Publications by authors named "Joachim Schulz"

44 Publications

The XBI BioLab for life science experiments at the European XFEL.

J Appl Crystallogr 2021 Feb 1;54(Pt 1):7-21. Epub 2021 Feb 1.

European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany.

The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.
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http://dx.doi.org/10.1107/S1600576720013989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7941304PMC
February 2021

Clinical Presentation and Management of a Dinutuximab Beta Extravasation in a Patient with Neuroblastoma.

Children (Basel) 2021 Jan 29;8(2). Epub 2021 Jan 29.

Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.

Extravasation can present serious accidental complication of intravenous drug application. While monoclonal antibodies do not show the necrotic potential of cytotoxic chemotherapy drugs, considerable inflammatory toxicity can occur, necessitating standardized operating procedures for the management of their extravasation. Here, we report the clinical course and management of dinutuximab beta extravasation in a 3-year-old child. Dinutuximab beta is a chimeric monoclonal antibody targeting the GD2 disialoganglioside on the surface of neuroblastoma cells that has in recent years gained significant importance in the treatment of high-risk neuroblastoma, now contributing to both first- and second-line therapy protocols. The dinutuximab beta extravasation reported here occurred when the patient received the antibody cycle as a continuous infusion over a 10-day period after haploidentical stem cell transplantation for relapsed high-risk neuroblastoma. The extravasated dinutuximab beta caused local pain, swelling, and hyperemia accompanied by fever and an overall deterioration in the general condition. Laboratory diagnostics demonstrated an increase in C-reactive protein level and total white blood cell count. Clinical complication management consisted of intravenous fluid therapy, local dabbing with dimethyl sulfoxide (DMSO), analgesia with dipyrone, as well as application of intravenous antibiotics to prevent bacterial superinfection in the severely immunocompromised host. The patient considerably improved after six days with this treatment regimen and fully recovered by day 20.
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http://dx.doi.org/10.3390/children8020091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7911257PMC
January 2021

Segmented flow generator for serial crystallography at the European X-ray free electron laser.

Nat Commun 2020 09 9;11(1):4511. Epub 2020 Sep 9.

School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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http://dx.doi.org/10.1038/s41467-020-18156-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7481229PMC
September 2020

The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation.

J Synchrotron Radiat 2019 May 12;26(Pt 3):660-676. Epub 2019 Apr 12.

European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany.

The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.
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http://dx.doi.org/10.1107/S1600577519003308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510195PMC
May 2019

Native mass spectrometry provides sufficient ion flux for XFEL single-particle imaging.

J Synchrotron Radiat 2019 May 11;26(Pt 3):653-659. Epub 2019 Apr 11.

European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany.

The SPB/SFX instrument at the European XFEL provides unique conditions for single-particle imaging (SPI) experiments due to its high brilliance, nano-focus and unique pulse structure. Promising initial results provided by the international LCLS (Linac Coherent Light Source) SPI initiative highlight the potential of SPI. Current available injection methods generally have high sample consumption and do not provide any options for pulsing, selection or orientation of particles, which poses a problem for data evaluation. Aerosol-injector-based sample delivery is the current method of choice for SPI experiments, although, to a lesser extent, electrospray and electrospinning are used. Single particles scatter only a limited number of photons providing a single orientation for data evaluation, hence large datasets are required from particles in multiple orientations in order to reconstruct a structure. Here, a feasibility study demonstrates that nano-electrospray ionization, usually employed in biomolecular mass spectrometry, provides enough ion flux for SPI experiments. A novel instrument setup at the SPB/SFX instrument is proposed, which has the benefit of extremely low background while delivering mass over charge and conformation-selected ions for SPI.
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http://dx.doi.org/10.1107/S1600577519002686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510201PMC
May 2019

Correction to: Experiences with a temporary synthetic skin substitute after decompressive craniectomy: a retrospective two-center analysis.

Acta Neurochir (Wien) 2019 Mar;161(3):501

Department of Neurosurgery, Trauma Center Murnau, Professor-Küntscher Straße 8, 82418, Murnau, Germany.

Incorrect given and family of Miron Yousif.
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http://dx.doi.org/10.1007/s00701-018-03776-2DOI Listing
March 2019

Experiences with a temporary synthetic skin substitute after decompressive craniectomy: a retrospective two-center analysis.

Acta Neurochir (Wien) 2019 03 4;161(3):493-499. Epub 2018 Dec 4.

Department of Neurosurgery, Trauma Center Murnau, Professor-Küntscher Straße 8, 82418, Murnau, Germany.

Background: Decompressive craniectomy is a commonly performed procedure. It reduces intracranial pressure, improves survival, and thus might have a positive impact on several neurosurgical diseases and emergencies. Sometimes primary skin closure is not possible due to cerebral herniation or extensive skin defects. In order to prevent further restriction of the underlying tissue, a temporary skin expansion might be necessary.

Methods And Material: We retrospectively reviewed patients in need for a temporary skin substitute because skin closure was not possible after craniectomy without violating brain tissue underneath in a time period of 6 years (2011-2016). With this study, we present initial experiences of Epigard (Biovision, Germany) as an artificial temporary skin replacement. We performed this analysis at two level-1 trauma centers (Trauma Center Murnau, Germany; University Hospital of St. Poelten, Austria). Demographic data, injury and surgical characteristics, and complication rates were analyzed via chart review. We identified nine patients within our study period. Six patients suffered from severe traumatic brain injury and developed pronounced cerebral herniation in the acute or subacute phase. Three patients presented with non-traumatic conditions (one atypical intracerebral hemorrhage and two patients with extensive destructive tumors invading the skull and scalp).

Results: A total of 20 Epigard exchanges (range 1-4) were necessary before skin closure was possible. A CSF fistula due to a leaky Epigard at the interface to the skin was observed in two patients (22%). Additional complications were four wound infections, three CNS infections, and three patients developed a shunt dependency. Three patients died within the first month after injury.

Conclusions: Temporary skin closure with Epigard as a substitute is feasible for a variety of neurosurgical conditions. The high complication and mortality rate reflect the complexity of the encountered pathologies and need to be considered when counseling the patient and their families.
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http://dx.doi.org/10.1007/s00701-018-3748-9DOI Listing
March 2019

Megahertz serial crystallography.

Authors:
Max O Wiedorn Dominik Oberthür Richard Bean Robin Schubert Nadine Werner Brian Abbey Martin Aepfelbacher Luigi Adriano Aschkan Allahgholi Nasser Al-Qudami Jakob Andreasson Steve Aplin Salah Awel Kartik Ayyer Saša Bajt Imrich Barák Sadia Bari Johan Bielecki Sabine Botha Djelloul Boukhelef Wolfgang Brehm Sandor Brockhauser Igor Cheviakov Matthew A Coleman Francisco Cruz-Mazo Cyril Danilevski Connie Darmanin R Bruce Doak Martin Domaracky Katerina Dörner Yang Du Hans Fangohr Holger Fleckenstein Matthias Frank Petra Fromme Alfonso M Gañán-Calvo Yaroslav Gevorkov Klaus Giewekemeyer Helen Mary Ginn Heinz Graafsma Rita Graceffa Dominic Greiffenberg Lars Gumprecht Peter Göttlicher Janos Hajdu Steffen Hauf Michael Heymann Susannah Holmes Daniel A Horke Mark S Hunter Siegfried Imlau Alexander Kaukher Yoonhee Kim Alexander Klyuev Juraj Knoška Bostjan Kobe Manuela Kuhn Christopher Kupitz Jochen Küpper Janine Mia Lahey-Rudolph Torsten Laurus Karoline Le Cong Romain Letrun P Lourdu Xavier Luis Maia Filipe R N C Maia Valerio Mariani Marc Messerschmidt Markus Metz Davide Mezza Thomas Michelat Grant Mills Diana C F Monteiro Andrew Morgan Kerstin Mühlig Anna Munke Astrid Münnich Julia Nette Keith A Nugent Theresa Nuguid Allen M Orville Suraj Pandey Gisel Pena Pablo Villanueva-Perez Jennifer Poehlsen Gianpietro Previtali Lars Redecke Winnie Maria Riekehr Holger Rohde Adam Round Tatiana Safenreiter Iosifina Sarrou Tokushi Sato Marius Schmidt Bernd Schmitt Robert Schönherr Joachim Schulz Jonas A Sellberg M Marvin Seibert Carolin Seuring Megan L Shelby Robert L Shoeman Marcin Sikorski Alessandro Silenzi Claudiu A Stan Xintian Shi Stephan Stern Jola Sztuk-Dambietz Janusz Szuba Aleksandra Tolstikova Martin Trebbin Ulrich Trunk Patrik Vagovic Thomas Ve Britta Weinhausen Thomas A White Krzysztof Wrona Chen Xu Oleksandr Yefanov Nadia Zatsepin Jiaguo Zhang Markus Perbandt Adrian P Mancuso Christian Betzel Henry Chapman Anton Barty

Nat Commun 2018 10 2;9(1):4025. Epub 2018 Oct 2.

Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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http://dx.doi.org/10.1038/s41467-018-06156-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168542PMC
October 2018

Rapid sample delivery for megahertz serial crystallography at X-ray FELs.

IUCrJ 2018 Sep 27;5(Pt 5):574-584. Epub 2018 Jul 27.

Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.
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http://dx.doi.org/10.1107/S2052252518008369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126653PMC
September 2018

MHz frame rate hard X-ray phase-contrast imaging using synchrotron radiation.

Opt Express 2017 Jun;25(12):13857-13871

Third generation synchrotron light sources offer high photon flux, partial spatial coherence, and ~10 s pulse widths. These enable hard X-ray phase-contrast imaging (XPCI) with single-bunch temporal resolutions. In this work, we exploited the MHz repetition rates of synchrotron X-ray pulses combined with indirect X-ray detection to demonstrate the potential of XPCI with millions of frames per second multiple-frame recording. This allows for the visualization of aperiodic or stochastic transient processes which are impossible to be realized using single-shot or stroboscopic XPCI. We present observations of various phenomena, such as crack tip propagation in glass, shock wave propagation in water and explosion during electric arc ignition, which evolve in the order of km/s (µm/ns).
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http://dx.doi.org/10.1364/OE.25.013857DOI Listing
June 2017

Idarucizumab elimination of dabigatran minutes before systemic thrombolysis in acute ischemic stroke.

J Neurol Sci 2016 11 9;370:44. Epub 2016 Sep 9.

Emergency Department, CHU Saint-Pierre, Université libre de Bruxelles, Rue Haute 322, 1000 Bruxelles, Belgium.

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http://dx.doi.org/10.1016/j.jns.2016.09.010DOI Listing
November 2016

Genes Related to Fatty Acid β-Oxidation Play a Role in the Functional Decline of the Drosophila Brain with Age.

PLoS One 2016 12;11(8):e0161143. Epub 2016 Aug 12.

Centro Biologia Molecular "Severo Ochoa", CSIC-UAM, Campus Universidad Autonoma de Madrid, 28049, Madrid, Spain.

In living organisms, ageing is widely considered to be the result of a multifaceted process consisting of the progressive accumulation of damage over time, having implications both in terms of function and survival. The study of ageing presents several challenges, from the different mechanisms implicated to the great diversity of systems affected over time. In the current study, we set out to identify genes involved in the functional decline of the brain with age and study its relevance in a tissue dependent manner using Drosophila melanogaster as a model system. Here we report the age-dependent upregulation of genes involved in the metabolic process of fatty acid β-oxidation in the nervous tissue of female wild-type flies. Downregulation of CG10814, dHNF4 and lipid mobilizing genes bmm and dAkh rescues the functional decline of the brain with age, both at the cellular and behaviour level, while over-expression worsens performance. Our data proposes the occurrence of a metabolic alteration in the fly brain with age, whereby the process of β-oxidation of fatty acids experiences a genetic gain-of-function. This event proved to be one of the main causes contributing to the functional decline of the brain with age.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161143PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982618PMC
August 2017

Open data set of live cyanobacterial cells imaged using an X-ray laser.

Sci Data 2016 Aug 1;3:160058. Epub 2016 Aug 1.

Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.
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http://dx.doi.org/10.1038/sdata.2016.58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968219PMC
August 2016

Acoustic Injectors Meet X-Ray Free-Electron Lasers.

Authors:
Joachim Schulz

Structure 2016 Apr;24(4):500-501

European XFEL GmbH, Sample Environment Group, Notkestraße 85, 22607 Hamburg, Germany. Electronic address:

In this issue of Structure, Roessler et al. (2016) present a new method to acoustically inject samples for serial femtosecond crystallography into the focus of free-electron lasers. This method can drastically reduce the sample consumption of this method. It will therefore play an important role in the mix of sample preparation technologies.
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http://dx.doi.org/10.1016/j.str.2016.03.014DOI Listing
April 2016

An organized co-assembly of clathrin adaptors is essential for endocytosis.

Dev Cell 2015 Apr;33(2):150-62

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, 69117 Heidelberg, Germany. Electronic address:

Clathrin-mediated endocytosis, the main trafficking route from the plasma membrane to the cytoplasm, is critical to many fundamental cellular processes. Clathrin, coupled to the membrane by adaptor proteins, is thought to play a major structural role in endocytosis by self-assembling into a cage-like lattice around the forming vesicle. Although clathrin adaptors are essential for endocytosis, little is known about their structural role in this process. Here we show that the membrane-binding domains of two conserved clathrin adaptors, Sla2 and Ent1, co-assemble in a PI(4,5)P2-dependent manner to form organized lattices on membranes. We determined the structure of the co-assembled lattice by electron cryo-microscopy and designed mutations that specifically impair the lattice formation in vitro. We show that these mutations block endocytosis in vivo. We suggest that clathrin adaptors not only link the polymerized clathrin to the membrane but also form an oligomeric structure, which is essential for membrane remodeling during endocytosis.
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http://dx.doi.org/10.1016/j.devcel.2015.02.023DOI Listing
April 2015

Imaging single cells in a beam of live cyanobacteria with an X-ray laser.

Nat Commun 2015 Feb 11;6:5704. Epub 2015 Feb 11.

Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.
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http://dx.doi.org/10.1038/ncomms6704DOI Listing
February 2015

Glial β-oxidation regulates Drosophila energy metabolism.

Sci Rep 2015 Jan 15;5:7805. Epub 2015 Jan 15.

1] VIB Center for the Biology of Disease, Leuven and Center for Human Genetics, KU Leuven, Leuven, Belgium [2] Centro Biología Molecular "Severo Ochoa" CSIC-UAM, Madrid, Spain.

The brain's impotence to utilize long-chain fatty acids as fuel, one of the dogmas in neuroscience, is surprising, since the nervous system is the tissue most energy consuming and most vulnerable to a lack of energy. Challenging this view, we here show in vivo that loss of the Drosophila carnitine palmitoyltransferase 2 (CPT2), an enzyme required for mitochondrial β-oxidation of long-chain fatty acids as substrates for energy production, results in the accumulation of triacylglyceride-filled lipid droplets in adult Drosophila brain but not in obesity. CPT2 rescue in glial cells alone is sufficient to restore triacylglyceride homeostasis, and we suggest that this is mediated by the release of ketone bodies from the rescued glial cells. These results demonstrate that the adult brain is able to catabolize fatty acids for cellular energy production.
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http://dx.doi.org/10.1038/srep07805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295106PMC
January 2015

Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

Faraday Discuss 2014 14;171:57-80. Epub 2014 Aug 14.

Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany.

This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.
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http://dx.doi.org/10.1039/c4fd00037dDOI Listing
June 2015

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers.

Opt Express 2013 Nov;21(23):28729-42

Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
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http://dx.doi.org/10.1364/OE.21.028729DOI Listing
November 2013

Sensing the wavefront of x-ray free-electron lasers using aerosol spheres.

Opt Express 2013 May;21(10):12385-94

PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.

Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
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http://dx.doi.org/10.1364/OE.21.012385DOI Listing
May 2013

Experimental results from a preclinical X-ray phase-contrast CT scanner.

Proc Natl Acad Sci U S A 2012 Sep 10;109(39):15691-6. Epub 2012 Sep 10.

Department of Physics and Institute of Medical Engineering, Technische Universität München, Garching, Germany.

To explore the future clinical potential of improved soft-tissue visibility with grating-based X-ray phase contrast (PC), we have developed a first preclinical computed tomography (CT) scanner featuring a rotating gantry. The main challenge in the transition from previous bench-top systems to a preclinical scanner are phase artifacts that are caused by minimal changes in the grating alignment during gantry rotation. In this paper, we present the first experimental results from the system together with an adaptive phase recovery method that corrects for these phase artifacts. Using this method, we show that the scanner can recover quantitatively accurate Hounsfield units in attenuation and phase. Moreover, we present a first tomography scan of biological tissue with complementary information in attenuation and phase contrast. The present study hence demonstrates the feasibility of grating-based phase contrast with a rotating gantry for the first time and paves the way for future in vivo studies on small animal disease models (in the mid-term future) and human diagnostics applications (in the long-term future).
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http://dx.doi.org/10.1073/pnas.1207503109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465429PMC
September 2012

Investigating the interaction of x-ray free electron laser radiation with grating structure.

Opt Lett 2012 Aug;37(15):3033-5

European XFEL GmbH, Hamburg, Germany.

The interaction of free electron laser pulses with grating structure is investigated using 4.6±0.1 nm radiation at the FLASH facility in Hamburg. For fluences above 63.7±8.7 mJ/cm2, the interaction triggers a damage process starting at the edge of the grating structure as evidenced by optical and atomic force microscopy. Simulations based on solution of the Helmholtz equation demonstrate an enhancement of the electric field intensity distribution at the edge of the grating structure. A procedure is finally deduced to evaluate damage threshold.
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http://dx.doi.org/10.1364/OL.37.003033DOI Listing
August 2012

Femtosecond free-electron laser x-ray diffraction data sets for algorithm development.

Opt Express 2012 Feb;20(4):4149-58

Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany.

We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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http://dx.doi.org/10.1364/OE.20.004149DOI Listing
February 2012

Time-resolved protein nanocrystallography using an X-ray free-electron laser.

Opt Express 2012 Jan;20(3):2706-16

Center for Free-Electron Laser Science, DESY, Notkestraße 85, 22607 Hamburg, Germany.

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413412PMC
http://dx.doi.org/10.1364/OE.20.002706DOI Listing
January 2012

In vivo protein crystallization opens new routes in structural biology.

Nat Methods 2012 Jan 29;9(3):259-62. Epub 2012 Jan 29.

Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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http://dx.doi.org/10.1038/nmeth.1859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429599PMC
January 2012

Lipidic phase membrane protein serial femtosecond crystallography.

Nat Methods 2012 Jan 29;9(3):263-5. Epub 2012 Jan 29.

Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.

X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
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http://dx.doi.org/10.1038/nmeth.1867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438231PMC
January 2012

Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements.

Nat Photonics 2012 ;6:35-40

Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.

X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology should enable structural determination from submicrometre protein crystals with atomic resolution.
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http://dx.doi.org/10.1038/nphoton.2011.297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783007PMC
January 2012

Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser.

Phys Rev B Condens Matter Mater Phys 2011 Dec;84(21):214111

Max-Planck Institut für medizinische Forschung, Jahnstrasse 29, DE-69120 Heidelberg, Germany ; Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, DE-22607 Hamburg, Germany.

X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
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http://dx.doi.org/10.1103/PhysRevB.84.214111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786679PMC
December 2011

Cytokinesis remnants define first neuronal asymmetry in vivo.

Nat Neurosci 2011 Nov 13;14(12):1525-33. Epub 2011 Nov 13.

Vlaams Instituut voor Biotechnologie, Department of Molecular and Developmental Genetics, Campus Gasthuisberg, Leuven, Belgium.

Polarization of a neuron begins with the appearance of the first neurite, thus defining the ultimate growth axis. Unlike late occurring polarity events (such as axonal growth), very little is known about this fundamental process. We show here that, in Drosophila melanogaster neurons in vivo, the first membrane deformation occurred 3.6 min after precursor division. Clustering of adhesion complex components (Bazooka (Par-3), cadherin-catenin) marked this place by 2.8 min after division; the upstream phosphatidylinositol 4,5-bisphosphate, by 0.7 min after division; and the furrow components RhoA and Aurora kinase, from the time of cytokinesis. Local DE-cadherin inactivation prevented sprout formation, whereas perturbation of division orientation did not alter polarization from the cytokinesis pole. This is, to our knowledge, the first molecular study of initial neuronal polarization in vivo. The mechanisms of polarization seem to be defined at the precursor stage.
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http://dx.doi.org/10.1038/nn.2976DOI Listing
November 2011