Atomic data from the IRON Project. I. Electron-impact scattering of Fe17+ using <I>R</I>-matrix theory with intermediate coupling

We present results for electron-impact excitation of F-like Fe calculated using R-matrix theory where an intermediate-coupling frame transformation (ICFT) is used to obtain level-resolved collision strengths. Two such calculations are performed, the first expands the target using 2s2 2p5, 2s 2p6, 2s2 2p4 3l, 2s 2p5 3l, and 2p6 3l configurations while the second calculation includes the 2s2 2p4 4l, 2s 2p5 4l, and 2p6 4l configurations as well. The effect of the additional structure in the latter calculation on the n=3 resonances is explored and compared with previous calculations. We find strong resonant enhancement of the effective collision strengths to the 2s2 2p4 3s levels. A comparison with a Chandra X-ray observation of Capella shows that the n=4 R-matrix calculation leads to good agreement with observation</p

Emission-Line Properties of the Optical Filaments of NGC 1275

Extended nebular filaments are seen at optical wavelengths in NGC 1275, the central galaxy in the Perseus cluster. The agents responsible for the excitation of these filaments remain poorly understood. In this paper we investigate possible mechanisms for powering the filaments, using measurements from an extensive spectroscopic data set acquired at the Lick Observatory 3-m Shane telescope. The results show that the filaments are in an extremely low ionization and excitation state. The high signal-to-noise ratio of the spectra allows us to measure or place sensitive upper limits on weak but important diagnostic lines. We compare the observed line intensity ratios to the predictions of various ionization models, including photoionization by an active galactic nucleus, shock heating, stellar photoionization, and photoionization by the intracluster medium. We also investigate possible roles for cluster extreme-ultraviolet emission, and filtering of cluster soft X-ray emission by an ionized screen, in the energetics of the filaments. None of these mechanisms provides an entirely satisfactory explanation for the physical state of the nebulae. Heating and ionization by reconnection of the intracluster magnetic field remains a potentially viable alternative, which merits further investigation through Faraday rotation studies.Comment: Accepted for publication in Ap

The coronal line regions of planetary nebulae NGC6302 and NGC6537: 3-13um grating and echelle spectroscopy

We report on advances in the study of the cores of NGC6302 and NGC6537 using infrared grating and echelle spectroscopy. In NGC6302, emission lines from species spanning a large range of ionization potential, and in particular [SiIX]3.934um, are interpreted using photoionization models (including CLOUDY), which allow us to reestimate the central star's temperature to be about 250000K. All of the detected lines are consistent with this value, except for [AlV] and [AlVI]. Aluminium is found to be depleted to one hundredth of the solar abundance, which provides further evidence for some dust being mixed with the highly ionized gas (with photons harder than 154eV). A similar depletion pattern is observed in NGC6537. Echelle spectroscopy of IR coronal ions in NGC6302 reveals a stratified structure in ionization potential, which confirms photoionization to be the dominant ionization mechanism. The lines are narrow (< 22km/s FWHM), with no evidence of the broad wings found in optical lines from species with similar ionization potentials, such as [NeV]3426A. We note the absence of a hot bubble, or a wind blown bipolar cavity filled with a hot plasma, at least on 1'' and 10km/s scales. We also provide accurate new wavelengths for several of the infrared coronal lines observed with the echelle.Comment: Accepted for publication in MNRA

The genome sequence of the European robin, Erithacus rubecula Linnaeus 1758

We present a genome assembly from an individual female Erithacus rubecula (the European robin; Chordata; Aves; Passeriformes; Turdidae). The genome sequence is 1.09 gigabases in span. The majority of the assembly is scaffolded into 36 chromosomal pseudomolecules, with both W and Z sex chromosomes assembled

The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758

We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled

Population genomics of the critically endangered kākāpō

Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead