<i>De novo</i> transcriptome analyses provide insights into opsin-based photoreception in the lanternshark <i>Etmopterus spinax</i>

The velvet belly lanternshark (Etmopterus spinax) is a small deep-sea shark commonly found in the Eastern Atlantic and the Mediterranean Sea. This bioluminescent species is able to emit a blue-green ventral glow used in counter-illumination camouflage, mainly. In this study, paired-end Illumina HiSeqTM technology has been employed to generate transcriptome data from eye and ventral skin tissues of the lanternshark. About 64 and 49 million Illumina reads were generated from skin and eye tissues respectively. The assembly allowed us to predict 119,749 total unigenes including 94,569 for the skin transcriptome and 94,365 for the eye transcriptome while 74,753 were commonly found in both transcriptomes. A taxonomy filtering was applied to extract a reference transcriptome containing 104,390 unigenes among which 38,836 showed significant similarities to known sequences in NCBI non-redundant protein sequences database. Around 58% of the annotated unigenes match with predicted genes from the Elephant shark (Callorhinchus milii) genome. The transcriptome completeness has been evaluated by successfully capturing around 98% of orthologous genes of the « Core eukaryotic gene dataset » within the E. spinax reference transcriptome. We identified potential “light-interacting toolkit” genes including multiple genes related to ocular and extraocular light perception processes such as opsins, phototransduction actors or crystallins. Comparative gene expression analysis reveals eye-specific expression of opsins, ciliary phototransduction actors, crystallins and vertebrate retinoid pathway actors. In particular, mRNAs from a single rhodopsin gene and its potentially associated peropsin were detected in the eye transcriptome, only, confirming a monochromatic vision of the lanternshark. Encephalopsin mRNAs were mainly detected in the ventral skin transcriptome. In parallel, immunolocalization of the encephalopsin within the ventral skin of the shark suggests a functional relation with the photophores, i.e. epidermal light-producing organs. We hypothesize that extraocular photoreception might be involved in the bioluminescence control possibly acting on the shutter opening and/or the photocyte activity itself. The newly generated reference transcriptome provides a valuable resource for further understanding of the shark biology

Placoid scales in bioluminescent sharks: Scaling their evolution using morphology and elemental composition

Elasmobranchs are characterised by the presence of placoid scales on their skin. These scales, structurally homologous to gnathostome teeth, are thought to have various ecological functions related to drag reduction, predator defense or abrasion reduction. Some scales, particularly those present in the ventral area, are also thought to be functionally involved in the transmission of bioluminescent light in deep-sea environments. In the deep parts of the oceans, elasmobranchs are mainly represented by squaliform sharks. This study compares ventral placoid scale morphology and elemental composition of more than thirty deep-sea squaliform species. Scanning Electron Microscopy and Energy Dispersive X-ray spectrometry, associated with morphometric and elemental composition measurements were used to characterise differences among species. A maximum likelihood molecular phylogeny was computed for 43 shark species incuding all known families of Squaliformes. Character mapping was based on this phylogeny to estimate ancestral character states among the squaliform lineages. Our results highlight a conserved and stereotypical elemental composition of the external layer among the examined species. Phosphorus-calcium proportion ratios (Ca/P) slightly vary from 1.8-1.9, and fluorine is typically found in the placoid scale. By contrast, there is striking variation in shape in ventral placoid scales among the investigated families. Character-mapping reconstructions indicated that the shield-shaped placoid scale morphotype is likely to be ancestral among squaliform taxa. The skin surface occupied by scales appears to be reduced in luminous clades which reflects a relationship between scale coverage and the ability to emit light. In luminous species, the placoid scale morphotypes are restricted to pavement, bristle- and spine-shaped except for the only luminescent somniosid, Zameus squamulosus, and the dalatiid Mollisquama mississippiensis. These results, deriving from an unprecedented sampling, show extensive morphological diversity in placoid scale shape but little variation in elemental composition among Squaliformes.publishedVersio

Validation and data characteristics of methane and nitrous oxide profiles observed by MIPAS and processed with Version 4.61 algorithm

The ENVISAT validation programme for the atmospheric instruments MIPAS, SCIAMACHY and GOMOS is based on a number of balloon-borne, aircraft, satellite and ground-based correlative measurements. In particular the activities of validation scientists were coordinated by ESA within the ENVISAT Stratospheric Aircraft and Balloon Campaign or ESABC. As part of a series of similar papers on other species [this issue] and in parallel to the contribution of the individual validation teams, the present paper provides a synthesis of comparisons performed between MIPAS CH4 and N2O profiles produced by the current ESA operational software (Instrument Processing Facility version 4.61 or IPF v4.61, full resolution MIPAS data covering the period 9 July 2002 to 26 March 2004) and correlative measurements obtained from balloon and aircraft experiments as well as from satellite sensors or from ground-based instruments. In the middle stratosphere, no significant bias is observed between MIPAS and correlative measurements, and MIPAS is providing a very consistent and global picture of the distribution of CH4 and N2O in this region. In average, the MIPAS CH4 values show a small positive bias in the lower stratosphere of about 5%. A similar situation is observed for N2O with a positive bias of 4%. In the lower stratosphere/upper troposphere (UT/LS) the individual used MIPAS data version 4.61 still exhibits some unphysical oscillations in individual CH4 and N2O profiles caused by the processing algorithm (with almost no regularization). Taking these problems into account, the MIPAS CH4 and N2O profiles are behaving as expected from the internal error estimation of IPF v4.61 and the estimated errors of the correlative measurements

A new method to detect long term trends of methane (CH₄) and nitrous oxide (N₂O) total columns measured within the NDACC ground-based high resolution solar FTIR network

Total columns measured with the ground-based solar FTIR technique are highly variable in time due to atmospheric chemistry and dynamics in the atmosphere above the measurement station. In this paper, a multiple regression model with anomalies of air pressure, total columns of hydrogen fluoride (HF) and carbon monoxide (CO) and tropopause height are used to reduce the variability in the methane (CH4) and nitrous oxide (N2O) total columns to estimate reliable linear trends with as small uncertainties as possible. The method is developed at the Harestua station (60°N, 11°E, 600ma.s.l.) and used on three other European FTIR stations, i.e. Jungfraujoch (47°N, 8°E, 3600ma.s.l.), Zugspitze (47°N, 11°E, 3000ma.s.l.), and Kiruna (68°N, 20°E, 400ma.s.l.). Linear CH4 trends between 0.13±0.01-0.25±0.02%yr−1 were estimated for all stations in the 1996-2009 period. A piecewise model with three separate linear trends, connected at change points, was used to estimate the short term fluctuations in the CH4 total columns. This model shows a growth in 1996–1999 followed by a period of steady state until 2007. From 2007 until 2009 the atmospheric CH4 amount increases between 0.57±0.22–1.15±0.17%yr−1. Linear N2O trends between 0.19±0.01–0.40±0.02%yr−1 were estimated for all stations in the 1996-2007 period, here with the strongest trend at Harestua and Kiruna and the lowest at the Alp stations. From the N2O total columns crude tropospheric and stratospheric partial columns were derived, indicating that the observed difference in the N2O trends between the FTIR sites is of stratospheric origin. This agrees well with the N2O measurements by the SMR instrument onboard the Odin satellite showing the highest trends at Harestua, 0.98±0.28%yr−1, and considerably smaller trends at lower latitudes, 0.27±0.25%yr−1. The multiple regression model was compared with two other trend methods, the ordinary linear regression and a Bootstrap algorithm. The multiple regression model estimated CH4 and N2O trends that differed up to 31% compared to the other two methods and had uncertainties that were up to 300% lower. Since the multiple regression method were carefully validated this stresses the importance to account for variability in the total columns when estimating trend from solar FTIR data

An approach to retrieve information on the carbonyl fluoride (COF₂) vertical distributions above Jungfraujoch by FTIR multi-spectrum multi-window fitting

We present an original multi-spectrum fitting procedure to retrieve volume mixing ratio (VMR) profiles of carbonyl fluoride (COF2) from ground-based high resolution Fourier transform infrared (FTIR) solar spectra. The multi-spectrum approach consists of simultaneously combining, during the retrievals, all spectra recorded consecutively during the same day and with the same resolution. Solar observations analyzed in this study with the SFIT-2 v3.91 fitting algorithm correspond to more than 2900 spectra recorded between January 2000 and December 2007 at high zenith angles, with a Fourier Transform Spectrometer operated at the high-altitude International Scientific Station of the Jungfraujoch (ISSJ, 46.5° N latitude, 8.0° E longitude, 3580m altitude), Switzerland. The goal of the retrieval strategy described here is to provide information about the vertical distribution of carbonyl fluoride. The microwindows used are located in the υ1 or in the υ4 COF2 infrared (IR) absorption bands. Averaging kernel and eigenvector analysis indicates that our FTIR retrieval is sensitive to COF2 inversion between 17 and 30 km, with the major contribution to the retrieved information always coming from the measurement. Moreover, there was no significant bias between COF2 partial columns, total columns or VMR profiles retrieved from the two bands. For each wavenumber region, a complete error budget including all identified sources has been carefully established. In addition, comparisons of FTIR COF2 17–30 km partial columns with KASIMA and SLIMCAT 3-D CTMs are also presented. If we do not notice any significant bias between FTIR and SLIMCAT time series, KASIMA COF2 17–30 km partial columns are lower of around 25%, probably due to incorrect lower boundary conditions. For each times series, linear trend estimation for the 2000–2007 time period as well as a seasonal variation study are also performed and critically discussed. For FTIR and KASIMA time series, very low COF2 growth rates (0.4±0.2%/year and 0.3±0.2%/year, respectively) have been derived. However, the SLIMCAT data set gives a slight negative trend (−0.5±0.2%/year), probably ascribable to discontinuities in the meteorological data used by this model. We further demonstrate that all time series are able to reproduce the COF2 seasonal cycle, which main seasonal characteristics deduced from each data set agree quite well

Carbon monoxide (CO) and ethane (C₂H₆) trends from ground-based solar FTIR measurements at six European stations, comparison and sensitivity analysis with the EMEP model

Trends in the CO and C2H6 partial columns (~0–15 km) have been estimated from four European groundbasedsolar FTIR (Fourier Transform InfraRed) stations for the 1996–2006 time period. The CO trends from the four stations Jungfraujoch, Zugspitze, Harestua and Kiruna have been estimated to −0.45±0.16%yr−1, −1.00 ± 0.24%yr−1, −0.62±0.19%yr−1 and −0.61±0.16%yr−1, respectively. The corresponding trends for C2H6 are−1.51±0.23%yr−1, −2.11±0.30%yr−1, −1.09±0.25%yr−1 and −1.14±0.18%yr−1. All trends are presented with their 2-σ confidence intervals. To find possible reasons for the CO trends, the global-scale EMEP MSC-W chemical transport model has been used in a series of sensitivity scenarios. It is shown that the trends are consistent with the combination of a 20% decrease in the anthropogenic CO emissions seen in Europe and North America during the 1996–2006 period and a 20% increase in the anthropogenic CO emissions in East Asia, during the same time period. The possible impacts of CH4 and biogenic volatile organic compounds (BVOCs) are also considered. The European and global-scale EMEP models have been evaluated against the measured CO and C2H6 partial columns from Jungfraujoch, Zugspitze, Bremen, Harestua, Kiruna and Ny-Ålesund. The European model reproduces, on average the measurements at the different sites fairly well and within 10–22% deviation for CO and 14–31% deviation for C2H6. Their seasonal amplitude is captured within 6–35% and 9–124% for CO and C2H6, respectively. However, 61–98% of the CO and C2H6 partial columns in the European model are shown to arise from the boundary conditions, making the globalscale model a more suitable alternative when modeling these two species. In the evaluation of the global model the average partial columns for 2006 are shown to be within 1–9% and 37–50% of the measurements for CO and C2H6, respectively. The global model sensitivity for assumptions made in this paper is also analyzed

Ground-based FTIR measurements of O3- and climate-related gases in the free troposphere and lower stratosphere

In the frame of the EC project UFTIR (Time series of Upper Free Troposphere observations from a European ground-based FTIR network), a common strategy for an optimal determination of the chemical composition in the free troposphere and lower stratosphere with ground-based Fourier-transform infrared (FTIR) spectrometers is being developed. The project focuses on 6 target species that are O3, CO, CH4, N2O, C2H6 and CHClF2 (HCFC-22). The strategy consists in selecting the most appropriate parameters to retrieve vertical concentration profiles from solar FTIR spectra. Among the important parameters are the spectral microwindows: they have been optimised to maximise the information content and to minimize the influence of poorly known spectroscopic data and interfering species