254 research outputs found
The ASCC2 CUE domain in the ALKBH3-ASCC DNA repair complex recognizes adjacent ubiquitins in K63-linked polyubiquitin
Alkylation of DNA and RNA is a potentially toxic lesion that can result in mutations and even cell death. In response to alkylation damage, K63-linked polyubiquitin chains are assembled that localize the Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3-Activating Signal Cointegrator 1 Complex Subunit (ASCC) repair complex to damage sites in the nucleus. The protein ASCC2, a subunit of the ASCC complex, selectively binds K63-linked polyubiquitin chains via its coupling of ubiquitin conjugation to ER degradation (CUE) domain. The basis for polyubiquitin-binding specificity was unclear, because CUE domains in other proteins typically bind a single ubiquitin and do not discriminate among different polyubiquitin linkage types. We report here that the ASCC2 CUE domain selectively binds K63-linked diubiquitin by contacting both the distal and proximal ubiquitin. The ASCC2 CUE domain binds the distal ubiquitin in a manner similar to that reported for other CUE domains bound to a single ubiquitin, whereas the contacts with the proximal ubiquitin are unique to ASCC2. Residues in the N-terminal portion of the ASCC2 α1 helix contribute to the binding interaction with the proximal ubiquitin of K63-linked diubiquitin. Mutation of residues within the N-terminal portion of the ASCC2 α1 helix decreases ASCC2 recruitment in response to DNA alkylation, supporting the functional significance of these interactions during the alkylation damage response. Our study reveals the versatility of CUE domains in ubiquitin recognition
Galaxy Formation and the Kinematics of Damped Lyman Alpha Systems
A model of damped lyman alpha systems is presented based on randomly moving
clouds in spherical halos. We use the Press-Schechter model for the abundance
of halos, and assume that each halo has a similar population of clouds, with
total mass and spatial distribution constrained to fit observations of the
column density distribution. We show that the kinematics of the multiple
absorbing components revealed in absorption profiles of the low-ionization
lines, presented by Prochaska & Wolfe, are consistent with our spherical halo
model.
The presence of multiple absorbing components with a large covering factor,
combined with the small impact parameters of the systems predicted in our
analytical model and in numerical simulations, implies a high rate of energy
dissipation in cloud collisions. We calculate the rate of energy dissipation in
our model, and show that it is far greater than the rate at which energy can be
supplied by gravitational mergers of halos. This poses a problem for the model
of merging protogalactic clumps of Haehnelt et al., based on numerical
simulations. We also present new constraints on the amplitude of the power
spectrum in hierarchical theories required to account for the observed velocity
dispersion in the absorbers. We find that the linearly extrapolated rms
fluctuation on spheres of radius HR = 100 km/s at z=4 must be greater than
0.75. Although this limit is obtained only for our specific model of the
absorbing components, it should not be highly model-dependent because the
velocity dispersion of the absorbers is essentially determined by the velocity
dispersion of the halos where the gas is moving.Comment: submitted to ApJ, 25 pages, 14 figure
A critical comparison of integral projection and matrix projection models for demographic analysis
Structured demographic models are among the most common and useful tools in population biology. However, the introduction of integral projection models (IPMs) has caused a profound shift in the way many demographic models are conceptualized. Some researchers have argued that IPMs, by explicitly representing demographic processes as continuous functions of state variables such as size, are more statistically efficient, biologically realistic, and accurate than classic matrix projection models, calling into question the usefulness of the many studies based on matrix models. Here, we evaluate how IPMs and matrix models differ, as well as the extent to which these differences matter for estimation of key model outputs, including population growth rates, sensitivity patterns, and life spans. First, we detail the steps in constructing and using each type of model. Second, we present a review of published demographic models, concentrating on size-based studies, which shows significant overlap in the way IPMs and matrix models are constructed and analyzed. Third, to assess the impact of various modeling decisions on demographic predictions, we ran a series of simulations based on size-based demographic data sets for five biologically diverse species. We found little evidence that discrete vital rate estimation is less accurate than continuous functions across a wide range of sample sizes or size classes (equivalently bin numbers or mesh points). Most model outputs quickly converged with modest class numbers (≥10), regardless of most other modeling decisions. Another surprising result was that the most commonly used method to discretize growth rates for IPM analyses can introduce substantial error into model outputs. Finally, we show that empirical sample sizes generally matter more than modeling approach for the accuracy of demographic outputs. Based on these results, we provide specific recommendations to those constructing and evaluating structured population models. Both our literature review and simulations question the treatment of IPMs as a clearly distinct modeling approach or one that is inherently more accurate than classic matrix models. Importantly, this suggests that matrix models, representing the vast majority of past demographic analyses available for comparative and conservation work, continue to be useful and important sources of demographic information.Support for this work was provided by NSF awards 1146489, 1242558, 1242355, 1353781, 1340024, 1753980, and 1753954, 1144807, 0841423, and 1144083. Support also came from USDA NIFA Postdoctoral Fellowship (award no. 2019-67012-29726/project accession no. 1019364) for R. K. Shriver; the Swiss Polar Institute of Food and Agriculture for N. I. Chardon; the ICREA under the ICREA Academia Programme for C. Linares; and SERDP contract RC-2512 and USDA National Institute of Food and Agriculture, Hatch project 1016746 for A .M. Louthan. This is Contribution no. 21-177-J from the Kansas Agricultural Experiment Station
Resonant nonlinear magneto-optical effects in atoms
In this article, we review the history, current status, physical mechanisms,
experimental methods, and applications of nonlinear magneto-optical effects in
atomic vapors. We begin by describing the pioneering work of Macaluso and
Corbino over a century ago on linear magneto-optical effects (in which the
properties of the medium do not depend on the light power) in the vicinity of
atomic resonances, and contrast these effects with various nonlinear
magneto-optical phenomena that have been studied both theoretically and
experimentally since the late 1960s. In recent years, the field of nonlinear
magneto-optics has experienced a revival of interest that has led to a number
of developments, including the observation of ultra-narrow (1-Hz)
magneto-optical resonances, applications in sensitive magnetometry, nonlinear
magneto-optical tomography, and the possibility of a search for parity- and
time-reversal-invariance violation in atoms.Comment: 51 pages, 23 figures, to appear in Rev. Mod. Phys. in Oct. 2002,
Figure added, typos corrected, text edited for clarit
LSST: from Science Drivers to Reference Design and Anticipated Data Products
(Abridged) We describe here the most ambitious survey currently planned in
the optical, the Large Synoptic Survey Telescope (LSST). A vast array of
science will be enabled by a single wide-deep-fast sky survey, and LSST will
have unique survey capability in the faint time domain. The LSST design is
driven by four main science themes: probing dark energy and dark matter, taking
an inventory of the Solar System, exploring the transient optical sky, and
mapping the Milky Way. LSST will be a wide-field ground-based system sited at
Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m
effective) primary mirror, a 9.6 deg field of view, and a 3.2 Gigapixel
camera. The standard observing sequence will consist of pairs of 15-second
exposures in a given field, with two such visits in each pointing in a given
night. With these repeats, the LSST system is capable of imaging about 10,000
square degrees of sky in a single filter in three nights. The typical 5
point-source depth in a single visit in will be (AB). The
project is in the construction phase and will begin regular survey operations
by 2022. The survey area will be contained within 30,000 deg with
, and will be imaged multiple times in six bands, ,
covering the wavelength range 320--1050 nm. About 90\% of the observing time
will be devoted to a deep-wide-fast survey mode which will uniformly observe a
18,000 deg region about 800 times (summed over all six bands) during the
anticipated 10 years of operations, and yield a coadded map to . The
remaining 10\% of the observing time will be allocated to projects such as a
Very Deep and Fast time domain survey. The goal is to make LSST data products,
including a relational database of about 32 trillion observations of 40 billion
objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures
available from https://www.lsst.org/overvie
Sensitivity of the Advanced LIGO detectors at the beginning of gravitational wave astronomy
The Laser Interferometer Gravitational Wave Observatory (LIGO) consists of two widely separated 4 km laser interferometers designed to detect gravitational waves from distant astrophysical sources in the frequency range from 10 Hz to 10 kHz. The first observation run of the Advanced LIGO detectors started in September 2015 and ended in January 2016. A strain sensitivity of better than 10−23/Hz−−−√ was achieved around 100 Hz. Understanding both the fundamental and the technical noise sources was critical for increasing the astrophysical strain sensitivity. The average distance at which coalescing binary black hole systems with individual masses of 30 M⊙ could be detected above a signal-to-noise ratio (SNR) of 8 was 1.3 Gpc, and the range for binary neutron star inspirals was about 75 Mpc. With respect to the initial detectors, the observable volume of the Universe increased by a factor 69 and 43, respectively. These improvements helped Advanced LIGO to detect the gravitational wave signal from the binary black hole coalescence, known as GW150914
Supplement: "Localization and broadband follow-up of the gravitational-wave transient GW150914" (2016, ApJL, 826, L13)
This Supplement provides supporting material for Abbott et al. (2016a). We briefly summarize past electromagnetic (EM) follow-up efforts as well as the organization and policy of the current EM follow-up program. We compare the four probability sky maps produced for the gravitational-wave transient GW150914, and provide additional details of the EM follow-up observations that were performed in the different bands
Effects of Data Quality Vetoes on a Search for Compact Binary Coalescences in Advanced LIGO's First Observing Run
The first observing run of Advanced LIGO spanned 4 months, from September 12,
2015 to January 19, 2016, during which gravitational waves were directly
detected from two binary black hole systems, namely GW150914 and GW151226.
Confident detection of gravitational waves requires an understanding of
instrumental transients and artifacts that can reduce the sensitivity of a
search. Studies of the quality of the detector data yield insights into the
cause of instrumental artifacts and data quality vetoes specific to a search
are produced to mitigate the effects of problematic data. In this paper, the
systematic removal of noisy data from analysis time is shown to improve the
sensitivity of searches for compact binary coalescences. The output of the
PyCBC pipeline, which is a python-based code package used to search for
gravitational wave signals from compact binary coalescences, is used as a
metric for improvement. GW150914 was a loud enough signal that removing noisy
data did not improve its significance. However, the removal of data with excess
noise decreased the false alarm rate of GW151226 by more than two orders of
magnitude, from 1 in 770 years to less than 1 in 186000 years.Comment: 27 pages, 13 figures, published versio
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