Proof-of-principle demonstration of vertical gravity gradient measurement using a single proof mass double-loop atom interferometer

We demonstrate a proof-of-principle of direct Earth gravity gradient measurement with an atom interferometer-based gravity gradiomter using a single proof mass of cold 87 rubidium atoms. The atomic gradiometer is implemented in the so-called double-loop configuration, hence providing a direct gravity gradient dependent phase shift insensitive do DC acceleration and constant rotation rate. The atom interferometer (AI) can be either operated as a gravimeter or a gradiomter by simply adding an extra Raman $\pi$-pulse. We demonstrate gravity gradient measurements first using a vibration isolation platform and second without seismic isolation using the correlation between the AI signal and the vibration signal measured by an auxilliary classical accelerometer. The simplicity of the experimental setup (a single atomic source and unique detection) and the immunity of the AI to rotation-induced contrast loss, make it a good candidate for onboard gravity gradient measurements.Comment: 11 pages, 7 figure

Protéines à motif tripartite (TRIM) chez le porc (Sus scrofa) et réplication du rétrovirus endogène porcin

Les études des interactions entre cellules hôtes et rétrovirus ont conduit à définir le concept de restriction virale dont les facteurs constituent une part de l'immunité innée des cellules hôtes. Ces facteurs contribuent au contrôle des rétrovirus endogènes (ERV) dont l'émergence peut être associée à certaines pathologies telles que des leucémies ou des immunodéficiences. Chez le porc, certains ERV (PERV) sont réplicatifs, pourtant aucune pathologie ne leur a, à ce jour, été associée. Les mécanismes de restriction virale impliqués dans ce phénomène ont fait l'objet de nombreuses études. Elles n'ont cependant concerné que certains facteurs. Les protéines porcines à motif tripartite (poTRIM) n'ont ainsi fait l'objet que de peu d'études. Pourtant, de nombreux membres de cette famille participent à la restriction virale chez d'autres organismes que le porc. La présente étude s'intéresse par conséquent aux orthologues porcins de ces protéines et à leur relation avec les PERV. L'élaboration d'une stratégie d'expression de ces protéines dans un modèle humain, sensible à l'infection par le PERV nous a permis d'évaluer et de caractériser les effets des TRIM sur le cycle infectieux du PERV. Cette stratégie a mis en évidence une activité de restriction par TRIM8 tandis que TRIM44 semble au contraire agir en faveur de la réplication virale. En ce qui concerne poTRIM11, elle favorise l'entrée du PERV tout en inhibant son expression. L'étude a également confirmé l'insensibilité du PERV vis-à-vis de poTRIM5a. L'ensemble de ces résultats contribuent à la compréhension de la relation entre la réplication des PERV et le contrôle mené par son hôte.From studies of pathogens and their host interaction has emerged the concept of viral restriction considered to be part of an innate immune system. These factors contribute to the control of endogenous retroviruses (ERV) whose emergence may be associated with several diseases such as leukemia or immunodeficiency. Three subgroups of the porcine ERV-g-1 group (PERV) are replicative. Nevertheless, these PERVs are not associated with any pathology in the pig. Several studies have been performed on viral restriction mechanism capabilities of the pig but these covered a very limited number of restriction factors. Regarding the porcine tripartite motif-containing (poTRIM) proteins, knowledge is weak although several members of this family have proved to be implicated in the viral restriction of other species. The purpose of this study is to investigate the relationship between these orthologous poTRIMs proteins and replicating PERVs. In order to explore this potential interaction, a TRIM protein expressing model in human cells, known to be sensitive to the PERV infection, has been developed. It has enabled us to assess and characterize potential TRIMs effects on the PERV infection cycle. We equally identified poTRIM8 as a restriction factor. Conversely, poTRIM44 seems to act as an enhancer of the PERV infection, while, TRIM11 displayed ambiguous effects including an enhancer effect of the early infectious stages and an inhibitor activity of the late infectious stages. In this study, we also confirmed the PERV insensitivity to the porcine TRIM5a protein. Finally, this work aims at contributing to the understanding of the relationship between PERV replication and their control leading by the host cells.RENNES1-Bibl. électronique (352382106) / SudocSudocFranceF

Zero-velocity atom interferometry using a retroreflected frequency chirped laser

International audienceAtom interferometry using stimulated Raman transitions in a retroreflected configuration is the first choice in high-precision measurements because it provides low phase noise, a high-quality Raman wave front, and a simple experimental setup. However, it cannot be used for atoms at zero velocity because two pairs of Raman lasers are simultaneously resonant. Here we report a method which allows this degeneracy to be lifted by using a frequency chirp on the Raman lasers. Using this technique, we realize a Mach-Zehnder atom interferometer hybridized with a force balanced accelerometer which provides horizontal acceleration measurements with a short-term sensitivity of 3.2×10−5ms−2/Hz. This technique could be used for multiaxis inertial sensors, tiltmeters, or atom interferometry in a microgravity environment

Open Access

Differential cellular gene expression in duck trachea infected with a highly or low pathogenic H5N1 avian influenza viru

Absolute airborne gravimetry with a cold atom sensor

Measuring gravity from an aircraft is essential in geodesy, geophysics and exploration. Today, only relative sensors are available for airborne gravimetry. This is a major drawback because of the calibration and drift estimation procedures which lead to important operational constraints and measurement errors. Here, we report an absolute airborne gravimeter based on atom interferometry. This instrument has been first tested on a motion simulator leading to gravity measurements noise of 0.3 mGal for 75 s filtering time constant. Then, we realized an airborne campaign across Iceland in April 2017. From a repeated line and crossing points, we obtain gravity measurements with an estimated error between 1.7 and 3.9 mGal. The airborne measurements have also been compared to upward continued ground gravity data and show differences with a standard deviation ranging from 3.3 to 6.2 mGal and a mean value ranging from-0.7 mGal to-1.9 mGal

Acute induction of cell death-related IFN stimulated genes (ISG) differentiates highly from moderately virulent CSFV strains

Classical swine fever (CSF) severity is dependent on the virulence of the CSF virus (CSFV) strain. The earliest event detected following CSFV infection is a decrease in lymphocytes number. With some CSFV strains this leads to lymphopenia, the severity varying according to strain virulence. This lymphocyte depletion is attributed to an induction of apoptosis in non-infected bystander cells. We collected peripheral blood mononuclear cells (PBMC) before and during 3 days post-infection with either a highly or moderately virulent CSFV strain and subjected them to comparative microarray analysis to decipher the transcriptomic modulations induced in these cells in relation to strain virulence. The results revealed that the main difference between strains resided in the kinetics of host response to the infection: strong and immediate with the highly virulent strain, progressive and delayed with the moderately virulent one. Also although cell death/apoptosis-related IFN stimulated genes (ISG) were strongly up-regulated by both strains, significant differences in their regulation were apparent from the observed differences in onset and extent of lymphopenia induced by the two strains. Furthermore, the death receptors apoptotic pathways (TRAIL-DR4, FASL-FAS and TNFa-TNFR1) were also differently regulated. Our results suggest that CSFV strains might exacerbate the interferon alpha response, leading to bystander killing of lymphocytes and lymphopenia, the severity of which might be due to the host’s loss of control of IFN production and downstream effectors regulation

An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material

Metagenomic shotgun sequencing (mNGS) can serve as a generic molecular diagnostic tool. An mNGS proficiency test (PT) was performed in six European veterinary and public health laboratories to detect porcine astroviruses in fecal material and the extracted RNA. While different mNGS workflows for the generation of mNGS data were used in the different laboratories, the bioinformatic analysis was standardized using a metagenomic read classifier as well as read mapping to selected astroviral reference genomes to assess the semiquantitative representation of astrovirus species mixtures. All participants successfully identified and classified most of the viral reads to the two dominant species. The normalized read counts obtained by aligning reads to astrovirus reference genomes by Bowtie2 were in line with Kraken read classification counts. Moreover, participants performed well in terms of repeatability when the fecal sample was tested in duplicate. However, the normalized read counts per detected astrovirus species differed substantially between participants, which was related to the different laboratory methods used for data generation. Further modeling of the mNGS data indicated the importance of selecting appropriate reference data for mNGS read classification. As virus- or sample-specific biases may apply, caution is needed when extrapolating this swine feces-based PT for the detection of other RNA viruses or using different sample types. The suitability of experimental design to a given pathogen/sample matrix combination, quality assurance, interpretation, and follow-up investigation remain critical factors for the diagnostic interpretation of mNGS results. IMPORTANCE: Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.</p

Probing the Universe with Weak Lensing

Gravitational lenses can provide crucial information on the geometry of the Universe, on the cosmological scenario of formation of its structures as well as on the history of its components with look-back time. In this review, I focus on the most recent results obtained during the last five years from the analysis of the weak lensing regime. The interest of weak lensing as a probe of dark matter and the for study of the coupling between light and mass on scales of clusters of galaxies, large scale structures and galaxies is discussed first. Then I present the impact of weak lensing for the study of distant galaxies and of the population of lensed sources as function of redshift. Finally, I discuss the potential interest of weak lensing to constrain the cosmological parameters, either from pure geometrical effects observed in peculiar lenses, or from the coupling of weak lensing with the CMB.Comment: To appear Annual Review of Astronomy and Astrophysiscs Vol. 37. Latex and psfig.sty. Version without figure, 54 pages, 73Kb. Complete version including 13 figures (60 pages) available on ftp.iap.fr anonymous account in /pub/from_users/mellier/AnnualReview ; file ARAAmellier.ps.gz 1.6 M

Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens

Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups

Genome Evolution of Two Genetically Homogeneous Infectious Bursal Disease Virus Strains During Passages in vitro and ex vivo in the Presence of a Mutagenic Nucleoside Analog

The avibirnavirus infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (Gallus gallus). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1. These viruses were serially passaged at controlled multiplicities of infection in several biological systems, including primary chickens B cells, the main cell type targeted by IBDV in vivo. Passages were also performed in the absence or presence of a strong selective pressure using the antiviral nucleoside analog 7-deaza-2′-C-methyladenosine (7DMA). Next Generation Sequencing (NGS) of viral genomes after the last passage in each biological system revealed that (i) a higher viral diversity was generated in segment A than in segment B, regardless 7DMA treatment and viral strain, (ii) diversity in segment B was increased by 7DMA treatment in both viruses, (iii) passaging of IBDV in primary chicken B cells, regardless of 7DMA treatment, did not select cell-culture adapted variants of rvv, preserving its capsid protein (VP2) properties, (iv) mutations in coding and non-coding regions of rCu-1 segment A could potentially associate to higher viral fitness, and (v) a specific selection, upon 7DMA addition, of a Thr329Ala substitution occurred in the viral polymerase VP1. The latter change, together with Ala270Thr change in VP2, proved to be associated with viral attenuation in vivo. These results identify genome sequences that are important for IBDV evolution in response to selection pressures. Such information will help tailor better strategies for controlling IBDV infection in chickens