Method for serial passage of infectious hematopoietic necrosis virus (IHNV) in rainbow trout

Transmission is a fundamental component of pathogen fitness. A better understanding of pathogen transmission can greatly improve disease management. In particular, controlled studies of multiple rounds of natural transmission (i.e. serial passage) can provide powerful epidemiological and evolutionary inferences. However, such studies are possible in only a few systems because of the challenges in successfully initiating and maintaining transmission in the laboratory. Here we developed an efficient and reproducible cohabitation method for conducting controlled experiments investigating the effects of serial passage on infectious hematopoietic necrosis virus (IHNV) in rainbow trout. This method was used to investigate the transmission efficiency and kinetics of viral shedding of IHNV over 3 serial passages. Transmission efficiency decreased from 100 to 62.5% over the passage steps and was associated with a decrease in virus shedding into water. A shift in the peak of viral shedding was also observed, from Day 2 post immersion for passage 0 to at least 24 h later for all subsequent passages. Finally, the characterization of viruses after 1 round of transmission and propagation on cells showed no change in glyco protein (G gene) sequences or viral virulence compared to the ancestral virus stock. The methods developed provide valuable tools for reproducible population-level studies of IHNV epidemiology and evolution

Within-host dynamics of the emergence of tomato yellow leaf curl virus recombinants

Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci . We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection-a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results anticipate the outcomes of natural encounters between TYLCV and ToLCKMV

First experimental results of very high accuracy centroiding measurements for the neat astrometric mission

NEAT is an astrometric mission proposed to ESA with the objectives of detecting Earth-like exoplanets in the habitable zone of nearby solar-type stars. NEAT requires the capability to measure stellar centroids at the precision of 5e-6 pixel. Current state-of-the-art methods for centroid estimation have reached a precision of about 2e-5 pixel at two times Nyquist sampling, this was shown at the JPL by the VESTA experiment. A metrology system was used to calibrate intra and inter pixel quantum efficiency variations in order to correct pixelation errors. The European part of the NEAT consortium is building a testbed in vacuum in order to achieve 5e-6 pixel precision for the centroid estimation. The goal is to provide a proof of concept for the precision requirement of the NEAT spacecraft. In this paper we present the metrology and the pseudo stellar sources sub-systems, we present a performance model and an error budget of the experiment and we report the present status of the demonstration. Finally we also present our first results: the experiment had its first light in July 2013 and a first set of data was taken in air. The analysis of this first set of data showed that we can already measure the pixel positions with an accuracy of about 1e-4 pixel.Comment: SPIE conference proceeding

Spectral performance of the Microchannel X-ray Telescope on board the SVOM mission

The Microchannel X-ray Telescope (MXT) is an innovative compact X-ray instrument on board the SVOM astronomical mission dedicated to the study of transient phenomena such as gamma-ray bursts. During 3 weeks, we have tested the MXT flight model at the Panter X-ray test facility under the nominal temperature and vacuum conditions that MXT will undergo in-flight. We collected data at series of characteristic energies probing the entire MXT energy range, from 0.28 keV up to 9 keV, for multiple source positions with the center of the point spread function (PSF) inside and outside the detector field of view (FOV). We stacked the data of the positions with the PSF outside the FOV to obtain a uniformly illuminated matrix and reduced all data sets using a dedicated pipeline. We determined the best spectral performance of MXT using an optimized data processing, especially for the energy calibration and the charge sharing effect induced by the pixel low energy thresholding. Our results demonstrate that MXT is compliant with the instrument requirement regarding the energy resolution (<80 eV at 1.5 keV), the low and high energy threshold, and the accuracy of the energy calibration ($\pm$20 eV). We also determined the charge transfer inefficiency (~$10^{-5}$) of the detector and modeled its evolution with energy prior to the irradiation that MXT will undergo during its in-orbit lifetime. Finally, we measured the relation of the energy resolution as function of the photon energy. We determined an equivalent noise charge of 4.9 $\pm$ 0.2 e- rms for the MXT detection chain and a Fano factor of 0.131 $\pm$ 0.003 in silicon at 208 K, in agreement with previous works. This campaign confirmed the promising scientific performance that MXT will be able to deliver during the mission lifetime.Comment: 20 pages, 10 figures, accepted for publication in Experimental Astronom

A detector interferometric calibration experiment for high precision astrometry

Context: Exoplanet science has made staggering progress in the last two decades, due to the relentless exploration of new detection methods and refinement of existing ones. Yet astrometry offers a unique and untapped potential of discovery of habitable-zone low-mass planets around all the solar-like stars of the solar neighborhood. To fulfill this goal, astrometry must be paired with high precision calibration of the detector. Aims: We present a way to calibrate a detector for high accuracy astrometry. An experimental testbed combining an astrometric simulator and an interferometric calibration system is used to validate both the hardware needed for the calibration and the signal processing methods. The objective is an accuracy of 5e-6 pixel on the location of a Nyquist sampled polychromatic point spread function. Methods: The interferometric calibration system produced modulated Young fringes on the detector. The Young fringes were parametrized as products of time and space dependent functions, based on various pixel parameters. The minimization of func- tion parameters was done iteratively, until convergence was obtained, revealing the pixel information needed for the calibration of astrometric measurements. Results: The calibration system yielded the pixel positions to an accuracy estimated at 4e-4 pixel. After including the pixel position information, an astrometric accuracy of 6e-5 pixel was obtained, for a PSF motion over more than five pixels. In the static mode (small jitter motion of less than 1e-3 pixel), a photon noise limited precision of 3e-5 pixel was reached

The ArT\'eMiS wide-field submillimeter camera: preliminary on-sky performances at 350 microns

ArTeMiS is a wide-field submillimeter camera operating at three wavelengths simultaneously (200, 350 and 450 microns). A preliminary version of the instrument equipped with the 350 microns focal plane, has been successfully installed and tested on APEX telescope in Chile during the 2013 and 2014 austral winters. This instrument is developed by CEA (Saclay and Grenoble, France), IAS (France) and University of Manchester (UK) in collaboration with ESO. We introduce the mechanical and optical design, as well as the cryogenics and electronics of the ArTeMiS camera. ArTeMiS detectors are similar to the ones developed for the Herschel PACS photometer but they are adapted to the high optical load encountered at APEX site. Ultimately, ArTeMiS will contain 4 sub-arrays at 200 microns and 2x8 sub-arrays at 350 and 450 microns. We show preliminary lab measurements like the responsivity of the instrument to hot and cold loads illumination and NEP calculation. Details on the on-sky commissioning runs made in 2013 and 2014 at APEX are shown. We used planets (Mars, Saturn, Uranus) to determine the flat-field and to get the flux calibration. A pointing model was established in the first days of the runs. The average relative pointing accuracy is 3 arcsec. The beam at 350 microns has been estimated to be 8.5 arcsec, which is in good agreement with the beam of the 12 m APEX dish. Several observing modes have been tested, like On-The-Fly for beam-maps or large maps, spirals or raster of spirals for compact sources. With this preliminary version of ArTeMiS, we concluded that the mapping speed is already more than 5 times better than the previous 350 microns instrument at APEX. The median NEFD at 350 microns is 600 mJy.s1/2, with best values at 300 mJy.s1/2. The complete instrument with 5760 pixels and optimized settings will be installed during the first half of 2015.Comment: 11 pages, 11 figures. Presented at SPIE Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy VII, June 24, 2014. To be published in Proceedings of SPIE Volume 915

Evidence of triggered star formation in G327.3-0.6. Dust-continuum mapping of an infrared dark cloud with P-ArT\'eMiS

Aims. Expanding HII regions and propagating shocks are common in the environment of young high-mass star-forming complexes. They can compress a pre-existing molecular cloud and trigger the formation of dense cores. We investigate whether these phenomena can explain the formation of high-mass protostars within an infrared dark cloud located at the position of G327.3-0.6 in the Galactic plane, in between two large infrared bubbles and two HII regions. Methods: The region of G327.3-0.6 was imaged at 450 ? m with the CEA P-ArT\'eMiS bolometer array on the Atacama Pathfinder EXperiment telescope in Chile. APEX/LABOCA and APEX-2A, and Spitzer/IRAC and MIPS archives data were used in this study. Results: Ten massive cores were detected in the P-ArT\'eMiS image, embedded within the infrared dark cloud seen in absorption at both 8 and 24 ?m. Their luminosities and masses indicate that they form high-mass stars. The kinematical study of the region suggests that the infrared bubbles expand toward the infrared dark cloud. Conclusions: Under the influence of expanding bubbles, star formation occurs in the infrared dark areas at the border of HII regions and infrared bubbles.Comment: 4 page

The Photodetector Array Camera and Spectrometer (PACS) on the Herschel Space Observatory

The Photodetector Array Camera and Spectrometer (PACS) is one of the three science instruments on ESA's far infrared and submillimetre observatory. It employs two Ge:Ga photoconductor arrays (stressed and unstressed) with 16x25 pixels, each, and two filled silicon bolometer arrays with 16x32 and 32x64 pixels, respectively, to perform integral-field spectroscopy and imaging photometry in the 60-210\mu\ m wavelength regime. In photometry mode, it simultaneously images two bands, 60-85\mu\ m or 85-125\mu\m and 125-210\mu\ m, over a field of view of ~1.75'x3.5', with close to Nyquist beam sampling in each band. In spectroscopy mode, it images a field of 47"x47", resolved into 5x5 pixels, with an instantaneous spectral coverage of ~1500km/s and a spectral resolution of ~175km/s. We summarise the design of the instrument, describe observing modes, calibration, and data analysis methods, and present our current assessment of the in-orbit performance of the instrument based on the Performance Verification tests. PACS is fully operational, and the achieved performance is close to or better than the pre-launch predictions

Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus

[EN] Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.The authors thank Francisca de la Iglesia and Paula Agudo for excellent technical assistance, our labmates for useful discussions and suggestions, and Dr Jose A. Daros for gifting us the pMTEV infectious clone. This work was supported by grants BFU2009-06993 and BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO), grant PROMETEOII/2014/021 from Generalitat Valenciana, and by the European Commission 7th Framework Programme (FP7-ICT-611640 FET Proactive: Evolving Living Technologies) EvoEvo project to S.F.E. J.M.C. was supported by a JAE-doc postdoctoral contract from CSIC. A.W. was supported by the EvoEvo project. J.H. was recipient of a predoctoral contract from MINECO. M.P.Z. was supported by a Juan de la Cierva postdoctoral contract from MINECO.Cuevas, JM.; Willemsen, A.; Hillung, J.; Zwart, MP.; Elena Fito, SF. (2015). Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus. Molecular Biology and Evolution. 32(5):1132-1147. https://doi.org/10.1093/molbev/msv028S1132114732