Crystallization and preliminary crystallographic analysis of the DNA gyrase B protein from B-stearothermophilus

DNA gyrase B (GyrB) from B. stearothermophilus has been crystallized in the presence of the non-hydrolyzable ATP analogue, 5'-adenylpl-beta-gamma-imidodiphosphate (ADPNP), by the dialysis method. A complete native data set to 3.7 Angstrom has been collected from crystals which belonged to the cubic space group I23 with unit-cell dimension a = 250.6 Angstrom. Self-rotation function analysis indicates the position of a molecular twofold axis. Low-resolution data sets of a thimerosal and a selenomethionine derivative have also been analysed. The heavy-atom positions are consistent with one dimer in the asymmetric unit

On the Tapping Mode Measurement for Young’s Modulus of Nanocrystalline Metal Coatings

Young’s modulus of nanocrystalline metal coatings is measured using the oscillating, that is, tapping, mode of a cantilever with a diamond tip. The resonant frequency of the cantilever changes when the diamond tip comes in contact with a sample surface. A Hertz-contact-based model is further developed using higher-order terms in a Taylor series expansion to determine a relationship between the reduced elastic modulus and the shift in the resonant frequency of the cantilever during elastic contact between the diamond tip and sample surface. The tapping mode technique can be used to accurately determine Young’s modulus that corresponds with the crystalline orientation of the sample surface as demonstrated for nanocrystalline nickel, vanadium, and tantalum coatings

Flexible Lipid Bilayers in Implicit Solvent

A minimalist simulation model for lipid bilayers is presented. Each lipid is represented by a flexible chain of beads in implicit solvent. The hydrophobic effect is mimicked through an intermolecular pair potential localized at the ``water''/hydrocarbon tail interface. This potential guarantees realistic interfacial tensions for lipids in a bilayer geometry. Lipids self assemble into bilayer structures that display fluidity and elastic properties consistent with experimental model membrane systems. Varying molecular flexibility allows for tuning of elastic moduli and area/molecule over a range of values seen in experimental systems.Comment: 5 pages, 5 figure

Evidence for CO depletion in the inner regions of gas-rich protoplanetary disks

We investigate the physical properties and spatial distribution of Carbon Monoxide (CO) gas in the disks around the Herbig Ae/Be stars HD 97048 and HD 100546. Using high-spectral-resolution 4.588-4.715 $\mu$m spectra containing fundamental CO emission taken with CRIRES on the VLT, we probe the circumstellar gas and model the kinematics of the emission lines. By using spectro-astrometry on the spatially resolved targets, we constrain the physical size of the emitting regions in the disks. We resolve, spectrally and spatially, the emission of the $^{13}$CO v(1-0) vibrational band and the $^{12}$CO $v=1-0, v=2-1, v=3-2$ and $v=4-3$ vibrational bands in both targets, as well as the $^{12}$CO $v=5-4$ band in HD 100546. Modeling of the CO emission with a homogeneous disk in Keplerian motion, yields a best fit with an inner and outer radius of the CO emitting region of 11 and $\geq$ 100 AU for HD 97048. HD 100546 is not fit well with our model, but we derive a lower limit on the inner radius of 8 AU. The fact that gaseous [OI] emission was previously detected in both targets at significantly smaller radii suggests that CO may be effectively destroyed at small radii in the surface layers of these disksComment: v2: Letter format has been changed to Paper format; Change in the focus of the paper towards CO depletion; Major changes in text; Change of title. Submitted to A&A, 14/10/2008. Accepted by A&A, 17/04/200

Polyunsaturated fatty acids inhibit a pentameric ligand-gated ion channel through one of two binding sites

Polyunsaturated fatty acids (PUFAs) inhibit pentameric ligand-gated ion channels (pLGICs) but the mechanism of inhibition is not well understood. The PUFA, docosahexaenoic acid (DHA), inhibits agonist responses of the pLGIC, ELIC, more effectively than palmitic acid, similar to the effects observed in the GAB

Tracing the origins of permitted emission lines in RU Lupi down to AU scales

Most of the observed emission lines and continuum excess from young accreting low mass stars (Classical T Tauri stars -- CTTSs) take place in the star-disk or inner disk region. These regions have a complex emission topology still largely unknown. In this paper the magnetospheric accretion and inner wind contributions to the observed permitted He and H near infrared (NIR) lines of the bright southern CTTS RU Lupi are investigated for the first time. Previous optical observations of RU Lupi showed a large H-alpha profile, due to the emission from a wind in the line wings, and a micro-jet detected in forbidden lines. We extend this analysis to NIR lines through seeing-limited high spectral resolution spectra taken with VLT/ISAAC, and adaptive optics (AO) aided narrow-band imaging and low spectral resolution spectroscopy with VLT/NACO. Using spectro-astrometric analysis we investigate the presence of extended emission down to very low spatial scales (a few AU). The HeI 10830 line presents a P Cygni profile whose absorption feature indicates the presence of an inner stellar wind. Moreover the spectro-astrometric analysis evidences the presence of an extended emission superimposed to the absorption feature and likely coming from the micro-jet detected in the optical. On the contrary, the origin of the Hydrogen Paschen and Brackett lines is difficult to address. We tried tentatively to explain the observed line profiles and flux ratios with both accretion and wind models showing the limits of both approaches. The lack of spectro-astrometric signal indicates that the HI emission is either compact or symmetric. Our analysis confirms the sensitivity of the HeI line to the presence of faint extended emission regions in the close proximity of the star.Comment: 11 pages, 4 figures, accepted for publication on A&

Seasonality of submesoscale flows in the ocean surface boundary layer

A signature of submesoscale flows in the upper ocean is skewness in the distribution of relative vorticity. Expected to result for high Rossby-number flows, such skewness has implications for mixing, dissipation and stratification within the upper ocean. An array of moorings deployed in the Northeast Atlantic for one year as part of the OSMOSIS experiment reveals that relative vorticity is positively skewed during winter even though the scale of the Rossby number is less than 0.5. Furthermore, this skewness is reduced to zero during spring and autumn. There is also evidence of modest seasonal variations in the gradient Rossby number. The proposed mechanism by which relative vorticity is skewed is that the ratio of lateral to vertical buoyancy gradients, as summarized by the inverse gradient Richardson number, restricts its range during winter but less so at other times of the year. These results support recent observations and model simulations suggesting the upper ocean is host to a seasonal cycle in submesoscale turbulence

The Orthologue of Sjögren's Syndrome Nuclear Autoantigen 1 (SSNA1) in Trypanosoma brucei Is an Immunogenic Self-Assembling Molecule

Primary Sjögren's Syndrome (PSS) is a highly prevalent autoimmune disease, typically manifesting as lymphocytic infiltration of the exocrine glands leading to chronically impaired lacrimal and salivary secretion. Sjögren's Syndrome nuclear autoantigen 1 (SSNA1 or NA14) is a major specific target for autoantibodies in PSS but the precise function and clinical relevance of this protein are largely unknown. Orthologues of the gene are absent from many of the commonly used model organisms but are present in Chlamyodomonas reinhardtii (in which it has been termed DIP13) and most protozoa. We report the functional characterisation of the orthologue of SSNA1 in the kinetoplastid parasite, Trypanosoma brucei. Both TbDIP13 and human SSNA1 are small coiled-coil proteins which are predicted to be remote homologues of the actin-binding protein tropomyosin. We use comparative proteomic methods to identify potential interacting partners of TbDIP13. We also show evidence that TbDIP13 is able to self-assemble into fibril-like structures both in vitro and in vivo, a property which may contribute to its immunogenicity. Endogenous TbDIP13 partially co-localises with acetylated α-tubulin in the insect procyclic stage of the parasite. However, deletion of the DIP13 gene in cultured bloodstream and procyclic stages of T. brucei has little effect on parasite growth or morphology, indicating either a degree of functional redundancy or a function in an alternative stage of the parasite life cycle

Disease prevention not decolonization – a model for fecal microbiota transplantation in patients colonized with multidrug-resistant organisms

Fecal microbiota transplantation (FMT) yields variable intestinal decolonization results for multidrug-resistant organisms (MDROs). This study showed significant reductions in antibiotic duration, bacteremia and length of stay in 20 patients colonized/ infected with MDRO receiving FMT (compared to pre-FMT history, and a matched group not receiving FMT), despite modest decolonization rates