I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[11282]
Abstract: Rivers are significant contributors of Fe to the ocean. However, the characteristics of chemically reactive Fe remain poorly constrained, especially in large Arctic rivers, which drain landscapes highly susceptible to climate change and carbon cycle alteration. The aim of this study was a detailed characterisation (size, mineralogy, and speciation) of riverine Fe-bearing particles (> 0.22 µm) and colloids (1 kDa – 0.22 µm) and their association with organic carbon (OC), in the Lena River and tributaries, which drain a catchment almost entirely underlain by permafrost. Samples from the main channel and tributaries representing watersheds that span a wide range in topography and lithology were taken after the spring flood in June 2013 and summer baseflow in July 2012. Fe-bearing particles were identified, using Transmission Electron Microscopy, as large (200 nm – 1 µm) aggregates of smaller (20 nm - 30 nm) spherical colloids of chemically-reactive ferrihydrite. In contrast, there were also large (500 nm – 1 µm) aggregates of clay (illite) particles and smaller (100 - 200 nm) iron oxide particles (dominantly hematite) that contain poorly reactive Fe. TEM imaging and Scanning Transmission X-ray microscopy (STXM) indicated that the ferrihydrite is present as discrete particles within networks of amorphous particulate organic carbon (POC) and attached to the surface of primary produced organic matter and clay particles. Together, these larger particles act as the main carriers of nanoscale ferrihydrite in the Lena River basin. The chemically reactive ferrihydrite accounts for on average 70 ± 15 % of the total suspended Fe in the Lena River and tributaries. These observations place important constraints on Fe and OC cycling in the Lena River catchment area and Fe-bearing particle transport to the Arctic Ocean.
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Jul 2017
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[2933]
Abstract: Synchrotron white beam X-ray topography has been used to characterise bulk crystal defects of thick vapour grown CdZnTe crystals. Whole 50 mm diameter wafers with thicknesses in the range of 2–3 mm were sliced from boules grown by the multi-tube physical vapour transport method and analysed by diffraction topography in a transmission geometry. A variety of defects were observed including cracks, voids and grain boundaries. The largest quantity of defects observed were sub-grains appearing as localised increased intensity in the topographs. The periphery of the wafers showed the highest number of defects, whereas central regions where largely defect-free. We failed to observe any inclusions or precipitates within these crystals. Surface damage from wire-saw cutting was also observed on poorly processed wafers; these defects were otherwise invisible to standard characterisation methods. X-ray topography has proven to be a useful tool for non-destructively investigating bulk extended defects in CdZnTe crystals for radiation detector applications.
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Jan 2012
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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
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Diamond Proposal Number(s):
[24622]
Open Access
Abstract: Active Virosomes (AVs) are derivatives of viruses, broadly similar to ‘parent’ pathogens, with an outer envelope that contains a bespoke genome coding for 4–5 viral proteins capable of eliciting an antigenic response. AVs are essentially novel vaccine formulations that present on their surface selected viral proteins as antigens. Once administered, they elicit an initial “anti-viral” immune response. AVs are also internalised by host cells where their cargo viral genes are used to express viral antigen(s) intracellularly. These can then be transported to the host cell surface resulting in a second wave of antigen exposure and a more potent immuno-stimulation. A new 3D correlative microscopy approach is used here to provide a robust analytical method for characterisation of Zika and Chikungunya-derivatised AV populations including vesicle size distribution and variations in antigen loading. Manufactured batches were compared to assess the extent and nature of batch-to-batch variations. We also show preliminary results that verify antigen expression on the surface of host cells. We present here a reliable and efficient high-resolution 3D imaging regime that allows the evaluation of the microstructure and biochemistry of novel vaccine formulations such as AVs.
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Aug 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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I08-Scanning X-ray Microscopy beamline (SXM)
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Alastair J. M.
Lough
,
Douglas P.
Connelly
,
William B.
Homoky
,
Jeffrey A.
Hawkes
,
Valerie
Chavagnac
,
Alain
Castillo
,
Majid
Kazemian
,
Ko-Ichi
Nakamura
,
Tohru
Araki
,
Burkhard
Kaulich
,
Rachel A.
Mills
Diamond Proposal Number(s):
[12738]
Open Access
Abstract: Iron (Fe) limits primary productivity and nitrogen fixation in large regions of the world’s oceans. Hydrothermal supply of Fe to the global deep ocean is extensive; however, most of the previous work has focused on examining high temperature, acidic, focused flow on ridge axes that create “black smoker” plumes. The contribution of other types of venting to the global ocean Fe cycle has received little attention. To thoroughly understand hydrothermal Fe sources to the ocean, different types of vent site must be compared. To examine the role of more diffuse, higher pH sources of venting, a hydrothermal plume above the Von Damm vent field (VDVF) was sampled for Total dissolvable Fe (unfiltered, TDFe), dissolved Fe (<0.2 μm, dFe) and soluble Fe (<0.02 μm, sFe). Plume particles sampled in situ were characterized using scanning electron microscopy and soft X-ray spectromicroscopy. The VDVF vents emit visibly clear fluids with particulate Fe (TDFe-dFe, >0.2 μm) concentrations up to 196 nmol kg–1 comparable to concentrations measured in black smoker plumes on the Mid-Atlantic Ridge. Colloidal Fe (cFe) and sFe increased as a fraction of TDFe with decreasing TDFe concentration. This increase in the percentage of sFe and cFe within the plume cannot be explained by settling of particulates or mixing with background seawater. The creation of new cFe and sFe within the plume from the breakdown of pFe is required to close the Fe budget. We suggest that the proportional increase in cFe and sFe reflects the entrainment, breakdown and recycling of Fe bearing organic particulates near the vents. Fe plume profiles from the VDVF differ significantly from previous studies of “black smoker” vents where formation of new pFe in the plume decreases the amount of cFe. Formation and removal of Fe-rich colloids and particles will control the amount and physico-chemical composition of dFe supplied to the deep ocean from hydrothermal systems. This study highlights the differences in the stabilization of hydrothermal Fe from an off-axis diffuse source compared to black smokers. Off-axis diffuse venting represent a potentially significant and previously overlooked Fe source to the ocean due to the difficulties in detecting and locating such sites.
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Jul 2019
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I08-Scanning X-ray Microscopy beamline (SXM)
I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[15230, 15854, 20809, 24526, 24531]
Abstract: Parkinson’s disease causes the loss of a particular group of brain cells, the neurons that produce the neurotransmitter dopamine. As these cells contain a dark pigment, neuromelanin, the change is evident from the loss of pigment in this brain region. Characterisation of neuromelanin in tissue remains dependent on visible pigmentation. Faint pigmentation may be interpreted as cell loss, and so contrast-
enhancing stains are commonly used. However, this staining constrains further chemical analysis of the tissue.
Researchers explored the use of synchrotron X-ray microscopy to visualise neuromelanin without relying on visible pigmentation or chemical staining. They performed combined imaging and spectroscopy (spectromicroscopy) on Diamond Light Source’s Scanning X-ray Microscopy beamline (I08), allowing the creation of images from distinct X-ray absorption features. Nanoscale spatial resolution using soft (low energy) X-rays allowed the researchers to probe the organic structure of neuromelanin to seek distinguishing spectral features. This revealed a characteristic feature in the absorption spectrum for neuromelanin. The team used this feature to create maps of neuromelanin distributions, which matched those observed in stained tissue sections.
The team also used nanoscale X-ray Fluorescence (XRF) with hard (high energy) X-rays on the Hard X-ray Nanoprobe beamline (I14) to discover a signature for identifying neuromelanin. This showed that neuromelanin could be identified by its elevated sulfur content. However, this approach is not as specific to neuromelanin as the soft X-ray method. The discovery of the soft X-ray neuromelanin signature offers significant potential for non-destructive studies of the relationships between depigmentation, metal binding and neurodegeneration in Parkinson’s disease.
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Jul 2021
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B16-Test Beamline
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Diamond Proposal Number(s):
[13464]
Abstract: During 4H silicon carbide (4H-SiC) homoepitaxy and post-growth processes, the development of stress relaxation has been observed, in which interfacial dislocations (IDs) are formed at the epilayer/substrate interface, relaxing the misfit strain induced by the nitrogen doping concentration difference between the epilayer and substrate. It is widely believed that an interfacial dislocation is created by the glide of a mobile segment of a basal plane dislocation (BPD) in the substrate or epilayer towards the interface, leaving a trailing edge component right at the interface.
However, direct observation of such mechanisms has not been made in SiC before. In this work, we present an in situ study of the stress relaxation process, in which a specimen cut from a commercial
4H-SiC homoepitaxial wafer undergoes the stress relaxation process during a high-temperature heat treatment while sequential synchrotron white beam X-ray topographs were recorded simultaneously. Based on the dynamic observation of this process, it can be concluded that thermal stress plays a role in the relaxation process while the increased misfit strain at elevated temperature most likely drives the formation of an interfacial dislocation.
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Jun 2018
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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[19228, 22730]
Open Access
Abstract: Hydrothermal carbonisation (HTC) has been demonstrated to be a sustainable thermochemical process, capable of producing functionalised carbon materials for a wide range of applications. In order to better apply such materials, the local chemistry and reaction pathways governing hydrothermal carbon growth must be understood. We report the use of scanning transmission X-ray microscopy (STXM) to observe chemical changes in functionality of carbon between the interface and bulk regions of HTC. Spatially-resolved, element-specific X-ray photo-absorption spectra show the presence of differing local carbon chemistry between bulk “core” and interface “shell” regions of a glucose-derived hydrothermal carbon spherule. STXM provides direct evidence to suggest that mechanistic pathways differ between the core and shell of the hydrothermal carbon. In the shell region, at the water-carbon interface, more aldehyde and/or carboxylic species are suspected to provide a reactive interface for bridging reactions to occur with local furan-based monomers. In contrast, condensation reactions appear to dominate in the core, removing aryl-linking units between polyfuranic domains. The application of STXM to HTC presents opportunities for a more comprehensive understanding of the spatial distribution of carbon species within hydrothermal carbon, especially at the solvent-carbon interface.
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Jan 2020
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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[14946]
Open Access
Abstract: Adsorption of prebiotic building blocks is proposed to have played a role in the emergence of life on Earth. The experimental and theoretical study of this phenomenon should be guided by our knowledge of the geochemistry of the habitable early Earth environments, which could have spanned a large range of settings. Adsorption being an interfacial phenomenon, experiments can be built around the minerals that probably exhibited the largest specific surface areas and were the most abundant, i.e., phyllosilicates. Our current work aims at understanding how nucleotides, the building blocks of RNA and DNA, might have interacted with phyllosilicates under various physico-chemical conditions. We carried out and refined batch adsorption studies to explore parameters such as temperature, pH, salinity, etc. We built a comprehensive, generalized model of the adsorption mechanisms of nucleotides onto phyllosilicate particles, mainly governed by phosphate reactivity. More recently, we used surface chemistry and geochemistry techniques, such as vibrational spectroscopy, low pressure gas adsorption, X-ray microscopy, and theoretical simulations, in order to acquire direct data on the adsorption configurations and localization of nucleotides on mineral surfaces. Although some of these techniques proved to be challenging, questioning our ability to easily detect biosignatures, they confirmed and complemented our pre-established model.
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Nov 2018
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