146 research outputs found
p53 Activation by Knockdown Technologies
Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected through the transferase-mediated dUTP nick end labeling assay, acridine orange, and p21 transcriptional activation assays. Concurrent knockdown of p53 specifically ameliorates the cell death induced by MO off-targeting. Importantly, reversal of p53-dependent cell death by p53 knockdown does not affect specific loss of gene function, such as the cell death caused by loss of function of chordin. Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. We show here that MO off-targeting results in induction of a p53-dependent cell death pathway. p53 activation has also recently been shown to be an unspecified off-target effect of siRNAs. Both commonly used knockdown technologies can thus induce secondary but sequence-specific p53 activation. p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies
Abundances of Baade's Window Giants from Keck/HIRES Spectra: I. Stellar Parameters and [Fe/H] Values
We present the first results of a new abundance survey of the Milky Way bulge
based on Keck/HIRES spectra of 27 K-giants in the Baade's Window (, ) field. The spectral data used in this study are of much higher resolution
and signal-to-noise than previous optical studies of Galactic bulge stars. The
[Fe/H] values of our stars, which range between -1.29 and , were used to
recalibrate large low resolution surveys of bulge stars. Our best value for the
mean [Fe/H] of the bulge is . This mean value is similar to the
mean metallicity of the local disk and indicates that there cannot be a strong
metallicity gradient inside the solar circle. The metallicity distribution of
stars confirms that the bulge does not suffer from the so-called ``G-dwarf''
problem. This paper also details the new abundance techniques necessary to
analyze very metal-rich K-giants, including a new Fe line list and regions of
low blanketing for continuum identification.Comment: Accepted for publication in January 2006 Astrophysical Journal. Long
tables 3--6 withheld to save space (electronic tables in journal paper). 53
pages, 10 figures, 9 table
Reply to Ellis et al.: human niche construction and evolutionary theory
We are pleased Ellis et al. found value in our recent synthesis of the deep history of human impacts on
global ecosystems and agree that our paper should influence the current debate on if and how an Anthropocene epoch is defined. We also agree that the ecological consequences of human niche construction have profound and growing effects on the evolutionary trajectories of humans and other species living within human-altered ecosystems. Niche construction theory (NCT) provides an explicit framework for linking evolutionary and ecological processes into a coherent theory of biological evolution. Of special appeal to us as archaeologists is that NCT bridges biological and cultural evolution by including human culture and social learning within the mechanisms of evolutionary change, allowing scientists to address issues at the interface of human and natural systems. Some of us have contributed significantly to human NCT, addressing some of the very issues raised by Ellis et al. Finally, we agree that human transformations of ecosystems are inherently social processes—clearly humans are intensely social organisms—and that such processes result from long-term melding of biological and cultural evolution
p53 Activation by Knockdown Technologies
Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected through the transferase-mediated dUTP nick end labeling assay, acridine orange, and p21 transcriptional activation assays. Concurrent knockdown of p53 specifically ameliorates the cell death induced by MO off-targeting. Importantly, reversal of p53-dependent cell death by p53 knockdown does not affect specific loss of gene function, such as the cell death caused by loss of function of chordin. Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. We show here that MO off-targeting results in induction of a p53-dependent cell death pathway. p53 activation has also recently been shown to be an unspecified off-target effect of siRNAs. Both commonly used knockdown technologies can thus induce secondary but sequence-specific p53 activation. p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies
Reply to Westaway and Lyman: emus, dingoes, and archaeology’s role in conservation biology
In a curious comment on our PNAS Perspective, Westaway and Lyman offer two Australian zooarchaeological case studies—one involving eggshells and the other dingoes—that they argue undercut one of our main points: that archaeological data and deep time perspectives have much to offer conservation biology. Neither example provides a specific substantive critique of our perspective: there are no dingoes in our article, no eggshells, and we mention the long and rich record of human management and alteration of Australian environments only briefly. Nor do we suggest that all archaeological assemblages can effectively inform current conservation biology efforts. Such datasets obviously vary in their quality and potential applicability to modern situations. When considered more closely, both of Westaway and Lyman’s case studies underscore rather than undercut the importance of archaeological and paleoecological data in conservation biology initiatives
The Origin of the Mass--Metallicity Relation: Insights from 53,000 Star-Forming Galaxies in the SDSS
We utilize Sloan Digital Sky Survey imaging and spectroscopy of ~53,000
star-forming galaxies at z~0.1 to study the relation between stellar mass and
gas-phase metallicity. We derive gas-phase oxygen abundances and stellar masses
using new techniques which make use of the latest stellar evolutionary
synthesis and photoionization models. We find a tight (+/-0.1 dex) correlation
between stellar mass and metallicity spanning over 3 orders of magnitude in
stellar mass and a factor of 10 in metallicity. The relation is relatively
steep from 10^{8.5} - 10^{10.5} M_sun, in good accord with known trends between
luminosity and metallicity, but flattens above 10^{10.5} M_sun. We use indirect
estimates of the gas mass based on the H-alpha luminosity to compare our data
to predictions from simple closed box chemical evolution models. We show that
metal loss is strongly anti-correlated with baryonic mass, with low mass dwarf
galaxies being 5 times more metal-depleted than L* galaxies at z~0.1. Evidence
for metal depletion is not confined to dwarf galaxies, but is found in galaxies
with masses as high as 10^{10} M_sun. We interpret this as strong evidence both
of the ubiquity of galactic winds and of their effectiveness in removing metals
from galaxy potential wells.Comment: ApJ accepted, 15 pages, 9 figures, emulateapj.st
Planetary Candidates Observed by Kepler VI: Planet Sample from Q1-Q16 (47 Months)
\We present the sixth catalog of Kepler candidate planets based on nearly 4
years of high precision photometry. This catalog builds on the legacy of
previous catalogs released by the Kepler project and includes 1493 new Kepler
Objects of Interest (KOIs) of which 554 are planet candidates, and 131 of these
candidates have best fit radii <1.5 R_earth. This brings the total number of
KOIs and planet candidates to 7305 and 4173 respectively. We suspect that many
of these new candidates at the low signal-to-noise limit may be false alarms
created by instrumental noise, and discuss our efforts to identify such
objects. We re-evaluate all previously published KOIs with orbital periods of
>50 days to provide a consistently vetted sample that can be used to improve
planet occurrence rate calculations. We discuss the performance of our planet
detection algorithms, and the consistency of our vetting products. The full
catalog is publicly available at the NASA Exoplanet Archive.Comment: 18 pages, to be published in the Astrophysical Journal Supplement
Serie
The Atacama Cosmology Telescope: A Measurement of the Cosmic Microwave Background Power Spectrum at 148 and 218 GHz from the 2008 Southern Survey
We present measurements of the cosmic microwave background (CMB) power
spectrum made by the Atacama Cosmology Telescope at 148 GHz and 218 GHz, as
well as the cross-frequency spectrum between the two channels. Our results
clearly show the second through the seventh acoustic peaks in the CMB power
spectrum. The measurements of these higher-order peaks provide an additional
test of the {\Lambda}CDM cosmological model. At l > 3000, we detect power in
excess of the primary anisotropy spectrum of the CMB. At lower multipoles 500 <
l < 3000, we find evidence for gravitational lensing of the CMB in the power
spectrum at the 2.8{\sigma} level. We also detect a low level of Galactic dust
in our maps, which demonstrates that we can recover known faint, diffuse
signals.Comment: 19 pages, 13 figures. Submitted to ApJ. This paper is a companion to
Hajian et al. (2010) and Dunkley et al. (2010
The Atacama Cosmology Telescope: Data Characterization and Map Making
We present a description of the data reduction and mapmaking pipeline used
for the 2008 observing season of the Atacama Cosmology Telescope (ACT). The
data presented here at 148 GHz represent 12% of the 90 TB collected by ACT from
2007 to 2010. In 2008 we observed for 136 days, producing a total of 1423 hours
of data (11 TB for the 148 GHz band only), with a daily average of 10.5 hours
of observation. From these, 1085 hours were devoted to a 850 deg^2 stripe (11.2
hours by 9.1 deg) centered on a declination of -52.7 deg, while 175 hours were
devoted to a 280 deg^2 stripe (4.5 hours by 4.8 deg) centered at the celestial
equator. We discuss sources of statistical and systematic noise, calibration,
telescope pointing, and data selection. Out of 1260 survey hours and 1024
detectors per array, 816 hours and 593 effective detectors remain after data
selection for this frequency band, yielding a 38% survey efficiency. The total
sensitivity in 2008, determined from the noise level between 5 Hz and 20 Hz in
the time-ordered data stream (TOD), is 32 micro-Kelvin sqrt{s} in CMB units.
Atmospheric brightness fluctuations constitute the main contaminant in the data
and dominate the detector noise covariance at low frequencies in the TOD. The
maps were made by solving the least-squares problem using the Preconditioned
Conjugate Gradient method, incorporating the details of the detector and noise
correlations. Cross-correlation with WMAP sky maps, as well as analysis from
simulations, reveal that our maps are unbiased at multipoles ell > 300. This
paper accompanies the public release of the 148 GHz southern stripe maps from
2008. The techniques described here will be applied to future maps and data
releases.Comment: 20 pages, 18 figures, 6 tables, an ACT Collaboration pape
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