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  • 1. Cheng, Kimberley
    et al.
    Ivanova, Natalia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Scheres, Sjors H. W.
    Pavlov, Michael Y.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Maria Carazo, Jose
    Hebert, Hans
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lindahl, Martin
    tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes.2010In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 169, no 3, p. 342-348Article in journal (Refereed)
    Abstract [en]

    Bacterial ribosomes stalled on faulty, often truncated, mRNAs lacking stop codons are rescued by trans-translation. It relies on an RNA molecule (tmRNA) capable of replacing the faulty mRNA with its own open reading frame (ORF). Translation of tmRNA ORF results in the tagging of faulty protein for degradation and its release from the ribosome. We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu). Three-dimensional reconstruction and heterogeneity analysis resulted in a 15 A resolution structure of the tmRNA-SmpB complex accommodated in the A site of the ribosome, which shows that SmpB mimics the anticodon- and D-stem of native tRNAs missing in the tRNA-like domain of tmRNA. We conclude that the tmRNA-SmpB complex accommodates in the ribosomal A site very much like an aminoacyl-tRNA during protein elongation.  

  • 2. Hertz, H. M.
    et al.
    von Hofsten, O.
    Bertilson, M.
    Vogt, U.
    Holmberg, A.
    Reinspach, J.
    Martz, D.
    Selin, M.
    Christakou, A. E.
    Jerlstrom-Hultqvist, Joel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Svärd, Staffan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Laboratory cryo soft X-ray microscopy2012In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 177, no 2, p. 267-272Article in journal (Refereed)
    Abstract [en]

    Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a lambda = 2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.

  • 3.
    Joffre, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Neagu, R. Cristian
    Bardage, Stig L.
    Gamstedt, Kristofer
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Modelling of the hygroelastic behaviour of normal and compression wood tracheids2014In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 185, no 1, p. 89-98Article in journal (Refereed)
    Abstract [en]

    Compression wood conifer tracheids show different swelling and stiffness properties than those of usual normal wood, which has a practical function in the living plant: when a conifer shoot is moved from its vertical position, compression wood is formed in the under part of the shoot. The growth rate of the compression wood is faster than in the upper part resulting in a renewed horizontal growth. The actuating and load-carrying function of the compression wood is addressed, on the basis of its special ultrastructure and shape of the tracheids. As a first step, a quantitative model is developed to predict the difference of moisture-induced expansion and axial stiffness between normal wood and compression wood. The model is based on a state space approach using concentric cylinders with anisotropic helical structure for each cell-wall layer, whose hygroelastic properties are in turn determined by a self-consistent concentric cylinder assemblage of the constituent wood polymers. The predicted properties compare well with experimental results found in the literature. Significant differences in both stiffness and hygroexpansion are found for normal and compression wood, primarily due to the large difference in microfibril angle and lignin content. On the basis of these numerical results, some functional arguments for the reason of high microfibril angle, high lignin content and cylindrical structure of compression wood tracheids are supported.

  • 4.
    Rubino, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Akhtar, Sultan
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Melin, Petter
    Dept of Microbiology, Swedish University of Agricultural Sciences, Uppsala.
    Searle, Andrew
    Gatan Inc, Abingdon Oxon, UK.
    Spellward, Paul
    Gatan Inc, Abingdon Oxon, UK.
    Leifer, Klaus
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    A site-specific focused-ion-beam lift-out method for cryo Transmission Electron Microscopy2012In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 180, no 3, p. 572-576Article in journal (Refereed)
    Abstract [en]

    The focused-ion-beam (FIB) is the method of choice for site-specific sample preparation for Transmission Electron Microscopy (TEM) in material sciences. A lamella can be physically lifted out from a specific region of a bulk specimen with submicrometer precision and thinned to electron transparency for high-resolution imaging in the TEM. The possibility to use this tool in life sciences applications has been limited by the lack of lift-out capabilities at the cryogenic temperatures often needed for biological samples. Conventional cryo-TEM sample preparation is mostly based on ultramicrotomy, a procedure that is not site-specific and known to produce artifacts. Here we demonstrate how a cooled nanomanipulator and a custom-built transfer station can be used to achieve cryo-preparation of TEM samples with the FIB, enabling high-resolution investigation of frozen-hydrated specimens in the TEM.

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