Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.

The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite-free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high-quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species

Ultralong-Range Rydberg Molecules in a Divalent-Atomic System

We report the creation of ultralong-range Sr$_2$ molecules comprising one ground-state $5s^2$ $^1S_0$ atom and one atom in a $5sns$ $^3S_1$ Rydberg state for $n$ ranging from 29 to 36. Molecules are created in a trapped ultracold atomic gas using two-photon excitation near resonant with the $5s5p$ $^3P_1$ intermediate state, and their formation is detected through ground-state atom loss from the trap. The observed molecular binding energies are fit with the aid of first-order perturbation theory that utilizes a Fermi pseudopotential with effective $s$-wave and $p$-wave scattering lengths to describe the interaction between an excited Rydberg electron and a ground-state Sr atom.Comment: 5 pages, 2 figure

Previously Identified Genetic Variants in ADGRL3 Are not Associated with Risk for Equine Degenerative Myeloencephalopathy across Breeds.

Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (eNAD/EDM) is a neurologic disease that has been reported in young horses from a wide range of breeds. The disease is inherited and associated with vitamin E deficiency during the first two years of life, resulting in bilateral symmetric ataxia. A missense mutation (chr3:71,917,591 C > T) within adhesion G protein-coupled receptor L3 (ADGRL3) was recently associated with risk for EDM in the Caspian breed. In order to confirm these findings, genotyping of this missense mutation, along with the three other associated single nucleotide polymorphisms (SNPs) in the genomic region, was carried out on 31 postmortem-confirmed eNAD/EDM cases and 43 clinically phenotyped controls from various breeds. No significant association was found between eNAD/EDM confirmed cases and genotype at any of the four identified SNPs (P > 0.05), including the nonsynonymous variant (EquCab2.0 chr3:71,917,591; allelic P = 0.85). These findings suggest that the four SNPs, including the missense variant in the ADGRL3 region, are not associated with risk for eNAD/EDM across multiple breeds of horses

A high flux source of cold strontium atoms

We describe an experimental apparatus capable of achieving a high loading rate of strontium atoms in a magneto-optical trap operating in a high vacuum environment. A key innovation of this setup is a two dimensional magneto-optical trap deflector located after a Zeeman slower. We find a loading rate of 6x10^9/s whereas the lifetime of the magnetically trapped atoms in the 3P2 state is 54s.Comment: 12 pages, 16 figure

Injection locking of a low cost high power laser diode at 461 nm

Stable laser sources at 461 nm are important for optical cooling of strontium atoms. In most existing experiments this wavelength is obtained by frequency doubling infrared lasers, since blue laser diodes either have low power or large emission bandwidths. Here, we show that injecting less than 10 mW of monomode laser radiation into a blue multimode 500 mW high power laser diode is capable of slaving at least 50% of the power to the desired frequency. We verify the emission bandwidth reduction by saturation spectroscopy on a strontium gas cell and by direct beating of the slave with the master laser. We also demonstrate that the laser can efficiently be used within the Zeeman slower for optical cooling of a strontium atomic beam.Comment: 2nd corrected version (minor revisions); Manuscript accepted for publication in Review of Scientific Instruments; 5 pages, 6 figure

Horses as Sources of Proprietary Information: Commercialization, Conservation, and Compensation Pursuant to the Convention on Biological Diversity

Horses indigenous to East and Southeast (E/SE) Asia, including native, landrace, feral, and wild populations, embody valuable genetic diversity. Conservation efforts for animals have largely been driven by humane altruism, with little consideration for the information value of genomes. Yet, if horses are viewed as archives of information as well as objects of affection, their conservation shifts to a market-based paradigm. Horse genetic resources (GR) likely contain significant value to the lucrative global horse industry, including veterinary applications such as diagnostics, therapeutics, genetic markers, gene therapies, and cloning technologies. As biotechnology becomes increasingly sophisticated, mining of horse GR will accelerate, thus facilitating identification, inventorying, bioprospecting, and commercialization of genetic information. Yet, establishing a value chain that balances equitable compensation for commercial applications while promoting conservation of horse populations remains a challenge. Recommendations presented here include establishing regional and national human resource and institutional capacity (competent national authorities), that catalog eco-geographical inventories of horse GR; monitor, manage, market and direct equitable value chains from horse to genetic information to commercial products; and ensure revenue flow back to support conservation. This system will foster market incentives to build capacity for sustainable conservation of the diverse horse populations of E/SE Asia

Modification of Graphene Properties due to Electron-Beam Irradiation

The authors report micro-Raman investigation of changes in the single and bilayer graphene crystal lattice induced by the low and medium energy electron-beam irradiation (5 and 20 keV). It was found that the radiation exposures results in appearance of the strong disorder D band around 1345 1/cm indicating damage to the lattice. The D and G peak evolution with the increasing radiation dose follows the amorphization trajectory, which suggests graphene's transformation to the nanocrystalline, and then to amorphous form. The results have important implications for graphene characterization and device fabrication, which rely on the electron microscopy and focused ion beam processing.Comment: 13 pages and 4 figure

State-Dependent Optical Lattices for the Strontium Optical Qubit

We demonstrate state-dependent optical lattices for the Sr optical qubit at the tune-out wavelength for its ground state. We tightly trap excited state atoms while suppressing the effect of the lattice on ground state atoms by more than four orders of magnitude. This highly independent control over the qubit states removes inelastic excited state collisions as the main obstacle for quantum simulation and computation schemes based on the Sr optical qubit. Our results also reveal large discrepancies in the atomic data used to calibrate the largest systematic effect of Sr optical lattice clocks.Comment: 6 pages, 4 figures + 6 pages supplemental materia