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  • Microscopy  (2)
  • X-ray lasersXFELsbiologystructuredynamics  (2)
  • perovskiteferroelectricpowder neutron diffraction  (2)
  • protein crystalscrystal lattices  (2)
  • ArenaviridaeendonucleasesLymphocytic choriomeningitis virusLCMVdiketo acidscompound optimizationmetal chelation  (1)
  • International Union of Crystallography (IUCr)  (7)
  • Cell Press  (2)
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  • 1
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-07-01
    Keywords: X-ray lasersXFELsbiologystructuredynamics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 4
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-05-11
    Description: The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump–probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallography to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
    Keywords: X-ray lasersXFELsbiologystructuredynamics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 5
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-04-27
    Keywords: perovskiteferroelectricpowder neutron diffraction
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 6
    Publication Date: 2017-03-09
    Description: The perovskite Li0.2Na0.8NbO3 is shown, by powder neutron diffraction, to display a unique sequence of phase transitions at elevated temperature. The ambient temperature polar phase (rhombohedral, space group R3c) transforms via a first-order transition to a polar tetragonal phase (space group P42mc) in the region 150–300°C; these two phases correspond to Glazer tilt systems a−a−a− and a+a+c−, respectively. At 500°C a ferroelectric–paraelectric transition takes place from P42mc to P42/nmc, retaining the a+a+c− tilt. Transformation to a single-tilt system, a0a0c+ (space group P4/mbm), occurs at 750°C, with the final transition to the aristotype cubic phase at 850°C. The P42mc and P42/nmc phases have each been seen only once and twice each, respectively, in perovskite crystallography, in each case in compositions prepared at high pressure.
    Keywords: perovskiteferroelectricpowder neutron diffraction
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 7
    Publication Date: 2018-02-23
    Description: The Arenaviridae family, together with the Bunyaviridae and Orthomyxoviridae families, is one of the three negative-stranded RNA viral families that encode an endonuclease in their genome. The endonuclease domain is at the N-terminus of the L protein, a multifunctional protein that includes the RNA-dependent RNA polymerase. The synthesis of mRNA in arenaviruses is a process that is primed by capped nucleotides that are `stolen' from the cellular mRNA by the endonuclease domain in cooperation with other domains of the L protein. This molecular mechanism has been demonstrated previously for the endonuclease of the prototype Lymphocytic choriomeningitis virus (LCMV). However, the mode of action of this enzyme is not fully understood as the original structure did not contain catalytic metal ions. The pivotal role played by the cap-snatching process in the life cycle of the virus and the highly conserved nature of the endonuclease domain make it a target of choice for the development of novel antiviral therapies. Here, the binding affinities of two diketo-acid (DKA) compounds (DPBA and L-742,001) for the endonuclease domain of LCMV were evaluated using biophysical methods. X-ray structures of the LCMV endonuclease domain with catalytic ions in complex with these two compounds were determined, and their efficacies were assessed in an in vitro endonuclease-activity assay. Based on these data and computational simulation, two new DKAs were synthesized. The LCMV endonuclease domain exhibits a good affinity for these DKAs, making them a good starting point for the design of arenavirus endonuclease inhibitors. In addition to providing the first example of an X-ray structure of an arenavirus endonuclease incorporating a ligand, this study provides a proof of concept that the design of optimized inhibitors against the arenavirus endonuclease is possible.
    Keywords: ArenaviridaeendonucleasesLymphocytic choriomeningitis virusLCMVdiketo acidscompound optimizationmetal chelation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirst, W. G., Kiefer, C., Abdosamadi, M. K., Schäffer, E., & Reber, S. In Vitro reconstitution and imaging of microtubule dynamics by fluorescence and label-free microscopy. STAR Protocols, 1(3), (2020): 100177, doi:10.1016/j.xpro.2020.100177.
    Description: Dynamic microtubules are essential for many processes in the lives of eukaryotic cells. To study and understand the mechanisms of microtubule dynamics and regulation, in vitro reconstitution with purified components has proven a vital approach. Imaging microtubule dynamics can be instructive for a given species, isoform composition, or biochemical modification. Here, we describe two methods that visualize microtubule dynamics at high speed and high contrast: (1) total internal reflection fluorescence microscopy and (2) label-free interference reflection microscopy.
    Description: We thank the AMBIO imaging facility (Charité, Berlin) and Nikon at MBL for imaging support. We thank all former and current members of the Reber lab for discussion and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding by the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University. C.K. thanks the Deutsche Forschungsgesellschaft (DFG, JA 2589/1-1). C.K. and M.A. thank Steve Simmert and Tobias Jachowski former and current members of the Schäffer lab.
    Keywords: Biophysics ; Cell Biology ; Microscopy
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geisterfer, Z. M., Oakey, J., & Gatlin, J. C. . Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography. STAR Protocols, 1(3), (2020): 100221, doi:10.1016/j.xpro.2020.100221.
    Description: Cell-free extract derived from the eggs of the African clawed frog Xenopus laevis is a well-established model system that has been used historically in bulk aliquots. Here, we describe a microfluidic approach for isolating discrete, biologically relevant volumes of cell-free extract, with more expansive and precise control of extract shape compared with extract-oil emulsions. This approach is useful for investigating the mechanics of intracellular processes affected by cell geometry or cytoplasmic volume, including organelle scaling and positioning mechanisms. For complete details on the use and execution of this protocol, please refer to Geisterfer et al. (2020).
    Description: This work was made possible by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant no. 2P20GM103432. It was also supported by additional funding provided by the NIGMS under grant no. R01GM113028, the NSF Faculty CAREER Program under award no. BBBE 1254608, Whitman Center fellowships at the Marine Biological Laboratory, and the Biomedical Scholars program of the Pew Charitable Trusts. We thank Drs. Aaron Groen and Tim Mitchison for their intellectual contributions and involvement in some of the pioneering experiments that set the foundation for this approach.
    Keywords: Biophysics ; Cell Biology ; Cell isolation ; Microscopy ; Model Organisms
    Repository Name: Woods Hole Open Access Server
    Type: Article
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