Compression of D_{2} to 460 GPa and Isotopic Effects in the Path to Metal Hydrogen.

How are nuclear quantum fluctuations affecting the properties of dense hydrogen approaching metallization? We report here Raman spectroscopy and synchrotron infrared absorption measurements on deuterium up to 460 GPa at 80 K. By comparing to a previous similar study on hydrogen, isotopic effects on the electronic and vibrational properties in phase III are disclosed. Also, evidence of a probable transition to metal deuterium is observed, shifted by about 35 GPa compared to that in hydrogen. Advanced calculations, quantifying a reduction of the band gap caused by nuclear quantum fluctuations, are compared to the present data.

The first infrared beamline at the Middle East SESAME synchrotron facility.

SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) is the only synchrotron light facility in the Middle East and neighboring regions, officially opened in 2017. Among the identification and construction of the first operational beamlines, infrared spectromicroscopy was selected as one of the two beamlines to be opened to the general users' program (the so-called Day-1 beamlines). Being one of the most demanded techniques by various scientific communities in the Middle East, the beamline has been designed and implemented in the framework of a collaboration agreement with the French synchrotron facility, SOLEIL. The design, construction and initial performances of the IR beamline (D02-IR), nowadays operational, are reported.

Composition of Carbon Clusters in Implanted Silicon Using Atom Probe Tomography.

Atom probe tomography was employed to observe and derive the composition of carbon clusters in implanted silicon. This value, which is of interest to the microelectronic industry when considering ion implantation defects, was estimated not to exceed 2 at%. This measurement has been done by fitting the distribution of first nearest neighbor distances between monoatomic carbon ions (C+ and C2+). Carbon quantification has been considerably improved through the detection of molecular ions, using lower electric field conditions as well as equal proportions of 12C and 13C. In these conditions and using another quantification method, we have shown that the carbon content in clusters approaches 50 at%. This result very likely indicates that clusters are nuclei of the SiC phase.

FTIR micro-spectroscopy using synchrotron-based and thermal source-based radiation for probing live bacteria.

Fourier transform infrared (FTIR) spectroscopy has proven to be a non-invasive tool to analyse cells without the hurdle of employing exogenous dyes or probes. Nevertheless, the study of single live bacteria in their aqueous environment has long remained a big challenge, due to the strong infrared absorption of water and the small size of bacteria compared to the micron-range infrared wavelengths of the probing photons. To record infrared spectra of bacteria in an aqueous environment, at different spatial resolutions, two setups were developed. A custom-built attenuated total reflection inverted microscope was coupled to a synchrotron-based FTIR spectrometer, using a germanium hemisphere. With such a setup, a projected spot size of 1 × 1 µm2 was achieved, which allowed spectral acquisition at the single-cell level in the 1800-1300 cm-1 region. The second setup used a demountable liquid micro-chamber with a thermal source-powered FTIR microscope, in transmission geometry, for probing clusters of a few thousands of live cells in the mid-IR region (4000-975 cm-1). Both setups were applied for studying two strains of a model lactic acid bacterium exhibiting different cryo-resistances. The two approaches allowed the discrimination of both strains and revealed population heterogeneity among bacteria at different spatial resolutions. The multivariate analysis of spectra indicated that the cryo-sensitive cells presented the highest cell heterogeneity and the highest content of proteins with the α-helix structure. Furthermore, the results from clusters of bacterial cells evidenced phosphate and peptidoglycan vibrational bands associated with the cell envelope, as potential markers of resistance to environmental conditions. Graphical Abstract.

Synchrotron infrared spectroscopic evidence of the probable transition to metal hydrogen.

Hydrogen has been an essential element in the development of atomic, molecular and condensed matter physics1. It is predicted that hydrogen should have a metal state2; however, understanding the properties of dense hydrogen has been more complex than originally thought, because under extreme conditions the electrons and protons are strongly coupled to each other and ultimately must both be treated as quantum particles3,4. Therefore, how and when molecular solid hydrogen may transform into a metal is an open question. Although the quest for metal hydrogen has pushed major developments in modern experimental high-pressure physics, the various claims of its observation remain unconfirmed5-7. Here a discontinuous change of the direct bandgap of hydrogen, from 0.6 electronvolts to below 0.1 electronvolts, is observed near 425 gigapascals. This result is most probably associated with the formation of the metallic state because the nucleus zero-point energy is larger than this lowest bandgap value. Pressures above 400 gigapascals are achieved with the recently developed toroidal diamond anvil cell8, and the structural changes and electronic properties of dense solid hydrogen at 80 kelvin are probed using synchrotron infrared absorption spectroscopy. The continuous downward shifts of the vibron wavenumber and the direct bandgap with increased pressure point to the stability of phase-III hydrogen up to 425 gigapascals. The present data suggest that metallization of hydrogen proceeds within the molecular solid, in good agreement with previous calculations that capture many-body electronic correlations9.

Monitoring the Kinetics of the Cellular Uptake of a Metal Carbonyl Conjugated with a Lipidic Moiety in Living Cells Using Synchrotron Infrared Spectromicroscopy.

Presented here is the exploitation of synchrotron infrared spectromicroscopy to evaluate the feasibility of monitoring the cellular uptake of rhenium-tris-carbonyl-tagged (Re(CO)3) lipophilic chains in living cells. To this aim, an in-house thermostated microfluidic device was used to limit water absorption while keeping cells alive. Indeed, cells showed a high survival rate in the microfluidic device over the course of the experiment, proving the short-term biocompatibility of the device. We recorded spectra of single, living, fully hydrated breast cancer MDA-MB231 cells and could follow the penetration of the rhenium complexes for up to 2 h. Despite the strong variations observed in the uptake kinetics between individual cells, the Re(CO)3 complex was traced inside the cells at low concentration and shown to enter them on the hour time scale by active transport.

Abiotic synthesis of amino acids in the recesses of the oceanic lithosphere.

Abiotic hydrocarbons and carboxylic acids are known to be formed on Earth, notably during the hydrothermal alteration of mantle rocks. Although the abiotic formation of amino acids has been predicted both from experimental studies and thermodynamic calculations, its occurrence has not been demonstrated in terrestrial settings. Here, using a multimodal approach that combines high-resolution imaging techniques, we obtain evidence for the occurrence of aromatic amino acids formed abiotically and subsequently preserved at depth beneath the Atlantis Massif (Mid-Atlantic Ridge). These aromatic amino acids may have been formed through Friedel-Crafts reactions catalysed by an iron-rich saponite clay during a late alteration stage of the massif serpentinites. Demonstrating the potential of fluid-rock interactions in the oceanic lithosphere to generate amino acids abiotically gives credence to the hydrothermal theory for the origin of life, and may shed light on ancient metabolisms and the functioning of the present-day deep biosphere.

Direct and rapid identification of T315I-Mutated BCR-ABL expressing leukemic cells using infrared microspectroscopy.

Despite the major success obtained by the use of tyrosine kinase inhibitors (TKI) in chronic myeloid leukemia (CML), resistances to therapies occur due to mutations in the ABL-kinase domain of the BCR-ABL oncogene. Amongst these mutations, the "gatekeeper" T315I is a major concern as it renders leukemic cells resistant to all licenced TKI except Ponatinib. We report here that Fourier transform infrared (FTIR) microspectroscopy is a powerful methodology allowing rapid and direct identification of a spectral signature in single cells expressing T315I-mutated BCR-ABL. The specificity of this spectral signature is confirmed using a Dox-inducible T315I-mutated BCR-ABL-expressing human UT-7 cells as well as in murine embryonic stem cells. Transcriptome analysis of UT-7 cells expressing BCR-ABL as compared to BCR-ABL T315I clearly identified a molecular signature which could be at the origin of the generation of metabolic changes giving rise to the spectral signature. Thus, these results suggest that this new methodology can be applied to the identification of leukemic cells harbouring the T315I mutation at the single cell level and could represent a novel early detection tool of mutant clones. It could also be applied to drug screening strategies to target T315I-mutated leukemic cells.

Low-aberration beamline optics for synchrotron infrared nanospectroscopy.

Synchrotron infrared nanospectroscopy is a recently developed technique that enables new possibilities in the broadband chemical analysis of materials in the nanoscale, far beyond the diffraction limit in this frequency domain. Synchrotron infrared ports have exploited mainly the high brightness advantage provided by electron storage rings across the whole infrared range. However, optical aberrations in the beam produced by the source depth of bending magnet emission at large angles prevent infrared nanospectroscopy to reach its maximum capability. In this work we present a low-aberration optical layout specially designed and constructed for a dedicated synchrotron infrared nanospectroscopy beamline. We report excellent agreement between simulated beam profiles (from standard wave propagation and raytracing optics simulations) with experimental measurements. We report an important improvement in the infrared nanospectroscopy experiment related to the improved beamline optics. Finally, we demonstrate the performance of the nanospectroscopy endstation by measuring a hyperspectral image of a polar material and we evaluate the setup sensitivity by measuring ultra-thin polymer films down to 6 nm thick.

Discrimination of cirrhotic nodules, dysplastic lesions and hepatocellular carcinoma by their vibrational signature.

BACKGROUND: Hepatocarcinogenesis is a multistep process characterized in patients with chronic liver diseases by a spectrum of hepatic nodules that mark the progression from regenerative nodules to dysplastic lesions followed by hepatocellular carcinoma (HCC). The differential diagnosis between precancerous dysplastic nodules and early HCC still represents a challenge for both radiologists and pathologists. We addressed the potential of Fourier transform-infrared (FTIR) microspectroscopy for grading cirrhotic nodules on frozen tissue sections. METHODS: The study was focused on 39 surgical specimens including normal livers (n = 11), dysplastic nodules (n = 6), early HCC (n = 1), progressed HCC on alcoholic cirrhosis (n = 10) or hepatitis C virus cirrhosis (n = 11). The use of the bright infrared source emitted by the synchrotron radiation allowed investigating the biochemical composition at the cellular level. Chemical mapping on whole tissue sections was further performed using a FTIR microscope equipped with a laboratory-based infrared source. The variance was addressed by principal component analysis. RESULTS: Profound alterations of the biochemical composition of the pathological liver were demonstrated by FTIR microspectroscopy. Indeed, dramatic changes were observed in lipids, proteins and sugars highlighting the metabolic reprogramming in carcinogenesis. Quantifiable spectral markers were characterized by calculating ratios of areas under specific bands along the infrared spectrum. These markers allowed the discrimination of cirrhotic nodules, dysplastic lesions and HCC. Finally, the spectral markers can be measured using a laboratory FTIR microscope that may be easily implemented at the hospital. CONCLUSION: Metabolic reprogramming in liver carcinogenesis can constitute a signature easily detectable using FTIR microspectroscopy for the diagnosis of precancerous and cancerous lesions.

Use of infrared microspectroscopy to elucidate a specific chemical signature associated with hypoxia levels found in glioblastoma.

Hypoxia is a common feature of solid tumours and is associated with poor prognosis, resistance to radio- and chemotherapy, and tumour aggressiveness. For predictive purposes as well as for improved therapeutic intervention, it is increasingly needed to have direct and specific diagnostic tools in order to measure the extent of, and changes in, tumour hypoxia. In this article, we have investigated the potential of Fourier Transform Infrared (FTIR) microspectroscopy, at cellular and subcellular resolution, for detecting hypoxia-induced metabolic changes in brain tumour (glioblastoma) cell lines and in short term primary cultures derived from patient samples. The most prominent and common changes observed were the increase in glycogen (specifically in the U87MG cell line) and lipids (all cell lines studied). Additionally, each cell line presented specific individual metabolic fingerprints. The metabolic changes did not evolve markedly with time (from 1 to 5 days hypoxic incubation), and yet were harder to detect under chronic hypoxic conditions, which is consistent with cellular adaptation occurring upon long term changes in the microenvironment. The metabolic signature was similar regardless of the severity of the hypoxic insult and was replicated by the hypoxia mimetic drug dimethyloxalylglycine (DMOG). To investigate any specific changes at subcellular levels and to improve the sensitivity of the detection method, spectra were recorded separately in the cytoplasm and in the nucleus of D566 glioblastoma cells, thanks to the use of a synchrotron source. We show that this method provides improved detection in both cell compartments. Whilst there was a high spectral variability between cell lines, we show that FTIR microspectroscopy allowed the detection of the common metabolic changes triggered by hypoxia regardless of cell type, providing a potential new approach for the detection of hypoxic tumours.

Understanding the cryotolerance of lactic acid bacteria using combined synchrotron infrared and fluorescence microscopies.

Freezing is widely used for preserving different types of cells. Frozen concentrates of lactic acid bacteria (LAB) are extensively used for manufacturing food, probiotic products and for green chemistry and medical applications. However, the freezing and thawing processes cause cell injuries that result in significant cell death. Producing homogeneous bacterial populations with high cryotolerance remains a real challenge. Our objective was to investigate the biochemical and physiological changes in a LAB model at the cell scale following fermentation and freezing in order to identify cellular biomarkers of cryotolerance. Infrared spectra of individual bacteria produced by applying different fermentation and freezing conditions were acquired using synchrotron radiation-based Fourier-transform infrared (SR-FTIR) microspectroscopy to achieve sub-cellular spatial resolution. Fluorescent microscopy was concomitantly assessed, thus making possible to simultaneously analyse the biochemistry and physiological state of a single cell for the first time. Principal component analysis was used to evaluate changes in cell composition, with particular focus on lipids, proteins and polysaccharides. SR-FTIR results indicated that before freezing, freeze-resistant cells grown in a rich medium presented a high content of CH3 groups from lipid chains, of cell proteins in an α-helix secondary structure and of charged polymers such as teichoic and lipoteichoic acids that constitute the Gram-positive bacterial wall. Moreover, SR-FTIR microspectroscopy made it possible to reveal cell heterogeneity within the cluster of resistant cells, which was ascribed to the diversity of potential substrates in the growth medium. Freezing and thawing processes induced losses of membrane integrity and cell viability in more than 90% of the freeze-sensitive bacterial population. These damages leading to cell death were ascribed to biochemical modification of cell membrane phospholipids, in particular a rigidification of the cytoplasmic membrane following freezing. Furthermore the freeze-resistant cells remained viable after freezing and thawing but a modification of protein secondary structure was detected by SR-FTIR analysis. These results highlighted the potential application of bimodal analysis by SR-FTIR and fluorescence microscopy to increase our knowledge about mechanisms related to cell damage.

Synthesis of lithium polyhydrides above 130 GPa at 300 K.

The prediction of novel lithium hydrides with nontraditional stoichiometries at high pressure has been seminal for highlighting a promising line of research on hydrogen-dense materials. Here, we report the evidences of the disproportionation of LiH above 130 GPa to form lithium hydrides containing H2 units. Measurements have been performed using the nonperturbing technique of synchrotron infrared absorption. The observed vibron frequencies match the predictions for LiH2 and LiH6. These polyhydrides remain insulating up to 215 GPa. A disproportionation mechanism based on the diffusion of lithium into the diamond anvil and a stratification of the sample into LiH6/LiH2/LiH layers is proposed. Polyhydrides containing an H2 sublattice do exist and could be ubiquitously stable at high pressure.

The biochemical changes in hippocampal formation occurring in normal and seizure experiencing rats as a result of a ketogenic diet.

In this study, ketogenic diet-induced biochemical changes occurring in normal and epileptic hippocampal formations were compared. Four groups of rats were analyzed, namely seizure experiencing animals and normal rats previously fed with ketogenic (KSE and K groups respectively) or standard laboratory diet (NSE and N groups respectively). Synchrotron radiation based Fourier-transform infrared microspectroscopy was used for the analysis of distributions of the main organic components (proteins, lipids, compounds containing phosphate group(s)) and their structural modifications as well as anomalies in creatine accumulation with micrometer spatial resolution. Infrared spectra recorded in the molecular layers of the dentate gyrus (DG) areas of normal rats on a ketogenic diet (K) presented increased intensity of the 1740 cm(-1) absorption band. This originates from the stretching vibrations of carbonyl groups and probably reflects increased accumulation of ketone bodies occurring in animals on a high fat diet compared to those fed with a standard laboratory diet (N). The comparison of K and N groups showed, moreover, elevated ratios of absorbance at 1634 and 1658 cm(-1) for DG internal layers and increased accumulation of creatine deposits in sector 3 of the Ammon's horn (CA3) hippocampal area of ketogenic diet fed rats. In multiform and internal layers of CA3, seizure experiencing animals on ketogenic diet (KSE) presented a lower ratio of absorbance at 1634 and 1658 cm(-1) compared to rats on standard laboratory diet (NSE). Moreover, in some of the examined cellular layers, the increased intensity of the 2924 cm(-1) lipid band as well as the massifs of 2800-3000 cm(-1) and 1360-1480 cm(-1), was found in KSE compared to NSE animals. The intensity of the 1740 cm(-1) band was diminished in DG molecular layers of KSE rats. The ketogenic diet did not modify the seizure induced anomalies in the unsaturation level of lipids or the number of creatine deposits.

Vibrational signatures to discriminate liver steatosis grades.

Non-alcoholic fatty liver disease (NAFLD) is a frequent lesion associated with obesity, diabetes and the metabolic syndrome. The hallmark feature of fatty liver disease is steatosis, which is the intra-cellular accumulation of lipids resulting in the formation of vesicles in hepatocytes. Steatosis is a precursor of steatohepatitis, a condition that may progress to hepatic fibrosis, cirrhosis and primary liver cancer. We addressed the potential of Fourier transform-infrared (FTIR) microspectroscopy for grading steatosis on frozen tissue sections. The use of the bright infrared source emitted by synchrotron radiation (SR) allowed the investigation of the biochemical composition at the cellular level. The variance in the huge number of spectra acquired was addressed by principal component analysis (PCA). The study demonstrated that the progression of steatosis corresponds not only to the accumulation of lipids but also to dramatic changes in the qualitative composition of the tissue. Indeed, a lower grade of steatosis showed a decrease in glycogen content and a concomitant increase in lipids in comparison with normal liver. Intermediate steatosis exhibited an increase in glycogen and major changes in lipids, with a significant contribution of esterified fatty acids with elongated carbon chains and unsaturated lipids, and these features were more pronounced in a high grade of steatosis. Furthermore, the approach allows a systematic discrimination of morphological features, leading to a separate investigation of steatotic vesicles and the non-steatotic counterpart of the tissue. This highlighted the fact that dramatic biochemical changes occur in the non-steatotic part of the tissue also despite its normal histological aspect, suggesting that the whole tissue reflects the grade of steatosis.

Pressure-induced chemistry in a nitrogen-hydrogen host-guest structure.

New topochemistry in simple molecular systems can be explored at high pressure. Here we examine the binary nitrogen/hydrogen system using Raman spectroscopy, synchrotron X-ray diffraction, synchrotron infrared microspectroscopy and visual observation. We find a eutectic-type binary phase diagram with two stable high-pressure van der Waals compounds, which we identify as (N2)6(H2)7 and N2(H2)2. The former represents a new type of van der Waals host-guest compound in which hydrogen molecules are contained within channels in a nitrogen lattice. This compound shows evidence for a gradual, pressure-induced change in bonding from van der Waals to ionic interactions near 50 GPa, forming an amorphous dinitrogen network containing ionized ammonia in a room-temperature analogue of the Haber-Bosch process. Hydrazine is recovered on decompression. The nitrogen-hydrogen system demonstrates the potential for new pressure-driven chemistry in high-pressure structures and the promise of tailoring molecular interactions for materials synthesis.

Study of gemcitabine-sensitive/resistant cancer cells by cell cloning and synchrotron FTIR microspectroscopy.

Over the last few years, significant scientific insight on the effects of chemotherapy drugs at cellular level using synchrotron-based FTIR (S-FTIR) microspectroscopy has been obtained. The work carried out so far has identified spectral differences in cancer cells before and after the addition of drugs. However, this had to account for the following issues. First, chemotherapy agents cause both chemical and morphological changes in cells, the latter being responsible for changes in the spectral profile not correlated with biochemical characteristics. Second, as the work has been carried out in mixed populations of cells (resistant and sensitive), it is important to distinguish the spectral differences which are due to sensitivity/resistance to those due to cell morphology and/or cell mixture. Here, we successfully cloned resistant and sensitive lung cancer cells to a chemotherapy drug. This allowed us to study a more uniform population and, more important, allowed us to study sensitive and resistant cells prior to the addition of the drug with S-FTIR microscopy. Principal component analysis (PCA) did not detect major differences in resistant cells prior to and after adding the drug. However, PCA separated sensitive cells prior to and after the addition of the drug. This would indicate that the spectral differences between cells prior to and after adding a drug might reside on those more or less sensitive cells that have been able to remain alive when they were collected to be studied with S-FTIR microspectroscopy. This is a proof of concept and a feasibility study showing a methodology that opens a new way to identify the effects of drugs on more homogeneous cell populations using vibrational spectroscopy.

Protein matrix involved in the lipid retention of foie gras during cooking: a multimodal hyperspectral imaging study.

Denaturation of the protein matrix during heat treatment of duck foie gras was studied in relationship to the amount of fat loss during cooking. A low fat loss group was compared with a high fat loss group by histochemistry, FT-IR, and synchrotron UV microspectroscopy combination to characterize their protein matrix at different scales. After cooking, the high fat loss group showed higher densification of its matrix, higher ultraviolet tyrosine autofluorescence, and an infrared shift of the amide I band. These results revealed a higher level of protein denaturation and aggregation during cooking in high fat loss than in low fat loss foie gras. In addition, the fluorescence and infrared responses of the raw tissue revealed differences according to the level of fat losses after cooking. These findings highlight the importance of the supramolecular state of the protein matrix in determining the fat loss of foie gras.

Medical approach to the treatment of feline injection site sarcoma with masitinib: a case report.

Feline injection site sarcoma is a common tumor among cats, for which existing medical treatments do not prove to be entirely satisfactory. In this tumor, the platelet-derived growth factor receptor, a tyrosine kinase receptor, is frequently hyperactivated. In the past, clinical case reports with imatinib, a tyrosine kinase inhibitor (TKI), have demonstrated tumoral stabilization. Here we describe the use of another TKI, masitinib, which specifically inhibits c-Kit, platelet-derived growth factor receptor, and Lyn, and is currently licensed for veterinary use in canine mast cell tumors. The therapeutic results were initially satisfactory, with regression of the tumor followed by tumoral recurrence which was stabilized and moderately reduced. Further studies are suggested, in order to evaluate the relevance of TKIs in the treatment and prevention of recurrences of feline injection site sarcoma. Tumoral stabilization by means of an inexpensive and reasonably well tolerated treatment would prove to be of true therapeutic relevance, in particular for inoperable feline injection site sarcomas. Another indication for such TKIs could be in preoperative treatment as a means of facilitating surgical excision by reduction of adhesions.