480 research outputs found
Genome Sequencing of a Marine Spirillum, Oceanospirillum multiglobuliferum ATCC 33336T, from Japan
Oceanospirillum multiglobuliferum ATCC 33336T is a motile gammaproteobacterium with bipolar tufted flagella, noted for its low salt tolerance compared to other marine spirilla. This strain was originally isolated from the putrid infusions of Crassostrea gigas near Hiroshima, Japan. This paper presents a draft genome sequence for O. multiglobuliferum ATCC 33336T
Draft Genome Sequence of the Salt Water Bacterium Oceanospirillum linum ATCC 11336T
Oceanospirillum linum ATCC 11336T is an aerobic, bipolar-tufted gammaproteobacterium first isolated in the Long Island Sound in the 1950s. This announcement offers a genome sequence for O. linum ATCC 11336T, which has a predicted genome size of 3,782,189 bp (49.13% G+C content) containing 3,540 genes and 3,361 coding sequences
Cautionary Tale of Using Tris(alkyl)phosphine Reducing Agents with NAD+-Dependent Enzymes
Protein biochemistry protocols typically include disulfide bond reducing agents to guard against unwanted thiol oxidation and protein aggregation. Commonly used disulfide bond reducing agents include dithiothreitol, β-mercaptoethanol, glutathione, and the tris(alkyl)phosphine compounds tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP). While studying the catalytic activity of the NAD(P)H-dependent enzyme Δ1-pyrroline-5-carboxylate reductase, we unexpectedly observed a rapid non-enzymatic chemical reaction between NAD+ and the reducing agents TCEP and THPP. The product of the reaction exhibits a maximum ultraviolet absorbance peak at 334 nm and forms with an apparent association rate constant of 231–491 M−1 s−1. The reaction is reversible, and nuclear magnetic resonance characterization (1H, 13C, and 31P) of the product revealed a covalent adduct between the phosphorus of the tris(alkyl)phosphine reducing agent and the C4 atom of the nicotinamide ring of NAD+. We also report a 1.45 Å resolution crystal structure of short-chain dehydrogenase/reductase with the NADP+–TCEP reaction product bound in the cofactor binding site, which shows that the adduct can potentially inhibit enzymes. These findings serve to caution researchers when using TCEP or THPP in experimental protocols with NAD(P)+. Because NAD(P)+-dependent oxidoreductases are widespread in nature, our results may be broadly relevant
The Time-Domain Spectroscopic Survey: Understanding the Optically Variable Sky with SEQUELS in SDSS-III
The Time-Domain Spectroscopic Survey (TDSS) is an SDSS-IV eBOSS subproject
primarily aimed at obtaining identification spectra of ~220,000
optically-variable objects systematically selected from SDSS/Pan-STARRS1
multi-epoch imaging. We present a preview of the science enabled by TDSS, based
on TDSS spectra taken over ~320 deg^2 of sky as part of the SEQUELS survey in
SDSS-III, which is in part a pilot survey for eBOSS in SDSS-IV. Using the
15,746 TDSS-selected single-epoch spectra of photometrically variable objects
in SEQUELS, we determine the demographics of our variability-selected sample,
and investigate the unique spectral characteristics inherent in samples
selected by variability. We show that variability-based selection of quasars
complements color-based selection by selecting additional redder quasars, and
mitigates redshift biases to produce a smooth quasar redshift distribution over
a wide range of redshifts. The resulting quasar sample contains systematically
higher fractions of blazars and broad absorption line quasars than from
color-selected samples. Similarly, we show that M-dwarfs in the TDSS-selected
stellar sample have systematically higher chromospheric active fractions than
the underlying M-dwarf population, based on their H-alpha emission. TDSS also
contains a large number of RR Lyrae and eclipsing binary stars with
main-sequence colors, including a few composite-spectrum binaries. Finally, our
visual inspection of TDSS spectra uncovers a significant number of peculiar
spectra, and we highlight a few cases of these interesting objects. With a
factor of ~15 more spectra, the main TDSS survey in SDSS-IV will leverage the
lessons learned from these early results for a variety of time-domain science
applications.Comment: 17 pages, 14 figures, submitted to Ap
Baryon Acoustic Oscillations in the Ly{\alpha} forest of BOSS DR11 quasars
We report a detection of the baryon acoustic oscillation (BAO) feature in the
flux-correlation function of the Ly{\alpha} forest of high-redshift quasars
with a statistical significance of five standard deviations. The study uses
137,562 quasars in the redshift range from the Data Release
11 (DR11) of the Baryon Oscillation Spectroscopic Survey (BOSS) of SDSS-III.
This sample contains three times the number of quasars used in previous
studies. The measured position of the BAO peak determines the angular distance,
and expansion rate, , both on a scale set by the sound
horizon at the drag epoch, . We find
and
where . The optimal
combination, is determined with a precision of
. For the value , consistent with the CMB power
spectrum measured by Planck, we find
and . Tests with mock
catalogs and variations of our analysis procedure have revealed no systematic
uncertainties comparable to our statistical errors. Our results agree with the
previously reported BAO measurement at the same redshift using the
quasar-Ly{\alpha} forest cross-correlation. The auto-correlation and
cross-correlation approaches are complementary because of the quite different
impact of redshift-space distortion on the two measurements. The combined
constraints from the two correlation functions imply values of and
that are, respectively, 7% low and 7% high compared to the
predictions of a flat CDM cosmological model with the best-fit Planck
parameters. With our estimated statistical errors, the significance of this
discrepancy is .Comment: Accepted for publication in A&A. 17 pages, 18 figure
The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : cosmological implications of the full shape of the clustering wedges in the data release 10 and 11 galaxy samples
We explore the cosmological implications of the angle-averaged correlation function, ξ(s), and the clustering wedges, ξ⊥(s) and ξ∥(s), of the LOWZ and CMASS galaxy samples from Data Releases 10 and 11 of the Sloan Digital Sky Survey III (SDSS-III) Baryon Oscillation Spectroscopic Survey. Our results show no significant evidence for a deviation from the standard Λ cold dark matter model. The combination of the information from our clustering measurements with recent data from the cosmic microwave background is sufficient to constrain the curvature of the Universe to Ωk = 0.0010 ± 0.0029, the total neutrino mass to ∑mν < 0.23 eV (95 per cent confidence level), the effective number of relativistic species to Neff = 3.31 ± 0.27 and the dark energy equation of state to wDE = −1.051 ± 0.076. These limits are further improved by adding information from Type Ia supernovae and baryon acoustic oscillations from other samples. In particular, this data set combination is completely consistent with a time-independent dark energy equation of state, in which case we find wDE = −1.024 ± 0.052. We explore the constraints on the growth rate of cosmic structures assuming f(z) = Ωm(z)γ and obtain γ = 0.69 ± 0.15, consistent with the predictions of general relativity of γ = 0.55.Publisher PDFPeer reviewe
Galactic Globular and Open Clusters in the Sloan Digital Sky Survey. I. Crowded Field Photometry and Cluster Fiducial Sequences in ugriz
We present photometry for globular and open cluster stars observed with the
Sloan Digital Sky Survey (SDSS). In order to exploit over 100 million stellar
objects with r < 22.5 mag observed by SDSS, we need to understand the
characteristics of stars in the SDSS ugriz filters. While star clusters provide
important calibration samples for stellar colors, the regions close to globular
clusters, where the fraction of field stars is smallest, are too crowded for
the standard SDSS photometric pipeline to process. To complement the SDSS
imaging survey, we reduce the SDSS imaging data for crowded cluster fields
using the DAOPHOT/ALLFRAME suite of programs and present photometry for 17
globular clusters and 3 open clusters in a SDSS value-added catalog. Our
photometry and cluster fiducial sequences are on the native SDSS 2.5-meter
ugriz photometric system, and the fiducial sequences can be directly applied to
the SDSS photometry without relying upon any transformations. Model photometry
for red giant branch and main-sequence stars obtained by Girardi et al. cannot
be matched simultaneously to fiducial sequences; their colors differ by
~0.02-0.05 mag. Good agreement (< ~0.02 mag in colors) is found with Clem et
al. empirical fiducial sequences in u'g'r'i'z' when using the transformation
equations in Tucker et al.Comment: 30 pages, 25 figures. Accepted for publication in ApJS. Version with
high resolution figures available at
http://www.astronomy.ohio-state.edu/~deokkeun/AnJohnson.pd
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