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18 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2 [Next/Last]

Instruments / Technical Area	Publication Details	Published
	Development of crystal optics for X-ray multi-projection imaging for synchrotron and XFEL sources Valerio Bellucci , Sarlota Birnsteinova , Tokushi Sato , Romain Letrun , Jayanath C. P. Koliyadu , Chan Kim , Gabriele Giovanetti , Carsten Deiter , Liubov Samoylova , Ilia Petrov , Luis Lopez Morillo , Rita Graceffa , Luigi Adriano , Helge Huelsen , Heiko Kollmann , Thu Nhi Tran Calliste , Dusan Korytar , Zdenko Zaprazny , Andrea Mazzolari , Marco Romagnoni , Eleni Myrto Asimakopoulou , Zisheng Yao , Yuhe Zhang , Jozef Ulicny , Alke Meents , Henry N. Chapman , Richard Bean , Adrian Mancuso , Pablo Villanueva-Perez , Patrik Vagovic Journal Of Synchrotron Radiation 31 DOI: 10.1107/S1600577524008488 Open Access Show Abstract ▼ Abstract: X-ray multi-projection imaging (XMPI) is an emerging experimental technique for the acquisition of rotation-free, time-resolved, volumetric information on stochastic processes. The technique is developed for high-brilliance light-source facilities, aiming to address known limitations of state-of-the-art imaging methods in the acquisition of 4D sample information, linked to their need for sample rotation. XMPI relies on a beam-splitting scheme, that illuminates a sample from multiple, angularly spaced viewpoints, and employs fast, indirect, X-ray imaging detectors for the collection of the data. This approach enables studies of previously inaccessible phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. In this work, we discuss in detail the beam-splitting scheme of XMPI. More specifically, we explore the relevant properties of X-ray splitter optics for their use in XMPI schemes, both at synchrotron insertion devices and XFEL facilities. Furthermore, we describe two distinct XMPI schemes, designed to faciliate large samples and complex sample environments. Finally, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL. This detailed overview aims to state the challenges and the potential of XMPI and act as a stepping stone for future development of the technique.	Nov 2024
	Development of MHz X-ray phase contrast imaging at the European XFEL Jayanath C. P. Koliyadu , Daniel Moško , Eleni Myrto Asimakopoulou , Valerio Bellucci , Šarlota Birnšteinová , Richard Bean , Romain Letrun , Chan Kim , Henry Kirkwood , Gabriele Giovanetti , Nerea Jardon , Janusz Szuba , Trey Guest , Andreas Koch , Jan Grünert , Peter Szeles , Pablo Villanueva-Perez , Fabian Reuter , Claus-Dieter Ohl , Mike Andreas Noack , Francisco Garcia-Moreno , Zuzana Kuglerová-Valdová , Libor Juha , Martin Nikl , Wataru Yashiro , Hitoshi Soyama , Daniel Eakins , Alexander M. Korsunsky , Jozef Ulicny , Alke Meents , Henry N. Chapman , Adrian P. Mancuso , Tokushi Sato , Patrik Vagovic Journal Of Synchrotron Radiation 32 DOI: 10.1107/S160057752400986X Show Abstract ▼ Abstract: We report on recent developments that enable megahertz hard X-ray phase contrast imaging (MHz XPCI) experiments at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL facility (EuXFEL). We describe the technical implementation of the key components, including an MHz fast camera and a modular indirect X-ray microscope system based on fast scintillators coupled through a high-resolution optical microscope, which enable full-field X-ray microscopy with phase contrast of fast and irreversible phenomena. The image quality for MHz XPCI data showed significant improvement compared with a pilot demonstration of the technique using parallel beam illumination, which also allows access to up to 24 keV photon energies at the SPB/SFX instrument of the EuXFEL. With these developments, MHz XPCI was implemented as a new method offered for a broad user community (academic and industrial) and is accessible via standard user proposals. Furthermore, intra-train pulse diagnostics with a high few-micrometre spatial resolution and recording up to 128 images of consecutive pulses in a train at up to 1.1 MHz repetition rate is available upstream of the instrument. Together with the diagnostic camera upstream of the instrument and the MHz XPCI setup at the SPB/SFX instrument, simultaneous two-plane measurements for future beam studies and feedback for machine parameter tuning are now possible.	Nov 2024
I03-Macromolecular Crystallography	Crystal structures of cables formed by the acetylated and unacetylated forms of the Schizosaccharomyces pombe tropomyosin orthologue TpmCdc8 Patrick Y. A. Reinke , Robin S. Heiringhoff , Theresia Reindl , Karen Baker , Manuel H. Taft , Alke Meents , Daniel P. Mulvihill , Owen R. Davies , Roman Fedorov , Michael Zahn , Dietmar J. Manstein Journal Of Biological Chemistry 6 DOI: 10.1016/j.jbc.2024.107925 Diamond Proposal Number(s): [35775] Open Access Show Abstract ▼ Abstract: Cables formed by head-to-tail polymerization of tropomyosin, localized along the length of sarcomeric and cytoskeletal actin filaments, play a key role in regulating a wide range of motile and contractile processes. The stability of tropomyosin cables, their interaction with actin filaments and the functional properties of the resulting co-filaments are thought to be affected by N-terminal acetylation of tropomyosin. Here, we present high–resolution structures of cables formed by acetylated and unacetylated Schizosaccharomyces pombe tropomyosin orthologue TpmCdc8. The crystal structures represent different types of cables, each consisting of TpmCdc8 homodimers in a different conformation. The structures show how the interactions of the residues in the overlap junction contribute to cable formation and how local structural perturbations affect the conformational dynamics of the protein and its ability to transmit allosteric signals. In particular, N-terminal acetylation increases the helicity of the adjacent region, which leads to a local reduction in conformational dynamics and consequently to less fraying of the N-terminal region. This creates a more consistent complementary surface facilitating the formation of specific interactions across the overlap junction.	Oct 2024
	Online dynamic flat-field correction for MHz microscopy data at European XFEL Sarlota Birnsteinova , Danilo E. Ferreira De Lima , Egor Sobolev , Henry J. Kirkwood , Valerio Bellucci , Richard J. Bean , Chan Kim , Jayanath C. P. Koliyadu , Tokushi Sato , Fabio Dall'Antonia , Eleni Myrto Asimakopoulou , Zisheng Yao , Khachiwan Buakor , Yuhe Zhang , Alke Meents , Henry N. Chapman , Adrian P. Mancuso , Pablo Villanueva-Perez , Patrik Vagovic Journal Of Synchrotron Radiation 30 DOI: 10.1107/S1600577523007336 Open Access Show Abstract ▼ Abstract: The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.	Nov 2023
	Laser-induced, single droplet fragmentation dynamics revealed through megahertz x-ray microscopy Fabian Reuter , Tokushi Sato , Valerio Bellucci , Sarlota Birnsteinova , Carsten Deiter , Jayanath C. P. Koliyadu , Romain Letrun , Pablo Villanueva-Perez , Richard Bean , Adrian P. Mancuso , Alke Meents , Patrik Vagovic , Claus-Dieter Ohl Physics Of Fluids 35 DOI: 10.1063/5.0171225 Open Access Show Abstract ▼ Abstract: The fragmentation dynamics of single water droplets from laser irradiation is studied with megahertz frame rate x-ray microscopy. Owed to the nearly refraction-free and penetrating imaging technique, we could look into the interior of the droplet and reveal that two mechanisms are responsible for the initial explosive fragmentation of the droplet. First, reflection and diffraction of the laser beam at the droplet interface result in the formation of laser ray caustics that lead to non-homogeneous heating of the droplet, locally above the critical temperature. Second, homogeneous cavitation in the droplet that is likely caused from shockwaves reflected as tension waves at the acoustic soft boundaries of the droplet. Further atomization occurs in three stages, first a fine sub-micrometer sized mist forms on the side of the droplet posterior to laser incidence, then micrometer sized droplets are expelled from the rim of an expanding liquid sheet, and finally into droplets of larger size through hole and ligament formation in the thinning liquid sheet where ligaments pinch off.	Nov 2023
I13-1-Coherence	Hard X-ray stereographic microscopy for single-shot differential phase imaging Valerio Bellucci , Marie-Christine Zdora , Ladislav Mikes , Šarlota Birnšteinová , Peter Oberta , Marco Romagnoni , Andrea Mazzolari , Pablo Villanueva-Perez , Rajmund Mokso , Christian David , Mikako Makita , Silvia Cipiccia , Jozef Ulicny , Alke Meents , Adrian P. Mancuso , Henry N. Chapman , Patrik Vagovic Optics Express 31 DOI: 10.1364/OE.492137 Diamond Proposal Number(s): [17739] Open Access Show Abstract ▼ Abstract: The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.	May 2023
	Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease Vasundara Srinivasan , Hévila Brognaro , Prince R. Prabhu , Edmarcia Elisa De Souza , Sebastian Günther , Patrick Y. A. Reinke , Thomas J. Lane , Helen Ginn , Huijong Han , Wiebke Ewert , Janina Sprenger , Faisal H. M. Koua , Sven Falke , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Bruno Alves Franca , Mengying Wang , Angélica Luana C. Barra , Markus Perbandt , Martin Schwinzer , Christina Schmidt , Lea Brings , Kristina Lorenzen , Robin Schubert , Rafael Rahal Guaragna Machado , Erika Donizette Candido , Danielle Bruna Leal Oliveira , Edison Luiz Durigon , Stephan Niebling , Angelica Struve Garcia , Oleksandr Yefanov , Julia Lieske , Luca Gelisio , Martin Domaracky , Philipp Middendorf , Michael Groessler , Fabian Trost , Marina Galchenkova , Aida Rahmani Mashhour , Sofiane Saouane , Johanna Hakanpää , Markus Wolf , Maria Garcia Alai , Dusan Turk , Arwen R. Pearson , Henry N. Chapman , Winfried Hinrichs , Carsten Wrenger , Alke Meents , Christian Betzel Communications Biology 5 DOI: 10.1038/s42003-022-03737-7 Open Access Show Abstract ▼ Abstract: SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.	Aug 2022
	Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals J. Mia Lahey-Rudolph , Robert Schönherr , Miriam Barthelmess , Pontus Fischer , Carolin Seuring , Armin Wagner , Alke Meents , Lars Redecke Iucrj 8, 665 - 677 DOI: 10.1107/S2052252521005297 Open Access Show Abstract ▼ Abstract: The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.	Jul 2021
	X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease Sebastian Gunther , Patrick Y. A. Reinke , Yaiza Fernández-García , Julia Lieske , Thomas J. Lane , Helen M. Ginn , Faisal H. M. Koua , Christiane Ehrt , Wiebke Ewert , Dominik Oberthuer , Oleksandr Yefanov , Susanne Meier , Kristina Lorenzen , Boris Krichel , Janine-Denise Kopicki , Luca Gelisio , Wolfgang Brehm , Ilona Dunkel , Brandon Seychell , Henry Gieseler , Brenna Norton-Baker , Beatriz Escudero-Pérez , Martin Domaracky , Sofiane Saouane , Alexandra Tolstikova , Thomas A. White , Anna Hänle , Michael Groessler , Holger Fleckenstein , Fabian Trost , Marina Galchenkova , Yaroslav Gevorkov , Chufeng Li , Salah Awel , Ariana Peck , Miriam Barthelmess , Frank Schluenzen , Paulraj Lourdu Xavier , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Sven Falke , Vasundara Srinivasan , Bruno Alves França , Martin Schwinzer , Hévila Brognaro , Cromarte Rogers , Diogo Melo , Joanna J. Zaitseva-Doyle , Juraj Knoska , Gisel E. Peña-Murillo , Aida Rahmani Mashhour , Vincent Hennicke , Pontus Fischer , Johanna Hakanpää , Jan Meyer , Philip Gribbon , Bernhard Ellinger , Maria Kuzikov , Markus Wolf , Andrea R. Beccari , Gleb Bourenkov , David Von Stetten , Guillaume Pompidor , Isabel Bento , Saravanan Panneerselvam , Ivars Karpics , Thomas R. Schneider , Maria Marta Garcia-Alai , Stephan Niebling , Christian Günther , Christina Schmidt , Robin Schubert , Huijong Han , Juliane Boger , Diana C. F. Monteiro , Linlin Zhang , Xinyuanyuan Sun , Jonathan Pletzer-Zelgert , Jan Wollenhaupt , Christian G. Feiler , Manfred S. Weiss , Eike-Christian Schulz , Pedram Mehrabi , Katarina Karničar , Aleksandra Usenik , Jure Loboda , Henning Tidow , Ashwin Chari , Rolf Hilgenfeld , Charlotte Uetrecht , Russell Cox , Andrea Zaliani , Tobias Beck , Matthias Rarey , Stephan Günther , Dusan Turk , Winfried Hinrichs , Henry N. Chapman , Arwen R. Pearson , Christian Betzel , Alke Meents Science DOI: 10.1126/science.abf7945 Open Access Show Abstract ▼ Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.	Apr 2021
	Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene Carolin Seuring , Kartik Ayyer , Eleftheria Filippaki , Miriam Barthelmess , Jean-Nicolas Longchamp , Philippe Ringler , Tommaso Pardini , David H. Wojtas , Matthew A. Coleman , Katerina Dörner , Silje Fuglerud , Greger Hammarin , Birgit Habenstein , Annette E. Langkilde , Antoine Loquet , Alke Meents , Roland Riek , Henning Stahlberg , Sébastien Boutet , Mark S. Hunter , Jason Koglin , Mengning Liang , Helen M. Ginn , Rick P. Millane , Matthias Frank , Anton Barty , Henry N. Chapman Nature Communications 9 DOI: 10.1038/s41467-018-04116-9 Open Access Show Abstract ▼ Abstract: Here we present a new approach to diffraction imaging of amyloid fibrils, combining a free-standing graphene support and single nanofocused X-ray pulses of femtosecond duration from an X-ray free-electron laser. Due to the very low background scattering from the graphene support and mutual alignment of filaments, diffraction from tobacco mosaic virus (TMV) filaments and amyloid protofibrils is obtained to 2.7 Å and 2.4 Å resolution in single diffraction patterns, respectively. Some TMV diffraction patterns exhibit asymmetry that indicates the presence of a limited number of axial rotations in the XFEL focus. Signal-to-noise levels from individual diffraction patterns are enhanced using computational alignment and merging, giving patterns that are superior to those obtainable from synchrotron radiation sources. We anticipate that our approach will be a starting point for further investigations into unsolved structures of filaments and other weakly scattering objects.	May 2018

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