Three-dimensional mapping of a deformation field inside a nanocrystal

Coherent X-ray diffraction imaging is a rapidly advancing form of microscopy: diffraction patterns, measured using the latest third-generation synchrotron radiation sources, can be inverted to obtain full three-dimensional images of the interior density within nanocrystals. Diffraction from an ideal crystal lattice results in an identical copy of this continuous diffraction pattern at every Bragg peak. This symmetry is broken by the presence of strain fields, which arise from the epitaxial contact forces that are inevitable whenever nanocrystals are prepared on a substrate. When strain is present, the diffraction copies at different Bragg peaks are no longer identical and contain additional information, appearing as broken local inversion symmetry about each Bragg point. Here we show that one such pattern can nevertheless be inverted to obtain a 'complex' crystal density, whose phase encodes a projection of the lattice deformation. A lead nanocrystal was crystallized in ultrahigh vacuum from a droplet on a silica substrate and equilibrated close to its melting point. A three-dimensional image of the density, obtained by inversion of the coherent X-ray diffraction, shows the expected facetted morphology, but in addition reveals a real-space phase that is consistent with the three-dimensional evolution of a deformation field arising from interfacial contact forces. Quantitative three-dimensional imaging of lattice strain on the nanometre scale will have profound consequences for our fundamental understanding of grain interactions and defects in crystalline materials. Our method of measuring and inverting diffraction patterns from nanocrystals represents a vital step towards the ultimate goal of atomic resolution single-molecule imaging that is a prominent justification for development of X-ray free-electron lasers.     

The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates

Ataxia oculomotor apraxia-1 (AOA1) is a neurological disorder caused by mutations in the gene (APTX) encoding aprataxin. Aprataxin is a member of the histidine triad (HIT) family of nucleotide hydrolases and transferases, and inactivating mutations are largely confined to this HIT domain. Aprataxin associates with the DNA repair proteins XRCC1 and XRCC4, which are partners of DNA ligase III and ligase IV, respectively, suggestive of a role in DNA repair. Consistent with this, APTX-defective cell lines are sensitive to agents that cause single-strand breaks and exhibit an increased incidence of induced chromosomal aberrations. It is not, however, known whether aprataxin has a direct or indirect role in DNA repair, or what the physiological substrate of aprataxin might be. Here we show, using purified aprataxin protein and extracts derived from either APTX-defective chicken DT40 cells or Aptx-/- mouse primary neural cells, that aprataxin resolves abortive DNA ligation intermediates. Specifically, aprataxin catalyses the nucleophilic release of adenylate groups covalently linked to 5'-phosphate termini at single-strand nicks and gaps, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. These data indicate that neurological disorders associated with APTX mutations may be caused by the gradual accumulation of unrepaired DNA strand breaks resulting from abortive DNA ligation events.     

A sensing array of radically coupled genetic 'biopixels'

Although there has been considerable progress in the development of engineering principles for synthetic biology, a substantial challenge is the construction of robust circuits in a noisy cellular environment. Such an environment leads to considerable intercellular variability in circuit behaviour, which can hinder functionality at the colony level. Here we engineer the synchronization of thousands of oscillating colony 'biopixels' over centimetre-length scales through the use of synergistic intercellular coupling involving quorum sensing within a colony and gas-phase redox signalling between colonies. We use this platform to construct a liquid crystal display (LCD)-like macroscopic clock that can be used to sense arsenic via modulation of the oscillatory period. Given the repertoire of sensing capabilities of bacteria such as Escherichia coli, the ability to coordinate their behaviour over large length scales sets the stage for the construction of low cost genetic biosensors that are capable of detecting heavy metals and pathogens in the field.     

Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand

In a variety of cells, the Ca2+ signalling process is mediated by the endoplasmic-reticulum-membrane-associated Ca2+ release channel, inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R). Being ubiquitous and present in organisms ranging from humans to Caenorhabditis elegans, InsP3R has a vital role in the control of cellular and physiological processes as diverse as cell division, cell proliferation, apoptosis, fertilization, development, behaviour, memory and learning. Mouse type I InsP3R (InsP3R1), found in high abundance in cerebellar Purkinje cells, is a polypeptide with three major functionally distinct regions: the amino-terminal InsP3-binding region, the central modulatory region and the carboxy-terminal channel region. Here we present a 2.2-A crystal structure of the InsP3-binding core of mouse InsP3R1 in complex with InsP3. The asymmetric, boomerang-like structure consists of an N-terminal beta-trefoil domain and a C-terminal alpha-helical domain containing an 'armadillo repeat'-like fold. The cleft formed by the two domains exposes a cluster of arginine and lysine residues that coordinate the three phosphoryl groups of InsP3. Putative Ca2+-binding sites are identified in two separate locations within the InsP3-binding core.