B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[15393]
Open Access
Abstract: Glycosaminoglycans (GAGs)/proteoglycans (PGs) play a pivotal role in the metastasis of inflammatory breast cancer (IBC). They represent biomarkers and targets in diagnosis and treatment of different cancers including breast cancer. Thus, GAGs/PGs could represent potential prognostic/diagnostic biomarkers for IBC. In the present study, non-IBC MDA-MB-231, MCF7, SKBR3 cells and IBC SUM149 cells, as well as their GAG secretome were analyzed. The latter was measured in toto as dried drops with high-throughput (HT) Fourier Transform InfraRed (FTIR) spectroscopy and imaging. FTIR imaging was also employed to investigate single whole breast cancer cells while synchrotron-FTIR microspectroscopy was used to specifically target their cytoplasms. Data were analyzed by hierarchical cluster analysis and principal components analysis. Results obtained from HT-FTIR analysis of GAG drops showed that the inter-group variability enabled us to delineate between cell types in the GAG absorption range 1350–800 cm−1. Similar results were obtained for FTIR imaging of GAG extracts and fixed single whole cells. Synchrotron-FTIR data from cytoplasms allowed discrimination between non-IBC and IBC. Thus, by using GAG specific region, not only different breast cancer cell lines could be differentiated, but also non-IBC from IBC cells. This could be a potential diagnostic spectral marker for IBC detection useful for patient management.
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Sep 2020
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[17737, 20810, 20855]
Abstract: We report the use of a surfactant molecule during the epitaxy of graphene on SiC(0001) that leads to the growth in an unconventional orientation, namely
R
0
°
rotation with respect to the SiC lattice. It yields a very high-quality single-layer graphene with a uniform orientation with respect to the substrate, on the wafer scale. We find an increased quality and homogeneity compared to the approach based on the use of a preoriented template to induce the unconventional orientation. Using spot profile analysis low-energy electron diffraction, angle-resolved photoelectron spectroscopy, and the normal incidence x-ray standing wave technique, we assess the crystalline quality and coverage of the graphene layer. Combined with the presence of a covalently bound graphene layer in the conventional orientation underneath, our surfactant-mediated growth offers an ideal platform to prepare epitaxial twisted bilayer graphene via intercalation.
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Sep 2020
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B21-High Throughput SAXS
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[16258]
Open Access
Abstract: Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin’s Gly76. Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD+. Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD+ bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.
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Sep 2020
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Yanchun
Peng
,
Alexander J.
Mentzer
,
Guihai
Liu
,
Xuan
Yao
,
Zixi
Yin
,
Danning
Dong
,
Wanwisa
Dejnirattisai
,
Timothy
Rostron
,
Piyada
Supasa
,
Chang
Liu
,
César
López-camacho
,
Jose
Slon-campos
,
Yuguang
Zhao
,
David I.
Stuart
,
Guido C.
Paesen
,
Jonathan M.
Grimes
,
Alfred A.
Antson
,
Oliver W.
Bayfield
,
Dorothy E. D. P.
Hawkins
,
De-sheng
Ker
,
Beibei
Wang
,
Lance
Turtle
,
Krishanthi
Subramaniam
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Paul
Thomson
,
Ping
Zhang
,
Christina
Dold
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Jeremy
Ratcliff
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Peter
Simmonds
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Thushan
De Silva
,
Paul
Sopp
,
Dannielle
Wellington
,
Ushani
Rajapaksa
,
Yi-ling
Chen
,
Mariolina
Salio
,
Giorgio
Napolitani
,
Wayne
Paes
,
Persephone
Borrow
,
Benedikt M.
Kessler
,
Jeremy W.
Fry
,
Nikolai F.
Schwabe
,
Malcolm G.
Semple
,
J. Kenneth
Baillie
,
Shona C.
Moore
,
Peter J. M.
Openshaw
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M. Azim
Ansari
,
Susanna
Dunachie
,
Eleanor
Barnes
,
John
Frater
,
Georgina
Kerr
,
Oliver
Gould
,
Teresa
Lockett
,
Robert
Levin
,
Yonghong
Zhang
,
Ronghua
Jing
,
Ling-pei
Ho
,
Richard J.
Cornall
,
Christopher P.
Conlon
,
Paul
Klenerman
,
Gavin R.
Screaton
,
Juthathip
Mongkolsapaya
,
Andrew
Mcmichael
,
Julian C.
Knight
,
Graham
Ogg
,
Tao
Dong
Open Access
Abstract: The development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and therapeutics will depend on understanding viral immunity. We studied T cell memory in 42 patients following recovery from COVID-19 (28 with mild disease and 14 with severe disease) and 16 unexposed donors, using interferon-γ-based assays with peptides spanning SARS-CoV-2 except ORF1. The breadth and magnitude of T cell responses were significantly higher in severe as compared with mild cases. Total and spike-specific T cell responses correlated with spike-specific antibody responses. We identified 41 peptides containing CD4+ and/or CD8+ epitopes, including six immunodominant regions. Six optimized CD8+ epitopes were defined, with peptide–MHC pentamer-positive cells displaying the central and effector memory phenotype. In mild cases, higher proportions of SARS-CoV-2-specific CD8+ T cells were observed. The identification of T cell responses associated with milder disease will support an understanding of protective immunity and highlights the potential of including non-spike proteins within future COVID-19 vaccine design.
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Sep 2020
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B18-Core EXAFS
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Diamond Proposal Number(s):
[14239]
Open Access
Abstract: Materials that display strong capabilities for lithium insertion without significant change in unit cell size on cycling are of considerable importance for electrochemical applications. Here, we present V2O3(SO4)2 as a host for lithium-ion batteries. Electrochemically, 2.0 Li+ ions can be inserted, giving Li2V2O3(SO4)2 with an oxidation state of V4+, as determined by X-ray absorption spectroscopy. The capacity of V2O3(SO4)2 can be increased from 157 mA h g−1 to 313 mA h g−1 with the insertion of two additional Li+ ions which would drastically improve the energy density of this material, but this would be over a wider potential range. Chemical lithiation using n-butyllithium was performed and characterisation using a range of techniques showed that a composition of Li4V2O3(SO4)2 can be obtained with an oxidation state of V3+. Structural studies of the lithiated materials by X-ray diffraction showed that up to 4.0 Li+ ions can be inserted into V2O3(SO4)2 whilst maintaining its framework structure.
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Sep 2020
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Open Access
Abstract: Hard X-ray nanotomography enables 3D investigations of a wide range of samples with high resolution (<100 nm) with both synchrotron-based and laboratory-based setups. However, the advantage of synchrotron-based setups is the high flux, enabling time resolution, which cannot be achieved at laboratory sources. Here, the nanotomography setup at the imaging beamline P05 at PETRA III is presented, which offers high time resolution not only in absorption but for the first time also in Zernike phase contrast. Two test samples are used to evaluate the image quality in both contrast modalities based on the quantitative analysis of contrast-to-noise ratio (CNR) and spatial resolution. High-quality scans can be recorded in 15 min and fast scans down to 3 min are also possible without significant loss of image quality. At scan times well below 3 min, the CNR values decrease significantly and classical image-filtering techniques reach their limitation. A machine-learning approach shows promising results, enabling acquisition of a full tomography in only 6 s. Overall, the transmission X-ray microscopy instrument offers high temporal resolution in absorption and Zernike phase contrast, enabling in situ experiments at the beamline.
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Sep 2020
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[18039]
Abstract: Cu2O is an attractive photocathode for important renewable energy reactions such as water splitting and CO2 reduction. Electrodeposition is commonly used to deposit Cu2O films on conductive substrates due to its simplicity and consistency. However, structural descriptors, linking electrodeposition parameters, film structure and the catalytic properties are elusive. A variety of Cu2O films reported by many research groups would often display vastly different electronic properties and catalytic activity, while appear indistinguishable under common characterisation tools. In this work, we take a systematic look into electrochemically deposited Cu2O and investigate the impact of deposition parameters towards the bulk and surface chemistry of the deposited film. Specifically, we employ high resolution XANES for thorough quantitative analysis of the Cu2O films, alongside more common characterisation methods like XRD, SEM and Raman spectroscopy. Photoelectrochemical (PEC) studies reveal an unexpected trend, where the highest PEC activity appears to correlate with the amount of Cu2+ content. Other factors which also affect the PEC activity and stability are film thickness and crystallite grain size. Our study shows that the use of high resolution XANES, though not perfect due to possible self-absorption issue, is apt for extracting compositional descriptor in concentrated thin film samples from the pre-edge energy position analysis. This descriptor can serve as a guide for future development of more active Cu2O based films for wide range of PEC processes as well as for solar cell applications.
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Sep 2020
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[2257]
Open Access
Abstract: The use of silica as a lithium‐ion battery anode material requires a pretreatment step to induce electrochemical activity. The partially reversible electrochemical reduction reaction between silica and lithium has been postulated to produce silicon, which can subsequently reversibly react with lithium, providing stable capacities higher than graphite materials. Up to now, the electrochemical reduction pathway and the nature of the products were unknown, thereby hampering the design, optimization, and wider uptake of silica‐based anodes. Here, the electrochemical reduction pathway is uncovered and, for the first time, elemental silicon is identified as a reduction product. These insights, gleaned from analysis of the current response and capacity increase during reduction, conclusively demonstrated that silica must be reduced to introduce reversible capacity and the highest capacities of 600 mAh g−1 are achieved by using a constant load discharge at elevated temperature. Characterization via total scattering X‐ray pair distribution function analysis reveal the reduction products are amorphous in nature, highlighting the need for local structural methods to uncover vital information often inaccessible by traditional diffraction. These insights contribute toward understanding the electrochemical reduction of silica and can inform the development of pretreatment processes to enable their incorporation into next‐generation lithium‐ion batteries.
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Sep 2020
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I15-Extreme Conditions
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Abstract: The occurrence and characterization of a new member of the dundasite group are reported. Grguricite, ideally CaCr2(CO3)2(OH)4·4H2O, is the Cr-analogue of alumohydrocalcite, CaAl2(CO3)2(OH)4·4H2O and occurs as lilac crusts of very fine-grained crystalline aggregates in
the Pb-Ba-V mineralization found at the Adeghoual Mine, Mibladen, Morocco (32°46′0′′ N, 4°37′59′′ W). The identification was based upon a close match with the X-ray powder diffraction data for alumohydrocalcite, the confirmation of anion components identified by Raman spectroscopy and the cation composition determined by electron-probe microanalysis. The empirical formula based upon 14 oxygen atoms per formula unit is Ca0.84Pb0.03Cr1.65Al0.39Mg0.02(CO3)2(OH)4·4H2O, with carbonate, hydroxyl and water contents set to those of the alumohydrocalcite stoichiometry. The fine-grained nature of the crystals (c. 0.5 x 0.1 x 5 μm) precluded a single-crystal X-ray study and both density and optical determinations. Grguricite is triclinic with space group P1 ̄. Unit-cell parameters refined from the powder diffraction data are: a = 5.724(2) Å, b = 6.5304(9) Å, c = 14.646(4) Å, α = 81.682(1)°, β = 83.712(2)°, γ = 86.365(2)°, V = 537.8(2) Å3, Z = 2. The five strongest peaks in the powder pattern are [dhkl , I/Imax, (hkl)]: [6.222, 100, (011)], [3.227, 87, (020)], [6.454, 63, (010)], [2.883, 58, (005, 023, 121)], [7.208, 45, (002)]. The mineral is named after Australian geologist Ben Grguric.
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Sep 2020
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Wout
Oosterheert
,
Katerina T.
Xenaki
,
Viviana
Neviani
,
Wouter
Pos
,
Sofia
Doulkeridou
,
Jip
Manshande
,
Nicholas M.
Pearce
,
Loes M. J.
Kroon-batenburg
,
Martin
Lutz
,
Paul M. P.
Van Bergen En Henegouwen
,
Piet
Gros
Diamond Proposal Number(s):
[19800]
Open Access
Abstract: Tetraspanins are eukaryotic membrane proteins that contribute to a variety of signaling processes by organizing partner-receptor molecules in the plasma membrane. How tetraspanins bind and cluster partner receptors into tetraspanin-enriched microdomains is unknown. Here, we present crystal structures of the large extracellular loop of CD9 bound to nanobodies 4C8 and 4E8 and, the cryo-EM structure of 4C8-bound CD9 in complex with its partner EWI-F. CD9–EWI-F displays a tetrameric arrangement with two central EWI-F molecules, dimerized through their ectodomains, and two CD9 molecules, one bound to each EWI-F transmembrane helix through CD9-helices h3 and h4. In the crystal structures, nanobodies 4C8 and 4E8 bind CD9 at loops C and D, which is in agreement with the 4C8 conformation in the CD9–EWI-F complex. The complex varies from nearly twofold symmetric (with the two CD9 copies nearly anti-parallel) to ca. 50° bent arrangements. This flexible arrangement of CD9–EWI-F with potential CD9 homo-dimerization at either end provides a “concatenation model” for forming short linear or circular assemblies, which may explain the occurrence of tetraspanin-enriched microdomains.
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Sep 2020
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