I12-JEEP: Joint Engineering, Environmental and Processing
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A.
Koko
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S.
Singh
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S.
Barhli
,
T.
Connolley
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N. T.
Vo
,
T.
Wigger
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D.
Liu
,
Y.
Fu
,
J.
Réthoré
,
J.
Lechambre
,
J.-Y.
Buffiere
,
T. J.
Marrow
Diamond Proposal Number(s):
[12585]
Open Access
Abstract: The propagation rate of a fatigue crack in a nodular cast iron, loaded in cyclic tension, has been studied in situ by X-ray computed tomography and digital volume correlation. The semi-elliptical crack initiated from an asymmetric corner notch and evolved to a semi-circular shape, initially with a higher growth rate towards one edge of the notch before the propagation rate along the crack front became essentially independent of po-sition. The phase congruency of the displacement field was used to measure the crack shape. The three-dimensional stress intensity factors were calculated via a linear elastic finite element model that used the displacement fields around the crack front as the boundary conditions. Closure of the crack tip region was observed. The cyclic change in the local mode I opening of the crack tip determined the local fatigue crack propaga-tion rate along the crack front.
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May 2023
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I07-Surface & interface diffraction
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Diamond Proposal Number(s):
[22995]
Open Access
Abstract: Hypothesis: The attractive interaction between a cationic surfactant monolayer at the air–water interface and vesicles, incorporating anionic lipids, is sufficient to drive the adsorption and deformation of the vesicles. Osmotic rupture of the vesicles produces a continuous lipid bilayer beneath the monolayer. Experimental: Specular neutron reflectivity has been measured from the surface of a purpose-built laminar flow trough, which allows for rapid adsorption of vesicles, the changes in salt concentration required for osmotic rupture of the adsorbed vesicles into a bilayer, and for neutron contrast variation of the sub-phase without disturbing the monolayer. Findings: The neutron reflectivity profiles measured after vesicle addition are consistent with the adsorption and flattening of the vesicles beneath the monolayer. An increase in the buffer salt concentration results in further flattening and fusion of the adsorbed vesicles, which are ruptured by a subsequent decrease in the salt concentration. This process results in a continuous, high coverage, bilayer suspended 11 Å beneath the monolayer. As the bilayer is not constrained by a solid substrate, this new mimetic is well-suited to studying the structure of lipid bilayers that include transmembrane proteins.
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Mar 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[18548, 25402]
Open Access
Abstract: The liver isoform of pyruvate kinase (PKL) has gained interest due to its potential capacity to regulate fatty acid synthesis involved in the progression of non-alcoholic fatty liver disease (NAFLD). Here we describe a novel series of PKL modulators that can either activate or inhibit the enzyme allosterically, from a cryptic site at the interface of two protomers in the tetrameric enzyme. Starting from urolithin D, we designed and synthesised 42 new compounds. The effect of these compounds on PKL enzymatic activity was assessed after incubation with cell lysates obtained from a liver cell line. Pronounced activation of PKL activity, up to 3.8-fold, was observed for several compounds at 10 μM, while other compounds were prominent PKL inhibitors reducing its activity to 81% at best. A structure-activity relationship identified linear-shaped sulfone-sulfonamides as activators and non-linear compounds as inhibitors. Crystal structures revealed the conformations of these modulators, which were used as a reference for designing new modulators.
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Mar 2023
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I02-Macromolecular Crystallography
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Christos
Stergiou
,
Rhys
Williams
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Jennifer R.
Fleming
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Vasiliki
Zouvelou
,
Elpinickie
Ninou
,
Francesca
Andreetta
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Elena
Rinaldi
,
Ornella
Simoncini
,
Renato
Mantegazza
,
Julius
Bogomolovas
,
John
Tzartos
,
Siegfried
Labeit
,
Olga
Mayans
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Socrates
Tzartos
Open Access
Abstract: Myasthenia gravis (MG) is an autoimmune disease caused by antibodies targeting the neuromuscular junction (NJ) of skeletal muscles. The major MG autoantigen is nicotinic acetylcholine receptor. Other autoantigens at the NJ include MuSK, LRP4 and agrin. Autoantibodies to the intra-sarcomeric striated muscle-specific gigantic protein titin, although not directed to the NJ, are invaluable biomarkers for thymoma and MG disease severity. Thymus and thymoma are critical in MG mechanisms and management. Titin autoantibodies bind to a 30 KDa titin segment, the main immunogenic region (MIR), consisting of an Ig-FnIII-FnIII 3-domain tandem, termed I109-I111. In this work, we further resolved the localization of titin epitope(s) to facilitate the development of more specific anti-titin diagnostics. For this, we expressed protein samples corresponding to 8 MIR and non-MIR titin fragments and tested 77 anti-titin sera for antibody binding using ELISA, competition experiments and Western blots. All anti-MIR antibodies were bound exclusively to the central MIR domain, I110, and to its containing titin segments. Most antibodies were bound also to SDS-denatured I110 on Western blots, suggesting that their epitope(s) are non-conformational. No significant difference was observed between thymoma and non-thymoma patients or between early- and late-onset MG. In addition, atomic 3D-structures of the MIR and its subcomponents were elucidated using X-ray crystallography. These immunological and structural data will allow further studies into the atomic determinants underlying titin-based autoimmunity, improved diagnostics and how to eventually treat titin autoimmunity associated co-morbidities.
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Feb 2023
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B21-High Throughput SAXS
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Tobias
Schmidt
,
Adrianna
Dabrowska
,
Joseph A.
Waldron
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Kelly
Hodge
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Grigorios
Koulouras
,
Mads
Gabrielsen
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June
Munro
,
David C.
Tack
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Gemma
Harris
,
Ewan
Mcghee
,
David
Scott
,
Leo m.
Carlin
,
Danny
Huang
,
John
Le quesne
,
Sara
Zanivan
,
Ania
Wilczynska
,
Martin
Bushell
Diamond Proposal Number(s):
[21657]
Open Access
Abstract: Altered eIF4A1 activity promotes translation of highly structured, eIF4A1-dependent oncogene mRNAs at root of oncogenic translational programmes. It remains unclear how these mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate their preferential translation. Here, we show that single-stranded RNA sequence motifs specifically activate eIF4A1 unwinding allowing local RNA structural rearrangement and translation of eIF4A1-dependent mRNAs in cells. Our data demonstrate that eIF4A1-dependent mRNAs contain AG-rich motifs within their 5’UTR which specifically activate eIF4A1 unwinding of local RNA structure to facilitate translation. This mode of eIF4A1 regulation is used by mRNAs encoding components of mTORC-signalling and cell cycle progression, and renders these mRNAs particularly sensitive to eIF4A1-inhibition. Mechanistically, we show that binding of eIF4A1 to AG-rich sequences leads to multimerization of eIF4A1 with eIF4A1 subunits performing distinct enzymatic activities. Our structural data suggest that RNA-binding of multimeric eIF4A1 induces conformational changes in the RNA resulting in an optimal positioning of eIF4A1 proximal to the RNA duplex enabling efficient unwinding. Our data proposes a model in which AG-motifs in the 5’UTR of eIF4A1-dependent mRNAs specifically activate eIF4A1, enabling assembly of the helicase-competent multimeric eIF4A1 complex, and positioning these complexes proximal to stable localised RNA structure allowing ribosomal subunit scanning.
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Feb 2023
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[25427, 23814]
Open Access
Abstract: We describe nNPipe for the automated analysis of morphologically diverse catalyst materials. Automated imaging routines and direct-electron detectors have enabled the collection of large data stacks over a wide range of sample positions at high temporal resolution. Simultaneously, traditional image analysis approaches are slow and hence unsuitable for large data stacks and consequently, researchers have progressively turned towards machine learning and deep learning approaches. Previous studies often detail work on morphologically uniform material systems with clearly discernible features, limited workable image sizes and training data that may be biased due to manual labelling. The nNPipe data-processing method consists of two standalone convolutional neural networks that were exclusively trained on multislice image simulations and enables fast analysis of 2048 × 2048 pixel images. Inference performance compared between idealised and real industrial catalytic samples and insights derived from subsequent data analysis are placed into the context of an automated imaging scenario.
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Feb 2023
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[26476]
Abstract: Two new multicomponent crystalline phases of fenbendazole (FNB), a benzimidazole-based anthelmintic drug, with maleic and oxalic acids have been obtained, and their structural and physicochemical properties carefully investigated. The crystal structures of the solid forms have been determined from powder X-ray diffraction data. The positions of dynamic hydrogen atoms have been further refined via dispersion-corrected density functional theory calculations, which validated the salt nature of the resulting solid forms by demonstrating proton transport from the corresponding acids to the FNB molecule. The in vitro dissolution performance of the solid forms in aqueous media at different pH values, as well as the in vivo anthelmintic efficacy of fenbendazole on the laboratory model of Trichinella spiralis infection in mice have been evaluated and compared to that of the previously reported salt of FNB with p-toluenesulfonic acid. A relationship between the in vitro dissolution characteristics and the in vivo therapeutic action has been revealed and discussed.
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Feb 2023
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Xiaojie
Yu
,
Christian M.
Orr
,
H. T. Claude
Chan
,
Sonya
James
,
Christine A.
Penfold
,
Jinny
Kim
,
Tatyana
Inzhelevskaya
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C. Ian
Mockridge
,
Kerry L.
Cox
,
Jonathan W.
Essex
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Ivo
Tews
,
Martin J.
Glennie
,
Mark S.
Cragg
Abstract: Antibody responses during infection and vaccination typically undergo affinity maturation to achieve high-affinity binding for efficient neutralization of pathogens1,2. Similarly, high affinity is routinely the goal for therapeutic antibody generation. However, in contrast to naturally occurring or direct-targeting therapeutic antibodies, immunomodulatory antibodies, which are designed to modulate receptor signalling, have not been widely examined for their affinity–function relationship. Here we examine three separate immunologically important receptors spanning two receptor superfamilies: CD40, 4-1BB and PD-1. We show that low rather than high affinity delivers greater activity through increased clustering. This approach delivered higher immune cell activation, in vivo T cell expansion and antitumour activity in the case of CD40. Moreover, an inert anti-4-1BB monoclonal antibody was transformed into an agonist. Low-affinity variants of the clinically important antagonistic anti-PD-1 monoclonal antibody nivolumab also mediated more potent signalling and affected T cell activation. These findings reveal a new paradigm for augmenting agonism across diverse receptor families and shed light on the mechanism of antibody-mediated receptor signalling. Such affinity engineering offers a rational, efficient and highly tuneable solution to deliver antibody-mediated receptor activity across a range of potencies suitable for translation to the treatment of human disease.
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Feb 2023
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B18-Core EXAFS
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Yunpeng
Zuo
,
Nikolaos
Antonatos
,
Lukáš
Děkanovský
,
Jan
Luxa
,
Joshua D.
Elliott
,
Diego
Gianolio
,
Jiří
Šturala
,
Fabrizio
Guzzetta
,
Stefanos
Mourdikoudis
,
Jakub
Regner
,
Roman
Málek
,
Zdenek
Sofer
Diamond Proposal Number(s):
[31795]
Abstract: As a fascinating innovative class of effective catalysts
for hydrogen evolution reaction (HER), transition-metal tellurides
have emerged as attractive materials, but they are still suffering
from their intrinsic activity for practical applications. Defect
engineering constitutes a promising strategy to optimize the
electronic configuration of the catalyst and further improve the
HER activity. Herein, we present the successful fabrication of
PdTe2-based catalysts with three different types of vacancies (dPdTex), including single Pd, Te defect site, and double Te defect
sites, by using a two-step method. The obtained d-PdTex
demonstrated a remarkable HER activity with an overpotential of
76 mV at 10 mA cm−2 without iR compensation, which is far lower
than that of bulk PdTe2 (259 mV). The procedure followed in this
work may be extended to generate defect sites in a range of
different two-dimensional materials, thus further expanding their potential application fields.
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Feb 2023
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B16-Test Beamline
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Open Access
Abstract: Alanine pellets with a nominal thickness of 0.5 mm and diameter of 5 mm were irradiated with monoenergetic x-rays at the Diamond Light Source synchrotron, to quantify their response in the 8 to 20 keV range relative to 60Co radiation. The absorbed dose to graphite was measured with a small portable graphite calorimeter, and the DOSRZnrc code in the EGSnrc Monte Carlo package was used to calculate conversion factors between the measured dose to graphite and the absorbed dose to water delivered to the alanine pellets. GafChromic EBT3 films were used to measure the beam profile for modelling in the MC simulations. The relative responses measured in this energy range were found to range from 0.616 to 0.643, with a combined relative expanded uncertainty of 3.4% to 3.5% (k = 2), where the majority of the uncertainty originated from the uncertainty in the alanine readout, due to the small size of the pellets used. The measured values were in good agreement with previously published data in the overlapping region of x-ray energies, while this work extended the dataset to lower energies. By measuring the response to monoenergetic x-rays, the response to a more complex broad-spectrum x-ray source can be inferred if the spectrum is known, meaning that this work supports the establishment of alanine as a secondary standard dosimeter for low-energy x-ray sources.
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Feb 2023
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