Search Results

You searched for all publications:

with publication states 'Published (Approved)'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

12,029 items found (0 items not approved), displaying 11 to 20.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
	Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images Nina Vyas , Stephan Kunne , Thomas M. Fish , Ian M. Dobbie , Maria Harkiolaki , Perrine Paul-Gilloteaux Star Protocols 2 DOI: 10.1016/j.xpro.2021.100529 Open Access Show Abstract ▼ Abstract: Correlation of 3D images acquired on different microscopes can be a daunting prospect even for experienced users. This protocol describes steps for registration of images from soft X-ray absorption contrast imaging and super-resolution fluorescence imaging of hydrated biological materials at cryogenic temperatures. Although it is developed for data generated at synchrotron beamlines that offer the above combination of microscopies, it is applicable to all analogous imaging systems where the same area of a sample is examined using successive non-destructive imaging techniques.	Jun 2021
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength)	Phosphorylation of the LIR domain of SCOC modulates ATG8 binding affinity and specificity Martina Wirth , Stephane Mouilleron , Wenxin Zhang , Eva Sjøttem , Yakubu Princely Abudu , Ashish Jain , Hallvard Lauritz Olsvik , Jack-Ansgar Bruun , Minoo Razi , Harold B. J. Jefferies , Rebecca Lee , Dhira Joshi , Nicola O'Reilly , Terje Johansen , Sharon A. Tooze Journal Of Molecular Biology 433 DOI: 10.1016/j.jmb.2021.166987 Diamond Proposal Number(s): [9826] Open Access Show Abstract ▼ Abstract: Autophagy is a highly conserved degradative pathway, essential for cellular homeostasis and implicated in diseases including cancer and neurodegeneration. Autophagy-related 8 (ATG8) proteins play a central role in autophagosome formation and selective delivery of cytoplasmic cargo to lysosomes by recruiting autophagy adaptors and receptors. The LC3-interacting region (LIR) docking site (LDS) of ATG8 proteins binds to LIR motifs present in autophagy adaptors and receptors. LIR-ATG8 interactions can be highly selective for specific mammalian ATG8 family members (LC3A-C, GABARAP, and GABARAPL1-2) and how this specificity is generated and regulated is incompletely understood. We have identified a LIR motif in the Golgi protein SCOC (short coiled-coil protein) exhibiting strong binding to GABARAP, GABARAPL1, LC3A and LC3C. The residues within and surrounding the core LIR motif of the SCOC LIR domain were phosphorylated by autophagy-related kinases (ULK1-3, TBK1) increasing specifically LC3 family binding. More distant flanking residues also contributed to ATG8 binding. Loss of these residues was compensated by phosphorylation of serine residues immediately adjacent to the core LIR motif, indicating that the interactions of the flanking LIR regions with the LDS are important and highly dynamic. Our comprehensive structural, biophysical and biochemical analyses support and provide novel mechanistic insights into how phosphorylation of LIR domain residues regulates the affinity and binding specificity of ATG8 proteins towards autophagy adaptors and receptors.	Jun 2021
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	The development of highly potent and selective small molecule correctors of Z α1-antitrypsin misfolding John Liddle , Andrew C. Pearce , Christopher Arico-Muendel , Svetlana Belyanskaya , Andrew Brewster , Murray Brown , Chun-Wa Chung , Alexis Denis , Nerina Dodic , Anthony Dossang , Peter Eddershaw , Diana Klimaszewska , Imran Haq , Duncan S. Holmes , Alistair Jagger , Toral Jakhria , Emilie Jigorel , Ken Lind , Jeff Messer , Margaret Neu , Allison Olszewski , Riccardo Ronzoni , James Rowedder , Martin Rüdiger , Steve Skinner , Kathrine J. Smith , Lionel Trottet , Iain Uings , Zhengrong Zhu , James A. Irving , David A. Lomas Bioorganic & Medicinal Chemistry Letters 41 DOI: 10.1016/j.bmcl.2021.127973 Diamond Proposal Number(s): [23853, 17201] Show Abstract ▼ Abstract: α1-antitrypsin deficiency is characterised by the misfolding and intracellular polymerisation of mutant α1-antitrypsin protein within the endoplasmic reticulum (ER) of hepatocytes. Small molecules that bind and stabilise Z α1-antitrypsin were identified via a DNA-encoded library screen. A subsequent structure based optimisation led to a series of highly potent, selective and cellular active α1-antitrypsin correctors.	Jun 2021
I03-Macromolecular Crystallography	Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme Joao Ramos , Valerie Laux , Michael Haertlein , Elisabetta Boeri Erba , Katherine E. Mcauley , V. Trevor Forsyth , Estelle Mossou , Sine Larsen , Annette E. Langkilde Iucrj 8 DOI: 10.1107/S2052252521001299 Diamond Proposal Number(s): [24717] Open Access Show Abstract ▼ Abstract: This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97–Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.	May 2021
I07-Surface & interface diffraction	Heads or tails: Nanostructure and molecular orientations in organised erucamide surface layers Dajana Gubala , Laura Fox , Robert Harniman , Hadeel Hussain , Eric Robles , Meng Chen , Wuge H. Briscoe Journal Of Colloid And Interface Science 590, 506 - 517 DOI: 10.1016/j.jcis.2021.01.087 Diamond Proposal Number(s): [22176] Show Abstract ▼ Abstract: Hypothesis: Despite the widespread industrial usage of erucamide as a slip additive to modify polymer surface properties, a controversy appears to have persisted regarding the nanostructure of erucamide surface layers, particularly the molecular orientation at the outermost layer. The erucamide nanostructure and molecular orientation, along with its surface coverage, hydrophobicity, and adhesive response, can be tuned by simply varying the erucamide concentration in the solution from which the spin coated layer is prepared. Experiments: Synchrotron X-ray reflectivity (XRR) allowed a comprehensive characterisation of the out-of-plane structural parameters (e.g. molecular packing and thickness) of the erucamide layers prepared via spin coating from nonaqueous solution on silica. Complementary Atomic Force Microscopy (AFM) imaging with high lateral resolution revealed localised in-plane structures. Contact angle measurements provided information on the wettability of erucamide-coated surfaces. Peak Force Quantitative Nanomechanical Mapping (QNM) allowed a correlation between the erucamide nanostructure with the surface nanomechanical properties (i.e. adhesive response). Findings: Our results reveal erucamide surface nanostructures on silica as patchy monolayers, isolated circular bilayers/rounded rectangle-like aggregates and overlapping plate-like multilayers as the erucamide concentration in the spin coating solution was varied. In all the cases, XRR and AFM results were consistent with the picture that the erucamide tails were oriented outwards. The QNM adhesion force mapping of all the observed morphologies also supported this molecular orientation at the outermost erucamide monolayer. The wettability study further confirmed this conclusion with the observed increase in the surface hydrophobicity and coverage upon increasing erucamide concentration, with the macroscopic water contact angle θ = 92.9° ± 2.9° at the highest erucamide concentration of 2 wt%.	May 2021
I12-JEEP: Joint Engineering, Environmental and Processing	Observation of microstructure evolution during inertia friction welding using in-situ synchrotron X-ray diffraction Matthew Rowson , Chris J. Bennett , Mohammed Azeem , Oxana Magdysyuk , James Rouse , Ryan Lye , Joshua Davies , Simon Bray , Peter D. Lee Journal Of Synchrotron Radiation 28 DOI: 10.1107/S1600577521001569 Diamond Proposal Number(s): [19235] Open Access Show Abstract ▼ Abstract: The widespread use and development of inertia friction welding is currently restricted by an incomplete understanding of the deformation mechanisms and microstructure evolution during the process. Understanding phase transformations and lattice strains during inertia friction welding is essential for the development of robust numerical models capable of determining optimized process parameters and reducing the requirement for costly experimental trials. A unique compact rig has been designed and used in-situ with a high-speed synchrotron X-ray diffraction instrument to investigate the microstructure evolution during inertia friction welding of a high-carbon steel (BS1407). At the contact interface, the transformation from ferrite to austenite was captured in great detail, allowing for analysis of the phase fractions during the process. Measurement of the thermal response of the weld reveals that the transformation to austenite occurs 230 °C below the equilibrium start temperature of 725 °C. It is concluded that the localization of large strains around the contact interface produced as the specimens deform assists this non-equilibrium phase transformation.	May 2021
I23-Long wavelength MX	X-ray tomographic reconstruction and segmentation pipeline for the long-wavelength macromolecular crystallography beamline at Diamond Light Source Daniil Kazantsev , Ramona Duman , Armin Wagner , Vitaliy Mykhaylyk , Kazimir Wanelik , Mark Basham , Nicola Wadeson Journal Of Synchrotron Radiation 28 DOI: 10.1107/S1600577521003453 Open Access Show Abstract ▼ Abstract: In this paper a practical solution for the reconstruction and segmentation of low-contrast X-ray tomographic data of protein crystals from the long-wavelength macromolecular crystallography beamline I23 at Diamond Light Source is provided. The resulting segmented data will provide the path lengths through both diffracting and non-diffracting materials as basis for analytical absorption corrections for X-ray diffraction data taken in the same sample environment ahead of the tomography experiment. X-ray tomography data from protein crystals can be difficult to analyse due to very low or absent contrast between the different materials: the crystal, the sample holder and the surrounding mother liquor. The proposed data processing pipeline consists of two major sequential operations: model-based iterative reconstruction to improve contrast and minimize the influence of noise and artefacts, followed by segmentation. The segmentation aims to partition the reconstructed data into four phases: the crystal, mother liquor, loop and vacuum. In this study three different semi-automated segmentation methods are experimented with by using Gaussian mixture models, geodesic distance thresholding and a novel morphological method, RegionGrow, implemented specifically for the task. The complete reconstruction-segmentation pipeline is integrated into the MPI-based data analysis and reconstruction framework Savu, which is used to reduce computation time through parallelization across a computing cluster and makes the developed methods easily accessible.	May 2021
I15-Extreme Conditions	In situ poling X-ray diffraction studies of lead-free BiFeO3-SrTiO3 ceramics Zhilun Lu , Ge Wang , Linhao Li , Yuhe Huang , Antonio Feteira , Weichao Bao , Annette K. Kleppe , Fangfang Xu , Dawei Wang , Ian M. Reaney Materials Today Physics 71 DOI: 10.1016/j.mtphys.2021.100426 Diamond Proposal Number(s): [21714] Open Access Show Abstract ▼ Abstract: The origin of the large electrostrain in BiFeO3-BaTiO3 (BF-BT) ceramics is controversial and has been attributed to either a field-induced transition to a long-range ferroelectric (FE) state or to multi-symmetry, polar nanoregions within a pseudocubic matrix whose vectors approximately align with the direction of the applied field. The (1-x)BiFeO3-xSrTiO3 (BF-xST) solid solution is structurally and microstructurally similar to BF-BT and provides a further case study to assess the origin of electrostrain. In BF-xST, electrostrain is optimised at x = 0.4 (0.15%) which zero field, room temperature full-pattern X-ray diffraction (XRD) Rietveld refinement and scanning/transmission electron microscopy suggest is composed of 15% rhombohedral (R) cores, surrounded by 85% pseudocubic (PC) shells. In-situ poling synchrotron XRD revealed that all peaks remained singlet and exhibited no change in full width half maximum up to 100 kV cm-1, confirming the absence of long-range FE order and the retention of short-range polar order, despite the large applied field. Strain anisotropy (calculated from individual peaks) of ε220 > ε111 > ε200 and the associated strain orientation distribution however, indicate the existence of local orthorhombic (O), rhombohedral (R) and tetragonal (T) symmetries. The data therefore imply the existence under poling of multi-symmetry polar nanoregions in BF-0.4ST rather than a long FE phase, supporting the model described by Wang and co-workers (2019) for BF-BT compositions.	May 2021
I03-Macromolecular Crystallography	SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site Mark D. Allen , Stefan M. V. Freund , Mark Bycroft , Giovanna Zinzalla Communications Biology 4 DOI: 10.1038/s42003-021-02050-z Open Access Show Abstract ▼ Abstract: SWI/SNF (BAF) chromatin remodelling complexes are key regulators of gene expression programs, and attractive drug targets for cancer therapies. Here we show that the N-terminus of the BAF155/SMARCC1 subunit contains a putative DNA-binding MarR-like domain, a chromodomain and a BRCT domain that are interconnected to each other to form a distinct module. In this structure the chromodomain makes interdomain interactions and has lost its canonical function to bind to methylated lysines. The structure provides new insights into the missense mutations that target this module in cancer. This study also reveals two adjacent, highly-conserved pockets in a cleft between the domains that form a potential binding site, which can be targeted with small molecules, offering a new strategy to target SWI/SNF complexes.	May 2021
I15-Extreme Conditions	Solidification microstructure and residual stress correlations in direct energy deposited type 316L stainless steel Da Guo , Kun Yan , Mark D. Callaghan , Dominik Daisenberger , Mark Chatterton , Jiadong Chen , Andrew Wisbey , Wajira Mirihanage Materials & Design DOI: 10.1016/j.matdes.2021.109782 Diamond Proposal Number(s): [20605] Open Access Show Abstract ▼ Abstract: Localized fluctuation in residual stress distribution for direct energy deposited 316L stainless steel thin plate was revealed through high-energy synchrotron X-ray diffraction. The macroscopic residual stress levels are changed steadily across the article according to the characteristic cooling rates, as implied by the measured dendrite arm lengths. Localized fluctuations of residual stress in the length scale, between 500 to 600 µm, coincides well with the morphological variations of the solidification microstructure that formed during direct energy deposition. Computations indicate a greater propensity for related mesoscopic thermal gradient fluctuations along the solidification front of the moving melt pool. Novel perspectives on residual stress across multiple length-scales and its relevance to the formation of solidification microstructure in metal additive manufacturing is analysed by considering the experimental results.	May 2021

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User