Disentangling the chemistry of Australian plant exudates from a unique historical collection.

For thousands of years, the unique physicochemical properties of plant exudates have defined uses in material culture and practical applications. Native Australian plant exudates, including resins, kinos, and gums, have been used and continue to be used by Aboriginal Australians for numerous technical and cultural purposes. A historic collection of well-preserved native Australian plant exudates, assembled a century ago by plant naturalists, gives a rare window into the history and chemical composition of these materials. Here we report the full hierarchical characterization of four genera from this collection, Xanthorrhoea, Callitris, Eucalyptus, and Acacia, from the local elemental speciation, to functional groups and main molecular markers. We use high-resolution X-ray Raman spectroscopy (XRS) to achieve bulk-sensitive chemical speciation of these plant exudates, including insoluble, amorphous, and cross-linked fractions, without the limitation of invasive and/or surface specific methods. Combinatorial testing of the XRS data allows direct classification of these complex natural species as terpenoid, aromatic, phenolic, and polysaccharide materials. Differences in intragenera chemistry was evidenced by detailed interpretation of the XRS spectral features. We complement XRS with Fourier-transform infrared (FT-IR) spectroscopy, gas chromatography­mass spectrometry (GC-MS), and pyrolysis­GC-MS (Py-GC-MS). This multimodal approach provides a fundamental understanding of the chemistry of these natural materials long used by Aboriginal Australian peoples.

X-ray Raman Scattering: A Hard X-ray Probe of Complex Organic Systems.

This paper provides a review of the characterization of organic systems via X-ray Raman scattering (XRS) and a step-by-step guidance for its application. We present the fundamentals of XRS required to use the technique and discuss the main parameters of the experimental set-ups to optimize spectral and spatial resolution while maximizing signal-to-background ratio. We review applications that target the analysis of mixtures of organic compounds, the identification of minor spectral features, and the spatial discrimination in heterogeneous systems. We discuss the recent development of the direct tomography technique, which utilizes the XRS process as a contrast mechanism for assessing the three-dimensional spatially resolved carbon chemistry of complex organic materials. We conclude by exposing the current limitations and provide an outlook on how to overcome some of the existing challenges and advance future developments and applications of this powerful technique for complex organic systems.

Triple Thorpe-Ingold Effect in the Synthesis of 18-Membered C3 Symmetric Lactams Stacking as Endless Supramolecular Tubes.

Three C3 symmetric macrolactams were very efficiently cyclized from their linear precursors. Adequately located substituents are responsible for the enhancement of reactivity that is not observed in the unsubstituted parent. DFT calculations show that the properly folded cyclization precursor, the reactive conformer, is more populated than other conformers, leading to a decrease of free energy of activation. The crystal structure of the ring substituted with three very bulky esters indicates that tubular stacking is preserved.

XANES-Based Quantification of Carbon Functional Group Concentrations.

X-ray absorption spectroscopy in the soft X-ray range is used in many research fields to identify the nature of functional groups in organic compounds and carbon materials. However, the concentrations of these functional groups have so far remained difficult to quantify. Using X-ray absorption near edge structure (XANES) spectra of reference materials (polymers and compounds of known molecular composition), we established a correlation between measured optical densities and functional groups concentration. This methodology relies on an alternative method for normalization to the total amount of carbon and for deconvolution of the spectra. It allows precisely quantifying the N/C atomic ratio (σ1 = 0.02 atom %) as well as the concentration of [aromatic + olefinic] groups (σ1 = 3.7 atom %), [ketone + phenol + nitrile] groups (σ1 = 2.2 atom %), [aliphatic] groups (σ1 = 11.2 atom %) and [carboxylic] groups (σ1 = 7.4 atom %). We validated this quantification by comparing with nuclear magnetic resonance data obtained on pyrolized lignin samples. We also provide an easy-to-use python program automating XANES-based quantification of carbon functional group concentrations.

Noninvasive Synchrotron-Based X-ray Raman Scattering Discriminates Carbonaceous Compounds in Ancient and Historical Materials.

Carbon compounds are ubiquitous and occur in a diversity of chemical forms in many systems including ancient and historic materials ranging from cultural heritage to paleontology. Determining their speciation cannot only provide unique information on their origin but may also elucidate degradation processes. Synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy at the carbon K-edge (280-350 eV) is a very powerful method to probe carbon speciation. However, the short penetration depth of soft X-rays imposes stringent constraints on sample type, preparation, and analytical environment. A hard X-ray probe such as X-ray Raman scattering (XRS) can overcome many of these difficulties. Here we report the use of XRS at ∼6 keV incident energy to collect carbon K-edge XANES data and probe the speciation of organic carbon in several specimens relevant to cultural heritage and natural history. This methodology enables the measurement to be done in a nondestructive way, in air, and provides information that is not compromised by surface contamination by ensuring that the dominant signal contribution is from the bulk of the probed material. Using the backscattering geometry at large photon momentum transfer maximizes the XRS signal at the given X-ray energy and enhances nondipole contributions compared to conventional XANES, thereby augmenting the speciation sensitivity. The capabilities and limitations of the technique are discussed. We show that despite its small cross section, for a range of systems the XRS method can provide satisfactory signals at realistic experimental conditions. XRS constitutes a powerful complement to FT-IR, Raman, and conventional XANES spectroscopy, overcoming some of the limitations of these techniques.

Burden of rotavirus disease: A population-based study in Eastern Townships, Quebec.

BACKGROUND: Since July 2010, the National Advisory Committee on Immunization of Canada has recommended rotavirus vaccination for all healthy infants. However, before implementing this vaccine in routine health programs, Canadian provinces need to establish current epidemiological data on rotavirus-associated acute gastroenteritis (AGE). METHODS: A retrospective cohort study of children <5 years of age with AGE from 2002 to 2008 was performed in Eastern Townships, Quebec (population in 2006: 298,780). Data were collected on visits to outpatient clinics, emergency department (ED) visits, hospitalizations (standard and short-stay units) and nosocomial AGE. The winter residual estimation and Brandt methods were used to estimate the proportion of AGE attributable to rotaviruses. RESULTS: During the six-year study period, a total of 1435 hospitalizations, 3631 ED visits and 6220 ambulatory care visits were attributed to AGE. The specific rotavirus burden was estimated to be 449 to 666 for hospitalizations, 1050 to 1361 for ED visits and 1633 to 1687 for outpatient visits. The epidemic curve showed a periodicity with higher incidence in March and April. Short-stay unit hospitalizations represented 58% of all hospitalizations. The annual incidence rate of rotaviruses was estimated to be 50 to 74 per 10,000 children for hospitalizations, 117 to 152 per 10,000 children for ED visits and 182 to 188 per 10,000 children for outpatient visits. CONCLUSION: Most available retrospective studies probably underestimate rotavirus-associated hospitalizations because they do not take into account short-stay unit hospitalizations. Furthermore, these data on emergency and outpatient visits provide an exhaustive appraisal of the rotavirus burden, which serves as crucial information for the evaluation of immunization programs.

HISTORIQUE: Depuis juillet 2010, le Comité consultatif national de l'immunisation recommande de vacciner tous les nourrissons en santé contre le rotavirus. Cependant, avant d'ajouter ce vaccin aux programmes de vaccination systématique, les provinces canadiennes doivent obtenir des données épidémiologiques à jour sur la gastro-entérite aiguë (GEA) associée au rotavirus. MÉTHODOLOGIE: Les chercheurs ont effectué une étude de cohorte rétrospective auprès d'enfants de moins de cinq ans ayant eu une GEA entre 2002 et 2008 en Estrie, au Québec (population de 298 780 habitants en 2006). Ils ont colligé les données aux consultations externes, au département d'urgence (DU), chez les patients hospitalisés (unités standard et de courte durée) et relatives aux cas de GEA nosocomiales. Ils ont utilisé l'estimation hivernale résiduelle et les méthodologies de Brandt pour évaluer la proportion de GEA attribuables aux rotavirus. RÉSULTATS: Pendant la période d'étude de six ans, 1 435 hospitalisations, 3 631 consultations au DU et 6 220 consultations externes étaient attribuables à la GEA. On estimait que le fardeau propre à la GEA se situait entre 449 et 666 pour les hospitalisations, entre 1 050 et 1 361 pour les consultations au DU et entre 1 633 et 1 687 pour les consultations externes. La courbe épidémique a révélé une périodicité à l'incidence plus élevée en mars et avril. Les hospitalisations de courte durée représentaient 58 % de toutes les hospitalisations. On estime que le taux d'incidence annuel des rotavirus oscille entre 50 et 74 cas sur 10 000 enfants sur le plan des hospitalisations, entre 117 et 152 cas sur 10 000 enfants sur le plan des consultations au DU et entre 182 et 188 cas sur 10 000 enfants sur le plan des consultations externes. CONCLUSION: Selon toute probabilité, la plupart des études rétrospectives disponibles sous-estiment le nombre d'hospitalisations associées au rotavirus parce qu'elles ne tiennent pas compte des hospitalisations dans les unités de courte durée. De plus, ces données sur les consultations externes et à l'urgence fournissent une évaluation détaillée du fardeau du rotavirus, qui contient de l'information capitale pour évaluer les programmes de vaccination.

Production of carbon-containing pyrite spherules induced by hyperthermophilic Thermococcales: a biosignature?

Thermococcales, a major order of hyperthermophilic archaea inhabiting iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, are known to induce the formation of iron phosphates, greigite (Fe3S4) and abundant quantities of pyrite (FeS2), including pyrite spherules. In the present study, we report the characterization of the sulfide and phosphate minerals produced in the presence of Thermococcales using X-ray diffraction, synchrotron-based X ray absorption spectroscopy and scanning and transmission electron microscopies. Mixed valence Fe(II)-Fe(III) phosphates are interpreted as resulting from the activity of Thermococcales controlling phosphorus-iron-sulfur dynamics. The pyrite spherules (absent in abiotic control) consist of an assemblage of ultra-small nanocrystals of a few ten nanometers in size, showing coherently diffracting domain sizes of few nanometers. The production of these spherules occurs via a sulfur redox swing from S0 to S-2 and then to S-1, involving a comproportionation of (-II) and (0) oxidation states of sulfur, as supported by S-XANES data. Importantly, these pyrite spherules sequester biogenic organic compounds in small but detectable quantities, possibly making them good biosignatures to be searched for in extreme environments.

Rapid grain boundary diffusion in foraminifera tests biases paleotemperature records.

The oxygen isotopic compositions of fossil foraminifera tests constitute a continuous proxy record of deep-ocean and sea-surface temperatures spanning the last 120 million years. Here, by incubating foraminifera tests in 18O-enriched artificial seawater analogues, we demonstrate that the oxygen isotopic composition of optically translucent, i.e., glassy, fossil foraminifera calcite tests can be measurably altered at low temperatures through rapid oxygen grain-boundary diffusion without any visible ultrastructural changes. Oxygen grain boundary diffusion occurs sufficiently fast in foraminifera tests that, under normal upper oceanic sediment conditions, their grain boundaries will be in oxygen isotopic equilibrium with the surrounding pore fluids on a time scale of <100 years, resulting in a notable but correctable bias of the paleotemperature record. When applied to paleotemperatures from 38,400 foraminifera tests used in paleoclimate reconstructions, grain boundary diffusion can be shown to bias prior paleotemperature estimates by as much as +0.86 to -0.46 °C. The process is general and grain boundary diffusion corrections can be applied to other polycrystalline biocarbonates composed of small nanocrystallites (<100 nm), such as those produced by corals, brachiopods, belemnites, and molluscs, the fossils of which are all highly susceptible to the effects of grain boundary diffusion.

Gardnerella vaginalis as a rare cause of prosthetic joint infection.

We describe a septic loosening of a hip prosthesis in a 71-year-old woman caused by Gardnerella vaginalis. Infection was confirmed by culture and molecular identification of this bacterium. The patient was treated by a one-step exchange of prosthesis and antibiotic therapy combining trimethoprim-sulfamethoxazole and rifampin, with favorable evolution.

Fast and pervasive diagenetic isotope exchange in foraminifera tests is species-dependent.

Oxygen isotope compositions of fossil foraminifera tests are commonly used proxies for ocean paleotemperatures, with reconstructions spanning the last 112 million years. However, the isotopic composition of these calcitic tests can be substantially altered during diagenesis without discernible textural changes. Here, we investigate fluid-mediated isotopic exchange in pristine tests of three modern benthic foraminifera species (Ammonia sp., Haynesina germanica, and Amphistegina lessonii) following immersion into an 18O-enriched artificial seawater at 90 °C for hours to days. Reacted tests remain texturally pristine but their bulk oxygen isotope compositions reveal rapid and species-dependent isotopic exchange with the water. NanoSIMS imaging reveals the 3-dimensional intra-test distributions of 18O-enrichment that correlates with test ultra-structure and associated organic matter. Image analysis is used to quantify species level differences in test ultrastructure, which explains the observed species-dependent rates of isotopic exchange. Consequently, even tests considered texturally pristine for paleo-climatic reconstruction purposes may have experienced substantial isotopic exchange; critical paleo-temperature record re-examination is warranted.

Compositionally and density stratified igneous terrain in Jezero crater, Mars.

Before Perseverance, Jezero crater's floor was variably hypothesized to have a lacustrine, lava, volcanic airfall, or aeolian origin. SuperCam observations in the first 286 Mars days on Mars revealed a volcanic and intrusive terrain with compositional and density stratification. The dominant lithology along the traverse is basaltic, with plagioclase enrichment in stratigraphically higher locations. Stratigraphically lower, layered rocks are richer in normative pyroxene. The lowest observed unit has the highest inferred density and is olivine-rich with coarse (1.5 millimeters) euhedral, relatively unweathered grains, suggesting a cumulate origin. This is the first martian cumulate and shows similarities to martian meteorites, which also express olivine disequilibrium. Alteration materials including carbonates, sulfates, perchlorates, hydrated silicates, and iron oxides are pervasive but low in abundance, suggesting relatively brief lacustrine conditions. Orbital observations link the Jezero floor lithology to the broader Nili-Syrtis region, suggesting that density-driven compositional stratification is a regional characteristic.

Simultaneous chirality transfer and structured aggregation of a cyclopeptide in a liquid crystal.

We report the finding that a chiral cyclopeptide dissolved in a nematic liquid crystal (LC) host could aggregate in a manner that is controlled by the texture (LC director configuration) of a cholesteric phase that is induced by the cyclopeptide itself. On one hand, with the fingerprint texture, where the helical axis formed by rotating LC molecules, that lies in the substrate plane, the cyclopeptide can use the LC texture as a template to aggregate and form long-range-ordered ribbons that mimic the helical configuration of the LC director. On the other hand, with the planar texture, where the helical axis is normal to the substrate plane, the cyclopeptide can migrate into the "oily-streak" defect regions of the cholesteric phase and stabilize a network of defects that dictates the electrooptical response of the LC. This is the first example of a molecular species exhibiting such a structured aggregation and defect stabilization effect in a cholesteric LC, but similar phenomena were previously reported for platinum nanoparticles and silica colloidal particles, respectively, dispersed in a cholesteric LC host. This study provides more evidence for the potential interest of exploring LCs as an anisotropic medium for mediating the aggregation and assembly of cyclopeptides.

Multiple stages of plant root calcification deciphered by chemical and micromorphological analyses.

Rhizoliths, that is, roots fossilized by secondary carbonates, have been known for ages and are increasingly used for paleoenvironmental reconstructions. However, knowledge about their formation mechanisms remains limited. This study reports the mineralogical and chemical characterization of rhizoliths at different stages of mineralization and fossilization in the Late Pleistocene loess-paleosol sequence of Nussloch (SW Germany). Scanning electron microscopy coupled with elemental mapping and 13 C solid-state nuclear magnetic resonance were used to concomitantly characterize the mineral and organic matter of the rhizoliths. These joint analyses showed for the first time that large rhizoliths are not necessarily remains of single large roots but consist of numerous microrhizoliths as remains of fine roots, formed mainly by calcium carbonates with only low amounts of Mg and Si. They further revealed that the precipitation of secondary carbonates occurs not only around, but also within the plant root and that fossilization leads to the selective preservation of recalcitrant root biopolymers-lignin and suberin. The precipitation of secondary carbonates was observed to occur first around fine roots, the epidermis acting as a first barrier, and then within the root, within the cortex cells, and even sometimes around the phloem and within the xylem. This study suggests that the calcification of plant roots starts during the lifetime of the plant and continues after its death. This has to be systematically investigated to understand the stratigraphic context before using (micro)rhizoliths for paleoenvironmental reconstructions in terrestrial sediments.

Martian Magmatic Clay Minerals Forming Vesicles: Perfect Niches for Emerging Life?

Mars was habitable in its early history, but the consensus is that it is quite inhospitable today, in particular because its modern climate cannot support stable liquid water at the surface. Here, we report the presence of magmatic Fe/Mg clay minerals within the mesostasis of the martian meteorite NWA 5790, an unaltered 1.3 Ga nakhlite archetypal of the martian crust. These magmatic clay minerals exhibit a vesicular texture that forms a network of microcavities or pockets, which could serve as microreactors and allow molecular crowding, a necessary step for the emergence of life. Because their formation does not depend on climate, such niches for emerging life may have been generated on Mars at many periods throughout its history, regardless of the stability or availability of liquid water at the surface.

Infrared spectroscopy quantification of functional carbon groups in kerogens and coals: A calibration procedure.

The determination of the abundances of the CHx, C = O and aromatic groups in chondritic Insoluble Organic Matter (IOM) and coals by Infrared (IR) spectroscopy is a challenging issue due to insufficient knowledge on the absorption cross-sections and their sensitivity to the molecular environment. Here, we report a calibration approach based on a 13C synthetic model material whose composition was unambiguously determined by Direct-Pulse/Magic Angle Spinning Nuclear Magnetic Resonance (DP/MAS NMR). Ratios of the cross-sections of the CHx, C = O and aromatic groups have been determined, and the method has been applied to IOM samples extracted from four chondrites as Orgueil (CI), Murchison (CM), Tagish Lake (C2-ungrouped) and EET 92042 (CR2), and to a series of coals. The estimate of the aliphatic to aromatic carbon ratio (nCHx/nAro) in IOM samples from Orgueil, Murchison and Tagish Lake chondrites is in good agreement with Single-Pulse/NMR estimates earlier published, and is lower by a factor of 1.3 in the case of the CR chondrite EET 92042 (but the error bars overlap). In contrast, the aliphatic to carbonyl ratio (nCHx/nC=O) is overestimated for the four chondrites. These discrepancies are likely due to the control of the absorption cross-section of the C = O and C = C bonds by the local molecular environment. Regarding coals, the use of published NMR analyses has brought to light that the integrated cross-section ratio ACHx/AAro varies with the vitrinite reflectance over an order of magnitude. Here as well, the local oxygen speciation plays a critical control in AAro, which decreases with increasing the vitrinite reflectance. We provide an analytical law that links ACHx/AAro and vitrinite reflectance, which will allow the determination of nCHx/nAro for any coal sample, provided its vitrinite reflectance is known.

The SuperCam Instrument Suite on the NASA Mars 2020 Rover: Body Unit and Combined System Tests.

The SuperCam instrument suite provides the Mars 2020 rover, Perseverance, with a number of versatile remote-sensing techniques that can be used at long distance as well as within the robotic-arm workspace. These include laser-induced breakdown spectroscopy (LIBS), remote time-resolved Raman and luminescence spectroscopies, and visible and infrared (VISIR; separately referred to as VIS and IR) reflectance spectroscopy. A remote micro-imager (RMI) provides high-resolution color context imaging, and a microphone can be used as a stand-alone tool for environmental studies or to determine physical properties of rocks and soils from shock waves of laser-produced plasmas. SuperCam is built in three parts: The mast unit (MU), consisting of the laser, telescope, RMI, IR spectrometer, and associated electronics, is described in a companion paper. The on-board calibration targets are described in another companion paper. Here we describe SuperCam's body unit (BU) and testing of the integrated instrument. The BU, mounted inside the rover body, receives light from the MU via a 5.8 m optical fiber. The light is split into three wavelength bands by a demultiplexer, and is routed via fiber bundles to three optical spectrometers, two of which (UV and violet; 245-340 and 385-465 nm) are crossed Czerny-Turner reflection spectrometers, nearly identical to their counterparts on ChemCam. The third is a high-efficiency transmission spectrometer containing an optical intensifier capable of gating exposures to 100 ns or longer, with variable delay times relative to the laser pulse. This spectrometer covers 535-853 nm ( 105 - 7070 cm - 1 Raman shift relative to the 532 nm green laser beam) with 12 cm - 1 full-width at half-maximum peak resolution in the Raman fingerprint region. The BU electronics boards interface with the rover and control the instrument, returning data to the rover. Thermal systems maintain a warm temperature during cruise to Mars to avoid contamination on the optics, and cool the detectors during operations on Mars. Results obtained with the integrated instrument demonstrate its capabilities for LIBS, for which a library of 332 standards was developed. Examples of Raman and VISIR spectroscopy are shown, demonstrating clear mineral identification with both techniques. Luminescence spectra demonstrate the utility of having both spectral and temporal dimensions. Finally, RMI and microphone tests on the rover demonstrate the capabilities of these subsystems as well.

A new polychelidan lobster preserved with its eggs in a 165 Ma nodule.

Crustacean eggs are rare in the fossil record. Here we report the exquisite preservation of a fossil polychelidan embedded within an unbroken nodule from the Middle Jurassic La Voulte-sur-Rhône Lagerstätte (France) and found with hundreds of eggs attached to the pleon. This specimen belongs to a new species, Palaeopolycheles nantosueltae sp. nov. and offers unique clues to discuss the evolution of brooding behaviour in polychelidan lobsters. In contrast to their development, which now relies on a long-lived planktic larval stage that probably did not exist in the early evolutionary steps of the group, the brood size of polychelidan lobsters seems to have remained unchanged and comparatively small since the Jurassic. This finding is at odds with reproductive strategies in other lobster groups, in which a long-lived planktic larval stage is associated with a large brood size.

Efficient synthesis of nevirapine analogs to study its metabolic profile by click fishing.

Knowledge of the biotransformation and pharmacokinetics of the antiretroviral agent nevirapine is still insufficient. In order to trace rash inducing metabolites of nevirapine, we devised a short and efficient multi-gram synthesis of a nevirapine analog that can be coupled to azide containing compounds by click chemistry.

The degradation of organic compounds impacts the crystallization of clay minerals and vice versa.

Expanding our capabilities to unambiguously identify ancient traces of life in ancient rocks requires laboratory experiments to better constrain the evolution of biomolecules during advanced fossilization processes. Here, we submitted RNA to hydrothermal conditions in the presence of a gel of Al-smectite stoichiometry at 200 °C for 20 days. NMR and STXM-XANES investigations revealed that the organic fraction of the residues is no longer RNA, nor the quite homogeneous aromatic-rich residue obtained in the absence of clays, but rather consists of particles of various chemical composition including amide-rich compounds. Rather than the pure clays obtained in the absence of RNA, electron microscopy (SEM and TEM) and diffraction (XRD) data showed that the mineralogy of the experimental residues includes amorphous silica and aluminosilicates mixed together with nanoscales phosphates and clay minerals. In addition to the influence of clay minerals on the degradation of organic compounds, these results evidence the influence of the presence of organic compounds on the nature of the mineral assemblage, highlighting the importance of fine-scale mineralogical investigations when discussing the nature/origin of organo-mineral microstructures found in ancient rocks.

Carbon speciation in organic fossils using 2D to 3D x-ray Raman multispectral imaging.

The in situ two-dimensional (2D) and 3D imaging of the chemical speciation of organic fossils is an unsolved problem in paleontology and cultural heritage. Here, we use x-ray Raman scattering (XRS)-based imaging at the carbon K-edge to form 2D and 3D images of the carbon chemistry in two exceptionally preserved specimens, a fossil plant dating back from the Carboniferous and an ancient insect entrapped in 53-million-year-old amber. The 2D XRS imaging of the plant fossil reveals a homogeneous chemical composition with micrometric "pockets" of preservation, likely inherited from its geological history. The 3D XRS imaging of the insect cuticle displays an exceptionally well preserved remaining chemical signature typical of polysaccharides such as chitin around a largely hollowed-out inclusion. Our results open up new perspectives for in situ chemical speciation imaging of fossilized organic materials, with the potential to enhance our understanding of organic specimens and their paleobiology.