Integrated DNA walking system to characterize a broad spectrum of GMOs in food/feed matrices

Background: In order to provide a system fully integrated with qPCR screening, usually used in GMO routine analysis, as well as being able to detect, characterize and identify a broad spectrum of GMOs in food/feed matrices, two bidirectional DNA walking methods targeting p35S or tNOS, the most common transgenic elements found in GM crops, were developed. These newly developed DNA walking methods are completing the previously implemented DNA walking method targeting the t35S pCAMBIA element. Results: First, the newly developed DNA walking methods, anchored on the sequences used for the p35S or tNOS qPCR screening, were tested on Bt rice that contains these two transgenic elements. Second, the methods were assessed on a maize sample containing a low amount of the GM MON863 event, representing a more complex matrix in terms of genome size and sensitivity. Finally, to illustrate its applicability in GMO routine analysis by enforcement laboratories, the entire workflow of the integrated strategy, including qPCR screening to detect the potential presence of GMOs and the subsequent DNA walking methods to characterize and identify the detected GMOs, was applied on a GeMMA Scheme Proficiency Test matrix. Via the characterization of the transgene flanking region between the transgenic cassette and the plant genome as well as of a part of the transgenic cassette, the presence of GMOs was properly confirmed or infirmed in all tested samples. Conclusion: Due to their simple procedure and their short time-frame to get results, the developed DNA walking methods proposed here can be easily implemented in GMO routine analysis by the enforcement laboratories. In providing crucial information about the transgene flanking regions and/or the transgenic cassettes, this DNA walking strategy is a key molecular tool to prove the presence of GMOs in any given food/feed matrix

Segmented Beam Dump for Time Resolved Spectrometry on a High Current Electron Beam

In the CLIC Test Facility 3 (CTF3), the strong coupling between the beam and the accelerating cavities induces transient effects such that the head of the pulse is accelerated twice as much as the rest of the pulse. Three spectrometer lines are installed along the linac with the aim of measuring energy spread versus time with a 20ns resolution. A major difficulty is due to the high power carried by the beam which imposes extreme constraints of thermal and radiation resistances on the detector. This paper presents the design and the performances of a simple and easy-to-maintain device, called âsegmented dump'. In this device, the particles are stopped inside metallic plates and the deposited charge is measured in the same way as in Faraday cups. Simulations were carried out with the Monte Carlo code âFLUKA' to evaluate the problems arising from the energy deposition and to find ways to prevent or reduce them. The detector resolution was optimized by an adequate choice of material and thickness of the plates. The overall layout of the monitor is described with special emphasis on its mechanical assembly. Finally, limitations arising at higher beam energies are discussed

An Upper Limit on the Mass of the Circumplanetary Disk for DH Tau b

Indexación: Scopus.DH Tau is a young (sim;1 Myr) classical T Tauri star. It is one of the few young PMS stars known to be associated with a planetary mass companion, DH Tau b, orbiting at large separation and detected by direct imaging. DH Tau b is thought to be accreting based on copious Ha emission and exhibits variable Paschen Beta emission. NOEMA observations at 230 GHz allow us to place constraints on the disk dust mass for both DH Tau b and the primary in a regime where the disks will appear optically thin. We estimate a disk dust mass for the primary, DH Tau A of 17.2 ± 1.7 MÅ, which gives a disk to star mass ratio of 0.014 (assuming the usual gas to dust mass ratio of 100 in the disk). We find a conservative disk dust mass upper limit of 0.42M⊕ for DH Tau b, assuming that the disk temperature is dominated by irradiation from DH Tau b itself. Given the environment of the circumplanetary disk, variable illumination from the primary or the equilibrium temperature of the surrounding cloud would lead to even lower disk mass estimates. A MCFOST radiative transfer model, including heating of the circumplanetary disk by DH Tau b and DH Tau A, suggests that a mass-averaged disk temperature of 22 K is more realistic, resulting in a dust disk mass upper limit of 0.09M⊕ for DH Tau b. We place DH Tau b in context with similar objects and discuss the consequences for planet formation models.http://iopscience.iop.org/article/10.3847/1538-3881/aa74cd/met

Recent MOST space photometry

The Microvariability and Oscillations of STars (MOST) photometric satellite has already undertaken more than 64 primary campaigns which include some clusters and has obtained observations of >850 secondary stars of which ~180 are variable. More than half of the variables pulsate, with the majority being of B-type. Since 2006 January, MOST has operated with only a single CCD for both guiding and science. The resulting increase in read-out cadence has improved precision for the brightest stars. The 2007 light curve for Procyon confirms the lack of predicted p-modes with photometric amplitudes exceeding 8 ppm as we found in 2004 and 2005. p-modes have been detected in other solar-type stars as well as pre-main sequence objects, roAp and delta Scuti variables. g-modes have been detected in a range of slowly pulsating B stars, Be stars and beta Cephei variables. Differential rotation has been defined for several spotted solar-type stars and limits set to the albedo of certain transiting planets and the presence of other perturbing planets. The mission is expected to continue as long as the experiment operates.Comment: 9 pages, 7 figures, from HELAS-II meetin

Massive Increase, Spread, and Exchange of Extended Spectrum {beta}-Lactamase-Encoding Genes Among Intestinal Enterobacteriaceae in Hospitalized Children With Severe Acute Malnutrition in Niger.

Background. From the time of CTX-M emergence, extended-spectrum β-lactamase-producing enterobacteria (ESBL-E) have spread worldwide in community settings as well as in hospitals, particularly in developing countries. Although their dissemination appears linked to Escherichia coli intestinal carriage, precise paths of this dynamic are largely unknown. Methods. Children from a pediatric renutrition center were prospectively enrolled in a fecal carriage study. Antibiotic exposure was recorded. ESBL-E strains were isolated using selective media from fecal samples obtained at admission and, when negative, also at discharge. ESBL-encoding genes were identified, their environments and plasmids were characterized, and clonality was assessed with polymerase chain reaction-based methods and pulsed-field gel electrophoresis for E. coli and Klebsiella pneumoniae. E. coli strains were subjected to multilocus sequence typing. Results. The ESBL-E carriage rate was 31% at admission in the 55 children enrolled. All children enrolled received antibiotics during hospitalization. Among the ESBL-E-negative children, 16 were resampled at discharge, and the acquisition rate was 94%. The bla(CTX-M-15) gene was found in >90% of the carriers. Genetic environments and plasmid characterization evidenced the roles of a worldwide, previously described, multidrug-resistant region and of IncF plasmids in CTX-M-15 E. coli dissemination. Diversity of CTX-M-15-carrying genetic structures and clonality of acquired ESBL E. coli suggested horizontal genetic transfer and underlined the potential of some ST types for nosocomial cross-transmission. Conclusions. Cross-transmission and high selective pressure lead to very high acquisition of ESBL-E carriage, contributing to dissemination in the community. Strict hygiene measures as well as careful balancing of benefit-risk ratio of current antibiotic policies need to be reevaluated

Genomic Expansion of Magnetotactic Bacteria Reveals an Early Common Origin of Magnetotaxis with Lineage-specific Evolution

The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth’s magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and “Candidatus Lambdaproteobacteria” classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB

Metastability in zero-temperature dynamics: Statistics of attractors

The zero-temperature dynamics of simple models such as Ising ferromagnets provides, as an alternative to the mean-field situation, interesting examples of dynamical systems with many attractors (absorbing configurations, blocked configurations, zero-temperature metastable states). After a brief review of metastability in the mean-field ferromagnet and of the droplet picture, we focus our attention onto zero-temperature single-spin-flip dynamics of ferromagnetic Ising models. The situations leading to metastability are characterized. The statistics and the spatial structure of the attractors thus obtained are investigated, and put in perspective with uniform a priori ensembles. We review the vast amount of exact results available in one dimension, and present original results on the square and honeycomb lattices.Comment: 21 pages, 6 figures. To appear in special issue of JPCM on Granular Matter edited by M. Nicodem

Apolipoprotein E mediates evasion from hepatitis C virus−neutralizing antibodies

Background & Aims Efforts to develop an effective vaccine against hepatitis C virus (HCV) have been hindered by the propensity of the virus to evade host immune responses. HCV particles in serum and in cell culture associate with lipoproteins, which contribute to viral entry. Lipoprotein association has also been proposed to mediate viral evasion of the humoral immune response, though the mechanisms are poorly defined. Methods We used small interfering RNAs to reduce levels of apolipoprotein E (apoE) in cell culture−derived HCV−producing Huh7.5-derived hepatoma cells and confirmed its depletion by immunoblot analyses of purified viral particles. Before infection of naïve hepatoma cells, we exposed cell culture−derived HCV strains of different genotypes, subtypes, and variants to serum and polyclonal and monoclonal antibodies isolated from patients with chronic HCV infection. We analyzed the interaction of apoE with viral envelope glycoprotein E2 and HCV virions by immunoprecipitation. Results Through loss-of-function studies on patient-derived HCV variants of several genotypes and subtypes, we found that the HCV particle apoE allows the virus to avoid neutralization by patient-derived antibodies. Functional studies with human monoclonal antiviral antibodies showed that conformational epitopes of envelope glycoprotein E2 domains B and C were exposed after depletion of apoE. The level and conformation of virion-associated apoE affected the ability of the virus to escape neutralization by antibodies. Conclusions In cell-infection studies, we found that HCV-associated apoE helps the virus avoid neutralization by antibodies against HCV isolated from chronically infected patients. This method of immune evasion poses a challenge for the development of HCV vaccines

Metastable configurations of spin models on random graphs

One-flip stable configurations of an Ising-model on a random graph with fluctuating connectivity are examined. In order to perform the quenched average of the number of stable configurations we introduce a global order-parameter function with two arguments. The analytical results are compared with numerical simulations.Comment: 11 pages Revtex, minor changes, to appear in Phys. Rev.

Time resolved spectrometry on the CLIC Test Facility 3

The high charge (>6ìC) electron beam produced in the CLIC Test Facility 3 (CTF3) is accelerated in fully beam loaded cavities. To be able to measure the resulting strong transient effects, the time evolution of the beam energy and its energy spread must be determined with at least 50MHz bandwidth. Three spectrometer lines are installed along the linac in order to control and tune the beam. The electrons are deflected by dipole magnets onto Optical Transition Radiation (OTR) screens which are observed by CCD cameras. The measured horizontal beam size is then directly related to the energy spread. In order to provide time-resolved energy spectra, a fraction of the OTR photons is sent onto a multi-channel photomultiplier. The overall setup is described, special focus is given to the design of the OTR screen with its synchrotron radiation shielding. The performance of the time-resolved measurements are discussed in detail. Finally, the limitations of the system, mainly due to radiation problems are discussed