I22-Small angle scattering & Diffraction
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Minghui
Sun
,
Zheng
Dong
,
Liyuan
Wu
,
Haodong
Yao
,
Wenchao
Niu
,
Deting
Xu
,
Ping
Chen
,
Himadri S.
Gupta
,
Yi
Zhang
,
Yuhui
Dong
,
Chunying
Chen
,
Lina
Zhao
Open Access
Abstract: Structural disclosure of biological materials can help our understanding of design disciplines in nature and inspire research for artificial materials. Synchrotron microfocus X-ray diffraction is one of the main techniques for characterizing hierarchically structured biological materials, especially the 3D orientation distribution of their interpenetrating nanofiber networks. However, extraction of 3D fiber orientation from X-ray patterns is still carried out by iterative parametric fitting, with disadvantages of time consumption and demand for expertise and initial parameter estimates. When faced with high-throughput experiments, existing analysis methods cannot meet the real time analysis challenges. In this work, using the assumption that the X-ray illuminated volume is dominated by two groups of nanofibers in a gradient biological composite, a machine-learning based method is proposed for fast and automatic fiber orientation metrics prediction from synchrotron X-ray micro-focused diffraction data. The simulated data were corrupted in the training procedure to guarantee the prediction ability of the trained machine-learning algorithm in real-world experimental data predictions. Label transformation was used to resolve the jump discontinuity problem when predicting angle parameters. The proposed method shows promise for application in the automatic data-processing pipeline for fast analysis of the vast data generated from multiscale diffraction-based tomography characterization of textured biomaterials.
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May 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[20481, 27656]
Open Access
Abstract: We outline techniques for the control and measurement of the nucleation of crystalline material.
SAXS/WAXS XRD measurements are presented that demonstrate the impact of low power,
continuous, non-cavitational ultrasound on the nucleation and crystallisation of a wax; n-eicosane
dissolved in heptane/toluene solvent. A mathematical-physical approach based on rectification of
heat and mass transport by such a low power oscillating pressure field is outlined and it is suggested
that this approach be combined with dissipative particle dynamics (DPD) computational modelling to
develop a predictive method capable of modelling the impact of low power oscillating pressure
fields (acoustics and ultrasonics) on a wide range of nucleating systems. Combining ultrasound pitch
and catch speed of sound measurements with low power harmonically oscillating pressure fields to
monitor and control nucleation presents the prospect of entirely new industrially significant
methods of process control in crystallisation. It also offers new insights into nucleation processes in
general. However, for the acoustic control technique to be applied widely, further theoretical and
modelling work will be necessary since at present, we are unable to predict the precise effect of low
power ultrasound in any given situation.
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May 2023
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B21-High Throughput SAXS
B23-Circular Dichroism
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Philip
Bardelang
,
Ewan J.
Murray
,
Isobel
Blower
,
Sara
Zandomeneghi
,
Alice
Goode
,
Rohanah
Hussain
,
Divya
Kumari
,
Giuliano
Siligardi
,
Katsuaki
Inoue
,
Jeni
Luckett
,
James
Doutch
,
Jonas
Emsley
,
Weng C.
Chan
,
Philip
Hill
,
Paul
Williams
,
Boyan B.
Bonev
Diamond Proposal Number(s):
[5098, 12923, 13185, 13634, 15146]
Open Access
Abstract: Virulence gene expression in the human pathogen, S. aureus is regulated by the agr (accessory gene regulator) quorum sensing (QS) system which is conserved in diverse Gram-positive bacteria. The agr QS signal molecule is an autoinducing peptide (AIP) generated via the initial processing of the AgrD pro-peptide by the transmembrane peptidase AgrB. Since structural information for AgrB and AgrBD interactions are lacking, we used homology modelling and molecular dynamics (MD) annealing to characterise the conformations of AgrB and AgrD in model membranes and in solution. These revealed a six helical transmembrane domain (6TMD) topology for AgrB. In solution, AgrD behaves as a disordered peptide, which binds N-terminally to membranes in the absence and in the presence of AgrB. In silico, membrane complexes of AgrD and dimeric AgrB show non-equivalent AgrB monomers responsible for initial binding and for processing, respectively. By exploiting split luciferase assays in Staphylococcus aureus, we provide experimental evidence that AgrB interacts directly with itself and with AgrD. We confirmed the in vitro formation of an AgrBD complex and AIP production after Western blotting using either membranes from Escherichia coli expressing AgrB or with purified AgrB and T7-tagged AgrD. AgrB and AgrD formed stable complexes in detergent micelles revealed using synchrotron radiation CD (SRCD) and Landau analysis consistent with the enhanced thermal stability of AgrB in the presence of AgrD. Conformational alteration of AgrB following provision of AgrD was observed by small angle X-ray scattering from proteodetergent micelles. An atomistic description of AgrB and AgrD has been obtained together with confirmation of the AgrB 6TMD membrane topology and existence of AgrBD molecular complexes in vitro and in vivo.
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May 2023
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B21-High Throughput SAXS
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Ália
Dos Santos
,
Daniel E.
Rollins
,
Yukti
Hari-Gupta
,
Hannah
Mcarthur
,
Mingxue
Du
,
Sabrina Yong Zi
Ru
,
Kseniia
Pidlisna
,
Ane
Stranger
,
Faeeza
Lorgat
,
Danielle
Lambert
,
Ian
Brown
,
Kevin
Howland
,
Jesse
Aaron
,
Lin
Wang
,
Peter J. I.
Ellis
,
Teng-Leong
Chew
,
Marisa
Martin-Fernandez
,
Alice L. B.
Pyne
,
Christopher P.
Toseland
Diamond Proposal Number(s):
[16207]
Open Access
Abstract: NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.
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May 2023
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B21-High Throughput SAXS
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[31323, 31668]
Open Access
Abstract: The allosteric regulation of biomolecules, such as enzymes, enables them to adapt and alter their conformation to fit specific substrates, expressing different functionalities in response to stimuli. Different stimuli can also trigger synthetic coordination cages to change their shape, size, and nuclearity by reconfiguring the dynamic metal–ligand bonds that hold them together. Here we demonstrate an abiological system consisting of different organic subcomponents and ZnII metal ions, which can respond to simple stimuli in complex ways. A ZnII20L12 dodecahedron transforms to give a larger ZnII30L12 icosidodecahedron through subcomponent exchange, as an aldehyde that forms bidentate ligands is displaced in favor of one that forms tridentate ligands together with a penta-amine subcomponent. In the presence of a chiral template guest, the same system that produced the icosidodecahedron instead gives a ZnII15L6 truncated rhombohedral architecture through enantioselective self-assembly. Under specific crystallization conditions, a guest induces a further reconfiguration of either the ZnII30L12 or ZnII15L6 cages to yield an unprecedented ZnII20L8 pseudo-truncated octahedral structure. The transformation network of these cages shows how large synthetic hosts can undergo structural adaptation through the application of chemical stimuli, opening pathways to broader applications.
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May 2023
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[26855]
Open Access
Abstract: Monkeypox virus (MPXV) is a double-stranded DNA virus from the family Poxviridae, which is endemic in West and Central Africa. Various human outbreaks occurred in the 1980s, resulting from a cessation of smallpox vaccination. Recently, MPXV cases have reemerged in non-endemic nations, and the 2022 outbreak has been declared a public health emergency. Treatment optionsare limited, and many countries lack the infrastructure to provide symptomatic treatments. The development of cost-effective antivirals could ease severe health outcomes. G-quadruplexes have been a target of interest in treating viral infections with different chemicals. In the present work, a genomic-scale mapping of different MPXV isolates highlighted two conserved putative quadruplex-forming sequences MPXV-exclusive in 590 isolates. Subsequently, we assessed the G-quadruplex formation using circular dichroism spectroscopy and solution small-angle X-ray scattering. Furthermore, biochemical assays indicated the ability of MPXV quadruplexes to be recognized by two specific G4-binding partners—Thioflavin T and DHX36. Additionally, our work also suggests that a quadruplex binding small-molecule with previously reported antiviral activity, TMPyP4, interacts with MPXV G-quadruplexes with nanomolar affinity in the presence and absence of DHX36. Finally, cell biology experiments suggests that TMPyP4 treatment substantially reduced gene expression of MPXV proteins. In summary, our work provides insights into the G-quadruplexes from the MPXV genome that can be further exploited to develop therapeutics.
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May 2023
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DL-SAXS-Offline SAXS and Sample Environment Development
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Diamond Proposal Number(s):
[2617]
Abstract: Utilizing carbon dioxide (CO2) to make polycarbonates through the ring-opening copolymerization (ROCOP) of CO2 and epoxides valorizes and recycles CO2 and reduces pollution in polymer manufacturing. Recent developments in catalysis provide access to polycarbonates with well-defined structures and allow for copolymerization with biomass-derived monomers; however, the resulting material properties are under-investigated. Here, new types of CO2-derived thermoplastic elastomers (TPEs) are described together with a generally applicable method to augment tensile mechanical strength and Young's modulus without requiring material re-design. These TPEs combine high glass transition temperature (Tg) amorphous blocks comprising CO2-derived poly(carbonates) (A-block), with low Tg poly(ε-decalactone), from castor oil, (B-block) in ABA structures. The poly(carbonate) blocks are selectively functionalized with metal-carboxylates, where the metals are Na(I), Mg(II), Ca(II), Zn(II) and Al(III). The colorless polymers, featuring <1 wt% metal, show tunable thermal (Tg), and mechanical (elongation at break, elasticity, creep-resistance) properties. The best elastomers show >50-fold higher Young's modulus and 21-times greater tensile strength, without compromise to elastic recovery, compared with the starting block polymers. They have wide operating temperatures (-20 to 200 ˚C), high creep-resistance and yet remain recyclable. In future, these materials could substitute high-volume petrochemical elastomers and be utilized in high-growth fields like medicine, robotics and electronics.
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May 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[21871]
Open Access
Abstract: β-NaYF4 nanocrystals are a popular class of optical materials. They can be doped with optically active lanthanide ions and shaped into core–multi-shell geometries with controlled dopant distributions. Here, we follow the synthesis of β-NaYF4 nanocrystals from α-NaYF4 precursor particles using in situ small-angle and wide-angle X-ray scattering and ex-situ electron microscopy. We observe an evolution from a monomodal particle size distribution to bimodal, and eventually back to monomodal. The final size distribution is narrower in absolute numbers than the initial distribution. These peculiar growth dynamics happen in large part before the α-to-β phase transformation. We propose that the splitting of the size distribution is caused by variations in the reactivity of α-NaYF4 precursor particles, potentially due to inter-particle differences in stoichiometry. Rate equation modeling confirms that a continuous distribution of reactivities can result in the observed particle growth dynamics.
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May 2023
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I15-1-X-ray Pair Distribution Function (XPDF)
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Elsebeth J.
Pedersen
,
Theany
To
,
Søren S.
Sørensen
,
Rasmus
Christensen
,
Johan F. S.
Christensen
,
Lars R.
Jensen
,
Michal
Bockowski
,
Oxana V.
Magdysyuk
,
Maria
Diaz-Lopez
,
Yuanzheng
Yue
,
Morten M.
Smedskjaer
Diamond Proposal Number(s):
[30401]
Abstract: Methods to improve the fracture toughness of oxide glasses are needed since low fracture toughness is a major bottleneck for their applications. To overcome this, it is critically important to investigate the effect of both short- and medium-range structural features on fracture toughness. Recent work reported a record-high fracture toughness for a bulk lithium aluminoborate glass subjected to hot compression. Here, we further explore the structural origin of this high fracture toughness by subjecting different alkali aluminoborate glasses to hot compression. Through a combination of x-ray total scattering experiments and atomistic simulations, we find that hot compression causes significant changes to both the short- and medium-range order structure of the glasses, e.g., increased coordination numbers (CNs) of network forming species and decreased average size of ring-type structures. To this end, we reveal positive correlations between the pressure-induced increase in fracture toughness and (i) the increase in average CN of network forming species and (ii) the area of the first sharp diffraction peak in the structure factor. Our study thus improves the understanding of which structural features benefit intrinsic toughening of oxide glasses.
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May 2023
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I21-Resonant Inelastic X-ray Scattering (RIXS)
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Open Access
Abstract: A photon carrying one unit of angular momentum can change the spin angular momentum of a magnetic system with one unit (ΔMs = ±1) at most. This implies that a two-photon scattering process can manipulate the spin angular momentum of the magnetic system with a maximum of two units. Herein we describe a triple-magnon excitation in α-Fe2O3, which contradicts this conventional wisdom that only 1- and 2-magnon excitations are possible in a resonant inelastic X-ray scattering experiment. We observe an excitation at exactly three times the magnon energy, along with additional excitations at four and five times the magnon energy, suggesting quadruple and quintuple-magnons as well. Guided by theoretical calculations, we reveal how a two-photon scattering process can create exotic higher-rank magnons and the relevance of these quasiparticles for magnon-based applications.
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May 2023
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