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Abstract: Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are found in a high proportion of diffuse gliomas. The presence of the IDH1 mutation is a valuable diagnostic, prognostic and predictive biomarker for the management of patients with glial tumours. Techniques involving vibrational spectroscopy, e.g., Fourier transform infrared (FTIR) spectroscopy, have previously demonstrated analytical capabilities for cancer detection, and have the potential to contribute to diagnostics. The implementation of FTIR microspectroscopy during surgical biopsy could present a fast, label-free method for molecular genetic classification. For example, the rapid determination of IDH1 status in a patient with a glioma diagnosis could inform intra-operative decision-making between alternative surgical strategies. In this study, we utilized synchrotron-based FTIR microanalysis to probe tissue microarray sections from 79 glioma patients, and distinguished the positive class (IDH1-mutated) from the IDH1-wildtype glioma, with a sensitivity and specificity of 82.4% and 83.4%, respectively. We also examined the ability of attenuated total reflection (ATR)-FTIR spectroscopy in detecting the biomolecular events and global epigenetic and metabolic changes associated with mutations in the IDH1 enzyme, in blood serum samples collected from an additional 72 brain tumour patients. Centrifugal filtration enhanced the diagnostic ability of the classification models, with balanced accuracies up to ~69%. Identification of the molecular status from blood serum prior to biopsy could further direct some patients to alternative treatment strategies.

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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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Abstract: Bubble nucleation and growth dynamics exert a primary control on the explosivity of volcanic eruptions. Numerous theoretical and experimental studies aim to capture the complex process of melt vesiculation, whereas textural studies use vesicle populations to reconstruct magma behaviour. However, post-fragmentation vesiculation in rhyolitic bombs can create final quenched bubble (vesicle) textures that are not representative of the nature of fragmenting magma within the conduit. To examine bubble growth in hydrous rhyolitic bombs, we have used heated stage microscopy to directly observe vesiculation of a Chaitén rhyolite melt (with an initial dissolved water content of ∼0.95 wt %) at atmospheric pressure and magmatic temperatures upon reheating. Thin wafers of obsidian were held from 5 min up to two days in the heated stage at temperatures between 575 °C and 875 °C. We found that bubble growth rates, measured through changes in bubble diameter, increased with both temperature and bubble size. The average growth rate at the highest temperature of 875 °C is ∼1.27 μm s−1, which is substantially faster than the lowest detected growth rate of ∼0.02 μm s−1 at 725 °C; below this temperature no growth was observed. Average growth rate Vr follows an exponential relationship with temperature, T and inferred melt viscosity η, where Vr = 5.57 10−7e0.016 and Vr = 3270.26e−1.117η. Several stages of evolving bubble morphology were directly observed, including initial relaxation of deformed bubbles into spheres, extensive growth of spheres, and, at higher temperatures, close packing and foam formation. Bubble deformation due to bubble-bubble interaction and coalescence was observed in most experiments. We use our simple, experimentally-determined relationship between melt viscosity and bubble growth rates to model post-fragmentation vesicle growth in a cooling 1 m-diameter rhyolitic bomb. The results, which indicate negligible vesicle growth within 2–3 cm of the bomb surface, correspond well with the observed dense margin thickness of a Chaitén bomb of comparable dimensions. The experiments described can be used to effectively reconstruct the post-fragmentation vesiculation history of bombs through simple analytical expressions which provide a useful tool for aiding in the interpretation of pumiceous endmember textures in hydrous rhyolitic bombs.

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Abstract: Mudstone-hosted microfossils are a major component of the Proterozoic fossil record, particularly dominating the record of early eukaryotic life. Early organisms possessed no biomineralized parts to resist decay and controls on their fossilization in mudstones are poorly understood. Consequently, the Proterozoic fossil record is compromised—we do not know whether changing temporal/spatial patterns of microfossil occurrences reflect evolution or the distribution of favourable fossilization conditions. We investigated fossilization within the approximately 1000 Ma Lakhanda Group (Russia) and the approximately 800 Ma Svanbergfjellet and Wynniatt formations (Svalbard and Arctic Canada). Vertical sections of microfossils and surrounding matrices were extracted from thin sections by focused ion beam milling. Elemental mapping and synchrotron-based infrared microspectroscopy revealed that microfossils are surrounded by haloes rich in aluminium, probably hosted in kaolinite. Kaolinite has been implicated in Cambrian Burgess Shale-type (BST) fossilization and is known to slow the growth of degraders. The Neoproterozoic mudstone microfossil record may be biased to tropical settings conducive to kaolinite formation. These deposits lack metazoan fossils even though they share fossilization conditions with younger BST deposits that are capable of preserving non-mineralizing metazoans. Thus metazoans, at least those typically preserved in BST deposits, were probably absent from sedimentary environments before approximately 800 Ma.

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Abstract: Synchrotron resonance-enhanced infrared-atomic force microscopy (RE-AFM-IR) is a near-field photothermal vibrational nanoprobe developed at the Diamond Light Source (DLS), capable of measuring mid-infrared absorption spectra with spatial resolution around 100 nm. The present study reports a first application of synchrotron RE-AFM-IR to interrogate biological soft matter at subcellular level, in this case on a cellular model of drug-induced phospholipidosis (DIPL). J774A-1 macrophages were exposed to amiodarone (10 µM) or medium for 24 hours and chemically fixed. AFM topography maps revealed amiodarone-treated cells with enlarged cytoplasm and very thin regions corresponding to collapsed vesicles. IR maps of the whole cell were analysed by exploiting the RE-AFM-IR overall signal, i.e. the integrated RE-AFM-IR signal amplitude versus AFM-derived cell thickness, also on lateral resolution around 100 nm. Results shown that vibrational band assignment was possible and all characteristic peaks for lipids, proteins and DNA/RNA were identified. Both peak ratio and unsupervised chemometric analysis of RE-AFM-IR nanospectra generated from the nuclear and perinuclear regions of untreated and amiodarone-treated cells showed that the perinuclear region (i.e. cytoplasm) of amiodarone-treated cells had significantly elevated band intensities in the regions corresponding to phosphate and carbonyl groups, indicating detection of phospholipid-rich inclusion bodies typical for cells with DIPL. The results of this study are of importance to demonstrate not only the applicability of Synchrotron RE-AFM-IR to soft biological matters with subcellular spatial resolution, but also that the spectral information gathered from an individual sub-micron sample volume enables chemometric identification of treatment and biochemical differences between mammalian cells.