Statistical analysis of pulse propagation driven by polarization-mode dispersion

International audienceThe linear propagation of pulses driven by random polarization-mode dispersion is considered. Analytical expressions are derived for the probability-density functions of the pulse width, timing displacement, and degree of polarization. The study is performed in Stokes space, and frequency correlation between modes is shown to play an important role in it

Contribution à l'étude des transmissions optiques sous-marines multiplexées en longueur d'onde à 40Gbit/s par l'étude de la gestion de dispersion et du format

PARIS-EST Marne-la-Vallee-BU (774682101) / SudocSudocFranceF

Inactivation of the RRB1-Pescadillo pathway involved in ribosome biogenesis induces chromosomal instability

International audienceSince chromosomal instability (CIN) is a hallmark of most cancer cells, it is essential to identify genes whose alteration results into this genetic instability. Using a yeast CIN indicator strain, we show that inactivation of the YMR131c/RRB1 gene, which is involved in early ribosome assembly and whose expression is induced when the spindle checkpoint is activated, alters chromosome segregation and blocks mitosis at the metaphase/anaphase transition. We demonstrate that RRB1 interacts with YPH1 (yeast pescadillo homologue 1) and other members of the Yph1 complex, RPL3, ERB1 and ORC6, involved in ribosome biogenesis and DNA replication. Transient depletion of the human homologues GRWD, Pescadillo, Rpl3, Bop1 and Orc6L resulted in an increase of abnormal mitoses with appearance of binucleate or hyperploid cells, of cells with multipolar spindles and of aberrant metaphase plates. If deregulation of proteins involved in ribosome biogenesis, commonly observed in malignant tumors, could contribute to cancer through an aberrant protein synthesis, our study demonstrates that alteration of proteins linking ribosome biogenesis and DNA replication may directly cause CIN

Pneumocystis jirovecii haplotypes at the internal transcribed spacers of the rRNA operon in French HIV-negative patients with diverse clinical presentations of Pneumocystis infections.

International audiencePneumocystis jirovecii, a transmissible fungus, is the causative agent of pulmonary infections. Its genomic diversity has appeared in reports from around the world but data on P. jirovecii genotypes in France are still limited. This study describes the typing of P. jirovecii isolates from 81 HIV-negative patients monitored at Brest University Hospital, Brittany, France, 40 of whom developed Pneumocystis pneumonia (PcP), and remaining 41 patients were colonized by the fungus. The isolates were assayed at the internal transcribed spacer (ITS)1 and ITS2 under improved amplification conditions to avoid in vitro ITS recombination. P. jirovecii ITS haplotypes were identified in 56/81 patients (31 PcP patients and 25 patients who were colonized) which revealed a high diversity in that 27 different haplotypes were identified. Eg was the most frequent haplotype (31/56, 55.3%), followed by Ec and Ai (5/56, 8.9% each). In contrast, Ne, usually the second most frequent haplotype in Europe and the USA, was observed in only 2/56 patients (3.6%). Mixed infections were detected in 18/56 patients (32.1%; 12 PcP patients and six who were colonized). No significant differences were observed in haplotype diversity, frequency of peculiar haplotypes, and mixed infection occurrence, between the two patient populations. The study, conducted with the largest HIV-negative patient population investigated so far, shows that ITS typing remains an efficient method for characterizing P. jirovecii among human populations, whatever their clinical presentation of Pneumocystis infections

Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation

International audienceThe detection of copy-number variations (CNVs) from NGS data is underexploited as chip-based or targeted techniques are still commonly used. We assessed the performances of a workflow centered on CANOES, a bioinformatics tool based on read depth information. We applied our workflow to gene panel (GP) and whole-exome sequencing (WES) data, and compared CNV calls to quantitative multiplex PCR of short fluorescent fragments (QMSPF) or array comparative genomic hybridization (aCGH) results. From GP data of 3776 samples, we reached an overall positive predictive value (PPV) of 87.8%. This dataset included a complete comprehensive QMPSF comparison of four genes (60 exons) on which we obtained 100% sensitivity and specificity. From WES data, we first compared 137 samples with aCGH and filtered comparable events (exonic CNVs encompassing enough aCGH probes) and obtained an 87.25% sensitivity. The overall PPV was 86.4% following the targeted confirmation of candidate CNVs from 1056 additional WES. In addition, our CANOES-centered workflow on WES data allowed the detection of CNVs with a resolution of single exons, allowing the detection of CNVs that were missed by aCGH. Overall, switching to an NGS-only approach should be cost-effective as it allows a reduction in overall costs together with likely stable diagnostic yields. Our bioinformatics pipeline is available at: https://gitlab.bioinfo-diag.fr/nc4gpm/canoes-centered-workflow

Polyols and glucose particulate species as tracers of primary biogenic organic aerosols at 28 French sites

A growing number of studies are using specific primary sugar species, such as sugar alcohols or primary saccharides, as marker compounds to characterize and apportion primary biogenic organic aerosols (PBOAs) in the atmosphere. To better understand their annual cycles, as well as their spatiotemporal abundance in terms of concentrations and sources, we conducted a large study focusing on three major atmospheric primary sugar compounds (i.e., arabitol, mannitol, and glucose) measured in various environmental conditions for about 5300 filter samples collected at 28 sites in France. Our results show significant atmospheric concentrations of polyols (defined here as the sum of arabitol and mannitol) and glucose at each sampling location, highlighting their ubiquity. Results also confirm that polyols and glucose are mainly associated with the coarse rather than the fine aerosol mode. At nearly all sites, atmospheric concentrations of polyols and glucose display a well-marked seasonal pattern, with maximum concentrations from late spring to early autumn, followed by an abrupt decrease in late autumn, and a minimum concentration during wintertime. Such seasonal patterns support biogenic emissions associated with higher biological metabolic activities (sporulation, growth, etc.) during warmer periods. Results from a previous comprehensive study using positive matrix factorization (PMF) based on an extended aerosol chemical composition dataset of up to 130 species for 16 of the same sample series have also been used in the present work. The polyols-to-PMPBOA ratio is 0.024 +/- 0.010 on average for all sites, with no clear distinction between traffic, urban, or rural typology. Overall, even if the exact origin of the PBOA source is still under investigation, it appears to be an important source of particulate matter (PM), especially during summertime. Results also show that PBOAs are significant sources of total organic matter (OM) in PM10 (13 +/- 4% on a yearly average, and up to 40% in some environments in summer) at most of the investigated sites. The mean PBOA chemical profile is clearly dominated by contribution from OM (78 +/- 9% of the mass of the PBOA PMF on average), and only a minor contribution from the dust class (3 +/- 4 %), suggesting that ambient polyols are most likely associated with biological particle emissions (e.g., active spore discharge) rather than soil dust resuspension

Arabitol, mannitol, and glucose as tracers of primary biogenic organic aerosol : the influence of environmental factors on ambient air concentrations and spatial distribution over France

The primary sugar compounds (SCs, defined as glucose, arabitol, and mannitol) are widely recognized as suitable molecular markers to characterize and apportion primary biogenic organic aerosol emission sources. This work improves our understanding of the spatial behavior and distribution of these chemical species and evidences their major effective environmental drivers. We conducted a large study focusing on the daily (24 h) PM10 SC concentrations for 16 increasing space scale sites (local to nationwide), over at least 1 complete year. These sites are distributed in several French geographic areas of different environmental conditions. Our analyses, mainly based on the examination of the short-term evolutions of SC concentrations, clearly show distance-dependent correlations. SC concentration evolutions are highly synchronous at an urban city scale and remain well correlated throughout the same geographic regions, even if the sites are situated in different cities. However, sampling sites located in two distinct geographic areas are poorly correlated. Such a pattern indicates that the processes responsible for the evolution of the atmospheric SC concentrations present a spatial homogeneity over typical areas of at least tens of kilometers. Local phenomena, such as the resuspension of topsoil and associated microbiota, do no account for the major emissions processes of SC in urban areas not directly influenced by agricultural activities. The concentrations of SC and cellulose display remarkably synchronous temporal evolution cycles at an urban site in Grenoble, indicating a common source ascribed to vegetation. Additionally, higher concentrations of SC at another site located in a crop field region occur during each harvest periods, indicating resuspension processes of plant materials (crop detritus, leaf debris) and associated microbiota for agricultural and nearby urbanized areas. Finally, ambient air temperature, relative humidity, and vegetation density constitute the main effective drivers of SC atmospheric concentrations