283 research outputs found
The proteasomal ATPase complex is required for stress-induced transcription in yeast
Sug1 and Sug2 are two of six ATPases in the 19S regulatory particle of the 26S proteasome. We have shown previously that these proteins play a non-proteolytic role in the transcription of the GAL genes in yeast. In this study, we probe the requirement for these factors in stress-induced transcription in yeast. It is known that proteasomal proteolysis is not required for these events. Indeed, proteasome inhibitors strongly stimulate expression of these stress response genes. However, shifting strains carrying temperature-sensitive alleles of SUG1 and SUG2 to the restrictive temperature strongly inhibited the expression of HSP26, HSP104 and GAD1 in response to heat shock or treatment with menadione bisulfate. Furthermore, chromatin immunoprecipitation analysis revealed the recruitment of Sug1, Sug2 and Cim5 (another of the ATPases), but not 20S proteasome core proteins, to the promoters of these genes. These data show that the non-proteolytic requirement for the proteasomal ATPases extends beyond the GAL genes in yeast and includes at least the heat and oxidative stress-responsive genes
Higher Order Moments of the Angular Distribution of Galaxies from Early SDSS Data
We present initial results for counts in cells statistics of the angular
distribution of galaxies in early data from the Sloan Digital Sky Survey
(SDSS). We analyze a rectangular stripe wide, covering
approximately 160 sq. degrees, containing over galaxies in the apparent
magnitude range , with areas of bad seeing, contamination
from bright stars, ghosts, and high galactic extinction masked out. This survey
region, which forms part of the SDSS Early Data Release, is the same as that
for which two-point angular clustering statistics have recently been computed.
The third and fourth moments of the cell counts, (skewness) and
(kurtosis), constitute the most accurate measurements to date of these
quantities (for ) over angular scales .
They display the approximate hierarchical scaling expected from non-linear
structure formation models and are in reasonable agreement with the predictions
of -dominated cold dark matter models with galaxy biasing that
suppresses higher order correlations at small scales. The results are in
general consistent with previous measurements in the APM, EDSGC, and Deeprange
surveys. These results suggest that the SDSS imaging data are free of
systematics to a high degree and will therefore enable determination of the
skewness and kurtosis to 1% and less then 10%, as predicted by Colombi,
Szapudi, & Szalay (1998).Comment: 24 pages, submitted to Ap
KL Estimation of the Power Spectrum Parameters from the Angular Distribution of Galaxies in Early SDSS Data
We present measurements of parameters of the 3-dimensional power spectrum of
galaxy clustering from 222 square degrees of early imaging data in the Sloan
Digital Sky Survey. The projected galaxy distribution on the sky is expanded
over a set of Karhunen-Loeve eigenfunctions, which optimize the signal-to-noise
ratio in our analysis. A maximum likelihood analysis is used to estimate
parameters that set the shape and amplitude of the 3-dimensional power
spectrum. Our best estimates are Gamma=0.188 +/- 0.04 and sigma_8L = 0.915 +/-
0.06 (statistical errors only), for a flat Universe with a cosmological
constant. We demonstrate that our measurements contain signal from scales at or
beyond the peak of the 3D power spectrum. We discuss how the results scale with
systematic uncertainties, like the radial selection function. We find that the
central values satisfy the analytically estimated scaling relation. We have
also explored the effects of evolutionary corrections, various truncations of
the KL basis, seeing, sample size and limiting magnitude. We find that the
impact of most of these uncertainties stay within the 2-sigma uncertainties of
our fiducial result.Comment: Fig 1 postscript problem correcte
The Angular Correlation Function of Galaxies from Early SDSS Data
The Sloan Digital Sky Survey is one of the first multicolor photometric and
spectroscopic surveys designed to measure the statistical properties of
galaxies within the local Universe. In this Letter we present some of the
initial results on the angular 2-point correlation function measured from the
early SDSS galaxy data. The form of the correlation function, over the
magnitude interval 18<r*<22, is shown to be consistent with results from
existing wide-field, photographic-based surveys and narrower CCD galaxy
surveys. On scales between 1 arcminute and 1 degree the correlation function is
well described by a power-law with an exponent of ~ -0.7. The amplitude of the
correlation function, within this angular interval, decreases with fainter
magnitudes in good agreement with analyses from existing galaxy surveys. There
is a characteristic break in the correlation function on scales of
approximately 1-2 degrees. On small scales, < 1', the SDSS correlation function
does not appear to be consistent with the power-law form fitted to the 1'<
theta <0.5 deg data. With a data set that is less than 2% of the full SDSS
survey area, we have obtained high precision measurements of the power-law
angular correlation function on angular scales 1' < theta < 1 deg, which are
robust to systematic uncertainties. Because of the limited area and the highly
correlated nature of the error covariance matrix, these initial results do not
yet provide a definitive characterization of departures from the power-law form
at smaller and larger angles. In the near future, however, the area of the SDSS
imaging survey will be sufficient to allow detailed analysis of the small and
large scale regimes, measurements of higher-order correlations, and studies of
angular clustering as a function of redshift and galaxy type
The Angular Power Spectrum of Galaxies from Early SDSS Data
We compute the angular power spectrum C_l from 1.5 million galaxies in early
SDSS data on large angular scales, l<600. The data set covers about 160 square
degrees, with a characteristic depth of order 1 Gpc/h in the faintest (21<r<22)
of our four magnitude bins. Cosmological interpretations of these results are
presented in a companion paper by Dodelson et al (2001). The data in all four
magnitude bins are consistent with a simple flat ``concordance'' model with
nonlinear evolution and linear bias factors of order unity. Nonlinear evolution
is particularly evident for the brightest galaxies. A series of tests suggest
that systematic errors related to seeing, reddening, etc., are negligible,
which bodes well for the sixtyfold larger sample that the SDSS is currently
collecting. Uncorrelated error bars and well-behaved window functions make our
measurements a convenient starting point for cosmological model fitting.Comment: Replaced to match accepted ApJ version (14 pages). Data, window
functions etc available at http://www.hep.upenn.edu/~max/sdss.html or from
[email protected]
Sloan Digital Sky Survey Imaging of Low Galactic Latitude Fields: Technical Summary and Data Release
The Sloan Digital Sky Survey (SDSS) mosaic camera and telescope have obtained
five-band optical-wavelength imaging near the Galactic plane outside of the
nominal survey boundaries. These additional data were obtained during
commissioning and subsequent testing of the SDSS observing system, and they
provide unique wide-area imaging data in regions of high obscuration and star
formation, including numerous young stellar objects, Herbig-Haro objects and
young star clusters. Because these data are outside the Survey regions in the
Galactic caps, they are not part of the standard SDSS data releases. This paper
presents imaging data for 832 square degrees of sky (including repeats), in the
star-forming regions of Orion, Taurus, and Cygnus. About 470 square degrees are
now released to the public, with the remainder to follow at the time of SDSS
Data Release 4. The public data in Orion include the star-forming region NGC
2068/NGC 2071/HH24 and a large part of Barnard's loop.Comment: 31 pages, 9 figures (3 missing to save space), accepted by AJ, in
press, see http://photo.astro.princeton.edu/oriondatarelease for data and
paper with all figure
Cosmological parameters from SDSS and WMAP
We measure cosmological parameters using the three-dimensional power spectrum
P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in
combination with WMAP and other data. Our results are consistent with a
``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt,
tensor modes or massive neutrinos. Adding SDSS information more than halves the
WMAP-only error bars on some parameters, tightening 1 sigma constraints on the
Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter
density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on
neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when
dropping prior assumptions about curvature, neutrinos, tensor modes and the
equation of state. Our results are in substantial agreement with the joint
analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive
consistency check with independent redshift survey data and analysis
techniques. In this paper, we place particular emphasis on clarifying the
physical origin of the constraints, i.e., what we do and do not know when using
different data sets and prior assumptions. For instance, dropping the
assumption that space is perfectly flat, the WMAP-only constraint on the
measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to
t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running
tilt, neutrino mass and equation of state in the list of free parameters, many
constraints are still quite weak, but future cosmological measurements from
SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt
figures available at http://www.hep.upenn.edu/~max/sdsspars.htm
The Fifth Data Release of the Sloan Digital Sky Survey
This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky
Survey (SDSS). DR5 includes all survey quality data taken through June 2005 and
represents the completion of the SDSS-I project (whose successor, SDSS-II will
continue through mid-2008). It includes five-band photometric data for 217
million objects selected over 8000 square degrees, and 1,048,960 spectra of
galaxies, quasars, and stars selected from 5713 square degrees of that imaging
data. These numbers represent a roughly 20% increment over those of the Fourth
Data Release; all the data from previous data releases are included in the
present release. In addition to "standard" SDSS observations, DR5 includes
repeat scans of the southern equatorial stripe, imaging scans across M31 and
the core of the Perseus cluster of galaxies, and the first spectroscopic data
from SEGUE, a survey to explore the kinematics and chemical evolution of the
Galaxy. The catalog database incorporates several new features, including
photometric redshifts of galaxies, tables of matched objects in overlap regions
of the imaging survey, and tools that allow precise computations of survey
geometry for statistical investigations.Comment: ApJ Supp, in press, October 2007. This paper describes DR5. The SDSS
Sixth Data Release (DR6) is now public, available from http://www.sdss.or
Discovery of High-Affinity Protein Binding Ligands – Backwards
BACKGROUND: There is a pressing need for high-affinity protein binding ligands for all proteins in the human and other proteomes. Numerous groups are working to develop protein binding ligands but most approaches develop ligands using the same strategy in which a large library of structured ligands is screened against a protein target to identify a high-affinity ligand for the target. While this methodology generates high-affinity ligands for the target, it is generally an iterative process that can be difficult to adapt for the generation of ligands for large numbers of proteins. METHODOLOGY/PRINCIPAL FINDINGS: We have developed a class of peptide-based protein ligands, called synbodies, which allow this process to be run backwards--i.e. make a synbody and then screen it against a library of proteins to discover the target. By screening a synbody against an array of 8,000 human proteins, we can identify which protein in the library binds the synbody with high affinity. We used this method to develop a high-affinity synbody that specifically binds AKT1 with a K(d)<5 nM. It was found that the peptides that compose the synbody bind AKT1 with low micromolar affinity, implying that the affinity and specificity is a product of the bivalent interaction of the synbody with AKT1. We developed a synbody for another protein, ABL1 using the same method. CONCLUSIONS/SIGNIFICANCE: This method delivered a high-affinity ligand for a target protein in a single discovery step. This is in contrast to other techniques that require subsequent rounds of mutational improvement to yield nanomolar ligands. As this technique is easily scalable, we believe that it could be possible to develop ligands to all the proteins in any proteome using this approach
Type I IFN controls chikungunya virus via its action on nonhematopoietic cells
Chikungunya virus (CHIKV) is the causative agent of an outbreak that began in La Réunion in 2005 and remains a major public health concern in India, Southeast Asia, and southern Europe. CHIKV is transmitted to humans by mosquitoes and the associated disease is characterized by fever, myalgia, arthralgia, and rash. As viral load in infected patients declines before the appearance of neutralizing antibodies, we studied the role of type I interferon (IFN) in CHIKV pathogenesis. Based on human studies and mouse experimentation, we show that CHIKV does not directly stimulate type I IFN production in immune cells. Instead, infected nonhematopoietic cells sense viral RNA in a Cardif-dependent manner and participate in the control of infection through their production of type I IFNs. Although the Cardif signaling pathway contributes to the immune response, we also find evidence for a MyD88-dependent sensor that is critical for preventing viral dissemination. Moreover, we demonstrate that IFN-α/β receptor (IFNAR) expression is required in the periphery but not on immune cells, as IFNAR−/−→WT bone marrow chimeras are capable of clearing the infection, whereas WT→IFNAR−/− chimeras succumb. This study defines an essential role for type I IFN, produced via cooperation between multiple host sensors and acting directly on nonhematopoietic cells, in the control of CHIKV
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