Characterisation of the photolytic HONO-source in the atmosphere simulation chamber SAPHIR

HONO formation has been proposed as an important OH radical source in simulation chambers for more than two decades. Besides the heterogeneous HONO formation by the dark reaction of NO₂ and adsorbed water, a photolytic source has been proposed to explain the elevated reactivity in simulation chamber experiments. However, the mechanism of the photolytic process is not well understood so far. As expected, production of HONO and NO_x was also observed inside the new atmospheric simulation chamber SAPHIR under solar irradiation. This photolytic HONO and NO_x formation was studied with a sensitive HONO instrument under reproducible controlled conditions at atmospheric concentrations of other trace gases. It is shown that the photolytic HONO source in the SAPHIR chamber is not caused by NO₂ reactions and that it is the only direct NO_y source under illuminated conditions. In addition, the photolysis of nitrate which was recently postulated for the observed photolytic HONO formation on snow, ground, and glass surfaces, can be excluded in the chamber. A photolytic HONO source at the surface of the chamber is proposed which is strongly dependent on humidity, on light intensity, and on temperature. An empirical function describes these dependencies and reproduces the observed HONO formation rates to within 10%. It is shown that the photolysis of HONO represents the dominant radical source in the SAPHIR chamber for typical tropospheric O₃/H₂O concentrations. For these conditions, the HONO concentrations inside SAPHIR are similar to recent observations in ambient air

Genome, proteome and structure of a T7-like bacteriophage of the kiwifruit canker phytopathogen pseudomonas syringae pv. actinidiae

La pseudomonas syringae pv. actinidiae es un patógeno responsable significativo de la afta bacteriana severa del kiwi (Actinidia sp.). Los bacteriófagos infectados de este fitopatógeno tienen potencial como agentes de control biológico como parte de un enfoque integrado de la gestión del cancro bacteriano, y para su uso como herramientas molecular para el estudio de esta bacteria. Una variedad de bacteriófagos fueron previamente aislados, antes de ser infectados con P. syringae pv. Actinidiae; y sus propiedades básicas fueron caracterizadas para proporcionar un marco para la formulación de estos fagos, como agentes de biocontrol. Aquí, hemos examinado con más detalle el φPsa17, un fago con la capacidad de infectar a una amplia gama de cepas P. syringae pv. Actinidiae, único miembro de la Podoviridae en esta colección. La morfología de partículas fue visualizada mediante criomicroscopía electrónica, el genoma fue secuenciado, y sus proteínas estructurales fueron analizados usando shotgun proteomics. Estos estudios demostraron que 40,525 φPsa17 tiene un genoma de BP, es un miembro de género T7likevirus y está estrechamente relacionada con la pseudomonada llamada fágicas φPSA2 y GH-1. Once proteínas estructurales (andamios) fueron detectados por la proteómica y φPsa17 tiene una cápside de aproximadamente 60 nm de diámetro. No fueron identificados genes indicativos de un ciclo de vida lisogénica, sugiriendo que el fago es necesariamente lítico. Estas características indican que φPsa17 pueden ser adecuadas para la formulación como un agente de biocontrol de P. syringae pv. actinidiaePseudomonas syringae pv. actinidiae is an economically significant pathogen responsible for severe bacterial canker of kiwifruit (Actinidia sp.). Bacteriophages infecting this phytopathogen have potential as biocontrol agents as part of an integrated approach to the management of bacterial canker, and for use as molecular tools to study this bacterium. A variety of bacteriophages were previously isolated that infect P. syringae pv. actinidiae, and their basic properties were characterized to provide a framework for formulation of these phages as biocontrol agents. Here, we have examined in more detail φPsa17, a phage with the capacity to infect a broad range of P. syringae pv. actinidiae strains and the only member of the Podoviridae in this collection. Particle morphology was visualized using cryo-electron microscopy, the genome was sequenced, and its structural proteins were analysed using shotgun proteomics. These studies demonstrated that φPsa17 has a 40,525 bp genome, is a member of the T7likevirus genus and is closely related to the pseudomonad phages φPSA2 and gh-1. Eleven structural proteins (one scaffolding) were detected by proteomics and φPsa17 has a capsid of approximately 60 nm in diameter. No genes indicative of a lysogenic lifecycle were identified, suggesting the phage is obligately lytic. These features indicate that φPsa17 may be suitable for formulation as a biocontrol agent of P. syringae pv. actinidiaeTrabajo patrocinado por. Royal Society. Fellowship Rutherford, para Peter C. Fineran Otago School of Medical Sciences Summer Research Scholarship, para Danni ChenpeerReviewe

Modelling chemistry in the nocturnal boundary layer above tropical rainforest and a generalised effective nocturnal ozone deposition velocity for sub-ppbv NOx conditions

Measurements of atmospheric composition have been made over a remote rainforest landscape. A box model has previously been demonstrated to model the observed daytime chemistry well. However the box model is unable to explain the nocturnal measurements of relatively high [NO] and [O3], but relatively low observed [NO2]. It is shown that a one-dimensional (1-D) column model with simple O3 -NOx chemistry and a simple representation of vertical transport is able to explain the observed nocturnal concentrations and predict the likely vertical profiles of these species in the nocturnal boundary layer (NBL). Concentrations of tracers carried over from the end of the night can affect the atmospheric chemistry of the following day. To ascertain the anomaly introduced by using the box model to represent the NBL, vertically-averaged NBL concentrations at the end of the night are compared between the 1-D model and the box model. It is found that, under low to medium [NOx] conditions (NOx <1 ppbv), a simple parametrisation can be used to modify the box model deposition velocity of ozone, in order to achieve good agreement between the box and 1-D models for these end-of-night concentrations of NOx and O3. This parametrisation would could also be used in global climate-chemistry models with limited vertical resolution near the surface. Box-model results for the following day differ significantly if this effective nocturnal deposition velocity for ozone is implemented; for instance, there is a 9% increase in the following day’s peak ozone concentration. However under medium to high [NOx] conditions (NOx > 1 ppbv), the effect on the chemistry due to the vertical distribution of the species means no box model can adequately represent chemistry in the NBL without modifying reaction rate constants

Understanding in situ ozone production in the summertime through radical observations and modelling studies during the Clean air for London project (ClearfLo)

Measurements of OH, HO2, RO2i (alkene and aromatic-related RO2) and total RO2 radicals taken during the ClearfLo campaign in central London in the summer of 2012 are presented. A photostationary steady-state calculation of OH which considered measured OH reactivity as the OH sink term and the measured OH sources (of which HO2+ NO reaction and HONO photolysis dominated) compared well with the observed levels of OH. Comparison with calculations from a detailed box model utilising the Master Chemical Mechanism v3.2, however, highlighted a substantial discrepancy between radical observations under lower NOx conditions ([NO] 3 ppbv) the box model increasingly underpredicted total [RO2]. The modelled and observed HO2 were in agreement, however, under elevated NO concentrations ranging from 7 to 15 ppbv. The model uncertainty under low NO conditions leads to more ozone production predicted using modelled peroxy radical concentrations ( ≈ 3 ppbv h-1) versus ozone production from peroxy radicals measured ( ≈ 1 ppbv h-1). Conversely, ozone production derived from the predicted peroxy radicals is up to an order of magnitude lower than from the observed peroxy radicals as [NO] increases beyond 7 ppbv due to the model underprediction of RO2 under these conditions

Intercomparison of four different in-situ techniques for ambient formaldehyde measurements in urban air

International audienceResults from an intercomparison of several currently used in-situ techniques for the measurement of atmospheric formaldehyde (CH2O) are presented. The measurements were carried out at Bresso, an urban site in the periphery of Milan (Italy) as part of the FORMAT-I field campaign. Eight instruments were employed by six independent research groups using four different techniques: Differential Optical Absorption Spectroscopy (DOAS), Fourier Transform Infra Red (FTIR) interferometry, the fluorimetric Hantzsch reaction technique (five instruments) and a chromatographic technique employing C18-DNPH-cartridges (2,4-dinitrophenylhydrazine). White type multi-reflection systems were employed for the optical techniques in order to avoid spatial CH2O gradients and ensure the sampling of nearly the same air mass by all instruments. Between 23 and 31 July 2002, up to 13 ppbv of CH2O were observed. The concentrations lay well above the detection limits of all instruments. The formaldehyde concentrations determined with DOAS, FTIR and the Hantzsch instruments were found to agree within ±11%, with the exception of one Hantzsch instrument, which gave systematically higher values. The two hour integrated samples by DNPH yielded up to 25% lower concentrations than the data of the continuously measuring instruments averaged over the same time period. The consistency between the DOAS and the Hantzsch method was better than during previous intercomparisons in ambient air with slopes of the regression line not significantly differing from one. The differences between the individual Hantzsch instruments could be attributed in part to the calibration standards used. Possible systematic errors of the methods are discussed

SUBA: the Arabidopsis Subcellular Database

Knowledge of protein localisation contributes towards our understanding of protein function and of biological inter-relationships. A variety of experimental methods are currently being used to produce localisation data that need to be made accessible in an integrated manner. Chimeric fluorescent fusion proteins have been used to define subcellular localisations with at least 1100 related experiments completed in Arabidopsis. More recently, many studies have employed mass spectrometry to undertake proteomic surveys of subcellular components in Arabidopsis yielding localisation information for ∼2600 proteins. Further protein localisation information may be obtained from other literature references to analysis of locations (AmiGO: ∼900 proteins), location information from Swiss-Prot annotations (∼2000 proteins); and location inferred from gene descriptions (∼2700 proteins). Additionally, an increasing volume of available software provides location prediction information for proteins based on amino acid sequence. We have undertaken to bring these various data sources together to build SUBA, a SUBcellular location database for Arabidopsis proteins. The localisation data in SUBA encompasses 10 distinct subcellular locations, >6743 non-redundant proteins and represents the proteins encoded in the transcripts responsible for 51% of Arabidopsis expressed sequence tags. The SUBA database provides a powerful means by which to assess protein subcellular localisation in Arabidopsis ()

Noncoding RNA Mediated Traffic of Foreign mRNA into Chloroplasts Reveals a Novel Signaling Mechanism in Plants

Communication between chloroplasts and the nucleus is one of the milestones of the evolution of plants on earth. Proteins encoded by ancestral chloroplast-endogenous genes were transferred to the nucleus during the endosymbiotic evolution and originated this communication, which is mainly dependent on specific transit-peptides. However, the identification of nuclear-encoded proteins targeted to the chloroplast lacking these canonical signals suggests the existence of an alternative cellular pathway tuning this metabolic crosstalk. Non-coding RNAS (NcRNAs) are increasingly recognized as regulators of gene expression as they play roles previously believed to correspond to proteins. Avsunviroidae family viroids are the only noncoding functional RNAs that have been reported to traffic inside the chloroplasts. Elucidating mechanisms used by these pathogens to enter this organelle will unearth novel transport pathways in plant cells. Here we show that a viroid-derived NcRNA acting as a 5′UTR-end mediates the functional import of Green Fluorescent Protein (GFP) mRNA into chloroplast. This claim is supported by the observation at confocal microscopy of a selective accumulation of GFP in the chloroplast of the leaves expressing the chimeric vd-5′UTR/GFP and by the detection of the GFP mRNA in chloroplasts isolated from cells expressing this construct. These results support the existence of an alternative signaling mechanism in plants between the host cell and chloroplasts, where an ncRNA functions as a key regulatory molecule to control the accumulation of nuclear-encoded proteins in this organelle. In addition, our findings provide a conceptual framework to develop new biotechnological tools in systems using plant chloroplast as bioreactors. Finally, viroids of the family Avsunviroidae have probably evolved to subvert this signaling mechanism to regulate their differential traffic into the chloroplast of infected cells

Assessing chemistry schemes and constraints in air quality models used to predict ozone in London against the detailed Master Chemical Mechanism

Air pollution is the environmental factor with the greatest impact on human health in Europe. Understanding the key processes driving air quality across the relevant spatial scales, especially during pollution exceedances and episodes, is essential to provide effective predictions for both policymakers and the public. It is particularly important for policy regulators to understand the drivers of local air quality that can be regulated by national policies versus the contribution from regional pollution transported from mainland Europe or elsewhere. One of the main objectives of the Coupled Urban and Regional processes: Effects on AIR quality (CUREAIR) project is to determine local and regional contributions to ozone events. A detailed zero-dimensional (0-D) box model run with the Master Chemical Mechanism (MCMv3.2) is used as the benchmark model against which the less explicit chemistry mechanisms of the Generic Reaction Set (GRS) and the Common Representative Intermediates (CRIv2-R5) schemes are evaluated. GRS and CRI are used by the Atmospheric Dispersion Modelling System (ADMS-Urban) and the regional chemistry transport model EMEP4UK, respectively. The MCM model uses a near-explicit chemical scheme for the oxidation of volatile organic compounds (VOCs) and is constrained to observations of VOCs, NOx, CO, HONO (nitrous acid), photolysis frequencies and meteorological parameters measured during the ClearfLo (Clean Air for London) campaign. The sensitivity of the less explicit chemistry schemes to different model inputs has been investigated: Constraining GRS to the total VOC observed during ClearfLo as opposed to VOC derived from ADMS-Urban dispersion calculations, including emissions and background concentrations, led to a significant increase (674% during winter) in modelled ozone. The inclusion of HONO chemistry in this mechanism, particularly during wintertime when other radical sources are limited, led to substantial increases in the ozone levels predicted (223%). When the GRS and CRIv2-R5 schemes are run with the equivalent model constraints to the MCM, they are able to reproduce the level of ozone predicted by the near-explicit MCM to within 40% and 20% respectively for the majority of the time. An exception to this trend was observed during pollution episodes experienced in the summer, when anticyclonic conditions favoured increased temperatures and elevated O3. The in situ O3 predicted by the MCM was heavily influenced by biogenic VOCs during these conditions and the low GRS [O3] : MCM [O3] ratio (and low CRIv2-R5 [O3] : MCM [O3] ratio) demonstrates that these less explicit schemes under-represent the full O3 creation potential of these VOCs. To fully assess the influence of the in situ O3 generated from local emissions versus O3 generated upwind of London and advected in, the time since emission (and, hence, how far the real atmosphere is from steady state) must be determined. From estimates of the mean transport time determined from the NOx : NOy ratio observed at North Kensington during the summer and comparison of the O3 predicted by the MCM model after this time, ∼60% of the median observed [O3] could be generated from local emissions. During the warmer conditions experienced during the easterly flows, however, the observed [O3] may be even more heavily influenced by London's emissions