Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions

<p>Abstract</p> <p>Background</p> <p>Sequence closure often represents the end-point of a genome project, without a system in place for subsequent improvement and refinement. Building on the genome project of <it>Vibrio fischeri </it>ES114, we used a comparative approach to identify and investigate genes that had a high likelihood of sequence error.</p> <p>Results</p> <p>Comparison of the <it>V. fischeri </it>ES114 genome with that of conspecific strain MJ11 identified 82 target loci in ES114 as containing likely errors, and thus of high-priority for resequencing. Analysis of the targets identified 75 loci in which an error had occurred, resulting in the correction of 10,457 base pairs to generate the new ES114 genomic sequence. A majority of the inaccurate loci involved frameshift errors, correction of which fused adjacent ORFs. Although insertions/deletions are thought to be rare in microbial genome assemblies, fourteen of the loci contained extraneous sequence of over 300 bp, likely due to imperfect contig ends that were misassembled in tandem rather than as overlapping segments. Additionally we updated the entire genome annotation with 113 new features including previously uncalled protein-coding genes, regulatory RNA genes and operon leader peptides, and we analyzed the transcriptional apparatus encoded by ES114.</p> <p>Conclusion</p> <p>We demonstrate that errors in microbial genome sequences, thought to largely be confined to point mutations, may also consist of other prevalent large-scale rearrangements such as insertions. Ongoing genome quality control and annotation programs are necessary to accompany technological advancements in data generation. These updates further advance <it>V. fischeri </it>as an important model for understanding intercellular communication and colonization of animal tissue.</p

ORFEUS-II Far-Ultraviolet Observations of 3C273: 1. Interstellar and Intergalactic Absorption Lines

We present the first intermediate-resolution (lambda / 3000) spectrum of the bright quasi-stellar object 3C273 at wavelengths between 900 and 1200 A. Observations were performed with the Berkeley spectrograph aboard the ORFEUS-SPAS II mission. We detect Lyman beta counterparts to previously-identified intergalactic Lyman-alpha features at cz = 19900, 1600, and 1000 km/s; counterparts to other putative Lyman-alpha clouds along the sight line are below our detection limit. The strengths of the two very low redshift Lyman-beta features, which are believed to arise in Virgo intracluster gas, exceed preflight expectations, suggesting that the previous determination of the cloud parameters may underestimate the true column densities. A curve-of-growth analysis sets a minimum H I column density of 4 E14/cm^2 for the 1600 km/s cloud. We find marginally significant evidence for Galactic H_2 along the sight line, with a total column density of about 1 E15/cm^2. We detect the stronger interstellar O VI doublet member unambiguously; the weaker member is blended with other features. If the Doppler b value for O VI is comparable to that determined for N V then the O VI column density is 7 +/- 2 E14/cm^2, significantly above the only previous estimate. The O VI / N V ratio is about 10, consistent with the low end of the range observed in the disk. Additional interstellar species detected for the first time toward 3C273 (at modest statistical significance) include P II, Fe III, Ar I, and S III.Comment: LaTeX file, 11 pages, 4 encapsulated PostScript figures. Uses aaspp4.sty and astrobib.sty. (Astrobib is available from http://www.stsci.edu/software/TeX.html .) The ORFEUS telescope is described at http://sag-www.ssl.berkeley.edu/orfeus/ . To appear in ApJ (Letters

Viral Gene Delivery Selectively Restores Feeding and Prevents Lethality of Dopamine-Deficient Mice

AbstractDopamine-deficient mice (DA−/−), lacking tyrosine hydroxylase (TH) in dopaminergic neurons, become hypoactive and aphagic and die by 4 weeks of age. They are rescued by daily treatment with L-3,4-dihydroxyphenylalanine (L-DOPA); each dose restores dopamine (DA) and feeding for less than 24 hr. Recombinant adeno-associated viruses expressing human TH or GTP cyclohydrolase 1 (GTPCH1) were injected into the striatum of DA−/− mice. Bilateral coinjection of both viruses restored feeding behavior for several months. However, locomotor activity and coordination were partially improved. A virus expressing only TH was less effective, and one expressing GTPCH1 alone was ineffective. TH immunoreactivity and DA were detected in the ventral striatum and adjacent posterior regions of rescued mice, suggesting that these regions mediate a critical DA-dependent aspect of feeding behavior

Quantum cryptography with squeezed states

A quantum key distribution scheme based on the use of displaced squeezed vacuum states is presented. The states are squeezed in one of two field quadrature components, and the value of the squeezed component is used to encode a character from an alphabet. The uncertainty relation between quadrature components prevents an eavesdropper from determining both with enough precision to determine the character being sent. Losses degrade the performance of this scheme, but it is possible to use phase-sensitive amplifiers to boost the signal and partially compensate for their effect.Comment: 15 pages, no figure

The Transit Light Curve Project. XII. Six Transits of the Exoplanet XO-2b

We present photometry of six transits of the exoplanet XO-2b. By combining the light-curve analysis with theoretical isochrones to determine the stellar properties, we find the planetary radius to be 0.996 +0.031/-0.018 rjup and the planetary mass to be 0.565 +/- 0.054 mjup. These results are consistent with those reported previously, and are also consistent with theoretical models for gas giant planets. The mid-transit times are accurate to within 1 min and are consistent with a constant period. However, the period we derive differs by 2.5 sigma from the previously published period. More data are needed to tell whether the period is actually variable (as it would be in the presence of an additional body) or if the timing errors have been underestimated.Comment: Accepted for publication in AJ. 20 pages, 3 tables, 4 figure

Speckle from phase ordering systems

The statistical properties of coherent radiation scattered from phase-ordering materials are studied in detail using large-scale computer simulations and analytic arguments. Specifically, we consider a two-dimensional model with a nonconserved, scalar order parameter (Model A), quenched through an order-disorder transition into the two-phase regime. For such systems it is well established that the standard scaling hypothesis applies, consequently the average scattering intensity at wavevector _k and time t' is proportional to a scaling function which depends only on a rescaled time, t ~ |_k|^2 t'. We find that the simulated intensities are exponentially distributed, with the time-dependent average well approximated using a scaling function due to Ohta, Jasnow, and Kawasaki. Considering fluctuations around the average behavior, we find that the covariance of the scattering intensity for a single wavevector at two different times is proportional to a scaling function with natural variables mt = |t_1 - t_2| and pt = (t_1 + t_2)/2. In the asymptotic large-pt limit this scaling function depends only on z = mt / pt^(1/2). For small values of z, the scaling function is quadratic, corresponding to highly persistent behavior of the intensity fluctuations. We empirically establish a connection between the intensity covariance and the two-time, two-point correlation function of the order parameter. This connection allows sensitive testing, either experimental or numerical, of existing theories for two-time correlations in systems undergoing order-disorder phase transitions. Comparison between theory and our numerical results requires no adjustable parameters.Comment: 18 pgs RevTeX, to appear in PR

A Prograde, Low-Inclination Orbit for the Very Hot Jupiter WASP-3b

We present new spectroscopic and photometric observations of the transiting exoplanetary system WASP-3. Spectra obtained during two separate transits exhibit the Rossiter-McLaughlin (RM) effect and allow us to estimate the sky-projected angle between the planetary orbital axis and the stellar rotation axis, lambda = 3.3^{+2.5}_{-4.4} degrees. This alignment between the axes suggests that WASP-3b has a low orbital inclination relative to the equatorial plane of its parent star. During our first night of spectroscopic measurements, we observed an unexpected redshift briefly exceeding the expected sum of the orbital and RM velocities by 140 m/s. This anomaly could represent the occultation of material erupting from the stellar photosphere, although it is more likely to be an artifact caused by moonlight scattered into the spectrograph.Comment: 23 pages, 4 figures, Accepted for publication in The Astrophysical Journal, Replacement includes revised citation

NLTT 41135: a field M-dwarf + brown dwarf eclipsing binary in a triple system, discovered by the MEarth observatory

We report the discovery of an eclipsing companion to NLTT 41135, a nearby M5 dwarf that was already known to have a wider, slightly more massive common proper motion companion, NLTT 41136, at 2.4 arcsec separation. Analysis of combined-light and radial velocity curves of the system indicates that NLTT 41135B is a 31-34 +/- 3 MJup brown dwarf (where the range depends on the unknown metallicity of the host star) on a circular orbit. The visual M-dwarf pair appears to be physically bound, so the system forms a hierarchical triple, with masses approximately in the ratio 8:6:1. The eclipses are grazing, preventing an unambiguous measurement of the secondary radius, but follow-up observations of the secondary eclipse (e.g. with the James Webb Space Telescope) could permit measurements of the surface brightness ratio between the two objects, and thus place constraints on models of brown dwarfs.Comment: 15 pages, 6 figures, 10 tables, emulateapj format. Accepted for publication in Ap