Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes.

A number of recent papers report that standing genetic variation in natural populations includes ubiquitous polymorphisms within target sites for Cas9-based gene drive (CGD) and that these "drive resistant alleles" (DRA) preclude the successful application of CGD for managing these populations. Here we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that ~90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of ≥1.0%. We conclude that the abundance of conserved target sites in mosquito genomes and the inherent flexibility in CGD design obviates the concern that DRAs present in the standing genetic variation of mosquito populations will be detrimental to the deployment of this technology for population modification strategies

Gaussian processes for choosing laser parameters for driven, dissipative Rydberg aggregates

To facilitate quantum simulation of open quantum systems at finite temperatures, an important ingredient is to achieve thermalization on a given time-scale. We consider a Rydberg aggregate (an arrangement of Rydberg atoms that interact via long-range interactions) embedded in a laser-driven atomic environment. For the smallest aggregate (two atoms), suitable laser parameters can be found by brute force scanning of the four tunable laser parameters. For more atoms, however, such parameter scans are too computationally costly. Here we apply Gaussian processes to predict the thermalization performance as a function of the laser parameters for two-atom and four-atom aggregates. These predictions perform remarkably well using just 1000 simulations, demonstrating the utility of Gaussian processes in an atomic physics setting. Using this approach, we find and present effective laser parameters for generating thermalization, the robustness of these parameters to variation, as well as different thermalization dynamics

Cosmic homogeneity demonstrated with luminous red galaxies

We test the homogeneity of the Universe at $z\sim 0.3$ with the Luminous Red Galaxy (LRG) spectroscopic sample of the Sloan Digital Sky Survey. First, the mean number $N(R)$ of LRGs within completely surveyed LRG-centered spheres of comoving radius $R$ is shown to be proportional to $R^3$ at radii greater than $R\sim 70 h^{-1} \mathrm{Mpc}$. The test has the virtue that it does not rely on the assumption that the LRG sample has a finite mean density; its results show, however, that there \emph{is} such a mean density. Secondly, the survey sky area is divided into 10 disjoint solid angular regions and the fractional rms density variations of the LRG sample in the redshift range $0.2<z<0.35$ among these ($\sim 2\times10^7 h^{-3} \mathrm{Mpc^3}$) regions is found to be 7 percent of the mean density. This variance is consistent with typical biased \lcdm models and puts very strong constraints on the quality of SDSS photometric calibration.Comment: submitted to Ap

First results from the CRESST-III low-mass dark matter program

The CRESST experiment is a direct dark matter search which aims to measure interactions of potential dark matter particles in an earth-bound detector. With the current stage, CRESST-III, we focus on a low energy threshold for increased sensitivity towards light dark matter particles. In this manuscript we describe the analysis of one detector operated in the first run of CRESST-III (05/2016-02/2018) achieving a nuclear recoil threshold of 30.1eV. This result was obtained with a 23.6g CaWO$_4$ crystal operated as a cryogenic scintillating calorimeter in the CRESST setup at the Laboratori Nazionali del Gran Sasso (LNGS). Both the primary phonon/heat signal and the simultaneously emitted scintillation light, which is absorbed in a separate silicon-on-sapphire light absorber, are measured with highly sensitive transition edge sensors operated at ~15mK. The unique combination of these sensors with the light element oxygen present in our target yields sensitivity to dark matter particle masses as low as 160MeV/c$^2$.Comment: 9 pages, 9 figure

An age-of-allele test of neutrality for transposable element insertions

How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, many previous studies have used models of transposition-selection equilibrium that rely on the assumption of a constant rate of transposition. However, since TE invasions are known to happen in bursts through time, this assumption may not be reasonable in natural populations. Here we propose a test of neutrality for TE insertions that does not rely on the assumption of a constant transposition rate. We consider the case of TE insertions that have been ascertained from a single haploid reference genome sequence and have subsequently had their allele frequency estimated in a population sample. By conditioning on the age of an individual TE insertion (using information contained in the number of substitutions that have occurred within the TE sequence since insertion), we determine the probability distribution for the insertion allele frequency in a population sample under neutrality. Taking models of varying population size into account, we then evaluate predictions of our model against allele frequency data from 190 retrotransposon insertions sampled from North American and African populations of Drosophila melanogaster. Using this non-equilibrium model, we are able to explain about 80% of the variance in TE insertion allele frequencies based on age alone. Controlling both for nonequilibrium dynamics of transposition and host demography, we provide evidence for negative selection acting against most TEs as well as for positive selection acting on a small subset of TEs. Our work establishes a new framework for the analysis of the evolutionary forces governing large insertion mutations like TEs, gene duplications or other copy number variants.Comment: 40 pages, 6 figures, Supplemental Data available: [email protected]

Bulk NaI(Tl) scintillation low energy events selection with the ANAIS-0 module

Dark matter particles scattering off some target nuclei are expected to deposit very small energies in form of nuclear recoils (below 100 keV). Because of the low scintillation efficiency for nuclear recoils vs. electron recoils, in most of the scintillating targets considered in the search for dark matter, the region below 10 keVee concentrates most of the expected dark matter signal. For this reason, very low energy threshold (at or below 2 keVee) and very low background are required. This is the case of the ANAIS (Annual modulation with NaI Scintillators) experiment. A good knowledge of the detector response function for real scintillation events, a good characterization of other anomalous or noise event populations contributing in that energy range, and the development of convenient filtering procedures for the latter are mandatory to achieve the required low background at such a low energy. In this work we will present the specific protocols developed to select bulk scintillation events in NaI(Tl), and its application to data obtained with the ANAIS-0 prototype. Slight differences in time constants are expected in scintillation pulses produced by nuclear or electron recoils in NaI(Tl), so in order to analyze the effect of these filtering procedures in the case of a recoil population attributable to dark matter, data from a neutron calibration have been used.Comment: 13 pages, 22 figure

The Chandra Galactic Bulge Survey: optical catalogue and point-source counterparts to X-ray sources

As part of the Chandra Galactic Bulge Survey (GBS), we present a catalogue of optical sources in the GBS footprint. This consists of two regions centered at Galactic latitude b = 1.5 degrees above and below the Galactic Centre, spanning (l x b) = (6x1) degrees. The catalogue consists of 2 or more epochs of observations for each line of sight in r', i' and H{\alpha} filters. It is complete down to r' = 20.2 and i' = 19.2 mag; the mean 5{\sigma} depth is r' = 22.5 and i' = 21.1 mag. The mean root-mean-square residuals of the astrometric solutions is 0.04 arcsec. We cross-correlate this optical catalogue with the 1640 unique X-ray sources detected in Chandra observations of the GBS area, and find candidate optical counterparts to 1480 X-ray sources. We use a false alarm probability analysis to estimate the contamination by interlopers, and expect ~ 10 per cent of optical counterparts to be chance alignments. To determine the most likely counterpart for each X-ray source, we compute the likelihood ratio for all optical sources within the 4{\sigma} X-ray error circle. This analysis yields 1480 potential counterparts (~ 90 per cent of the sample). 584 counterparts have saturated photometry (r'<17, i'<16), indicating these objects are likely foreground sources and the real counterparts. 171 candidate counterparts are detected only in the i'-band. These sources are good qLMXB and CV candidates as they are X-ray bright and likely located in the Bulge.Comment: 18 pages, 18 figures. Published in MNRAS. 2016MNRAS.458.4530