40 research outputs found
Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes.
INTRODUCTION: Genomic base composition ranges from less than 25% AT to more than 85% AT in prokaryotes. Since only a small fraction of prokaryotic genomes is not protein coding even a minor change in genomic base composition will induce profound protein changes. We examined how amino acid and codon frequencies were distributed in over 2000 microbial genomes and how these distributions were affected by base compositional changes. In addition, we wanted to know how genome-wide amino acid usage was biased in the different genomes and how changes to base composition and mutations affected this bias. To carry this out, we used a Generalized Additive Mixed-effects Model (GAMM) to explore non-linear associations and strong data dependences in closely related microbes; principal component analysis (PCA) was used to examine genomic amino acid- and codon frequencies, while the concept of relative entropy was used to analyze genomic mutation rates. RESULTS: We found that genomic amino acid frequencies carried a stronger phylogenetic signal than codon frequencies, but that this signal was weak compared to that of genomic %AT. Further, in contrast to codon usage bias (CUB), amino acid usage bias (AAUB) was differently distributed in AT- and GC-rich genomes in the sense that AT-rich genomes did not prefer specific amino acids over others to the same extent as GC-rich genomes. AAUB was also associated with relative entropy; genomes with low AAUB contained more random mutations as a consequence of relaxed purifying selection than genomes with higher AAUB. CONCLUSION: Genomic base composition has a substantial effect on both amino acid- and codon frequencies in bacterial genomes. While phylogeny influenced amino acid usage more in GC-rich genomes, AT-content was driving amino acid usage in AT-rich genomes. We found the GAMM model to be an excellent tool to analyze the genomic data used in this study
Photometric Response Functions of the SDSS Imager
The monochromatic illumination system is constructed to carry out in situ
measurements of the response function of the mosaicked CCD imager used in the
Sloan Digital Sky Survey (SDSS). The system is outlined and the results of the
measurements, mostly during the first 6 years of the SDSS, are described. We
present the reference response functions for the five colour passbands derived
from these measurements, and discuss column to column variations and variations
in time, and also their effects on photometry. We also discuss the effect
arising from various, slightly different response functions of the associated
detector systems that were used to give SDSS photometry. We show that the
calibration procedures of SDSS remove these variations reasonably well with the
resulting final errors from variant response functions being unlikely to be
larger than 0.01 mag for g, r, i, and z bands over the entire duration of the
survey. The considerable aging effect is uncovered in the u band, the response
function showing a 30% decrease in the throughput in the short wavelength side
during the survey years, which potentially causes a systematic error in
photometry. The aging effect is consistent with variation of the instrumental
sensitivity in u-band, which is calibrated out. The expected colour variation
is consistent with measured colour variation in the catalog of repeated
photometry. The colour variation is delta (u-g) ~ 0.01 for most stars, and at
most delta (u-g) ~ 0.02 mag for those with extreme colours. We verified in the
final catalogue that no systematic variations in excess of 0.01 mag are
detected in the photometry which can be ascribed to aging and/or seasonal
effects except for the secular u-g colour variation for stars with extreme
colours.Comment: 54 pages, 18 figures, 7 tables, accepted for publication in A
First-year Sloan Digital Sky Survey-II (SDSS-II) Supernova Results: Hubble Diagram and Cosmological Parameters
We present measurements of the Hubble diagram for 103 Type Ia supernovae
(SNe) with redshifts 0.04 < z < 0.42, discovered during the first season (Fall
2005) of the Sloan Digital Sky Survey-II (SDSS-II) Supernova Survey. These data
fill in the redshift "desert" between low- and high-redshift SN Ia surveys. We
combine the SDSS-II measurements with new distance estimates for published SN
data from the ESSENCE survey, the Supernova Legacy Survey, the Hubble Space
Telescope, and a compilation of nearby SN Ia measurements. Combining the SN
Hubble diagram with measurements of Baryon Acoustic Oscillations from the SDSS
Luminous Red Galaxy sample and with CMB temperature anisotropy measurements
from WMAP, we estimate the cosmological parameters w and Omega_M, assuming a
spatially flat cosmological model (FwCDM) with constant dark energy equation of
state parameter, w. For the FwCDM model and the combined sample of 288 SNe Ia,
we find w = -0.76 +- 0.07(stat) +- 0.11(syst), Omega_M = 0.306 +- 0.019(stat)
+- 0.023(syst) using MLCS2k2 and w = -0.96 +- 0.06(stat) +- 0.12(syst), Omega_M
= 0.265 +- 0.016(stat) +- 0.025(syst) using the SALT-II fitter. We trace the
discrepancy between these results to a difference in the rest-frame UV model
combined with a different luminosity correction from color variations; these
differences mostly affect the distance estimates for the SNLS and HST
supernovae. We present detailed discussions of systematic errors for both
light-curve methods and find that they both show data-model discrepancies in
rest-frame -band. For the SALT-II approach, we also see strong evidence for
redshift-dependence of the color-luminosity parameter (beta). Restricting the
analysis to the 136 SNe Ia in the Nearby+SDSS-II samples, we find much better
agreement between the two analysis methods but with larger uncertainties.Comment: Accepted for publication by ApJ
The Sloan Digital Sky Survey-II: Photometry and Supernova Ia Light Curves from the 2005 data
We present ugriz light curves for 146 spectroscopically confirmed or
spectroscopically probable Type Ia supernovae from the 2005 season of the
SDSS-II Supernova survey. The light curves have been constructed using a
photometric technique that we call scene modelling, which is described in
detail here; the major feature is that supernova brightnesses are extracted
from a stack of images without spatial resampling or convolution of the image
data. This procedure produces accurate photometry along with accurate estimates
of the statistical uncertainty, and can be used to derive photometry taken with
multiple telescopes. We discuss various tests of this technique that
demonstrate its capabilities. We also describe the methodology used for the
calibration of the photometry, and present calibrated magnitudes and fluxes for
all of the spectroscopic SNe Ia from the 2005 season
Maternal plasma folate impacts differential DNA methylation in an epigenome-wide meta-analysis of newborns
Folate is vital for fetal development. Periconceptional folic acid supplementation and food fortification are recommended to prevent neural tube defects. Mechanisms whereby periconceptional folate influences normal development and disease are poorly understood: epigenetics may be involved. We examine the association between maternal plasma folate during pregnancy and epigenome-wide DNA methylation using Illumina" s HumanMethyl450 Beadchip in 1,988 newborns from two European cohorts. Here we report the combined covariate-adjusted results using meta-analysis and employ pathway and gene expression analyses. Four-hundred forty-three CpGs (320 genes) are significantly associated with maternal plasma folate levels during pregnancy (false discovery rate 5%); 48 are significant after Bonferroni correction. Most genes are not known for folate biology, including APC2, GRM8, SLC16A12, OPCML, PRPH, LHX1, KLK4 and PRSS21. Some relate to birth defects other than neural tube defects, neurological functions or varied aspects of embryonic development. These findings may inform how maternal folate impacts the developing epigenome and health outcomes in offspring
The Highly Virulent 2006 Norwegian EHEC O103:H25 Outbreak Strain Is Related to the 2011 German O104:H4 Outbreak Strain
In 2006, a severe foodborne EHEC outbreak occured in Norway. Seventeen cases were recorded and the HUS frequency was 60%. The causative strain, Esherichia coli O103:H25, is considered to be particularly virulent. Sequencing of the outbreak strain revealed resemblance to the 2011 German outbreak strain E. coli O104:H4, both in genome and Shiga toxin 2-encoding (Stx2) phage sequence. The nucleotide identity between the Stx2 phages from the Norwegian and German outbreak strains was 90%. During the 2006 outbreak, stx2-positive O103:H25 E. coli was isolated from two patients. All the other outbreak associated isolates, including all food isolates, were stx-negative, and carried a different phage replacing the Stx2 phage. This phage was of similar size to the Stx2 phage, but had a distinctive early phage region and no stx gene. The sequence of the early region of this phage was not retrieved from the bacterial host genome, and the origin of the phage is unknown. The contaminated food most likely contained a mixture of E. coli O103:H25 cells with either one of the phages
The Fifteenth Data Release of the Sloan Digital Sky Surveys: First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 Julyâ2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGAâwe release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020â2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data
The James Webb Space Telescope Mission
Twenty-six years ago a small committee report, building on earlier studies,
expounded a compelling and poetic vision for the future of astronomy, calling
for an infrared-optimized space telescope with an aperture of at least .
With the support of their governments in the US, Europe, and Canada, 20,000
people realized that vision as the James Webb Space Telescope. A
generation of astronomers will celebrate their accomplishments for the life of
the mission, potentially as long as 20 years, and beyond. This report and the
scientific discoveries that follow are extended thank-you notes to the 20,000
team members. The telescope is working perfectly, with much better image
quality than expected. In this and accompanying papers, we give a brief
history, describe the observatory, outline its objectives and current observing
program, and discuss the inventions and people who made it possible. We cite
detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space
Telescope Overview, 29 pages, 4 figure