ALBERT

Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.

Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.

Description: Laboratory studies of immersion and deposition mode ice nucleation of ozone aged mineral dust particles Atmospheric Chemistry and Physics, 13, 9097-9118, 2013 Author(s): Z. A. Kanji, A. Welti, C. Chou, O. Stetzer, and U. Lohmann Ice nucleation in the atmosphere is central to the understanding the microphysical properties of mixed-phase and cirrus clouds. Ambient conditions such as temperature ( T ) and relative humidity (RH), as well as aerosol properties such as chemical composition and mixing state play an important role in predicting ice formation in the troposphere. Previous field studies have reported the absence of sulfate and organic compounds on mineral dust ice crystal residuals sampled at mountain top stations or aircraft based measurements despite the long-range transport mineral dust is subjected to. We present laboratory studies of ice nucleation for immersion and deposition mode on ozone aged mineral dust particles for 233 〈 T 〈 263 K. Heterogeneous ice nucleation of untreated kaolinite (Ka) and Arizona Test Dust (ATD) particles is compared to corresponding aged particles that are subjected to ozone concentrations of 0.4–4.3 ppmv in a stainless steel aerosol tank. The portable ice nucleation counter (PINC) and immersion chamber combined with the Zurich ice nucleation chamber (IMCA-ZINC) are used to conduct deposition and immersion mode measurements, respectively. Ice active fractions as well as ice active surface site densities ( n s ) are reported and observed to increase as a function of decreasing temperature. We present first results that demonstrate enhancement of the ice nucleation ability of aged mineral dust particles in both the deposition and immersion mode due to ageing. We also present the first results to show a suppression of heterogeneous ice nucleation activity without the condensation of a coating of (in)organic material. In immersion mode, low ozone exposed Ka particles showed enhanced ice activity requiring a median freezing temperature of 1.5 K warmer than that of untreated Ka, whereas high ozone exposed ATD particles showed suppressed ice nucleation requiring a median freezing temperature of 3 K colder than that of untreated ATD. In deposition mode, low exposure Ka had ice active fractions of an order of magnitude higher than untreated Ka, whereas high ozone exposed ATD had ice active fractions up to a factor of 4 lower than untreated ATD. From our results, we derive and present parameterizations in terms of n s ( T ) that can be used in models to predict ice nuclei concentrations based on available aerosol surface area.

Description: A plume-in-grid approach to characterize air quality impacts of aircraft emissions at the Hartsfield–Jackson Atlanta International Airport Atmospheric Chemistry and Physics, 13, 9285-9302, 2013 Author(s): J. Rissman, S. Arunachalam, M. Woody, J. J. West, T. BenDor, and F. S. Binkowski This study examined the impacts of aircraft emissions during the landing and takeoff cycle on PM 2.5 concentrations during the months of June and July 2002 at the Hartsfield–Jackson Atlanta International Airport. Primary and secondary pollutants were modeled using the Advanced Modeling System for Transport, Emissions, Reactions, and Deposition of Atmospheric Matter (AMSTERDAM). AMSTERDAM is a modified version of the Community Multiscale Air Quality (CMAQ) model that incorporates a plume-in-grid process to simulate emissions sources of interest at a finer scale than can be achieved using CMAQ's model grid. Three fundamental issues were investigated: the effects of aircraft on PM 2.5 concentrations throughout northern Georgia, the differences resulting from use of AMSTERDAM's plume-in-grid process rather than a traditional CMAQ simulation, and the concentrations observed in aircraft plumes at subgrid scales. Comparison of model results with an air quality monitor located in the vicinity of the airport found that normalized mean bias ranges from −77.5% to 6.2% and normalized mean error ranges from 40.4% to 77.5%, varying by species. Aircraft influence average PM 2.5 concentrations by up to 0.232 μg m −3 near the airport and by 0.001–0.007 μg m −3 throughout the Atlanta metro area. The plume-in-grid process increases concentrations of secondary PM pollutants by 0.005–0.020 μg m −3 (compared to the traditional grid-based treatment) but reduces the concentration of non-reactive primary PM pollutants by up to 0.010 μg m −3 , with changes concentrated near the airport. Examination of subgrid-scale results indicates that median aircraft contribution to grid cells is higher than median puff concentration in the airport's grid cell and outside of a 20 km × 20 km square area centered on the airport, while in a 12 km × 12 km square ring centered on the airport, puffs have median concentrations over an order of magnitude higher than aircraft contribution to the grid cells. Maximum puff impacts are seen within the 12 km × 12 km ring, not in the airport's own grid cell, while maximum grid cell impacts occur within the airport's grid cell. Twenty-one (21)% of all aircraft-related puffs from the Atlanta airport have at least 0.1 μg m −3 PM 2.5 concentrations. Near the airport, median daily puff concentrations vary between 0.017 and 0.134 μg m −3 (0.05 and 0.35 μg m −3 at ground level), while maximum daily puff concentrations vary between 6.1 and 42.1 μg m −3 (7.5 and 42.1 μg m −3 at ground level) during the 2-month period. In contrast, median daily aircraft contribution to grid concentrations varies between 0.015 and 0.091 μg m −3 (0.09 and 0.40 μg m −3 at ground level), while the maximum varies between 0.75 and 2.55 μg m −3 (0.75 and 2.0 μg m −3 at ground level). Future researchers may consider using a plume-in-grid process, such as the one used here, to understand the impacts of aircraft emissions at other airports, for proposed future airports, for airport expansion projects under various future scenarios, and for other national-scale studies specifically when the maximum impacts at fine scales are of interest.

Description: Corrigendum to "Atmospheric column-averaged mole fractions of carbon dioxide at 53 aircraft measurement sites" published in Atmos. Chem. Phys. 13, 5265–5275, 2013 Atmospheric Chemistry and Physics, 13, 9213-9216, 2013 Author(s): Y. Miyamoto, M. Inoue, I. Morino, O. Uchino, T. Yokota, T. Machida, Y. Sawa, H. Matsueda, C. Sweeney, P. P. Tans, A. E. Andrews, S. C. Biraud, and P. K. Patra No abstract available.

Description: Regional CO 2 flux estimates for 2009–2010 based on GOSAT and ground-based CO 2 observations Atmospheric Chemistry and Physics, 13, 9351-9373, 2013 Author(s): S. Maksyutov, H. Takagi, V. K. Valsala, M. Saito, T. Oda, T. Saeki, D. A. Belikov, R. Saito, A. Ito, Y. Yoshida, I. Morino, O. Uchino, R. J. Andres, and T. Yokota We present the application of a global carbon cycle modeling system to the estimation of monthly regional CO 2 fluxes from the column-averaged mole fractions of CO 2 ( X CO 2 ) retrieved from spectral observations made by the Greenhouse gases Observing SATellite (GOSAT). The regional flux estimates are to be publicly disseminated as the GOSAT Level 4 data product. The forward modeling components of the system include an atmospheric tracer transport model, an anthropogenic emissions inventory, a terrestrial biosphere exchange model, and an oceanic flux model. The atmospheric tracer transport was simulated using isentropic coordinates in the stratosphere and was tuned to reproduce the age of air. We used a fossil fuel emission inventory based on large point source data and observations of nighttime lights. The terrestrial biospheric model was optimized by fitting model parameters to observed atmospheric CO 2 seasonal cycle, net primary production data, and a biomass distribution map. The oceanic surface p CO 2 distribution was estimated with a 4-D variational data assimilation system based on reanalyzed ocean currents. Monthly CO 2 fluxes of 64 sub-continental regions, between June 2009 and May 2010, were estimated from GOSAT FTS SWIR Level 2 X CO 2 retrievals (ver. 02.00) gridded to 5° × 5° cells and averaged on a monthly basis and monthly-mean GLOBALVIEW-CO 2 data. Our result indicated that adding the GOSAT X CO 2 retrievals to the GLOBALVIEW data in the flux estimation brings changes to fluxes of tropics and other remote regions where the surface-based data are sparse. The uncertainties of these remote fluxes were reduced by as much as 60% through such addition. Optimized fluxes estimated for many of these regions, were brought closer to the prior fluxes by the addition of the GOSAT retrievals. In most of the regions and seasons considered here, the estimated fluxes fell within the range of natural flux variabilities estimated with the component models.

Description: Global ozone–CO correlations from OMI and AIRS: constraints on tropospheric ozone sources Atmospheric Chemistry and Physics, 13, 9321-9335, 2013 Author(s): P. S. Kim, D. J. Jacob, X. Liu, J. X. Warner, K. Yang, K. Chance, V. Thouret, and P. Nedelec We present a global data set of free tropospheric ozone–CO correlations with 2° × 2.5° spatial resolution from the Ozone Monitoring Instrument (OMI) and Atmospheric Infrared Sounder (AIRS) satellite instruments for each season of 2008. OMI and AIRS have near-daily global coverage of ozone and CO respectively and observe coincident scenes with similar vertical sensitivities. The resulting ozone–CO correlations are highly statistically significant (positive or negative) in most regions of the world, and are less noisy than previous satellite-based studies that used sparser data. Comparison with ozone–CO correlations and regression slopes ( d O 3 / d CO) from MOZAIC (Measurements of OZone, water vapour, carbon monoxide and nitrogen oxides by in-service AIrbus airCraft) aircraft profiles shows good general agreement. We interpret the observed ozone–CO correlations with the GEOS (Goddard Earth Observing System)-Chem chemical transport model to infer constraints on ozone sources. Driving GEOS-Chem with different meteorological fields generally shows consistent ozone–CO correlation patterns, except in some tropical regions where the correlations are strongly sensitive to model transport error associated with deep convection. GEOS-Chem reproduces the general structure of the observed ozone–CO correlations and regression slopes, although there are some large regional discrepancies. We examine the model sensitivity of d O 3 / d CO to different ozone sources (combustion, biosphere, stratosphere, and lightning NO x ) by correlating the ozone change from that source to CO from the standard simulation. The model reproduces the observed positive d O 3 / d CO in the extratropical Northern Hemisphere in spring–summer, driven by combustion sources. Stratospheric influence there is also associated with a positive d O 3 / d CO because of the interweaving of stratospheric downwelling with continental outflow. The well-known ozone maximum over the tropical South Atlantic is associated with negative d O 3 / d CO in the observations; this feature is reproduced in GEOS-Chem and supports a dominant contribution from lightning to the ozone maximum. A major model discrepancy is found over the northeastern Pacific in summer–fall where d O 3 / d CO is positive in the observations but negative in the model, for all ozone sources. We suggest that this reflects a model overestimate of lightning at northern midlatitudes combined with an underestimate of the East Asian CO source.

Description: Emission ratio and isotopic signatures of molecular hydrogen emissions from tropical biomass burning Atmospheric Chemistry and Physics, 13, 9401-9413, 2013 Author(s): F. A. Haumann, A. M. Batenburg, G. Pieterse, C. Gerbig, M. C. Krol, and T. Röckmann In this study, we identify a biomass-burning signal in molecular hydrogen (H 2 ) over the Amazonian tropical rainforest. To quantify this signal, we measure the mixing ratios of H 2 and several other species as well as the H 2 isotopic composition in air samples that were collected in the BARCA (Balanço Atmosférico Regional de Carbono na Amazônia) aircraft campaign during the dry season. We derive a relative H 2 emission ratio with respect to carbon monoxide (CO) of 0.31 ± 0.04 ppb ppb −1 and an isotopic source signature of −280 ± 41‰ in the air masses influenced by tropical biomass burning. In order to retrieve a clear source signal that is not influenced by the soil uptake of H 2 , we exclude samples from the atmospheric boundary layer. This procedure is supported by data from a global chemistry transport model. The ΔH 2 / ΔCO emission ratio is significantly lower than some earlier estimates for the tropical rainforest. In addition, our results confirm the lower values of the previously conflicting estimates of the H 2 isotopic source signature from biomass burning. These values for the emission ratio and isotopic source signatures of H 2 from tropical biomass burning can be used in future bottom-up and top-down approaches aiming to constrain the strength of the biomass-burning source for H 2 . Hitherto, these two quantities relied only on combustion experiments or on statistical relations, since no direct signal had been obtained from in-situ observations.

Description: Cloud and boundary layer interactions over the Arctic sea ice in late summer Atmospheric Chemistry and Physics, 13, 9379-9399, 2013 Author(s): M. D. Shupe, P. O. G. Persson, I. M. Brooks, M. Tjernström, J. Sedlar, T. Mauritsen, S. Sjogren, and C. Leck Observations from the Arctic Summer Cloud Ocean Study (ASCOS), in the central Arctic sea-ice pack in late summer 2008, provide a detailed view of cloud–atmosphere–surface interactions and vertical mixing processes over the sea-ice environment. Measurements from a suite of ground-based remote sensors, near-surface meteorological and aerosol instruments, and profiles from radiosondes and a helicopter are combined to characterize a week-long period dominated by low-level, mixed-phase, stratocumulus clouds. Detailed case studies and statistical analyses are used to develop a conceptual model for the cloud and atmosphere structure and their interactions in this environment. Clouds were persistent during the period of study, having qualities that suggest they were sustained through a combination of advective influences and in-cloud processes, with little contribution from the surface. Radiative cooling near cloud top produced buoyancy-driven, turbulent eddies that contributed to cloud formation and created a cloud-driven mixed layer. The depth of this mixed layer was related to the amount of turbulence and condensed cloud water. Coupling of this cloud-driven mixed layer to the surface boundary layer was primarily determined by proximity. For 75% of the period of study, the primary stratocumulus cloud-driven mixed layer was decoupled from the surface and typically at a warmer potential temperature. Since the near-surface temperature was constrained by the ocean–ice mixture, warm temperatures aloft suggest that these air masses had not significantly interacted with the sea-ice surface. Instead, back-trajectory analyses suggest that these warm air masses advected into the central Arctic Basin from lower latitudes. Moisture and aerosol particles likely accompanied these air masses, providing necessary support for cloud formation. On the occasions when cloud–surface coupling did occur, back trajectories indicated that these air masses advected at low levels, while mixing processes kept the mixed layer in equilibrium with the near-surface environment. Rather than contributing buoyancy forcing for the mixed-layer dynamics, the surface instead simply appeared to respond to the mixed-layer processes aloft. Clouds in these cases often contained slightly higher condensed water amounts, potentially due to additional moisture sources from below.

Description: Multiannual changes of CO 2 emissions in China: indirect estimates derived from satellite measurements of tropospheric NO 2 columns Atmospheric Chemistry and Physics, 13, 9415-9438, 2013 Author(s): E. V. Berezin, I. B. Konovalov, P. Ciais, A. Richter, S. Tao, G. Janssens-Maenhout, M. Beekmann, and E.-D. Schulze Multiannual satellite measurements of tropospheric NO 2 columns are used for evaluation of CO 2 emission changes in China in the period from 1996 to 2008. Indirect top-down annual estimates of CO 2 emissions are derived from the satellite NO 2 column measurements by means of a simple inverse modeling procedure involving simulations performed with the CHIMERE mesoscale chemistry–transport model and the CO 2 -to-NO x emission ratios from the Emission Database for Global Atmospheric Research (EDGAR) global anthropogenic emission inventory and Regional Emission Inventory in Asia (REAS). Exponential trends in the normalized time series of annual emissions are evaluated separately for the periods from 1996 to 2001 and from 2001 to 2008. The results indicate that the both periods manifest strong positive trends in the CO 2 emissions, and that the trend in the second period was significantly larger than the trend in the first period. Specifically, the trends in the first and second periods are best estimated to be in the range from 3.7 to 8.3 and from 11.0 to 13.2% per year, respectively, taking into account statistical uncertainties and differences between the CO 2 -to-NO x emission ratios from the EDGAR and REAS inventories. Comparison of our indirect top-down estimates of the CO 2 emission changes with the corresponding bottom-up estimates provided by the EDGAR (version 4.2) and Global Carbon Project (GCP) glomal emission inventories reveals that while acceleration of the CO 2 emission growth in the considered period is a common feature of both kinds of estimates, nonlinearity in the CO 2 emission changes may be strongly exaggerated in the global emission inventories. Specifically, the atmospheric NO 2 observations do not confirm the existence of a sharp bend in the emission inventory data time series in the period from 2000 to 2002. A significant quantitative difference is revealed between the bottom-up and indirect top-down estimates of the CO 2 emission trend in the period from 1996 to 2001 (specifically, the trend was not positive according to the global emission inventories, but is strongly positive in our estimates). These results confirm the findings of earlier studies that indicated probable large uncertainties in the energy production and other activity data for China from international energy statistics used as the input information in the global emission inventories. For the period from 2001 to 2008, some quantitative differences between the different kinds of estimates are found to be in the range of possible systematic uncertainties associated with our estimation method. In general, satellite measurements of tropospheric NO 2 are shown to be a useful source of information on CO 2 sources collocated with sources of nitrogen oxides; the corresponding potential of these measurements should be exploited further in future studies.

Description: Air quality over Europe: modelling gaseous and particulate pollutants Atmospheric Chemistry and Physics, 13, 9661-9673, 2013 Author(s): E. Tagaris, R. E. P. Sotiropoulou, N. Gounaris, S. Andronopoulos, and D. Vlachogiannis Air quality over Europe using Models-3 (i.e., CMAQ, MM5, SMOKE) modelling system is performed for winter (i.e., January 2006) and summer (i.e., July 2006) months with the 2006 TNO gridded anthropogenic emissions database. Higher ozone mixing ratios are predicted in southern Europe while higher NO 2 levels are simulated over western Europe. Elevated SO 2 values are simulated over eastern Europe and higher PM 2.5 concentrations over eastern and western Europe. Regional average results suggest that NO 2 and PM 2.5 are underpredicted, SO 2 is overpredicted, while Max8hrO 3 is overpredicted for low mixing ratios and is underpredicted for the higher mixing ratios. However, in a number of countries observed and predicted values are in good agreement for the pollutants examined here. Speciated PM 2.5 components suggest that NO 3 is dominant during winter over western Europe and in a few eastern countries due to the high NO 2 mixing ratios. During summer NO 3 is dominant only in regions with elevated NH 3 emissions. For the rest of the domain SO 4 is dominant. Low OC concentrations are simulated mainly due to the uncertain representation of SOA formation.

Description: On the uses of a new linear scheme for stratospheric methane in global models: water source, transport tracer and radiative forcing Atmospheric Chemistry and Physics, 13, 9641-9660, 2013 Author(s): B. M. Monge-Sanz, M. P. Chipperfield, A. Untch, J.-J. Morcrette, A. Rap, and A. J. Simmons This study evaluates effects and applications of a new linear parameterisation for stratospheric methane and water vapour. The new scheme (CoMeCAT) is derived from a 3-D full-chemistry-transport model (CTM). It is suitable for any global model, and is shown here to produce realistic profiles in the TOMCAT/SLIMCAT 3-D CTM and the ECMWF (European Centre for Medium-Range Weather Forecasts) general circulation model (GCM). Results from the new scheme are in good agreement with the full-chemistry CTM CH 4 field and with observations from the Halogen Occultation Experiment (HALOE). The scheme is also used to derive stratospheric water increments, which in the CTM produce vertical and latitudinal H 2 O variations in fair agreement with satellite observations. Stratospheric H 2 O distributions in the ECMWF GCM show realistic overall features, although concentrations are smaller than in the CTM run (up to 0.5 ppmv smaller above 10 hPa). The potential of the new CoMeCAT tracer for evaluating stratospheric transport is exploited to assess the impacts of nudging the free-running GCM to ERA-40 and ERA-Interim reanalyses. The nudged GCM shows similar transport patterns to the offline CTM forced by the corresponding reanalysis data. The new scheme also impacts radiation and temperature in the model. Compared to the default CH 4 climatology and H 2 O used by the ECMWF radiation scheme, the main effect on ECMWF temperatures when considering both CH 4 and H 2 O from CoMeCAT is a decrease of up to 1.0 K over the tropical mid/low stratosphere. The effect of using the CoMeCAT scheme for radiative forcing (RF) calculations is investigated using the offline Edwards–Slingo radiative transfer model. Compared to the default model option of a tropospheric global 3-D CH 4 value, the CoMeCAT distribution produces an overall change in the annual mean net RF of up to −30 mW m −2 .

Description: A global historical ozone data set and prominent features of stratospheric variability prior to 1979 Atmospheric Chemistry and Physics, 13, 9623-9639, 2013 Author(s): S. Brönnimann, J. Bhend, J. Franke, S. Flückiger, A. M. Fischer, R. Bleisch, G. Bodeker, B. Hassler, E. Rozanov, and M. Schraner We present a vertically resolved zonal mean monthly mean global ozone data set spanning the period 1901 to 2007, called HISTOZ.1.0. It is based on a new approach that combines information from an ensemble of chemistry climate model (CCM) simulations with historical total column ozone information. The CCM simulations incorporate important external drivers of stratospheric chemistry and dynamics (in particular solar and volcanic effects, greenhouse gases and ozone depleting substances, sea surface temperatures, and the quasi-biennial oscillation). The historical total column ozone observations include ground-based measurements from the 1920s onward and satellite observations from 1970 to 1976. An off-line data assimilation approach is used to combine model simulations, observations, and information on the observation error. The period starting in 1979 was used for validation with existing ozone data sets and therefore only ground-based measurements were assimilated. Results demonstrate considerable skill from the CCM simulations alone. Assimilating observations provides additional skill for total column ozone. With respect to the vertical ozone distribution, assimilating observations increases on average the correlation with a reference data set, but does not decrease the mean squared error. Analyses of HISTOZ.1.0 with respect to the effects of El Niño–Southern Oscillation (ENSO) and of the 11 yr solar cycle on stratospheric ozone from 1934 to 1979 qualitatively confirm previous studies that focussed on the post-1979 period. The ENSO signature exhibits a much clearer imprint of a change in strength of the Brewer–Dobson circulation compared to the post-1979 period. The imprint of the 11 yr solar cycle is slightly weaker in the earlier period. Furthermore, the total column ozone increase from the 1950s to around 1970 at northern mid-latitudes is briefly discussed. Indications for contributions of a tropospheric ozone increase, greenhouse gases, and changes in atmospheric circulation are found. Finally, the paper points at several possible future improvements of HISTOZ.1.0.

Description: Naphthalene SOA: redox activity and naphthoquinone gas–particle partitioning Atmospheric Chemistry and Physics, 13, 9731-9744, 2013 Author(s): R. D. McWhinney, S. Zhou, and J. P. D. Abbatt Chamber secondary organic aerosol (SOA) from low-NO x photooxidation of naphthalene by hydroxyl radical was examined with respect to its redox cycling behaviour using the dithiothreitol (DTT) assay. Naphthalene SOA was highly redox-active, consuming DTT at an average rate of 118 ± 14 pmol per minute per μg of SOA material. Measured particle-phase masses of the major previously identified redox active products, 1,2- and 1,4-naphthoquinone, accounted for only 21 ± 3% of the observed redox cycling activity. The redox-active 5-hydroxy-1,4-naphthoquinone was identified as a new minor product of naphthalene oxidation, and including this species in redox activity predictions increased the predicted DTT reactivity to 30 ± 5% of observations. These results suggest that there are substantial unidentified redox-active SOA constituents beyond the small quinones that may be important toxic components of these particles. A gas-to-SOA particle partitioning coefficient was calculated to be (7.0 ± 2.5) × 10 −4 m 3 μg −1 for 1,4-naphthoquinone at 25 °C. This value suggests that under typical warm conditions, 1,4-naphthoquinone is unlikely to contribute strongly to redox behaviour of ambient particles, although further work is needed to determine the potential impact under conditions such as low temperatures where partitioning to the particle is more favourable. Also, higher order oxidation products that likely account for a substantial fraction of the redox cycling capability of the naphthalene SOA are likely to partition much more strongly to the particle phase.

Description: Satellite observation of lowermost tropospheric ozone by multispectral synergism of IASI thermal infrared and GOME-2 ultraviolet measurements over Europe Atmospheric Chemistry and Physics, 13, 9675-9693, 2013 Author(s): J. Cuesta, M. Eremenko, X. Liu, G. Dufour, Z. Cai, M. Höpfner, T. von Clarmann, P. Sellitto, G. Foret, B. Gaubert, M. Beekmann, J. Orphal, K. Chance, R. Spurr, and J.-M. Flaud We present a new multispectral approach for observing lowermost tropospheric ozone from space by synergism of atmospheric radiances in the thermal infrared (TIR) observed by IASI (Infrared Atmospheric Sounding Interferometer) and earth reflectances in the ultraviolet (UV) measured by GOME-2 (Global Ozone Monitoring Experiment-2). Both instruments are onboard the series of MetOp satellites (in orbit since 2006 and expected until 2022) and their scanning capabilities offer global coverage every day, with a relatively fine ground pixel resolution (12 km-diameter pixels spaced by 25 km for IASI at nadir). Our technique uses altitude-dependent Tikhonov–Phillips-type constraints, which optimize sensitivity to lower tropospheric ozone. It integrates the VLIDORT (Vector Linearized Discrete Ordinate Radiative Transfer) and KOPRA (Karlsruhe Optimized and Precise Radiative transfer Algorithm) radiative transfer codes for simulating UV reflectance and TIR radiance, respectively. We have used our method to analyse real observations over Europe during an ozone pollution episode in the summer of 2009. The results show that the multispectral synergism of IASI (TIR) and GOME-2 (UV) enables the observation of the spatial distribution of ozone plumes in the lowermost troposphere (LMT, from the surface up to 3 km a.s.l., above sea level), in good agreement with the CHIMERE regional chemistry-transport model. In this case study, when high ozone concentrations extend vertically above 3 km a.s.l., they are similarly observed over land by both the multispectral and IASI retrievals. On the other hand, ozone plumes located below 3 km a.s.l. are only clearly depicted by the multispectral retrieval (both over land and over ocean). This is achieved by a clear enhancement of sensitivity to ozone in the lowest atmospheric layers. The multispectral sensitivity in the LMT peaks at 2 to 2.5 km a.s.l. over land, while sensitivity for IASI or GOME-2 only peaks at 3 to 4 km a.s.l. at lowest (above the LMT). The degrees of freedom for the multispectral retrieval increase by 0.1 (40% in relative terms) with respect to IASI only retrievals for the LMT. Validations with ozonesondes (over Europe during summer 2009) show that our synergetic approach for combining IASI (TIR) and GOME-2 (UV) measurements retrieves lowermost tropospheric ozone with a mean bias of 1% and a precision of 16%, when smoothing by the retrieval vertical sensitivity (1% mean bias and 21% precision for direct comparisons).

Description: Tethered balloon-borne aerosol measurements: seasonal and vertical variations of aerosol constituents over Syowa Station, Antarctica Atmospheric Chemistry and Physics, 13, 9119-9139, 2013 Author(s): K. Hara, K. Osada, and T. Yamanouchi Tethered balloon-borne aerosol measurements were conducted at Syowa Station, Antarctica, during the 46th Japanese Antarctic expedition (2005–2006). Direct aerosol sampling was operated from near the surface to the lower free troposphere (approximately 2500 m) using a balloon-borne aerosol impactor. Individual aerosol particles were analyzed using a scanning electron microscope equipped with an energy dispersive X-ray spectrometer. Seasonal and vertical features of aerosol constituents and their mixing states were investigated. Results show that sulfate particles were predominant in the boundary layer and lower free troposphere in summer, whereas sea-salt particles were predominant during winter through spring. Minerals, MgSO 4 , and sulfate containing K were identified as minor aerosol constituents in both boundary layer and free troposphere over Syowa Station. Although sea-salt particles were predominant during winter through spring, the relative abundance of sulfate particles increased in the boundary layer when air masses fell from the free troposphere over the Antarctic coast and continent. Sea-salt particles were modified considerably through heterogeneous reactions with SO 4 2− CH 3 SO 3 − and their precursors during summer, and were modified slightly through heterogeneous reactions with NO 3 − and its precursors. During winter through spring, sea-salt modification was insignificant, particularly in the cases of high relative abundance of sea-salt particles and higher number concentrations. In August, NO 3 − and its precursors contributed greatly to sea-salt modification over Syowa Station. Because of the occurrence of sea-salt fractionation on sea ice, Mg-rich sea-salt particles were identified during the months of April through November. In contrast, Mg-free sea-salt particles and slightly Mg-rich sea-salt particles coexisted in the lower troposphere during summer. Thereby, Mg separation can proceed by sea-salt fractionation during summer in Antarctic regions.

Description: Regional inversion of CO 2 ecosystem fluxes from atmospheric measurements: reliability of the uncertainty estimates Atmospheric Chemistry and Physics, 13, 9039-9056, 2013 Author(s): G. Broquet, F. Chevallier, F.-M. Bréon, N. Kadygrov, M. Alemanno, F. Apadula, S. Hammer, L. Haszpra, F. Meinhardt, J. A. Morguí, J. Necki, S. Piacentino, M. Ramonet, M. Schmidt, R. L. Thompson, A. T. Vermeulen, C. Yver, and P. Ciais The Bayesian framework of CO 2 flux inversions permits estimates of the retrieved flux uncertainties. Here, the reliability of these theoretical estimates is studied through a comparison against the misfits between the inverted fluxes and independent measurements of the CO 2 Net Ecosystem Exchange (NEE) made by the eddy covariance technique at local (few hectares) scale. Regional inversions at 0.5° resolution are applied for the western European domain where ~ 50 eddy covariance sites are operated. These inversions are conducted for the period 2002–2007. They use a mesoscale atmospheric transport model, a prior estimate of the NEE from a terrestrial ecosystem model and rely on the variational assimilation of in situ continuous measurements of CO 2 atmospheric mole fractions. Averaged over monthly periods and over the whole domain, the misfits are in good agreement with the theoretical uncertainties for prior and inverted NEE, and pass the chi-square test for the variance at the 30% and 5% significance levels respectively, despite the scale mismatch and the independence between the prior (respectively inverted) NEE and the flux measurements. The theoretical uncertainty reduction for the monthly NEE at the measurement sites is 53% while the inversion decreases the standard deviation of the misfits by 38%. These results build confidence in the NEE estimates at the European/monthly scales and in their theoretical uncertainty from the regional inverse modelling system. However, the uncertainties at the monthly (respectively annual) scale remain larger than the amplitude of the inter-annual variability of monthly (respectively annual) fluxes, so that this study does not engender confidence in the inter-annual variations. The uncertainties at the monthly scale are significantly smaller than the seasonal variations. The seasonal cycle of the inverted fluxes is thus reliable. In particular, the CO 2 sink period over the European continent likely ends later than represented by the prior ecosystem model.

Description: Key chemical NO x sink uncertainties and how they influence top-down emissions of nitrogen oxides Atmospheric Chemistry and Physics, 13, 9057-9082, 2013 Author(s): T. Stavrakou, J.-F. Müller, K. F. Boersma, R. J. van der A, J. Kurokawa, T. Ohara, and Q. Zhang Triggered by recent developments from laboratory and field studies regarding major NO x sink pathways in the troposphere, this study evaluates the influence of chemical uncertainties in NO x sinks for global NO x distributions calculated by the IMAGESv2 chemistry-transport model, and quantifies their significance for top-down NO x emission estimates. Our study focuses on five key chemical parameters believed to be of primary importance, more specifically, the rate of the reaction of NO 2 with OH radicals, the newly identified HNO 3 -forming channel in the reaction of NO with HO 2 , the reactive uptake of N 2 O 5 and HO 2 by aerosols, and the regeneration of OH in the oxidation of isoprene. Sensitivity simulations are performed to estimate the impact of each source of uncertainty. The model calculations show that, although the NO 2 +OH reaction is the largest NO x sink globally accounting for ca. 60% of the total sink, the reactions contributing the most to the overall uncertainty are the formation of HNO 3 in NO+HO 2 , leading to NO x column changes exceeding a factor of two over tropical regions, and the uptake of HO 2 by aqueous aerosols, in particular over East and South Asia. Emission inversion experiments are carried out using model settings which either minimise (MINLOSS) or maximise (MAXLOSS) the total NO x sink, both constrained by one year of OMI NO 2 column data from the DOMINO v2 KNMI algorithm. The choice of the model setup is found to have a major impact on the top-down flux estimates, with 75% higher emissions for MAXLOSS compared to the MINLOSS inversion globally. Even larger departures are found for soil NO (factor of 2) and lightning (1.8). The global anthropogenic source is better constrained (factor of 1.57) than the natural sources, except over South Asia where the combined uncertainty primarily associated to the NO+HO 2 reaction in summer and HO 2 uptake by aerosol in winter lead to top-down emission differences exceeding a factor of 2. Evaluation of the emission optimisation is performed against independent satellite observations from the SCIAMACHY sensor, with airborne NO 2 measurements of the INTEX-A and INTEX-B campaigns, as well as with two new bottom-up inventories of anthropogenic emissions in Asia (REASv2) and China (MEIC). Neither the MINLOSS nor the MAXLOSS setup succeeds in providing the best possible match with all independent datasets. Whereas the minimum sink assumption leads to better agreement with aircraft NO 2 profile measurements, consistent with the results of a previous analysis (Henderson et al., 2012), the same assumption leads to unrealistic features in the inferred distribution of emissions over China. Clearly, although our study addresses an important issue which was largely overlooked in previous inversion exercises, and demonstrates the strong influence of NO x loss uncertainties on top-down emission fluxes, additional processes need to be considered which could also influence the inferred source.

Description: Airborne hydrogen cyanide measurements using a chemical ionisation mass spectrometer for the plume identification of biomass burning forest fires Atmospheric Chemistry and Physics, 13, 9217-9232, 2013 Author(s): M. Le Breton, A. Bacak, J. B. A. Muller, S. J. O'Shea, P. Xiao, M. N. R. Ashfold, M. C. Cooke, R. Batt, D. E. Shallcross, D. E. Oram, G. Forster, S. J.-B. Bauguitte, and C. J. Percival A chemical ionisation mass spectrometer (CIMS) was developed for measuring hydrogen cyanide (HCN) from biomass burning events in Canada using I − reagent ions on board the FAAM BAe-146 research aircraft during the BORTAS campaign in 2011. The ionisation scheme enabled highly sensitive measurements at 1 Hz frequency through biomass burning plumes in the troposphere. A strong correlation between the HCN, carbon monoxide (CO) and acetonitrile (CH 3 CN) was observed, indicating the potential of HCN as a biomass burning (BB) marker. A plume was defined as being 6 standard deviations above background for the flights. This method was compared with a number of alternative plume-defining techniques employing CO and CH 3 CN measurements. The 6-sigma technique produced the highest R 2 values for correlations with CO. A normalised excess mixing ratio (NEMR) of 3.68 ± 0.149 pptv ppbv −1 was calculated, which is within the range quoted in previous research (Hornbrook et al., 2011). The global tropospheric model STOCHEM-CRI incorporated both the observed ratio and extreme ratios derived from other studies to generate global emission totals of HCN via biomass burning. Using the ratio derived from this work, the emission total for HCN from BB was 0.92 Tg (N) yr −1 .

Description: Modeling of very low frequency (VLF) radio wave signal profile due to solar flares using the GEANT4 Monte Carlo simulation coupled with ionospheric chemistry Atmospheric Chemistry and Physics, 13, 9159-9168, 2013 Author(s): S. Palit, T. Basak, S. K. Mondal, S. Pal, and S. K. Chakrabarti X-ray photons emitted during solar flares cause ionization in the lower ionosphere (~60 to 100 km) in excess of what is expected to occur due to a quiet sun. Very low frequency (VLF) radio wave signals reflected from the D-region of the ionosphere are affected by this excess ionization. In this paper, we reproduce the deviation in VLF signal strength during solar flares by numerical modeling. We use GEANT4 Monte Carlo simulation code to compute the rate of ionization due to a M-class flare and a X-class flare. The output of the simulation is then used in a simplified ionospheric chemistry model to calculate the time variation of electron density at different altitudes in the D-region of the ionosphere. The resulting electron density variation profile is then self-consistently used in the LWPC code to obtain the time variation of the change in VLF signal. We did the modeling of the VLF signal along the NWC (Australia) to IERC/ICSP (India) propagation path and compared the results with observations. The agreement is found to be very satisfactory.

Description: Absorption properties of Mediterranean aerosols obtained from multi-year ground-based remote sensing observations Atmospheric Chemistry and Physics, 13, 9195-9210, 2013 Author(s): M. Mallet, O. Dubovik, P. Nabat, F. Dulac, R. Kahn, J. Sciare, D. Paronis, and J. F. Léon Aerosol absorption properties are of high importance to assess aerosol impact on regional climate. This study presents an analysis of aerosol absorption products obtained over the Mediterranean basin or land stations in the region from multi-year ground-based AERONET observations with a focus on the Absorbing Aerosol Optical Depth (AAOD), Single Scattering Albedo (SSA) and their spectral dependence. The AAOD and Absorption Angström Exponent (AAE) dataset is composed of daily averaged AERONET level 2 data from a total of 22 Mediterranean stations having long time series, mainly under the influence of urban-industrial aerosols and/or soil dust. This dataset covers the 17-yr period 1996–2012 with most data being from 2003–2011 (~89% of level-2 AAOD data). Since AERONET level-2 absorption products require a high aerosol load (AOD at 440 nm 〉 0.4), which is most often related to the presence of desert dust, we also consider level-1.5 SSA data, despite their higher uncertainty, and filter out data with an Angström exponent 〈 1.0 in order to study absorption by carbonaceous aerosols. The SSA dataset includes AERONET level-2 products. Sun-photometer observations show that values of AAOD at 440 nm vary between 0.024 ± 0.01 (resp. 0.040 ± 0.01) and 0.050 ± 0.01 (0.055 ± 0.01) for urban (dusty) sites. Analysis shows that the Mediterranean urban-industrial aerosols appear "moderately" absorbing with values of SSA close to ~0.94–0.95 ± 0.04 (at 440 nm) in most cases except over the large cities of Rome and Athens, where aerosol appears more absorbing (SSA ~0.89–0.90 ± 0.04). The aerosol Absorption Angström Exponent (AAE, estimated using 440 and 870 nm) is found to be larger than 1 for most sites over the Mediterranean, a manifestation of mineral dust (iron) and/or brown carbon producing the observed absorption. AERONET level-2 sun-photometer data indicate a possible East-West gradient, with higher values over the eastern basin (AAE East = 1.39/AAE West = 1.33). The North-South AAE gradient is more pronounced, especially over the western basin. Our additional analysis of AERONET level-1.5 data also shows that organic absorbing aerosols significantly affect some Mediterranean sites. These results indicate that current climate models treating organics as nonabsorbing over the Mediterranean certainly underestimate the warming effect due to carbonaceous aerosols.

Description: Optical, microphysical, mass and geometrical properties of aged volcanic particles observed over Athens, Greece, during the Eyjafjallajökull eruption in April 2010 through synergy of Raman lidar and sunphotometer measurements Atmospheric Chemistry and Physics, 13, 9303-9320, 2013 Author(s): P. Kokkalis, A. Papayannis, V. Amiridis, R. E. Mamouri, I. Veselovskii, A. Kolgotin, G. Tsaknakis, N. I. Kristiansen, A. Stohl, and L. Mona Vertical profiles of the optical (extinction and backscatter coefficients, lidar ratio and Ångström exponent), microphysical (mean effective radius, mean refractive index, mean number concentration) and geometrical properties as well as the mass concentration of volcanic particles from the Eyjafjallajökull eruption were retrieved at selected heights over Athens, Greece, using multi-wavelength Raman lidar measurements performed during the period 21–24 April 2010. Aerosol Robotic Network (AERONET) particulate columnar measurements along with inversion schemes were initialized together with lidar observations to deliver the aforementioned products. The well-known FLEXPART (FLEXible PARTicle dispersion model) model used for volcanic dispersion simulations is initiated as well in order to estimate the horizontal and vertical distribution of volcanic particles. Compared with the lidar measurements within the planetary boundary layer over Athens, FLEXPART proved to be a useful tool for determining the state of mixing of ash with other, locally emitted aerosol types. The major findings presented in our work concern the identification of volcanic particles layers in the form of filaments after 7-day transport from the volcanic source (approximately 4000 km away from our site) from the surface and up to 10 km according to the lidar measurements. Mean hourly averaged lidar signals indicated that the layer thickness of volcanic particles ranged between 1.5 and 2.2 km. The corresponding aerosol optical depth was found to vary from 0.01 to 0.18 at 355 nm and from 0.02 up to 0.17 at 532 nm. Furthermore, the corresponding lidar ratios ( S ) ranged between 60 and 80 sr at 355 nm and 44 and 88 sr at 532 nm. The mean effective radius of the volcanic particles estimated by applying inversion scheme to the lidar data found to vary within the range 0.13–0.38 μm and the refractive index ranged from 1.39+0.009 i to 1.48+0.006 i . This high variability is most probably attributed to the mixing of aged volcanic particles with other aerosol types of local origin. Finally, the LIRIC (LIdar/Radiometer Inversion Code) lidar/sunphotometric combined inversion algorithm has been applied in order to retrieve particle concentrations. These have been compared with FLEXPART simulations of the vertical distribution of ash showing good agreement concerning not only the geometrical properties of the volcanic particles layers but also the particles mass concentration.

Description: Corrigendum to "The magnitude and causes of uncertainty in global model simulations of cloud condensation nuclei" published in Atmos. Chem. Phys., 13, 8879–8914, 2013 Atmospheric Chemistry and Physics, 13, 9375-9377, 2013 Author(s): L. A. Lee, K. J. Pringle, C. L. Reddington, G. W. Mann, P. Stier, D. V. Spracklen, J. R. Pierce, and K. S. Carslaw No abstract available.

Description: Spinal muscular atrophy (SMA) is caused by mutations of the survival motor neuron 1 ( SMN1 ) gene, retention of the survival motor neuron 2 ( SMN2 ) gene and insufficient expression of full-length survival motor neuron (SMN) protein. Quinazolines increase SMN2 promoter activity and inhibit the ribonucleic acid scavenger enzyme DcpS. The quinazoline derivative RG3039 has advanced to early phase clinical trials. In preparation for efficacy studies in SMA patients, we investigated the effects of RG3039 in severe SMA mice. Here, we show that RG3039 distributed to central nervous system tissues where it robustly inhibited DcpS enzyme activity, but minimally activated SMN expression or the assembly of small nuclear ribonucleoproteins. Nonetheless, treated SMA mice showed a dose-dependent increase in survival, weight and motor function. This was associated with improved motor neuron somal and neuromuscular junction synaptic innervation and function and increased muscle size. RG3039 also enhanced survival of conditional SMA mice in which SMN had been genetically restored to motor neurons. As this systemically delivered drug may have therapeutic benefits that extend beyond motor neurons, it could act additively with SMN-restoring therapies delivered directly to the central nervous system such as antisense oligonucleotides or gene therapy.

Description: Coronary heart disease (CHD) is the leading cause of death worldwide. Mitochondrial genetic determinant for the development of CHD remains poorly explored. We report there the clinical, genetic, molecular and biochemical characterization of a four-generation Chinese family with maternally inherited CHD. Thirteen of 32 adult members in this family exhibited variable severity and age-at-onset of CHD. Mutational analysis of their mitochondrial genomes identified the tRNA Thr 15927G〉A mutation belonging to the Eastern Asian haplogroup B5. The anticipated destabilization of a highly conserved base-pairing (28C-42G) by the 15927G〉A mutation affects structure and function of tRNA Thr . Northern analysis revealed 80% decrease in the steady-state level of tRNA Thr in the mutant cell lines carrying the 15927G〉A mutation. The 15927G〉A mutation changed the conformation of tRNA Thr , as suggested by slower electrophoretic mobility of mutated tRNA with respect to the wild-type molecule. In addition, ~39% reduction in aminoacylated efficiency of tRNA Thr was observed in mutant cells derived from this Chinese family. An in vivo mitochondrial protein labeling analysis showed ~53% reduction in the rate of mitochondrial translation in mutant cells. The impaired mitochondrial protein synthesis leads to defects in overall respiratory capacity or malate/glutamate-promoted respiration or succinate/glycerol-3-phosphate-promoted respiration, or N,N,N',N '-tetramethyl-pphenylenediamine/ascorbate-promoted respiration in mutant cells. An increasing production of reactive oxygen species was observed in the mutant cells carrying the 15927G〉A mutation. These results provide the direct evidence that the tRNA Thr 15927G〉A mutation is associated with CHD. Our findings may provide new insights into pathophysiology and intervention targets of this disorder.

Description: Spinal muscular atrophy (SMA) is a devastating neuromuscular disorder that stems from low levels of survival of motor neuron (SMN) protein. The processes that cause motor neurons and muscle cells to become dysfunctional are incompletely understood. We are interested in neuromuscular homeostasis and the stresses put upon that system by loss of SMN. We recently reported that α-COP, a member of the coatomer complex of coat protein I (COPI) vesicles, is an SMN-binding partner, implicating this protein complex in normal SMN function. To investigate the functional significance of the interaction between α-COP and SMN, we constructed an inducible NSC-34 cell culture system to model the consequences of SMN depletion and find that depletion of SMN protein results in shortened neurites. Heterologous expression of human SMN, and interestingly over-expression of α-COP, restores normal neurite length and morphology. Mutagenesis of the canonical COPI dilysine motifs in exon 2b results in failure to bind to α-COP and abrogates the ability of human SMN to restore neurite outgrowth in SMN-depleted motor neuron-like NSC-34 cells. We conclude that the interaction between SMN and α-COP serves an important function in the growth and maintenance of motor neuron processes and may play a significant role in the pathogenesis of SMA.

Description: Human cortical malformations, including lissencephaly, polymicrogyria and other diseases of neurodevelopment, have been associated with mutations in microtubule subunits and microtubule-associated proteins. Here we report our cloning of the brain dimple ( brdp ) mouse mutation, which we recovered from an ENU screen for recessive perinatal phenotypes affecting neurodevelopment. We identify the causal mutation in the tubulin, beta-2b ( Tubb2b) gene as a missense mutation at a highly conserved residue (N247S). Brdp/brdp homozygous mutants have significant thinning of the cortical epithelium, which is markedly more severe in the caudo-lateral portion of the telencephalon, and do not survive past birth. The cortical defects are largely due to a major increase in apoptosis and we note abnormal proliferation of the basal progenitors. Adult brdp/+ mice are viable and fertile but exhibit behavioral phenotypes. This allele of Tubb2b represents the most severely affected mouse tubulin phenotype reported to date and this is the first report of a tubulin mutation affecting neuronal proliferation and survival.

Description: CCDC28B encodes a coiled coil domain-containing protein involved in ciliogenesis that was originally identified as a second site modifier of the ciliopathy Bardet–Biedl syndrome. We have previously shown that the depletion of CCDC28B leads to shortened cilia; however, the mechanism underlying how this protein controls ciliary length is unknown. Here, we show that CCDC28B interacts with SIN1, a component of the mTOR complex 2 (mTORC2), and that this interaction is important both in the context of mTOR signaling and in a hitherto unknown, mTORC-independent role of SIN1 in cilia biology. We show that CCDC28B is a positive regulator of mTORC2, participating in its assembly/stability and modulating its activity, while not affecting mTORC1 function. Further, we show that Ccdc28b regulates cilia length in vivo , at least in part, through its interaction with Sin1. Importantly, depletion of Rictor, another core component of mTORC2, does not result in shortened cilia. Taken together, our findings implicate CCDC28B in the regulation of mTORC2, and uncover a novel function of SIN1 regulating cilia length that is likely independent of mTOR signaling.

Description: Spinal muscular atrophy (SMA) is caused by insufficient levels of the survival motor neuron (SMN) protein due to the functional loss of the SMN1 gene and the inability of its paralog, SMN2 , to fully compensate due to reduced exon 7 splicing efficiency. Since SMA patients have at least one copy of SMN2 , drug discovery campaigns have sought to identify SMN2 inducers. C5-substituted quinazolines increase SMN2 promoter activity in cell-based assays and a derivative, RG3039, has progressed to clinical testing. It is orally bioavailable, brain-penetrant and has been shown to be an inhibitor of the mRNA decapping enzyme, DcpS. Our pharmacological characterization of RG3039, reported here, demonstrates that RG3039 can extend survival and improve function in two SMA mouse models of varying disease severity (Taiwanese 5058 Hemi and 2B/– SMA mice), and positively impacts neuromuscular pathologies. In 2B/– SMA mice, RG3039 provided a 〉600% survival benefit (median 18 days to 〉112 days) when dosing began at P4, highlighting the importance of early intervention. We determined the minimum effective dose and the associated pharmacokinetic (PK) and exposure relationship of RG3039 and DcpS inhibition ex vivo . These data support the long PK half-life with extended pharmacodynamic outcome of RG3039 in 2B/– SMA mice. In motor neurons, RG3039 significantly increased both the average number of cells with gems and average number of gems per cell, which is used as an indirect measure of SMN levels. These studies contribute to dose selection and exposure estimates for the first studies with RG3039 in human subjects.

Description: Amyotrophic lateral sclerosis (ALS) is a devastating neurological disorder characterized by selective degeneration of upper and lower motoneurons. The primary triggers for motoneuron degeneration are still unknown, but inflammation is considered an important contributing factor. P2X7 receptor is a key player in microglia response to toxic insults and was previously shown to increase pro-inflammatory actions of SOD1-G93A ALS microglia. We therefore hypothesized that lack of P2X7 receptor could modify disease features in the SOD1-G93A mice. Hetero- and homozygous P2X7 receptor knock-out SOD1-G93A mice were thus generated and analysed for body weight, disease onset and progression (by behavioural scores, grip and rotarod tests) and survival. Although the lifespan of P2X7 +/– and P2X7 –/– /SOD1-G93A female mice was extended by 6–7% with respect to SOD1-G93A mice, to our surprise the clinical onset was significantly anticipated and the disease progression worsened in both male and female P2X7 –/– /SOD1-G93A mice. Consistently, we found increased astrogliosis, microgliosis, motoneuron loss, induction of the pro-inflammatory markers NOX2 and iNOS and activation of the MAPKs pathway in the lumbar spinal cord of end-stage P2X7 –/– /SOD1-G93A mice. These results show that the constitutive deletion of P2X7 receptor aggravates the ALS pathogenesis, suggesting that the receptor might have beneficial effects in at least definite stages of the disease. This study unravels a complex dual role of P2X7 receptor in ALS and strengthens the importance of a successful time window of therapeutic intervention in contrasting the pathology.

Description: There are certain de novo germline mutations associated with genetic disorders whose mutation rates per generation are orders of magnitude higher than the genome average. Moreover, these mutations occur exclusively in the male germ line and older men have a higher probability of having an affected child than younger ones, known as the paternal age effect (PAE). The classic example of a genetic disorder exhibiting a PAE is achondroplasia, caused predominantly by a single-nucleotide substitution (c.1138G〉A) in FGFR3 . To elucidate what mechanisms might be driving the high frequency of this mutation in the male germline, we examined the spatial distribution of the c.1138G〉A substitution in a testis from an 80-year-old unaffected man. Using a technology based on bead-emulsion amplification, we were able to measure mutation frequencies in 192 individual pieces of the dissected testis with a false-positive rate lower than 2.7 x 10 –6 . We observed that most mutations are clustered in a few pieces with 95% of all mutations occurring in 27% of the total testis. Using computational simulations, we rejected the model proposing an elevated mutation rate per cell division at this nucleotide site. Instead, we determined that the observed mutation distribution fits a germline selection model, where mutant spermatogonial stem cells have a proliferative advantage over unmutated cells. Combined with data on several other PAE mutations, our results support the idea that the PAE, associated with a number of Mendelian disorders, may be explained primarily by a selective mechanism.

Description: microRNAs (miRNAs) are dysregulated in a variety of disease states, suggesting that this newly discovered class of gene expression repressors may be viable therapeutic targets. A microarray of miRNA changes in ALS-model superoxide dismutase 1 (SOD1) G93A rodents identified 12 miRNAs as significantly changed. Six miRNAs tested in human ALS tissues were confirmed increased. Specifically, miR-155 was increased 5-fold in mice and 2-fold in human spinal cords. To test miRNA inhibition in the central nervous system (CNS) as a potential novel therapeutic, we developed oligonucleotide-based miRNA inhibitors (anti-miRs) that could inhibit miRNAs throughout the CNS and in the periphery. Anti-miR-155 caused global derepression of targets in peritoneal macrophages and, following intraventricular delivery, demonstrated widespread functional distribution in the brain and spinal cord. After treating SOD1 G93A mice with anti-miR-155, we significantly extended survival by 10 days and disease duration by 15 days (38%) while a scrambled control anti-miR did not significantly improve survival or disease duration. Therefore, antisense oligonucleotides may be used to successfully inhibit miRNAs throughout the brain and spinal cord, and miR-155 is a promising new therapeutic target for human ALS.

Description: Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system (CNS). It is characterized by the infiltration of autoreactive immune cells into the CNS, which target the myelin sheath, leading to the loss of neuronal function. Although it is accepted that MS is a multifactorial disorder with both genetic and environmental factors influencing its development and course, the molecular pathogenesis of MS has not yet been fully elucidated. Here, we studied the longitudinal gene expression profiles of whole-blood RNA from a cohort of 195 MS patients and 66 healthy controls. We analyzed these transcriptomes at both the individual transcript and the biological pathway level. We found 62 transcripts to be significantly up-regulated in MS patients; the expression of 11 of these genes was counter-regulated by interferon treatment, suggesting partial restoration of a ‘healthy’ gene expression profile. Global pathway analyses linked the proteasome and Wnt signaling to MS disease processes. Since genotypes from a subset of individuals were available, we were able to identify expression quantitative trait loci (eQTL), a number of which involved two genes of the MS gene signature. However, all these eQTL were also present in healthy controls. This study highlights the challenge posed by analyzing transcripts from whole blood and how these can be mitigated by using large, well-characterized cohorts of patients with longitudinal follow-up and multi-modality measurements.

Description: Cornelia de Lange syndrome (CdLS) is a developmental disorder caused by mutations in NIPBL, a protein which has functionally been associated with the cohesin complex. Mutations in core cohesin complex components have also been reported in individuals with CdLS-like phenotypes. In addition to its role in sister chromatid cohesion, cohesin is thought to play a role in regulating gene expression during development. The mechanism of this gene regulation remains unclear, but NIPBL and cohesin have been reported to affect long-range chromosomal interactions, both independently and through interactions with CTCF. We used fluorescence in situ hybridization to investigate whether the disruption of NIPBL affects chromosome architecture. We show that cells from CdLS patients exhibit visible chromatin decompaction, that is most pronounced across gene-rich regions of the genome. Cells carrying mutations predicted to have a more severe effect on NIPBL function show more extensive chromatin decompaction than those carrying milder mutations. This cellular phenotype was reproduced in normal cells depleted for NIPBL with siRNA, but was not seen following the knockdown of either the cohesin component SMC3, or CTCF. We conclude that NIPBL has a function in modulating chromatin architecture, particularly for gene-rich areas of the chromosome, that is not dependent on SMC3/cohesin or CTCF, raising the possibility that the aetiology of disorders associated with the mutation of core cohesin components is distinct from that associated with the disruption of NIPBL itself in classical CdLS.

Description: Skin barrier function is primarily assigned to the outer epidermal layer, the stratum corneum (SC), mainly composed of corneocytes and lipid-enriched extracellular matrix. Epidermal ceramides (Cers) are essential barrier lipids, containing ultra-long-chain (ULC) fatty acids (FAs) with a unique -hydroxy group, which is necessary for binding to corneocyte proteins. In the SC, Cers are believed to derive from glucosylated intermediates, namely glucosylceramides (GlcCers), as surmised from human Gaucher's disease and related mouse models. Tamoxifen (TAM)-induced deletion of the endogenous GlcCer-synthesizing enzyme UDP-glucose:ceramide glucosyltransferase (UGCG) in keratin K14-positive cells resulted in epidermal GlcCer depletion. Although free extractable Cers were elevated in total epidermis and as well in SC, protein-bound Cers decreased significantly in Ugcg f/fK14CreERT2 mice, indicating glucosylation to be required for regular Cer processing as well as arrangement and extrusion of lipid lamellae. The almost complete loss of protein-bound Cers led to a disruption of the water permeability barrier (WPB). UGCG-deficient mice developed an ichthyosis-like skin phenotype marked by impaired keratinocyte differentiation associated with delayed wound healing. Gene expression profiling of Ugcg -mutant skin revealed a subset of differentially expressed genes involved in lipid signaling and epidermal differentiation/proliferation, correlating to human skin diseases such as psoriasis and atopic dermatitis. Peroxisome proliferator-activated receptor beta/delta (PPARβ/), a Cer-sensitive transcription factor was identified as potential mediator of the altered gene sets.

Description: A long-standing pathomechanistic model proposes that the polyglutamine (polyQ)-length-dependent toxicity threshold observed in all polyQ diseases is triggered by a conformational change within the monomer that occurs only above a certain polyQ length. If true, this yet undefined and elusive mutant-specific toxic conformation would constitute a direct therapeutic target. Three anti-polyQ antibodies—MW1, 1C2 and 3B5H10—have been extensively used to probe the conformation of polyQ. The crystal structure of the MW1 epitope reveals a linear, non-pathogenic polyQ. In contrast, although the detailed structure of its epitope is unknown, the 3B5H10 antibody is widely advertised and used as a conformational antibody that recognizes the toxic conformation of expanded polyQ. We solved the crystal structure of the 1C2 antigen-binding domain (1C2-Fab) and performed a direct comparison between the 1C2, MW1 and 3B5H10 structures. The MW1 and 1C2 antibodies have similar sequences and structures, consistent with their binding to short polyQ and their polyQ length-discrimination properties. Unexpectedly, the 3B5H10 antibody also shares striking features with MW1 and 1C2, which prompted us to revisit its binding properties. We show that the 3B5H10 epitope is actually a short, non-pathogenic polyQ. All three antibodies MW1, 1C2 and 3B5H10 interact similarly with polyQ of various lengths, and bind small polyQ epitopes in similar linear and extended conformations. Together with studies published during the recent years, our work argues against the hypothesis that a mutant-specific conformation in monomeric polyQ molecules is the toxic entity responsible for polyQ diseases.

Description: Charcot–Marie–Tooth disease (CMT) comprises a clinically and genetically heterogeneous group of peripheral neuropathies characterized by progressive distal muscle weakness and atrophy, foot deformities and distal sensory loss. Following the analysis of two consanguineous families affected by a medium to late-onset recessive form of intermediate CMT, we identified overlapping regions of homozygosity on chromosome 1p36 with a combined maximum LOD score of 5.4. Molecular investigation of the genes from this region allowed identification of two homozygous mutations in PLEKHG5 that produce premature stop codons and are predicted to result in functional null alleles. Analysis of Plekhg5 in the mouse revealed that this gene is expressed in neurons and glial cells of the peripheral nervous system, and that knockout mice display reduced nerve conduction velocities that are comparable with those of affected individuals from both families. Interestingly, a homozygous PLEKHG5 missense mutation was previously reported in a recessive form of severe childhood onset lower motor neuron disease (LMND) leading to loss of the ability to walk and need for respiratory assistance. Together, these observations indicate that different mutations in PLEKHG5 lead to clinically diverse outcomes (intermediate CMT or LMND) affecting the function of neurons and glial cells.

Description: Disappearance of TAR-DNA-binding protein 43 kDa (TDP-43) from the nucleus contributes to the pathogenesis of amyotrophic lateral sclerosis (ALS), but the nuclear function of TDP-43 is not yet fully understood. TDP-43 associates with nuclear bodies including Gemini of coiled bodies (GEMs). GEMs contribute to the biogenesis of uridine-rich small nuclear RNA (U snRNA), a component of splicing machinery. The number of GEMs and a subset of U snRNAs decrease in spinal muscular atrophy, a lower motor neuron disease, suggesting that alteration of U snRNAs may also underlie the molecular pathogenesis of ALS. Here, we investigated the number of GEMs and U11/12-type small nuclear ribonucleoproteins (snRNP) by immunohistochemistry and the level of U snRNAs using real-time quantitative RT-PCR in ALS tissues. GEMs decreased in both TDP-43-depleted HeLa cells and spinal motor neurons in ALS patients. Levels of several U snRNAs decreased in TDP-43-depleted SH-SY5Y and U87-MG cells. The level of U12 snRNA was decreased in tissues affected by ALS (spinal cord, motor cortex and thalamus) but not in tissues unaffected by ALS (cerebellum, kidney and muscle). Immunohistochemical analysis revealed the decrease in U11/12-type snRNP in spinal motor neurons of ALS patients. These findings suggest that loss of TDP-43 function decreases the number of GEMs, which is followed by a disturbance of pre-mRNA splicing by the U11/U12 spliceosome in tissues affected by ALS.

Description: Uromodulin-associated kidney disease (UAKD) is a dominant heritable renal disease in humans which is caused by mutations in the uromodulin ( UMOD) gene and characterized by heterogeneous clinical appearance. To get insights into possible causes of this heterogeneity of UAKD, we describe the new mutant mouse line Umod C93F , leading to disruption of a putative disulfide bond which is also absent in a known human UMOD mutation, and compare the phenotype of this new mouse line with the recently published mouse line Umod A227T . In both mutant mouse lines, which were both bred on the C3H background, the Umod mutations cause a gain-of-toxic function due to a maturation defect of the mutant uromodulin leading to a dysfunction of thick ascending limb of Henle's loop (TALH) cells of the kidney. Umod mutant mice exhibit increased plasma urea and Cystatin levels, impaired urinary concentration ability, reduced fractional excretion of uric acid and nephropathological alterations including uromodulin retention in TALH cells, interstitial fibrosis and inflammatory cell infiltrations, tubular atrophy and occasional glomerulo- und tubulocystic changes, a phenotype highly similar to UAKD in humans. The maturation defect of mutant uromodulin leads to the accumulation of immature uromodulin in the endoplasmic reticulum (ER) and to ER hyperplasia. Further, this study was able to demonstrate for the first time in vivo that the severity of the uromodulin maturation defect as well as onset and speed of progression of renal dysfunction and morphological alterations are strongly dependent on the particular Umod mutation itself and the zygosity status.

Description: Hepatitis B virus (HBV) infection is the predominant risk factor for chronic hepatitis B (CHB), liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Recently, several genome-wide association studies (GWASs) of CHB identified human leukocyte antigen (HLA) loci, including HLA-DP and HLA-DQ in Asian populations, as being associated with the risk of CHB. To confirm and identify the host genetic factors related to CHB infection, we performed another GWAS using a higher-density chip in Korean CHB carriers. We analyzed 1400 samples from Korean population (400 CHB cases and 1000 population controls) using a higher-density GWAS chip [1 140 419 single nucleotide polymorphisms (SNPs)]. In subsequent replication analysis, we further analyzed in an independent study of a Korean CHB cohort consisting of 2909 Korean samples (971 cases and 1938 controls). Logistic regression methods were used for statistical analysis adjusting for age and sex as covariates. This study identified two new risk-associated loci for CHB on the HLA region of chromosome 6, e.g. rs652888 on euchromatic histone-lysine-methyltransferase 2 (EHMT2, P = 7.07 x 10 –13 ) and rs1419881 on transcription factor 19 (TCF19, P = 1.26 x 10 –18 ). Conditional analysis with nearby HLA CHB loci that were previously known, confirmed the independent genetic effects of these two loci on CHB. Conclusion : The GWAS and the subsequent validation study identified new variants associated with the risk of CHB. These findings may advance the understanding of genetic susceptibility to CHB.

Description: Facio-scapulo-humeral dystrophy (FSHD) results from deletions in the subtelomeric macrosatellite D4Z4 array on the 4q35 region. Upregulation of the DUX4 retrogene from the last D4Z4 repeated unit is thought to underlie FSHD pathophysiology. However, no one knows what triggers muscle defect and when alteration arises. To gain further insights into the molecular mechanisms of the disease, we evaluated at the molecular level, the perturbation linked to the FSHD genotype with no a priori on disease onset, severity or penetrance and prior to any infiltration by fibrotic or adipose tissue in biopsies from fetuses carrying a short pathogenic D4Z4 array ( n = 6) compared with fetuses with a non-pathogenic D4Z4 array ( n = 21). By measuring expression of several muscle-specific markers and 4q35 genes including the DUX4 retrogene by an RT-PCR and western blotting, we observed a global dysregulation of genes involved in myogenesis including MYOD1 in samples with 〈11 D4Z4 . The DUX4-fl pathogenic transcript was detected in FSHD biopsies but also in controls. Importantly, in FSHD fetuses, we mainly detected the non-spliced DUX4-fl isoform. In addition, several other genes clustered at the 4q35 locus are upregulated in FSHD fetuses. Our study is the first to examine fetuses carrying an FSHD-linked genotype and reveals an extensive dysregulation of several muscle-specific and 4q35 genes at early development stage at a distance from any muscle defect. Overall, our work suggests that even if FSHD is an adult-onset muscular dystrophy, the disease might also involve early molecular defects arising during myogenesis or early differentiation.

Description: Introduction to special issue: the TransBrom Sonne expedition in the tropical West Pacific Atmospheric Chemistry and Physics, 13, 9439-9446, 2013 Author(s): K. Krüger and B. Quack This special section of Atmospheric Chemistry and Physics gives an overview of scientific results, collected during a West Pacific ship expedition in October 2009 with the Research Vessel (R/V) Sonne . The cruise focussed on chemical interactions between the ocean surface and the atmosphere above the tropical West Pacific and was planned within the national research project TransBrom ( www.geomar.de/~transbrom ). TransBrom aimed to particularly investigate very short lived bromine compounds in the ocean and their transport to and relevance for the stratosphere. For this purpose, chemical and biological parameters were analysed in the ocean and in the atmosphere, accompanied by a high frequency of meteorological measurements, to derive new insights into the multidisciplinary research field. This introduction paper presents the scientific goals and the meteorological and oceanographic background. The main research findings of the TransBrom Sonne expedition are highlighted.

Description: Quantitative determination of carbonaceous particle mixing state in Paris using single-particle mass spectrometer and aerosol mass spectrometer measurements Atmospheric Chemistry and Physics, 13, 9479-9496, 2013 Author(s): R. M. Healy, J. Sciare, L. Poulain, M. Crippa, A. Wiedensohler, A. S. H. Prévôt, U. Baltensperger, R. Sarda-Estève, M. L. McGuire, C.-H. Jeong, E. McGillicuddy, I. P. O'Connor, J. R. Sodeau, G. J. Evans, and J. C. Wenger Single-particle mixing state information can be a powerful tool for assessing the relative impact of local and regional sources of ambient particulate matter in urban environments. However, quantitative mixing state data are challenging to obtain using single-particle mass spectrometers. In this study, the quantitative chemical composition of carbonaceous single particles has been determined using an aerosol time-of-flight mass spectrometer (ATOFMS) as part of the MEGAPOLI 2010 winter campaign in Paris, France. Relative peak areas of marker ions for elemental carbon (EC), organic aerosol (OA), ammonium, nitrate, sulfate and potassium were compared with concurrent measurements from an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), a thermal–optical OCEC analyser and a particle into liquid sampler coupled with ion chromatography (PILS-IC). ATOFMS-derived estimated mass concentrations reproduced the variability of these species well ( R 2 = 0.67–0.78), and 10 discrete mixing states for carbonaceous particles were identified and quantified. The chemical mixing state of HR-ToF-AMS organic aerosol factors, resolved using positive matrix factorisation, was also investigated through comparison with the ATOFMS dataset. The results indicate that hydrocarbon-like OA (HOA) detected in Paris is associated with two EC-rich mixing states which differ in their relative sulfate content, while fresh biomass burning OA (BBOA) is associated with two mixing states which differ significantly in their OA / EC ratios. Aged biomass burning OA (OOA 2 -BBOA) was found to be significantly internally mixed with nitrate, while secondary, oxidised OA (OOA) was associated with five particle mixing states, each exhibiting different relative secondary inorganic ion content. Externally mixed secondary organic aerosol was not observed. These findings demonstrate the range of primary and secondary organic aerosol mixing states in Paris. Examination of the temporal behaviour and chemical composition of the ATOFMS classes also enabled estimation of the relative contribution of transported emissions of each chemical species and total particle mass in the size range investigated. Only 22% of the total ATOFMS-derived particle mass was apportioned to fresh, local emissions, with 78% apportioned to regional/continental-scale emissions.

Description: Contact freezing: a review of experimental studies Atmospheric Chemistry and Physics, 13, 9745-9769, 2013 Author(s): L. A. Ladino Moreno, O. Stetzer, and U. Lohmann This manuscript compiles both theoretical and experimental information on contact freezing with the aim to better understand this potentially important but still not well quantified heterogeneous freezing mode. There is no complete theory that describes contact freezing and how the energy barrier has to be overcome to nucleate an ice crystal by contact freezing. Experiments on contact freezing conducted using the cold plate technique indicate that it can initiate ice formation at warmer temperatures than immersion freezing. Additionally, a qualitative difference in the freezing temperatures between contact and immersion freezing has been found using different instrumentation and different ice nuclei. There is a lack of data on collision rates in most of the reported data, which inhibits a quantitative calculation of the freezing efficiencies. Thus, new or modified instrumentation to study contact nucleation in the laboratory and in the field are needed to identify the conditions at which contact nucleation could occur in the atmosphere. Important questions concerning contact freezing and its potential role for ice cloud formation and climate are also summarized.

Description: Validation of XCO 2 derived from SWIR spectra of GOSAT TANSO-FTS with aircraft measurement data Atmospheric Chemistry and Physics, 13, 9771-9788, 2013 Author(s): M. Inoue, I. Morino, O. Uchino, Y. Miyamoto, Y. Yoshida, T. Yokota, T. Machida, Y. Sawa, H. Matsueda, C. Sweeney, P. P. Tans, A. E. Andrews, S. C. Biraud, T. Tanaka, S. Kawakami, and P. K. Patra Column-averaged dry air mole fractions of carbon dioxide (XCO 2 ) retrieved from Greenhouse gases Observing SATellite (GOSAT) Short-Wavelength InfraRed (SWIR) observations were validated with aircraft measurements by the Comprehensive Observation Network for TRace gases by AIrLiner (CONTRAIL) project, the National Oceanic and Atmospheric Administration (NOAA), the US Department of Energy (DOE), the National Institute for Environmental Studies (NIES), the HIAPER Pole-to-Pole Observations (HIPPO) program, and the GOSAT validation aircraft observation campaign over Japan. To calculate XCO 2 based on aircraft measurements (aircraft-based XCO 2 ), tower measurements and model outputs were used for additional information near the surface and above the tropopause, respectively. Before validation, we investigated the impacts of GOSAT SWIR column averaging kernels (CAKs) and the shape of a priori profiles on the aircraft-based XCO 2 calculation. The differences between aircraft-based XCO 2 with and without the application of GOSAT CAK were evaluated to be less than ±0.4 ppm at most, and less than ±0.1 ppm on average. Therefore, we concluded that the GOSAT CAK produces only a minor effect on the aircraft-based XCO 2 calculation in terms of the overall uncertainty of GOSAT XCO 2 . We compared GOSAT data retrieved within ±2 or ±5° latitude/longitude boxes centered at each aircraft measurement site to aircraft-based data measured on a GOSAT overpass day. The results indicated that GOSAT XCO 2 over land regions agreed with aircraft-based XCO 2 , except that the former is biased by −0.68 ppm (−0.99 ppm) with a standard deviation of 2.56 ppm (2.51 ppm), whereas the averages of the differences between the GOSAT XCO 2 over ocean and the aircraft-based XCO 2 were −1.82 ppm (−2.27 ppm) with a standard deviation of 1.04 ppm (1.79 ppm) for ±2° (±5°) boxes.

Description: A comparison of atmospheric composition using the Carbon Bond and Regional Atmospheric Chemistry Mechanisms Atmospheric Chemistry and Physics, 13, 9695-9712, 2013 Author(s): G. Sarwar, J. Godowitch, B. H. Henderson, K. Fahey, G. Pouliot, W. T. Hutzell, R. Mathur, D. Kang, W. S. Goliff, and W. R. Stockwell We incorporate the recently developed Regional Atmospheric Chemistry Mechanism (version 2, RACM2) into the Community Multiscale Air Quality modeling system for comparison with the existing 2005 Carbon Bond mechanism with updated toluene chemistry (CB05TU). Compared to CB05TU, RACM2 enhances the domain-wide monthly mean hydroxyl radical concentrations by 46% and nitric acid by 26%. However, it reduces hydrogen peroxide by 2%, peroxyacetic acid by 94%, methyl hydrogen peroxide by 19%, peroxyacetyl nitrate by 40%, and organic nitrate by 41%. RACM2 enhances ozone compared to CB05TU at all ambient levels. Although it exhibited greater overestimates at lower observed concentrations, it displayed an improved performance at higher observed concentrations. The RACM2 ozone predictions are also supported by increased ozone production efficiency that agrees better with observations. Compared to CB05TU, RACM2 enhances the domain-wide monthly mean sulfate by 10%, nitrate by 6%, ammonium by 10%, anthropogenic secondary organic aerosols by 42%, biogenic secondary organic aerosols by 5%, and in-cloud secondary organic aerosols by 7%. Increased inorganic and organic aerosols with RACM2 agree better with observed data. Any air pollution control strategies developed using the two mechanisms do not differ appreciably.

Description: Climate and chemistry effects of a regional scale nuclear conflict Atmospheric Chemistry and Physics, 13, 9713-9729, 2013 Author(s): A. Stenke, C. R. Hoyle, B. Luo, E. Rozanov, J. Gröbner, L. Maag, S. Brönnimann, and T. Peter Previous studies have highlighted the severity of detrimental effects for life on earth after an assumed regionally limited nuclear war. These effects are caused by climatic, chemical and radiative changes persisting for up to one decade. However, so far only a very limited number of climate model simulations have been performed, giving rise to the question how realistic previous computations have been. This study uses the coupled chemistry climate model (CCM) SOCOL, which belongs to a different family of CCMs than previously used, to investigate the consequences of such a hypothetical nuclear conflict. In accordance with previous studies, the present work assumes a scenario of a nuclear conflict between India and Pakistan, each applying 50 warheads with an individual blasting power of 15 kt ("Hiroshima size") against the major population centers, resulting in the emission of tiny soot particles, which are generated in the firestorms expected in the aftermath of the detonations. Substantial uncertainties related to the calculation of likely soot emissions, particularly concerning assumptions of target fuel loading and targeting of weapons, have been addressed by simulating several scenarios, with soot emissions ranging from 1 to 12 Tg. Their high absorptivity with respect to solar radiation leads to a rapid self-lofting of the soot particles into the strato- and mesosphere within a few days after emission, where they remain for several years. Consequently, the model suggests earth's surface temperatures to drop by several degrees Celsius due to the shielding of solar irradiance by the soot, indicating a major global cooling. In addition, there is a substantial reduction of precipitation lasting 5 to 10 yr after the conflict, depending on the magnitude of the initial soot release. Extreme cold spells associated with an increase in sea ice formation are found during Northern Hemisphere winter, which expose the continental land masses of North America and Eurasia to a cooling of several degrees. In the stratosphere, the strong heating leads to an acceleration of catalytic ozone loss and, consequently, to enhancements of UV radiation at the ground. In contrast to surface temperature and precipitation changes, which show a linear dependence to the soot burden, there is a saturation effect with respect to stratospheric ozone chemistry. Soot emissions of 5 Tg lead to an ozone column reduction of almost 50% in northern high latitudes, while emitting 12 Tg only increases ozone loss by a further 10%. In summary, this study, though using a different chemistry climate model, corroborates the previous investigations with respect to the atmospheric impacts. In addition to these persistent effects, the present study draws attention to episodically cold phases, which would likely add to the severity of human harm worldwide. The best insurance against such a catastrophic development would be the delegitimization of nuclear weapons.

Description: Observations of peroxyacetyl nitrate (PAN) in the upper troposphere by the Atmospheric Chemistry Experiment-Fourier Transform Spectrometer (ACE-FTS) Atmospheric Chemistry and Physics, 13, 5601-5613, 2013 Author(s): K. A. Tereszchuk, D. P. Moore, J. J. Harrison, C. D. Boone, M. Park, J. J. Remedios, W. J. Randel, and P. F. Bernath Peroxyacetyl nitrate (CH 3 CO·O 2 NO 2 , abbreviated as PAN) is a trace molecular species present in the troposphere and lower stratosphere due primarily to pollution from fuel combustion and the pyrogenic outflows from biomass burning. In the lower troposphere, PAN has a relatively short lifetime and is principally destroyed within a few hours through thermolysis, but it can act as a reservoir and carrier of NO x in the colder temperatures of the upper troposphere, where UV photolysis becomes the dominant loss mechanism. Pyroconvective updrafts from large biomass burning events can inject PAN into the upper troposphere and lower stratosphere (UTLS), providing a means for the long-range transport of NO x . Given the extended lifetimes at these higher altitudes, PAN is readily detectable via satellite remote sensing. A new PAN data product is now available for the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) version 3.0 data set. We report observations of PAN in boreal biomass burning plumes recorded during the BORTAS (quantifying the impact of BOReal forest fires on Tropospheric oxidants over the Atlantic using Aircraft and Satellites) campaign (12 July to 3 August 2011). The retrieval method employed by incorporating laboratory-recorded absorption cross sections into version 3.0 of the ACE-FTS forward model and retrieval software is described in full detail. The estimated detection limit for ACE-FTS PAN is 5 pptv, and the total systematic error contribution to the ACE-FTS PAN retrieval is ~ 16%. The retrieved volume mixing ratio (VMR) profiles are compared to coincident measurements made by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument on the European Space Agency (ESA) Environmental Satellite (ENVISAT). The MIPAS measurements demonstrated good agreement with the ACE-FTS VMR profiles for PAN, where the measured VMR values are well within the associated measurement errors for both instruments and comparative measurements differ no more than 70 pptv. The ACE-FTS PAN data set is used to obtain zonal mean distributions of seasonal averages from ~ 5–20 km. A strong seasonality is clearly observed for PAN concentrations in the global UTLS. Since the principal source of PAN in the UTLS is due to lofted biomass burning emissions from the pyroconvective updrafts created by large fires, the observed seasonality in enhanced PAN coincides with fire activity in different geographical regions throughout the year.

Description: Multiple daytime nucleation events in semi-clean savannah and industrial environments in South Africa: analysis based on observations Atmospheric Chemistry and Physics, 13, 5523-5532, 2013 Author(s): A. Hirsikko, V. Vakkari, P. Tiitta, J. Hatakka, V.-M. Kerminen, A.-M. Sundström, J. P. Beukes, H. E. Manninen, M. Kulmala, and L. Laakso Recent studies have shown very high frequencies of atmospheric new particle formation in different environments in South Africa. Our aim here was to investigate the causes for two or three consecutive daytime nucleation events, followed by subsequent particle growth during the same day. We analysed 108 and 31 such days observed in a polluted industrial and moderately polluted rural environments, respectively, in South Africa. The analysis was based on two years of measurements at each site. After rejecting the days having notable changes in the air mass origin or local wind direction, i.e. two major reasons for observed multiple nucleation events, we were able to investigate other factors causing this phenomenon. Clouds were present during, or in between most of the analysed multiple particle formation events. Therefore, some of these events may have been single events, interrupted somehow by the presence of clouds. From further analysis, we propose that the first nucleation and growth event of the day was often associated with the mixing of a residual air layer rich in SO 2 (oxidized to sulphuric acid) into the shallow surface-coupled layer. The second nucleation and growth event of the day usually started before midday and was sometimes associated with renewed SO 2 emissions from industrial origin. However, it was also evident that vapours other than sulphuric acid were required for the particle growth during both events. This was especially the case when two simultaneously growing particle modes were observed. Based on our analysis, we conclude that the relative contributions of estimated H 2 SO 4 and other vapours on the first and second nucleation and growth events of the day varied from day to day, depending on anthropogenic and natural emissions, as well as atmospheric conditions.

Description: Evolution of particle composition in CLOUD nucleation experiments Atmospheric Chemistry and Physics, 13, 5587-5600, 2013 Author(s): H. Keskinen, A. Virtanen, J. Joutsensaari, G. Tsagkogeorgas, J. Duplissy, S. Schobesberger, M. Gysel, F. Riccobono, J. G. Slowik, F. Bianchi, T. Yli-Juuti, K. Lehtipalo, L. Rondo, M. Breitenlechner, A. Kupc, J. Almeida, A. Amorim, E. M. Dunne, A. J. Downard, S. Ehrhart, A. Franchin, M.K. Kajos, J. Kirkby, A. Kürten, T. Nieminen, V. Makhmutov, S. Mathot, P. Miettinen, A. Onnela, T. Petäjä, A. Praplan, F. D. Santos, S. Schallhart, M. Sipilä, Y. Stozhkov, A. Tomé, P. Vaattovaara, D. Wimmer, A. Prevot, J. Dommen, N. M. Donahue, R.C. Flagan, E. Weingartner, Y. Viisanen, I. Riipinen, A. Hansel, J. Curtius, M. Kulmala, D. R. Worsnop, U. Baltensperger, H. Wex, F. Stratmann, and A. Laaksonen Sulphuric acid, ammonia, amines, and oxidised organics play a crucial role in nanoparticle formation in the atmosphere. In this study, we investigate the composition of nucleated nanoparticles formed from these compounds in the CLOUD (Cosmics Leaving Outdoor Droplets) chamber experiments at CERN (Centre européen pour la recherche nucléaire). The investigation was carried out via analysis of the particle hygroscopicity, ethanol affinity, oxidation state, and ion composition. Hygroscopicity was studied by a hygroscopic tandem differential mobility analyser and a cloud condensation nuclei counter, ethanol affinity by an organic differential mobility analyser and particle oxidation level by a high-resolution time-of-flight aerosol mass spectrometer. The ion composition was studied by an atmospheric pressure interface time-of-flight mass spectrometer. The volume fraction of the organics in the particles during their growth from sizes of a few nanometers to tens of nanometers was derived from measured hygroscopicity assuming the Zdanovskii–Stokes–Robinson relationship, and compared to values gained from the spectrometers. The ZSR-relationship was also applied to obtain the measured ethanol affinities during the particle growth, which were used to derive the volume fractions of sulphuric acid and the other inorganics (e.g. ammonium salts). In the presence of sulphuric acid and ammonia, particles with a mobility diameter of 150 nm were chemically neutralised to ammonium sulphate. In the presence of oxidation products of pinanediol, the organic volume fraction of freshly nucleated particles increased from 0.4 to ~0.9, with an increase in diameter from 2 to 63 nm. Conversely, the sulphuric acid volume fraction decreased from 0.6 to 0.1 when the particle diameter increased from 2 to 50 nm. The results provide information on the composition of nucleated aerosol particles during their growth in the presence of various combinations of sulphuric acid, ammonia, dimethylamine and organic oxidation products.

Description: Comparison of three vertically resolved ozone data sets: climatology, trends and radiative forcings Atmospheric Chemistry and Physics, 13, 5533-5550, 2013 Author(s): B. Hassler, P. J. Young, R. W. Portmann, G. E. Bodeker, J. S. Daniel, K. H. Rosenlof, and S. Solomon Climate models that do not simulate changes in stratospheric ozone concentrations require the prescription of ozone fields to accurately calculate UV fluxes and stratospheric heating rates. In this study, three different global ozone time series that are available for this purpose are compared: the data set of Randel and Wu (2007) (RW07), Cionni et al. (2011) (SPARC), and Bodeker et al. (2013) (BDBP). All three data sets represent multiple-linear regression fits to vertically resolved ozone observations, resulting in a spatially and temporally continuous stratospheric ozone field covering at least the period from 1979 to 2005. The main differences among the data sets result from regression models, which use different observations and include different basis functions. The data sets are compared against ozonesonde and satellite observations to assess how the data sets represent concentrations, trends and interannual variability. In the Southern Hemisphere polar region, RW07 and SPARC underestimate the ozone depletion in spring ozonesonde measurements. A piecewise linear trend regression is performed to estimate the 1979–1996 ozone decrease globally, covering a period of extreme depletion in most regions. BDBP overestimates Arctic and tropical ozone depletion over this period relative to the available measurements, whereas the depletion is underestimated in RW07 and SPARC. While the three data sets yield ozone concentrations that are within a range of different observations, there is a large spread in their respective ozone trends. One consequence of this is differences of almost a factor of four in the calculated stratospheric ozone radiative forcing between the data sets (RW07: −0.038 Wm −2 , SPARC: −0.033 Wm −2 , BDBP: −0.119 Wm −2 ), important in assessing the contribution of stratospheric ozone depletion to the total anthropogenic radiative forcing.

Description: Two siblings from consanguineous parents died perinatally with a condition characterized by generalized hypotonia, respiratory insufficiency, arthrogryposis, microcephaly, congenital brain malformations and hyperglycinemia. Catalytic activities of the mitochondrial respiratory complexes I and II were deficient in skeletal muscle, a finding suggestive of an inborn error in mitochondrial biogenesis. Homozygosity mapping identified IBA57 located in the largest homozygous region on chromosome 1 as a culprit candidate gene. IBA57 is known to be involved in the biosynthesis of mitochondrial [4Fe-4S] proteins. Sequence analysis of IBA57 revealed the homozygous mutation c.941A 〉 C, p.Gln314Pro. Severely decreased amounts of IBA57 protein were observed in skeletal muscle and cultured skin fibroblasts from the affected subjects. HeLa cells depleted of IBA57 showed biochemical defects resembling the ones found in patient-derived cells, including a decrease in various mitochondrial [4Fe-4S] proteins and in proteins covalently linked to lipoic acid (LA), a cofactor produced by the [4Fe-4S] protein LA synthase. The defects could be complemented by wild-type IBA57 and partially by mutant IBA57 . As a result of the mutation, IBA57 protein was excessively degraded, an effect ameliorated by protease inhibitors. Hence, we propose that the mutation leads to partial functional impairment of IBA57, yet the major pathogenic impact is due to its proteolytic degradation below physiologically critical levels. In conclusion, the ensuing lethal complex biochemical phenotype of a novel metabolic syndrome results from multiple Fe/S protein defects caused by a deficiency in the Fe/S cluster assembly protein IBA57.

Description: Duchenne muscular dystrophy (DMD) is characterized by severe degeneration and necrosis of both skeletal and cardiac muscle. While many experimental therapies have shown great promise in treating skeletal muscle disease, an effective therapy for Duchenne cardiomyopathy remains a challenge in large animal models and human patients. The current views on cardiac consequences of skeletal muscle-centered therapy are controversial. Studies performed in young adult mdx mice (a mild DMD mouse model) have yielded opposing results. Since mdx mice do not develop dystrophic cardiomyopathy until ≥21 months of age, we reasoned that old mdx mice may represent a better model to assess the impact of skeletal muscle rescue on dystrophic heart disease. Here, we aged skeletal muscle-specific micro-dystrophin transgenic mdx mice to 23 months and examined the cardiac phenotype. As expected, transgenic mdx mice had minimal skeletal muscle disease and they also outperformed original mdx mice on treadmill running. On cardiac examination, the dystrophin-null heart of transgenic mdx mice displayed severe cardiomyopathy matching that of non-transgenic mdx mice. Specifically, both the strains showed similar heart fibrosis and cardiac function deterioration in systole and diastole. Cardiac output and ejection fraction were also equally compromised. Our results suggest that skeletal muscle rescue neither aggravates nor alleviates cardiomyopathy in aged mdx mice. These findings underscore the importance of treating both skeletal and cardiac muscles in DMD therapy.

Description: Mutations in Parkin or PINK1 are the most common cause of recessively inherited parkinsonism. Parkin and PINK1 function in a conserved mitochondrial quality control pathway, in which PINK1, a putative mitochondrial kinase, directs Parkin, a cytosolic E3 ubiquitin ligase, selectively to dysfunctional mitochondria to promote their isolation, immobilization and degradation by macroautophagy (hereafter, mitophagy). As Parkin recruitment to mitochondria is robustly induced by PINK1 expression on the outer mitochondrial membrane, Parkin recruitment to mitochondria was used as an assay for PINK1 function. Unexpectedly, mutation of serine residues within the activation segment of PINK1 uncovered a temperature-sensitive variant of PINK1 (tsPINK1). tsPINK1 allowed for the first time the disassociation of PINK1 activity from its expression and localization. Additionally, extensive mutagenesis identified three disease-associated variants in the activation segment and one in an α-helix N-terminal to kinase domain (Q126P) that are similarly thermally labile, suggesting that their activity could be restored post-translationally (e.g. by reducing the temperature or by a chemical or pharmacologic chaperone). Together, these findings suggest that tsPINK1 may represent a valuable tool for the analysis of the PINK1/Parkin pathway in human cells; additionally, as the serine residue promoting thermal lability is conserved among Mus musculus , Danio rerio , Drosophila melanogaster and Caenorhabditis elegans , it may serve as the basis for developing other temperature-sensitive models for the study of recessive parkinsonism and mitophagy. Finally, these results suggest that PINK1 kinase function could be restored for a subset of patients with PINK1 mutations, and perhaps alter the course of their disease.

Description: Newly observed peroxides and the water effect on the formation and removal of hydroxyalkyl hydroperoxides in the ozonolysis of isoprene Atmospheric Chemistry and Physics, 13, 5671-5683, 2013 Author(s): D. Huang, Z. M. Chen, Y. Zhao, and H. Liang The ozonolysis of alkenes is considered to be an important source of atmospheric peroxides, which serve as oxidants, reservoirs of HO x radicals, and components of secondary organic aerosols (SOAs). Recent laboratory investigations of this reaction identified hydrogen peroxide (H 2 O 2 ) and hydroxymethyl hydroperoxide (HMHP) in ozonolysis of isoprene. Although larger hydroxyalkyl hydroperoxides (HAHPs) were also expected, their presence is not currently supported by experimental evidence. In the present study, we investigated the formation of peroxides in the gas phase ozonolysis of isoprene at various relative humidities on a time scale of tens of seconds, using a quartz flow tube reactor coupled with the online detection of peroxides. We detected a variety of conventional peroxides, including H 2 O 2 , HMHP, methyl hydroperoxide, bis-hydroxymethyl hydroperoxide, and ethyl hydroperoxide, and interestingly found three unknown peroxides. The molar yields of the conventional peroxides fell within the range of values provided in the literature. The three unknown peroxides had a combined molar yield of ~ 30% at 5% relative humidity (RH), which was comparable with that of the conventional peroxides. Unlike H 2 O 2 and HMHP, the molar yields of these three unknown peroxides were inversely related to the RH. On the basis of experimental kinetic and box model analysis, we tentatively assigned these unknown peroxides to C2−C4 HAHPs, which are produced by the reactions of different Criegee intermediates with water. Our study provides experimental evidence for the formation of large HAHPs in the ozonolysis of isoprene (one of the alkenes). These large HAHPs have a sufficiently long lifetime, estimated as tens of minutes, which allows them to become involved in atmospheric chemical processes, e.g., SOA formation and radical recycling.

Description: The Vesicle-associated membrane protein ( V AMP)- A ssociated P rotein B (VAPB) is the causative gene of amyotrophic lateral sclerosis 8 (ALS8) in humans. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by selective death of motor neurons leading to spasticity, muscle atrophy and paralysis. VAP proteins have been implicated in various cellular processes, including intercellular signalling, synaptic remodelling, lipid transport and membrane trafficking and yet, the molecular mechanisms underlying ALS8 pathogenesis remain poorly understood. We identified the conserved phosphoinositide phosphatase Sac1 as a Drosophila VAP (DVAP)-binding partner and showed that DVAP is required to maintain normal levels of phosphoinositides. Downregulating either Sac1 or DVAP disrupts axonal transport, synaptic growth, synaptic microtubule integrity and the localization of several postsynaptic components. Expression of the disease-causing allele ( DVAP-P58S ) in a fly model for ALS8 induces neurodegeneration, elicits synaptic defects similar to those of DVAP or Sac1 downregulation and increases phosphoinositide levels. Consistent with a role for Sac1-mediated increase of phosphoinositide levels in ALS8 pathogenesis, we found that Sac1 downregulation induces neurodegeneration in a dosage-dependent manner. In addition, we report that Sac1 is sequestered into the DVAP-P58S-induced aggregates and that reducing phosphoinositide levels rescues the neurodegeneration and suppresses the synaptic phenotypes associated with DVAP-P58S transgenic expression. These data underscore the importance of DVAP–Sac1 interaction in controlling phosphoinositide metabolism and provide mechanistic evidence for a crucial role of phosphoinositide levels in VAP-induced ALS.

Description: The pubertal height growth spurt is a distinctive feature of childhood growth reflecting both the central onset of puberty and local growth factors. Although little is known about the underlying genetics, growth variability during puberty correlates with adult risks for hormone-dependent cancer and adverse cardiometabolic health. The only gene so far associated with pubertal height growth, LIN28B, pleiotropically influences childhood growth, puberty and cancer progression, pointing to shared underlying mechanisms. To discover genetic loci influencing pubertal height and growth and to place them in context of overall growth and maturation, we performed genome-wide association meta-analyses in 18 737 European samples utilizing longitudinally collected height measurements. We found significant associations ( P 〈 1.67 x 10 –8 ) at 10 loci, including LIN28B . Five loci associated with pubertal timing, all impacting multiple aspects of growth. In particular, a novel variant correlated with expression of MAPK3 , and associated both with increased prepubertal growth and earlier menarche. Another variant near ADCY3-POMC associated with increased body mass index, reduced pubertal growth and earlier puberty. Whereas epidemiological correlations suggest that early puberty marks a pathway from rapid prepubertal growth to reduced final height and adult obesity, our study shows that individual loci associating with pubertal growth have variable longitudinal growth patterns that may differ from epidemiological observations. Overall, this study uncovers part of the complex genetic architecture linking pubertal height growth, the timing of puberty and childhood obesity and provides new information to pinpoint processes linking these traits.

Description: Visual refractive errors (REs) are complex genetic traits with a largely unknown etiology. To date, genome-wide association studies (GWASs) of moderate size have identified several novel risk markers for RE, measured here as mean spherical equivalent (MSE). We performed a GWAS using a total of 7280 samples from five cohorts: the Age-Related Eye Disease Study (AREDS); the KORA study (‘Cooperative Health Research in the Region of Augsburg’); the Framingham Eye Study (FES); the Ogliastra Genetic Park-Talana (OGP-Talana) Study and the Multiethnic Study of Atherosclerosis (MESA). Genotyping was performed on Illumina and Affymetrix platforms with additional markers imputed to the HapMap II reference panel. We identified a new genome-wide significant locus on chromosome 16 (rs10500355, P = 3.9 x 10 –9 ) in a combined discovery and replication set (26 953 samples). This single nucleotide polymorphism (SNP) is located within the RBFOX1 gene which is a neuron-specific splicing factor regulating a wide range of alternative splicing events implicated in neuronal development and maturation, including transcription factors, other splicing factors and synaptic proteins.

Description: Small intestinal epithelial cells (sIECs) have a significant share in whole body metabolism as they perform enzymatic digestion and absorption of nutrients. Furthermore, the diet plays a key role in a number of complex diseases including obesity and diabetes. The impact of diet and altered genetic backgrounds on human metabolism may be studied by using computational modeling. A metabolic reconstruction of human sIECs was manually assembled using the literature. The resulting sIEC model was subjected to two different diets to obtain condition-specific metabolic models. Fifty defined metabolic tasks evaluated the functionalities of these models, along with the respective secretion profiles, which distinguished between impacts of different dietary regimes. Under the average American diet, the sIEC model resulted in higher secretion flux for metabolites implicated in metabolic syndrome. In addition, enzymopathies were analyzed in the context of the sIEC metabolism. Computed results were compared with reported gastrointestinal (GI) pathologies and biochemical defects as well as with biomarker patterns used in their diagnosis. Based on our simulations, we propose that (i) sIEC metabolism is perturbed by numerous enzymopathies, which can be used to study cellular adaptive mechanisms specific for such disorders, and in the identification of novel co-morbidities, (ii) porphyrias are associated with both heme synthesis and degradation and (iii) disturbed intestinal gamma-aminobutyric acid synthesis may be linked to neurological manifestations of various enzymopathies. Taken together, the sIEC model represents a comprehensive, biochemically accurate platform for studying the function of sIEC and their role in whole body metabolism.

Description: Large intronic expansions of the triplet-repeat sequence (GAA.TTC) cause transcriptional repression of the Frataxin gene ( FXN ) leading to Friedreich's ataxia (FRDA). We previously found that GAA-triplet expansions stimulate heterochromatinization in vivo in transgenic mice. We report here using chromosome conformation capture (3C) coupled with high-throughput sequencing that the GAA-repeat expansion in FRDA cells stimulates a higher-order structure as a fragment containing the GAA-repeat expansion showed an increased interaction frequency with genomic regions along the FXN locus. This is consistent with a more compacted chromatin and coincided with an increase in both constitutive H3K9me3 and facultative H3K27me3 heterochromatic marks in FRDA. Consistent with this, DNase I accessibility in regions flanking the GAA repeats in patients was decreased compared with healthy controls. Strikingly, this effect could be antagonized with the class III histone deactylase (HDAC) inhibitor vitamin B3 (nicotinamide) which activated the silenced FXN gene in several FRDA models. Examination of the FXN locus revealed a reduction of H3K9me3 and H3K27me3, an increased accessibility to DNase I and an induction of euchromatic H3 and H4 histone acetylations upon nicotinamide treatment. In addition, transcriptomic analysis of nicotinamide treated and untreated FRDA primary lymphocytes revealed that the expression of 67% of genes known to be dysregulated in FRDA was ameliorated by the treatment. These findings show that nictotinamide can up-regulate the FXN gene and reveal a potential mechanism of action for nicotinamide in reactivating the epigenetically silenced FXN gene and therefore support the further assessment of HDAC inhibitors (HDACi's) in FRDA and diseases caused by a similar mechanism.

Description: Neuronal ceroid lipofuscinosis (NCL), commonly referred to as Batten disease, is a group of autosomal recessive neurodegenerative diseases of childhood characterized by seizures, blindness, motor and cognitive decline and premature death. Currently, there are over 400 known mutations in 14 different genes, leading to five overlapping clinical variants of NCL. A large portion of these mutations lead to premature stop codons (PTCs) and are predicted to predispose mRNA transcripts to nonsense-mediated decay (NMD). Nonsense-mediated decay is associated with a number of other genetic diseases and is an important regulator of disease pathogenesis. We contend that NMD targets PTCs in NCL gene transcripts for degradation. A number of PTC mutations in CLN1 , CLN2 and CLN3 lead to a significant decrease in mRNA transcripts and a corresponding decrease in protein levels and function in patient-derived lymphoblast cell lines. Inhibiting NMD leads to an increased transcript level, and where protein function is known, increased activity. Treatment with read-through drugs also leads to increased protein function. Thus, NMD provides a promising therapeutic target that would allow read-through of transcripts to enhance protein function and possibly ameliorate Batten disease pathogenesis.

Description: Megacity impacts on regional ozone formation: observations and WRF-Chem modeling for the MIRAGE-Shanghai field campaign Atmospheric Chemistry and Physics, 13, 5655-5669, 2013 Author(s): X. Tie, F. Geng, A. Guenther, J. Cao, J. Greenberg, R. Zhang, E. Apel, G. Li, A. Weinheimer, J. Chen, and C. Cai The MIRAGE-Shanghai experiment was designed to characterize the factors controlling regional air pollution near a Chinese megacity (Shanghai) and was conducted during September 2009. This paper provides information on the measurements conducted for this study. In order to have some deep analysis of the measurements, a regional chemical/dynamical model (version 3 of Weather Research and Forecasting Chemical model – WRF-Chemv3) is applied for this study. The model results are intensively compared with the measurements to evaluate the model capability for calculating air pollutants in the Shanghai region, especially the chemical species related to ozone formation. The results show that the model is able to calculate the general distributions (the level and the variability) of air pollutants in the Shanghai region, and the differences between the model calculation and the measurement are mostly smaller than 30%, except the calculations of HONO (nitrous acid) at PD (Pudong) and CO (carbon monoxide) at DT (Dongtan). The main scientific focus is the study of ozone chemical formation not only in the urban area, but also on a regional scale of the surrounding area of Shanghai. The results show that during the experiment period, the ozone photochemical formation was strongly under the VOC (volatile organic compound)-limited condition in the urban area of Shanghai. Moreover, the VOC-limited condition occurred not only in the city, but also in the larger regional area. There was a continuous enhancement of ozone concentrations in the downwind of the megacity of Shanghai, resulting in a significant enhancement of ozone concentrations in a very large regional area in the surrounding region of Shanghai. The sensitivity study of the model suggests that there is a threshold value for switching from VOC-limited condition to NO x (nitric oxide and nitrogen dioxide)-limited condition. The threshold value is strongly dependent on the emission ratio of NO x / VOCs. When the ratio is about 0.4, the Shanghai region is under a strong VOC-limited condition over the regional scale. In contrast, when the ratio is reduced to about 0.1, the Shanghai region is under a strong NO x -limited condition. The estimated threshold value (on the regional scale) for switching from VOC-limited to NO x -limited condition ranges from 0.1 to 0.2. This result has important implications for ozone production in this region and will facilitate the development of effective O 3 control strategies in the Shanghai region.

Description: Estimate of surface direct radiative forcing of desert dust from atmospheric modulation of the aerosol optical depth Atmospheric Chemistry and Physics, 13, 5647-5654, 2013 Author(s): A. di Sarra, D. Fuà, and D. Meloni Measurements carried out on the island of Lampedusa, in the central Mediterranean, on 7 September 2005, show the occurrence of a quasi-periodic oscillation of aerosol optical depth, column water vapour, and surface irradiance in different spectral bands. The oscillation has a period of about 13 min and is attributed to the propagation of a gravity wave able to modify the vertical structure of the planetary boundary layer, as also confirmed by satellite images. The wave occurred during a Saharan dust event. The oscillation amplitude is about 0.1 for the aerosol optical depth, and about 0.4 cm for the column water vapour. The modulation of the downward surface irradiances is in opposition of phase with respect to aerosol optical depth and water vapour column variations. The perturbation of the downward irradiance produced by the aerosols is determined by comparing the measured irradiances with estimated irradiances at a fixed value of the aerosol optical depth, and by correcting for the effect of the water vapour in the shortwave spectral range. The direct radiative forcing efficiency, i.e., the radiative perturbation of the net surface irradiance produced by a unit of optical depth aerosol layer, is determined at different solar zenith angles as the slope of the irradiance perturbation versus the aerosol optical depth. The estimated direct surface forcing efficiency at about 60° solar zenith angle is −(181 ± 17) W m −2 in the shortwave, and −(83 ± 7) W m −2 in the photosynthetic spectral range. The estimated daily average forcing efficiencies are of about −79 and −46 W m −2 for the shortwave and photosynthetic spectral range, respectively.

Description: On the "well-mixed" assumption and numerical 2-D tracing of atmospheric moisture Atmospheric Chemistry and Physics, 13, 5567-5585, 2013 Author(s): H. F. Goessling and C. H. Reick Atmospheric water vapour tracers (WVTs) are an elegant tool to determine source–sink relations of moisture "online" in atmospheric general circulation models (AGCMs). However, it is sometimes desirable to establish such relations "offline" based on already existing atmospheric data (e.g. reanalysis data). One simple and frequently applied offline method is 2-D moisture tracing. It makes use of the "well-mixed" assumption, which allows for treating the vertical dimension integratively. Here we scrutinise the "well-mixed" assumption and 2-D moisture tracing by means of analytical considerations in combination with AGCM-WVT simulations. We find that vertically well-mixed conditions are seldom met. Due to the presence of vertical inhomogeneities, 2-D moisture tracing (i) neglects a significant degree of fast-recycling, and (ii) results in erroneous advection where the direction of the horizontal winds varies vertically. The latter is not so much the case in the extratropics, but in the tropics this can lead to large errors. For example, computed by 2-D moisture tracing, the fraction of precipitation in the western Sahel that originates from beyond the Sahara is ~40%, whereas the fraction that originates from the tropical and Southern Atlantic is only ~4%. According to full (i.e. 3-D) moisture tracing, however, both regions contribute roughly equally, showing that the errors introduced by the 2-D approximation can be substantial.

Description: Southern hemispheric halon trends and global halon emissions, 1978–2011 Atmospheric Chemistry and Physics, 13, 5551-5565, 2013 Author(s): M. J. Newland, C. E. Reeves, D. E. Oram, J. C. Laube, W. T. Sturges, C. Hogan, P. Begley, and P. J. Fraser The atmospheric records of four halons, H-1211 (CBrClF 2 ), H-1301 (CBrF 3 ), H-2402 (CBrF 2 CBrF 2 ) and H-1202 (CBr 2 F 2 ), measured from air collected at Cape Grim, Tasmania, between 1978 and 2011, are reported. Mixing ratios of H-1211, H-2402 and H-1202 began to decline in the early to mid-2000s, but those of H-1301 continue to increase up to mid-2011. These trends are compared to those reported by NOAA (National Oceanic and Atmospheric Administration) and AGAGE (Advanced Global Atmospheric Experiment). The observations suggest that the contribution of the halons to total tropospheric bromine at Cape Grim has begun to decline from a peak in 2008 of about 8.1 ppt. An extrapolation of halon mixing ratios to 2060, based on reported banks and predicted release factors, shows this decline becoming more rapid in the coming decades, with a contribution to total tropospheric bromine of about 3 ppt in 2060. Top-down global annual emissions of the halons were derived using a two-dimensional atmospheric model. The emissions of all four have decreased since peaking in the late 1980s–mid-1990s, but this decline has slowed recently, particularly for H-1301 and H-2402 which have shown no decrease in emissions over the past five years. The UEA (University of East Anglia) top-down model-derived emissions are compared to those reported using a top-down approach by NOAA and AGAGE and the bottom-up estimates of HTOC (Halons Technical Options Committee). The implications of an alternative set of steady-state atmospheric lifetimes are discussed. Using a lifetime of 14 yr or less for H-1211 to calculate top-down emissions estimates would lead to small, or even negative, estimated banks given reported production data. Finally emissions of H-1202, a product of over-bromination during the production process of H-1211, have continued despite reported production of H-1211 ceasing in 2010. This raises questions as to the source of these H-1202 emissions.

Description: Impacts of aircraft emissions on the air quality near the ground Atmospheric Chemistry and Physics, 13, 5505-5522, 2013 Author(s): H. Lee, S. C. Olsen, D. J. Wuebbles, and D. Youn The continuing increase in demand for commercial aviation transport raises questions about the effects of resulting emissions on the environment. The purpose of this study is to investigate, using a global chemistry transport model, to what extent aviation emissions outside the boundary layer influence air quality in the boundary layer. The large-scale effects of current levels of aircraft emissions were studied through comparison of multiple simulations allowing for the separated effects of aviation emissions occurring in the low, middle and upper troposphere. We show that emissions near cruise altitudes (9–11 km in altitude) rather than emissions during landing and take-off are responsible for most of the total odd-nitrogen (NO y ), ozone (O 3 ) and aerosol perturbations near the ground with a noticeable seasonal difference. Overall, the perturbations of these species are smaller than 1 ppb even in winter when the perturbations are greater than in summer. Based on the widely used air quality standards and uncertainty of state-of-the-art models, we conclude that aviation-induced perturbations have a negligible effect on air quality even in areas with heavy air traffic. Aviation emissions lead to a less than 1% aerosol enhancement in the boundary layer due to a slight increase in ammonium nitrate (NH 4 NO 3 ) during cold seasons and a statistically insignificant aerosol perturbation in summer. In addition, statistical analysis using probability density functions, Hellinger distance, and p value indicate that aviation emissions outside the boundary layer do not affect the occurrence of extremely high aerosol concentrations in the boundary layer. An additional sensitivity simulation assuming the doubling of surface ammonia emissions demonstrates that the aviation induced aerosol increase near the ground is highly dependent on background ammonia concentrations whose current range of uncertainty is large.

Description: Otitis media with effusion (OME) is the most common cause of hearing loss in children and tympanostomy to alleviate the condition remains the commonest surgical intervention in children in the developed world. Chronic and recurrent forms of OM are known to have a very significant genetic component, however, until recently little was known of the underlying genes involved. The identification of mouse models of chronic OM has indicated a role of transforming growth factor beta (TGFβ) signalling and its impact on responses to hypoxia in the inflamed middle ear. We have, therefore, investigated the role of TGFβ signalling and identified and characterized a new model of chronic OM carrying a mutation in the gene for transforming growth interacting factor 1 ( Tgif1 ). Tgif1 homozygous mutant mice have significantly raised auditory thresholds due to a conductive deafness arising from a chronic effusion starting at around 3 weeks of age. The OM is accompanied by a significant thickening of the middle ear mucosa lining, expansion of mucin-secreting goblet cell populations and raised levels of vascular endothelial growth factor, TNF-α and IL-1β in ear fluids. We also identified downstream effects on TGFβ signalling in middle ear epithelia at the time of development of chronic OM. Both phosphorylated SMAD2 and p21 levels were lowered in the homozygous mutant, demonstrating a suppression of the TGFβ pathway. The identification and characterization of the Tgif mutant supports the role of TGFβ signalling in the development of chronic OM and provides an important candidate gene for genetic studies in the human population.

Description: Mutations in the epithelial cell adhesion molecule (EpCAM; CD326) gene are causal for congenital tufting enteropathy (CTE), a disease characterized by intestinal abnormalities resulting in lethal diarrhea in newborns. Why the different mutations all lead to the same disease is not clear. Here, we report that most mutations, including a novel intronic variant, will result in lack of EpCAM's transmembrane domain, whereas two mutations allow transmembrane localization. We find that these mutants are not routed to the plasma membrane, and that truncated mutants are secreted or degraded. Thus, all epcam mutations lead to loss of cell-surface EpCAM, resulting in CTE.

Description: Rett syndrome (RTT), an X-linked postnatal disorder, results from mutations in Methyl CpG-binding protein 2 ( MECP2 ). Survival and breathing in Mecp2 NULL/Y animals are improved by an N-terminal tripeptide of insulin-like growth factor I (IGF-I) treatment. We determined that Mecp2 NULL/Y animals also have a metabolic syndrome and investigated whether IGF-I treatment might improve this phenotype. Mecp2 NULL/Y mice were treated with a full-length IGF-I modified with the addition of polyethylene glycol (PEG-IGF-I), which improves pharmacological properties. Low-dose PEG-IGF-I treatment slightly improved lifespan and heart rate in Mecp2 NULL/Y mice; however, high-dose PEG-IGF-I decreased lifespan. To determine whether insulinotropic off-target effects of PEG-IGF-I caused the detrimental effect, we treated Mecp2 NULL/Y mice with insulin, which also decreased lifespan. Thus, the clinical benefit of IGF-I treatment in RTT may critically depend on the dose used, and caution should be taken when initiating clinical trials with these compounds because the beneficial therapeutic window is narrow.

Description: Abnormal metabolism of the tau protein is central to the pathogenesis of a number of dementias, including Alzheimer's disease. Aberrant alternative splicing of exon 10 in the tau pre-mRNA resulting in an imbalance of tau isoforms is one of the molecular causes of the inherited tauopathy, FTDP-17. We showed previously in heterologous systems that exon 10 inclusion in tau mRNA could be modulated by spliceosome-mediated RNA trans -splicing (SMaRT). Here, we evaluated the potential of trans -splicing RNA reprogramming to correct tau mis-splicing in differentiated neurons in a mouse model of tau mis-splicing, the htau transgenic mouse line, expressing the human MAPT gene in a null mouse Mapt background. Trans -splicing molecules designed to increase exon 10 inclusion were delivered to neurons using lentiviral vectors. We demonstrate reprogramming of tau transcripts at the RNA level after transduction of cultured neurons or after direct delivery and long-term expression of viral vectors into the brain of htau mice in vivo . Tau RNA trans -splicing resulted in an increase in exon 10 inclusion in the mature tau mRNA. Importantly, we also show that the trans -spliced product is translated into a full-length chimeric tau protein. These results validate the potential of SMaRT to correct tau mis-splicing and provide a framework for its therapeutic application to neurodegenerative conditions linked to aberrant RNA processing.

Description: Proper function of the motor unit is dependent upon the correct development of dendrites and axons. The infant/childhood onset motoneuron disease spinal muscular atrophy (SMA), caused by low levels of the survival motor neuron (SMN) protein, is characterized by muscle denervation and paralysis. Although different SMA models have shown neuromuscular junction defects and/or motor axon defects, a comprehensive analysis of motoneuron development in vivo under conditions of low SMN will give insight into why the motor unit becomes dysfunctional. We have generated genetic mutants in zebrafish expressing low levels of SMN from the earliest stages of development. Analysis of motoneurons in these mutants revealed motor axons were often shorter and had fewer branches. We also found that motoneurons had significantly fewer dendritic branches and those present were shorter. Analysis of motor axon filopodial dynamics in live embryos revealed that mutants had fewer filopodia and their average half-life was shorter. To determine when SMN was needed to rescue motoneuron development, SMN was conditionally induced in smn mutants during embryonic stages. Only when SMN was added back soon after motoneurons were born, could later motor axon development be rescued. Importantly, analysis of motor behavior revealed that animals with motor axon defects had significant deficits in motor output. We also show that SMN is required earlier for motoneuron development than for survival. These data support that SMN is needed early in development of motoneuron dendrites and axons to develop normally and that this is essential for proper connectivity and movement.

Description: Environmental factors including ionizing radiation and chemical agents have been known to be able to induce DNA rearrangements and cause genomic structural variations (SVs); however, the roles of intrinsic characteristics of the human genome, such as regional genome architecture, in SV formation and the potential mechanisms underlying genomic instability remain to be further elucidated. Recently, locus-specific observations showed that ‘self-chain’ (SC), a group of short low-copy repeats (LCRs) in the human genome, can induce autism-associated SV mutations of the MECP2 and NRXN1 genes. In this study, we conducted a genome-wide analysis to investigate SCs and their potential roles in genomic SV formation. Utilizing a vast amount of human SV data, we observed a significant biased distribution of human germline SV breakpoints to SC regions. Notably, the breakpoint distribution pattern is different between SV types across deletion, duplication, inversion and insertion. Our observations were coincident with a mechanism of SC-induced DNA replicative errors, whereas SC may sporadically be used as substrates of nonallelic homologous recombination (NAHR). This contention was further supported by our consistent findings in somatic SV mutations of cancer genomes, suggesting a general mechanism of SC-induced genome instability in human germ and somatic cells.

Description: Mowat–Wilson syndrome (MWS) is a severe intellectual disability (ID)-distinctive facial gestalt-multiple congenital anomaly syndrome, commonly associating microcephaly, epilepsy, corpus callosum agenesis, conotruncal heart defects, urogenital malformations and Hirschsprung disease (HSCR). MWS is caused by de novo heterozygous mutations in the ZEB2 gene. The majority of mutations lead to haplo-insufficiency through premature stop codons or large gene deletions. Only three missense mutations have been reported so far; none of which resides in a known functional domain of ZEB2. In this study, we report and analyze the functional consequences of three novel missense mutations, p.Tyr1055Cys, p.Ser1071Pro and p.His1045Arg, identified in the highly conserved C-zinc-finger (C-ZF) domain of ZEB2 . Patients' phenotype included the facial gestalt of MWS and moderate ID, but no microcephaly, heart defects or HSCR. In vitro studies showed that all the three mutations prevented binding and repression of the E-cadherin promoter, a characterized ZEB2 target gene. Taking advantage of the zebrafish morphant technology, we performed rescue experiments using wild-type (WT) and mutant human ZEB2 mRNAs. Variable, mutation-dependent, embryo rescue, correlating with the severity of patients' phenotype, was observed. Our data provide evidence that these missense mutations cause a partial loss of function of ZEB2, suggesting that its role is not restricted to repression of E-cadherin. Functional domains other than C-ZF may play a role in early embryonic development. Finally, these findings broaden the clinical spectrum of ZEB2 mutations, indicating that MWS ought to be considered in patients with lesser degrees of ID and a suggestive facial gestalt, even in the absence of congenital malformation.

Description: Mutations in the gene encoding Fused in Sarcoma ( FUS ) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. FUS is a predominantly nuclear DNA- and RNA-binding protein that is involved in RNA processing. Large FUS-immunoreactive inclusions fill the perikaryon of surviving motor neurons of ALS patients carrying mutations at post-mortem. This sequestration of FUS is predicted to disrupt RNA processing and initiate neurodegeneration. Here, we demonstrate that C-terminal ALS mutations disrupt the nuclear localizing signal (NLS) of FUS resulting in cytoplasmic accumulation in transfected cells and patient fibroblasts. FUS mislocalization is rescued by the addition of the wild-type FUS NLS to mutant proteins. We also show that oxidative stress recruits mutant FUS to cytoplasmic stress granules where it is able to bind and sequester wild-type FUS. While FUS interacts with itself directly by protein–protein interaction, the recruitment of FUS to stress granules and interaction with PABP are RNA dependent. These findings support a two-hit hypothesis, whereby cytoplasmic mislocalization of FUS protein, followed by cellular stress, contributes to the formation of cytoplasmic aggregates that may sequester FUS, disrupt RNA processing and initiate motor neuron degeneration.

Description: Genome-wide association studies (GWASs) have identified multiple common genetic variants associated with an increased risk of testicular germ cell tumors (TGCTs). A previous GWAS reported a possible TGCT susceptibility locus on chromosome 1q23 in the UCK2 gene, but failed to reach genome-wide significance following replication. We interrogated this region by conducting a meta-analysis of two independent GWASs including a total of 940 TGCT cases and 1559 controls for 122 single-nucleotide polymorphisms (SNPs) on chromosome 1q23 and followed up the most significant SNPs in an additional 2202 TGCT cases and 2386 controls from four case–control studies. We observed genome-wide significant associations for several UCK2 markers, the most significant of which was for rs3790665 ( P Combined = 6.0 x 10 –9 ). Additional support is provided from an independent familial study of TGCT where a significant over-transmission for rs3790665 with TGCT risk was observed ( P FBAT = 2.3 x 10 –3 ). Here, we provide substantial evidence for the association between UCK2 genetic variation and TGCT risk.

Description: Corrigendum to "Tropospheric NO 2 vertical column densities over Beijing: results of the first three years of ground-based MAX-DOAS measurements (2008–2011) and satellite validation" published in Atmos. Chem. Phys., 13, 1547–1567, 2013 Atmospheric Chemistry and Physics, 13, 5629-5629, 2013 Author(s): J. Z. Ma, S. Beirle, J. L. Jin, R. Shaiganfar, P. Yan, and T. Wagner No abstract available.

Description: Large-eddy simulation of organized precipitating trade wind cumulus clouds Atmospheric Chemistry and Physics, 13, 5631-5645, 2013 Author(s): A. Seifert and T. Heus Trade wind cumulus clouds often organize in along-wind cloud streets and across-wind mesoscale arcs. We present a benchmark large-eddy simulation which resolves the individual clouds as well as the mesoscale organization on scales of O(10 km). Different methods to quantify organization of cloud fields are applied and discussed. Using perturbed physics large-eddy simulation experiments, the processes leading to the formation of cloud clusters and the mesoscale arcs are revealed. We find that both cold pools as well as the sub-cloud layer moisture field are crucial to understand the organization of precipitating shallow convection. Further sensitivity studies show that microphysical assumptions can have a pronounced impact on the onset of cloud organization.

Description: Investigation of gaseous and particulate emissions from various marine vessel types measured on the banks of the Elbe in Northern Germany Atmospheric Chemistry and Physics, 13, 3603-3618, 2013 Author(s): J.-M. Diesch, F. Drewnick, T. Klimach, and S. Borrmann Measurements of the ambient aerosol, various trace gases and meteorological quantities using a mobile laboratory (MoLa) were performed on the banks of the Lower Elbe in an emission control area (ECA) which is passed by numerous private and commercial marine vessels reaching and leaving the port of Hamburg, Germany. From 25–29 April 2011 a total of 178 vessels were probed at a distance of about 0.8–1.2 km with high temporal resolution. 139 ship emission plumes were of sufficient quality to be analyzed further and to determine emission factors (EFs). Concentrations of aerosol number and mass as well as polycyclic aromatic hydrocarbons (PAH) and black carbon were measured in PM 1 and size distribution instruments covered the diameter range from 6 nm up to 32 μm. The chemical composition of the non-refractory submicron aerosol was measured by means of an Aerosol Mass Spectrometer (Aerodyne HR-ToF-AMS). Gas phase species analyzers monitored various trace gases (O 3 , SO 2 , NO, NO 2 , CO 2 ) in the air and a weather station provided wind, precipitation, solar radiation data and other quantities. Together with ship information for each vessel obtained from Automatic Identification System (AIS) broadcasts a detailed characterization of the individual ship types and of features affecting gas and particulate emissions is provided. Particle number EFs (average 2.6 e +16 # kg −1 ) and PM 1 mass EFs (average 2.4 g kg −1 ) tend to increase with the fuel sulfur content. Observed PM 1 composition of the vessel emissions was dominated by organic matter (72%), sulfate (22%) and black carbon (6%) while PAHs only account for 0.2% of the submicron aerosol mass. Measurements of gaseous components showed an increase of SO 2 (average EF: 7.7 g kg −1 ) and NO x (average EF: 53 g kg −1 ) while O 3 decreased when a ship plume reached the sampling site. The particle number size distributions of the vessels are generally characterized by a bimodal size distribution, with the nucleation mode in the 10–20 nm diameter range and a combustion aerosol mode centered at about 35 nm while particles \textgreater 1 μm were not found. "High particle number emitters" are characterized by a dominant nucleation mode. By contrast, increased particle concentrations around 150 nm primarily occurred for "high black carbon emitters". Classifying the vessels according to their gross tonnage shows a decrease of the number, black carbon and PAH EFs while EFs of SO 2 , NO, NO 2 , NO x , AMS species (particulate organics, sulfate) and PM 1 mass concentration increase with increasing gross tonnages.

Description: Modeling of daytime HONO vertical gradients during SHARP 2009 Atmospheric Chemistry and Physics, 13, 3587-3601, 2013 Author(s): K. W. Wong, C. Tsai, B. Lefer, N. Grossberg, and J. Stutz Nitrous acid (HONO) acts as a major precursor of the hydroxyl radical (OH) in the urban atmospheric boundary layer in the morning and throughout the day. Despite its importance, HONO formation mechanisms are not yet completely understood. It is generally accepted that conversion of NO 2 on surfaces in the presence of water is responsible for the formation of HONO in the nocturnal boundary layer, although the type of surface on which the mechanism occurs is still under debate. Recent observations of higher than expected daytime HONO concentrations in both urban and rural areas indicate the presence of unknown daytime HONO source(s). Various formation pathways in the gas phase, and on aerosol and ground surfaces have been proposed to explain the presence of daytime HONO. However, it is unclear which mechanism dominates and, in the cases of heterogeneous mechanisms, on which surfaces they occur. Vertical concentration profiles of HONO and its precursors can help in identifying the dominant HONO formation pathways. In this study, daytime HONO and NO 2 vertical profiles, measured in three different height intervals (20–70, 70–130, and 130–300 m) in Houston, TX, during the 2009 Study of Houston Atmospheric Radical Precursors (SHARP) are analyzed using a one-dimensional (1-D) chemistry and transport model. Model results with various HONO formation pathways suggested in the literature are compared to the the daytime HONO and HONO/NO 2 ratios observed during SHARP. The best agreement of HONO and HONO/NO 2 ratios between model and observations is achieved by including both a photolytic source of HONO at the ground and on the aerosol. Model sensitivity studies show that the observed diurnal variations of the HONO/NO 2 ratio are not reproduced by the model if there is only a photolytic HONO source on aerosol or in the gas phase from NO 2 * + H 2 O. Further analysis of the formation and loss pathways of HONO shows a vertical dependence of HONO chemistry during the day. Photolytic HONO formation at the ground is the major formation pathway in the lowest 20 m, while a combination of gas-phase, photolytic formation on aerosol, and vertical transport is responsible for daytime HONO between 200–300 m a.g.l. HONO removal is dominated by vertical transport below 20 m and photolysis between 200–300 m a.g.l.

Description: Antarctic new particle formation from continental biogenic precursors Atmospheric Chemistry and Physics, 13, 3527-3546, 2013 Author(s): E.-M. Kyrö, V.-M. Kerminen, A. Virkkula, M. Dal Maso, J. Parshintsev, J. Ruíz-Jimenez, L. Forsström, H. E. Manninen, M.-L. Riekkola, P. Heinonen, and M. Kulmala Over Antarctica, aerosol particles originate almost entirely from marine areas, with minor contribution from long-range transported dust or anthropogenic material. The Antarctic continent itself, unlike all other continental areas, has been thought to be practically free of aerosol sources. Here we present evidence of local aerosol production associated with melt-water ponds in continental Antarctica. We show that in air masses passing such ponds, new aerosol particles are efficiently formed and these particles grow up to sizes where they may act as cloud condensation nuclei (CCN). The precursor vapours responsible for aerosol formation and growth originate very likely from highly abundant cyanobacteria Nostoc commune (Vaucher) communities of local ponds. This is the first time freshwater vegetation has been identified as an aerosol precursor source. The influence of the new source on clouds and climate may increase in future Antarctica, and possibly elsewhere undergoing accelerating summer melting of semi-permanent snow cover.

Description: The influence of snow grain size and impurities on the vertical profiles of actinic flux and associated NO x emissions on the Antarctic and Greenland ice sheets Atmospheric Chemistry and Physics, 13, 3547-3567, 2013 Author(s): M. C. Zatko, T. C. Grenfell, B. Alexander, S. J. Doherty, J. L. Thomas, and X. Yang We use observations of the absorption properties of black carbon and non-black carbon impurities in near-surface snow collected near the research stations at South Pole and Dome C, Antarctica, and Summit, Greenland, combined with a snowpack actinic flux parameterization to estimate the vertical profile and e-folding depth of ultraviolet/near-visible (UV/near-vis) actinic flux in the snowpack at each location. We have developed a simple and broadly applicable parameterization to calculate depth and wavelength dependent snowpack actinic flux that can be easily integrated into large-scale (e.g., 3-D) models of the atmosphere. The calculated e-folding depths of actinic flux at 305 nm, the peak wavelength of nitrate photolysis in the snowpack, are 8–12 cm near the stations and 15–31 cm away (〉11 km) from the stations. We find that the e-folding depth is strongly dependent on impurity content and wavelength in the UV/near-vis region, which explains the relatively shallow e-folding depths near stations where local activities lead to higher snow impurity levels. We calculate the lifetime of NO x in the snowpack interstitial air produced by photolysis of snowpack nitrate against wind pumping (τ wind pumping ) from the snowpack, and compare this to the calculated lifetime of NO x against chemical conversion to HNO 3 (τ chemical ) to determine whether the NO x produced at a given depth can escape from the snowpack to the overlying atmosphere. Comparison of τ wind pumping and τ chemical suggests efficient escape of photoproduced NO x in the snowpack to the overlying atmosphere throughout most of the photochemically active zone. Calculated vertical actinic flux profiles and observed snowpack nitrate concentrations are used to estimate the potential flux of NO x from the snowpack. Calculated NO x fluxes of 4.4 × 10 8 –3.8 × 10 9 molecules cm −2 s −1 in remote polar locations and 3.2–8.2 × 10 8 molecules cm −2 s −1 near polar stations for January at Dome C and South Pole and June at Summit suggest that NO x flux measurements near stations may be underestimating the amount of NO x emitted from the clean polar snowpack.

Description: The relative importance of impacts from climate change vs. emissions change on air pollution levels in the 21st century Atmospheric Chemistry and Physics, 13, 3569-3585, 2013 Author(s): G. B. Hedegaard, J. H. Christensen, and J. Brandt So far several studies have analysed the impacts of climate change on future air pollution levels. Significant changes due to impacts of climate change have been made clear. Nevertheless, these changes are not yet included in national, regional or global air pollution reduction strategies. The changes in future air pollution levels are caused by both impacts from climate change and anthropogenic emission changes, the importance of which needs to be quantified and compared. In this study we use the Danish Eulerian Hemispheric Model (DEHM) driven by meteorological input data from the coupled Atmosphere-Ocean General Circulation Model ECHAM5/MPI-OM and forced with the newly developed RCP4.5 emissions. The relative importance of the climate signal and the signal from changes in anthropogenic emissions on the future ozone, black carbon (BC), total particulate matter with a diameter below 2.5 μm (total PM 2.5 including BC, primary organic carbon (OC), mineral dust and secondary inorganic aerosols (SIA)) and total nitrogen (including NH x + NO y ) has been determined. For ozone, the impacts of anthropogenic emissions dominate, though a climate penalty is found in the Arctic region and northwestern Europe, where the signal from climate change dampens the effect from the projected emission reductions of anthropogenic ozone precursors. The investigated particles are even more dominated by the impacts from emission changes. For black carbon the emission signal dominates slightly at high latitudes, with an increase up to an order of magnitude larger, close to the emission sources in temperate and subtropical areas. Including all particulate matter with a diameter below 2.5 μm (total PM 2.5 ) enhances the dominance from emissions change. In contrast, total nitrogen (NH x + NO y ) in parts of the Arctic and at low latitudes is dominated by impacts of climate change.

Description: Pollution transport from North America to Greenland during summer 2008 Atmospheric Chemistry and Physics, 13, 3825-3848, 2013 Author(s): J. L. Thomas, J.-C. Raut, K. S. Law, L. Marelle, G. Ancellet, F. Ravetta, J. D. Fast, G. Pfister, L. K. Emmons, G. S. Diskin, A. Weinheimer, A. Roiger, and H. Schlager Ozone pollution transported to the Arctic is a significant concern because of the rapid, enhanced warming in high northern latitudes, which is caused, in part, by short-lived climate forcers, such as ozone. Long-range transport of pollution contributes to background and episodic ozone levels in the Arctic. However, the extent to which plumes are photochemically active during transport, particularly during the summer, is still uncertain. In this study, regional chemical transport model simulations are used to examine photochemical production of ozone in air masses originating from boreal fire and anthropogenic emissions over North America and during their transport toward the Arctic during early July 2008. Model results are evaluated using POLARCAT aircraft data collected over boreal fire source regions in Canada (ARCTAS-B) and several days downwind over Greenland (POLARCAT-France and POLARCAT-GRACE). Model results are generally in good agreement with the observations, except for certain trace gas species over boreal fire regions, in some cases indicating that the fire emissions are too low. Anthropogenic and biomass burning pollution (BB) from North America was rapidly uplifted during transport east and north to Greenland where pollution plumes were observed in the mid- and upper troposphere during POLARCAT. A model sensitivity study shows that CO levels are in better agreement with POLARCAT measurements (fresh and aged fire plumes) upon doubling CO emissions from fires. Analysis of model results, using ΔO 3 /ΔCO enhancement ratios, shows that pollution plumes formed ozone during transport towards the Arctic. Fresh anthropogenic plumes have average ΔO 3 /ΔCO enhancement ratios of 0.63 increasing to 0.92 for aged anthropogenic plumes, indicating additional ozone production during aging. Fresh fire plumes are only slightly enhanced in ozone (ΔO 3 /ΔCO=0.08), but form ozone downwind with ΔO 3 /ΔCO of 0.49 for aged BB plumes (model-based run). We estimate that aged anthropogenic and BB pollution together made an important contribution to ozone levels with an average contribution for latitudes 〉55° N of up to 6.5 ppbv (18%) from anthropogenic pollution and 3 ppbv (5.2%) from fire pollution in the model domain in summer 2008.

Description: Validation of an hourly resolved global aerosol model in answer to solar electricity generation information needs Atmospheric Chemistry and Physics, 13, 3777-3791, 2013 Author(s): M. Schroedter-Homscheidt and A. Oumbe Solar energy applications need global aerosol optical depth (AOD) information to derive historic surface solar irradiance databases from geostationary meteorological satellites reaching back to the 1980's. This paper validates the MATCH/DLR model originating in the climate community against AERONET ground measurements. Hourly or daily mean AOD model output is evaluated individually for all stations in Europe, Africa and the Middle East – an area highly interesting for solar energy applications being partly dominated by high aerosol loads. Overall, a bias of 0.02 and a root-mean-square error (RMSE) of 0.23 are found for daily mean AOD values, while the RMSE increases to 0.28 for hourly mean AOD values. Large differences between various regions and stations are found providing a feedback loop for the aerosol modelling community. The difference in using daily means versus hourly resolved modelling with respect to hourly resolved observations is evaluated. Nowadays state-of-the-art in solar resource assessment relies on monthly turbidity or AOD climatologies while at least hourly resolved irradiance time series are needed by the solar sector. Therefore, the contribution of higher temporally modelled AOD is evaluated.

Description: Montreal Protocol Benefits simulated with CCM SOCOL Atmospheric Chemistry and Physics, 13, 3811-3823, 2013 Author(s): T. Egorova, E. Rozanov, J. Gröbner, M. Hauser, and W. Schmutz Ozone depletion is caused by the anthropogenic increase of halogen-containing species in the atmosphere, which results in the enhancement of the concentration of reactive chlorine and bromine in the stratosphere. To reduce the influence of anthropogenic ozone-depleting substances (ODS), the Montreal Protocol was agreed by Governments in 1987, with several Amendments and Adjustments adopted later. In order to assess the benefits of the Montreal Protocol and its Amendments and Adjustments (MPA) on ozone and UV radiation, two different runs of the chemistry-climate model (CCM) SOCOL have been carried out. The first run was driven by the emission of ozone depleting substances (ODS) prescribed according to the restrictions of the MPA. For the second run we allow the ODS to grow by 3% annually. We find that the MPA would have saved up to 80% of the global annual total ozone by the end of the 21st century. Our calculations also show substantial changes of the stratospheric circulation pattern as well as in surface temperature and precipitations that could occur in the world without MPA implementations. To illustrate the changes in UV radiation at the surface and to emphasise certain features, which can only be seen for some particular regions if the influence of the cloud cover changes is accounted for, we calculate geographical distribution of the erythemally weighted irradiance ( E ery ). For the no Montreal Protocol simulation E ery increases by factor of 4 to 16 between the 1970s and 2100. For the scenario including the Montreal Protocol it is found that UV radiation starts to decrease in 2000, with continuous decline of 5% to 10% at middle latitudes in the both Northern and Southern Hemispheres.

Description: CLARA-SAL: a global 28 yr timeseries of Earth's black-sky surface albedo Atmospheric Chemistry and Physics, 13, 3743-3762, 2013 Author(s): A. Riihelä, T. Manninen, V. Laine, K. Andersson, and F. Kaspar We present a novel 28 yr dataset of Earth's black-sky surface albedo, derived from AVHRR instruments. The dataset is created using algorithms to separately derive the surface albedo for different land use areas globally. Snow, sea ice, open water and vegetation are all treated independently. The product features corrections for the atmospheric effect in satellite-observed surface radiances, a BRDF correction for the anisotropic reflectance properties of natural surfaces, and a novel topography correction of geolocation and radiometric accuracy of surface reflectance observations over mountainous areas. The dataset is based on a homogenized AVHRR radiance timeseries. The product is validated against quality-controlled in situ observations of clear-sky surface albedo at various BSRN sites around the world. Snow and ice albedo retrieval validation is given particular attention using BSRN sites over Antarctica, Greenland Climate Network stations on the Greenland Ice Sheet (GrIS), as well as sea ice albedo data from the SHEBA and Tara expeditions. The product quality is found to be comparable to other previous long-term surface albedo datasets from AVHRR.

Description: Spectral albedo of seasonal snow during intensive melt period at Sodankylä, beyond the Arctic Circle Atmospheric Chemistry and Physics, 13, 3793-3810, 2013 Author(s): O. Meinander, S. Kazadzis, A. Arola, A. Riihelä, P. Räisänen, R. Kivi, A. Kontu, R. Kouznetsov, M. Sofiev, J. Svensson, H. Suokanerva, V. Aaltonen, T. Manninen, J.-L. Roujean, and O. Hautecoeur We have measured spectral albedo, as well as ancillary parameters, of seasonal European Arctic snow at Sodankylä, Finland (67°22' N, 26°39' E). The springtime intensive melt period was observed during the Snow Reflectance Transition Experiment (SNORTEX) in April 2009. The upwelling and downwelling spectral irradiance, measured at 290–550 nm with a double monochromator spectroradiometer, revealed albedo values of ~0.5–0.7 for the ultraviolet and visible range, both under clear sky and variable cloudiness. During the most intensive snowmelt period of four days, albedo decreased from 0.65 to 0.45 at 330 nm, and from 0.72 to 0.53 at 450 nm. In the literature, the UV and VIS albedo for clean snow are ~0.97–0.99, consistent with the extremely small absorption coefficient of ice in this spectral region. Our low albedo values were supported by two independent simultaneous broadband albedo measurements, and simulated albedo data. We explain the low albedo values to be due to (i) large snow grain sizes up to ~3 mm in diameter; (ii) meltwater surrounding the grains and increasing the effective grain size; (iii) absorption caused by impurities in the snow, with concentration of elemental carbon (black carbon) in snow of 87 ppb, and organic carbon 2894 ppb, at the time of albedo measurements. The high concentrations of carbon, detected by the thermal–optical method, were due to air masses originating from the Kola Peninsula, Russia, where mining and refining industries are located.

Description: Top-down estimate of surface flux in the Los Angeles Basin using a mesoscale inverse modeling technique: assessing anthropogenic emissions of CO, NO x and CO 2 and their impacts Atmospheric Chemistry and Physics, 13, 3661-3677, 2013 Author(s): J. Brioude, W. M. Angevine, R. Ahmadov, S.-W. Kim, S. Evan, S. A. McKeen, E.-Y. Hsie, G. J. Frost, J. A. Neuman, I. B. Pollack, J. Peischl, T. B. Ryerson, J. Holloway, S. S. Brown, J. B. Nowak, J. M. Roberts, S. C. Wofsy, G. W. Santoni, T. Oda, and M. Trainer We present top-down estimates of anthropogenic CO, NO x and CO 2 surface fluxes at mesoscale using a Lagrangian model in combination with three different WRF model configurations, driven by data from aircraft flights during the CALNEX campaign in southern California in May–June 2010. The US EPA National Emission Inventory 2005 (NEI 2005) was the prior in the CO and NO x inversion calculations. The flux ratio inversion method, based on linear relationships between chemical species, was used to calculate the CO 2 inventory without prior knowledge of CO 2 surface fluxes. The inversion was applied to each flight to estimate the variability of single-flight-based flux estimates. In Los Angeles (LA) County, the uncertainties on CO and NO x fluxes were 10% and 15%, respectively. Compared with NEI 2005, the CO posterior emissions were lower by 43% in LA County and by 37% in the South Coast Air Basin (SoCAB). NO x posterior emissions were lower by 32% in LA County and by 27% in the SoCAB. NO x posterior emissions were 40% lower on weekends relative to weekdays. The CO 2 posterior estimates were 183 Tg yr −1 in SoCAB. A flight during ITCT (Intercontinental Transport and Chemical Transformation) in 2002 was used to estimate emissions in the LA Basin in 2002. From 2002 to 2010, the CO and NO x posterior emissions decreased by 41% and 37%, respectively, in agreement with previous studies. Over the same time period, CO 2 emissions increased by 10% in LA County but decreased by 4% in the SoCAB, a statistically insignificant change. Overall, the posterior estimates were in good agreement with the California Air Resources Board (CARB) inventory, with differences of 15% or less. However, the posterior spatial distribution in the basin was significantly different from CARB for NO x emissions. WRF-Chem mesoscale chemical-transport model simulations allowed an evaluation of differences in chemistry using different inventory assumptions, including NEI 2005, a gridded CARB inventory and the posterior inventories derived in this study. The biases in WRF-Chem ozone were reduced and correlations were increased using the posterior from this study compared with simulations with the two bottom-up inventories, suggesting that improving the spatial distribution of ozone precursor surface emissions is also important in mesoscale chemistry simulations.

Description: Arctic aerosol life cycle: linking aerosol size distributions observed between 2000 and 2010 with air mass transport and precipitation at Zeppelin station, Ny-Ålesund, Svalbard Atmospheric Chemistry and Physics, 13, 3643-3660, 2013 Author(s): P. Tunved, J. Ström, and R. Krejci In this study we present a qualitative and quantitative assessment of more than 10 yr of aerosol number size distribution data observed in the Arctic environment (Mt. Zeppelin (78°56' N, 11°53' E, 474 m a.s.l.), Ny Ålesund, Svalbard). We provide statistics on both seasonal and diurnal characteristics of the aerosol observations and conclude that the Arctic aerosol number size distribution and related parameters such as integral mass and surface area exhibit a very pronounced seasonal variation. This seasonal variation seems to be controlled by both dominating source as well as meteorological conditions. Three distinctly different periods can be identified during the Arctic year: the haze period characterized by a dominating accumulation mode aerosol (March–May), followed by the sunlit summer period with low abundance of accumulation mode particles but high concentration of small particles which are likely to be recently and locally formed (June–August). The rest of the year is characterized by a comparably low concentration of accumulation mode particles and negligible abundance of ultrafine particles (September–February). A minimum in aerosol mass and number concentration is usually observed during September/October. We further show that the transition between the different regimes is fast, suggesting rapid change in the conditions defining their appearance. A source climatology based on trajectory analysis is provided, and it is shown that there is a strong seasonality of dominating source areas, with Eurasia dominating during the Autumn–Winter period and dominance of North Atlantic air during the summer months. We also show that new-particle formation events are rather common phenomena in the Arctic during summer, and this is the result of photochemical production of nucleating/condensing species in combination with low condensation sink. It is also suggested that wet removal may play a key role in defining the Arctic aerosol year, via the removal of accumulation mode size particles, which in turn have a pivotal role in facilitating the conditions favorable for new-particle formation events. In summary the aerosol Arctic year seems to be at least qualitatively predictable based on the knowledge of seasonality of transport paths and associated source areas, meteorological conditions and removal processes.

Description: Assessment of the interannual variability and influence of the QBO and upwelling on tracer–tracer distributions of N 2 O and O 3 in the tropical lower stratosphere Atmospheric Chemistry and Physics, 13, 3619-3641, 2013 Author(s): F. Khosrawi, R. Müller, J. Urban, M. H. Proffitt, G. Stiller, M. Kiefer, S. Lossow, D. Kinnison, F. Olschewski, M. Riese, and D. Murtagh A modified form of tracer–tracer correlations of N 2 O and O 3 has been used as a tool for the evaluation of atmospheric photochemical models. Applying this method, monthly averages of N 2 O and O 3 are derived for both hemispheres by partitioning the data into altitude (or potential temperature) bins and then averaging over a fixed interval of N 2 O. In a previous study, the method has been successfully applied to the evaluation of two chemical transport models (CTMs) and one chemistry–climate model (CCM) using a 1 yr climatology derived from the Odin Sub-Millimetre Radiometer (Odin/SMR). However, the applicability of a 1 yr climatology of monthly averages of N 2 O and O 3 has been questioned due to the inability of some CCMs to simulate a specific year for the evaluation of CCMs. In this study, satellite measurements from Odin/SMR, the Aura Microwave Limb Sounder (Aura/MLS), the Michelson Interferometer for Passive Atmospheric Sounding on ENVISAT (ENVISAT/MIPAS), and the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere (CRISTA-1 and CRISTA-2) as well as model simulations from the Whole Atmosphere Community Climate Model (WACCM) are considered. By using seven to eight years of satellite measurements derived between 2003 and 2010 from Odin/SMR, Aura/MLS, ENVISAT/MIPAS and six years of model simulations from WACCM, the interannual variability of lower stratospheric monthly averages of N 2 O and O 3 is assessed. It is shown that the interannual variability of the monthly averages of N 2 O and O 3 is low, and thus can be easily distinguished from model deficiencies. Furthermore, it is investigated why large differences are found between Odin/SMR observations and model simulations from the Karlsruhe Simulation Model of the Middle Atmosphere (KASIMA) and the atmospheric general circulation model ECHAM5/Messy1 for the Northern and Southern Hemisphere tropics (0° to 30° N and 0° to −30° S, respectively). The differences between model simulations and observations are most likely caused by an underestimation of the quasi-biennial oscillation and tropical upwelling by the models as well as due to biases and/or instrument noise from the satellite instruments. A realistic consideration of the QBO in the model reduces the differences between model simulation and observations significantly. Finally, an intercomparison between Odin/SMR, Aura/MLS, ENVISAT/MIPAS and WACCM was performed. The comparison shows that these data sets are generally in good agreement, although some known biases of the data sets are clearly visible in the monthly averages. Nevertheless, the differences caused by the uncertainties of the satellite data sets are sufficiently small and can be clearly distinguished from model deficiencies. Thus, the method applied in this study is not only a valuable tool for model evaluation, but also for satellite data intercomparisons.

Description: Corrigendum to "Quantifying the uncertainty in simulating global tropospheric composition due to the variability in global emission estimates of Biogenic Volatile Organic Compounds" published in Atmos. Chem. Phys., 13, 2857–2891, 2013 Atmospheric Chemistry and Physics, 13, 3693-3694, 2013 Author(s): J. E. Williams, P. F. J. van Velthoven, and C. A. M. Brenninkmeijer No abstract available.

Description: The TP53 tumor suppressor pathway is abrogated by TP53 mutations in the majority of human cancers. Increased levels of wild-type TP53 in aggressive neuroblastomas appear paradox but are tolerated by tumor cells due to co-activation of the TP53 ubiquitin ligase, MDM2. The role of the MDM2 antagonist, p14 ARF , in controlling the TP53-MDM2 balance in neuroblastoma is unresolved. In the present study, we show that conditional p14 ARF expression substantially suppresses viability, clonogenicity and anchorage-independent growth in p14 ARF -deficient or MYCN -amplified neuroblastoma cell lines. Furthermore, ectopic 14 ARF expression induced accumulation of cells in the G1 phase and apoptosis, which was paralleled by accumulation of TP53 and its targets. Comparative genomic hybridization analysis of 193 primary neuroblastomas detected one homozygous deletion of CDKN2A (encoding both p14 ARF and p16 INK4A ) and heterozygous loss of CDKN2A in 22% of tumors. Co-expression analysis of p14 ARF and its transactivator, E2F1, in a set of 68 primary tumors revealed only a weak correlation, suggesting that further regulatory mechanisms govern p14 ARF expression in neuroblastomas. Intriguingly, analyses utilizing chromatin immunoprecipitation revealed different histone mark-defined epigenetic activity states of p14 ARF in neuroblastoma cell lines that correlated with endogenous p14 ARF expression but not with episomal p14 ARF promoter reporter activity, indicating that the native chromatin context serves to epigenetically repress p14 ARF in neuroblastoma cells. Collectively, the data pinpoint p14 ARF as a critical factor for efficient TP53 response in neuroblastoma cells and assign p14 ARF as a neuroblastoma suppressor candidate that is impaired by genomic loss and epigenetic repression.

Description: Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in TSC1 or TSC2 resulting in hyperactivity of the mammalian target of rapamycin and disabling brain lesions. These lesions contain misplaced neurons enriched in hypoxia-inducible factor 1a (HIF1a). However, the relationship between TSC1/2 and HIF1a and the function of HIF1a in TSC neurons remain unexplored. Here, we examine the degree of HIF1a activity and its function in newborn Tsc1 null neurons in a mouse model of TSC. Using single cell electroporation in the neurogenic subventricular zone (SVZ) of neonatal mice, we deleted Tsc1 and generated olfactory lesions containing misplaced Tsc1 null neurons as previously reported. These newborn neurons displayed elevated HIF1a-mediated transcriptional activity when compared with Tsc1 heterozygote neurons and a marked resistance to cell death induced by a HIF1a antagonist. Electroporation of Hif1a targeting short hairpin RNA (shRNA) or dominant negative HIF1a constructs resulted in 80–90% loss of Tsc1 null newborn neurons although sparing SVZ stem cells. Consistent with this later finding, induction of Hif1a shRNA expression during synaptic integration thus bypassing neuron production also resulted in newborn neuron death. Collectively, these results suggest that HIF1a acts as a molecular determinant of newborn neuron survival and that its TSC1-dependent up-regulation gave Tsc1 null neurons a survival advantage, despite their misplacement in a novel microenvironment.

Description: Several known or putative glycosyltransferases are required for the synthesis of laminin-binding glycans on alpha-dystroglycan (αDG), including POMT1, POMT2, POMGnT1, LARGE, Fukutin, FKRP, ISPD and GTDC2. Mutations in these glycosyltransferase genes result in defective αDG glycosylation and reduced ligand binding by αDG causing a clinically heterogeneous group of congenital muscular dystrophies, commonly referred to as dystroglycanopathies. The most severe clinical form, Walker–Warburg syndrome (WWS), is characterized by congenital muscular dystrophy and severe neurological and ophthalmological defects. Here, we report two homozygous missense mutations in the β-1,3- N -acetylglucosaminyltransferase 1 ( B3GNT1 ) gene in a family affected with WWS. Functional studies confirmed the pathogenicity of the mutations. First, expression of wild-type but not mutant B3GNT1 in human prostate cancer (PC3) cells led to increased levels of αDG glycosylation. Second, morpholino knockdown of the zebrafish b3gnt1 orthologue caused characteristic muscular defects and reduced αDG glycosylation. These functional studies identify an important role of B3GNT1 in the synthesis of the uncharacterized laminin-binding glycan of αDG and implicate B3GNT1 as a novel causative gene for WWS.