T-loop phosphorylation of Arabidopsis CDKA;1 is required for its function and can be partially substituted by an aspartate residue

As in other eukaryotes, progression through the cell cycle in plants is governed by cyclin-dependent kinases. Phosphorylation of a canonical Thr residue in the T-loop of the kinases is required for high enzyme activity in animals and yeast. We show that the Arabidopsis thaliana Cdc21/Cdc28 homolog CDKA; 1 is also phosphorylated in the T-loop and that phosphorylation at the conserved Thr-161 residue is essential for its function. A phospho-mimicry T161D substitution restored the primary defect of cdka; 1 mutants, and although the T161D substitution displayed a dramatically reduced kinase activity with a compromised ability to bind substrates, homozygous mutant plants were recovered. The rescue by the T161D substitution, however, was not complete, and the resulting plants displayed various developmental abnormalities. For instance, even though flowers were formed, these plants were completely sterile as a result of a failure of the meiotic program, indicating that different requirements for CDKA; 1 function are needed during plant development

A simplified protocol for the detection of blood, saliva, and semen from a single biological trace using immunochromatographic tests.

The detection of body fluids (e.g., blood, saliva or semen) provides information that is important both for the investigation and for the choice of the analytical protocols. Because of their sensitivity, specificity, as well as their simplicity of use, immunochromatographic tests are widely applied. These tests target different body fluids and generally require specific buffer solutions. If one needs to investigate whether the material is of a specific nature (e.g., blood), this is fine. However, if the material can also contain other material (e.g., saliva or semen) then the use of different tests can be problematic. Indeed, if the different tests require different buffers, it will not be possible to perform all tests on the exact same specimen.In this study, we assess the use of the RSID™-universal buffer to perform three immunochromatographic tests (HEXAGON OBTI, RSID-saliva, and PSA Semiquant) as well as spermatozoa detection. We use the same eluate for the detection of all three body fluids. The proposed protocol provides similar results to those obtained when each test is conducted independently. Furthermore, it does not affect the quality of the DNA profiles. The main advantage of this protocol is that the results of the presumptive test(s) and of the DNA analyses are representative of the exact same specimen

Modeling secondary organic aerosol formation through cloud processing of organic compounds

Interest in the potential formation of secondary organic aerosol (SOA) through reactions of organic compounds in condensed aqueous phases is growing. In this study, the potential formation of SOA from irreversible aqueous-phase reactions of organic species in clouds was investigated. A new proposed aqueous-phase chemistry mechanism (AqChem) is coupled with the existing gas-phase Caltech Atmospheric Chemistry Mechanism (CACM) and the Model to Predict the Multiphase Partitioning of Organics (MPMPO) that simulate SOA formation. AqChem treats irreversible organic reactions that lead mainly to the formation of carboxylic acids, which are usually less volatile than the corresponding aldehydic compounds. Zero-dimensional model simulations were performed for tropospheric conditions with clouds present for three consecutive hours per day. Zero-dimensional model simulations show that 48-h average SOA formation is increased by 27% for a rural scenario with strong monoterpene emissions and 7% for an urban scenario with strong emissions of aromatic compounds, respectively, when irreversible organic reactions in clouds are considered. AqChem was also incorporated into the Community Multiscale Air Quality Model (CMAQ) version 4.4 with CACM/MPMPO and applied to a previously studied photochemical episode (3–4 August 2004) focusing on the eastern United States. The CMAQ study indicates that the maximum contribution of SOA formation from irreversible reactions of organics in clouds is 0.28 μg m<sup>−3</sup> for 24-h average concentrations and 0.60 μg m<sup>−3</sup> for one-hour average concentrations at certain locations. On average, domain-wide surface SOA predictions for the episode are increased by 9% when irreversible, in-cloud processing of organics is considered. Because aldehydes of carbon number greater than four are assumed to convert fully to the corresponding carboxylic acids upon reaction with OH in cloud droplets and this assumption may overestimate carboxylic acid formation from this reaction route, the present study provides an upper bound estimate of SOA formation via this pathway

The effect of harmonized emissions on aerosol properties in global models – an AeroCom experiment

The effects of unified aerosol sources on global aerosol fields simulated by different models are examined in this paper. We compare results from two AeroCom experiments, one with different (ExpA) and one with unified emissions, injection heights, and particle sizes at the source (ExpB). Surprisingly, harmonization of aerosol sources has only a small impact on the simulated diversity for aerosol burden, and consequently optical properties, as the results are largely controlled by model-specific transport, removal, chemistry (leading to the formation of secondary aerosols) and parameterizations of aerosol microphysics (e.g. the split between deposition pathways) and to a lesser extent on the spatial and temporal distributions of the (precursor) emissions. The burdens of black carbon and especially sea salt become more coherent in ExpB only, because the large ExpA diversity for these two species was caused by few outliers. The experiment also indicated that despite prescribing emission fluxes and size distributions, ambiguities in the implementation in individual models can lead to substantial differences. These results indicate the need for a better understanding of aerosol life cycles at process level (including spatial dispersal and interaction with meteorological parameters) in order to obtain more reliable results from global aerosol simulations. This is particularly important as such model results are used to assess the consequences of specific air pollution abatement strategies

Analysis and quantification of the diversities of aerosol life cycles within AeroCom

Simulation results of global aerosol models have been assembled in the framework of the AeroCom intercomparison exercise. In this paper, we analyze the life cycles of dust, sea salt, sulfate, black carbon and particulate organic matter as simulated by sixteen global aerosol models. The diversities among the models for the sources and sinks, burdens, particle sizes, water uptakes, and spatial dispersals have been established. These diversities have large consequences for the calculated radiative forcing and the aerosol concentrations at the surface. The AeroCom all-models-average emissions are dominated by the mass of sea salt (SS), followed by dust (DU), sulfate (SO_4), particulate organic matter (POM), and finally black carbon (BC). Interactive parameterizations of the emissions and contrasting particles sizes of SS and DU lead generally to higher diversities of these species, and for total aerosol. The lower diversity of the emissions of the fine aerosols, BC, POM, and SO_4, is due to the use of similar emission inventories, and does therefore not necessarily indicate a better understanding of their sources. The diversity of SO_4-sources is mainly caused by the disagreement on depositional loss of precursor gases and on chemical production. The diversities of the emissions are passed on to the burdens, but the latter are also strongly affected by the model-specific treatments of transport and aerosol processes. The burdens of dry masses decrease from largest to smallest: DU, SS, SO_4, POM, and BC. The all-models-average residence time is shortest for SS with about half a day, followed by S_O4 and DU with four days, and POM and BC with six and seven days, respectively. The wet deposition rate is controlled by the solubility and increases from DU, BC, POM to SO_4 and SS. It is the dominant sink for SO_4, BC, and POM, and contributes about one third to the total removal rate coefficients of SS and DU species. For SS and DU we find high diversities for the removal rate coefficients and deposition pathways. Models do neither agree on the split between wet and dry deposition, nor on that between sedimentation and turbulent dry Deposition. We diagnose an extremely high diversity for the uptake of ambient water vapor that influences the particle size and thus the sink rate coefficients. Furthermore, we find little agreement among the model results for the partitioning of wet removal into scavenging by convective and stratiform rain. Large differences exist for aerosol dispersal both in the vertical and in the horizontal direction. In some models, a minimum of total aerosol concentration is simulated at the surface. Aerosol dispersal is most pronounced for SO4 and BC and lowest for SS. Diversities are higher for meridional than for vertical dispersal, they are similar for a given species and highest for SS and DU. For these two components we do not find a correlation between vertical and meridional aerosol dispersal. In addition the degree of dispersals of SS and DU is not related to their residence times. SO_4, BC, and POM, however, show increased meridional dispersal in models with larger vertical dispersal, and dispersal is larger for longer simulated residence times

An AeroCom initial assessment – optical properties in aerosol component modules of global models

The AeroCom exercise diagnoses multi-component aerosol modules in global modeling. In an initial assessment simulated global distributions for mass and mid-visible aerosol optical thickness (aot) were compared among 20 different modules. Model diversity was also explored in the context of previous comparisons. For the component combined aot general agreement has improved for the annual global mean. At 0.11 to 0.14, simulated aot values are at the lower end of global averages suggested by remote sensing from ground (AERONET ca. 0.135) and space (satellite composite ca. 0.15). More detailed comparisons, however, reveal that larger differences in regional distribution and significant differences in compositional mixture remain. Of particular concern are large model diversities for contributions by dust and carbonaceous aerosol, because they lead to significant uncertainty in aerosol absorption (aab). Since aot and aab, both, influence the aerosol impact on the radiative energy-balance, the aerosol (direct) forcing uncertainty in modeling is larger than differences in aot might suggest. New diagnostic approaches are proposed to trace model differences in terms of aerosol processing and transport: These include the prescription of common input (e.g. amount, size and injection of aerosol component emissions) and the use of observational capabilities from ground (e.g. measurements networks) or space (e.g. correlations between aerosol and clouds)

The ASH1 HOMOLOG 2 (ASHH2) Histone H3 Methyltransferase Is Required for Ovule and Anther Development in Arabidopsis

BACKGROUND:SET-domain proteins are histone lysine (K) methyltransferases (HMTase) implicated in defining transcriptionally permissive or repressive chromatin. The Arabidopsis ASH1 HOMOLOG 2 (ASHH2) protein (also called SDG8, EFS and CCR1) has been suggested to methylate H3K4 and/or H3K36 and is similar to Drosophila ASH1, a positive maintainer of gene expression, and yeast Set2, a H3K36 HMTase. Mutation of the ASHH2 gene has pleiotropic developmental effects. Here we focus on the role of ASHH2 in plant reproduction. METHODOLOGY/PRINCIPAL FINDINGS:A slightly reduced transmission of the ashh2 allele in reciprocal crosses implied involvement in gametogenesis or gamete function. However, the main requirement of ASHH2 is sporophytic. On the female side, close to 80% of mature ovules lack embryo sac. On the male side, anthers frequently develop without pollen sacs or with specific defects in the tapetum layer, resulting in reduction in the number of functional pollen per anther by up to approximately 90%. In consistence with the phenotypic findings, an ASHH2 promoter-reporter gene was expressed at the site of megaspore mother cell formation as well as tapetum layers and pollen. ashh2 mutations also result in homeotic changes in floral organ identity. Transcriptional profiling identified more than 300 up-regulated and 600 down-regulated genes in ashh2 mutant inflorescences, whereof the latter included genes involved in determination of floral organ identity, embryo sac and anther/pollen development. This was confirmed by real-time PCR. In the chromatin of such genes (AP1, AtDMC1 and MYB99) we observed a reduction of H3K36 trimethylation (me3), but not H3K4me3 or H3K36me2. CONCLUSIONS/SIGNIFICANCE:The severe distortion of reproductive organ development in ashh2 mutants, argues that ASHH2 is required for the correct expression of genes essential to reproductive development. The reduction in the ashh2 mutant of H3K36me3 on down-regulated genes relevant to the observed defects, implicates ASHH2 in regulation of gene expression via H3K36 trimethylation in chromatin of Arabidopsis inflorescences

Evaluation of global simulations of aerosol particle and cloud condensation nuclei number, with implications for cloud droplet formation

A total of 16 global chemistry transport models and general circulation models have participated in this study; 14 models have been evaluated with regard to their ability to reproduce the near-surface observed number concentration of aerosol particles and cloud condensation nuclei (CCN), as well as derived cloud droplet number concentration (CDNC). Model results for the period 2011-2015 are compared with aerosol measurements (aerosol particle number, CCN and aerosol particle composition in the submicron fraction) from nine surface stations located in Europe and Japan. The evaluation focuses on the ability of models to simulate the average across time state in diverse environments and on the seasonal and short-term variability in the aerosol properties. There is no single model that systematically performs best across all environments represented by the observations. Models tend to underestimate the observed aerosol particle and CCN number concentrations, with average normalized mean bias (NMB) of all models and for all stations, where data are available, of -24 % and -35 % for particles with dry diameters > 50 and > 120 nm, as well as -36 % and -34 % for CCN at supersaturations of 0.2 % and 1.0 %, respectively. However, they seem to behave differently for particles activating at very low supersaturations (<0.1 %) than at higher ones. A total of 15 models have been used to produce ensemble annual median distributions of relevant parameters. The model diversity (defined as the ratio of standard deviation to mean) is up to about 3 for simulated N-3 (number concentration of particles with dry diameters larger than 3 nm) and up to about 1 for simulated CCN in the extra-polar regions. A global mean reduction of a factor of about 2 is found in the model diversity for CCN at a supersaturation of 0.2 % (CCN0.2) compared to that for N-3, maximizing over regions where new particle formation is important. An additional model has been used to investigate potential causes of model diversity in CCN and bias compared to the observations by performing a perturbed parameter ensemble (PPE) accounting for uncertainties in 26 aerosol-related model input parameters. This PPE suggests that biogenic secondary organic aerosol formation and the hygroscopic properties of the organic material are likely to be the major sources of CCN uncertainty in summer, with dry deposition and cloud processing being dominant in winter. Models capture the relative amplitude of the seasonal variability of the aerosol particle number concentration for all studied particle sizes with available observations (dry diameters larger than 50, 80 and 120 nm). The short-term persistence time (on the order of a few days) of CCN concentrations, which is a measure of aerosol dynamic behavior in the models, is underestimated on average by the models by 40 % during winter and 20 % in summer. In contrast to the large spread in simulated aerosol particle and CCN number concentrations, the CDNC derived from simulated CCN spectra is less diverse and in better agreement with CDNC estimates consistently derived from the observations (average NMB -13 % and -22 % for updraft velocities 0.3 and 0.6 m s(-1), respectively). In addition, simulated CDNC is in slightly better agreement with observationally derived values at lower than at higher updraft velocities (index of agreement 0.64 vs. 0.65). The reduced spread of CDNC compared to that of CCN is attributed to the sublinear response of CDNC to aerosol particle number variations and the negative correlation between the sensitivities of CDNC to aerosol particle number concentration (partial derivative N-d/partial derivative N-a) and to updraft velocity (partial derivative N-d/partial derivative w). Overall, we find that while CCN is controlled by both aerosol particle number and composition, CDNC is sensitive to CCN at low and moderate CCN concentrations and to the updraft velocity when CCN levels are high. Discrepancies are found in sensitivities partial derivative N-d/partial derivative N-a and partial derivative N-d/partial derivative w; models may be predisposed to be too "aerosol sensitive" or "aerosol insensitive" in aerosol-cloud-climate interaction studies, even if they may capture average droplet numbers well. This is a subtle but profound finding that only the sensitivities can clearly reveal and may explain intermodel biases on the aerosol indirect effect.Peer reviewe

Evaluation of Global Simulations of Aerosol Particle and Cloud Condensation Nuclei Number, with Implications for Cloud Droplet Formation

A total of 16 global chemistry transport models and general circulation models have participated in this study; 14 models have been evaluated with regard to their ability to reproduce the near-surface observed number concentration of aerosol particles and cloud condensation nuclei (CCN), as well as derived cloud droplet number concentration (CDNC). Model results for the period 2011-2015 are compared with aerosol measurements (aerosol particle number, CCN and aerosol particle composition in the submicron fraction) from nine surface stations located in Europe and Japan. The evaluation focuses on the ability of models to simulate the average across time state in diverse environments and on the seasonal and short-term variability in the aerosol properties. There is no single model that systematically performs best across all environments represented by the observations. Models tend to underestimate the observed aerosol particle and CCN number concentrations, with average normalized mean bias (NMB) of all models and for all stations, where data are available, of -24% and -35% for particles with dry diameters > 50 and > 120nm, as well as -36% and -34% for CCN at supersaturations of 0.2% and 1.0%, respectively. However, they seem to behave differently for particles activating at very low supersaturations (< 0.1%) than at higher ones. A total of 15 models have been used to produce ensemble annual median distributions of relevant parameters. The model diversity (defined as the ratio of standard deviation to mean) is up to about 3 for simulated N3 (number concentration of particles with dry diameters larger than 3 nm) and up to about 1 for simulated CCN in the extra-polar regions. A global mean reduction of a factor of about 2 is found in the model diversity for CCN at a supersaturation of 0.2% (CCN(0.2)) compared to that for N3, maximizing over regions where new particle formation is important. An additional model has been used to investigate potential causes of model diversity in CCN and bias compared to the observations by performing a perturbed parameter ensemble (PPE) accounting for uncertainties in 26 aerosol-related model input parameters. This PPE suggests that biogenic secondary organic aerosol formation and the hygroscopic properties of the organic material are likely to be the major sources of CCN uncertainty in summer, with dry deposition and cloud processing being dominant in winter. Models capture the relative amplitude of the seasonal variability of the aerosol particle number concentration for all studied particle sizes with available observations (dry diameters larger than 50, 80 and 120nm). The short-term persistence time (on the order of a few days) of CCN concentrations, which is a measure of aerosol dynamic behavior in the models, is underestimated on average by the models by 40% during winter and 20% in summer