Search

Accurate and temporally resolved fields of free-troposphere ozone are of major importance to quantify the intercontinental transport of pollution and the ozone radiative forcing. In this study we examine the impact of assimilating ozone observations from the Microwave Limb Sounder (MLS) and the Infrared Atmospheric Sounding Interferometer (IASI) in a global chemical transport model (MOdèle de Chimie Atmosphérique à Grande Échelle, MOCAGE). The assimilation of the two instruments is performed by means of a variational algorithm (4-D-VAR) and allows to constrain stratospheric and tropospheric ozone simultaneously. The analysis is first computed for the months of August and November 2008 and validated against ozone-sondes measurements to verify the presence of observations and model biases. It is found that the IASI Tropospheric Ozone Column (TOC, 1000-225 hPa) should be bias-corrected prior to assimilation and MLS lowermost level (215 hPa) excluded from the analysis. Furthermore, a longer analysis of 6 months (July--August 2008) showed that the combined assimilation of MLS and IASI is able to globally reduce the uncertainty (Root Mean Square Error, RMSE) of the modeled ozone columns from 30% to 15% in the Upper- Troposphere/Lower-Stratosphere (UTLS, 70-225 hPa) and from 25% to 20% in the free troposphere. The positive effect of assimilating IASI tropospheric observations is very significant at low latitudes (30° S-30° N), whereas it is not demonstrated at higher latitudes. Results are confirmed by a comparison with additional ozone datasets like the Measurements of OZone and wAter vapour by aIrbus in-service airCraft (MOZAIC) data, the Ozone Monitoring Instrument (OMI) total ozone columns and several highaltitude surface measurements. Finally, the analysis is found to be little sensitive to the assimilation parameters and the model chemical scheme, due to the high frequency of satellite observations compared to the average life-time of free-troposphere/low-stratosphere ozone. [ABSTRACT FROM AUTHOR]

The pixel size of the Infrared Atmospheric Sounding Interferometer (IASI) remote sensor is much smaller than the horizontal grid size of current Chemical Transport Models (CTMs). In order to assimilate the maximum of information from the IASI retrievals, we have increased the horizontal resolution of our model MOCAGE to be consistent with the IASI pixel size. Experiments are carried out with the Valentina data assimilation system using the standard and the high resolution versions of the model. Two resolutions of the horizontal Gaussian grid have been used for the model: with a T42 and a T170 triangular truncations. Our study is based on the combination of data from the IASI instrument and from the Microwave Limb Sounder (MLS), since this latter dataset allows the information to be spread through the whole atmospheric columns at a low computational cost. Two datasets of ozone super-observations have been constructed by averaging the IASI data on the two model grids. Direct model simulations without data assimilation first show that the increase of the horizontal resolution modifies the ozone smallest scale structures as well as the ozone meridional distribution. This modification results from a better representation of the vertical velocity with the T170 configuration. When the ozone assimilation is performed there is less influence of the horizontal resolution of the model. Nevertheless, in a general way, comparisons with independent data show large reductions of the ozone standard deviations when the resolution is increased. When the ozone assimilation is performed with the high resolution dataset, the high resolution model does not improve the ozone analysis compared to the one obtained with the same model resolution but with the low resolution IASI dataset. This result is due to the difficulty to combine IASI data and MLS data. For assimilating IASI data at high resolution the horizontal correlation length-scale has to be decreased to catch the small scale structures present in the dataset. By doing so the indluence of the coarser resolution MLS data is decreased and part of the information brought on the vertical shape of the ozone profile is lost. It is concluded that it is essential to add information on the vertical distribution of ozone column when the IASI data is assimilated at a resolution close to the pixel size. Using IASI averaging kernels would likely improve the simulations, but the computational cost would be much higher. Alternatively, better results might be obtained by a careful tuning of the horizontal correlation length-scale. [ABSTRACT FROM AUTHOR]

The article presents a study which compares observing system simulation experiments (OSSEs) with geostationary (GEO) thermal infrared (TIR) instruments to measure ozone (O3) and carbon monoxide (CO) for monitoring air quality (AQ) in Europe. The study aims on using OSSEs to assess how infrared instruments restrain different errors affecting AQ. Based on results, GEO-TIR has a significant impact on O3 and CO analyses, and that its impact can improve surface analyses in the lowermost troposphere.

This paper presents a comprehensive characterization of a very deep stratospheric intrusion which occurred over the British Isles on 15 August 2007. The signature of this event is diagnosed using ozonesonde measurements over Lerwick, UK (60.14° N, 1.19° W) and is also well characterized using meteorological analyses from the global operational weather prediction model of Météo-France, ARPEGE. Modelled as well as assimilated fields of both ozone (O3) and carbon monoxide (CO) have been used in order to better document this event. O3 and CO from Aura/MLS and Terra/MOPITT instruments, respectively, are assimilated into the three-dimensional chemical transport model MOCAGE of Météo-France using a variational 3-DFGAT (First Guess at Appropriate Time) method. The validation of O3 and CO assimilated fields is done using selfconsistency diagnostics and by comparison with independent observations such as MOZAIC (O3 and CO), AIRS (CO) and OMI (O3). It particularly shows in the upper troposphere and lower stratosphere region that the assimilated fields are closer to MOZAIC than the free model run. The O3 bias between MOZAIC and the analyses is -11.5 ppbv with a RMS of 22.4 ppbv and a correlation coefficient of 0.93, whereas between MOZAIC and the free model run, the corresponding values are 33 ppbv, 38.5 ppbv and 0.83, respectively. In the same way, for CO, the bias, RMS and correlation coefficient between MOZAIC and the analyses are -3.16 ppbv, 13 ppbv and 0.79, respectively, whereas between MOZAIC and the free model they are 6.3 ppbv, 16.6 ppbv and 0.71, respectively. The paper also presents a demonstration of the capability of O3 and CO assimilated fields to better describe a stratosphere-troposphere exchange (STE) event in comparison with the free run modelled O3 and CO fields. Although the assimilation of MLS data improves the distribution of O3 above the tropopause compared to the free model run, it is not sufficient to reproduce the STE event well. Assimilated MOPITT CO allows a better qualitative description of the stratospheric intrusion event. The MOPITT CO analyses appear more promising than the MLS O3 analyses in terms of their ability to capture a deep STE event. Therefore, the results of this study open the perspectives for using MOPITT CO in the STE studies. [ABSTRACT FROM AUTHOR]

This paper presents a complete characterization of a very deep stratospheric intrusion which occurred over the British Isles on 15 August 2007. The signature of this event is diagnosed using ozonesonde measurements over Lerwick, UK (60.14° N, 1.19° W) and is also well characterized using meteorological analyses from the global operational weather prediction model of Météo-France, ARPEGE. Modelled as well as assimilated fields of both ozone (O3) and carbon monoxide (CO) have been used in order to better document this event. The paper also presents a demonstration of the capability of O3 and CO assimilated fields to better describe a stratosphere-troposphere exchange (STE) event in comparison with the free run modelled O3 and CO fields. O3 and CO from Aura/MLS and Terra/MOPITT instruments, respectively, are assimilated into the three-dimensional chemical transport model MOCAGE of Météo-France using a variational 3-D-FGAT (First Guess at Appropriate Time) method within the MOCAGE-PALM assimilation system. The usefulness of assimilated MOPITT CO data in a STE study is demonstrated in this novel result. The study shows that the use of the model MOCAGE gives consistent 3-D fields capable of describing the synoptic evolution of the event. However, modelled O3 and CO vertical distributions do not provide a quantitative evaluation of the intrusion. Although the assimilation of MLS data improves the distribution of O3 above the tropopause compared to the free model run, it is not sufficient to reproduce the stratospheric intrusion event well. Conversely, assimilated MOPITT CO allows a better description of the stratospheric intrusion event. Indeed, the horizontal distribution of the CO assimilated field is consistent with meteorological analyses. Moreover, the vertical distribution of the CO assimilated field is in accordance with the potential vorticity distribution and reveals a deeper intrusion from the lower stratosphere downward to the mid-troposphere compared to the O3 assimilated field. This study clearly demonstrates the capability of the assimilation of MOPITT CO to improve the CO distribution in the upper troposphere and lower stratosphere region. In addition, the behaviour of CO assimilated field is consistent with the synoptic evolution of the meteorological conditions. Therefore, the results of this study open the perspectives for using MOPITT CO in the STE studies. [ABSTRACT FROM AUTHOR]

Recent technological development of molecular methods has led to the proliferation of new rapid PCR or reverse-transcriptase (RT)-PCR-derived diagnostic tests for plant viruses. Nevertheless, for routine use, the reliability of all these new methods is not widely established and there is still an apprehension to adopt them in official diagnostic for certification of plant material. This is partly because of the lack of confidence in the obtained results and the poor knowledge on the reproducibility and limits of the RT-PCR protocols. There is a lack of information on the adequate risk assessment in the use of this new technology. An interlaboratory evaluation of two RT-PCR duplex protocols for the detection of four different fruit tree viruses was performed to address these questions. Identical samples were sent as crude extract preparation to each of the participant laboratories. Samples were coded to ensure a double-blind test. General principles of result analysis are described, for example calculation of parameters such as specificity, sensitivity, repeatability, reproducibility, likelihood ratios and post-test probabilities. These parameters and the integration of the protocols within official certification scheme are discussed. Finally, guidelines for researchers desirous of validating their new plant virus diagnostic protocols through interlaboratory evaluation are suggested. [ABSTRACT FROM AUTHOR]

The presence of Peach latent mosaic viroid (PLMVd) was monitored during 2 years in peach orchards located in the North of Tunisia. PLMVd population was surveyed using a specific RT-PCR test adapted to crude sap extract. During the first year (2004), 228 samples were randomly selected in 22 peach orchards (eight cultivars) and tested for the presence of PLMVd. Results showed that PLMVd is highly and equally present in four regions of the North of Tunisia. Analyses of some key factors in relation to PLMVd incidence revealed that the tree age did not influence the infection rate. The eight studied cultivars were clustered in three groups according to their PLMVd incidence. Furthermore, the early and season cultivars were statistically more infected than the late cultivars. Prospections in May and October 2005 were performed in four selected orchards. Each two orchards contained Early May Crest (early cultivar) and Carnival (late cultivar) cultivars, respectively. The difference in PLMVd incidence observed in 2004 was confirmed. Furthermore, no correlation between the tree physiological state and the viroid detection was observed. Further investigations on the origin of the differences in PLMVd incidence between Early May Crest and Carnival cultivars would be of interest. [ABSTRACT FROM AUTHOR]

VALITEST is an EU‐funded project built to improve the reliability of diagnostic tests performed in plant health laboratories across the European and Mediterranean region. The project is undertaken by a consortium of 16 partners composed of research institutions, private companies (such as diagnostic kit providers), national plant protection organizations and one intergovernmental organization (EPPO). Current harmonized procedures for the validation and organization of test performance studies will be improved based on the experience gained from the project and by including appropriate statistical approaches, by adapting the process for new promising technologies (e.g. high‐throughput sequencing) and by providing new guidelines for the production of reference materials for validation studies. The project will provide a more complete and precise description of the performance of 82 diagnostic tests targeting 11 pests of interest for stakeholders of the region. It will also tackle the need for proficient users by developing a horizontal approach for the evaluation of laboratories' proficiency and by organizing training activities on the concept of validation. The outcomes of the project will stimulate, optimize and strengthen the interactions between stakeholders in plant health for better diagnostics and lay the foundations for structuring the quality and the commercial offers for plant health diagnostics tools thanks to the creation of a dedicated association and a quality charter. [ABSTRACT FROM AUTHOR]

Background Chemotherapy is commonly used as myeloablative conditioning treatment to prepare patients for haematopoietic stem cell transplantation ( HSCT). Chemotherapy leads to several side effects, with gastrointestinal ( GI) mucositis being one of the most frequent. Current models of GI mucositis pathophysiology are generally silent on the role of the intestinal microbiome. Aim To identify functional mechanisms by which the intestinal microbiome may play a key role in the pathophysiology of GI mucositis, we applied high-throughput DNA-sequencing analysis to identify microbes and microbial functions that are modulated following chemotherapy. Methods We amplified and sequenced 16S rRNA genes from faecal samples before and after chemotherapy in 28 patients with non-Hodgkin's lymphoma who received the same myeloablative conditioning regimen and no other concomitant therapy such as antibiotics. Results We found that faecal samples collected after chemotherapy exhibited significant decreases in abundances of Firmicutes ( P = 0.0002) and Actinobacteria ( P = 0.002) and significant increases in abundances of Proteobacteria ( P = 0.0002) compared to samples collected before chemotherapy. Following chemotherapy, patients had reduced capacity for nucleotide metabolism ( P = 0.0001), energy metabolism ( P = 0.001), metabolism of cofactors and vitamins ( P = 0.006), and increased capacity for glycan metabolism ( P = 0.0002), signal transduction ( P = 0.0002) and xenobiotics biodegradation ( P = 0.002). Conclusions Our study identifies a severe compositional and functional imbalance in the gut microbial community associated with chemotherapy-induced GI mucositis. The functional pathways implicated in our analysis suggest potential directions for the development of intestinal microbiome-targeted interventions in cancer patients. [ABSTRACT FROM AUTHOR]

The cultivation of pineapple ( Ananas comosus ) is threatened worldwide by mealybug wilt disease of pineapple (MWP), whose etiology is not yet fully elucidated. In this study, we characterized pineapple mealybug wilt-associated ampeloviruses (PMWaVs, family Closteroviridae ) from a diseased pineapple plant collected from Reunion Island, using a high-throughput sequencing approach combining Illumina short reads and Nanopore long reads. Reads co-assembly resulted in complete or near-complete genomes for six distinct ampeloviruses, including the first complete genome of pineapple mealybug wilt-associated virus 5 (PMWaV5) and that of a new species tentatively named pineapple mealybug wilt-associated virus 7 (PMWaV7). Short reads data provided high genome coverage and sequencing depths for all six viral genomes, contrary to long reads data. The 5' and 3' ends of the genome for most of the six ampeloviruses could be recovered from long reads, providing an alternative to RACE-PCRs. Phylogenetic analyses did not unveil any geographic structuring of the diversity of PMWaV1, PMWaV2 and PMWaV3 isolates, supporting the current hypothesis that PMWaVs were mainly spread by human activity and vegetative propagation., Competing Interests: The authors declare no conflicts of interest.

Phosphorus constitutes a crucial macronutrient for crop growth, yet its availability often limits food production. Efficient phosphorus management is crucial for enhancing crop yields and ensuring food security. This study aimed to enhance the efficiency of a short-chain polyphosphate (PolyP) fertilizer by integrating it with plant growth-promoting bacteria (PGPB) to improve nutrient solubilization and wheat growth. Specifically, the study investigated the effects of various bacterial strains on wheat germination and growth when used in conjunction with PolyP. To achieve this, a greenhouse experiment was conducted in which the wheat rhizosphere was amended with a short-chain PolyP fertilizer. Based on the morphological aspect, eight bacteria, designated P1 to P8, were isolated and further characterized. Plant growth-promoting traits were observed in all bacterial strains, as they presented the ability to produce Indole Acetic Acid (IAA) in significant amounts ranging from 7.5 ± 0.3 µg/mL to 44.1 ± 2 µg/mL, expressed by B. tropicus P4 and P. soyae P1, respectively. They also produced ammonia, hydrogen cyanide (HCN), and siderophores. Their effect against the plant pathogen Fusarium culmorum was also assessed, with P. reinekei P2 demonstrating the highest biocontrol activity as it presented a total inhibitory effect. Additionally, some strains exhibited the ability to solubilize/hydrolyze phosphorus, potassium, and zinc. In vivo, the initial growth potential of wheat seeds indicated that those inoculated with the isolated strains exhibited elevated germination rates and enhanced root growth. Based on their plant growth-promoting traits and performance in the germination assay, three strains were selected for producing the best results, specifically phosphorus hydrolyzation/solubilization, zinc solubilization, IAA production, HCN, and siderophores production. Wheat seeds were inoculated by drenching in a bacterial suspension containing 10 10 CFU/mL of log phase culture, and an in planta bioassay was conducted in a growth chamber using three selected strains ( Pseudomonas soyae P1, Pseudomonas reinekei P2, and Bacillus tropicus P4), applied either individually or with PolyP on a P-deficient soil (28 mg/kg of P Olsen). Our findings demonstrated that the combination of Pseudomonas soyae P1 and PolyP achieved the highest shoot biomass, averaging 41.99 ± 0.87 g. Notably, applying P. soyae P1 or Bacillus tropicus P4 alone yielded similar results to the use of PolyP alone. At the heading growth stage, the combination of Bacillus tropicus P4 and PolyP significantly increased the Chlorophyll Content Index (CCI) to 37.02 µmol/m 2 , outperforming both PolyP alone (24.07 µmol/m 2 ) and the control (23.06 µmol/m 2 ). This study presents an innovative approach combining short-chain PolyP with bacterial biostimulants to enhance nutrient availability and plant growth. By identifying and characterizing effective bacterial strains, it offers a sustainable alternative to conventional fertilizers.