Chlamydia psittaci infected cell studies by 4Pi Raman and atomic force microscopy.

Chlamydia psittaci is an avian bacterial pathogen that can cause atypical pneumonia in humans via zoonotic transmission. It is a Gram-negative intracellular bacterium that proliferates inside membrane bound inclusions in the cytoplasm of living eukaryotic cells. The study of such cells with C. psittaci inside without destroying them poses a significant challenge. We demonstrated in this work the utility of a combined multitool approach to analyze such complex samples. Atomic force microscopy was applied to obtain high-resolution images of the surface of infected cells upon entrance of bacteria. Atomic force microscopy scans revealed the morphological changes of the cell membrane of Chlamydia infected cells such as changes in roughness of cell membrane and the presence of micro vesicles. 4Pi Raman microscopy was used to image and probe the molecular composition of intracellular bacteria inside intact cells. Information about the structure of the inclusion produced by C. psittaci was obtained and it was found to have a similar molecular fingerprint as that of an intracellular lipid droplet but with less proteins and unsaturated lipids. The presented approach demonstrates complementarity of various microscopy-based approaches and might be useful for characterization of intracellular bacteria.

Directional Aspects of Vegetation Linear and Circular Polarization Biosignatures.

Homochirality is a generic and unique property of all biochemical life and it is considered a universal and agnostic biosignature. Upon interaction with unpolarized light, homochirality induces fractional circular polarization in the light that is scattered from it, which can be sensed remotely. As such, it can be a prime candidate biosignature in the context of future life detection missions and observatories. The linear polarizance of vegetation is also sometimes envisaged as a biosignature, although it does not share the same molecular origin as circular polarization. It is known that linear polarization of surfaces is strongly dependent on the phase angle. The relationship between the phase angle and circular polarization stemming from macromolecular assemblies such as in vegetation, however, remained unclear. In this study, using the average of 27 different species, we demonstrate that the circular polarization-phase angle dependency of vegetation induces relatively small changes in spectral shape and mostly affects the signal magnitude. With these results, we underline the use of circular spectropolarimetry as a promising agnostic biosignature complementary to the use of linear spectropolarimetry and scalar reflectance.

UV photonic integrated circuits for far-field structured illumination autofluorescence microscopy.

Ultra-violet (UV) light has still a limited scope in optical microscopy despite its potential advantages over visible light in terms of optical resolution and of interaction with a wide variety of biological molecules. The main challenge is to control in a robust, compact and cost-effective way UV light beams at the level of a single optical spatial mode and concomitantly to minimize the light propagation loss. To tackle this challenge, we present here photonic integrated circuits made of aluminum oxide thin layers that are compatible with both UV light and high-volume manufacturing. These photonic circuits designed at a wavelength of 360 nm enable super-resolved structured illumination microscopy with conventional wide-field microscopes and without modifying the usual protocol for handling the object to be imaged. As a biological application, we show that our UV photonic chips enable to image the autofluorescence of yeast cells and reveal features unresolved with standard wide-field microscopy.

Mars and the ESA Science Programme - the case for Mars polar science.

Current plans within the European Space Agency (ESA) for the future investigation of Mars (after the ExoMars programme) are centred around participation in the Mars Sample Return (MSR) programme led by NASA. This programme is housed within the Human and Robotic Exploration (HRE) Directorate of ESA. This White Paper, in response to the Voyage 2050 call, focuses on the important scientific objectives for the investigation of Mars outside the present HRE planning. The achievement of these objectives by Science Directorate missions is entirely consistent with ESA's Science Programme. We illustrate this with a theme centred around the study of the Martian polar caps and the investigation of recent (Amazonian) climate change produced by known oscillations in Mars' orbital parameters. Deciphering the record of climate contained within the polar caps would allow us to learn about the climatic evolution of another planet over the past few to hundreds of millions of years, and also addresses the more general goal of investigating volatile-related dynamic processes in the Solar System.

Morphological and Spectral Diversity of the Clay-Bearing Unit at the ExoMars Landing Site Oxia Planum.

The European Space Agency and Roscosmos' ExoMars rover mission, which is planned to land in the Oxia Planum region, will be dedicated to exobiology studies at the surface and subsurface of Mars. Oxia Planum is a clay-bearing site that has preserved evidence of long-term interaction with water during the Noachian era. Fe/Mg-rich phyllosilicates have previously been shown to occur extensively throughout the landing area. Here, we analyze data from the High Resolution Imaging Science Experiment (HiRISE) and from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) instruments onboard NASA's Mars Reconnaissance Orbiter and the Colour and Stereo Surface Imaging System (CaSSIS) onboard ESA's Trace Gas Orbiter to characterize, at a high spatial resolution, the morphological and spectral variability of Oxia Planum's surface deposits. Two main types of bedrocks are identified within the clay-bearing, fractured unit observed throughout the landing site: (1) an orange type in HiRISE correlated with the strongest detections of secondary minerals (dominated by Fe/Mg-rich clay minerals) with, in some locations, an additional spectral absorption near 2.5 µm, suggesting the mixture with an additional mineral, plausibly carbonate or another type of clay mineral; (2) a more bluish bedrock associated with weaker detections of secondary minerals, which exhibits at certain locations a ∼1 µm broad absorption feature consistent with olivine. Coanalysis of the same terrains with the recently acquired CaSSIS images confirms the variability in the color and spectral properties of the fractured unit. Of interest for the ExoMars mission, both types of bedrocks are extensively outcropping in the Oxia Planum region, and the one corresponding to the most intense spectral signals of clay minerals (the primary scientific target) is well exposed within the landing area, including near its center.

Ultra-sensitive slot-waveguide-enhanced Raman spectroscopy for aqueous solutions of non-polar compounds using a functionalized silicon nitride photonic integrated circuit.

We demonstrate an ultra-sensitive waveguide-enhanced Raman sensor for low concentration organic compounds dissolved in water. The spectra are obtained using silicon nitride slot waveguides coated with a thin film of hexamethyldisilazane-modified mesoporous silica. Enriched locally by 600-fold within the coating, a micromolar level of cyclohexanone is probed. The sensor is also capable of simultaneous quantification of multiple analytes, and the adsorbed analytes can be completely released from the coating. These properties make this on-chip Raman sensor promising for diverse applications, especially for the monitoring of non-polar organics and biomolecules in aqueous environments.

Early volumetric changes of hippocampus and medial prefrontal cortex following medial temporal lobe resection.

Previous studies have shown that cognitive demands and physical exercise stimulate adult neurogenesis in the dentate gyrus and hippocampus. Recent observations in healthy humans and patients with mild cognitive impairment moreover suggest that training-induced increases in hippocampal volume may be associated with improved memory performance. The corresponding plasticity processes in hippocampal volume may occur on timescales of months to years. For patients with focal lesions in this region, previous functional imaging studies suggest that increased recruitment of the contralateral hippocampus and extratemporal regions may be an important part of the reorganization of episodic memory. However, it is currently unclear whether focal damage to the medial temporal lobe (MTL) induces gray matter (GM) volume changes in the intact contralateral hippocampus and in connected network regions on a shorter timescale. We therefore investigated whether unilateral resection of the MTL, including the hippocampus, induces measurable volumetric changes in the contralateral hippocampus and in the default mode network (DMN). We recruited 31 patients with unilateral left (N = 19) or right (N = 12) hippocampal sclerosis undergoing MTL resection for treatment of drug-resistant epilepsy. Structural MRI was acquired immediately before and 3 months after surgery. Longitudinal voxel-based morphometry (VBM) analysis revealed a significant increase of right hippocampal volume following resection of the left anterior MTL. Furthermore, this patient group showed GM volume increases in the DMN. These results demonstrate significant structural plasticity of the contralateral hippocampus, even in patients with a long-standing unilateral hippocampal dysfunction and structural reorganization processes extending to distant, but functionally connected brain regions.

Ammonium salts are a reservoir of nitrogen on a cometary nucleus and possibly on some asteroids.

The measured nitrogen-to-carbon ratio in comets is lower than for the Sun, a discrepancy which could be alleviated if there is an unknown reservoir of nitrogen in comets. The nucleus of comet 67P/Churyumov-Gerasimenko exhibits an unidentified broad spectral reflectance feature around 3.2 micrometers, which is ubiquitous across its surface. On the basis of laboratory experiments, we attribute this absorption band to ammonium salts mixed with dust on the surface. The depth of the band indicates that semivolatile ammonium salts are a substantial reservoir of nitrogen in the comet, potentially dominating over refractory organic matter and more volatile species. Similar absorption features appear in the spectra of some asteroids, implying a compositional link between asteroids, comets, and the parent interstellar cloud.

High index contrast photonic platforms for on-chip Raman spectroscopy.

Nanophotonic waveguide enhanced Raman spectroscopy (NWERS) is a sensing technique that uses a highly confined waveguide mode to excite and collect the Raman scattered signal from molecules in close vicinity of the waveguide. The most important parameters defining the figure of merit of an NWERS sensor include its ability to collect the Raman signal from an analyte, i.e. "the Raman conversion efficiency" and the amount of "Raman background" generated from the guiding material. Here, we compare different photonic integrated circuit (PIC) platforms capable of on-chip Raman sensing in terms of the aforementioned parameters. Among the four photonic platforms under study, tantalum oxide and silicon nitride waveguides exhibit high signal collection efficiency and low Raman background. In contrast, the performance of titania and alumina waveguides suffers from a strong Raman background and a weak signal collection efficiency, respectively.

Low-power optical beam steering by microelectromechanical waveguide gratings.

Optical beam steering is key for optical communications, laser mapping (lidar), and medical imaging. For these applications, integrated photonics is an enabling technology that can provide miniaturized, lighter, lower-cost, and more power-efficient systems. However, common integrated photonic devices are too power demanding. Here, we experimentally demonstrate, for the first time, to the best of our knowledge, beam steering by microelectromechanical (MEMS) actuation of a suspended silicon photonic waveguide grating. Our device shows up to 5.6° beam steering with 20 V actuation and power consumption below the µW level, i.e., more than five orders of magnitude lower power consumption than previous thermo-optic tuning methods. The novel combination of MEMS with integrated photonics presented in this work lays ground for the next generation of power-efficient optical beam steering systems.

Cometary Dust.

This review presents our understanding of cometary dust at the end of 2017. For decades, insight about the dust ejected by nuclei of comets had stemmed from remote observations from Earth or Earth's orbit, and from flybys, including the samples of dust returned to Earth for laboratory studies by the Stardust return capsule. The long-duration Rosetta mission has recently provided a huge and unique amount of data, obtained using numerous instruments, including innovative dust instruments, over a wide range of distances from the Sun and from the nucleus. The diverse approaches available to study dust in comets, together with the related theoretical and experimental studies, provide evidence of the composition and physical properties of dust particles, e.g., the presence of a large fraction of carbon in macromolecules, and of aggregates on a wide range of scales. The results have opened vivid discussions on the variety of dust-release processes and on the diversity of dust properties in comets, as well as on the formation of cometary dust, and on its presence in the near-Earth interplanetary medium. These discussions stress the significance of future explorations as a way to decipher the formation and evolution of our Solar System.

Superresolution 4π Raman microscopy.

The advent of 4π microscopy broke the conventional optical resolution limit in the axial direction of the microscope. In combination with fluorescence microscopy, it broadened the knowledge of cell biology at the expense of perturbing the samples with extrinsic fluorescent labels. In contrast, Raman microscopy acquires the molecular fingerprint of the sample without the need of extrinsic labels, and therefore improving its resolution can make an even greater impact. Here, we take advantage of the improved axial resolution of a 4π configuration to form a 4π Raman microscope. With this microscope, we independently and simultaneously analyzed different nanolayers in a multilayer stack. We identified their chemical composition and retrieved their relative subwavelength optical separation with a precision of 6 nm.

Bioinspired bright noniridescent photonic melanin supraballs.

Structural colors enable the creation of a spectrum of nonfading colors without pigments, potentially replacing toxic metal oxides and conjugated organic pigments. However, significant challenges remain to achieve the contrast needed for a complete gamut of colors and a scalable process for industrial application. We demonstrate a feasible solution for producing structural colors inspired by bird feathers. We have designed core-shell nanoparticles using high-refractive index (RI) (~1.74) melanin cores and low-RI (~1.45) silica shells. The design of these nanoparticles was guided by finite-difference time-domain simulations. These nanoparticles were self-assembled using a one-pot reverse emulsion process, which resulted in bright and noniridescent supraballs. With the combination of only two ingredients, synthetic melanin and silica, we can generate a full spectrum of colors. These supraballs could be directly added to paints, plastics, and coatings and also used as ultraviolet-resistant inks or cosmetics.

Silicon Nitride Background in Nanophotonic Waveguide Enhanced Raman Spectroscopy.

Recent studies have shown that evanescent Raman spectroscopy using a silicon nitride (SiN) nanophotonic waveguide platform has higher signal enhancement when compared to free-space systems. However, signal-to-noise ratio from the waveguide at a low analyte concentration is constrained by the shot-noise from the background light originating from the waveguide itself. Hence, understanding the origin and properties of this waveguide background luminescence (WGBL) is essential to developing mitigation strategies. Here, we identify the dominating component of the WGBL spectrum composed of a broad Raman scattering due to momentum selection-rule breaking in amorphous materials, and several peaks specific to molecules embedded in the core. We determine the maximum of the Raman scattering efficiency of the WGBL at room temperature for 785 nm excitation to be 4.5 ± 1 × 10-9 cm-1·sr-1, at a Stokes shift of 200 cm-1. This efficiency decreases monotonically for higher Stokes shifts. Additionally, we also demonstrate the use of slotted waveguides and quasi-transverse magnetic polarization as some mitigation strategies.

Remote Sensing of Potential Biosignatures from Rocky, Liquid, or Icy (Exo)Planetary Surfaces.

To detect signs of life by remote sensing on objects of our Solar System and on exoplanets, the characterization of light scattered by surface life material could complement possible clues given by the atmospheric composition. We reviewed the reflectance spectra of a broad selection of major biomolecules that constitute terrestrial carbon-based life from 0.4 to 2.4 µm, and we discuss their detectability through atmospheric spectral windows. Biomolecule features in the near-infrared (0.8-2.4 µm) will likely be obscured by water spectral features and some atmospheric gases. The visible range (0.4-0.8 µm), including the strong spectral features of pigments, is the most favorable. We investigated the detectability of a pigmented microorganism (Deinococcus radiodurans) when mixed with silica sand, liquid water, and water-ice particles representative of diverse surfaces of potentially habitable worlds. We measured the visible to near-infrared reflectance spectra (0.4-2.4 µm) and the visible phase curves (at 0.45 and 0.75 µm) of the mixtures to assess how the surface medium and the viewing geometry affect the detectability of the microorganisms. The results show that ice appears to be the most favorable medium for the detection of pigments. Water ice is bright and featureless from 0.4 to 0.8 µm, allowing the absorption of any pigment present in the ice to be well noticeable. We found that the visible phase curve of water ice is the most strongly affected by the presence of pigments, with variations of the spectral slope by more than a factor of 3 with phase angles. Finally, we show that the sublimation of the ice results in the concentration of the biological material onto the surface and the consequent increase of its signal. These results have applications to the search for life on icy worlds, such as Europa or Enceladus. Key Words: Remote sensing-Biosignatures-Reflectance spectroscopy-Exoplanets-Spectroscopic biosignatures-Pigments. Astrobiology 17, 231-252.

Paleomicrobiology to investigate copper resistance in bacteria: isolation and description of Cupriavidus necator B9 in the soil of a medieval foundry.

Remains of a medieval foundry were excavated by archaeologists in 2013 in Verdun (France). Ancient workshops specialized in brass and copper alloys were found with an activity between 13th to 16th c. Levels of Cu, Zn and Pb reached 20000, 7000 and 6000 mg kg-1 (dw), respectively, in several soil horizons. The objective of the present work was to examine the microbial community in this contaminated site. A total of 8-22 106 reads were obtained by shotgun metagenomics in four soil horizons. Bioinformatic analyses suggest the presence of complex bacterial communities dominated by Proteobacteria. The structure of the community was not affected by metals, contrary to the set of metal-resistance genes. Using selective media, a novel strain of Cupriavidus necator (eutrophus), strain B9, was isolated. Its genome was sequenced and a novel metal resistance gene cluster with Hg resistance genes (merRTPCA) followed by 24 copper-resistance genes (actP, cusCBAF, silP, copK1, copH4QLOFGJH3IDCBARS, copH2H1, copK2) was found. This cluster is partly homologous to the cop genes of Cupriavidus gilardii CR3 and C. metallidurans CH34. Proteomics indicated that the four copH genes were differentially expressed: CopH1 and CopH2 were mostly induced by Cd while CopH4 was highly expressed by Cu.

Understanding Texts with the Help of Experimentation: The Example of Cupellation in Arabic Scientific Literature.

The article aims to show how experimentation can help us understand historical texts, by focusing on the specific case of cupellation in Arabic scientific literature. It also provides new information about cupellation in the Arab-Muslim Middle Ages. The article consists of translations of three of the most detailed accounts of cupellation: Hamdani's Kitab al-jawharatayn al-'atiqatayn (first half of the fourth/tenth century), Maslama b. Qasim al-Qurtubi, Rutbat al-hakim (339-342/950-953), and Mansur b. Ba'ra, Kitab kashf al-asrar al-'ilmiyya bi-dar al-darb al-misriyya (615-635/1218-1238). These are accompanied by commentaries based on a series of experiments carried out in the course of archaeological research on cupellation, which are here used to shed new light on the medieval texts and resolve several problems in interpreting them.

Single mode waveguide platform for spontaneous and surface-enhanced on-chip Raman spectroscopy.

We review an on-chip approach for spontaneous Raman spectroscopy and surface-enhanced Raman spectroscopy based on evanescent excitation of the analyte as well as evanescent collection of the Raman signal using complementary metal oxide semiconductor (CMOS)-compatible single mode waveguides. The signal is either directly collected from the analyte molecules or via plasmonic nanoantennas integrated on top of the waveguides. Flexibility in the design of the geometry of the waveguide, and/or the geometry of the antennas, enables optimization of the collection efficiency. Furthermore, the sensor can be integrated with additional functionality (sources, detectors, spectrometers) on the same chip. In this paper, the basic theoretical concepts are introduced to identify the key design parameters, and some proof-of-concept experimental results are reviewed.