zfishbook: connecting you to a world of zebrafish revertible mutants

zfishbook is an internet-based openly accessible database of revertible protein trap gene-breaking transposon (GBT) insertional mutants in the zebrafish, Danio rerio. In these lines, a monomeric red fluorescent protein (mRFP) is encoded by an artificial 3′ exon, resulting in a translational fusion to endogenous loci. The natural transparency of the zebrafish embryo and larvae greatly facilitates the expression annotation of tagged loci using new capillary-based SCORE imaging methods. Molecular annotation of each line is facilitated by cloning methods such as 5′-Rapid Amplification of cDNA Ends (RACE) and inverse polymerase chain reaction (PCR). zfishbook (http://zfishbook.org) represents a central hub for molecular, expression and mutational information about GBT lines from the International Zebrafish Protein Trap Consortium (IZPTC) that includes researchers from around the globe. zfishbook is open to community-wide contributions including expression and functional annotation. zfishbook also represents a central location for information on how to obtain these lines from diverse members of the IZPTC and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information

Optimising fusion detection through sequential DNA and RNA molecular profiling of non-small cell lung cancer

OBJECTIVES: There is an increasing number of driver fusions in NSCLC which are amenable to targeted therapy. Panel testing for fusions is increasingly appropriate but can be costly and requires adequate good quality biopsy material. In light of the typical mutual exclusivity of driver events in NSCLC, the objective of this study was to trial a novel testing pathway, supported by industrial collaboration, in which only patients negative for driver mutations on DNA-NGS were submitted for fusion panel analysis. MATERIALS AND METHODS: Over 18 months, all patients from a single centre with non-squamous NSCLC were submitted for DNA-NGS, plus ALK and ROS1 immunohistochemistry +/− FISH. Those which were negative for a driver mutation were then recalled for RNA panel testing. RESULTS: 307 samples were referred for DNA-NGS mutation analysis, of which, 10% of cases were unsuitable for or failed DNA-NGS analysis. Driver mutations were detected in 61% (167/275) of all those successfully tested. Of those without a driver mutation and with some remaining tissue available, 28% had insufficient tissue/extracted RNA or failed RNA-NGS. Of those successfully tested, 24% (17/72) had a fusion gene detected involving either ALK, ROS, MET, RET, FGFR or EGFR. Overall, 66% (184/277) of patients had a driver event detected through the combination of DNA and RNA panels. CONCLUSION: Sequential DNA and RNA based molecular profiling increased the efficacy of detecting fusion driven NSCLCs. Continued optimisation of tissue procurement, handling and the diagnostic pathways for gene fusion analysis is necessary to reduce analysis failure rates and improve detection rate for treatment with the next generation of small molecule inhibitors

Paisia, an Early Cretaceous eudicot angiosperm flower with pantoporate pollen from Portugal

A new fossil angiosperm, Paisia pantoporata, is described from the Early Cretaceous Catefica mesofossil flora, Portugal, based on coalified floral buds, flowers and isolated floral structures. The flowers are actinomorphic and structurally bisexual with a single whorl of five fleshy tepals, a single whorl of five stamens and a single whorl of five carpels. Tepals, stamens and carpels are opposite, arranged on the same radii and tepals are involute at the base clasping the stamens. Stamens have a massive filament that grades without a joint into the anther. The anthers are dithecate and tetrasporangiate with extensive connective tissue between the tiny pollen sacs. Pollen grains are pantoporate and spiny. The carpels are free, apparently plicate, with many ovules borne in two rows along the ventral margins. Paisia pantoporata is the oldest known flower with pantoporate pollen. Similar pantoporate pollen was also recognised in the associated dispersed palynoflora. Paisia is interpreted as a possibly insect pollinated, herbaceous plant with low pollen production and low dispersal potential of the pollen. The systematic position of Paisia is uncertain and Paisia pantoporata most likely belongs to an extinct lineage. Pantoporate pollen occurs scattered among all major groups of angiosperms and a close match to the fossils has not been identified. The pentamerous floral organisation together with structure of stamen, pollen and carpel suggests a phylogenetic position close to the early diverging eudicot lineages, probably in the Ranunculales.Swiss Light Source at the Paul Scherrer Institute (European Union FP6 projects) [20130185, 20141047]; Swedish Research Council [2014-5228]; Portuguese Science Foundation (FCT) [UID/MAR/00350/2013]; CretaCarbo project [PTDC/CTE-GIX/113983/2009

Stellar Diameters and Temperatures II. Main Sequence K & M Stars

We present interferometric diameter measurements of 21 K- and M- dwarfs made with the CHARA Array. This sample is enhanced by literature radii measurements to form a data set of 33 K-M dwarfs with diameters measured to better than 5%. For all 33 stars, we compute absolute luminosities, linear radii, and effective temperatures (Teff). We develop empirical relations for \simK0 to M4 main- sequence stars between the stellar Teff, radius, and luminosity to broad-band color indices and metallicity. These relations are valid for metallicities between [Fe/H] = -0.5 and +0.1 dex, and are accurate to ~2%, ~5%, and ~4% for Teff, radius, and luminosity, respectively. Our results show that it is necessary to use metallicity dependent transformations to convert colors into stellar Teffs, radii, and luminosities. We find no sensitivity to metallicity on relations between global stellar properties, e.g., Teff-radius and Teff-luminosity. Robust examinations of single star Teffs and radii compared to evolutionary model predictions on the luminosity-Teff and luminosity-radius planes reveals that models overestimate the Teffs of stars with Teff < 5000 K by ~3%, and underestimate the radii of stars with radii < 0.7 R\odot by ~5%. These conclusions additionally suggest that the models overestimate the effects that the stellar metallicity may have on the astrophysical properties of an object. By comparing the interferometrically measured radii for single stars to those of eclipsing binaries, we find that single and binary star radii are consistent. However, the literature Teffs for binary stars are systematically lower compared to Teffs of single stars by ~ 200 to 300 K. Lastly, we present a empirically determined HR diagram for a total of 74 nearby, main-sequence, A- to M-type stars, and define regions of habitability for the potential existence of sub-stellar mass companions in each system. [abridged]Comment: 73 pages, 12 Tables, 18 Figures. Accepted for publication in The Astrophysical Journa

A Planet Orbiting the Star Rho Coronae Borealis

We report the discovery of near-sinusoidal radial velocity variations of the G0V star rhoCrB, with period 39.6 days and amplitude 67 m/s. These variations are consistent with the existence of an orbital companion in a circular orbit. Adopting a mass of 1.0 M(Sun) for the primary, the companion has minimum mass about 1.1 Jupiter masses, and orbital radius about 0.23 AU. Such an orbital radius is too large for tidal circularization of an initially eccentric orbit during the lifetime of the star, and hence we suggest that the low eccentricity is primordial, as would be expected for a planet formed in a dissipative circumstellar disk.Comment: 9 pages, LaTeX, accepted in Astrophys. J. Letter

The Palomar Testbed Interferometer Calibrator Catalog

The Palomar Testbed Interferometer (PTI) archive of observations between 1998 and 2005 is examined for objects appropriate for calibration of optical long-baseline interferometer observations - stars that are predictably point-like and single. Approximately 1,400 nights of data on 1,800 objects were examined for this investigation. We compare those observations to an intensively studied object that is a suitable calibrator, HD217014, and statistically compare each candidate calibrator to that object by computing both a Mahalanobis distance and a Principal Component Analysis. Our hypothesis is that the frequency distribution of visibility data associated with calibrator stars differs from non-calibrator stars such as binary stars. Spectroscopic binaries resolved by PTI, objects known to be unsuitable for calibrator use, are similarly tested to establish detection limits of this approach. From this investigation, we find more than 350 observed stars suitable for use as calibrators (with an additional $\approx 140$ being rejected), corresponding to $\gtrsim 95$ sky coverage for PTI. This approach is noteworthy in that it rigorously establishes calibration sources through a traceable, empirical methodology, leveraging the predictions of spectral energy distribution modeling but also verifying it with the rich body of PTI's on-sky observations.Comment: 100 pages, 7 figures, 7 tables; to appear in the May 2008ApJS, v176n

PKS 1502+106: a new and distant gamma-ray blazar in outburst discovered by the Fermi Large Area Telescope

The Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope discovered a rapid (about 5 days duration), high-energy (E >100 MeV) gamma-ray outburst from a source identified with the blazar PKS 1502+106 (OR 103, S3 1502+10, z=1.839) starting on August 05, 2008 and followed by bright and variable flux over the next few months. Results on the gamma-ray localization and identification, as well as spectral and temporal behavior during the first months of the Fermi all-sky survey are reported here in conjunction with a multi-waveband characterization as a result of one of the first Fermi multi-frequency campaigns. The campaign included a Swift ToO (followed up by 16-day observations on August 07-22, MJD 54685-54700), VLBA (within the MOJAVE program), Owens Valley (OVRO) 40m, Effelsberg-100m, Metsahovi-14m, RATAN-600 and Kanata-Hiroshima radio/optical observations. Results from the analysis of archival observations by INTEGRAL, XMM-Newton and Spitzer space telescopes are reported for a more complete picture of this new gamma-ray blazar.Comment: 17 pages, 11 figures, accepted for The Astrophysical Journa

55 Cancri: Stellar Astrophysical Parameters, a Planet in the Habitable Zone, and Implications for the Radius of a Transiting Super-Earth

The bright star 55 Cancri is known to host five planets, including a transiting super-Earth. The study presented here yields directly determined values for 55 Cnc's stellar astrophysical parameters based on improved interferometry: $R=0.943 \pm 0.010 R_{\odot}$, $T_{\rm EFF} = 5196 \pm 24$ K. We use isochrone fitting to determine 55 Cnc's age to be 10.2 $\pm$ 2.5 Gyr, implying a stellar mass of $0.905 \pm 0.015 M_{\odot}$. Our analysis of the location and extent of the system's habitable zone (0.67--1.32 AU) shows that planet f, with period $\sim$ 260 days and $M \sin i = 0.155 M_{Jupiter}$, spends the majority of the duration of its elliptical orbit in the circumstellar habitable zone. Though planet f is too massive to harbor liquid water on any planetary surface, we elaborate on the potential of alternative low-mass objects in planet f's vicinity: a large moon, and a low-mass planet on a dynamically stable orbit within the habitable zone. Finally, our direct value for 55 Cancri's stellar radius allows for a model-independent calculation of the physical diameter of the transiting super-Earth 55 Cnc e (\sim 2.05 \pm 0.15 R_{\earth}), which, depending on the planetary mass assumed, implies a bulk density of 0.76 \rho_{\earth} or 1.07 \rho_{\earth}.Comment: revised version after incorporating referee's comments and suggestions by members of the astronomical community; 7 pages, 4 figures, 2 tables; accepted for publication in Ap

Deep MMT Transit Survey of the Open Cluster M37 III: Stellar Rotation at 550 Myr

In the course of conducting a deep (14.5 ~< r ~< 23), 20 night survey for transiting planets in the rich ~550 Myr old open cluster M37 we have measured the rotation periods of 575 stars which lie near the cluster main sequence, with masses 0.2 Msun ~< M ~< 1.3 Msun. This is the largest sample of rotation periods for a cluster older than 500 Myr. Using this rich sample we investigate a number of relations between rotation period, color and the amplitude of photometric variability. Stars with M >~ 0.8 Msun show a tight correlation between period and mass with heavier stars rotating more rapidly. There is a group of 4 stars with P > 15 days that fall well above this relation, which, if real, would present a significant challenge to theories of stellar angular momentum evolution. Below 0.8 Msun the stars continue to follow the period-mass correlation but with a broad tail of rapid rotators that expands to shorter periods with decreasing mass. We combine these results with observations of other open clusters to test the standard theory of lower-main sequence stellar angular momentum evolution. We find that the model reproduces the observations for solar mass stars, but discrepancies are apparent for stars with 0.6 ~< M ~< 1.0 Msun. We also find that for late-K through early-M dwarf stars in this cluster rapid rotators tend to be bluer than slow rotators in B-V but redder than slow rotators in V-I_{C}. This result supports the hypothesis that the significant discrepancy between the observed and predicted temperatures and radii of low-mass main sequence stars is due to stellar activity.Comment: Replaced with version accepted to ApJ. 104 pages, 7 tables, 26 figure