riege SP, London RA, Szoke A. Dynamics of biological molecules irradiated by short x-ray pulses. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 69:051906. [PMID: 15244846 DOI: 10.1103/physreve.69.051906] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Indexed: 05/24/2023]
Abstract
Very short and intense x-ray pulses can be used for diffraction imaging of single biological molecules. Inevitably, x-ray absorption initiates damage that degrades the molecule's image. This paper presents a continuum model of the physics that leads to damage when a small particle absorbs a large x-ray dose. The main processes are found to be ionization and Coulomb-force driven atomic motion. Trapping of electrons, Debye shielding, and nonuniform collisional ionization all have a significant effect on the overall damage kinetics.
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Affiliation(s)
- Stefan P Hau-Riege
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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31
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Marchesini S, Chapman H, Hau-Riege S, London R, Szoke A, He H, Howells M, Padmore H, Rosen R, Spence J, Weierstall U. Coherent X-ray diffractive imaging: applications and limitations. OPTICS EXPRESS 2003; 11:2344-2353. [PMID: 19471343 DOI: 10.1364/oe.11.002344] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The inversion of a diffraction pattern offers aberration-free diffraction-limited 3D images without the resolution and depth-of-field limitations of lens-based tomographic systems, the only limitation being radiation damage. We review our experimental results, discuss the fundamental limits of this technique and future plans.
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32
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Miao J, Hodgson KO, Ishikawa T, Larabell CA, LeGros MA, Nishino Y. Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction. Proc Natl Acad Sci U S A 2003; 100:110-2. [PMID: 12518059 PMCID: PMC140897 DOI: 10.1073/pnas.232691299] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the first experimental recording, to our knowledge, of the diffraction pattern from intact Escherichia coli bacteria using coherent x-rays with a wavelength of 2 A. By using the oversampling phasing method, a real space image at a resolution of 30 nm was directly reconstructed from the diffraction pattern. An R factor used for characterizing the quality of the reconstruction was in the range of 5%, which demonstrated the reliability of the reconstruction process. The distribution of proteins inside the bacteria labeled with manganese oxide has been identified and this distribution confirmed by fluorescence microscopy images. Compared with lens-based microscopy, this diffraction-based imaging approach can examine thicker samples, such as whole cultured cells, in three dimensions with resolution limited only by radiation damage. Looking forward, the successful recording and reconstruction of diffraction patterns from biological samples reported here represent an important step toward the potential of imaging single biomolecules at near-atomic resolution by combining single-particle diffraction with x-ray free electron lasers.
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Affiliation(s)
- Jianwei Miao
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Stanford University, CA 94309-0210, USA.
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33
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Abstract
This second article in the series shows how fluorescence lifetime imaging allows natural biochemical and physiological properties of tissues to act as contrast agents and so provide a basis for distinguishing normal and diseased tissue components. When combined with methods for imaging through non-transparent tissues and tomographic reconstruction it shows promise as a new optical biopsy technique. In addition to this, specially designed vital fluorescent probes of specific biochemical, secondary messenger and receptor activity in living cells may be imaged using FLIM. This is the youngest of the techniques covered in these review articles on imaging, the first FLIM images of cells having been produced in 1994.
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Affiliation(s)
- P J Tadrous
- Department of Histopathology, Imperial College School of Medicine, The Hammersmith Hospital, London, UK.
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34
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Takaki Y, Ohzu H. Fast numerical reconstruction technique for high-resolution hybrid holographic microscopy. APPLIED OPTICS 1999; 38:2204-2211. [PMID: 18319782 DOI: 10.1364/ao.38.002204] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A numerical reconstruction method believed to be new is proposed for hybrid holographic microscopy in which the hologram of a microscopic object is recorded by an image sensor and is then reconstructed by a computer. Because the Fresnel-Kirchhoff integral must be used for numerical reconstruction to achieve high resolution, we propose an approximation technique for reducing the calculation time. This approximation technique is suitable for microscopic application. The numerical reconstruction of 1-microm-sized objects was demonstrated with a He-Ne laser (lambda = 0.6328 microm).
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Affiliation(s)
- Y Takaki
- Department of Applied Physics, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
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35
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Yang S, Xie X, Jia C, Zhao Y, Jiang S, Zhang Y, Shan X, Zhang X. Soft X-ray in-line holographic experiment. CHINESE SCIENCE BULLETIN-CHINESE 1998. [DOI: 10.1007/bf02883564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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37
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Boyer K, Solem JC, Longworth JW, Borisov AB, Rhodes CK. Biomedical three-dimensional holographic microimaging at visible, ultraviolet and X-ray wavelengths. Nat Med 1996; 2:939-41. [PMID: 8705867 DOI: 10.1038/nm0896-939] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A new imaging technology is under advanced development that has several key advantages over conventional forms of microimaging performed with standard light microscopes, confocal light microscopes, and electron microscopes. The image created by this microscope possesses several unique features: It is intrinsically three-dimensional; it can be formed with very high contrast, a characteristic of the phase-sensitive nature of the recording; the information contained in the image is obtained in a single exposure of the specimen, a feature that eliminates the accumulation of damage to living systems that can occur with techniques utilizing multiple exposures; the method of image construction is fundamentally free from aberration (distortion), thereby obviating the need to employ complex procedures for correction; the exact focal plane of any optical section is digitally determined through computation and is not based on any mechanical adjustments; and the principles of operation, including the computational processes and modalities of image presentation, are uniform over the full range of spectral coverage spanning from the visible (approximately 500 nm) to the X-ray (approximately 0.3 nm) regions. The application of this new technology is expected to open new cost-effective avenues to the understanding, prevention and treatment of broad areas of human disease.
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Affiliation(s)
- K Boyer
- Department of Physics (M/C 273), University of Illinois at Chicago 60607-7059, USA
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38
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Guo-xin C. Fully relativistic distorted-wave Born procedure for electron-impact excitation. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1996; 53:3227-3236. [PMID: 9913264 DOI: 10.1103/physreva.53.3227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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39
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Abstract
In this review we propose to address the question: for the life-science researcher, what does X-ray microscopy have to offer that is not otherwise easily available?We will see that the answer depends on a combination of resolution, penetrating power, analytical sensitivity, compatibility with wet specimens, and the ease of image interpretation.
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Affiliation(s)
- J Kirz
- Physics Department, State University of New York, Stony Brook 11794-3800, USA
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40
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McPherson A, Thompson BD, Borisov AB, Boyer K, Rhodes CK. Multiphoton-induced X-ray emission at 4–5 keV from Xe atoms with multiple core vacancies. Nature 1994. [DOI: 10.1038/370631a0] [Citation(s) in RCA: 354] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Ade H, Zhang X, Cameron S, Costello C, Kirz J, Williams S. Chemical contrast in X-ray microscopy and spatially resolved XANES spectroscopy of organic specimens. Science 1992; 258:972-5. [PMID: 1439809 DOI: 10.1126/science.1439809] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The scanning transmission x-ray microscope at the National Synchrotron Light Source has been used to record x-ray absorption near-edge structure (XANES) spectra from 0.01-square-micrometer regions of organic specimens. The spectral features observed reflect the molecular structure of the dominant absorbing atoms and provide the contrast mechanism for high-resolution imaging with chemical sensitivity. This technique was used with x-ray energies near the carbon K absorption edge to identify and map separate phases in various polymer blends and to map the DNA distribution in chromosomes with a spatial resolution of 55 nanometers.
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Affiliation(s)
- H Ade
- Department of Physics, State University of New York, Stony Brook, NY 11794
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Boyer K, Borisov AB, Borovskiy AV, Shiryaev OB, Tate DA, Bouma BE, Shi X, McPherson A, Luk TS, Rhodes CK. Method of concentration of power in materials for x-ray amplification. APPLIED OPTICS 1992; 31:3433-3437. [PMID: 20725308 DOI: 10.1364/ao.31.003433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Recent experimental and theoretical results indicate that a new technique for the controlled concentration of power in materials may be feasible. The power levels that are potentially achievable are sufficient for the generation of amplification of x-ray wavelengths in the kilovolt range. The method of power concentration involves the combination of (1) a new ultrahigh brightness subpicosecond laser technology, (2) multiphoton coupling to atoms and molecules, and (3) a new channeled mode of electromagnetic propagation. The energy scaling of this approach is the most important consideration, and it is shown that the control of the propagation is the key factor that enables high levels of amplification in the kilovolt regime to be achieved with a total excitation energy of ~1 J.
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MacGowan BJ, Maxon S, Fields DJ, Keane CJ, Matthews DL, Osterheld AL, Scofield JH, Shimkaveg G, Stone GF. Demonstration of x-ray amplifiers near the carbon K edge. PHYSICAL REVIEW LETTERS 1990; 65:420-423. [PMID: 10042916 DOI: 10.1103/physrevlett.65.420] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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London RA, Rosen MD, Trebes JE. Wavelength choice for soft x-ray laser holography of biological samples. APPLIED OPTICS 1989; 28:3397-3404. [PMID: 20555712 DOI: 10.1364/ao.28.003397] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The choice of an optimal wavelength for soft x-ray holography is discussed, based on a description of scattering by biological structures within an aqueous environment. We conclude that wavelengths slightly longer than the 43.7-A carbon K-edge provide a good trade off between minimizing the necessary source power and the dose absorbed by the sample and maximizing the penetrability of the x-rays through wet samples. This differs from the previous notion that wavelengths within the water window (between 23.2 A and 43.7 A) would be the best for holography. The problem of motion resulting from the absorption of x rays during a short exposure is described. The possibility of using ultrashort exposures in order to capture the image before motion can compromise the resolution is explored. The impact of these calculations on the question of the feasibility of using an x-ray laser for holography of biological structures is discussed.
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Yamanaka R, Yamamoto K, Handa N, Yoshikura H. A 3D display with a linearly moving mirror to reflect a series of 2D cross sections and its application to noninvasive angiography. IEEE TRANSACTIONS ON MEDICAL IMAGING 1988; 7:193-197. [PMID: 18230468 DOI: 10.1109/42.7781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A 3D display equipped with a linearly moving mirror reflecting a series of 2D cross sections pictures has been devised. The pictures were displayed by a CRT in perfect synchronization with the back-and-forth movements of the mirror. The 80x80x80 mm(3) 3D space contained 128x128 pixels; with each pixel having 256 grades of intensity, enough to produce a satisfactory 3D image of an ultrasonic echogram of hepatic vessels. The images can be observed from different angles by changing the observer's position or by prompt rotation of the image through a console. Mechanical problems inherent in using moving parts have been solved.
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Howells M, Jacobsen C, Kirz J, Feder R, McQuaid K, Rothman S. X-ray holograms at improved resolution: a study of zymogen granules. Science 1987; 238:514-7. [PMID: 3659925 DOI: 10.1126/science.3659925] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
X-ray holography offers the possibility of three-dimensional microscopy with resolution higher than that of the light microscope and with contrast based on x-ray edges. In principle, the method is especially advantageous for biological samples if x-rays in the wavelength region between the carbon and oxygen K edges are used. However, until now the achieved resolution has not exceeded that of the light microscope because of the poor coherence properties of the x-ray sources and the low resolution of the detectors that were available. With a recently developed x-ray source based on an undulator on an electron storage ring, and high resolution x-ray resist, a hologram has been recorded at about 400-angstrom resolution. The experiment utilized x-rays with wavelengths of 24.7 angstroms and required a 1-hour exposure of the pancreatic zymogen granules under study.
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Affiliation(s)
- M Howells
- Center for X-ray Optics, Lawrence Berkeley Laboratory, University of California, Berkeley 94720
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