B24-Cryo Soft X-ray Tomography
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Mohamed A.
Koronfel
,
Ilias
Kounatidis
,
Dennis M.
Mwangangi
,
Nina
Vyas
,
Chidinma
Okolo
,
Archana
Jadhav
,
Tom
Fish
,
Phatcharin
Chotchuang
,
Albert
Schulte
,
Robert
Robinson
,
Maria
Harkiolaki
Diamond Proposal Number(s):
[23033, 23073]
Open Access
Abstract: Imaging of actin filaments is crucial due to the integral role that they play in many cellular functions such as intracellular transport, membrane remodelling and cell motility. Visualizing actin filaments has so far relied on fluorescence microscopy and electron microscopy/tomography. The former lacks the capacity to capture the overall local ultrastructure, while the latter requires rigorous sample preparation that can lead to potential artefacts, and only delivers relatively small volumes of imaging data at the thinnest areas of a cell. In this work, a correlative approach utilizing in situ super-resolution fluorescence imaging and cryo X-ray tomography was used to image bundles of actin filaments deep inside cells under near-native conditions. In this case, fluorescence 3D imaging localized the actin bundles within the intracellular space, while X-ray tomograms of the same areas provided detailed views of the local ultrastructure. Using this new approach, actin trails connecting vesicles in the perinuclear area and hotspots of actin presence within and around multivesicular bodies were observed. The characteristic prevalence of filamentous actin in cytoplasmic extensions was also documented.
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Dec 2021
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B24-Cryo Soft X-ray Tomography
Krios II-Titan Krios II at Diamond
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Luiza
Mendonca
,
Andrew
Howe
,
James B.
Gilchrist
,
Yuewen
Sheng
,
Dapeng
Sun
,
Michael L.
Knight
,
Laura C.
Zanetti-Domingues
,
Benji
Bateman
,
Anna-Sophia
Krebs
,
Long
Chen
,
Julika
Radecke
,
Vivian D.
Li
,
Tao
Ni
,
Ilias
Kounatidis
,
Mohamed A.
Koronfel
,
Marta
Szynkiewicz
,
Maria
Harkiolaki
,
Marisa
Martin-Fernandez
,
William
James
,
Peijun
Zhang
Diamond Proposal Number(s):
[21004, 26987]
Open Access
Abstract: Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events – e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
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Jul 2021
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Open Access
Abstract: Lithium ion battery technology is the state-of-the-art rechargeable energy storage technology for electric vehicles, stationary energy storage and personal electronics. However, a wide variety of degradation effects still contribute to performance limitations. The metallic copper and aluminium current collectors in a lithium ion battery can be subject to dissolution or other reactions with the electrolytes. Corrosion of these metal foils is significantly detrimental to the overall performance of a lithium ion battery, however the mechanisms of this degradation are poorly understood. This review summarises the key effects contributing to metal current collector degradation in lithium ion batteries as well as introduces relevant corrosion and lithium ion battery principles. By developing the understanding of these complex chemistries, lithium ion battery degradation can be mitigated, enabling safer operation and longer lifetimes.
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Jun 2021
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I14-Hard X-ray Nanoprobe
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Miguel A.
Gomez-Gonzalez
,
Mohamed A.
Koronfel
,
Huw
Pullin
,
Julia E.
Parker
,
Paul D.
Quinn
,
Maria D.
Inverno
,
Thomas B.
Scott
,
Fang
Xie
,
Nikolaos
Voulvoulis
,
Marian L.
Yallop
,
Mary P.
Ryan
,
Alexandra E.
Porter
Diamond Proposal Number(s):
[17784]
Open Access
Abstract: Understanding nanomaterial transformations within wastewater treatment plants is an important step to better predict their potential impact on the environment. Here, spatially resolved, in situ nano‐X‐ray fluorescence microscopy is applied to directly observe nanometer‐scale dissolution, morphological, and chemical evolution of individual and aggregated ZnO nanorods in complex “real‐world” conditions: influent water and primary sludge collected from a municipal wastewater system. A complete transformation of isolated ZnO nanorods into ZnS occurs after only 1 hour in influent water, but larger aggregates of the ZnO nanorods transform only partially, with small contributions of ZnS and Zn‐phosphate (Zn3(PO4)2) species, after 3 hours. Transformation of aggregates of the ZnO nanorods toward mixed ZnS, Zn adsorbed to Fe‐oxyhydroxides, and a large contribution of Zn3(PO4)2 phases are observed during their incubation in primary sludge for 3 hours. Discrete, isolated ZnO regions are imaged with unprecedented spatial resolution, revealing their incipient transformation toward Zn3(PO4)2. Passivation by transformation(s) into mixtures of less soluble phases may influence the subsequent bioreactivity of these nanomaterials. This work emphasizes the importance of imaging the nanoscale chemistry of mixtures of nanoparticles in highly complex, heterogeneous semi‐solid matrices for improved prediction of their impacts on treatment processes, and potential environmental toxicity following release.
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May 2021
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B24-Cryo Soft X-ray Tomography
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Chidinma
Okolo
,
Ilias
Kounatidis
,
Johannes
Groen
,
Kamal
Nahas
,
Stefan
Balint
,
Thomas M.
Fish
,
Mohamed A.
Koronfel
,
Aitziber L.
Cortajarena
,
Ian M.
Dobbie
,
Eva
Pereiro
,
Maria
Harkiolaki
Diamond Proposal Number(s):
[18737, 20321, 22274, 23046, 25162]
Abstract: 3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2–50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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May 2021
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B24-Cryo Soft X-ray Tomography
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Nina
Vyas
,
Nina
Perry
,
Chidinma A.
Okolo
,
Ilias
Kounatidis
,
Thomas M.
Fish
,
Kamal L.
Nahas
,
Archana
Jadhav
,
Mohamed A.
Koronfel
,
Johannes
Groen
,
Eva
Pereiro
,
Ian M.
Dobbie
,
Maria
Harkiolaki
Diamond Proposal Number(s):
[25512]
Open Access
Abstract: Three-dimensional (3D) structured illumination microscopy (SIM) allows imaging of fluorescently labelled cellular structures at higher resolution than conventional fluorescence microscopy. This super-resolution (SR) technique enables visualization of molecular processes in whole cells and has the potential to be used in conjunction with electron microscopy and X-ray tomography to correlate structural and functional information. A SIM microscope for cryogenically preserved samples (cryoSIM) has recently been commissioned at the correlative cryo-imaging beamline B24 at the UK synchrotron.
It was designed specifically for 3D imaging of biological samples at cryogenic temperatures in a manner compatible with subsequent imaging of the same samples by X-ray microscopy methods such as cryo-soft X-ray tomography. This video article provides detailed methods and protocols for successful imaging using the cryoSIM. In addition to instructions on the operation of the cryoSIM microscope, recommendations have been included regarding the choice of samples, fluorophores, and parameter settings. The protocol is demonstrated in U2OS cell samples whose mitochondria and tubulin have been fluorescently labelled.
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May 2021
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Abstract: Despite their ubiquitous usage and increasing societal dependence on Li-ion batteries, there remains a lack of detailed empirical evidence of Li intercalation/deintercalation into graphite even though this process dictates the performance, longevity, and safety of the system. Here, we report direct detection and dissociation of specific crystallographic phases in the lithiated graphite, which form through a stepwise staging process. Using operando measurements, LiC18, LiC12, and LiC6 phases are observed via distinct low-frequency Raman features, which are the result of displacement of the graphite lattice by induced local strain. Density functional theory calculations confirm the nature of the Raman-active vibrational modes, to the layer breathing modes (LBMs) of the lithiated graphite. The new findings indicate graphene-like characteristics in the lithiated graphite under the deep charged condition due to the imposed strain by the inserted Li. Moreover, our approach also provides a simple experimental tool to measure induced strain in the graphite structure under full intercalation conditions.
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Apr 2021
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B24-Cryo Soft X-ray Tomography
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Diamond Proposal Number(s):
[21046, 18314]
Open Access
Abstract: This protocol illustrates the steps necessary to deposit correlated 3D cryo-imaging data from cryo-structured illumination microscopy and cryo-soft X-ray tomography with the BioStudies and EMPIAR deposition databases of the European Bioinformatics Institute. There is currently a real need for a robust method of data deposition to ensure unhindered access to and independent validation of correlative light and X-ray microscopy data to allow use in further comparative studies, educational activities, and data mining.
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Mar 2021
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I14-Hard X-ray Nanoprobe
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Miguel A.
Gomez-Gonzalez
,
Mohamed A.
Koronfel
,
Angela Erin
Goode
,
Maryam
Al-Ejji
,
Nikolaos
Voulvoulis
,
Julia E.
Parker
,
Paul D.
Quinn
,
Thomas Bligh
Scott
,
Fang
Xie
,
Marian L.
Yallop
,
Alexandra E.
Porter
,
Mary P.
Ryan
Diamond Proposal Number(s):
[17784]
Abstract: Zinc oxide engineered nanomaterials (ZnO ENMs) are used in a variety of applications worldwide due to their optoelectronic and antibacterial properties with potential contaminant risk to the environment following their disposal. One of the main potential pathways for ZnO nanomaterials to reach the environment is via urban wastewater treatment plants. So far there is no technique that can provide spatiotemporal nanoscale information about the rates and mechanisms by which the individual nanoparticles transform. Fundamental knowledge of how the surface chemistry of individual particles change, and the heterogeneity of transformations within the system, will reveal the critical physicochemical properties determining environmental damage and deactivation. We applied a methodology based on spatially resolved in situ X-ray fluorescence microscopy (XFM), allowing observation of real-time dissolution and morphological and chemical evolution of synthetic template-grown ZnO nanorods (∼725 nm length, ∼140 nm diameter). Core–shell ZnO-ZnS nanostructures were formed rapidly within 1 h, and significant amounts of ZnS species were generated, with a corresponding depletion of ZnO after 3 h. Diffuse nanoparticles of ZnS, Zn3(PO4)2, and Zn adsorbed to Fe-oxyhydroxides were also imaged in some nonsterically impeded regions after 3 h. The formation of diffuse nanoparticles was affected by ongoing ZnO dissolution (quantified by inductively coupled plasma mass spectrometry) and the humic acid content in the simulated sludge. Complementary ex situ X-ray absorption spectroscopy and scanning electron microscopy confirmed a significant decrease in the ZnO contribution over time. Application of time-resolved XFM enables predictions about the rates at which ZnO nanomaterials transform during their first stages of the wastewater treatment process.
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Sep 2019
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Mohamed A.
Koronfel
,
Angela E.
Goode
,
Miguel Angel
Gomez-Gonzalez
,
Johanna
Nelson Weker
,
Thiago Araujo
Simões
,
Rik
Brydson
,
Paul
Quinn
,
Michael F.
Toney
,
Alister
Hart
,
Alexandra E.
Porter
,
Mary P.
Ryan
Abstract: The unexpected high failure rates of CoCrMo hip-implants is associated with the release of a large number of inflammatory wear particles. CoCrMo is nominally a stable material, however, previous chemical speciation studies on CoCrMo wear particles obtained from periprosthetic tissue revealed only trace amounts of Co remaining despite Co being the major component of the alloy. The unexpected high levels of Co dissolution in-vivo raised significant clinical concerns particularly related to the Cr speciation in the dissolution process. At high electrochemical potentials, the alloy’s Cr-rich passive film breaks down (transpassive polarisation) facilitating alloy dissolution. The potential release of the carcinogenic Cr(VI) species in vivo has been a subject of debate. While the large scale Co dissolution observed on in vivo produced particles could indicate a highly oxidising in vivo environment, Cr(VI) species were not previously detected in periprosthetic tissue samples. However, Cr(VI) is likely to be an unstable (transient) species in biological environments and studies on periprosthetic tissue does not provide information on intermediate reaction products nor the exposure history of the wear particles. Here, an in situ spectro-microscopy approach was developed, utilising the high chemical resolution of synchrotron radiation, in order to study CoCrMo reactivity as a function of time and oxidising conditions. The results reveal limited Co dissolution from CoCrMo particles, which increases dramatically at a critical electrochemical potential. Furthermore, in-situ XAS detected only Cr(III) dissolution, even at potentials where Cr(VI) is known to be produced, suggesting that Cr(VI) species are extremely transient in simulated biological environments where the oxidation zone is small.
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Apr 2019
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