Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont.

Animal guts are often colonized by host-specialized bacterial species to the exclusion of other transient microorganisms, but the genetic basis of colonization ability is largely unknown. The bacterium Snodgrassella alvi is a dominant gut symbiont in honey bees, specialized in colonizing the hindgut epithelium. We developed methods for transposon-based mutagenesis in S. alvi and, using high-throughput DNA sequencing, screened genome-wide transposon insertion (Tn-seq) and transcriptome (RNA-seq) libraries to characterize both the essential genome and the genes facilitating host colonization. Comparison of Tn-seq results from laboratory cultures and from monoinoculated worker bees reveal that 519 of 2,226 protein-coding genes in S. alvi are essential in culture, whereas 399 are not essential but are beneficial for gut colonization. Genes facilitating colonization fall into three broad functional categories: extracellular interactions, metabolism, and stress responses. Extracellular components with strong fitness benefits in vivo include trimeric autotransporter adhesins, O antigens, and type IV pili (T4P). Experiments with T4P mutants establish that T4P in S. alvi likely function in attachment and biofilm formation, with knockouts experiencing a competitive disadvantage in vivo. Metabolic processes promoting colonization include essential amino acid biosynthesis and iron acquisition pathways, implying nutrient scarcity within the hindgut environment. Mechanisms to deal with various stressors, such as for the repair of double-stranded DNA breaks and protein quality control, are also critical in vivo. This genome-wide study identifies numerous genetic networks underlying colonization by a gut commensal in its native host environment, including some known from more targeted studies in other host-microbe symbioses

The Dynamics of a Rigid Body in Potential Flow with Circulation

We consider the motion of a two-dimensional body of arbitrary shape in a planar irrotational, incompressible fluid with a given amount of circulation around the body. We derive the equations of motion for this system by performing symplectic reduction with respect to the group of volume-preserving diffeomorphisms and obtain the relevant Poisson structures after a further Poisson reduction with respect to the group of translations and rotations. In this way, we recover the equations of motion given for this system by Chaplygin and Lamb, and we give a geometric interpretation for the Kutta-Zhukowski force as a curvature-related effect. In addition, we show that the motion of a rigid body with circulation can be understood as a geodesic flow on a central extension of the special Euclidian group SE(2), and we relate the cocycle in the description of this central extension to a certain curvature tensor.Comment: 28 pages, 2 figures; v2: typos correcte

Self-assembly of quantum dots: effect of neighbor islands on the wetting in coherent Stranski-Krastanov growth

The wetting of the homogeneously strained wetting layer by dislocation-free three-dimensional islands belonging to an array has been studied. The array has been simulated as a chain of islands in 1+1 dimensions. It is found that the wetting depends on the density of the array, the size distribution and the shape of the neighbor islands. Implications for the self-assembly of quantum dots grown in the coherent Stranski-Krastanov mode are discussed.Comment: 4 pages, 6 figures, accepted version, minor change

Acceleration of the universe, vacuum metamorphosis, and the large-time asymptotic form of the heat kernel

We investigate the possibility that the late acceleration observed in the rate of expansion of the universe is due to vacuum quantum effects arising in curved spacetime. The theoretical basis of the vacuum cold dark matter (VCDM), or vacuum metamorphosis, cosmological model of Parker and Raval is revisited and improved. We show, by means of a manifestly nonperturbative approach, how the infrared behavior of the propagator (related to the large-time asymptotic form of the heat kernel) of a free scalar field in curved spacetime causes the vacuum expectation value of its energy-momentum tensor to exhibit a resonance effect when the scalar curvature R of the spacetime reaches a particular value related to the mass of the field. we show that the back reaction caused by this resonance drives the universe through a transition to an accelerating expansion phase, very much in the same way as originally proposed by Parker and Raval. Our analysis includes higher derivatives that were neglected in the earlier analysis, and takes into account the possible runaway solutions that can follow from these higher-derivative terms. We find that the runaway solutions do not occur if the universe was described by the usual classical FRW solution prior to the growth of vacuum energy-density and negative pressure (i.e., vacuum metamorphosis) that causes the transition to an accelerating expansion of the universe in this theory.Comment: 33 pages, 3 figures. Submitted to Physical Review D15 (Dec 23, 2003). v2: 1 reference added. No other change

WD + MS systems as the progenitor of SNe Ia

We show the initial and final parameter space for SNe Ia in a ($\log P^{\rm i}, M_{\rm 2}^{\rm i}$) plane and find that the positions of some famous recurrent novae, as well as a supersoft X-ray source (SSS), RX J0513.9-6951, are well explained by our model. The model can also explain the space velocity and mass of Tycho G, which is now suggested to be the companion star of Tycho's supernova. Our study indicates that the SSS, V Sge, might be the potential progenitor of supernovae like SN 2002ic if the delayed dynamical-instability model due to Han & Podsiadlowski (2006) is appropriate. Following the work of Meng, Chen & Han (2009), we found that the SD model (WD + MS) with an optically thick wind can explain the birth rate of supernovae like SN 2006X and reproduce the distribution of the color excess of SNe Ia. The model also predicts that at least 75% of all SNe Ia may show a polarization signal in their spectra.Comment: 6 pages, 2 figures, accepted for publication in Astrophysics & Space Science (Proceeding of the 4th Meeting on Hot Subdwarf Stars and Related Objects, edited by Zhanwen Han, Simon Jeffery & Philipp Podsiadlowski

PTF11iqb: cool supergiant mass-loss that bridges the gap between Type IIn and normal supernovae

The supernova (SN) PTF11iqb was initially classified as a Type IIn event caught very early after explosion. It showed narrow Wolf–Rayet (WR) spectral features on day 2 (as in SN 1998S and SN 2013cu), but the narrow emission weakened quickly and the spectrum morphed to resemble Types II-L and II-P. At late times, H? exhibited a complex, multipeaked profile reminiscent of SN 1998S. In terms of spectroscopic evolution, we find that PTF11iqb was a near twin of SN 1998S, although with somewhat weaker interaction with circumstellar material (CSM) at early times, and stronger interaction at late times. We interpret the spectral changes as caused by early interaction with asymmetric CSM that is quickly (by day 20) enveloped by the expanding SN ejecta photosphere, but then revealed again after the end of the plateau when the photosphere recedes. The light curve can be matched with a simple model for CSM interaction (with a mass-loss rate of roughly 10?4 M? yr?1) added to the light curve of a normal SN II-P. The underlying plateau requires a progenitor with an extended hydrogen envelope like a red supergiant at the moment of explosion, consistent with the slow wind speed (<80?km?s?1) inferred from narrow H? emission. The cool supergiant progenitor is significant because PTF11iqb showed WR features in its early spectrum – meaning that the presence of such WR features does not necessarily indicate a WR-like progenitor. Overall, PTF11iqb bridges SNe IIn with weaker pre-SN mass-loss seen in SNe II-L and II-P, implying a continuum between these types

PTF11iqb: cool supergiant mass-loss that bridges the gap between Type IIn and normal supernovae

The supernova (SN) PTF11iqb was initially classified as a Type IIn event caught very early after explosion. It showed narrow Wolf–Rayet (WR) spectral features on day 2 (as in SN 1998S and SN 2013cu), but the narrow emission weakened quickly and the spectrum morphed to resemble Types II-L and II-P. At late times, H? exhibited a complex, multipeaked profile reminiscent of SN 1998S. In terms of spectroscopic evolution, we find that PTF11iqb was a near twin of SN 1998S, although with somewhat weaker interaction with circumstellar material (CSM) at early times, and stronger interaction at late times. We interpret the spectral changes as caused by early interaction with asymmetric CSM that is quickly (by day 20) enveloped by the expanding SN ejecta photosphere, but then revealed again after the end of the plateau when the photosphere recedes. The light curve can be matched with a simple model for CSM interaction (with a mass-loss rate of roughly 10?4 M? yr?1) added to the light curve of a normal SN II-P. The underlying plateau requires a progenitor with an extended hydrogen envelope like a red supergiant at the moment of explosion, consistent with the slow wind speed (<80?km?s?1) inferred from narrow H? emission. The cool supergiant progenitor is significant because PTF11iqb showed WR features in its early spectrum – meaning that the presence of such WR features does not necessarily indicate a WR-like progenitor. Overall, PTF11iqb bridges SNe IIn with weaker pre-SN mass-loss seen in SNe II-L and II-P, implying a continuum between these types

Field Measurements of Terrestrial and Martian Dust Devils

Surface-based measurements of terrestrial and martian dust devils/convective vortices provided from mobile and stationary platforms are discussed. Imaging of terrestrial dust devils has quantified their rotational and vertical wind speeds, translation speeds, dimensions, dust load, and frequency of occurrence. Imaging of martian dust devils has provided translation speeds and constraints on dimensions, but only limited constraints on vertical motion within a vortex. The longer mission durations on Mars afforded by long operating robotic landers and rovers have provided statistical quantification of vortex occurrence (time-of-sol, and recently seasonal) that has until recently not been a primary outcome of more temporally limited terrestrial dust devil measurement campaigns. Terrestrial measurement campaigns have included a more extensive range of measured vortex parameters (pressure, wind, morphology, etc.) than have martian opportunities, with electric field and direct measure of dust abundance not yet obtained on Mars. No martian robotic mission has yet provided contemporaneous high frequency wind and pressure measurements. Comparison of measured terrestrial and martian dust devil characteristics suggests that martian dust devils are larger and possess faster maximum rotational wind speeds, that the absolute magnitude of the pressure deficit within a terrestrial dust devil is an order of magnitude greater than a martian dust devil, and that the time-of-day variation in vortex frequency is similar. Recent terrestrial investigations have demonstrated the presence of diagnostic dust devil signals within seismic and infrasound measurements; an upcoming Mars robotic mission will obtain similar measurement types

Towards Machine Wald

The past century has seen a steady increase in the need of estimating and predicting complex systems and making (possibly critical) decisions with limited information. Although computers have made possible the numerical evaluation of sophisticated statistical models, these models are still designed \emph{by humans} because there is currently no known recipe or algorithm for dividing the design of a statistical model into a sequence of arithmetic operations. Indeed enabling computers to \emph{think} as \emph{humans} have the ability to do when faced with uncertainty is challenging in several major ways: (1) Finding optimal statistical models remains to be formulated as a well posed problem when information on the system of interest is incomplete and comes in the form of a complex combination of sample data, partial knowledge of constitutive relations and a limited description of the distribution of input random variables. (2) The space of admissible scenarios along with the space of relevant information, assumptions, and/or beliefs, tend to be infinite dimensional, whereas calculus on a computer is necessarily discrete and finite. With this purpose, this paper explores the foundations of a rigorous framework for the scientific computation of optimal statistical estimators/models and reviews their connections with Decision Theory, Machine Learning, Bayesian Inference, Stochastic Optimization, Robust Optimization, Optimal Uncertainty Quantification and Information Based Complexity.Comment: 37 page