Using a high finesse optical resonator to provide a long light path for differential optical absorption spectroscopy: CE-DOAS

International audienceCavity enhanced methods in absorption spectroscopy have seen a considerable increase in popularity during the past decade. Especially Cavity Enhanced Absorption Spectroscopy (CEAS) established itself in atmospheric trace gas detection by providing tens of kilometers of effective light path length using a cavity as short as 1 m. In this paper we report on the construction and testing of a compact and power efficient light emitting diode based broadband Cavity Enhanced Differential Optical Absorption Spectrometer (CE-DOAS) for in situ field observation of atmospheric NO3. This device combines the small size of the cavity with the enormous advantages of the DOAS approach in terms of sensitivity and specificity. In particular, no selective removal of the analyte (here NO3) is necessary, thus the CE-DOAS technique can ? in principle ? measure any gas detectable by DOAS. We will discuss the advantages of using a light emitting diode (LED) as light source particularly the precautions which have to be satisfied for the use of LEDs. The instrument was tested in the lab by detecting NO3 in a mixture of NO2 and O3 in air. It was then compared to other trace gas detection techniques in an intercomparison campaign in the atmosphere simulation chamber SAPHIR at NO3 concentrations as low as 6.3 ppt

Accounting for the effect of horizontal gradients in limb measurements of scattered sunlight

Limb measurements provided by the SCanning Imaging Absorption spectrometer for Atmospheric CHartographY (SCIAMACHY) on the ENVISAT satellite allow retrieving stratospheric profiles of various trace gases on a global scale, among them BrO for the first time. For limb observations in the UV/VIS spectral region the instrument measures scattered light with a complex distribution of light paths: the light is measured at different tangent heights and can be scattered or absorbed in the atmosphere or reflected by the ground. By means of spectroscopy and radiative transfer modelling these measurements can be inverted to retrieve the vertical distribution of stratospheric trace gases. <br></br> The fully spherical 3-D Monte Carlo radiative transfer model "Tracy-II" is applied in this study. The Monte Carlo method benefits from conceptual simplicity and allows realizing the concept of full spherical geometry of the atmosphere and also its 3-D properties, which is important for a realistic description of the limb geometry. Furthermore it allows accounting for horizontal gradients in the distribution of trace gases. <br></br> In this study the effect of horizontally inhomogeneous distributions of trace gases along flight/viewing direction on the retrieval of profiles is investigated. We introduce a tomographic method to correct for this effect by combining consecutive limb scanning sequences and utilizing the overlap in their measurement sensitivity regions. It is found that if horizontal inhomogenity is not properly accounted for, typical errors of 20% for NO<sub>2</sub> and up to 50% for OClO around the altitude of the profile peak can arise for measurements close to the Arctic polar vortex boundary in boreal winter

Extending differential optical absorption spectroscopy for limb measurements in the UV

Methods of UV/VIS absorption spectroscopy to determine the constituents in the Earth's atmosphere from measurements of scattered light are often based on the Beer-Lambert law, like e.g. Differential Optical Absorption Spectroscopy (DOAS). While the Beer-Lambert law is strictly valid for a single light path only, the relation between the optical depth and the concentration of any absorber can be approximated as linear also for scattered light observations at a single wavelength if the absorption is weak. If the light path distribution is approximated not to vary with wavelength, also linearity between the optical depth and the product of the cross-section and the concentration of an absorber can be assumed. These assumptions are widely made for DOAS applications for scattered light observations. <br><br> For medium and strong absorption of scattered light (e.g. along very long light-paths like in limb geometry) the relation between the optical depth and the concentration of an absorber is no longer linear. In addition, for broad wavelength intervals the differences in the travelled light-paths at different wavelengths become important, especially in the UV, where the probability for scattering increases strongly with decreasing wavelength. <br><br> However, the DOAS method can be extended to cases with medium to strong absorptions and for broader wavelength intervals by the so called air mass factor modified (or extended) DOAS and the weighting function modified DOAS. These approaches take into account the wavelength dependency of the slant column densities (SCDs), but also require a priori knowledge for the air mass factor or the weighting function from radiative transfer modelling. <br><br> We describe an approach that considers the fitting results obtained from DOAS, the SCDs, as a function of wavelength and vertical optical depth and expands this function into a Taylor series of both quantities. The Taylor coefficients are then applied as additional fitting parameters in the DOAS analysis. Thus the variability of the SCD in the fit window is determined by the retrieval itself. <br><br> This new approach provides a description of the SCD the exactness of which depends on the order of the Taylor expansion, and is independent from any assumptions or a priori knowledge of the considered absorbers. <br><br> In case studies of simulated and measured spectra in the UV range (332–357 nm), we demonstrate the improvement by this approach for the retrieval of vertical profiles of BrO from the SCIAMACHY limb observations. The results for BrO obtained from the simulated spectra are closer to the true profiles, when applying the new method for the SCDs of ozone, than when the standard DOAS approach is used. For the measured spectra the agreement with validation measurements is also improved significantly, especially for cases with strong ozone absorption. <br><br> While the focus of this article is on the improvement of the BrO profile retrieval from the SCIAMACHY limb measurements, the novel approach may be applied to a wide range of DOAS retrievals

Corrigendum to "Broadband Cavity Enhanced Differential Optical Absorption Spectroscopy (CE-DOAS) – applicability and corrections" published in Atmos. Meas. Tech., 2, 713–723, 2009

No abstract available

Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge

Retrieval interval mapping: a tool to visualize the impact of the spectral retrieval range on differential optical absorption spectroscopy evaluations

Remote sensing via differential optical absorption spectroscopy (DOAS) has become a standard technique to identify and quantify trace gases in the atmosphere. Due to the wide range of measurement conditions, atmospheric compositions and instruments used, a specific challenge of a DOAS retrieval is to optimize the retrieval parameters for each specific case and particular trace gas of interest. Of these parameters, the retrieval wavelength range is one of the most important ones. Although for many trace gases the overall dependence of common DOAS retrieval on the evaluation wavelength interval is known, a systematic approach for finding the optimal retrieval wavelength range and quantitative assessment is missing. Here we present a novel tool to visualize the effect of different evaluation wavelength ranges. It is based on mapping retrieved column densities in the retrieval wavelength space and thus visualizing the consequences of different choices of spectral retrieval ranges caused by slightly erroneous absorption cross sections, cross correlations and instrumental features. Based on the information gathered, an optimal retrieval wavelength range may be determined systematically

Disease classification from capillary electrophoresis: mass spectrometry

We investigate the possibility of using pattern recognition techniques to classify various disease types using data produced by a new form of rapid Mass Spectrometry. The data format has several advantages over other high-throughput technologies and as such could become a useful diagnostic tool. We investigate the binary and multi-class performances obtained using standard classifiers as the number of features is varied and conclude that there is potential in this technique and suggest research directions that would improve performance

Satellite Chartography of Atmospheric Methane and carbon monoxide from SCIAMACHY onboard ENVISAT

The UV/Vis/near infrared spectrometer SCIAMACHY on board the European ENVISAT satellite enables total column retrieval of atmospheric methane with high sensitivity to the lower troposphere. The vertical column density of methane is converted to column averaged mixing ratio by using carbon dioxide retrievals as proxy for the probed atmospheric column. For this purpose, we apply concurrent total column measurements of CO_2 in combination with modeled column-averaged CO_2 mixing ratios. Possible systematic errors are discussed in detail while the precision error is 1.8% on average. This paper focuses on methane retrievals from January 2003 through December 2004. The measurements with global coverage over continents are compared with model results from the chemistry–transport model TM4. In the retrievals, the north-south gradient as well as regions with enhanced methane levels can be clearly identified. The highest abundances are found in the Red Basin of China, followed by northern South America, the Gangetic plains of India and central parts of Africa. Especially the abundances in northern South America and the Red Basin are generally higher than modeled. Further, we present the seasonal variations within the investigated time period. Peak values in Asia due to rice emissions are observed from August through October. We expand earlier investigations that suggest underestimated emissions in the tropics. It is shown that these underestimations show a seasonal behavior that peaks from August through December. The global measurements may be used for inverse modeling and are thus an important step towards better quantification of the methane budget