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

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

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry

BACKGROUND: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. FINDINGS: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. CONCLUSIONS: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets

Genomic landscape of TP53-mutated myeloid malignancies

TP53-mutated myeloid malignancies are associated with complex cytogenetics and extensive structural variants, which complicates detailed genomic analysis by conventional clinical techniques. We performed whole-genome sequencing (WGS) of 42 acute myeloid leukemia (AML)/myelodysplastic syndromes (MDS) cases with paired normal tissue to better characterize the genomic landscape of TP53-mutated AML/MDS. WGS accurately determines TP53 allele status, a key prognostic factor, resulting in the reclassification of 12% of cases from monoallelic to multihit. Although aneuploidy and chromothripsis are shared with most TP53-mutated cancers, the specific chromosome abnormalities are distinct to each cancer type, suggesting a dependence on the tissue of origin. ETV6 expression is reduced in nearly all cases of TP53-mutated AML/MDS, either through gene deletion or presumed epigenetic silencing. Within the AML cohort, mutations of NF1 are highly enriched, with deletions of 1 copy of NF1 present in 45% of cases and biallelic mutations in 17%. Telomere content is increased in TP53-mutated AMLs compared with other AML subtypes, and abnormal telomeric sequences were detected in the interstitial regions of chromosomes. These data highlight the unique features of TP53-mutated myeloid malignancies, including the high frequency of chromothripsis and structural variation, the frequent involvement of unique genes (including NF1 and ETV6) as cooperating events, and evidence for altered telomere maintenance

Far infrared Fourier transform spectrometer breadboard activities for the FORUM mission, ESA's 9th Earth Explorer

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Overview of the 2010 Carbonaceous Aerosols and Radiative Effects Study (CARES)

Substantial uncertainties still exist in the scientific understanding of the possible interactions between urban and natural (biogenic) emissions in the production and transformation of atmospheric aerosol and the resulting impact on climate change. The US Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program's Carbonaceous Aerosol and Radiative Effects Study (CARES) carried out in June 2010 in Central Valley, California, was a comprehensive effort designed to improve this understanding. The primary objective of the field study was to investigate the evolution of secondary organic and black carbon aerosols and their climate-related properties in the Sacramento urban plume as it was routinely transported into the forested Sierra Nevada foothills area. Urban aerosols and trace gases experienced significant physical and chemical transformations as they mixed with the reactive biogenic hydrocarbons emitted from the forest. Two heavily-instrumented ground sites – one within the Sacramento urban area and another about 40 km to the northeast in the foothills area – were set up to characterize the evolution of meteorological variables, trace gases, aerosol precursors, aerosol size, composition, and climate-related properties in freshly polluted and "aged" urban air. On selected days, the DOE G-1 aircraft was deployed to make similar measurements upwind and across the evolving Sacramento plume in the morning and again in the afternoon. The NASA B-200 aircraft, carrying remote sensing instruments, was also deployed to characterize the vertical and horizontal distribution of aerosols and aerosol optical properties within and around the plume. This overview provides: (a) the scientific background and motivation for the study, (b) the operational and logistical information pertinent to the execution of the study, (c) an overview of key observations and initial findings from the aircraft and ground-based sampling platforms, and (d) a roadmap of planned data analyses and focused modeling efforts that will facilitate the integration of new knowledge into improved representations of key aerosol processes and properties in climate models.United States. Dept. of Energy. Atmospheric System Research Program (Contract DE-AC06-76RLO 1830)United States. National Oceanic and Atmospheric AdministrationUnited States. National Aeronautics and Space Administration. HQ Science Mission Directorate Radiation Sciences ProgramUnited States. National Aeronautics and Space Administration. CALIPSO ProgramUnited States. Dept. of Energy. Atmospheric Radiation Measurement Program (Interagency Agreement No. DE-AI02-05ER63985

Comparative Analysis of Expressed Sequence Tag (EST) Libraries in the Seagrass Zostera marina Subjected to Temperature Stress

Global warming is associated with increasing stress and mortality on temperate seagrass beds, in particular during periods of high sea surface temperatures during summer months, adding to existing anthropogenic impacts, such as eutrophication and habitat destruction. We compare several expressed sequence tag (EST) in the ecologically important seagrass Zostera marina (eelgrass) to elucidate the molecular genetic basis of adaptation to environmental extremes. We compared the tentative unigene (TUG) frequencies of libraries derived from leaf and meristematic tissue from a control situation with two experimentally imposed temperature stress conditions and found that TUG composition is markedly different among these conditions (all P < 0.0001). Under heat stress, we find that 63 TUGs are differentially expressed (d.e.) at 25°C compared with lower, no-stress condition temperatures (4°C and 17°C). Approximately one-third of d.e. eelgrass genes were characteristic for the stress response of the terrestrial plant model Arabidopsis thaliana. The changes in gene expression suggest complex photosynthetic adjustments among light-harvesting complexes, reaction center subunits of photosystem I and II, and components of the dark reaction. Heat shock encoding proteins and reactive oxygen scavengers also were identified, but their overall frequency was too low to perform statistical tests. In all conditions, the most abundant transcript (3–15%) was a putative metallothionein gene with unknown function. We also find evidence that heat stress may translate to enhanced infection by protists. A total of 210 TUGs contain one or more microsatellites as potential candidates for gene-linked genetic markers. Data are publicly available in a user-friendly database at http://www.uni-muenster.de/Evolution/ebb/Services/zostera

Novel inhibitors of the calcineurin/NFATc hub - alternatives to CsA and FK506?

The drugs cyclosporine A (CsA) and tacrolimus (FK506) revolutionized organ transplantation. Both compounds are still widely used in the clinic as well as for basic research, even though they have dramatic side effects and modulate other pathways than calcineurin-NFATc, too. To answer the major open question - whether the adverse side effects are secondary to the actions of the drugs on the calcineurin-NFATc pathway - alternative inhibitors were developed. Ideal inhibitors should discriminate between the inhibition of (i) calcineurin and peptidyl-prolyl cis-trans isomerases (PPIases; the matchmaker proteins of CsA and FK506), (ii) calcineurin and the other Ser/Thr protein phosphatases, and (iii) NFATc and other transcription factors. In this review we summarize the current knowledge about novel inhibitors, synthesized or identified in the last decades, and focus on their mode of action, specificity, and biological effects

CD164 identifies CD4+ T cells highly expressing genes associated with malignancy in Sézary syndrome: the Sézary signature genes, FCRL3, Tox, and miR-214

Sézary syndrome (SS), a leukemic variant of cutaneous T-cell lymphoma (CTCL), is associated with a significantly shorter life expectancy compared to skin-restricted mycosis fungoides. Early diagnosis of SS is, therefore, key to achieving enhanced therapeutic responses. However, the lack of a biomarker(s) highly specific for malignant CD4+ T cells in SS patients has been a serious obstacle in making an early diagnosis. We recently demonstrated the high expression of CD164 on CD4+ T cells from Sézary syndrome patients with a wide range of circulating tumor burdens. To further characterize CD164 as a potential biomarker for malignant CD4+ T cells, CD164+ and CD164-CD4+ T cells isolated from patients with high-circulating tumor burden, B2 stage, and medium/low tumor burden, B1-B0 stage, were assessed for the expression of genes reported to differentiate SS from normal controls, and associated with malignancy and poor prognosis. The expression of Sézary signature genes: T plastin, GATA-3, along with FCRL3, Tox, and miR-214, was significantly higher, whereas STAT-4 was lower, in CD164+ compared with CD164-CD4+ T cells. While Tox was highly expressed in both B2 and B1-B0 patients, the expression of Sézary signature genes, FCRL3, and miR-214 was associated predominantly with advanced B2 disease. High expression of CD164 mRNA and protein was also detected in skin from CTCL patients. CD164 was co-expressed with KIR3DL2 on circulating CD4+ T cells from high tumor burden SS patients, further providing strong support for CD164 as a disease relevant surface biomarker