I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[23540]
Open Access
Abstract: Mineral-associated organic matter is an integral part of soil carbon pool. Biological processes contribute to the formation of such organo-mineral complexes when soil microbes, and in particular soil fungi, deposit a suite of extracellular metabolic compounds and their necromass on the mineral surfaces. While studied in bulk, micro- to nanoscale fungal–mineral interactions remain elusive. Of particular interest are the mutual effects at the interface between the fungal exometabolites and proximal mineral particles. In this work, we have grown saprotrophic and symbiotic fungi in contact with two soil minerals with contrasting properties: quartz and goethite, on top of X-ray transparent silicon nitride membrane windows and analyzed fungal hyphae by synchrotron-based scanning transmission X-ray microscopy in combination with near edge X-ray fine structure spectroscopy at C(K) and Fe(L) absorption edges. In the resultant chemical maps, we were able to visualize and differentiate organic compounds constituting the fungal cells, their extracellular metabolites, and the exometabolites adsorbing on the minerals. We found that the composition of the exometabolites differed between the fungal functional guilds, particularly, in their sugar to protein ratio and potassium concentration. In samples with quartz and goethite, we observed adsorption of the exometabolic compounds on the mineral surfaces with variations in their chemical composition around the particles. Although we did not observe clear alteration in the exometabolite chemistry upon mineral encounters, we show that fungal–mineral interaction result in reduction of Fe(III) in goethite. This process has been demonstrated for bulk systems, but, to our knowledge, this is the first observation on a single hypha scale offering insight into its underlying biological mechanisms. This demonstrates the link between processes initiated at the single-cell level to macroscale phenomena. Thus, spatially resolved chemical characterization of the microbial–mineral interfaces is crucial for an increased understanding of overall carbon cycling in soil.
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Jun 2022
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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[20567]
Abstract: To assess the safety of engineered nanomaterials (ENMs) and to evaluate and improve ENMs’ targeting ability for medical application, it is necessary to analyze the fate of these materials in biological media. This protocol presents a workflow that allows researchers to determine, characterize and quantify metal-bearing ENMs (M-ENMs) in biological tissues and cells and quantify their dynamic behavior at trace-level concentrations. Sample preparation methods to enable analysis of M-ENMs in a single cell, a cell layer, tissue, organ and physiological media (e.g., blood, gut content, hemolymph) of different (micro)organisms, e.g., bacteria, animals and plants are presented. The samples are then evaluated using fit-for-purpose analytical techniques e.g., single-cell inductively coupled plasma mass spectrometry, single-particle inductively coupled plasma mass spectrometry and synchrotron X-ray absorption fine structure, providing a protocol that allows comprehensive characterization and quantification of M-ENMs in biological matrices. Unlike previous methods, the protocol uses no fluorescent dyes or radiolabels to trace M-ENMs in biota and enables analysis of most M-ENMs at cellular, tissue and organism levels. The protocols can be applied by a wide variety of users depending on the intended purpose of the application, e.g., to correlate toxicity with a specific particle form, or to understand the absorption, distribution and excretion of M-ENMs. The results facilitate an understanding of the biological fate of M-ENMs and their dynamic behavior in biota. Performing the protocol may take 7–30 d, depending on which combination of methods is applied.
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Jun 2022
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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[20839]
Open Access
Abstract: Minerals are widely proposed to protect organic carbon from degradation and thus promote the persistence of organic carbon in soils and sediments, yet a direct link between mineral adsorption and retardation of microbial remineralisation is often presumed and a mechanistic understanding of the protective preservation hypothesis is lacking. We find that methylamines, the major substrates for cryptic methane production in marine surface sediment, are strongly adsorbed by marine sediment clays, and that this adsorption significantly reduces their concentrations in the dissolved pool (up to 40.2 ± 0.2%). Moreover, the presence of clay minerals slows methane production and reduces final methane produced (up to 24.9 ± 0.3%) by a typical methylotrophic methanogen—Methanococcoides methylutens TMA-10. Near edge X-ray absorption fine structure spectroscopy shows that reversible adsorption and occlusive protection of methylamines in clay interlayers are responsible for the slow-down and reduction in methane production. Here we show that mineral-OC interactions strongly control methylotrophic methanogenesis and potentially cryptic methane cycling in marine surface sediments.
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May 2022
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I08-Scanning X-ray Microscopy beamline (SXM)
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Dawn M.
Buchanan
,
Laura
Newsome
,
Jonathan R.
Lloyd
,
Majid
Kazemian
,
Burkhard
Kaulich
,
Tohru
Araki
,
Heath
Bagshaw
,
John
Waters
,
Gerrit
Van Der Laan
,
Alpha
N’diaye
,
Victoria S.
Coker
Diamond Proposal Number(s):
[17626]
Open Access
Abstract: Cobalt is an essential element for life and plays a crucial role in supporting the drive to clean energy, due to its importance in rechargeable batteries. Co is often associated with Fe in the environment, but the fate of Co in Fe-rich biogeochemically-active environments is poorly understood. To address this, synchrotron-based scanning X-ray microscopy (SXM) was used investigate the behaviour of cobalt at the nanoscale in Co-Fe(III)-oxyhydroxides undergoing microbial reduction. SXM can assess spatial changes in metal speciation and organic compounds helping to elucidate the electron transfer processes occurring at the cell-mineral interface and inform on the fate of cobalt in redox horizons. G. sulfurreducens was used to reduce synthetic Co-ferrihydrite as an analogue of natural cobalt-iron-oxides. Magnetite [Fe(II)/Fe(III)3O4] production was confirmed by powder X-ray diffraction (XRD), SXM and X-ray magnetic circular dichroism (XMCD) data, where best fits of the latter suggested Co-bearing magnetite. Macro-scale XAS techniques suggested Co(III) reduction occurred and complementary SXM at the nanoscale, coupled with imaging, found localised biogenic Co(III) reduction at the cell-mineral interface via direct contact with outer membrane cytochromes. No discernible localised changes in Fe speciation were detected in the reordered cobalt-iron-oxides that were formed and at the end point of the experiment only 11% Co and 1.5% Fe had been solubilised. The solid phase retention, alongside the highly localised and preferential cobalt bioreduction observed at the nanoscale is consistent with retention of Co in redox zones. This work improves our fundamental molecular-scale understanding of the fate of Co in complex environmental systems and supports the development of biogenic Co-doped magnetite for industrial applications from drug delivery systems to magnetic recording media.
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May 2022
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I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[22484]
Open Access
Abstract: We have spatially investigated lattice spacing, twist, and bending in individual laterally (110)-oriented Ge nanowires (NWs) on pre-patterned Si(001) substrates. A combination of synchrotron-based scanning x-ray diffraction microscopy with an x-ray focus size of 50 nm and numerical finite element calculations on the elastic strain reveals a three-dimensional relaxation scenario, which becomes particularly complex next to NW nucleation points. Despite a lattice mismatch of 4.2%, lattice compliance is preserved, since strain can effectively be released close to the seeding window. Areas in the NWs other than that appear fully relaxed. The resulting NW twist, i.e., lattice rotations around the growth axis, amounts to less than 0.1°.
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Mar 2022
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I08-Scanning X-ray Microscopy beamline (SXM)
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A.
Steele
,
L. G
Benning
,
R.
Writh
,
A.
Schreiber
,
T.
Araki
,
F. M.
Mccubbin
,
M. R.
Fries
,
L. R.
Nittler
,
J.
Wang
,
L. J.
Hallis
,
P. G.
Conrad
,
C.
Conley
,
S.
Vitale
,
A. C.
O'Brien
,
V.
Riggi
,
K.
Rogers
Diamond Proposal Number(s):
[2444]
Abstract: Water-rock interactions are relevant to planetary habitability, influencing mineralogical diversity and the production of organic molecules. We examine carbonates and silicates in the martian meteorite Allan Hills 84001 (ALH 84001), using colocated nanoscale analyses, to characterize the nature of water-rock reactions on early Mars. We find complex refractory organic material associated with mineral assemblages that formed by mineral carbonation and serpentinization reactions. The organic molecules are colocated with nanophase magnetite; both formed in situ during water-rock interactions on Mars. Two potentially distinct mechanisms of abiotic organic synthesis operated on early Mars during the late Noachian period (3.9 to 4.1 billion years ago).
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Jan 2022
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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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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[21323, 20839, 23049]
Open Access
Abstract: The coprecipitation of organic carbon with iron minerals is important for its preservation in soils and sediments, but the mechanisms for carbon-iron interactions and thus the controls on organic carbon cycling are far from understood. Here we coprecipitate carboxylic acids with iron (oxyhydr)oxide ferrihydrite and use near-edge X-ray absorption fine structure spectroscopy and wet chemical treatments to determine the relationship between sequestration mechanism and organic carbon stability against its release and chemical oxidative remineralisation. We show that organic carbon sequestration, stabilisation and persistence increase with an increasing number of carboxyl functional groups. We suggest that carboxyl-richness provides an important control on organic carbon preservation in the natural environment. Our work offers a mechanistic basis for understanding the stability and persistence of organic carbon in soils and sediments, which might be used to develop an overarching relationship between organic functional group-richness, mineral interactions and organic carbon preservation in the Earth system.
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Nov 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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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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