Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography

Our understanding of metabolic interactions between small symbi-otic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histologi -cal changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrom-etry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metab-olites to the same animal's three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridiza-tion for the taxonomic identification and localization of the associ-ated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an in-teractive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning

MAX-DOAS measurements of atmospheric trace gases in Ny-Ålesund - Radiative transfer studies and their application

International audienceA new approach to derive tropospheric concentrations of some atmospheric trace gases from ground-based UV/vis measurements is described. The instrument, referred to as the MAX-DOAS, is based on the well-known UV/vis instruments, which use the sunlight scattered in the zenith sky as the light source and the method of Differential Optical Absorption Spectroscopy (DOAS) to derive column amounts of absorbers like ozone and nitrogen dioxide. Substantial enhancements have been applied to this standard setup to use different lines of sight near to the horizon as additional light sources (MAX - multi axis). Results from measurements at Ny-Ålesund (79° N, 12° E) are presented and interpreted with the full-spherical radiative transfer model SCIATRAN. In particular, measurements of the oxygen dimer O4 which has a known column and vertical distribution in the atmosphere are used to evaluate the sensitivity of the retrieval to parameters such as multiple scattering, solar azimuth, surface albedo and refraction in the atmosphere and also to validate the radiative transfer model. As a first application, measurements of NO2 emissions from a ship lying in Ny-Ålesund harbour are presented. The results of this study demonstrate the feasibility of long term UV/vis multi axis measurement that can be used to derive not only column amounts of different trace gases but also some information on the vertical location of these absorbers

Emissivity retrievals with FORUM's end-to-end simulator: challenges and recommendations

Spectral emissivity is a key property of the Earth's surface, of which only very few measurements exist so far in the far-infrared (FIR) spectral region, even though recent work has shown that the FIR is important for accurate modelling of the global climate. The European Space Agency's 9th Earth Explorer, FORUM (Far-infrared Outgoing Radiation Understanding and Monitoring) will provide the first global spectrally resolved measurements of the Earth's top-of-the-atmosphere (TOA) spectrum in the FIR. In clear-sky conditions with low water vapour content, these measurements will provide a unique opportunity to retrieve spectrally resolved FIR surface emissivity. In preparation for the FORUM mission with an expected launch in 2027, this study takes the first steps towards the development of an operational emissivity retrieval for FORUM by investigating the sensitivity of the emissivity product of a full spectrum optimal estimation retrieval method to different physical and operational parameters. The tool used for the sensitivity tests is the FORUM mission's end-to-end simulator. These tests show that the spectral emissivity of most surface types can be retrieved for dry scenes in the 350–600 cm−1 region, with an absolute uncertainty ranging from 0.005 to 0.01. In addition, the quality of the retrieval is quantified with respect to the precipitable water vapour content of the scene, and the uncertainty caused by the correlation of emissivity with surface temperature is investigated. Based on these investigations, a road map is recommended for the development of the operational emissivity product

Retrieval of tropospheric water vapour from airborne far-infrared measurements: a case study

We describe studies undertaken in support of the Far-infrared Outgoing Radiation Understanding and Monitoring (FORUM) mission, ESA’s ninth Earth Explorer, designed to investigate whether airborne observations of far-infrared radiances can provide beneficial information on mid and upper tropospheric water vapour concentrations.Initially we perform a joint temperature and water vapour retrieval and show that the water vapour retrieval exploiting far-infrared measurements from the Tropospheric Airborne Fourier Transform Spectrometer (TAFTS) shows improvement over the a-priori Unified Model global forecast when compared to in situ dropsonde measurements. For this case the improvement is particularly noticeable in the mid-upper troposphere. Equivalent retrievals using mid-infrared radiances measured by the Airborne Research Interferometer Evaluation System (ARIES) show much reduced performance, with the degrees of freedom for signal (DFS), reduced by a factor of almost 2. Further sensitivity studies show that this advantage is decreased, but still present when the spectral resolution of the TAFTS measurements is reduced to match that of ARIES.The beneficial role of the far infrared for this case is further confirmed by performing water vapour only retrievals using ARIES and TAFTS individually, and then in combination. We find that the combined retrieval has a DFS value of 6.7 for water vapour, marginally larger than that obtained for the TAFTS retrieval and almost twice as large as that obtained for ARIES.These results provide observational support of theoretical studies highlighting the potential improvement that far-infrared observations could bring for the retrieval of tropospheric water vapour

Cirrus cloud identification from airborne far-infrared and mid-infrared spectra

Airborne interferometric data, obtained from the Cirrus Coupled Cloud-Radiation Experiment (CIRCCREX) and from the PiknMix-F field campaign, are used to test the ability of a machine learning cloud identification and classification algorithm (CIC). Data comprise a set of spectral radiances measured by the Tropospheric Airborne Fourier Transform Spectrometer (TAFTS) and the Airborne Research Interferometer Evaluation System (ARIES). Co-located measurements of the two sensors allow observations of the upwelling radiance for clear and cloudy conditions across the far-and mid-infrared part of the spectrum. Theoretical sensitivity studies show that the performance of the CIC algorithm improves with cloud altitude. These tests also suggest that, for conditions encompassing those sampled by the flight campaigns, the additional information contained within the far-infrared improves the algorithm's performance compared to using mid-infrared data only. When the CIC is applied to the airborne radiance measurements, the classification performance of the algorithm is very high. However, in this case, the limited temporal and spatial variability in the measured spectra results in a less obvious advantage being apparent when using both mid-and far-infrared radiances compared to using mid-infrared information only. These results suggest that the CIC algorithm will be a useful addition to existing cloud classification tools but that further analyses of nadir radiance observations spanning the infrared and sampling a wider range of atmospheric and cloud conditions are required to fully probe its capabilities. This will be realised with the launch of the Far-infrared Outgoing Radiation Understanding and Monitoring (FORUM) mission, ESA's 9th Earth Explorer

A test of the ability of current bulk optical models to represent the radiative properties of cirrus cloud across the mid-and far-infrared

Measurements of mid- to far-infrared nadir radiances obtained from the UK Facility for Airborne Atmospheric Measurements (FAAM) BAe-146 aircraft during the Cirrus Coupled Cloud-Radiation Experiment (CIRCCREX) are used to assess the performance of various ice cloud bulk optical (single-scattering) property models. Through use of a minimisation approach, we find that the simulations can reproduce the observed spectra in the mid-infrared to within measurement uncertainty but are unable to simultaneously match the observations over the far-infrared frequency range. When both mid and far-infrared observations are used to minimise residuals, first order estimates of the flux differences between the best performing simulations and observations indicate a strong compensation effect between the mid and far infrared such that the absolute broadband difference is < 0.7 W m−2. However, simply matching the spectra using the mid-infrared observations in isolation leads to substantially larger discrepancies, with absolute differences reaching ~ 1.8 W m−2. These results highlight the benefit of far infrared observations for better constraining retrievals of cirrus cloud properties and their radiative impact, and provide guidance for the development of more realistic ice cloud optical models

Structural Amyloid Plaque Polymorphism is Associated with Distinct Lipid Accumulations Revealed by Trapped Ion Mobility Mass Spectrometry Imaging (TIMS MSI)

Understanding of Alzheimer’s disease (AD) pathophysiology, requires molecular assessment of how key pathological factors, specifically amyloid β (Aβ) plaques, influence the surrounding microenvironment. Here, neuronal lipids have been implicated in Aβ) plaque pathology, though the lipid microenvironment in direct proximity to Aβ plaques are still not fully resolved. A further challenge is the microenvironmental molecular heterogeneity, across structurally polymorphic Aβ features - such as diffuse, immature and mature, fibrillary aggregates, whose resolution requires the integration of advanced, multimodal chemical imaging tools. Herein, we used matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) trapped ion mobility spectrometry Time-of-Flight (TIMS TOF) in combination with hyperspectral confocal microscopy to probe the lipidomic microenvironment associated with structural polymorphism of Aβ plaques in transgenic Alzheimer’s disease mice (tgAPPSWE). Using on tissue and ex situ validation, TIMS MS/MS facilitated unambiguous identification of isobaric lipid species that showed plaque pathology associated localizations. Integrated multivariate imaging data analysis revealed multiple, Aβ plaque enriched lipid patterns for gangliosides (GM), phosphoinositols (PI), phosphoethanolamines (PE) and phosphatidic acids (PA). Conversely, sulfatides (ST), cardiolipins (CL) and polyunsaturated fatty acid conjugated -phosphoserines (PS) and - PE were depleted at plaques. Hyperspectral amyloid imaging further delineated unique distribution of PA, PE to mature plaque core regions, while PI, LPI, GM2 and GM3 localized to immature Aβ aggregates present within the periphery of individual Aβ plaques. Finally, we followed AD pathology associated lipid changes over time, identifying plaque growth and maturation to be characterized by peripheral accumulation of PI (18:0/22:6). Together, these data demonstrate the potential of multimodal imaging approaches to overcome limitations associated with conventional advanced MS imaging applications. This allowed for differentiation of both distinct lipid components in a complex micro environment, as well as their correlation to disease relevant amyloid plaque polymorphs

The FORUM end-to-end simulator project: architecture and results

FORUM (Far-infrared Outgoing Radiation Understanding and Monitoring) will fly as the ninth ESA's Earth Explorer mission, and an end-to-end simulator (E2ES) has been developed as a support tool for the mission selection process and the subsequent development phases. The current status of the FORUM E2ES project is presented together with the characterization of the capabilities of a full physics retrieval code applied to FORUM data. We show how the instrument characteristics and the observed scene conditions impact on the spectrum measured by the instrument, accounting for the main sources of error related to the entire acquisition process, and the consequences on the retrieval algorithm. Both homogeneous and heterogeneous case studies are simulated in clear and cloudy conditions, validating the E2ES against appropriate well-established correlative codes. The performed tests show that the performance of the retrieval algorithm is compliant with the project requirements both in clear and cloudy conditions. The far-infrared (FIR) part of the FORUM spectrum is shown to be sensitive to surface emissivity, in dry atmospheric conditions, and to cirrus clouds, resulting in improved performance of the retrieval algorithm in these conditions. The retrieval errors increase with increasing the scene heterogeneity, both in terms of surface characteristics and in terms of fractional cloud cover of the scene

Measurements of iodine monoxide at a semi polluted coastal location

Point source measurements of IO by laser induced fluorescence spectroscopy were made at a semi-polluted coastal location during the Reactive Halogens in the Marine Boundary Layer (RHaMBLe) campaign in September 2006. The site, on the NW French coast in Roscoff, was characterised by extensive intertidal macroalgae beds which were exposed at low tide. The closest known iodine active macroalgae beds were at least 300 m from the measurement point. From 20 days of measurements, IO was observed above the instrument limit of detection on 14 days, of which a clear diurnal profile was observed on 11 days. The maximum IO mixing ratio was 30.0 pptv (10 s integration period) during the day, amongst the highest concentrations ever observed in the atmosphere, and 1–2 pptv during the night. IO concentrations were strongly dependent on tidal height, the intensity of solar irradiation and meteorological conditions. An intercomparison of IO measurements made using point source and spatially averaged DOAS instruments confirms the presence of hot-spots of IO caused by an inhomogeneous distribution of macroalgae. The co-incident, point source measurement of IO and ultra fine particles (2.5 nm&amp;ge;&lt;i&gt;d&lt;/i&gt;&amp;ge;10 nm) displayed a strong correlation, providing evidence that IO is involved in the production pathway of ultra fine particles at coastal locations. Finally, a modelling study shows that high IO concentrations which are likely to be produced in a macrolagae rich environment can significantly perturb the concentrations of OH and HO&lt;sub&gt;2&lt;/sub&gt; radicals. The effect of IO on HO&lt;sub&gt;x&lt;/sub&gt; is reduced as NO&lt;sub&gt;x&lt;/sub&gt; concentrations increase