The PLATO Dome A Site-Testing Observatory : instrumentation and first results

The PLATeau Observatory (PLATO) is an automated self-powered astrophysical observatory that was deployed to Dome A, the highest point on the Antarctic plateau, in 2008 January. PLATO consists of a suite of site-testing instruments designed to quantify the benefits of the Dome A site for astronomy, and science instruments designed to take advantage of the unique observing conditions. Instruments include CSTAR, an array of optical telescopes for transient astronomy; Gattini, an instrument to measure the optical sky brightness and cloud cover statistics; DASLE, an experiment to measure the statistics of the meteorological conditions within the near-surface layer; Pre-HEAT, a submillimeter tipping radiometer measuring the atmospheric transmission and water vapor content and performing spectral line imaging of the Galactic plane; and Snodar, an acoustic radar designed to measure turbulence within the near-surface layer. PLATO has run completely unattended and collected data throughout the winter 2008 season. Here we present a detailed description of the PLATO instrument suite and preliminary results obtained from the first season of operation

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Mean-field analysis of the stability of a K-Rb Fermi-Bose mixture

We compare the experimental stability diagram of a Fermi-Bose mixture of K-40 and Rb-87 atoms with attractive interaction to the predictions of a mean-field theoretical model. We discuss how this comparison can be used to give a better estimate of the interspecies scattering length, which is currently known from collisional measurements with larger uncertainty.Comment: 5 pages, 4 figure

Finite temperature excitations of a trapped Bose-Fermi mixture

We present a detailed study of the low-lying collective excitations of a spherically trapped Bose-Fermi mixture at finite temperature in the collisionless regime. The excitation frequencies of the condensate are calculated self-consistently using the static Hartree-Fock-Bogoliubov theory within the Popov approximation. The frequency shifts and damping rates due to the coupled dynamics of the condensate, noncondensate, and degenerate Fermi gas are also taken into account by means of the random phase approximation and linear response theory. In our treatment, the dipole excitation remains close to the bare trapping frequency for all temperatures considered, and thus is consistent with the generalized Kohn theorem. We discuss in some detail the behavior of monopole and quadrupole excitations as a function of the Bose-Fermi coupling. At nonzero temperatures we find that, as the mixture moves towards spatial separation with increasing Bose-Fermi coupling, the damping rate of the monopole (quadrupole) excitation increases (decreases). This provides us a useful signature to identify the phase transition of spatial separation.Comment: 10 pages, 8 figures embedded; to be published in Phys. Rev.

Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage.

Colibactin is an assumed human gut bacterial genotoxin, whose biosynthesis is linked to the clb genomic island that has a widespread distribution in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumour formation and enhance the progression of colorectal cancer via cellular senescence and death induced by DNA double-strand breaks (DSBs); however, the chemical basis that contributes to the pathogenesis at the molecular level has not been fully characterized. Here, we report the discovery of colibactin-645, a macrocyclic colibactin metabolite that recapitulates the previously assumed genotoxicity and cytotoxicity. Colibactin-645 shows strong DNA DSB activity in vitro and in human cell cultures via a unique copper-mediated oxidative mechanism. We also delineate a complete biosynthetic model for colibactin-645, which highlights a unique fate of the aminomalonate-building monomer in forming the C-terminal 5-hydroxy-4-oxazolecarboxylic acid moiety through the activities of both the polyketide synthase ClbO and the amidase ClbL. This work thus provides a molecular basis for colibactin's DNA DSB activity and facilitates further mechanistic study of colibactin-related colorectal cancer incidence and prevention

Protein trafficking through the endosomal system prepares intracellular parasites for a home invasion

Toxoplasma (toxoplasmosis) and Plasmodium (malaria) use unique secretory organelles for migration, cell invasion, manipulation of host cell functions, and cell egress. In particular, the apical secretory micronemes and rhoptries of apicomplexan parasites are essential for successful host infection. New findings reveal that the contents of these organelles, which are transported through the endoplasmic reticulum (ER) and Golgi, also require the parasite endosome-like system to access their respective organelles. In this review, we discuss recent findings that demonstrate that these parasites reduced their endosomal system and modified classical regulators of this pathway for the biogenesis of apical organelles

Photoinduced absorption and photoluminescence in poly(2,5-dimethoxy-p- phenylene vinylene)

We report a study of the photoexcited states in the conjugated polymer poly(2,5-dimethoxy-p-phenylene vinylene). Photoluminescence due to radiative recombination of singlet excitons is observed at energiesjust below the onset of the pi-pi* absorption band at 2.1 eV. Photoinduced absorption at 80 K shows bands peaking at 0.68, 1.35, and 1.80 eV. The features at 0.68 and 1.8 eV are associated with the same excited state which we propose is a doubly charged bipolaron, while the third at 1.35 eV is unrelated. We assign this 1.35-eV absorption to a triplet-triplet transition of a triplet exciton. The bipolarons are long lived with significant numbers surviving in excess of 100 ms at 80 K, and have a weak temperature dependence such that photoinduced absorption is readily detectable even at room temperature. The triplet exciton has a lifetime of order 2.5 ms at 80 K but this falls rapidly at higher temperature and the response is not detected at room temperature. We contrast these results with those obtained previously for the related poly(arylene vinylene) polymers poly(p-phenylene vinylene), and poly(2,5-thienylene vinylene) and for other conjugated polymers, and draw attention to the important role played in the photophysics of these materials by neutral excited states

Long-lived photoexcited states in polydiacetylenes with different molecular and supramolecular organization

With the aim of determining the importance of the molecular and supramolecular organization on the excited states of polydiacetylenes, we have studied the photoinduced absorption spectra of the red form of poly[1,6-bis(3,6-didodecyl-N-carbazolyl)-2,4-hexadiyne] (polyDCHD-S) and the results compared with those of the blue form of the same polymer. An interpretation of the data is given in terms of both the conjugation length and the interbackbone separation also in relation to the photoinduced absorption spectra of both blue and red forms of poly[1,6-bis(N-carbazolyl)-2,4-hexadiyne] (polyDCHD), which does not carry the alkyl substituents on the carbazolyl side groups. Information on the above properties is derived from the analysis of the absorption and Raman spectra of this class of polydiacetylenes

Possible realization of Josephson charge qubits in two coupled Bose-Einstein condensates

We demonstrate that two coupled Bose-Einstein condensates (BEC) at zero temperature can be used to realize a qubit which is the counterpart of Josephson charge qubits. The two BEC are weakly coupled and confined in an asymmetric double-well trap. When the "charging energy" of the system is much larger than the Josephson energy and the system is biased near a degeneracy point, the two BEC represent a qubit with two states differing only by one atom. The realization of the BEC qubits in realistic BEC experiments is briefly discussed.Comment: 4 pages; comments are welcome / Corrected typos in Eq. (16); a note adde

Astrometry with Hubble Space Telescope: A Parallax of the Fundamental Distance Calibrator RR Lyrae

We present an absolute parallax and relative proper motion for the fundamental distance scale calibrator, RR Lyr. We obtain these with astrometric data from FGS 3, a white-light interferometer on HST. We find $\pi_{abs} = 3.82 \pm 0.2$ mas. Spectral classifications and VRIJHKT$_2$M and DDO51 photometry of the astrometric reference frame surrounding RR Lyr indicate that field extinction is low along this line of sight. We estimate =0.07\pm0.03 for these reference stars. The extinction suffered by RR Lyr becomes one of the dominant contributors to the uncertainty in its absolute magnitude. Adopting the average field absorption, =0.07 \pm 0.03, we obtain M_V^{RR} = 0.61 ^{-0.11}_{+0.10}. This provides a distance modulus for the LMC, m-M = 18.38 - 18.53^{-0.11}_{+0.10} with the average extinction-corrected magnitude of RR Lyr variables in the LMC, , remaining a significant uncertainty. We compare this result to more than 80 other determinations of the distance modulus of the LMC.Comment: Several typos corrected. To appear in The Astronomical Journal, January 200