ALBERT

Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.

Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.

Description: Calibration of the passive cavity aerosol spectrometer probe for airborne determination of the size distribution Atmospheric Measurement Techniques, 6, 2349-2358, 2013 Author(s): Y. Cai, J. R. Snider, and P. Wechsler This work describes calibration methods for the particle sizing and particle concentration systems of the passive cavity aerosol spectrometer probe (PCASP). Laboratory calibrations conducted over six years, in support of the deployment of a PCASP on a cloud physics research aircraft, are analyzed. Instead of using the many calibration sizes recommended by the PCASP manufacturer, a relationship between particle diameter and scattered light intensity is established using three sizes of mobility-selected polystyrene latex particles, one for each amplifier gain stage. In addition, studies of two factors influencing the PCASP's determination of the particle size distribution – amplifier baseline and particle shape – are conducted. It is shown that the PCASP-derived size distribution is sensitive to adjustments of the sizing system's baseline voltage, and that for aggregates of spheres, a PCASP-derived particle size and a sphere-equivalent particle size agree within uncertainty dictated by the PCASP's sizing resolution. Robust determinations of aerosol concentration, and size distribution, also require calibration of the PCASP's aerosol flowrate sensor. Sensor calibrations, calibration drift, and the sensor's non-linear response are documented.

Description: Experimental quantification of contact freezing in an electrodynamic balance Atmospheric Measurement Techniques, 6, 2373-2382, 2013 Author(s): N. Hoffmann, A. Kiselev, D. Rzesanke, D. Duft, and T. Leisner Heterogeneous nucleation of ice in a supercooled water droplet induced by external contact with a dry aerosol particle has long been known to be more effective than freezing induced by the same nucleus immersed in the droplet. However, the experimental quantification of contact freezing is challenging. Here we report an experimental method to determine the temperature-dependent ice nucleation probability of size-selected aerosol particles. The method is based on the suspension of supercooled charged water droplets in a laminar flow of air containing aerosol particles as contact freezing nuclei. The rate of droplet–particle collisions is calculated numerically with account for Coulomb attraction, drag force and induced dipole interaction between charged droplet and aerosol particles. The calculation is verified by direct counting of aerosol particles collected by a levitated droplet. By repeating the experiment on individual droplets for a sufficient number of times, we are able to reproduce the statistical freezing behavior of a large ensemble of supercooled droplets and measure the average rate of freezing events. The freezing rate is equal to the product of the droplet–particle collision rate and the probability of freezing on a single contact, the latter being a function of temperature, size and composition of the contact ice nuclei. Based on these observations, we show that for the types of particles investigated so far, contact freezing is the dominating freezing mechanism on the timescale of our experiment.

Description: Wolbachia , endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis , revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event.

Description: Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola , of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia- ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia- ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia -ALF is most closely related to Zinderia , the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia / Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs 〉200 Ma, and possibly since the origin of the Auchenorrhyncha, 〉260 Ma.

Description: Validation and empirical correction of MODIS AOT and AE over ocean Atmospheric Measurement Techniques, 6, 2455-2475, 2013 Author(s): N. A. J. Schutgens, M. Nakata, and T. Nakajima We present a validation study of Collection 5 MODIS level 2 Aqua and Terra AOT (aerosol optical thickness) and AE (Ångström exponent) over ocean by comparison to coastal and island AERONET (AErosol RObotic NETwork) sites for the years 2003–2009. We show that MODIS (MODerate-resolution Imaging Spectroradiometer) AOT exhibits significant biases due to wind speed and cloudiness of the observed scene, while MODIS AE, although overall unbiased, exhibits less spatial contrast on global scales than the AERONET observations. The same behaviour can be seen when MODIS AOT is compared against Maritime Aerosol Network (MAN) data, suggesting that the spatial coverage of our datasets does not preclude global conclusions. Thus, we develop empirical correction formulae for MODIS AOT and AE that significantly improve agreement of MODIS and AERONET observations. We show these correction formulae to be robust. Finally, we study random errors in the corrected MODIS AOT and AE and show that they mainly depend on AOT itself, although small contributions are present due to wind speed and cloud fraction in AOT random errors and due to AE and cloud fraction in AE random errors. Our analysis yields significantly higher random AOT errors than the official MODIS error estimate (0.03 + 0.05 τ), while random AE errors are smaller than might be expected. This new dataset of bias-corrected MODIS AOT and AE over ocean is intended for aerosol model validation and assimilation studies, but also has consequences as a stand-alone observational product. For instance, the corrected dataset suggests that much less fine mode aerosol is transported across the Pacific and Atlantic oceans.

Description: Thanks to the microarray technology, our understanding of transcriptome evolution at the genome level has been considerably advanced in the past decade. Yet, further investigation was challenged by several technical limitations of this technology. Recent innovation of next-generation sequencing, particularly the invention of RNA-seq technology, has shed insightful lights on resolving this problem. Though a number of statistical and computational methods have been developed to analyze RNA-seq data, the analytical framework specifically designed for evolutionary genomics remains an open question. In this article we develop a new method for estimating the genome expression distance from the RNA-seq data, which has explicit interpretations under the model of gene expression evolution. Moreover, this distance measure takes the data overdispersion, gene length variation, and sequencing depth variation into account so that it can be applied to multiple genomes from different species. Using mammalian RNA-seq data as example, we demonstrated that this expression distance is useful in phylogenomic analysis.

Description: The control of RNA splicing is often modulated by exonic motifs near splice sites. Chief among these are exonic splice enhancers (ESEs). Well-described ESEs in mammals are purine rich and cause predictable skews in codon and amino acid usage toward exonic ends. Looking across species, those with relatively abundant intronic sequence are those with the more profound end of exon skews, indicative of exonization of splice site recognition. To date, the only intron-rich species that have been analyzed are mammals, precluding any conclusions about the likely ancestral condition. Here, we examine the patterns of codon and amino acid usage in the vicinity of exon–intron junctions in the brown alga Ectocarpus siliculosus , a species with abundant large introns, known SR proteins, and classical splice sites. We find that amino acids and codons preferred/avoided at both 3' and 5' ends in Ectocarpus , of which there are many, tend, on average, to also be preferred/avoided at the same exon ends in humans. Moreover, the preferences observed at the 5' ends of exons are largely the same as those at the 3' ends, a symmetry trend only previously observed in animals. We predict putative hexameric ESEs in Ectocarpus and show that these are purine rich and that there are many more of these identified as functional ESEs in humans than expected by chance. These results are consistent with deep phylogenetic conservation of SR protein binding motifs. Assuming codons preferred near boundaries are "splice optimal" codons, in Ectocarpus , unlike Drosophila, splice optimal and translationally optimal codons are not mutually exclusive. The exclusivity of translationally optimal and splice optimal codon sets is thus not universal.

Description: Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila , applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard ( Anolis carolinensis ). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis . We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites.

Description: Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and " Candidatus Methanomethylophilus alvus," provide insights into its evolutionary history and metabolic features. Phylogenetic analysis of ribosomal proteins robustly indicates a monophyletic group independent of any previously known methanogenic order, which shares ancestry with the Marine Benthic Group D, the Marine Group II, the DHVE2 group, and the Thermoplasmatales. This phylogenetic position, along with the analysis of enzymes involved in core methanogenesis, strengthens a single ancient origin of methanogenesis in the Euryarchaeota and indicates further multiple independent losses of this metabolism in nonmethanogenic lineages than previously suggested. Genomic analysis revealed an unprecedented loss of the genes coding for the first six steps of methanogenesis from H 2 /CO 2 and the oxidative part of methylotrophic methanogenesis, consistent with the fact that M. luminyensis and " Ca. M. alvus" are obligate H 2 -dependent methylotrophic methanogens. Genomic data also suggest that these methanogens may use a large panel of methylated compounds. Phylogenetic analysis including homologs retrieved from environmental samples indicates that methylotrophic methanogenesis (regardless of dependency on H 2 ) is not restricted to gut representatives but may be an ancestral characteristic of the whole order, and possibly also of ancient origin in the Euryarchaeota. 16S rRNA and McrA trees show that this new order of methanogens is very diverse and occupies environments highly relevant for methane production, therefore representing a key lineage to fully understand the diversity and evolution of methanogenesis.

Description: A neural network algorithm for cloud fraction estimation using NASA-Aura OMI VIS radiance measurements Atmospheric Measurement Techniques, 6, 2301-2309, 2013 Author(s): G. Saponaro, P. Kolmonen, J. Karhunen, J. Tamminen, and G. de Leeuw The discrimination of cloudy from cloud-free pixels is required in almost any estimate of a parameter retrieved from satellite data in the ultraviolet (UV), visible (VIS) or infrared (IR) parts of the electromagnetic spectrum. In this paper we report on the development of a neural network (NN) algorithm to estimate cloud fractions using radiances measured at the top of the atmosphere with the NASA-Aura Ozone Monitoring Instrument (OMI). We present and discuss the results obtained from the application of two different types of neural networks, i.e., extreme learning machine (ELM) and back propagation (BP). The NNs were trained with an OMI data sets existing of six orbits, tested with three other orbits and validated with another two orbits. The results were evaluated by comparison with cloud fractions available from the MODerate Resolution Imaging Spectrometer (MODIS) flying on Aqua in the same constellation as OMI, i.e., with minimal time difference between the OMI and MODIS observations. The results from the ELM and BP NNs are compared. They both deliver cloud fraction estimates in a fast and automated way, and they both performs generally well in the validation. However, over highly reflective surfaces, such as desert, or in the presence of dust layers in the atmosphere, the cloud fractions are not well predicted by the neural network. Over ocean the two NNs work equally well, but over land ELM performs better.

Description: Validation of stratospheric and mesospheric ozone observed by SMILES from International Space Station Atmospheric Measurement Techniques, 6, 2311-2338, 2013 Author(s): Y. Kasai, H. Sagawa, D. Kreyling, E. Dupuy, P. Baron, J. Mendrok, K. Suzuki, T. O. Sato, T. Nishibori, S. Mizobuchi, K. Kikuchi, T. Manabe, H. Ozeki, T. Sugita, M. Fujiwara, Y. Irimajiri, K. A. Walker, P. F. Bernath, C. Boone, G. Stiller, T. von Clarmann, J. Orphal, J. Urban, D. Murtagh, E. J. Llewellyn, D. Degenstein, A. E. Bourassa, N. D. Lloyd, L. Froidevaux, M. Birk, G. Wagner, F. Schreier, J. Xu, P. Vogt, T. Trautmann, and M. Yasui We observed ozone (O 3 ) in the vertical region between 250 and 0.0005 hPa (~ 12–96 km) using the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) on the Japanese Experiment Module (JEM) of the International Space Station (ISS) between 12 October 2009 and 21 April 2010. The new 4 K superconducting heterodyne receiver technology of SMILES allowed us to obtain a one order of magnitude better signal-to-noise ratio for the O 3 line observation compared to past spaceborne microwave instruments. The non-sun-synchronous orbit of the ISS allowed us to observe O 3 at various local times. We assessed the quality of the vertical profiles of O 3 in the 100–0.001 hPa (~ 16–90 km) region for the SMILES NICT Level 2 product version 2.1.5. The evaluation is based on four components: error analysis; internal comparisons of observations targeting three different instrumental setups for the same O 3 625.371 GHz transition; internal comparisons of two different retrieval algorithms; and external comparisons for various local times with ozonesonde, satellite and balloon observations (ENVISAT/MIPAS, SCISAT/ACE-FTS, Odin/OSIRIS, Odin/SMR, Aura/MLS, TELIS). SMILES O 3 data have an estimated absolute accuracy of better than 0.3 ppmv (3%) with a vertical resolution of 3–4 km over the 60 to 8 hPa range. The random error for a single measurement is better than the estimated systematic error, being less than 1, 2, and 7%, in the 40–1, 80–0.1, and 100–0.004 hPa pressure regions, respectively. SMILES O 3 abundance was 10–20% lower than all other satellite measurements at 8–0.1 hPa due to an error arising from uncertainties of the tangent point information and the gain calibration for the intensity of the spectrum. SMILES O 3 from observation frequency Band-B had better accuracy than that from Band-A. A two month period is required to accumulate measurements covering 24 h in local time of O 3 profile. However such a dataset can also contain variation due to dynamical, seasonal, and latitudinal effects.

Description: The Atmospheric radiation measurement (ARM) program network of microwave radiometers: instrumentation, data, and retrievals Atmospheric Measurement Techniques, 6, 2359-2372, 2013 Author(s): M. P. Cadeddu, J. C. Liljegren, and D. D. Turner The Climate Research Facility of the US Department of Energy's Atmospheric Radiation Measurement (ARM) Program operates a network of ground-based microwave radiometers. Data and retrievals from these instruments have been available to the scientific community for almost 20 yr. In the past five years the network has expanded to include a total of 22 microwave radiometers deployed in various locations around the world. The new instruments cover a frequency range between 22 and 197 GHz and are consistently and automatically calibrated. The latest addition to the network is a new generation of three-channel radiometers, currently in the early stage of deployment at all ARM sites. The network has been specifically designed to achieve increased accuracy in the retrieval of precipitable water vapor (PWV) and cloud liquid water path (LWP) with the long-term goal of providing the scientific community with reliable, calibrated radiometric data and retrievals of important geophysical quantities with well-characterized uncertainties. The radiometers provide high-quality, continuous datasets that can be utilized in a wealth of applications and scientific studies. This paper presents an overview of the microwave instrumentation, calibration procedures, data, and retrievals that are available for download from the ARM data archive.

Description: Airborne sun photometer PLASMA: concept, measurements, comparison of aerosol extinction vertical profile with lidar Atmospheric Measurement Techniques, 6, 2383-2389, 2013 Author(s): Y. Karol, D. Tanré, P. Goloub, C. Vervaerde, J. Y. Balois, L. Blarel, T. Podvin, A. Mortier, and A. Chaikovsky A 15-channel airborne sun-tracking photometer has been developed. The instrument provides aerosol optical depths over a wide spectral range (0.34–2.25 μm) with an accuracy (ΔAOD) of approximately 0.01. Taking measurements at different altitudes allow us to derive the aerosol extinction vertical profile. Thanks to the wide spectral range of the instrument, information on the aerosol size distribution along the vertical is also available.

Description: McClear: a new model estimating downwelling solar radiation at ground level in clear-sky conditions Atmospheric Measurement Techniques, 6, 2403-2418, 2013 Author(s): M. Lefèvre, A. Oumbe, P. Blanc, B. Espinar, B. Gschwind, Z. Qu, L. Wald, M. Schroedter-Homscheidt, C. Hoyer-Klick, A. Arola, A. Benedetti, J. W. Kaiser, and J.-J. Morcrette A new fast clear-sky model called McClear was developed to estimate the downwelling shortwave direct and global irradiances received at ground level under clear skies. It is a fully physical model replacing empirical relations or simpler models used before. It exploits the recent results on aerosol properties, and total column content in water vapour and ozone produced by the MACC project (Monitoring Atmosphere Composition and Climate). It accurately reproduces the irradiance computed by the libRadtran reference radiative transfer model with a computational speed approximately 10 5 times greater by adopting the abaci, or look-up table, approach combined with interpolation functions. It is therefore suited for geostationary satellite retrievals or numerical weather prediction schemes with many pixels or grid points, respectively. McClear irradiances were compared to 1 min measurements made in clear-sky conditions at several stations within the Baseline Surface Radiation Network in various climates. The bias for global irradiance comprises between −6 and 25 W m −2 . The RMSE ranges from 20 W m −2 (3% of the mean observed irradiance) to 36 W m −2 (5%) and the correlation coefficient ranges between 0.95 and 0.99. The bias for the direct irradiance comprises between −48 and +33 W m −2 . The root mean square error (RMSE) ranges from 33 W m −2 (5%) to 64 W m −2 (10%). The correlation coefficient ranges between 0.84 and 0.98. This work demonstrates the quality of the McClear model combined with MACC products, and indirectly the quality of the aerosol properties modelled by the MACC reanalysis.

Description: Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging human pathogen that causes life-threatening invasive infections such as streptococcal toxic shock syndrome. Recent epidemiological studies reveal that invasive SDSE infections have been increasing in Asia, Europe, and the United States. Almost all SDSE carry Lancefield group G or C antigen. We have determined the complete genome sequence of a human group C SDSE 167 strain. A comparison of its sequence with that of four SDSE strains, three in Lancefield group G and one in Lancefield group A, showed approximately 90% coverage. Most regions showing little or no homology were located in the prophages. There was no evidence of massive rearrangement in the genome of SDSE 167. Bayesian phylogeny using entire genome sequences showed that the most recent common ancestor of the five SDSE strains appeared 446 years ago. Interestingly, we found that SDSE 167 harbors sugar metabolizing enzymes in a unique region and streptodornase in the phage region, which presumably contribute to the degradation of host tissues and the prompted covRS mutation, respectively. A comparison of these five SDSE strains, which differ in Lancefield group antigens, revealed a gene cluster presumably responsible for the synthesis of the antigenic determinant. These results may provide the basis for molecular epidemiological research of SDSE.

Description: Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.

Description: Ten years of MIPAS measurements with ESA Level 2 processor V6 – Part 1: Retrieval algorithm and diagnostics of the products Atmospheric Measurement Techniques, 6, 2419-2439, 2013 Author(s): P. Raspollini, B. Carli, M. Carlotti, S. Ceccherini, A. Dehn, B. M. Dinelli, A. Dudhia, J.-M. Flaud, M. López-Puertas, F. Niro, J. J. Remedios, M. Ridolfi, H. Sembhi, L. Sgheri, and T. von Clarmann The MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) instrument on the Envisat (Environmental satellite) satellite has provided vertical profiles of the atmospheric composition on a global scale for almost ten years. The MIPAS mission is divided in two phases: the full resolution phase, from 2002 to 2004, and the optimized resolution phase, from 2005 to 2012, which is characterized by a finer vertical and horizontal sampling attained through a reduction of the spectral resolution. While the description and characterization of the products of the ESA processor for the full resolution phase has been already described in previous papers, in this paper we focus on the performances of the latest version of the ESA (European Space Agency) processor, named ML2PP V6 (MIPAS Level 2 Prototype Processor), which has been used for reprocessing the entire mission. The ESA processor had to perform the operational near real time analysis of the observations and its products needed to be available for data assimilation. Therefore, it has been designed for fast, continuous and automated analysis of observations made in quite different atmospheric conditions and for a minimum use of external constraints in order to avoid biases in the products. The dense vertical sampling of the measurements adopted in the second phase of the MIPAS mission resulted in sampling intervals finer than the instantaneous field of view of the instrument. Together with the choice of a retrieval grid aligned with the vertical sampling of the measurements, this made ill-conditioned the retrieval problem of the MIPAS operational processor. This problem has been handled with minimal changes to the original retrieval approach but with significant improvements nonetheless. The Levenberg–Marquardt method, already present in the retrieval scheme for its capability to provide fast convergence for nonlinear problems, is now also exploited for the reduction of the ill-conditioning of the inversion. An expression specifically designed for the regularizing Levenberg–Marquardt method has been implemented for the computation of the covariance matrices and averaging kernels of the retrieved products. The regularization of the Levenberg–Marquardt method is controlled by the convergence criteria and is deliberately kept weak. The resulting oscillations of the retrieved profile are a posteriori damped by an innovative self-adapting Tikhonov regularization. The convergence criteria and the weakness of the self-adapting regularization ensure that minimum constraints are used and the best vertical resolution obtainable from the measurements is achieved in all atmospheric conditions. Random and systematic errors, as well as vertical and horizontal resolution are compared in the two phases of the mission for all products, namely: temperature, H 2O , O 3 , HNO 3 , CH 4 , N 2O , NO 2 , CFC-11, CFC-12, N 2 O 5 and ClONO 2 . The use in the two phases of the mission of different optimized sets of spectral intervals ensures that, despite the different spectral resolutions, comparable performances are obtained in the whole MIPAS mission in terms of random and systematic errors, while the vertical resolution and the horizontal resolution are significantly better in the case of the optimized resolution measurements.

Description: Ground-based stratospheric O 3 and HNO 3 measurements at Thule, Greenland: an intercomparison with Aura MLS observations Atmospheric Measurement Techniques, 6, 2441-2453, 2013 Author(s): I. Fiorucci, G. Muscari, L. Froidevaux, and M. L. Santee In response to the need for improving our understanding of the evolution and the interannual variability of the winter Arctic stratosphere, in January 2009 a Ground-Based Millimeter-wave Spectrometer (GBMS) was installed at the Network for the Detection of Atmospheric Composition Change (NDACC) site in Thule (76.5° N, 68.8° W), Greenland. In this work, stratospheric GBMS O 3 and HNO 3 vertical profiles obtained from Thule during the winters 2010 (HNO 3 only), 2011 and 2012 are characterized and intercompared with co-located measurements of the Aura Microwave Limb Sounder (MLS) experiment. Using a recently developed algorithm based on Optimal Estimation, we find that the GBMS O 3 retrievals show good sensitivity (〉 80%) to atmospheric variations between ~ 17 and ~ 50 km, where their 1σ uncertainty is estimated to be the larger of ~ 11% or 0.2 ppmv. Similarly, HNO 3 profiles can be considered for scientific use between ~ 17 and ~ 45 km altitude, with a 1σ uncertainty that amounts to the larger of 15% or 0.2 ppbv. Comparisons with Aura MLS version 3.3 observations show that, on average, GBMS O 3 mixing ratios are biased negatively with respect to MLS throughout the stratosphere, with differences ranging between ~ 0.3 ppmv (8%) and 0.9 ppmv (18%) in the 17–50 km vertical range. GBMS HNO 3 values display instead a positive bias with respect to MLS up to 26 km, reaching a maximum of ~ 1 ppbv (10%) near the mixing ratio profile peak. O 3 and HNO 3 values from the two datasets prove to be well correlated at all altitudes, although their correlations worsen at the lower end of the altitude ranges considered. Column contents of GBMS and MLS O 3 (from 20 km upwards) and HNO 3 (from 17 km upwards) correlate very well and indicate that GBMS measurements can provide valuable estimates of column interannual and seasonal variations for these compounds.

Description: Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders ( Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus ( met1 ) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander ( Ambystoma tigrinum tigrinum ) and the paedomorphic Mexican axolotl ( Ambystoma mexicanum ). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the effect of met1 on larval growth, metamorphic timing, and gene expression in the brain. We show that met1 maps to the position of a urodele-specific chromosome rearrangement on linkage group 2 that uniquely brought functionally associated genes into linkage. Furthermore, we found that more than 200 genes were differentially expressed during larval development as a function of met1 genotype. This list of differentially expressed genes is enriched for proteins that function in the mitochondria, providing evidence of a link between met1 , thyroid hormone signaling, and mitochondrial energetics associated with metamorphosis. Finally, we found that met1 significantly affected metamorphic timing in hybrids, but not early larval growth rate. Collectively, our results show that met1 regulates species and morph-specific patterns of brain transcription and life history variation .

Description: Inter-calibration of polar imager solar channels using SEVIRI Atmospheric Measurement Techniques, 6, 2495-2508, 2013 Author(s): J. F. Meirink, R. A. Roebeling, and P. Stammes Accurate calibration of satellite imagers is a prerequisite for using their measurements in climate applications. Here we present a method for the inter-calibration of geostationary and polar-orbiting imager solar channels based on regressions of collocated near-nadir reflectances. Specific attention is paid to correcting for differences in spectral response between instruments. The method is used to calibrate the solar channels of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) on the geostationary Meteosat satellite with corresponding channels of the Moderate Resolution Imaging Spectroradiometer (MODIS) on the polar-orbiting Aqua satellite. The SEVIRI operational calibration is found to be stable during the years 2004 to 2009, but offset by −8, −6, and +3.5 % for channels 1 (0.6 μm), 2 (0.8 μm), and 3 (1.6 μm), respectively. These results are robust for a range of choices that can be made regarding data collocation and selection, as long as the viewing and illumination geometries of the two instruments are matched. Uncertainties in the inter-calibration method are estimated to be 1 % for channel 1 and 1.5 % for channels 2 and 3. A specific application of our method is the inter-calibration of polar imagers using SEVIRI as a transfer instrument. This offers an alternative to direct inter-calibration, which in general has to rely on high-latitude collocations. Using this method we have tied MODIS-Terra and Advanced Very High Resolution Radiometer (AVHRR) instruments on National Oceanic and Atmospheric Administration (NOAA) satellites 17 and 18 to MODIS-Aqua for the years 2007 to 2009. While reflectances of the two MODIS instruments differ less than 2 % for all channels considered, deviations of an existing AVHRR calibration from MODIS-Aqua reach −3.5 and +2.5 % for the 0.8 and 1.6 μm channels, respectively.

Description: Using ocean-glint scattered sunlight as a diagnostic tool for satellite remote sensing of greenhouse gases Atmospheric Measurement Techniques, 6, 2509-2520, 2013 Author(s): A. Butz, S. Guerlet, O. P. Hasekamp, A. Kuze, and H. Suto Spectroscopic measurements of sunlight backscattered by the Earth's surface is a technique widely used for remote sensing of atmospheric constituent concentrations from space. Thereby, remote sensing of greenhouse gases poses particularly challenging accuracy requirements for instrumentation and retrieval algorithms which, in general, suffer from various error sources. Here, we investigate a method that helps disentangle sources of error for observations of sunlight backscattered from the glint spot on the ocean surface. The method exploits the backscattering characteristics of the ocean surface, which is bright for glint geometry but dark for off-glint angles. This property allows for identifying a set of clean scenes where light scattering due to particles in the atmosphere is negligible such that uncertain knowledge of the lightpath can be excluded as a source of error. We apply the method to more than 3 yr of ocean-glint measurements by the Thermal And Near infrared Sensor for carbon Observation (TANSO) Fourier Transform Spectrometer (FTS) onboard the Greenhouse Gases Observing Satellite (GOSAT), which aims at measuring carbon dioxide (CO 2 ) and methane (CH 4 ) concentrations. The proposed method is able to clearly monitor recent improvements in the instrument calibration of the oxygen (O 2 ) A-band channel and suggests some residual uncertainty in our knowledge about the instrument. We further assess the consistency of CO 2 retrievals from several absorption bands between 6400 cm −1 (1565 nm) and 4800 cm −1 (2100 nm) and find that the absorption bands commonly used for monitoring of CO 2 dry air mole fractions from GOSAT allow for consistency better than 1.5 ppm. Usage of other bands reveals significant inconsistency among retrieved CO 2 concentrations pointing at inconsistency of spectroscopic parameters.

Description: Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most nu genes, maintenance of OXPHOS structural stability and functional efficiency may involve correlated evolution of mt and nu OXPHOS genes. The nu OXPHOS genes might be predicted to exhibit accelerated evolutionary rates to accommodate the elevated substitution rates of mt OXPHOS subunits with which they interact. Evolutionary rates of nu OXPHOS genes should, therefore, be higher than that of nu genes that are not involved in OXPHOS (nu non-OXPHOS). We tested the compensatory evolution hypothesis by comparing the evolutionary rates (synonymous substitution rate d S and nonsynonymous substitution rate d N ) among 13 mt OXPHOS genes, 60 nu OXPHOS genes, and 77 nu non-OXPHOS genes in vertebrates (7 fish and 40 mammal species). The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis. However, results from two OXPHOS complexes did not fit this pattern when analyzed separately. We found that the d N of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d N between genes for nu non-OXPHOS and core subunits. This latter finding suggests that compensatory changes play a minor role in the evolution of OXPHOS genes and that the observed accelerated nu substitution rates are due largely to reduced functional constraint on noncore subunits.

Description: Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

Description: Parameterizing radiative transfer to convert MAX-DOAS dSCDs into near-surface box-averaged mixing ratios Atmospheric Measurement Techniques, 6, 1521-1532, 2013 Author(s): R. Sinreich, A. Merten, L. Molina, and R. Volkamer We present a novel parameterization method to convert multi-axis differential optical absorption spectroscopy (MAX-DOAS) differential slant column densities (dSCDs) into near-surface box-averaged volume mixing ratios. The approach is applicable inside the planetary boundary layer under conditions with significant aerosol load, and builds on the increased sensitivity of MAX-DOAS near the instrument altitude. It parameterizes radiative transfer model calculations and significantly reduces the computational effort, while retrieving ~ 1 degree of freedom. The biggest benefit of this method is that the retrieval of an aerosol profile, which usually is necessary for deriving a trace gas concentration from MAX-DOAS dSCDs, is not needed. The method is applied to NO 2 MAX-DOAS dSCDs recorded during the Mexico City Metropolitan Area 2006 (MCMA-2006) measurement campaign. The retrieved volume mixing ratios of two elevation angles (1° and 3°) are compared to volume mixing ratios measured by two long-path (LP)-DOAS instruments located at the same site. Measurements are found to agree well during times when vertical mixing is expected to be strong. However, inhomogeneities in the air mass above Mexico City can be detected by exploiting the different horizontal and vertical dimensions probed by the MAX-DOAS and LP-DOAS instruments. In particular, a vertical gradient in NO 2 close to the ground can be observed in the afternoon, and is attributed to reduced mixing coupled with near-surface emission inside street canyons. The existence of a vertical gradient in the lower 250 m during parts of the day shows the general challenge of sampling the boundary layer in a representative way, and emphasizes the need of vertically resolved measurements.

Description: Polarization data from SCIAMACHY limb backscatter observations compared to vector radiative transfer model simulations Atmospheric Measurement Techniques, 6, 1503-1520, 2013 Author(s): P. Liebing, K. Bramstedt, S. Noël, V. Rozanov, H. Bovensmann, and J. P. Burrows SCIAMACHY is a passive imaging spectrometer onboard ENVISAT designed to obtain trace gas abundances from measured radiances and irradiances in the UV to SWIR range in nadir-, limb- and occultation-viewing modes. Its grating spectrometer introduces a substantial sensitivity to the polarization of the incoming light with nonnegligible effects on the radiometric calibration. To be able to correct for the polarization sensitivity, SCIAMACHY utilizes broadband Polarization Measurement Devices (PMDs). While for the nadir-viewing mode the measured atmospheric polarization has been validated against POLDER data (Tilstra and Stammes, 2007, 2010), a similar validation study regarding the limb-viewing mode has not yet been performed. This paper aims at an assessment of the quality of the SCIAMACHY limb polarization data. Since limb polarization measurements by other air/spaceborne instruments in the spectral range of SCIAMACHY are not available, a comparison with radiative transfer simulations by SCIATRAN V3.1 (Rozanov et al., 2013) using a wide range of atmospheric parameters is performed. SCIATRAN is a vector radiative transfer model (VRTM) capable of performing calculations of the multiply scattered radiance in a spherically symmetric atmosphere. The study shows that the limb polarization data exhibit a large time-dependent bias that decreases with wavelength. Possible reasons for this bias are a still unknown combination of insufficient accuracy or inconsistencies of the on-ground calibration data, scan mirror degradation and stress induced changes of the polarization response of components inside the optical bench of the instrument. It is shown that it should in principle be feasible to recalibrate the effective polarization sensitivity of the instrument using the in-flight data and VRTM simulations.

Description: Evaluating calibration strategies for isotope ratio infrared spectroscopy for atmospheric 13 CO 2 / 12 CO 2 measurement Atmospheric Measurement Techniques, 6, 1491-1501, 2013 Author(s): X.-F. Wen, Y. Meng, X.-Y. Zhang, X.-M. Sun, and X. Lee Isotope ratio infrared spectroscopy (IRIS) provides an in situ technique for measuring δ 13 C in atmospheric CO 2 . A number of methods have been proposed for calibrating the IRIS measurements, but few studies have systematically evaluated their accuracy for atmospheric applications. In this study, we carried out laboratory and ambient measurements with two commercial IRIS analyzers and compared the accuracy of four calibration strategies. We found that calibration based on the 12 C and 13 C mixing ratios (Bowling et al., 2003) and on linear interpolation of the measured delta using the mixing ratio of the major isotopologue (Lee et al., 2005) yielded accuracy better than 0.06‰. Over a 7-day atmospheric measurement in Beijing, the two analyzers agreed to within −0.02 ± 0.18‰ after proper calibration. However, even after calibration the difference between the two analyzers showed a slight correlation with concentration, and this concentration dependence propagated through the Keeling analysis, resulting in a much larger difference of 2.44‰ for the Keeling intercept. The high sensitivity of the Keeling analysis to the concentration dependence underscores the challenge of IRIS for atmospheric research.

Description: Cavity ring-down spectroscopy sensor development for high-time-resolution measurements of gaseous elemental mercury in ambient air Atmospheric Measurement Techniques, 6, 1477-1489, 2013 Author(s): A. Pierce, D. Obrist, H. Moosmüller, X. Faïn, and C. Moore We describe further development of a previous laboratory prototype pulsed cavity ring-down spectroscopy (CRDS) sensor into a field-deployable system for high-time-resolution, continuous, and automated measurement of gaseous elemental mercury (GEM) concentrations in ambient air. We employed an external, isotopically enriched Hg cell for automated locking and stabilization of the laser wavelength on the GEM peak absorption during measurements. Further, we describe implementation of differential absorption measurements via a piezoelectric tuning element for pulse-by-pulse tuning of the laser wavelength onto and off of the GEM absorption line. This allowed us to continuously correct (at 25 Hz) for system baseline extinction losses unrelated to GEM absorption. Extensive measurement and calibration data obtained with the system were based on spike addition in both GEM-free air and ambient air. Challenges and interferences that occurred during measurements (particularly in ambient air) are discussed including temperature and ozone (O 3 ) concentration fluctuations, and steps taken to reduce these. CRDS data were highly linear ( r 2 ≥ 0.98) with data from a commercial Tekran 2537 Hg analyzer across a wide range of GEM concentrations (0 to 127 ng m −3 ) in Hg-free and ambient air. Measurements during periods of stable background GEM concentrations provided a conservative instrument sensitivity estimate of 0.35 ng m −3 for the CRDS system when time averaged for 5 min. This sensitivity, along with concentration patterns observed in ambient air (with the CRDS system and verified with the Tekran analyzer), showed that the sensor was capable of characterizing GEM fluctuations in ambient air. The value of fast-response GEM measurements was shown by a series of GEM spike additions – highlighting that high-temporal-resolution measurement allowed for detailed characterization of fast concentration fluctuations not possible with traditional analyzers.

Description: Human hemoglobins, the oxygen carriers in the blood, are composed by two α-like and two β-like globin monomers. The β-globin gene cluster located at 11p15.5 comprises one pseudogene and five genes whose expression undergoes two critical switches: the embryonic-to-fetal and fetal-to-adult transition. HBD encodes the -globin chain of the minor adult hemoglobin (HbA 2 ), which is assumed to be physiologically irrelevant. Paradoxically, reduced diversity levels have been reported for this gene. In this study, we sought a detailed portrait of the genetic variation within the β-globin cluster in a large human population panel from different geographic backgrounds. We resequenced the coding and noncoding regions of the two adult β-globin genes ( HBD and HBB ) in European and African populations, and analyzed the data from the β-globin cluster ( HBE , HBG2 , HBG1 , HBBP1 , HBD, and HBB ) in 1,092 individuals representing 14 populations sequenced as part of the 1000 Genomes Project. Additionally, we assessed the diversity levels in nonhuman primates using chimpanzee sequence data provided by the PanMap Project. Comprehensive analyses, based on classic neutrality tests, empirical and haplotype-based studies, revealed that HBD and its neighbor pseudogene HBBP1 have mainly evolved under purifying selection, suggesting that their roles are essential and nonredundant. Moreover, in the light of recent studies on the chromatin conformation of the β-globin cluster, we present evidence sustaining that the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression.

Description: A tandem repeat’s (TR) propensity to mutate increases with repeat number, and can become very pronounced beyond a critical boundary, transforming it into a microsatellite (MS). However, a clear understanding of the mutational behavior of different TR classes and motifs and related mechanisms is lacking, as is a consensus on the existence of a boundary separating short TRs (STRs) from MSs. This hinders our understanding of MSs’ mutational properties and their effective use as genetic markers. Using indel calls for 179 individuals from 1000 Genomes Pilot-1 Project, we determined polymorphism incidence for four major TR classes, and formalized its varying relationship with repeat number using segmented regression. We observed a biphasic regime with a transition from a faster to a slower exponential growth at 9, 5, 4, and 4 repeats for mono-, di-, tri-, and tetranucleotide TRs, respectively. We used an in vitro mutagenesis assay to evaluate the contribution of strand slippage errors to mutability. STRs and MSs differ in their absolute polymorphism levels, but more importantly in their rates of mutability growth. Although strand slippage is a major factor driving mononucleotide polymorphism incidence, dinucleotide polymorphism incidence is greater than that expected due to strand slippage alone, indicating that additional cellular factors might be driving dinucleotide mutability in the human genome. Leveraging on hundreds of human genomes, we present the first comprehensive, genome-wide analysis of TR mutational behavior, encompassing several motif sizes and compositions.

Description: Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales ( Alphaproteobacteria ) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T . adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan’s aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host–microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.

Description: Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana–A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa . Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa ; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with "deletion" in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a "deletion machine" in the Brassica lineage.

Description: Understanding the molecular basis of within and between species phenotypic variation is one of the main goals of Biology. In Drosophila , most of the work regarding this issue has been performed in D. melanogaster , but other distantly related species must also be studied to verify the generality of the findings obtained for this species. Here, we make the case for D. americana , a species of the virilis group of Drosophila that has been diverging from the model species, D. melanogaster , for approximately 40 Myr. To determine the suitability of this species for such studies, polymorphism and recombination estimates are presented for D. americana based on the largest nucleotide sequence polymorphism data set so far analyzed (more than 100 data sets) for this species. The polymorphism estimates are also compared with those obtained from the comparison of the genome assembly of two D. americana strains (H5 and W11) here reported. As an example of the general utility of these resources, we perform a preliminary study on the molecular basis of lifespan differences in D. americana . First, we show that there are lifespan differences between D. americana populations from different regions of the distribution range. Then, we perform five F2 association experiments using markers for 21 candidate genes previously identified in D. melanogaster . Significant associations are found between polymorphism at two genes ( hep and Lim3 ) and lifespan. For the F2 association study involving the two sequenced strains (H5 and W11), we identify amino acid differences at Lim3 and Hep that could be responsible for the observed changes in lifespan. For both genes, no large gene expression differences were observed between the two strains.

Description: Broadband measurements of aerosol extinction in the ultraviolet spectral region Atmospheric Measurement Techniques, 6, 861-877, 2013 Author(s): R. A. Washenfelder, J. M. Flores, C. A. Brock, S. S. Brown, and Y. Rudich Aerosols influence the Earth's radiative budget by scattering and absorbing incoming solar radiation. The optical properties of aerosols vary as a function of wavelength, but few measurements have reported the wavelength dependence of aerosol extinction cross sections and complex refractive indices. We describe a new laboratory instrument to measure aerosol optical extinction as a function of wavelength, using cavity enhanced spectroscopy with a broadband light source. The instrument consists of two broadband channels which span the 360–390 and 385–420 nm spectral regions using two light emitting diodes (LED) and a grating spectrometer with charge-coupled device (CCD) detector. We determined aerosol extinction cross sections and directly observed Mie scattering resonances for aerosols that are purely scattering (polystyrene latex spheres and ammonium sulfate), slightly absorbing (Suwannee River fulvic acid), and strongly absorbing (nigrosin dye). We describe an approach for retrieving refractive indices as a function of wavelength from the measured extinction cross sections over the 360–420 nm wavelength region. The retrieved refractive indices for PSL and ammonium sulfate agree within uncertainty with the literature values for this spectral region. The refractive index determined for nigrosin is 1.78 (± 0.03) + 0.19 (± 0.08) i at 360 nm and 1.63 (± 0.03) + 0.21 (± 0.05) i at 420 nm. The refractive index determined for Suwannee River fulvic acid is 1.71 (± 0.02) + 0.07 (± 0.06) i at 360 nm and 1.66 (± 0.02) + 0.06 (± 0.04) i at 420 nm. These laboratory results support the potential for a field instrument capable of determining ambient aerosol optical extinction, average aerosol extinction cross section, and complex refractive index as a function of wavelength.

Description: Climatologies from satellite measurements: the impact of orbital sampling on the standard error of the mean Atmospheric Measurement Techniques, 6, 937-948, 2013 Author(s): M. Toohey and T. von Clarmann Climatologies of atmospheric observations are often produced by binning measurements according to latitude and calculating zonal means. The uncertainty in these climatological means is characterised by the standard error of the mean (SEM). However, the usual estimator of the SEM, i.e., the sample standard deviation divided by the square root of the sample size, holds only for uncorrelated randomly sampled measurements. Measurements of the atmospheric state along a satellite orbit cannot always be considered as independent because (a) the time-space interval between two nearest observations is often smaller than the typical scale of variations in the atmospheric state, and (b) the regular time-space sampling pattern of a satellite instrument strongly deviates from random sampling. We have developed a numerical experiment where global chemical fields from a chemistry climate model are sampled according to real sampling patterns of satellite-borne instruments. As case studies, the model fields are sampled using sampling patterns of the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) and Atmospheric Chemistry Experiment Fourier-Transform Spectrometer (ACE-FTS) satellite instruments. Through an iterative subsampling technique, and by incorporating information on the random errors of the MIPAS and ACE-FTS measurements, we produce empirical estimates of the standard error of monthly mean zonal mean model O 3 in 5° latitude bins. We find that generally the classic SEM estimator is a conservative estimate of the SEM, i.e., the empirical SEM is often less than or approximately equal to the classic estimate. Exceptions occur only when natural variability is larger than the random measurement error, and specifically in instances where the zonal sampling distribution shows non-uniformity with a similar zonal structure as variations in the sampled field, leading to maximum sensitivity to arbitrary phase shifts between the sample distribution and sampled field. The occurrence of such instances is thus very sensitive to slight changes in the sampling distribution, and to the variations in the measured field. This study highlights the need for caution in the interpretation of the oft-used classically computed SEM, and outlines a relatively simple methodology that can be used to assess one component of the uncertainty in monthly mean zonal mean climatologies produced from measurements from satellite-borne instruments.

Description: A chemical analyzer for charged ultrafine particles Atmospheric Measurement Techniques, 6, 2339-2348, 2013 Author(s): S. G. Gonser and A. Held New particle formation is a frequent phenomenon in the atmosphere and of major significance for the Earth's climate and human health. To date the mechanisms leading to the nucleation of particles as well as to aerosol growth are not completely understood. A lack of appropriate measurement equipment for online analysis of the chemical composition of freshly nucleated particles is one major limitation. We have developed a Chemical Analyzer for Charged Ultrafine Particles (CAChUP) capable of analyzing particles with diameters below 30 nm. A bulk of size-separated particles is collected electrostatically on a metal filament, resistively desorbed and subsequently analyzed for its molecular composition in a time of flight mass spectrometer. We report on technical details as well as characterization experiments performed with the CAChUP. Our instrument was tested in the laboratory for its detection performance as well as for its collection and desorption capabilities. The manual application of defined masses of camphene (C 10 H 16 ) to the desorption filament resulted in a detection limit between 0.5 and 5 ng, and showed a linear response of the mass spectrometer. Flow tube experiments of 25 nm diameter secondary organic aerosol from ozonolysis of alpha-pinene also showed a linear relation between collection time and the mass spectrometer's signal intensity. The resulting mass spectra from the collection experiments are in good agreement with published work on particles generated by the ozonolysis of alpha-pinene. A sensitivity study shows that the current setup of CAChUP is ready for laboratory measurements and for the observation of new particle formation events in the field.

Description: Comparison of AOD between CALIPSO and MODIS: significant differences over major dust and biomass burning regions Atmospheric Measurement Techniques, 6, 2391-2401, 2013 Author(s): X. Ma, K. Bartlett, K. Harmon, and F. Yu Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) provide global vertical profiles of aerosol optical properties for the first time. In this study, we employed about 6 yr (2006–2011) of CALIPSO level 3 monthly mean gridded aerosol optical depth (AOD) products (daytime and nighttime) for cloud-free conditions, to compare with the Moderate Resolution Imaging Spectroradiometer (MODIS) Terra/Aqua level 3 monthly mean AOD dataset for the same time period. While the spatial distribution and seasonal variability of CALIPSO AOD is generally consistent with that of MODIS, CALIPSO is overall lower than MODIS as MODIS has higher frequency than CALIPSO for most bins of AOD. The correlation between MODIS and CALIPSO is better over ocean than over land. We focused on four regions that have large systematic differences: two over dust regions (the Sahara and Northwest China) and two over biomass burning regions (South Africa and South America). It is found that CALIPSO AOD is significantly lower than MODIS AOD over dust regions during the whole time period, with a maximum difference of 0.3 over the Saharan region and 0.25 over Northwest China. For biomass burning regions, CALIPSO AOD is significantly higher than MODIS AOD over South Africa, with a maximum difference of 0.25. Additionally CALIPSO AOD is slightly higher than MODIS AOD over South America for most of the time period, with a few exceptions in 2006, 2007, and 2010, when biomass burning is significantly stronger than during other years. We analyzed the impact of the satellite spatial and temporal sampling issue by using level 2 CALIPSO and MODIS products, and these systematic differences can still be found. The results of this study indicate that systematic differences of CALIPSO relative to MODIS are closely associated with aerosol types, which vary by location and season. Large differences over dust and biomass burning regions may suggest that assumptions made in satellite retrievals, such as the assumed lidar ratios for CALIPSO retrievals over dust and biomass burning regions or the surface reflectance information and/or the aerosol model utilized by the MODIS algorithm, are not appropriate.

Description: Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms. AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes ( dpo ), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp. ) with substantial mtDNA synteny divergence, were sequenced and compared with available glomeromycotan mitochondrial genomes . We used an extensive nucleotide/protein similarity network-based approach to investigate dpo diversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo -induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity. We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.

Description: The study of genetic and phenotypic variation is fundamental for understanding the dynamics of bacterial genome evolution and untangling the evolution and epidemiology of bacterial pathogens. Neisseria meningitidis ( Nm ) is among the most intriguing bacterial pathogens in genomic studies due to its dynamic population structure and complex forms of pathogenicity. Extensive genomic variation within identical clonal complexes (CCs) in Nm has been recently reported and suggested to be the result of homologous recombination, but the extent to which recombination contributes to genomic variation within identical CCs has remained unclear. In this study, we sequenced two Nm strains of identical serogroup (C) and multi-locus sequence type (ST60), and conducted a systematic analysis with an additional 34 Nm genomes. Our results revealed that all gene content variation between the two ST60 genomes was introduced by homologous recombination at the conserved flanking genes, and 94.25% or more of sequence divergence was caused by homologous recombination. Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Nm . Recombination was also evident in genes of the restriction and modification systems, which may undermine barriers to DNA exchange. In conclusion, homologous recombination can drive both gene content variation and sequence divergence in Nm . These findings shed new light on the understanding of the rapid pathoadaptive evolution of Nm and other recombinogenic bacterial pathogens.

Description: Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna , we uncovered precisely this type of genic arrangement. The P. magna mitochondrial genome is linear and made up entirely of palindromes, each containing 1–7 unique coding regions. Consequently, every gene in the genome is duplicated and in an inverted orientation relative to its partner. And when these palindromic genes are folded into putative stem-loops, their predicted translational start sites are often positioned in the apex of the loop. Gel electrophoresis results support the linear, 28-kb monomeric conformation of the P. magna mitochondrial genome. Analyses of other Polytomella taxa suggest that palindromic mitochondrial genes were present in the ancestor of the Polytomella lineage and lost or retained to various degrees in extant species. The possible origins and consequences of this bizarre genomic architecture are discussed.

Description: Expression quantitative trait loci (eQTLs) have been found to be enriched in trait-associated single-nucleotide polymorphisms (SNPs). However, whether eQTLs are adaptive to different environmental factors and its relative evolutionary significance compared with nonsynonymous SNPs (NS SNPs) are still elusive. Compiling environmental correlation data from three studies for more than 500,000 SNPs and 42 environmental factors, including climate, subsistence, pathogens, and dietary patterns, we performed a systematic examination of the adaptive patterns of eQTLs to local environment. Compared with intergenic SNPs, eQTLs are significantly enriched in the lower tail of a transformed rank statistic in the environmental correlation analysis, indicating possible adaptation of eQTLs to the majority of 42 environmental factors. The mean enrichment of eQTLs across 42 environmental factors is as great as, if not greater than, that of NS SNPs. The enrichment of eQTLs, although significant across all levels of recombination rate, is inversely correlated with recombination rate, suggesting the presence of selective sweep or background selection. Further pathway enrichment analysis identified a number of pathways with possible environmental adaption from eQTLs. These pathways are mostly related with immune function and metabolism. Our results indicate that eQTLs might have played an important role in recent and ongoing human adaptation and are of special importance for some environmental factors and biological pathways.

Description: Microwave radiometer to retrieve temperature profiles from the surface to the stratopause Atmospheric Measurement Techniques, 6, 2477-2494, 2013 Author(s): O. Stähli, A. Murk, N. Kämpfer, C. Mätzler, and P. Eriksson TEMPERA (TEMPERature RAdiometer) is a new ground-based radiometer which measures in a frequency range from 51–57 GHz radiation emitted by the atmosphere. With this instrument it is possible to measure temperature profiles from ground to about 50 km. This is the first ground-based instrument with the capability to retrieve temperature profiles simultaneously for the troposphere and stratosphere. The measurement is done with a filterbank in combination with a digital fast Fourier transform spectrometer. A hot load and a noise diode are used as stable calibration sources. The optics consist of an off-axis parabolic mirror to collect the sky radiation. Due to the Zeeman effect on the emission lines used, the maximum height for the temperature retrieval is about 50 km. The effect is apparent in the measured spectra. The performance of TEMPERA is validated by comparison with nearby radiosonde and satellite data from the Microwave Limb Sounder on the Aura satellite. In this paper we present the design and measurement method of the instrument followed by a description of the retrieval method, together with a validation of TEMPERA data over its first year, 2012.

Description: Environmental or geological changes can create new niches that drive ecological species divergence without the immediate cessation of gene flow. However, few such cases have been characterized. On a recently formed volcano, Mt. Etna, Senecio aethnensis and S. chrysanthemifolius inhabit contrasting environments of high and low altitude, respectively. They have very distinct phenotypes, despite hybridizing promiscuously, and thus may represent an important example of ecological speciation "in action," possibly as a response to the rapid geological changes that Mt. Etna has recently undergone. To elucidate the species’ evolutionary history, and help establish the species as a study system for speciation genomics, we sequenced the transcriptomes of the two Etnean species, and the outgroup, S. vernalis , using Illumina sequencing. Despite the species’ substantial phenotypic divergence, synonymous divergence between the high- and low-altitude species was low (d S = 0.016 ± 0.017 [SD]). A comparison of species divergence models with and without gene flow provided unequivocal support in favor of the former and demonstrated a recent time of species divergence (153,080 ya ± 11,470 [SE]) that coincides with the growth of Mt. Etna to the altitudes that separate the species today. Analysis of d N /d S revealed wide variation in selective constraint between genes, and evidence that highly expressed genes, more "multifunctional" genes, and those with more paralogs were under elevated purifying selection. Taken together, these results are consistent with a model of ecological speciation, potentially as a response to the emergence of a new, high-altitude niche as the volcano grew.

Description: Retrieval of nitric oxide in the mesosphere and lower thermosphere from SCIAMACHY limb spectra Atmospheric Measurement Techniques, 6, 2521-2531, 2013 Author(s): S. Bender, M. Sinnhuber, J. P. Burrows, M. Langowski, B. Funke, and M. López-Puertas We use the ultra-violet (UV) spectra in the range 230–300 nm from the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) to retrieve the nitric oxide (NO) number densities from atmospheric emissions in the gamma-bands in the mesosphere and lower thermosphere. Using 3-D ray tracing, a 2-D retrieval grid, and regularisation with respect to altitude and latitude, we retrieve a whole semi-orbit simultaneously for the altitude range from 60 to 160 km. We present details of the retrieval algorithm, first results, and initial comparisons to data from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS). Our results agree on average well with MIPAS data and are in line with previously published measurements from other instruments. For the time of available measurements in 2008–2011, we achieve a vertical resolution of 5–10 km in the altitude range 70–140 km and a horizontal resolution of about 9° from 60° S–60° N. With this we have independent measurements of the NO densities in the mesosphere and lower thermosphere with approximately global coverage. This data can be further used to validate climate models or as input for them.

Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.

Description: Development and field testing of a rapid and ultra-stable atmospheric carbon dioxide spectrometer Atmospheric Measurement Techniques, 7, 4445-4453, 2014 Author(s): B. Xiang, D. D. Nelson, J. B. McManus, M. S. Zahniser, R. A. Wehr, and S. C. Wofsy We present field test results for a new spectroscopic instrument to measure atmospheric carbon dioxide (CO 2 ) with high precision (0.02 μmol mol −1 , or ppm at 1 Hz) and demonstrate high stability (within 0.1 ppm over more than 8 months), without the need for hourly, daily, or even monthly calibration against high-pressure gas cylinders. The technical novelty of this instrument (ABsolute Carbon dioxide, ABC) is the spectral null method using an internal quartz reference cell with known CO 2 column density. Compared to a previously described prototype, the field instrument has better stability and benefits from more precise thermal control of the optics and more accurate pressure measurements in the sample cell (at the mTorr level). The instrument has been deployed at a long-term ecological research site (the Harvard Forest, USA), where it has measured for 8 months without on-site calibration and with minimal maintenance, showing drift bounds of less than 0.1 ppm. Field measurements agree well with those of a commercially available cavity ring-down CO 2 instrument (Picarro G2301) run with a standard calibration protocol. This field test demonstrates that ABC is capable of performing high-accuracy, unattended, continuous field measurements with minimal use of reference gas cylinders.

Description: Investigating uptake of N 2 O in agricultural soils using a high-precision dynamic chamber method Atmospheric Measurement Techniques, 7, 4455-4462, 2014 Author(s): N. J. Cowan, D. Famulari, P. E. Levy, M. Anderson, D. S. Reay, and U. M. Skiba Uptake (or negative flux) of nitrous oxide (N 2 O) in agricultural soils is a controversial issue which has proved difficult to investigate in the past due to constraints such as instrumental precision and methodological uncertainties. Using a recently developed high-precision quantum cascade laser gas analyser combined with a closed dynamic chamber, a well-defined detection limit of 4 μg N 2 O-N m −2 h −1 could be achieved for individual soil flux measurements. 1220 measurements of N 2 O flux were made from a variety of UK soils using this method, of which 115 indicated uptake by the soil (i.e. a negative flux in the micrometeorological sign convention). Only four of these apparently negative fluxes were greater than the detection limit of the method, which suggests that the vast majority of reported negative fluxes from such measurements are actually due to instrument noise. As such, we suggest that the bulk of negative N 2 O fluxes reported for agricultural fields are most likely due to limits in detection of a particular flux measurement methodology and not a result of microbiological activity consuming atmospheric N 2 O.

Description: Rapid, optical measurement of the atmospheric pressure on a fast research aircraft using open-path TDLAS Atmospheric Measurement Techniques, 7, 3653-3666, 2014 Author(s): B. Buchholz, A. Afchine, and V. Ebert Because of the high travel speed, the complex flow dynamics around an aircraft, and the complex dependency of the fluid dynamics on numerous airborne parameters, it is quite difficult to obtain accurate pressure values at a specific instrument location of an aircraft's fuselage. Complex simulations using computational fluid dynamics (CFD) models can in theory computationally "transfer" pressure values from one location to another. However, for long flight patterns, this process is inconvenient and cumbersome. Furthermore, these CFD transfer models require a local experimental validation, which is rarely available. In this paper, we describe an integrated approach for a spectroscopic, calibration-free, in-flight pressure determination in an open-path White cell on an aircraft fuselage using ambient, atmospheric water vapour as the "sensor species". The presented measurements are realised with the HAI (Hygrometer for Atmospheric Investigations) instrument, built for multiphase water detection via calibration-free TDLAS (tunable diode laser absorption spectroscopy). The pressure determination is based on raw data used for H 2 O concentration measurement, but with a different post-flight evaluation method, and can therefore be conducted at deferred time intervals on any desired flight track. The spectroscopic pressure is compared in-flight with the static ambient pressure of the aircraft avionic system and a micro-mechanical pressure sensor, located next to the open-path cell, over a pressure range from 150 to 800 hPa, and a water vapour concentration range of more than 3 orders of magnitude. The correlation between the micro-mechanical pressure sensor measurements and the spectroscopic pressure measurements shows an average deviation from linearity of only 0.14% and a small offset of 9.5 hPa. For the spectroscopic pressure evaluation we derive measurement uncertainties under laboratory conditions of 3.2 and 5.1% during in-flight operation on the HALO airplane. Under certain flight conditions we quantified, for the first time, stalling-induced, dynamic pressure deviations of up to 30% (at 200 hPa) between the avionic sensor and the optical and mechanical pressure sensors integrated in HAI. Such severe local pressure deviations from the typically used avionic pressure are important to take into account for other airborne sensors employed on such fast flying platforms as the HALO aircraft.

Description: As an important subtype of structural variations, chromosomal translocation is associated with various diseases, especially cancers, by disrupting gene structures and functions. Traditional methods for identifying translocations are time consuming and have limited resolutions. Recently, a few studies have employed next-generation sequencing (NGS) technology for characterizing chromosomal translocations on human genome, obtaining high-throughput results with high resolutions. However, these studies are mainly focused on mechanism-specific or site-specific translocation mapping. In this study, we conducted a comprehensive genome-wide analysis on the characterization of human chromosomal material exchange with regard to the chromosome translocations. Using NGS data of 1,481 subjects from the 1000 Genomes Project, we identified 15,349,092 translocated DNA fragment pairs, ranging from 65 to 1,886 bp and with an average size of approximately 102 bp. On average, each individual genome carried about 10,364 pairs, covering approximately 0.069% of the genome. We identified 16 translocation hot regions, among which two regions did not contain repetitive fragments. Results of our study overlapped with a majority of previous results, containing approximately 79% of approximately 2,340 translocations characterized in three available translocation databases. In addition, our study identified five novel potential recurrent chromosomal material exchange regions with greater than 20% detection rates. Our results will be helpful for an accurate characterization of translocations in human genomes, and contribute as a resource for future studies of the roles of translocations in human disease etiology and mechanisms.

Description: Mixing-layer height retrieval with ceilometer and Doppler lidar: from case studies to long-term assessment Atmospheric Measurement Techniques, 7, 3685-3704, 2014 Author(s): J. H. Schween, A. Hirsikko, U. Löhnert, and S. Crewell Aerosol signatures observed by ceilometers are frequently used to derive mixing-layer height (MLH) which is an essential variable for air quality modelling. However, Doppler wind lidar measurements of vertical velocity can provide a more direct estimation of MLH via simple thresholding. A case study reveals difficulties in the aerosol-based MLH retrieval during transition times when the mixing layer builds up in the morning and when turbulence decays in the afternoon. The difficulties can be explained by the fact that the aerosol distribution is related to the history of the mixing process and aerosol characteristics are modified by humidification. The results of the case study are generalized by evaluating one year of joint measurements by a Vaisala CT25K and a HALO Photonics Streamline wind lidar. On average the aerosol-based retrieval gives higher MLH than the wind lidar with an overestimation of MLH by about 300 m (600 m) in the morning (late afternoon). Also, the daily aerosol-based maximum MLH is larger and occurs later during the day and the average morning growth rates are smaller than those derived from the vertical wind. In fair weather conditions classified by less than 4 octa cloud cover the mean diurnal cycle of cloud base height corresponds well to the mixing-layer height showing potential for a simplified MLH estimation.

Description: Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA ( mtpts ). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.

Description: Radio occultation bending angle anomalies during tropical cyclones Atmospheric Measurement Techniques, 4, 1053-1060, 2011 Author(s): R. Biondi, T. Neubert, S. Syndergaard, and J. K. Nielsen The tropical deep convection affects the radiation balance of the atmosphere changing the water vapor mixing ratio and the temperature of the upper troposphere lower stratosphere. The aim of this work is to better understand these processes and to investigate if severe storms leave a significant signature in radio occultation profiles in the tropical tropopause layer. Using tropical cyclone best track database and data from different GPS radio occultation missions (COSMIC, GRACE, CHAMP, SACC and GPSMET), we selected 1194 profiles in a time window of 3 h and a space window of 300 km from the eye of the cyclone. We show that the bending angle anomaly of a GPS radio occultation signal is typically larger than the climatology in the upper troposphere and lower stratosphere and that a double tropopause during deep convection can easily be detected using this technique. Comparisons with co-located radiosondes, climatology of tropopause altitudes and GOES analyses are also shown to support the hypothesis that the bending angle anomaly can be used as an indicator of convective towers. The results are discussed in connection to the GPS radio occultation receiver which will be part of the Atomic Clock Ensemble in Space (ACES) payload on the International Space Station.

Description: Assimilation of GPS radio occultation data at DWD Atmospheric Measurement Techniques, 4, 1105-1113, 2011 Author(s): H. Anlauf, D. Pingel, and A. Rhodin We describe the status of the assimilation of bending angles from GPS radio occultations in the 3D-Var for DWD's operational global forecast model GME ("Global Model for Europe"). Experiments show that the assimilation of GPSRO data leads to a significant reduction of biases in the analyses of temperature, humidity and wind in the upper troposphere and the stratosphere, as well as a better r. m. s. fit in the comparison to radiosondes. The impact on forecasts is most prominent in the data sparse Southern Hemisphere, but is also quite notable in the Northern Hemisphere extra-tropics. The positive results found in the impact experiments lead to the implementation of the assimilation of GPS radio occultations from GRACE-A, FORMOSAT-3/COSMIC and GRAS/MetOp-A into the operational suite on 3 August 2010. We also show some initial results from assimilation experiments using radio occultation data from the German research satellite TerraSAR-X.

Description: CIAO: the CNR-IMAA advanced observatory for atmospheric research Atmospheric Measurement Techniques, 4, 1191-1208, 2011 Author(s): F. Madonna, A. Amodeo, A. Boselli, C. Cornacchia, V. Cuomo, G. D'Amico, A. Giunta, L. Mona, and G. Pappalardo Long-term observations of aerosol and clouds are of crucial importance to understand the weather climate system. At the Istituto di Metodologie per l'Analisi Ambientale of the Italian National Research Council (CNR-IMAA) an advanced atmospheric observatory, named CIAO, is operative. CIAO (CNR-IMAA Atmospheric Observatory) main scientific objective is the long term measurement for the climatology of aerosol and cloud properties. Its equipment addresses the state-of-the-art for the ground-based remote sensing of aerosol, water vapour and clouds including active and passive sensors, like lidars, ceilometers, radiometers, and a radar. This paper describes the CIAO infrastructure, its scientific activities as well as the observation strategy. The observation strategy is mainly organized in order to provide quality assured measurements for satellite validation and model evaluation and to fully exploit the synergy and integration of the active and passive sensors for the improvement of atmospheric profiling. Data quality is ensured both by the application of protocols and dedicated quality assurance programs mainly related to the projects and networks in which the infrastructure is involved. The paper also introduces examples of observations performed at CIAO and of the synergies and integration algorithms (using Raman lidar and microwave profiler data) developed and implemented at the observatory for the optimization and improvement of water vapour profiling. CIAO database represents an optimal basis to study the synergy between different sensors and to investigate aerosol-clouds interactions, and can give a significant contribution to the validation programs of the incoming new generation satellite missions.

Description: Airborne DOAS limb measurements of tropospheric trace gas profiles: case studies on the profile retrieval of O 4 and BrO Atmospheric Measurement Techniques, 4, 1241-1260, 2011 Author(s): C. Prados-Roman, A. Butz, T. Deutschmann, M. Dorf, L. Kritten, A. Minikin, U. Platt, H. Schlager, H. Sihler, N. Theys, M. Van Roozendael, T. Wagner, and K. Pfeilsticker A novel limb scanning mini-DOAS spectrometer for the detection of UV/vis absorbing radicals (e.g., O 3 , BrO, IO, HONO) was deployed on the DLR-Falcon (Deutsches Zentrum für Luft- und Raumfahrt) aircraft and tested during the ASTAR 2007 campaign (Arctic Study of Tropospheric Aerosol, Clouds and Radiation) that took place at Svalbard (78° N) in spring 2007. Our main objectives during this campaign were to test the instrument, and to perform spectral and profile retrievals of tropospheric trace gases, with particular interest on investigating the distribution of halogen compounds (e.g., BrO) during the so-called ozone depletion events (ODEs). In the present work, a new method for the retrieval of vertical profiles of tropospheric trace gases from tropospheric DOAS limb observations is presented. Major challenges arise from modeling the radiative transfer in an aerosol and cloud particle loaded atmosphere, and from overcoming the lack of a priori knowledge of the targeted trace gas vertical distribution (e.g., unknown tropospheric BrO vertical distribution). Here, those challenges are tackled by a mathematical inversion of tropospheric trace gas profiles using a regularization approach constrained by a retrieved vertical profile of the aerosols extinction coefficient E M . The validity and limitations of the algorithm are tested with in situ measured E M , and with an absorber of known vertical profile (O 4 ). The method is then used for retrieving vertical profiles of tropospheric BrO. Results indicate that, for aircraft ascent/descent observations, the limit for the BrO detection is roughly 1.5 pptv (pmol mol −1 ), and the BrO profiles inferred from the boundary layer up to the upper troposphere and lower stratosphere have around 10 degrees of freedom. For the ASTAR 2007 deployments during ODEs, the retrieved BrO vertical profiles consistently indicate high BrO mixing ratios (∼15 pptv) within the boundary layer, low BrO mixing ratios (≤1.5 pptv) in the free troposphere, occasionally enhanced BrO mixing ratios (∼1.5 pptv) in the upper troposphere, and increasing BrO mixing ratios with altitude in the lowermost stratosphere. These findings agree reasonably well with satellite and balloon-borne soundings of total and partial BrO atmospheric column densities.

Description: Processing of GRAS/METOP radio occultation data recorded in closed-loop and raw-sampling modes Atmospheric Measurement Techniques, 4, 1021-1026, 2011 Author(s): M. E. Gorbunov, K. B. Lauritsen, H.-H. Benzon, G. B. Larsen, S. Syndergaard, and M. B. Sørensen Instrument GRAS (Global Navigation Satellite System Receiver for Atmospheric Sounding) on-board of the Metop-A satellite was activated on 27 October 2006. Currently, Metop-A is a fully operational satellite with GRAS providing from 650–700 occultations per day. We describe our processing of GRAS data based on the modification of our OCC software, which was modified to become capable of reading and processing GRAS data. We perform a statistical comparison of bending angles and refractivities derived from GRAS data with those derived from ECMWF analyses. We conclude that GRAS data have error characteristics close to those of COSMIC data. In the height range 10–30 km, the systematic refractivity difference GRAS–ECMWF is of the order of 0.1–0.2 %, and the standard deviation is 0.3–0.6 %. In the lower troposphere GRAS refractivity and bending angle indicate a negative bias, which reaches its maximum value in the tropics. In particular the retrieved refractivity is biased by up to 2.5 %. The negative bias pattern is similar to that found in the statistical validation of COSMIC data. This makes it probable that the bias should not be attributed to the instrument design or hardware.

Description: Eight-component retrievals from ground-based MAX-DOAS observations Atmospheric Measurement Techniques, 4, 1027-1044, 2011 Author(s): H. Irie, H. Takashima, Y. Kanaya, K. F. Boersma, L. Gast, F. Wittrock, D. Brunner, Y. Zhou, and M. Van Roozendael We attempt for the first time to retrieve lower-tropospheric vertical profile information for 8 quantities from ground-based Multi-Axis Differential Optical Absorption Spectroscopy (MAX-DOAS) observations. The components retrieved are the aerosol extinction coefficients at two wavelengths, 357 and 476 nm, and NO 2 , HCHO, CHOCHO, H 2 O, SO 2 , and O 3 volume mixing ratios. A Japanese MAX-DOAS profile retrieval algorithm, version 1 (JM1), is applied to observations performed at Cabauw, the Netherlands (51.97° N, 4.93° E), in June–July 2009 during the Cabauw Intercomparison campaign of Nitrogen Dioxide measuring Instruments (CINDI). Of the retrieved profiles, we focus here on the lowest-layer data (mean values at altitudes 0–1 km), where the sensitivity is usually highest owing to the longest light path. In support of the capability of the multi-component retrievals, we find reasonable overall agreement with independent data sets, including a regional chemical transport model (CHIMERE) and in situ observations performed near the surface (2–3 m) and at the 200-m height level of the tall tower in Cabauw. Plumes of enhanced HCHO and SO 2 were likely affected by biogenic and ship emissions, respectively, and an improvement in their emission strengths is suggested for better agreement between CHIMERE simulations and MAX-DOAS observations. Analysis of air mass factors indicates that the horizontal spatial representativeness of MAX-DOAS observations is about 3–15 km (depending mainly on aerosol extinction), comparable to or better than the spatial resolution of current UV-visible satellite observations and model calculations. These demonstrate that MAX-DOAS provides multi-component data useful for the evaluation of satellite observations and model calculations and can play an important role in bridging different data sets having different spatial resolutions.

Description: Preliminary validation of column-averaged volume mixing ratios of carbon dioxide and methane retrieved from GOSAT short-wavelength infrared spectra Atmospheric Measurement Techniques, 4, 1061-1076, 2011 Author(s): I. Morino, O. Uchino, M. Inoue, Y. Yoshida, T. Yokota, P. O. Wennberg, G. C. Toon, D. Wunch, C. M. Roehl, J. Notholt, T. Warneke, J. Messerschmidt, D. W. T. Griffith, N. M. Deutscher, V. Sherlock, B. Connor, J. Robinson, R. Sussmann, and M. Rettinger Column-averaged volume mixing ratios of carbon dioxide and methane retrieved from the Greenhouse gases Observing SATellite (GOSAT) Short-Wavelength InfraRed observation (GOSAT SWIR X CO 2 and X CH 4 ) were compared with the reference calibrated data obtained by ground-based high-resolution Fourier Transform Spectrometers (g-b FTSs) participating in the Total Carbon Column Observing Network (TCCON). Preliminary results are as follows: the GOSAT SWIR X CO 2 and X CH 4 (Version 01.xx) are biased low by 8.85 ± 4.75 ppm (2.3 ± 1.2 %) and 20.4 ± 18.9 ppb (1.2 ± 1.1 %), respectively. The standard deviation of the GOSAT SWIR X CO 2 and X CH 4 is about 1 % (1 σ) after correcting the negative biases of X CO 2 and X CH 4 by 8.85 ppm and 20.4 ppb, respectively. The latitudinal distributions of zonal means of the GOSAT SWIR X CO 2 and X CH 4 show similar features to those of the g-b FTS data except for the negative biases in the GOSAT data.

Description: Remote sensing of aerosols over snow using infrared AATSR observations Atmospheric Measurement Techniques, 4, 1133-1145, 2011 Author(s): L. G. Istomina, W. von Hoyningen-Huene, A. A. Kokhanovsky, E. Schultz, and J. P. Burrows Infrared (IR) retrievals of aerosol optical thickness (AOT) are challenging because of the low reflectance of aerosol layer at longer wavelengths. In this paper we present a closer analysis of this problem, performed with radiative transfer (RT) simulations for coarse and accumulation mode of four main aerosol components. It shows the strong angular dependence of aerosol IR reflectance at low solar elevations resulting from the significant asymmetry of aerosol phase function at these wavelengths. This results in detectable values of aerosol IR reflectance at certain non-nadir observation angles providing the advantage of multiangle remote sensing instruments for a retrieval of AOT at longer wavelengths. Such retrievals can be of importance e.g. in case of a very strong effect of the surface on the top of atmosphere (TOA) reflectance in the visible spectral range. In the current work, a new method to retrieve AOT of the coarse and accumulation mode particles over snow has been developed using the measurements of Advanced Along Track Scanning Radiometer (AATSR) on board the ENVISAT satellite. The algorithm uses AATSR channel at 3.7 μm and utilizes its dual-viewing observation technique, implying the forward view with an observation zenith angle of around 55 degrees and the nadir view. It includes cloud/snow discrimination, extraction of the atmospheric reflectance out of measured brightness temperature (BT) at 3.7 μm, and interpolation of look-up tables (LUTs) for a given aerosol reflectance. The algorithm uses LUTs, separately simulated with RT forward calculations. The resulting AOT at 500 nm is estimated from the value at 3.7 μm using a fixed Angström parameter. The presented method has been validated against ground-based Aerosol Robotic Network (AERONET) data for 4 high Arctic stations and shows good agreement. A case study has been performed at W-Greenland on 5 July 2008. The day before was characterized by a noticeable dust event. The retrieved AOT maps of the region show a clear increase of AOT in the Kangerlussuaq area. The area of increased AOT was detected on 5 July on the ice sheet east of Kangelussuaq, opposite to the observed north easterly wind at ground level. This position can be explained by a small scale atmospheric circulation transporting the mobilized mineral dust upslope, after its intrusion into the upper branch of the circulation. The performed study of atmospheric reflectance at 3.7 μm also shows possibilities for the detection and retrievals of cloud properties over snow surfaces.

Description: Analytical system for stable carbon isotope measurements of low molecular weight (C 2 -C 6 ) hydrocarbons Atmospheric Measurement Techniques, 4, 1161-1175, 2011 Author(s): A. Zuiderweg, R. Holzinger, and T. Röckmann We present setup, testing and initial results from a new automated system for stable carbon isotope ratio measurements on C 2 to C 6 atmospheric hydrocarbons. The inlet system allows analysis of trace gases from air samples ranging from a few liters for urban samples and samples with high mixing ratios, to many tens of liters for samples from remote unpolluted regions with very low mixing ratios. The centerpiece of the sample preparation is the separation trap, which is used to separate CO 2 and methane from the compounds of interest. The main features of the system are (i) the capability to sample up to 300 l of air, (ii) long term (since May 2009) operational δ 13 C accuracy levels in the range 0.3–0.8 ‰ (1-σ), and (iii) detection limits of order 1.5–2.5 ngC (collected amount of substance) for all reported compounds. The first application of this system was the analysis of 21 ambient air samples taken during 48 h in August 2009 in Utrecht, the Netherlands. Results obtained are generally in good agreement with those from similar urban ambient air studies. Short sample intervals allowed by the design of the instrument help to illustrate the complex diurnal behavior of hydrocarbons in an urban environment, where diverse sources, dynamical processes, and chemical reactions are present.

Description: Source brightness fluctuation correction of solar absorption fourier transform mid infrared spectra Atmospheric Measurement Techniques, 4, 1045-1051, 2011 Author(s): T. Ridder, T. Warneke, and J. Notholt The precision and accuracy of trace gas observations using solar absorption Fourier Transform infrared spectrometry depend on the stability of the light source. Fluctuations in the source brightness, however, cannot always be avoided. Current correction schemes, which calculate a corrected interferogram as the ratio of the raw DC interferogram and a smoothed DC interferogram, are applicable only to near infrared measurements. Spectra in the mid infrared spectral region below 2000 cm −1 are generally considered uncorrectable, if they are measured with a MCT detector. Such measurements introduce an unknown offset to MCT interferograms, which prevents the established source brightness fluctuation correction. This problem can be overcome by a determination of the offset using the modulation efficiency of the instrument. With known modulation efficiency the offset can be calculated, and the source brightness correction can be performed on the basis of offset-corrected interferograms. We present a source brightness fluctuation correction method which performs the smoothing of the raw DC interferogram in the interferogram domain by an application of a running mean instead of high-pass filtering the corresponding spectrum after Fourier transformation of the raw DC interferogram. This smoothing can be performed with the onboard software of commercial instruments. The improvement of MCT spectra and subsequent ozone profile and total column retrievals is demonstrated. Application to InSb interferograms in the near infrared spectral region proves the equivalence with the established correction scheme.

Description: An improved NO 2 retrieval for the GOME-2 satellite instrument Atmospheric Measurement Techniques, 4, 1147-1159, 2011 Author(s): A. Richter, M. Begoin, A. Hilboll, and J. P. Burrows Satellite observations of nitrogen dioxide (NO 2 ) provide valuable information on both stratospheric and tropospheric composition. Nadir measurements from GOME, SCIAMACHY, OMI, and GOME-2 have been used in many studies on tropospheric NO 2 burdens, the importance of different NO x emissions sources and their change over time. The observations made by the three GOME-2 instruments will extend the existing data set by more than a decade, and a high quality of the data as well as their good consistency with existing time series is of particular importance. In this paper, an improved GOME-2 NO 2 retrieval is described which reduces the scatter of the individual NO 2 columns globally but in particular in the region of the Southern Atlantic Anomaly. This is achieved by using a larger fitting window including more spectral points, and by applying a two step spike removal algorithm in the fit. The new GOME-2 data set is shown to have good consistency with SCIAMACHY NO 2 columns. Remaining small differences are shown to be linked to changes in the daily solar irradiance measurements used in both GOME-2 and SCIAMACHY retrievals. In the large retrieval window, a not previously identified spectral signature was found which is linked to deserts and other regions with bare soil. Inclusion of this empirically derived pseudo cross-section significantly improves the retrievals and potentially provides information on surface properties and desert aerosols. Using the new GOME-2 NO 2 data set, a long-term average of tropospheric columns was computed and high-pass filtered. The resulting map shows evidence for pollution from several additional shipping lanes, not previously identified in satellite observations. This illustrates the excellent signal to noise ratio achievable with the improved GOME-2 retrievals.

Description: Matching radiative transfer models and radiosonde data from the EPS/Metop Sodankylä campaign to IASI measurements Atmospheric Measurement Techniques, 4, 1177-1189, 2011 Author(s): X. Calbet, R. Kivi, S. Tjemkes, F. Montagner, and R. Stuhlmann Radiances observed from IASI are compared to calculated ones. Calculated radiances are obtained using several radiative transfer models (OSS, LBLRTM v11.3 and v11.6) on best estimates of the atmospheric state vectors. The atmospheric state vectors are derived from cryogenic frost point hygrometer and humidity dry bias corrected RS92 measurements flown on sondes launched 1 h and 5 min before IASI overpass time. The temperature and humidity best estimate profiles are obtained by interpolating or extrapolating these measurements to IASI overpass time. The IASI observed and calculated radiances match to within one sigma IASI instrument noise in the spectral region where water vapour is a strong absorber (wavenumber, ν, in the range of 1500 ≤ ν ≤ 1570 and 1615 ≤ ν ≤ 1800 cm −1 ).

Description: Eddy covariance measurements with high-resolution time-of-flight aerosol mass spectrometry: a new approach to chemically resolved aerosol fluxes Atmospheric Measurement Techniques, 4, 1275-1289, 2011 Author(s): D. K. Farmer, J. R. Kimmel, G. Phillips, K. S. Docherty, D. R. Worsnop, D. Sueper, E. Nemitz, and J. L. Jimenez Although laboratory studies show that biogenic volatile organic compounds (VOCs) yield substantial secondary organic aerosol (SOA), production of biogenic SOA as indicated by upward fluxes has not been conclusively observed over forests. Further, while aerosols are known to deposit to surfaces, few techniques exist to provide chemically-resolved particle deposition fluxes. To better constrain aerosol sources and sinks, we have developed a new technique to directly measure fluxes of chemically-resolved submicron aerosols using the high-resolution time-of-flight aerosol mass spectrometer (HR-AMS) in a new, fast eddy covariance mode. This approach takes advantage of the instrument's ability to quantitatively identify both organic and inorganic components, including ammonium, sulphate and nitrate, at a temporal resolution of several Hz. The new approach has been successfully deployed over a temperate ponderosa pine plantation in California during the BEARPEX-2007 campaign, providing both total and chemically resolved non-refractory (NR) PM 1 fluxes. Average deposition velocities for total NR-PM 1 aerosol at noon were 2.05 ± 0.04 mm s −1 . Using a high resolution measurement of the NH 2 + and NH 3 + fragments, we demonstrate the first eddy covariance flux measurements of particulate ammonium, which show a noon-time deposition velocity of 1.9 ± 0.7 mm s −1 and are dominated by deposition of ammonium sulphate.

Description: Space and ground segment performance and lessons learned of the FORMOSAT-3/COSMIC mission: four years in orbit Atmospheric Measurement Techniques, 4, 1115-1132, 2011 Author(s): C.-J. Fong, D. Whiteley, E. Yang, K. Cook, V. Chu, B. Schreiner, D. Ector, P. Wilczynski, T.-Y. Liu, and N. Yen The FORMOSAT-3/COSMIC (Constellation Observing System for Meteorology, Ionosphere, and Climate) Mission consisting of six Low-Earth-Orbit (LEO) satellites is the world's first demonstration constellation using radio occultation signals from Global Positioning System (GPS) satellites. The atmospheric profiles derived by processing radio occultation signals are retrieved in near real-time for global weather/climate monitoring, numerical weather prediction, and space weather research. The mission has processed, on average, 1400 to 1800 high-quality atmospheric sounding profiles per day. The atmospheric radio occultation data are assimilated into operational numerical weather prediction models for global weather prediction, including typhoon/hurricane/cyclone forecasts. The radio occultation data has shown a positive impact on weather predictions at many national weather forecast centers. A follow-on mission was proposed that transitions the current experimental research mission into a significantly improved real-time operational mission, which will reliably provide 8000 radio occultation soundings per day. The follow-on mission, as planned, will consist of 12 LEO satellites (compared to 6 satellites for the current mission) with data latency requirement of 45 min (compared to 3 h for the current mission), which will provide greatly enhanced opportunities for operational forecasts and scientific research. This paper will address the FORMOSAT-3/COSMIC system and mission overview, the spacecraft and ground system performance after four years in orbit, the lessons learned from the encountered technical challenges and observations, and the expected design improvements for the spacecraft and ground system for FORMOSAT-7/COSMIC-2.

Description: Exploring Earth's atmosphere with radio occultation: contributions to weather, climate and space weather Atmospheric Measurement Techniques, 4, 1077-1103, 2011 Author(s): R. A. Anthes The launch of the proof-of-concept mission GPS/MET (Global Positioning System/Meteorology) in 1995 began a revolution in profiling Earth's atmosphere through radio occultation (RO). GPS/MET; subsequent single-satellite missions CHAMP (CHAllenging Minisatellite Payload), SAC-C (Satellite de Aplicaciones Cientificas-C), GRACE (Gravity Recovery and Climate Experiment), METOP-A, and TerraSAR-X (Beyerle et al., 2010); and the six-satellite constellation, FORMOSAT-3/COSMIC (Formosa Satellite mission {#}3/Constellation Observing System for Meteorology, Ionosphere, and Climate) have proven the theoretical capabilities of RO to provide accurate and precise profiles of electron density in the ionosphere and refractivity, containing information on temperature and water vapor, in the stratosphere and troposphere. This paper summarizes results from these RO missions and the applications of RO observations to atmospheric research and operational weather analysis and prediction.

Description: Detection of HO 2 by laser-induced fluorescence: calibration and interferences from RO 2 radicals Atmospheric Measurement Techniques, 4, 1209-1225, 2011 Author(s): H. Fuchs, B. Bohn, A. Hofzumahaus, F. Holland, K. D. Lu, S. Nehr, F. Rohrer, and A. Wahner HO 2 concentration measurements are widely accomplished by chemical conversion of HO 2 to OH including reaction with NO and subsequent detection of OH by laser-induced fluorescence. RO 2 radicals can be converted to OH via a similar radical reaction sequence including reaction with NO, so that they are potential interferences for HO 2 measurements. Here, the conversion efficiency of various RO 2 species to HO 2 is investigated. Experiments were conducted with a radical source that produces OH and HO 2 by water photolysis at 185 nm, which is frequently used for calibration of LIF instruments. The ratio of HO 2 and the sum of OH and HO 2 concentrations provided by the radical source was investigated and was found to be 0.50 ± 0.02. RO 2 radicals are produced by the reaction of various organic compounds with OH in the radical source. Interferences via chemical conversion from RO 2 radicals produced by the reaction of OH with methane and ethane (H-atom abstraction) are negligible consistent with measurements in the past. However, RO 2 radicals from OH plus alkene- and aromatic-precursors including isoprene (mainly OH-addition) are detected with a relative sensitivity larger than 80 % with respect to that for HO 2 for the configuration of the instrument with which it was operated during field campaigns. Also RO 2 from OH plus methyl vinyl ketone and methacrolein exhibit a relative detection sensitivity of 60 %. Thus, previous measurements of HO 2 radical concentrations with this instrument were biased in the presence of high RO 2 radical concentrations from isoprene, alkenes or aromatics, but were not affected by interferences in remote clean environment with no significant emissions of biogenic VOCs, when the OH reactivity was dominated by small alkanes. By reducing the NO concentration and/or the transport time between NO addition and OH detection, interference from these RO 2 species are suppressed to values below 20 % relative to the HO 2 detection sensitivity. The HO 2 conversion efficiency is also smaller by a factor of four, but this is still sufficient for atmospheric HO 2 concentration measurements for a wide range of conditions.

Description: Diode laser-based cavity ring-down instrument for NO 3 , N 2 O 5 , NO, NO 2 and O 3 from aircraft Atmospheric Measurement Techniques, 4, 1227-1240, 2011 Author(s): N. L. Wagner, W. P. Dubé, R. A. Washenfelder, C. J. Young, I. B. Pollack, T. B. Ryerson, and S. S. Brown This article presents a diode laser-based, cavity ring-down spectrometer for simultaneous in situ measurements of four nitrogen oxide species, NO 3 , N 2 O 5 , NO, NO 2 , as well as O 3 , designed for deployment on aircraft. The instrument measures NO 3 and NO 2 by optical extinction at 662 nm and 405 nm, respectively; N 2 O 5 is measured by thermal conversion to NO 3 , while NO and O 3 are measured by chemical conversion to NO 2 . The instrument has several advantages over previous instruments developed by our group for measurement of NO 2 , NO 3 and N 2 O 5 alone, based on a pulsed Nd:YAG and dye laser. First, the use of continuous wave diode lasers reduces the requirements for power and weight and eliminates hazardous materials. Second, detection of NO 2 at 405 nm is more sensitive than our previously reported 532 nm instrument, and does not have a measurable interference from O 3 . Third, the instrument includes chemical conversion of NO and O 3 to NO 2 to provide measurements of total NO x (= NO + NO 2 ) and O x (= NO 2 + O 3 ) on two separate channels; mixing ratios of NO and O 3 are determined by subtraction of NO 2 . Finally, all five species are calibrated against a single standard based on 254 nm O 3 absorption to provide high accuracy. Disadvantages include an increased sensitivity to water vapor on the 662 nm NO 3 and N 2 O 5 channels and a modest reduction in sensitivity for these species compared to the pulsed laser instrument. The in-flight detection limit for both NO 3 and N 2 O 5 is 3 pptv (2 σ, 1 s) and for NO, NO 2 and O 3 is 140, 90, and 120 pptv (2 σ, 1 s) respectively. Demonstrated performance of the instrument in a laboratory/ground based environment is better by approximately a factor of 2–3. The NO and NO 2 measurements are less precise than research-grade chemiluminescence instruments. However, the combination of these five species in a single instrument, calibrated to a single analytical standard, provides a complete and accurate picture of nighttime nitrogen oxide chemistry. The instrument performance is demonstrated using data acquired during a recent field campaign in California.

Description: Retrieval of water vapor vertical distributions in the upper troposphere and the lower stratosphere from SCIAMACHY limb measurements Atmospheric Measurement Techniques, 4, 933-954, 2011 Author(s): A. Rozanov, K. Weigel, H. Bovensmann, S. Dhomse, K.-U. Eichmann, R. Kivi, V. Rozanov, H. Vömel, M. Weber, and J. P. Burrows This study describes the retrieval of water vapor vertical distributions in the upper troposphere and lower stratosphere (UTLS) altitude range from space-borne observations of the scattered solar light made in limb viewing geometry. First results using measurements from SCIAMACHY (Scanning Imaging Absorption spectroMeter for Atmospheric CHartographY) aboard ENVISAT (Environmental Satellite) are presented here. In previous publications, the retrieval of water vapor vertical distributions has been achieved exploiting either the emitted radiance leaving the atmosphere or the transmitted solar radiation. In this study, the scattered solar radiation is used as a new source of information on the water vapor content in the UTLS region. A recently developed retrieval algorithm utilizes the differential absorption structure of the water vapor in 1353–1410 nm spectral range and yields the water vapor content in the 11–25 km altitude range. In this study, the retrieval algorithm is successfully applied to SCIAMACHY limb measurements and the resulting water vapor profiles are compared to in situ balloon-borne observations. The results from both satellite and balloon-borne instruments are found to agree typically within 10 %.

Description: Fast NO 2 retrievals from Odin-OSIRIS limb scatter measurements Atmospheric Measurement Techniques, 4, 965-972, 2011 Author(s): A. E. Bourassa, C. A. McLinden, C. E. Sioris, S. Brohede, A. F. Bathgate, E. J. Llewellyn, and D. A. Degenstein The feasibility of retrieving vertical profiles of NO 2 from space-based measurements of limb scattered sunlight has been demonstrated using several different data sets since the 1980's. The NO 2 data product routinely retrieved from measurements made by the Optical Spectrograph and InfraRed Imaging System (OSIRIS) instrument onboard the Odin satellite uses a spectral fitting technique over the 437 to 451 nm range, over which there are 36 individual wavelength measurements. In this work we present a proof of concept technique for the retrieval of NO 2 using only 4 of the 36 OSIRIS measurements in this wavelength range, which reduces the computational cost by almost an order of magnitude. The method is an adaptation of a triplet analysis technique that is currently used for the OSIRIS retrievals of ozone at Chappuis band wavelengths. The results obtained are shown to be in very good agreement with the spectral fit method, and provide an important alternative for applications where the computational burden is very high. Additionally this provides a baseline for future instrument design in terms of cost effectiveness and reducing spectral range requirements.

Description: Intercomparison of stratospheric gravity wave observations with AIRS and IASI Atmospheric Measurement Techniques, 7, 4517-4537, 2014 Author(s): L. Hoffmann, M. J. Alexander, C. Clerbaux, A. W. Grimsdell, C. I. Meyer, T. Rößler, and B. Tournier Gravity waves are an important driver for the atmospheric circulation and have substantial impact on weather and climate. Satellite instruments offer excellent opportunities to study gravity waves on a global scale. This study focuses on observations from the Atmospheric Infrared Sounder (AIRS) onboard the National Aeronautics and Space Administration Aqua satellite and the Infrared Atmospheric Sounding Interferometer (IASI) onboard the European MetOp satellites. The main aim of this study is an intercomparison of stratospheric gravity wave observations of both instruments. In particular, we analyzed AIRS and IASI 4.3 μm brightness temperature measurements, which directly relate to stratospheric temperature. Three case studies showed that AIRS and IASI provide a clear and consistent picture of the temporal development of individual gravity wave events. Statistical comparisons based on a 5-year period of measurements (2008–2012) showed similar spatial and temporal patterns of gravity wave activity. However, the statistical comparisons also revealed systematic differences of variances between AIRS and IASI that we attribute to the different spatial measurement characteristics of both instruments. We also found differences between day- and nighttime data that are partly due to the local time variations of the gravity wave sources. While AIRS has been used successfully in many previous gravity wave studies, IASI data are applied here for the first time for that purpose. Our study shows that gravity wave observations from different hyperspectral infrared sounders such as AIRS and IASI can be directly related to each other, if instrument-specific characteristics such as different noise levels and spatial resolution and sampling are carefully considered. The ability to combine observations from different satellites provides an opportunity to create a long-term record, which is an exciting prospect for future climatological studies of stratospheric gravity wave activity.

Description: Collection efficiency of the soot-particle aerosol mass spectrometer (SP-AMS) for internally mixed particulate black carbon Atmospheric Measurement Techniques, 7, 4507-4516, 2014 Author(s): M. D. Willis, A. K. Y. Lee, T. B. Onasch, E. C. Fortner, L. R. Williams, A. T. Lambe, D. R. Worsnop, and J. P. D. Abbatt The soot-particle aerosol mass spectrometer (SP-AMS) uses an intra-cavity infrared laser to vaporize refractory black carbon (rBC) containing particles, making the particle beam–laser beam overlap critical in determining the collection efficiency (CE) for rBC and associated non-refractory particulate matter (NR-PM). This work evaluates the ability of the SP-AMS to quantify rBC and NR-PM mass in internally mixed particles with different thicknesses of organic coating. Using apparent relative ionization efficiencies for uncoated and thickly coated rBC particles, we report measurements of SP-AMS sensitivity to NR-PM and rBC, for Regal Black, the recommended particulate calibration material. Beam width probe (BWP) measurements are used to illustrate an increase in sensitivity for highly coated particles due to narrowing of the particle beam, which enhances the CE of the SP-AMS by increasing the laser beam–particle beam overlap. Assuming complete overlap for thick coatings, we estimate CE for bare Regal Black particles of 0.6 ± 0.1, which suggests that previously measured SP-AMS sensitivities to Regal Black were underestimated by up to a factor of 2. The efficacy of the BWP measurements is highlighted by studies at a busy road in downtown Toronto and at a non-roadside location, which show particle beam widths similar to, but greater than that of bare Regal Black and coated Regal Black, respectively. Further BWP measurements at field locations will help to constrain the range of CE for fresh and aged rBC-containing particles. The ability of the SP-AMS to quantitatively assess the composition of internally mixed particles is validated through measurements of laboratory-generated organic coated particles, which demonstrate that the SP-AMS can quantify rBC and NR-PM over a wide range of particle compositions and rBC core sizes.

Description: Reference quality upper-air measurements: GRUAN data processing for the Vaisala RS92 radiosonde Atmospheric Measurement Techniques, 7, 4463-4490, 2014 Author(s): R. J. Dirksen, M. Sommer, F. J. Immler, D. F. Hurst, R. Kivi, and H. Vömel The GCOS (Global Climate Observing System) Reference Upper-Air Network (GRUAN) data processing for the Vaisala RS92 radiosonde was developed to meet the criteria for reference measurements. These criteria stipulate the collection of metadata, the use of well-documented correction algorithms, and estimates of the measurement uncertainty. An important and novel aspect of the GRUAN processing is that the uncertainty estimates are vertically resolved. This paper describes the algorithms that are applied in version 2 of the GRUAN processing to correct for systematic errors in radiosonde measurements of pressure, temperature, humidity, and wind, as well as how the uncertainties related to these error sources are derived. Currently, the RS92 is launched on a regular basis at 13 out of 15 GRUAN sites. An additional GRUAN requirement for performing reference measurements with the RS92 is that the manufacturer-prescribed procedure for the radiosonde's preparation, i.e. heated reconditioning of the sensors and recalibration during ground check, is followed. In the GRUAN processing however, the recalibration of the humidity sensors that is applied during ground check is removed. For the dominant error source, solar radiation, laboratory experiments were performed to investigate and model its effect on the RS92's temperature and humidity measurements. GRUAN uncertainty estimates are 0.15 K for night-time temperature measurements and approximately 0.6 K at 25 km during daytime. The other uncertainty estimates are up to 6% relative humidity for humidity, 10–50 m for geopotential height, 0.6 hPa for pressure, 0.4–1 m s −1 for wind speed, and 1° for wind direction. Daytime temperature profiles for GRUAN and Vaisala processing are comparable and consistent within the estimated uncertainty. GRUAN daytime humidity profiles are up to 15% moister than Vaisala processed profiles, of which two-thirds is due to the radiation dry bias correction and one-third is due to an additional calibration correction. Redundant measurements with frost point hygrometers (CFH and NOAA FPH) show that GRUAN-processed RS92 humidity profiles and frost point data agree within 15% in the troposphere. No systematic biases occur, apart from a 5% dry bias for GRUAN data around −40 °C at night.

Description: Deployment of a sequential two-photon laser-induced fluorescence sensor for the detection of gaseous elemental mercury at ambient levels: fast, specific, ultrasensitive detection with parts-per-quadrillion sensitivity Atmospheric Measurement Techniques, 7, 4251-4265, 2014 Author(s): D. Bauer, S. Everhart, J. Remeika, C. Tatum Ernest, and A. J. Hynes The operation of a laser-based sensor for gas-phase elemental mercury, Hg(0), is described. It utilizes sequential two-photon laser excitation with detection of blue-shifted laser-induced fluorescence (LIF) to provide a highly specific detection scheme that precludes detection of anything other than atomic mercury. It has high sensitivity, fast temporal resolution, and can be deployed for in situ measurements in the open atmosphere with essentially no perturbation of the environment. An ambient sample can also be pulled through a fluorescence cell, allowing for standard addition calibrations of the concentration. No type of preconcentration is required and there appears to be no significant interferences from other atmospheric constituents, including gas-phase oxidized mercury species. As a consequence, it is not necessary to remove oxidized mercury, commonly referred to as reactive gaseous mercury (RGM), from the air sample. The instrument has been deployed as part of an instrument intercomparison and compares well with conventional instrumentation that utilizes preconcentration on gold followed by analysis using cold-vapor atomic fluorescence spectroscopy (CVAFS). Currently, the achievable detection sensitivity is ~ 15 pg m −3 (~ 5 × 10 4 atoms cm −3 , ~ 2 ppq) at a sampling rate of 0.1 Hz, i.e., averaging 100 shots with a 10 Hz laser system. Preliminary results are described for a 50 Hz instrument that utilizes a modified excitation sequence and has monitored ambient elemental mercury with an effective sampling rate of 10 Hz. Additional work is required to produce the precision necessary to perform eddy correlation measurements. Addition of a pyrolysis channel should allow for the measurement of total gaseous mercury (TGM) and hence RGM (by difference) with good sensitivity and time resolution.

Description: Prerequisites for application of hyperbolic relaxed eddy accumulation on managed grasslands and alternative net ecosystem exchange flux partitioning Atmospheric Measurement Techniques, 7, 4237-4250, 2014 Author(s): M. Riederer, J. Hübner, J. Ruppert, W. A. Brand, and T. Foken Relaxed eddy accumulation is still applied in ecosystem sciences for measuring trace gas fluxes. On managed grasslands, the length of time between management events and the application of relaxed eddy accumulation has an essential influence on the determination of the proportionality factor b and thus on the resulting flux. In this study this effect is discussed for the first time. Also, scalar similarity between proxy scalars and scalars of interest is affected until the ecosystem has completely recovered. Against this background, CO 2 fluxes were continuously measured and 13 CO 2 isofluxes were determined with a high measurement precision on two representative days in summer 2010. Moreover, a common method for the partitioning of the net ecosystem exchange into assimilation and respiration based on temperature and light response was compared with an isotopic approach directly based on the isotope discrimination of the biosphere. This approach worked well on the grassland site and could enhance flux partitioning results by better reproducing the environmental conditions.

Description: Extending the satellite data record of tropospheric ozone profiles from Aura-TES to MetOp-IASI: characterisation of optimal estimation retrievals Atmospheric Measurement Techniques, 7, 4223-4236, 2014 Author(s): H. Oetjen, V. H. Payne, S. S. Kulawik, A. Eldering, J. Worden, D. P. Edwards, G. L. Francis, H. M. Worden, C. Clerbaux, J. Hadji-Lazaro, and D. Hurtmans We apply the Tropospheric Emission Spectrometer (TES) ozone retrieval algorithm to Infrared Atmospheric Sounding Instrument (IASI) radiances and characterise the uncertainties and information content of the retrieved ozone profiles. This study focuses on mid-latitudes for the year 2008. We validate our results by comparing the IASI ozone profiles to ozone sondes. In the sonde comparisons, we find a negative bias (1–10%) in the IASI profiles in the lower to mid-troposphere and a positive bias (up to 14%) in the upper troposphere/lower stratosphere (UTLS) region. For the described cases, the degrees of freedom for signal are on average 3.2, 0.3, 0.8, and 0.9 for the columns 0 km – top of atmosphere, (0–6), (0–11), and (8–16) km, respectively. We find that our biases with respect to sondes and our degrees of freedom for signal for ozone are comparable to previously published results from other IASI ozone algorithms. In addition to evaluating biases, we validate the retrieval errors by comparing predicted errors to the sample covariance matrix of the IASI observations themselves. For the predicted versus empirical error comparison, we find that these errors are consistent and that the measurement noise and the interference of temperature and water vapour on the retrieval together mostly explain the empirically derived random errors. In general, the precision of the IASI ozone profiles is better than 20%.

Description: Solar irradiances measured using SPN1 radiometers: uncertainties and clues for development Atmospheric Measurement Techniques, 7, 4267-4283, 2014 Author(s): J. Badosa, J. Wood, P. Blanc, C. N. Long, L. Vuilleumier, D. Demengel, and M. Haeffelin The fast development of solar radiation and energy applications, such as photovoltaic and solar thermodynamic systems, has increased the need for solar radiation measurement and monitoring, for not only the global but also the diffuse and direct components. End users look for the best compromise between getting close to state-of-the-art measurements and keeping low capital, maintenance and operating costs. Among the existing commercial options, SPN1 is a relatively low cost solar radiometer that estimates global and diffuse solar irradiances from seven thermopile sensors under a shading mask and without moving parts. This work presents a comprehensive study of SPN1 accuracy and sources of uncertainty, drawing on laboratory experiments, numerical modelling and comparison studies between measurements from this sensor and state-of-the art instruments for six diverse sites. Several clues are provided for improving the SPN1 accuracy and agreement with state-of-the art measurements.

Description: Differences in aerosol absorption Ångström exponents between correction algorithms for a particle soot absorption photometer measured on the South African Highveld Atmospheric Measurement Techniques, 7, 4285-4298, 2014 Author(s): J. Backman, A. Virkkula, V. Vakkari, J. P. Beukes, P. G. Van Zyl, M. Josipovic, S. Piketh, P. Tiitta, K. Chiloane, T. Petäjä, M. Kulmala, and L. Laakso Absorption Ångström exponents (AAEs) calculated from filter-based absorption measurements are often used to give information on the origin of the ambient aerosol, for example, to distinguish between urban pollution and biomass burning aerosol. Filter-based absorption measurements are widely used and are common at aerosol monitoring stations globally. Several correction algorithms are used to account for artefacts associated with filter-based absorption techniques. These algorithms are of profound importance when determining the absolute amount of absorption by the aerosol. However, this study shows that there are substantial differences between the AAEs calculated from these corrections. Depending on the used correction, AAEs can change by as much as 46%. The study also highlights that the difference between AAEs calculated using different corrections can lead to conflicting conclusions on the type of aerosol when using the same data set. The AAE ranged between 1.17 for non-corrected data to 1.96 for the correction that gave the greatest values. Furthermore, the study implies that the AAEs reported for a site depend on at which filter transmittance the filter is changed. In this work, the AAEs were calculated from data measured with a three-wavelength particle soot absorption photometer (PSAP) at Elandsfontein on the South African Highveld for 23 months. The sample air of the PSAP was diluted to prolong filter change intervals, by a factor of 15. The correlation coefficient between the dilution-corrected PSAP and a non-diluted Multi-Angle Absorption Photometer (MAAP) was 0.9. Thus, the study also shows that the applicability of the PSAP can be extended to remote sites that are not often visited or suffer from high levels of pollution.

Description: Looking through the haze: evaluating the CALIPSO level 2 aerosol optical depth using airborne high spectral resolution lidar data Atmospheric Measurement Techniques, 7, 4317-4340, 2014 Author(s): R. R. Rogers, M. A. Vaughan, C. A. Hostetler, S. P. Burton, R. A. Ferrare, S. A. Young, J. W. Hair, M. D. Obland, D. B. Harper, A. L. Cook, and D. M. Winker The Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument onboard the Cloud–Aerosol Lidar and Pathfinder Satellite Observations (CALIPSO) spacecraft has provided over 8 yr of nearly continuous vertical profiling of Earth's atmosphere. In this paper we investigate the V3.01 and V3.02 CALIOP 532 nm aerosol layer optical depth (AOD) product (i.e the AOD of individual layers) and the column AOD product (i.e., the sum AOD of the complete column) using an extensive database of coincident measurements. The CALIOP AOD measurements and AOD uncertainty estimates are compared with collocated AOD measurements collected with the NASA High Spectral Resolution Lidar (HSRL) in the North American and Caribbean regions. In addition, the CALIOP aerosol lidar ratios are investigated using the HSRL measurements. In general, compared with the HSRL values, the CALIOP layer AOD are biased high by less than 50% for AOD 〈 0.3 with higher errors for higher AOD. Less than 60% of the HSRL AOD measurements are encompassed within the CALIOP layer 1 SD uncertainty range (around the CALIOP layer AOD), so an error estimate is created to encompass 68% of the HSRL data. Using this new metric, the CALIOP layer AOD error is estimated using the HSRL layer AOD as ±0.035 ± 0.05 · (HSRL layer AOD) at night and ±0.05 ± 0.05 · (HSRL layer AOD) during the daytime. Furthermore, the CALIOP layer AOD error is found to correlate with aerosol loading as well as aerosol subtype, with the AODs in marine and dust layers agreeing most closely with the HSRL values. The lidar ratios used by CALIOP for polluted dust, polluted continental, and biomass burning layers are larger than the values measured by the HSRL in the CALIOP layers, and therefore the AODs for these types retrieved by CALIOP were generally too large. We estimated the CALIOP column AOD error can be expressed as ±0.05 ± 0.07 · (HSRL column AOD) at night and ±0.08 ± 0.1 · (HSRL column AOD) during the daytime. Multiple sources of error contribute to both positive and negative errors in the CALIOP column AOD, including multiple layers in the column of different aerosol types, lidar ratio errors, cloud misclassification, and undetected aerosol layers. The undetected layers were further investigated and we found that the layer detection algorithm works well at night, although undetected aerosols in the free troposphere introduce a mean underestimate of 0.02 in the column AOD in the data set examined. The decreased signal-to-noise ratio (SNR) during the daytime led to poorer performance of the layer detection. This caused the daytime CALIOP column AOD to be less accurate than during the nighttime, because CALIOP frequently does not detect optically thin aerosol layers with AOD 〈 0.1. Given that the median vertical extent of aerosol detected within any column was 1.6 km during the nighttime and 1.5 km during the daytime, we can estimate the minimum extinction detection threshold to be 0.012 km −1 at night and 0.067 km −1 during the daytime in a layer median sense. This extensive validation of level 2 CALIOP AOD products extends previous validation studies to nighttime lighting conditions and provides independent measurements of the lidar ratio; thus, allowing the assessment of the effect on the CALIOP AOD of using inappropriate lidar ratio values in the extinction retrieval.

Description: The use of NO 2 absorption cross section temperature sensitivity to derive NO 2 profile temperature and stratospheric–tropospheric column partitioning from visible direct-sun DOAS measurements Atmospheric Measurement Techniques, 7, 4299-4316, 2014 Author(s): E. Spinei, A. Cede, W. H. Swartz, J. Herman, and G. H. Mount This paper presents a temperature sensitivity method (TESEM) to accurately calculate total vertical NO 2 column, atmospheric slant NO 2 profile-weighted temperature ( T ), and to separate stratospheric and tropospheric columns from direct-sun (DS), ground-based measurements using the retrieved T . TESEM is based on differential optical absorption spectroscopy (DOAS) fitting of the linear temperature-dependent NO 2 absorption cross section, σ ( T ), regression model (Vandaele et al., 2003). Separation between stratospheric and tropospheric columns is based on the primarily bimodal vertical distribution of NO 2 and an assumption that stratospheric effective temperature can be represented by temperature at 27 km ± 3 K, and tropospheric effective temperature is equal to surface temperature within 3–5 K. These assumptions were derived from the Global Modeling Initiative (GMI) chemistry-transport model (CTM) simulations over two northern midlatitude sites in 2011. TESEM was applied to the Washington State University Multi-Function DOAS instrument (MFDOAS) measurements at four midlatitude locations with low and moderate NO 2 anthropogenic emissions: (1) the Jet Propulsion Laboratory's Table Mountain Facility (JPL-TMF), CA, USA (34.38° N/117.68° W); (2) Pullman, WA, USA (46.73° N/117.17° W); (3) Greenbelt, MD, USA (38.99° N/76.84° W); and (4) Cabauw, the Netherlands (51.97° N/4.93° E) during July 2007, June–July 2009, July–August and October 2011, November 2012–May 2013, respectively. NO 2 T and total, stratospheric, and tropospheric NO 2 vertical columns were determined over each site.

Description: A Fabry–Perot interferometer-based camera for two-dimensional mapping of SO 2 distributions Atmospheric Measurement Techniques, 7, 3705-3715, 2014 Author(s): J. Kuhn, N. Bobrowski, P. Lübcke, L. Vogel, and U. Platt We examine a new imaging method for the remote sensing of volcanic gases, which relies on the regularly spaced narrow-band absorption structures in the UV–VIS of many molecules. A Fabry–Perot interferometer (FPI) is used to compare the scattered sunlight radiance at wavelengths corresponding to absorption bands with the radiance at wavelengths in between the bands, thereby identifying and quantifying the gas. In this first theoretical study, we present sample calculations for the detection of sulfur dioxide (SO 2 ). Optimum values for the FPI setup parameters are proposed. Furthermore, the performance of the FPI method is compared to SO 2 cameras. We show that camera systems using an FPI are far less influenced by changes in atmospheric radiative transfer (e.g., due to aerosol) and have a great potential as a future technique for examining emissions of SO 2 (or other gases) from volcanic sources and other point sources.

Description: Middle-atmospheric zonal and meridional wind profiles from polar, tropical and midlatitudes with the ground-based microwave Doppler wind radiometer WIRA Atmospheric Measurement Techniques, 7, 4491-4505, 2014 Author(s): R. Rüfenacht, A. Murk, N. Kämpfer, P. Eriksson, and S. A. Buehler WIRA is a ground-based microwave Doppler spectroradiometer specifically designed for the measurement of profiles of horizontal wind in the upper stratosphere and lower mesosphere region where no other continuously running measurement technique exists. A proof of principle has been delivered in a previous publication. A technical upgrade including a new high-frequency amplifier and sideband filter has improved the signal to noise ratio by a factor of 2.4. Since this upgrade the full horizontal wind field comprising zonal and meridional wind profiles is continuously measured. A completely new retrieval based on optimal estimation has been set up. Its characteristics are detailed in the present paper. Since the start of the routine operation of the first prototype in September 2010, WIRA has been measuring at four different locations at polar, mid- and tropical latitudes (67°22' N/26°38' E, 46°57' N/7°26' E, 43°56' N/5°43' E and 21°04' S/55°23' E) for time periods between 5.5 and 11 months. The data presented in this paper are daily average wind profiles with typical uncertainties and resolutions of 10 to 20 m s −1 and 10 to 16 km, respectively. A comparison between the data series from WIRA and European Centre for Medium-Range Weather Forecasts (ECMWF) model data revealed agreement within 10% in the stratospheric zonal wind. The meridional wind profiles agree within their error bars over the entire sensitive altitude range of WIRA. However, significant differences in the mesospheric zonal wind speed of up to 50% have been found.

Description: Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The evolution of NP has been intensively investigated in the last decade by studies focusing on their phylogeny and timescale. However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene trees within the proposed phylogenies. We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids. The molecular phylogeny of NP has been difficult to solve because of population-level phenomena at the early evolution of the lineage. The association of evolutionary variation with the distribution of gene trees within proposed phylogenies is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time. This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms.

Description: Dogs shared a much closer relationship with humans than any other domesticated animals, probably due to their unique social cognitive capabilities, which were hypothesized to be a by-product of selection for tameness toward humans. Here, we demonstrate that genes involved in glutamate metabolism, which account partially for fear response, indeed show the greatest population differentiation by whole-genome comparison of dogs and wolves. However, the changing direction of their expression supports a role in increasing excitatory synaptic plasticity in dogs rather than reducing fear response. Because synaptic plasticity are widely believed to be cellular correlates of learning and memory, this change may alter the learning and memory abilities of ancient scavenging wolves, weaken the fear reaction toward humans, and prompt the initial interspecific contact.

Description: Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism.

Description: Anopheles gambiae is a major mosquito vector of malaria in Africa. Although increased use of insecticide-based vector control tools has decreased malaria transmission, elimination is likely to require novel genetic control strategies. It can be argued that the absence of an A. gambiae inbred line has slowed progress toward genetic vector control . In order to empower genetic studies and enable precise and reproducible experimentation, we set out to create an inbred line of this species. We found that amenability to inbreeding varied between populations of A. gambiae . After full-sib inbreeding for ten generations, we genotyped 112 individuals—56 saved prior to inbreeding and 56 collected after inbreeding—at a genome-wide panel of single nucleotide polymorphisms (SNPs). Although inbreeding dramatically reduced diversity across much of the genome, we discovered numerous, discrete genomic blocks that maintained high heterozygosity. For one large genomic region, we were able to definitively show that high diversity is due to the persistent polymorphism of a chromosomal inversion. Inbred lines in other eukaryotes often exhibit a qualitatively similar retention of polymorphism when typed at a small number of markers. Our whole-genome SNP data provide the first strong, empirical evidence supporting associative overdominance as the mechanism maintaining higher than expected diversity in inbred lines. Although creation of A. gambiae lines devoid of nearly all polymorphism may not be feasible, our results provide critical insights into how more fully isogenic lines can be created.

Description: Analysis of internal gravity waves with GPS RO density profiles Atmospheric Measurement Techniques, 7, 4123-4132, 2014 Author(s): P. Šácha, U. Foelsche, and P. Pišoft GPS radio occultation (RO) data have proved to be a great tool for atmospheric monitoring and studies. In the past decade, they were frequently used for analyses of the internal gravity waves in the upper troposphere and lower stratosphere region. Atmospheric density is the first quantity of state gained in the retrieval process and is not burdened by additional assumptions. However, there are no studies elaborating in detail the utilization of GPS RO density profiles for gravity wave analyses. In this paper, we introduce a method for density background separation and a methodology for internal gravity wave analysis using the density profiles. Various background choices are discussed and the correspondence between analytical forms of the density and temperature background profiles is examined. In the stratosphere, a comparison between the power spectrum of normalized density and normalized dry temperature fluctuations confirms the suitability of the density profiles' utilization. In the height range of 8–40 km, results of the continuous wavelet transform are presented and discussed. Finally, the limits of our approach are discussed and the advantages of the density usage are listed.

Description: Characterization of model errors in the calculation of tangent heights for atmospheric infrared limb measurements Atmospheric Measurement Techniques, 7, 4117-4122, 2014 Author(s): M. Ridolfi and L. Sgheri We review the main factors driving the calculation of the tangent height of spaceborne limb measurements: the ray-tracing method, the refractive index model and the assumed atmosphere. We find that commonly used ray tracing and refraction models are very accurate, at least in the mid-infrared. The factor with largest effect in the tangent height calculation is the assumed atmosphere. Using a climatological model in place of the real atmosphere may cause tangent height errors up to ± 200 m. Depending on the adopted retrieval scheme, these errors may have a significant impact on the derived profiles.

Description: Recovering long-term aerosol optical depth series (1976–2012) from an astronomical potassium-based resonance scattering spectrometer Atmospheric Measurement Techniques, 7, 4103-4116, 2014 Author(s): A. Barreto, E. Cuevas, P. Pallé, P. M. Romero, C. Guirado, C. J. Wehrli, and F. Almansa A 37-year long-term series of monochromatic aerosol optical depth (AOD) has been recovered from solar irradiance measurements performed with the solar spectrometer Mark-I, deployed at Izaña mountain since 1976. The instrument operation is based on the method of resonant scattering, which affords wavelength absolute reference and stability (long-term stability and high precision) in comparison to other instruments based purely on interference filters. However, it has been specifically designed as a reference instrument for helioseismology, and its ability to determine AOD from transmitted and scattered monochromatic radiation at 769.9 nm inside a potassium vapour cell in the presence of a permanent magnetic field is evaluated in this paper. Particularly, the use of an exposed mirror arrangement to collect sunlight as well as the Sun–laboratory velocity dependence of the scattered component introduces some important inconveniences to overcome when we perform the instrument's calibration. We have solved this problem using a quasi-continuous Langley calibration technique and a refinement procedure to correct for calibration errors as well as for the fictitious diurnal cycle on AOD data. Our results showed similar calibration errors retrieved by means of this quasi-continuous Langley technique applied in different aerosol load events (from 0.04 to 0.3), provided aerosol concentration remains constant throughout the calibration interval. It assures the validity of this technique when it is applied in those periods with relatively high aerosol content. The comparative analysis between the recovered AOD data set from the Mark-I and collocated quasi-simultaneous data from the Cimel-AErosol RObotic NETwork (AERONET) and Precision Filter Radiometer (PFR) instruments showed an absolute mean bias ≤ 0.01 in the 10- and 12-year comparison, respectively. High correlation coefficients between AERONET and Mark-I and PFR/Mark-I pairs confirmed a very good linear relationship between instruments, proving that recovered AOD data series from Mark-I can be used together with PFR and AERONET AOD data to build a long-term AOD data series at the Izaña site (1976–now), suitable for future analysis of aerosols trends and inter-annual variability. Finally, the AOD preliminary trend analysis in the 29-year period from 1984 to 2012 with Mark-I AOD revealed no significant trends.

Description: Multistation intercomparison of column-averaged methane from NDACC and TCCON: impact of dynamical variability Atmospheric Measurement Techniques, 7, 4081-4101, 2014 Author(s): A. Ostler, R. Sussmann, M. Rettinger, N. M. Deutscher, S. Dohe, F. Hase, N. Jones, M. Palm, and B.-M. Sinnhuber Dry-air column-averaged mole fractions of methane (XCH 4 ) retrieved from ground-based solar Fourier transform infrared (FTIR) measurements provide valuable information for satellite validation, evaluation of chemical-transport models, and source-sink-inversions. In this context, Sussmann et al. (2013) have shown that midinfrared (MIR) soundings from the Network for the Detection of Atmospheric Composition Change (NDACC) can be combined with near-infrared (NIR) soundings from the Total Carbon Column Observing Network (TCCON) without the need to apply an overall intercalibration factor. However, in spite of efforts to reduce a priori impact, some residual seasonal biases were identified, and the reasons behind remained unclear. In extension to this previous work, which was based on multiannual quasi-coincident MIR and NIR measurements from the stations Garmisch (47.48° N, 11.06° E, 743 m a.s.l.) and Wollongong (34.41° S, 150.88° E, 30 m a.s.l.), we now investigate upgraded retrievals with longer temporal coverage and include three additional stations (Ny-Ålesund, 78.92° N, 11.93° E, 20 m a.s.l.; Karlsruhe, 49.08° N, 8.43° E, 110 m a.s.l.; Izaña, 28.31° N, 16.45° W, 2.370 m a.s.l.). Our intercomparison results (except for Ny-Ålesund) confirm that there is no overall bias between MIR and NIR XCH 4 retrievals, and all MIR and NIR time series reveal a quasi-periodic seasonal bias for all stations, except for Izaña. We find that dynamical variability causes MIR–NIR differences of up to ~ 30 ppb (parts per billion) for Ny-Ålesund, ~ 20 ppb for Wollongong, ~ 18 ppb for Garmisch, and ~ 12 ppb for Karlsruhe. The mechanisms behind this variability are elaborated via two case studies, one dealing with stratospheric subsidence induced by the polar vortex at Ny-Ålesund and the other with a deep stratospheric intrusion event at Garmisch. Smoothing effects caused by the dynamical variability during these events are different for MIR and NIR retrievals depending on the altitude of the perturbation area. MIR retrievals appear to be more realistic in the case of stratospheric subsidence, while NIR retrievals are more accurate in the case of stratosphere–troposphere exchange (STE) in the upper troposphere/lower stratosphere (UTLS) region. About 35% of the FTIR measurement days at Garmisch are impacted by STE, and about 23% of the measurement days at Ny-Ålesund are influenced by polar vortex subsidence. The exclusion of data affected by these dynamical situations resulted in improved agreement of MIR and NIR seasonal cycles for Ny-Ålesund and Garmisch. We found that dynamical variability is a key factor in constraining the accuracy of MIR and NIR seasonal cycles. To mitigate this impact it is necessary to use more realistic a priori profiles that take these dynamical events into account (e.g., via improved models), and/or to improve the FTIR retrievals to achieve a more uniform sensitivity at all altitudes (possibly including profile retrievals for the TCCON data).

Description: Assessment of BSRN radiation records for the computation of monthly means Atmospheric Measurement Techniques, 4, 339-354, 2011 Author(s): A. Roesch, M. Wild, A. Ohmura, E. G. Dutton, C. N. Long, and T. Zhang The integrity of the Baseline Surface Radiation Network (BSRN) radiation monthly averages are assessed by investigating the impact on monthly means due to the frequency of data gaps caused by missing or discarded high time resolution data. The monthly statistics, especially means, are considered to be important and useful values for climate research, model performance evaluations and for assessing the quality of satellite (time- and space-averaged) data products. The study investigates the spread in different algorithms that have been applied for the computation of monthly means from 1-min values. The paper reveals that the computation of monthly means from 1-min observations distinctly depends on the method utilized to account for the missing data. The intra-method difference generally increases with an increasing fraction of missing data. We found that a substantial fraction of the radiation fluxes observed at BSRN sites is either missing or flagged as questionable. The percentage of missing data is 4.4%, 13.0%, and 6.5% for global radiation, direct shortwave radiation, and downwelling longwave radiation, respectively. Most flagged data in the shortwave are due to nighttime instrumental noise and can reasonably be set to zero after correcting for thermal offsets in the daytime data. The study demonstrates that the handling of flagged data clearly impacts on monthly mean estimates obtained with different methods. We showed that the spread of monthly shortwave fluxes is generally clearly higher than for downwelling longwave radiation. Overall, BSRN observations provide sufficient accuracy and completeness for reliable estimates of monthly mean values. However, the value of future data could be further increased by reducing the frequency of data gaps and the number of outliers. It is shown that two independent methods for accounting for the diurnal and seasonal variations in the missing data permit consistent monthly means to within less than 1 W m −2 in most cases. The authors suggest using a standardized method for the computation of monthly means which addresses diurnal variations in the missing data in order to avoid a mismatch of future published monthly mean radiation fluxes from BSRN. The application of robust statistics would probably lead to less biased results for data records with frequent gaps and/or flagged data and outliers. The currently applied empirical methods should, therefore, be completed by the development of robust methods.

Description: Characterisation of a new Fast CPC and its application for atmospheric particle measurements Atmospheric Measurement Techniques, 4, 823-833, 2011 Author(s): B. Wehner, H. Siebert, M. Hermann, F. Ditas, and A. Wiedensohler A new Fast CPC (FCPC) using butanol as working fluid has been built based on the setup described by Wang et al. (2002). In this study, we describe the new instrument. The functionality and stable operation of the FCPC in the laboratory, as well as under atmospheric conditions, is demonstrated. The counting efficiency was measured for three temperature differences between FCPC saturator and condenser, 25, 27, and 29 K, subsequently resulting in a lower detection limit between 6.1 and 8.5 nm. Above 25 nm the FCPC reached 98–100% counting efficiency compared to an electrometer used as the reference instrument. The FCPC demonstrated its ability to perform continuous measurements over a few hours in the laboratory with respect to the total particle counting. The instrument has been implemented into the airborne measurement platform ACTOS to perform measurements in the atmospheric boundary layer. Therefore, a stable operation over two hours is required. The mixing time of the new FCPC was estimated in two ways using a time series with highly fluctuating particle number concentrations. The analysis of a sharp ramp due to a concentration change results in a mixing time of 5 ms while a spectral analysis of atmospheric data demonstrates that for frequencies up to 10 Hz coherent structures can be resolved before sampling noise dominates.

Description: A network of autonomous surface ozone monitors in Antarctica: technical description and first results Atmospheric Measurement Techniques, 4, 645-658, 2011 Author(s): S. J.-B. Bauguitte, N. Brough, M. M. Frey, A. E. Jones, D. J. Maxfield, H. K. Roscoe, M. C. Rose, and E. W. Wolff A suite of 10 autonomous ozone monitoring units, each powered using renewable energy, was developed and built to study surface ozone in Antarctica during the International Polar Year (2007–2009). The monitoring systems were deployed in a network around the Weddell Sea sector of coastal Antarctica with a transect up onto the Antarctic Plateau. The aim was to measure for a full year, thus gaining a much-improved broader view of boundary layer ozone seasonality at different locations as well as of factors affecting the budget of surface ozone in Antarctica. Ozone mixing ratios were measured based on UV photometry using a modified version of the commercial 2B Technologies Inc. Model 202 instrument. All but one of the autonomous units measured successfully within its predefined duty cycle throughout the year, with some differences in performance dependent on power availability and ambient temperature. Mean data recovery after removal of outliers was on average 70% (range 44–83%) and precision varied between 1.5 and 8 ppbv, thus was sufficiently good to resolve year-round the main ozone features of scientific interest. We conclude that, with adequate power, and noting a minor communication problem, our units would be able to operate successfully at ambient temperatures down to −60 °C. Systems such as the one described in this paper, or derivatives of it, could therefore be deployed either as local or regional networks elsewhere in the Arctic or Antarctic. Here we present technical information and first results from the experiment.

Description: Analysis of the application of the optical method to the measurements of the water vapor content in the atmosphere – Part 1: Basic concepts of the measurement technique Atmospheric Measurement Techniques, 4, 843-856, 2011 Author(s): V. D. Galkin, F. Immler, G. A. Alekseeva, F.-H. Berger, U. Leiterer, T. Naebert, I. N. Nikanorova, V. V. Novikov, V. P. Pakhomov, and I. B. Sal'nikov We retrieved the total content of the atmospheric water vapor (or Integrated Water Vapor, IWV) from extensive sets of photometric data obtained since 1995 at Lindenberg Meteorological Observatory with star and sun photometers. Different methods of determination of the empirical parameters that are necessary for the retrieval are discussed. The instruments were independently calibrated using laboratory measurements made at Pulkovo Observatory with the VKM-100 multi-pass vacuum cell. The empirical parameters were also calculated by the simulation of the atmospheric absorption by water vapor, using the MODRAN-4 program package for different model atmospheres. The results are compared to those presented in the literature, obtained with different instruments and methods of the retrieval. The reliability of the empirical parameters, used for the power approximation that links the water vapor content with the observed absorption, is analyzed. Currently, the total (from measurements, calibration, and calculations) errors yield the standard uncertainty of about 10 % in the total column water vapor. We discuss the possibilities for improving the accuracy of calibration to ~1 % as indispensable condition in order to make it possible to use data obtained by optical photometry as an independent reference for other methods (GPS, MW-radiometers, lidar, etc).

Description: Intercomparison of atmospheric water vapor soundings from the differential absorption lidar (DIAL) and the solar FTIR system on Mt. Zugspitze Atmospheric Measurement Techniques, 4, 835-841, 2011 Author(s): H. Vogelmann, R. Sussmann, T. Trickl, and T. Borsdorff We present an intercomparison of three years of measurements of integrated water vapor (IWV) performed by the mid-infrared solar FTIR (Fourier Transform Infra-Red) instrument on the summit of Mt. Zugspitze (2964 m a.s.l.) and by the nearby near-infrared differential absorption lidar (DIAL) at the Schneefernerhaus research station (2675 m a.s.l.). The solar FTIR was shown to be one of the most accurate and precise IWV sounders in recent work (Sussmann et al., 2009) and is taken as the reference here. By calculating the FTIR-DIAL correlation (22 min coincidence interval, 15 min integration time) we derive an almost ideal slope of 0.996 (10), a correlation coefficient of R = 0.99, an IWV intercept of −0.039 (42) mm (−1.2 % of the mean), and a bias of −0.052 (26) mm (−1.6 % of the mean) from the scatter plot. By selecting a subset of coincidences with an optimum temporal and spatial matching between DIAL and FTIR, we obtain a conservative estimate of the precision of the DIAL in measuring IWV which is better than 0.1 mm (3.2 % of the mean). We found that for a temporal coincidence interval of 22 min the difference in IWV measured by these two systems is dominated by the volume mismatch (horizontal distance: 680 m). The outcome from this paper is twofold: (1) the IWV soundings by FTIR and DIAL agree very well in spite of the differing wavelength regions with different spectroscopic line parameters and retrieval algorithms used. (2) In order to derive an estimate of the precision of state-of-the-art IWV sounders from intercomparison experiments, it is necessary to use a temporal matching on time scales shorter than 10 min and a spatial matching on the 100-m scale.

Description: An effective method for the detection of trace species demonstrated using the MetOp Infrared Atmospheric Sounding Interferometer Atmospheric Measurement Techniques, 4, 1567-1580, 2011 Author(s): J. C. Walker, A. Dudhia, and E. Carboni Fast and reliable methods for the detection of atmospheric trace species are needed for near-real-time applications including volcanic hazard avoidance. One common approach using hyperspectral instruments is to measure the difference in brightness temperature between a small number of target sensitive and background channels to determine the presence of the target species. Although fast and robust, current brightness temperature difference methods do not fully exploit the spectral range and resolution of hyperspectral instruments, and the noise associated with the measurements remains high. In this paper, we describe a way to make full use of the spectral information from hyperspectral sounders allowing the presence of the target species to be determined with much better sensitivity in near-real-time if required. The technique is demonstrated using the MetOp Infrared Atmospheric Sounding Interferometer considering two case studies: (a) the detection of sulphur dioxide from the eruption of the Kasatochi volcano in Alaska in August 2008, and (b) the detection of ammonia emissions related to agriculture over Southern Asia in May 2008. The performance of this method is compared against that of existing brightness temperature difference methods. It is found that the sensitivity of the detection of these trace species is improved by up to an order of magnitude.

Description: Statistically optimized inversion algorithm for enhanced retrieval of aerosol properties from spectral multi-angle polarimetric satellite observations Atmospheric Measurement Techniques, 4, 975-1018, 2011 Author(s): O. Dubovik, M. Herman, A. Holdak, T. Lapyonok, D. Tanré, J. L. Deuzé, F. Ducos, A. Sinyuk, and A. Lopatin The proposed development is an attempt to enhance aerosol retrieval by emphasizing statistical optimization in inversion of advanced satellite observations. This optimization concept improves retrieval accuracy relying on the knowledge of measurement error distribution. Efficient application of such optimization requires pronounced data redundancy (excess of the measurements number over number of unknowns) that is not common in satellite observations. The POLDER imager on board the PARASOL micro-satellite registers spectral polarimetric characteristics of the reflected atmospheric radiation at up to 16 viewing directions over each observed pixel. The completeness of such observations is notably higher than for most currently operating passive satellite aerosol sensors. This provides an opportunity for profound utilization of statistical optimization principles in satellite data inversion. The proposed retrieval scheme is designed as statistically optimized multi-variable fitting of all available angular observations obtained by the POLDER sensor in the window spectral channels where absorption by gas is minimal. The total number of such observations by PARASOL always exceeds a hundred over each pixel and the statistical optimization concept promises to be efficient even if the algorithm retrieves several tens of aerosol parameters. Based on this idea, the proposed algorithm uses a large number of unknowns and is aimed at retrieval of extended set of parameters affecting measured radiation. The algorithm is designed to retrieve complete aerosol properties globally. Over land, the algorithm retrieves the parameters of underlying surface simultaneously with aerosol. In all situations, the approach is anticipated to achieve a robust retrieval of complete aerosol properties including information about aerosol particle sizes, shape, absorption and composition (refractive index). In order to achieve reliable retrieval from PARASOL observations even over very reflective desert surfaces, the algorithm was designed as simultaneous inversion of a large group of pixels within one or several images. Such multi-pixel retrieval regime takes advantage of known limitations on spatial and temporal variability in both aerosol and surface properties. Specifically the variations of the retrieved parameters horizontally from pixel-to-pixel and/or temporary from day-to-day are enforced to be smooth by additional a priori constraints. This concept is expected to provide satellite retrieval of higher consistency, because the retrieval over each single pixel will be benefiting from coincident aerosol information from neighboring pixels, as well, from the information about surface reflectance (over land) obtained in preceding and consequent observations over the same pixel. The paper provides in depth description of the proposed inversion concept, illustrates the algorithm performance by a series of numerical tests and presents the examples of preliminary retrieval results obtained from actual PARASOL observations. It should be noted that many aspects of the described algorithm design considerably benefited from experience accumulated in the preceding effort on developments of currently operating AERONET and PARASOL retrievals, as well as several core software components were inherited from those earlier algorithms.