New families of single integration vectors and gene tagging plasmids for genetic manipulations in budding yeast.

The tractability of the budding yeast genome has provided many insights into the fundamental mechanisms regulating cellular life. With the advent of synthetic biology and single-cell measurements, novel tools are required to manipulate the yeast genome in a more controlled manner. We present, here, a new family of yeast shuttle vectors called single integration vectors (pSIV). Upon transformation in yeast, these plasmids replace the entire deficient auxotrophy marker locus by a cassette containing an exogenous marker. As shown using flow cytometry, this complete replacement results in a unique integration of the desired DNA fragment at the marker locus. In addition, a second transcriptional unit can be inserted to achieve the simultaneous integration of two constructs. The selection marker cassettes, present in the pSIV, were also used to generate a complete set of gene tagging plasmids (pGT) encompassing a large palette of fluorescent proteins, from a cyan fluorescent protein to a near-infrared tandem dimer red fluorescent protein. These tagging cassettes are orthogonal to each other thanks to the use of different TEF promoter and terminator couples, thereby avoiding marker cassette switching and favoring integration in the desired locus. In summary, we have created two sets of robust molecular tools for the precise genetic manipulation of the budding yeast

X-ray emission during the muonic cascade in hydrogen

We report our investigations of X rays emitted during the muonic cascade in hydrogen employing charge coupled devices as X-ray detectors. The density dependence of the relative X-ray yields for the muonic hydrogen lines (K_alpha, K_beta, K_gamma) has been measured at densities between 0.00115 and 0.97 of liquid hydrogen density. In this density region collisional processes dominate the cascade down to low energy levels. A comparison with recent calculations is given in order to demonstrate the influence of Coulomb deexcitation.Comment: 5 pages, Tex, 4 figures, submitted to Physical Review Letter

The SAMI Galaxy Survey: a statistical approach to an optimal classification of stellar kinematics in galaxy surveys

Large galaxy samples from multi-object IFS surveys now allow for a statistical analysis of the z~0 galaxy population using resolved kinematics. However, the improvement in number statistics comes at a cost, with multi-object IFS survey more severely impacted by the effect of seeing and lower S/N. We present an analysis of ~1800 galaxies from the SAMI Galaxy Survey and investigate the spread and overlap in the kinematic distributions of the spin parameter proxy $\lambda_{Re}$ as a function of stellar mass and ellipticity. For SAMI data, the distributions of galaxies identified as regular and non-regular rotators with \textsc{kinemetry} show considerable overlap in the $\lambda_{Re}$-$\varepsilon_e$ diagram. In contrast, visually classified galaxies (obvious and non-obvious rotators) are better separated in $\lambda_{Re}$ space, with less overlap of both distributions. Then, we use a Bayesian mixture model to analyse the observed $\lambda_{Re}$-$\log(M_*/M_{\odot})$ distribution. Below $\log(M_{\star}/M_{\odot})\sim10.5$, a single beta distribution is sufficient to fit the complete $\lambda_{Re}$ distribution, whereas a second beta distribution is required above $\log(M_{\star}/M_{\odot})\sim10.5$ to account for a population of low-$\lambda_{Re}$ galaxies. While the Bayesian mixture model presents the cleanest separation of the two kinematic populations, we find the unique information provided by visual classification of kinematic maps should not be disregarded in future studies. Applied to mock-observations from different cosmological simulations, the mixture model also predicts bimodal $\lambda_{Re}$ distributions, albeit with different positions of the $\lambda_{Re}$ peaks. Our analysis validates the conclusions from previous smaller IFS surveys, but also demonstrates the importance of using kinematic selection criteria that are dictated by the quality of the observed or simulated data.Comment: 30 pages and 17 figures, accepted for publication in MNRAS. Abstract abridged for Arxiv. The key figures of the paper are: 3, 7, 8, and 1

The SAMI Galaxy Survey: Data Release Two with absorption-line physics value-added products

Instrumentatio

A mesocosm approach to study the response of Sphagnum peatlands to hydrological changes: setup, optimisation and performance

Sphagnum-dominated peatlands are major carbon pools and sinks, but these functions are threatened by climate change. There is, therefore, a need to better understand how microclimatic changes (soil temperature, soil moisture and water table depth) are affecting their functioning. Experimental studies on Sphagnum peatlands conducted under precisely controlled (e.g. mesocosm) conditions are relatively rare, especially those aiming to understand the system as a whole. Furthermore, mesocosm designs are generally described only briefly in the literature. In this article we provide a comprehensive account of a mesocosm experiment designed to study the response of Sphagnum peatlands to water table manipulation. We describe our experimental setup (3 water levels × 3 amplitudes of water table fluctuation × 5 replicates); and explain how we built the mesocosms, the issues we faced and the solutions we chose to solve them. We provide a detailed description of the devices we conceived to manipulate the water level, including software codes and electronic diagrams (as supplementary material), and explain how to address data loss in such an experimental design. We show that it is possible to build a reliable and powerful experimental setup at moderate cost using standard technology. The aim of this article is to provide a useful resource for researchers wishing to design similar experiments in the future