159 research outputs found
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 being
rejected), corresponding to 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: , K.
We use isochrone fitting to determine 55 Cnc's age to be 10.2 2.5 Gyr,
implying a stellar mass of . Our analysis of the
location and extent of the system's habitable zone (0.67--1.32 AU) shows that
planet f, with period 260 days and ,
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
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