Pyrene Mineralization by Mycobacterium sp. Strain KMS in a Barley Rhizosphere

To determine whether the soil Mycobacterium isolate KMS would mineralize pyrene under rhizosphere conditions, a microcosm system was established to collect radioactive carbon dioxide released from the labeled polycyclic aromatic hydrocarbon. Microcosms were designed as sealed, flow-through systems that allowed the growth of plants. Experiments were conducted to evaluate mineralization of 14C-labeled pyrene in a sand amended with the polycyclic aromatic hydrocarbons degrading Mycobacterium isolate KMS, barley plants, or barley plants with roots colonized by isolate KMS. Mineralization was quantified by collecting the 14CO2 produced from 14C-labeled pyrene at intervals during the 10-d incubation period. Roots and foliar tissues were examined for 14C incorporation. Mass balances for microcosms were determined through combustion of sand samples and collection and quantification of 14CO2 evolved from radiolabeled pyrene. No pyrene mineralization was observed in the sterile control systems. Greater release of 14CO2 was observed in the system with barley colonized by KMS than in microcosms containing just the bacterium inoculum or sterile barley plants. These findings suggest that phytostimulation of polycyclic aromatic hydrocarbons mineralization could be applied in remediation schemes

Characterizing the cross dispersion reflection gratings of CRIRES+

The CRIRES+ project attempts to upgrade the CRIRES instrument into a cross dispersed Echelle spectrograph with a simultaneous recording of 8-10 diffraction orders. In order to transform the CRIRES spectrograph into a cross-dispersing instrument, a set of six reflection gratings, each one optimized for one of the wavelength bands CRIRES+ will operate in (YJHKLM), will be used as cross dispersion elements in CRIRES+. Due to the upgrade nature of the project, the choice of gratings depends on the fixed geometry of the instrument. Thus, custom made gratings would be required to achieve the ambitious design goals. Custom made gratings have the disadvantage, though, that they come at an extraordinary price and with lead times of more than 12 months. To mitigate this, a set of off-the-shelf gratings was obtained which had grating parameters very close to the ones being identified as optimal. To ensure that the rigorous specifications for CRIRES+ will be fulfilled, the CRIRES+ team started a collaboration with the Physikalisch-Technische Bundesanstalt Berlin (PTB) to characterize gratings underconditions similar to the operating conditions in CRIRES+ (angle of incidence, wavelength range). The respective test setup was designed in collaboration between PTB and the CRIRES+ consortium. The PTB provided optical radiation sources and calibrated detectors for each wavelength range. With this setup, it is possible to measure the absolute efficiency of the gratings both wavelength dependent and polarization state dependent in a wavelength range from 0.9 μm to 6 μm

The "+" for CRIRES: enabling better science at infrared wavelength and high spectral resolution at the ESO VLT

The adaptive optics (AO) assisted CRIRES instrument is an IR (0.92 - 5.2 μm) high-resolution spectrograph was in operation from 2006 to 2014 at the Very Large Telescope (VLT) observatory. CRIRES was a unique instrument, accessing a parameter space (wavelength range and spectral resolution) up to now largely uncharted. It consisted of a single-order spectrograph providing long-slit (40 arcsecond) spectroscopy with a resolving power up to R=100 000. However the setup was limited to a narrow, single-shot, spectral range of about 1/70 of the central wavelength, resulting in low observing efficiency for many scientific programmes requiring a broad spectral coverage. The CRIRES upgrade project, CRIRES+, transforms this VLT instrument into a cross-dispersed spectrograph to increase the simultaneously covered wavelength range by a factor of ten. A new and larger detector focal plane array of three Hawaii 2RG detectors with 5.3 μm cut-off wavelength will replace the existing detectors. For advanced wavelength calibration, custom-made absorption gas cells and an etalon system will be added. A spectro-polarimetric unit will allow the recording of circular and linear polarized spectra. This upgrade will be supported by dedicated data reduction software allowing the community to take full advantage of the new capabilities offered by CRIRES+. CRIRES+ has now entered its assembly and integration phase and will return with all new capabilities by the beginning of 2018 to the Very Large Telescope in Chile. This article will provide the reader with an update of the current status of the instrument as well as the remaining steps until final installation at the Paranal Observatory

A unique infrared spectropolarimetric unit for CRIRES+

High-resolution infrared spectropolarimetry has many science applications in astrophysics. One of them is measuring weak magnetic fields using the Zeeman effect. Infrared domain is particularly advantageous as Zeeman splitting of spectral lines is proportional to the square of the wavelength while the intrinsic width of the line cores increases only linearly. Important science cases include detection and monitoring of global magnetic fields on solar-type stars, study of the magnetic field evolution from stellar formation to the final stages of the stellar life with massive stellar winds, and the dynamo mechanism operation across the boundary between fully- and partially-convective stars. CRIRES+ (the CRIRES upgrade project) includes a novel spectropolarimetric unit (SPU) based on polar- ization gratings. The novel design allows to perform beam-splitting very early in the optical path, directly after the tertiary mirror of the telescope (the ESO Very Large Telescope, VLT), minimizing instrumental polariza- tion. The new SPU performs polarization beam-splitting in the near-infrared while keeping the telescope beam mostly unchanged in the optical domain, making it compatible with the adaptive optics system of the CRIRES+ instrument. The SPU consists of four beam-splitters optimized for measuring circular and linear polarization of spectral lines in YJ and HK bands. The SPU can perform beam switching allowing to correct for throughput in each beam and for variations in detector pixel sensitivity. Other new features of CRIRES+, such as substantially increased wavelength coverage, stability and advanced data reduction pipeline will further enhance the sensitivity of the polarimetric mode. The combination of the SPU, CRIRES+ and the VLT is a unique facility for making major progress in understanding stellar activity. In this article we present the design of the SPU, laboratory measurements of individual components and of the whole unit as well as the performance prediction for the operation at the VLT

Full system test and early preliminary acceptance Europe results for CRIRES+

CRIRES+ is the new high-resolution NIR echelle spectrograph intended to be operated at the platform B of VLT Unit telescope UT3. It will cover from Y to M bands (0.95-5.3um) with a spectral resolution of R = 50000 or R=100000. The main scientific goals are the search of super-Earths in the habitable zone of low-mass stars, the characterisation of transiting planets atmosphere and the study of the origin and evolution of stellar magnetic fields. Based on the heritage of the old adaptive optics (AO) assisted VLT instrument CRIRES, the new spectrograph will present improved optical layout, a new detector system and a new calibration unit providing optimal performances in terms of simultaneous wavelength coverage and radial velocity accuracy (a few m/s). The total observing efficiency will be enhanced by a factor of 10 with respect to CRIRES. An innovative spectro-polarimetry mode will be also offered and a new metrology system will ensure very high system stability and repeatability. Fiinally, the CRIRES+ project will also provide the community with a new data reduction software (DRS) package. CRIRES+ is currently at the initial phase of its Preliminary Acceptance in Europe (PAE) and it will be commissioned early in 2019 at VLT. This work outlines the main results obtained during the initial phase of the full system test at ESO HQ Garching

Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms

Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301–8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.Ministerio de Ciencia, Tecnología y Telecomunicaciones/[803-B4-510]/MICITT/Costa RicaFederal State of Lower Saxony/[VWZN2889/3215]//Baja SajoniaGerman Center for Infection Research/[ 8000-105-3]/DZIF/AlemaniaUniversidad de Costa Rica/[803-B5-770]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET)UCR::Vicerrectoría de Docencia::Salud::Facultad de Microbiologí