Investigation of the ALICE-MUON forward spectrometer performances for Upsilon measurement

ALICE, présenté par F. Guérin, à paraître dans les proceedings: European physical Journal CALICE (A Large Ion Collider Experiment) is the LHC detector dedicated to the study of nucleus-nucleus collisions, in which the formation of the Quark Gluon Plasma (QGP) is expected. Heavy quarkonia, especially the Upsilon states, are relevant for studying the QGP since they provide an essential probe of the earliest and hottest stages of heavy ion collisions. They will be measured via their dimuon decay channel in ALICE in the muon spectrometer. The muon spectrometer performance has been studied in simulations, the results will be presented with emphasis on the trigger efficiency and rate in Pb-Pb collisions. The expected yields of Upsilon states will be extracted from a simulation based on a global fit of the dimuon mass spectra for different collision centralities

Etude des performances du système de déclenchement du spectromètre à muons de l'expérience ALICE

ALICE (A Large Ion Collider Experiment) est une expérience dédiée à l'étude des collisions d'ions lourds ultra-relativistes qui opèrera au LHC (Large Hadron Collider) en 2007. Le but de cette expérience est de mettre en évidence et d'étudier le plasma de quarks et de gluons (QGP). Une des signatures possibles de ce nouvel état de la matière est la variation du taux de production des quarkonia lorsque l'on passe d'une phase purement hadronique à une phase de déconfinement. Le spectromètre à muons d'ALICE permettra de détecter les quarkonia via le canal de désintégration en dimuons. Un système de déclenchement appelé ``trigger'' associé au spectromètre permet de sélectionner les événements physiquement intéressants (contenant des quarkonia) en effectuant des coupures sur l'impulsion transverse des muons. Cet article présente les performances du système de déclenchement du spectromètre à muons d'ALICE en terme d'efficacité de détection et de taux de trigger

Sources and transfers of particulate organic matter in a tropical reservoir (Petit Saut, French Guiana): a multi-tracers analysis using d¹³C, C/N ratio and pigments

International audienceCarbon cycling and organic matter transfers in the tropical Sinnamary river system (French Guiana), including a mid-stream reservoir (Petit Saut) and its estuary on the Atlantic coast, were studied during the dry season by analyzing the organic carbon isotopic ratios (d13C-OC), C/N ratios and pigments contents of suspended matter, sediments, sediments traps and epiphytic and epilithic biofilms. In the River upstream as well as in surface sediments at the entrance of the reservoir and at the littoral zone of the reservoir, particulate organic matter (POM) was in majority of terrestrial origin, with a d13C-C/N signature close to the one of soil and litter collected in the surrounding forest and with high OC/total pigments ratios. High concentrations of Pheopigments a and b in these surface sediments showed that this terrestrial POM, either carried by the river and eolian transport or present in the soil before flooding, undergoes intense degradation. Deeper in the sediment, the d13C profile showed a decreasing trend with depth typical of what is found in soils, showing that the flooded soil still remains present at the reservoir bottom 10 years after flooding. At the center of the reservoir, POM in the water column, in sediment traps and in surface sediments was in majority of aquatic origin with low C/N and OC/total pigments ratios. In the oxic epilimnion at 3 m depth, Chl a, Chl b and Lutein showed the predominance of Chlorophyceae to the phytoplankton community. At this depth, a C/N ratio of 21 suggests a large contribution of transparent exopolymeric particles to the bulk POM, which, in addition, was 13C-depleted due to a significant contribution of methanotrophic bacteria. At 7 m depth, below the oxicline, high concentrations of BChl d and occasionally BChl c revealed the presence of anoxygenic phototrophic bacteria, namely Chlorobiaceae. In the sediment traps, Chl a, Chl b, Lutein and BChl c and BChl d confirmed the contribution of plankton to the sedimentary POM. This material was undergoing intense degradation as revealed by high concentration of pheopigments and by an increase in C/N ratio and an increase in d13C-OC with trap depth. Scytonemin was found in a biofilm developed on tree trunks at the reservoir surface and in all sediment traps. Other tracers showed however that the contribution of the biofilm to the sedimentary POM was minor compared to the planktonic source. In the Sinnamary downstream of the dam, POM became more 13C-depleted showing a larger contribution of methanotrophic bacteria. Chl b, Lutein and BChl c + BChl d originating from the reservoir progressively decreased downstream as the result of mineralization. At the estuarine mouth, fucoxanthin showed the presence of diatoms and the d13C-C/N signature matched the one of POM carried by the Amazonian coastal mobile mud belt

Increasing feed production using legume and cereal mixtures as a second crop (DiverIMPACTS Practice Abstract)

Improved feed diversity and more resilient feed production, less dependent on soybean imports. This strategy helps to mitigate droughts effects, through an “avoidance strategy”, with production of forage during seasons less likely to be affected by such phenomenon. Other benefits include improved soil biodiversity and soil health, reduced leaching during winter (as mixtures are used as cover crops) and benefits associated with incorporating residues from roots and crops (nitrogen availability for maize, carbon input to the soil, etc.)

An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022

During the recent avian influenza epizootics that occurred in France in 2020/21 and 2021/22, the virus was so contagiousness that it was impossible to control its spread between farms. The preventive slaughter of millions of birds consequently was the only solution available. In an effort to better understand the spread of avian influenza viruses (AIVs) in a rapid and innovative manner, we established an amplicon-based MinION sequencing workflow for the rapid genetic typing of circulating AIV strains. An amplicon-based MinION sequencing workflow based on a set of PCR primers targeting primarily the hemagglutinin gene but also the entire influenza virus genome was developed. Thirty field samples from H5 HPAIV outbreaks in France, including environmental samples, were sequenced using the MinION MK1C. A real-time alignment of the sequences with MinKNOW software allowed the sequencing run to be stopped as soon as enough data were generated. The consensus sequences were then generated and a phylogenetic analysis was conducted to establish links between the outbreaks. The whole sequence of the hemagglutinin gene was obtained for the 30 clinical samples of H5Nx HPAIV belonging to clade 2.3.4.4b. The consensus sequences comparison and the phylogenetic analysis demonstrated links between some outbreaks. While several studies have shown the advantages of MinION for avian influenza virus sequencing, this workflow has been applied exclusively to clinical field samples, without any amplification step on cell cultures or embryonated eggs. As this type of testing pipeline requires only a short amount of time to link outbreaks or demonstrate a new introduction, it could be applied to the real-time management of viral epizootics

Genome sequencing of Xanthomonas axonopodis pv. phaseoli CFBP4834-R reveals that flagellar motility is not a general feature of xanthomonads.

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap and filament) are absent in the genome of strain 4834-R that is not motile. Primers were designed to detect this deletion by PCR in a collection of more than 300 strains representing different species and pathovars of Xanthomonas, and less than 5% of the tested xanthomonads strains were found nonmotile because of a deletion in the flagellum gene cluster. We observed that half of the Xapf strains isolated from the same epidemic than strain 4834-R was non-motile and that this ratio was conserved in the strains colonizing the next bean seed generation. Isolation of such variants in a natural epidemic reveals that either flagellar motility is not a key function for fitness or that some complementation occurs within the bacterial population. (Résumé d'auteur