Pollution trace gas distributions and their transport in the Asian monsoon upper troposphere and lowermost stratosphere during the StratoClim campaign 2017

We present the first high-resolution measurements of pollutant trace gases in the Asian summer monsoon upper troposphere and lowermost stratosphere (UTLS) from the Gimballed Limb Observer for Radiance Imaging of the Atmosphere (GLORIA) during the StratoClim (Stratospheric and upper tropospheric processes for better climate predictions) campaign based in Kathmandu, Nepal, 2017. Measurements of peroxyacetyl nitrate (PAN), acetylene (C$_2$H$_2$), and formic acid (HCOOH) show strong local enhancements up to altitudes of 16\,km. More than 500\,pptv of PAN, more than 200\,pptv of C$_2$H$_2$, and more than 200\,pptv of HCOOH are observed. Air masses with increased volume mixing ratios of PAN and C$_2$H$_2$ at altitudes up to 18\,km, reaching to the lowermost stratosphere, were present at these altitudes for more than 10\,d, as indicated by trajectory analysis. A local minimum of HCOOH is correlated with a previously reported maximum of ammonia (NH$_3$), which suggests different washout efficiencies of these species in the same air masses. A backward trajectory analysis based on the models Alfred Wegener InsTitute LAgrangian Chemistry/Transport System (ATLAS) and TRACZILLA, using advanced techniques for detection of convective events, and starting at geolocations of GLORIA measurements with enhanced pollution trace gas concentrations, has been performed. The analysis shows that convective events along trajectories leading to GLORIA measurements with enhanced pollutants are located close to regions where satellite measurements by the Ozone Monitoring Instrument (OMI) indicate enhanced tropospheric columns of nitrogen dioxide (NO$_2$) in the days prior to the observation. A comparison to the global atmospheric models Copernicus Atmosphere Monitoring Service (CAMS) and ECHAM/MESSy Atmospheric Chemistry (EMAC) has been performed. It is shown that these models are able to reproduce large-scale structures of the pollution trace gas distributions for one part of the flight, while the other part of the flight reveals large discrepancies between models and measurement. These discrepancies possibly result from convective events that are not resolved or parameterized in the models, uncertainties in the emissions of source gases, and uncertainties in the rate constants of chemical reactions

Diurnal variations of BrONO₂ observed by MIPAS-B at midlatitudes and in the Arctic

The first stratospheric measurements of the diurnal variation in the inorganic bromine (Bry) reservoir species BrONO2 around sunrise and sunset are reported. Arctic flights of the balloon-borne Michelson Interferometer for Passive Atmospheric Sounding (MIPAS-B) were carried out from Kiruna (68° N, Sweden) in January 2010 and March 2011 inside the stratospheric polar vortices where diurnal variations of BrONO2 around sunrise have been observed. High nighttime BrONO2 volume mixing ratios of up to 21 pptv (parts per trillion by volume) were detected in late winter 2011 in the absence of polar stratospheric clouds (PSCs). In contrast, the amount of measured BrONO2 was significantly lower in January 2010 due to low available NO2 amounts (for the build-up of BrONO2), the heterogeneous destruction of BrONO2 on PSC particles, and the gas-phase interaction of BrO (the source to form BrONO2) with ClO. A further balloon flight took place at midlatitudes from Timmins (49° N, Canada) in September 2014. Mean BrONO2 mixing ratios of 22 pptv were observed after sunset in the altitude region between 21 and 29 km. Measurements are compared and discussed with the results of a multi-year simulation performed with the chemistry climate model ECHAM5/MESSy Atmospheric Chemistry (EMAC). The calculated temporal variation in BrONO2 largely reproduces the balloon-borne observations. Using the nighttime simulated ratio between BrONO2 and Bry, the amount of Bry observed by MIPAS-B was estimated to be about 21–25 pptv in the lower stratosphere

Unusual chlorine partitioning in the 2015/16 Arctic winter lowermost stratosphere: Observations and simulations

The Arctic winter 2015/16 was characterized by cold stratospheric temperatures. Here we present a comprehensive view of the temporal evolution of chlorine in the lowermost stratosphere over the course of the studied winter. We utilize two-dimensional vertical cross sections of ozone (\chem{O_3}) and chlorine nitrate (\chem{ClONO_2}), measured by the airborne limb imager GLORIA (Gimballed Limb Observer for Radiance Imaging of the Atmosphere) during the POLSTRACC/GW-LCYCLE~II/GWEX/SALSA campaigns, to investigate the tropopause region in detail. Observations from three long-distance flights in January, February, and March~2016 are discussed. \chem{ClONO_2} volume mixing ratios up to 1100\,pptv were measured at 380\,K potential temperature in mesoscale structures. Similar mesoscale structures are also visible in \chem{O_3} measurements. Both trace gas measurements are applied to evaluate simulation results from the chemistry transport model CLaMS (Chemical Lagrangian Model of the Stratosphere) and the chemistry--climate model EMAC (ECHAM5/MESSy Atmospheric Chemistry). These comparisons show agreement within the expected performance of these models. Satellite measurements from Aura/MLS (Microwave Limb Sounder) and SCISAT/ACE-FTS (Atmospheric Chemistry Experiment -- Fourier Transform Spectrometer) provide an overview over the whole winter and information about the stratospheric situation above the flight altitude. Time series of these satellite measurements reveal unusually low hydrochloric acid (HCl) and \chem{ClONO_2} at 380\,K from the beginning of January to the end of February~2016, while chlorine monoxide (ClO) is strongly enhanced. In March~2016, unusually rapid chlorine deactivation into HCl is observed instead of deactivation into \chem{ClONO_2}, the more typical pathway for deactivation in the Arctic. Chlorine deactivation observed in the satellite time series is well reproduced by CLaMS. Sensitivity simulations with CLaMS demonstrate the influence of low abundances of \chem{O_3} and reactive nitrogen (\chem{NO_\mathit{y}}) due to ozone depletion and sedimentation of \chem{NO_\mathit{y}}-containing particles, respectively. On the basis of the different altitude and time ranges of these effects, we conclude that the substantial chlorine deactivation into HCl at 380\,K arose as a result of very low ozone abundances together with low temperatures. Additionally, CLaMS estimates ozone depletion of at least 0.4\,ppmv at 380\,K and 1.75\,ppmv at 490\,K, which is comparable to other extremely cold Arctic winters. We have used CLaMS trajectories to analyze the history of enhanced \chem{ClONO_2} measured by GLORIA. In February, most of the enhanced \chem{ClONO_2} is traced back to chlorine deactivation that had occurred within the past few days prior to the GLORIA measurement. In March, after the final warming, air masses in which chlorine has previously been deactivated into \chem{ClONO_2} have been transported in the remnants of the polar vortex towards the location of measurement for at least~11\,d

Pollution trace gases C₂H₆, C₂H₂, HCOOH, and PAN in the North Atlantic UTLS: observations and simulations

Measurements of the pollution trace gases ethane (C2H6), ethyne (C2H2), formic acid (HCOOH), and peroxyacetyl nitrate (PAN) were performed in the North Atlantic upper troposphere and lowermost stratosphere (UTLS) region with the airborne limb imager GLORIA (Gimballed Limb Observer for Radiance Imaging of the Atmosphere) with high spatial resolution down to cloud top. Observations were made during flights with the German research aircraft HALO (High Altitude and LOng Range Research Aircraft) in the frame of the WISE (Wave-driven ISentropic Exchange) campaign, which was carried out in autumn 2017 from Shannon (Ireland) and Oberpfaffenhofen (Germany). Enhanced volume mixing ratios (VMRs) of up to 2.2 ppbv C2H6, 0.2 ppbv C2H2, 0.9 ppbv HCOOH, and 0.4 ppbv PAN were detected during the flight on 13 September 2017 in the upper troposphere and around the tropopause above the British Isles. Elevated quantities of PAN were measured even in the lowermost stratosphere (locally up to 14 km), likely reflecting the fact that this molecule has the longest lifetime of the four species discussed herein. Backward trajectory calculations as well as global three-dimensional Chemical Lagrangian Model of the Stratosphere (CLaMS) simulations with artificial tracers of air mass origin have shown that the main sources of the observed pollutant species are forest fires in North America and anthropogenic pollution in South Asia and Southeast Asia uplifted and moved within the Asian monsoon anticyclone (AMA) circulation system. After release from the AMA, these species or their precursor substances are transported by strong tropospheric winds over large distances, depending on their particular atmospheric lifetime of up to months. Observations are compared to simulations with the atmospheric models EMAC (ECHAM5/MESSy Atmospheric Chemistry) and CAMS (Copernicus Atmosphere Monitoring Service). These models are qualitatively able to reproduce the measured VMR enhancements but underestimate the absolute amount of the increase. Increasing the emissions in EMAC by a factor of 2 reduces the disagreement between simulated and measured results and illustrates the importance of the quality of emission databases used in chemical models

What do aquaporin knockout studies tell us about fluid transport in epithelia?

The investigation of near-isosmotic water transport in epithelia goes back over 100 years; however, debates over mechanism and pathway remain. Aquaporin (AQP) knockouts have been used by various research groups to test the hypothesis of an osmotic mechanism as well as to explore the paracellular versus transcellular pathway debate. Nonproportional reductions in the water permeability of a water-transporting epithelial cell (e.g., a reduction of around 80–90 %) compared to the reduction in overall water transport rate in the knockout animal (e.g., a reduction of 50–60 %) are commonly found. This nonproportionality has led to controversy over whether AQP knockout studies support or contradict the osmotic mechanism. Arguments raised for and against an interpretation supporting the osmotic mechanism typically have partially specified, implicit, or incorrect assumptions. We present a simple mathematical model of the osmotic mechanism with clear assumptions and, for models based on this mechanism, establish a baseline prediction of AQP knockout studies. We allow for deviations from isotonic/isosmotic conditions and utilize dimensional analysis to reduce the number of parameters that must be considered independently. This enables a single prediction curve to be used for multiple epithelial systems. We find that a simple, transcellular-only osmotic mechanism sufficiently predicts the results of knockout studies and find criticisms of this mechanism to be overstated. We note, however, that AQP knockout studies do not give sufficient information to definitively rule out an additional paracellular pathway

Integrated Genomic and Gene Expression Profiling Identifies Two Major Genomic Circuits in Urothelial Carcinoma

Similar to other malignancies, urothelial carcinoma (UC) is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21), and BCL2L1 (20q11). We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development

The Colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information

<p>Abstract</p> <p>Background</p> <p>To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome.</p> <p>Methods</p> <p>DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information.</p> <p>Results</p> <p>The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance.</p> <p>Conclusions</p> <p>Analysis from our <it>in vitro </it>and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including <it>IGF2BP2</it>, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.</p

Sharpey-Schafer Lecture Gas channels

The traditional dogma has been that all gases diffuse through all membranes simply by dissolving in the lipid phase of the membrane. Although this mechanism may explain how most gases move through most membranes, it is now clear that some membranes have no demonstrable gas permeability, and that at least two families of membrane proteins, the aquaporins (AQPs) and the Rhesus (Rh) proteins, can each serve as pathways for the diffusion of both CO2 and NH3. The knockout of RhCG in the renal collecting duct leads to the predicted consequences in acid–base physiology, providing a clear-cut role for at least one gas channel in the normal physiology of mammals. In our laboratory, we have found that surface-pH (pHS) transients provide a sensitive approach for detecting CO2 and NH3 movement across the cell membranes of Xenopus oocytes. Using this approach, we have found that each tested AQP and Rh protein has its own characteristic CO2/NH3 permeability ratio, which provides the first demonstration of gas selectivity by a channel. Our preliminary AQP1 data suggest that all the NH3 and less than half of the CO2 move along with H2O through the four monomeric aquapores. The majority of CO2 takes an alternative route through AQP1, possibly the central pore at the four-fold axis of symmetry. Preliminary data with two Rh proteins, bacterial AmtB and human erythroid RhAG, suggest a similar story, with all the NH3 moving through the three monomeric NH3 pores and the CO2 taking a separate route, perhaps the central pore at the three-fold axis of symmetry. The movement of different gases via different pathways is likely to underlie the gas selectivity that these channels exhibit

El Diario de Pontevedra : periódico liberal: Ano XXIV Número 7067 - 1907 novembro 8

Quantification of total fatty acids in complemented A. thaliana lines. GC measurements of seeds and seedlings for Fig. 8c are shown. (XLSX 127 kb