Real-time depth sectioning: Isolating the effect of stress on structure development in pressure-driven flow

Transient structure development at a specific distance from the channel wall in a pressure-driven flow is obtained from a set of real-time measurements that integrate contributions throughout the thickness of a rectangular channel. This “depth sectioning method” retains the advantages of pressure-driven flow while revealing flow-induced structures as a function of stress. The method is illustrated by applying it to isothermal shear-induced crystallization of an isotactic polypropylene using both synchrotron x-ray scattering and optical retardance. Real-time, depth-resolved information about the development of oriented precursors reveals features that cannot be extracted from ex-situ observation of the final morphology and that are obscured in the depth-averaged in-situ measurements. For example, at 137 °C and at the highest shear stress examined (65 kPa), oriented thread-like nuclei formed rapidly, saturated within the first 7 s of flow, developed significant crystalline overgrowth during flow and did not relax after cessation of shear. At lower stresses, threads formed later and increased at a slower rate. The depth sectioning method can be applied to the flow-induced structure development in diverse complex fluids, including block copolymers, colloidal systems, and liquid-crystalline polymers

GTC OSIRIS transiting exoplanet atmospheric survey: detection of sodium in XO-2b from differential long-slit spectroscopy

We present two transits of the hot-Jupiter exoplanet XO-2b using the Gran Telescopio Canarias (GTC). The time series observations were performed using long-slit spectroscopy of XO-2 and a nearby reference star with the OSIRIS instrument, enabling differential specrophotometric transit lightcurves capable of measuring the exoplanet's transmission spectrum. Two optical low-resolution grisms were used to cover the optical wavelength range from 3800 to 9300{\AA}. We find that sub-mmag level slit losses between the target and reference star prevent full optical transmission spectra from being constructed, limiting our analysis to differential absorption depths over ~1000{\AA} regions. Wider long slits or multi-object grism spectroscopy with wide masks will likely prove effective in minimising the observed slit-loss trends. During both transits, we detect significant absorption in the planetary atmosphere of XO-2b using a 50{\AA} bandpass centred on the Na I doublet, with absorption depths of Delta(R_pl/R_star)^2=0.049+/-0.017 % using the R500R grism and 0.047+/-0.011 % using the R500B grism (combined 5.2-sigma significance from both transits). The sodium feature is unresolved in our low-resolution spectra, with detailed modelling also likely ruling out significant line-wing absorption over an ~800{\AA} region surrounding the doublet. Combined with narrowband photometric measurements, XO-2b is the first hot Jupiter with evidence for both sodium and potassium present in the planet's atmosphere.Comment: 9 pages, 10 figures, 1 table, accepted for publication in MNRA

Gran Telescopio Canarias OSIRIS Transiting Exoplanet Atmospheric Survey: Detection of potassium in XO-2b from narrowband spectrophotometry

We present Gran Telescopio Canarias (GTC) optical transit narrow-band photometry of the hot-Jupiter exoplanet XO-2b using the OSIRIS instrument. This unique instrument has the capabilities to deliver high cadence narrow-band photometric lightcurves, allowing us to probe the atmospheric composition of hot Jupiters from the ground. The observations were taken during three transit events which cover four wavelengths at spectral resolutions near 500, necessary for observing atmospheric features, and have near-photon limited sub-mmag precisions. Precision narrow-band photometry on a large aperture telescope allows for atmospheric transmission spectral features to be observed for exoplanets around much fainter stars than those of the well studied targets HD209458b and HD189733b, providing access to the majority of known transiting planets. For XO-2b, we measure planet-to-star radius contrasts of R_pl/R_star=0.10508+/-0.00052 at 6792 Ang, 0.10640+/-0.00058 at 7582 Ang, and 0.10686+/-0.00060 at 7664.9 Ang, and 0.10362+/-0.00051 at 8839 Ang. These measurements reveal significant spectral features at two wavelengths, with an absorption level of 0.067+/-0.016% at 7664.9 Ang due to atmospheric potassium in the line core (a 4.1-sigma significance level), and an absorption level of 0.058+/-0.016% at 7582 Ang, (a 3.6-sigma significance level). When comparing our measurements to hot-Jupiter atmospheric models, we find good agreement with models which are dominated in the optical by alkali metals. This is the first evidence for potassium in an extrasolar planet, an element that has long been theorized along with sodium to be a dominant source of opacity at optical wavelengths for hot Jupiters.Comment: 11 pages, 6 figures, accepted in A&A, minor changes to wording, primarily section 4.2, and the title has also been slightly modifie

Voltage-gated sodium channels as targets for pyrethroid insecticides

The pyrethroid insecticides are a very successful group of compounds that have been used extensively for the control of arthropod pests of agricultural crops and vectors of animal and human disease. Unfortunately, this has led to the development of resistance to the compounds in many species. The mode of action of pyrethroids is known to be via interactions with the voltage-gated sodium channel. Understanding how binding to the channel is affected by amino acid substitutions that give rise to resistance has helped to elucidate the mode of action of the compounds and the molecular basis of their selectivity for insects vs mammals and between insects and other arthropods. Modelling of the channel/pyrethroid interactions, coupled with the ability to express mutant channels in oocytes and study function, has led to knowledge of both how the channels function and potentially how to design novel insecticides with greater species selectivity

Molecular Binding Mechanism of TtgR Repressor to Antibiotics and Antimicrobials

A disturbing phenomenon in contemporary medicine is the prevalence of multidrug-resistant pathogenic bacteria. Efflux pumps contribute strongly to this antimicrobial drug resistance, which leads to the subsequent failure of clinical treatments. The TtgR protein of Pseudomonas putida is a HTH-type transcriptional repressor that controls expression of the TtgABC efflux pump, which is the main contributor to resistance against several antimicrobials and toxic compounds in this microbe. One of the main strategies to modulate the bacterial resistance is the rational modification of the ligand binding target site. We report the design and characterization of four mutants-TtgRS77A, TtgRE78A, TtgRN110A and TtgRH114A - at the active ligand binding site. The biophysical characterization of the mutants, in the presence and in the absence of different antimicrobials, revealed that TtgRN110A is the variant with highest thermal stability, under any of the experimental conditions tested. EMSA experiments also showed a different dissociation pattern from the operator for TtgRN110A, in the presence of several antimicrobials, making it a key residue in the TtgR protein repression mechanism of the TtgABC efflux pump. We found that TtgRE78A stability is the most affected upon effector binding. We also probe that one mutation at the C-terminal half of helix-α4, TtgRS77A, provokes a severe protein structure distortion, demonstrating the important role of this residue in the overall protein structure and on the ligand binding site. The data provide new information and deepen the understanding of the TtgR-effector binding mechanism and consequently the TtgABC efflux pump regulation mechanism in Pseudomonas putida.This work was supported by Spanish Ministry of Economy and Competitiveness, National programme for Recruitment and Incorporation of Human Resources, Subprogramme: Ramon y Cajal RYC-2009-04570 and grant P11-CVI-7391 from Junta de Andalucía and EFDR (European Regional Development Fund)

Ensembl 2008.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure

Ensembl 2007

The Ensembl () project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees