Development of Sequence Tagged Microsatellite Site (STMS) markers in Azalea

A genomic library was constructed from DNA of two azalea genotypes: a Belgian pot azalea R. simsii hybrid Mevr. Van Belle and a Chinese R. simsii from Daoxian. An enrichment of microsatellite containing sequences was performed as in Van de Wiel et al. (1999). Fragments were sequenced and primers were designed that allow the amplification of the microsatellite repeat. About 220 microsatellite containing clones were selected from the enrichment procedure. Mainly dinucleotide repeats and some trinucleotide repeats were found. The selected primers were tested in a small set of reference varieties to check their value (specificity and polymorphic rate) and to set up the PCR-conditions. Five primer pairs have been tested, two of them gave a specific and polymorphic pattern. They were further screened by radioactive PCR on a selection of 5 plants from the azalea breeders gene pool which included the two genotypes used library construction. These 2 STMS markers uniquely identified the 5 plants

Semi-quantitative immunohistochemical detection of 5-hydroxymethyl-cytosine reveals conservation of its tissue distribution between amphibians and mammals

5-Hydroxymethyl-cytosine (5-hmC) is a form of modified cytosine, which has recently attracted a considerable attention due to its potential role in transcriptional regulation. According to several reports 5-hydroxymethyl-cytosine distribution is tissue-specific in mammals. Thus, 5-hmC is enriched in embryonic cell populations and in adult neuronal tissue. Here, we describe a novel method of semi-quantitative immunohistochemical detection of 5-hmC and utilize it to assess the levels of this modification in amphibian tissues. We show that, similar to mammalian embryos, 5-hmC is enriched in axolotl tadpoles compared with adult tissues. Our data demonstrate that 5-hmC distribution is tissue-specific in amphibians, and that strong 5-hmC enrichment in neuronal cells is conserved between amphibians and mammals. In addition, we identify 5-hmC-enriched cell populations that are distributed in amphibian skin and connective tissue in a mosaic manner. Our results illustrate that immunochemistry can be successfully used not only for spatial identification of cells enriched with 5-hmC, but also for the semi-quantitative assessment of the levels of this epigenetic modification in single cells of different tissues. © 2012 Landes Bioscience

Measurements and analysis of the upper critical field Hc2H_{c2} on an underdoped and overdoped La2−xSrxCuO4La_{2-x}Sr_xCuO_4 compounds

The upper critical field $H_{c2}$ is one of the many non conventional properties of high-$T_c$ cuprates. It is possible that the $H_{c2}(T)$ anomalies are due to the presence of inhomogeneities in the local charge carrier density $\rho$ of the $CuO_2$ planes. In order to study this point, we have prepared good quality samples of polycrystalline $La_{2-x}Sr_xCuO_{4}$ using the wet-chemical method, which has demonstrated to produce samples with a better cation distribution. In particular, we have studied the temperature dependence of the second critical field, $H_{c2}(T)$, through the magnetization measurements on two samples with opposite average carrier concentration ($\rho_m=x$) and nearly the same critical temperature, namely $\rho_m = 0.08$ (underdoped) and $\rho_m = 0.25$ (overdoped). The results close to $T_c$ do not follow the usual Ginzburg-Landau theory and are interpreted by a theory which takes into account the influence of the inhomogeneities.Comment: Published versio

New Light in Star-Forming Dwarf Galaxies: The PMAS Integral Field View of the Blue Compact Dwarf Galaxy Mrk 409

We present an integral field spectroscopic study of the central 2x2 kpc^2 of the blue compact dwarf galaxy Mrk 409, observed with the Potsdam MultiAperture Spectrophotometer. This study focuses on the morphology, two-dimensional chemical abundance pattern, excitation properties and kinematics of the ionized interstellar medium in the starburst component. We also investigate the nature of the extended ring of ionized gas emission surrounding the bright nuclear starburst region of Mrk 409. PMAS spectra of selected regions along the ring, interpreted with evolutionary and population synthesis models, indicate that their ionized emission is mainly due to a young stellar population with a total mass of ~1.5x10^6 M_sun, which started forming almost coevally ~10 Myr ago. This stellar component is likely confined to the collisional interface of a spherically expanding, starburst-driven super-bubble with denser, swept-up ambient gas, ~600 pc away from the central starburst nucleus. The spectroscopic properties of the latter imply a large extinction (C_H-beta>0.9), and the presence of an additional non-thermal ionization source, most likely a low-luminosity Active Galactic Nucleus. Mrk 409 shows a relatively large oxygen abundance (12+log(O/H)~8.4) and no chemical abundance gradients out to R~600 pc. The ionized gas kinematics displays an overall regular rotation on a northwest-southwest axis, with a maximum velocity of 60 km/s; the total mass inside the star-forming ring is about 1.4x10^9 M_sun.Comment: Accepted for publication in Ap

Comparative study of concatemer efficiency as an isotope-labelled internal standard for allergen quantification

Mass spectrometry-based methods coupled with stable isotope dilution have become effective and widely used methods for the detection and quantification of food allergens. Current methods target signature peptides resulting from proteolytic digestion of proteins of the allergenic ingredient. The choice of appropriate stable isotope-labelled internal standard is crucial, given the diversity of encountered food matrices which can affect sample preparation and analysis. We propose the use of concatemer, an artificial and stable isotope-labelled protein composed of several concatenated signature peptides as internal standard. With a comparative analysis of three matrices contaminated with four allergens (egg, milk, peanut, and hazelnut), the concatemer approach was found to offer advantages associated with the use of labelled proteins, ideal but unaffordable, and circumvent certain limitations of traditionally used synthetic peptides as internal standards. Although used in the proteomic field for more than a decade, concatemer strategy has not yet been applied for food analysis

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance

The stellar host in blue compact dwarf galaxies: the need for a two-dimensional fit

The structural properties of the low surface brightness stellar host in blue compact dwarf galaxies are often studied by fitting r^{1/n} models to the outer regions of their radial profiles. The limitations imposed by the presence of a large starburst emission overlapping the underlying component makes this kind of analysis a difficult task. We propose a two-dimensional fitting methodology in order to improve the extraction of the structural parameters of the LSB host. We discuss its advantages and weaknesses by using a set of simulated galaxies and compare the results for a sample of eight objects with those already obtained using a one-dimensional technique. We fit a PSF convolved Sersic model to synthetic galaxies, and to real galaxy images in the B, V, R filters. We restrict the fit to the stellar host by masking out the starburst region and take special care to minimize the sky-subtraction uncertainties. In order to test the robustness and flexibility of the method, we carry out a set of fits with synthetic galaxies. Furthermore consistency checks are performed to assess the reliability and accuracy of the derived structural parameters. The more accurate isolation of the starburst emission is the most important advantage and strength of the method. Thus, we fit the host galaxy in a range of surface brightness and in a portion of area larger than in previous published 1D fits with the same dataset. We obtain robust fits for all the sample galaxies, all of which, except one, show Sersic indices n very close to 1, with good agreement in the three bands. These findings suggest that the stellar hosts in BCDs have near-exponential profiles, a result that will help us to understand the mechanisms that form and shape BCD galaxies, and how they relate to the other dwarf galaxy classes.Comment: 22 pages, 15 figures (low resolution), accepted for publication in A&A. A higher resolution version of the figures can be provided upon reques

Imaging Jupiter's radiation belts down to 127 MHz with LOFAR

Context. Observing Jupiter's synchrotron emission from the Earth remains today the sole method to scrutinize the distribution and dynamical behavior of the ultra energetic electrons magnetically trapped around the planet (because in-situ particle data are limited in the inner magnetosphere). Aims. We perform the first resolved and low-frequency imaging of the synchrotron emission with LOFAR at 127 MHz. The radiation comes from low energy electrons (~1-30 MeV) which map a broad region of Jupiter's inner magnetosphere. Methods (see article for complete abstract) Results. The first resolved images of Jupiter's radiation belts at 127-172 MHz are obtained along with total integrated flux densities. They are compared with previous observations at higher frequencies and show a larger extent of the synchrotron emission source (>=4 $R_J$). The asymmetry and the dynamic of east-west emission peaks are measured and the presence of a hot spot at lambda_III=230 {\deg} $\pm$ 25 {\deg}. Spectral flux density measurements are on the low side of previous (unresolved) ones, suggesting a low-frequency turnover and/or time variations of the emission spectrum. Conclusions. LOFAR is a powerful and flexible planetary imager. The observations at 127 MHz depict an extended emission up to ~4-5 planetary radii. The similarities with high frequency results reinforce the conclusion that: i) the magnetic field morphology primarily shapes the brightness distribution of the emission and ii) the radiating electrons are likely radially and latitudinally distributed inside about 2 $R_J$. Nonetheless, the larger extent of the brightness combined with the overall lower flux density, yields new information on Jupiter's electron distribution, that may shed light on the origin and mode of transport of these particles.Comment: 10 pages, 12 figures, accepted for publication in A&A (27/11/2015) - abstract edited because of limited character