Sequence-Based Mapping and Genome Editing Reveal Mutations in Stickleback Hps5 Cause Oculocutaneous Albinism and the casper Phenotype.

Here, we present and characterize the spontaneous X-linked recessive mutation casper, which causes oculocutaneous albinism in threespine sticklebacks (Gasterosteus aculeatus). In humans, Hermansky-Pudlak syndrome results in pigmentation defects due to disrupted formation of the melanin-containing lysosomal-related organelle (LRO), the melanosome. casper mutants display not only reduced pigmentation of melanosomes in melanophores, but also reductions in the iridescent silver color from iridophores, while the yellow pigmentation from xanthophores appears unaffected. We mapped casper using high-throughput sequencing of genomic DNA from bulked casper mutants to a region of the stickleback X chromosome (chromosome 19) near the stickleback ortholog of Hermansky-Pudlak syndrome 5 (Hps5). casper mutants have an insertion of a single nucleotide in the sixth exon of Hps5, predicted to generate an early frameshift. Genome editing using CRISPR/Cas9 induced lesions in Hps5 and phenocopied the casper mutation. Injecting single or paired Hps5 guide RNAs revealed higher incidences of genomic deletions from paired guide RNAs compared to single gRNAs. Stickleback Hps5 provides a genetic system where a hemizygous locus in XY males and a diploid locus in XX females can be used to generate an easily scored visible phenotype, facilitating quantitative studies of different genome editing approaches. Lastly, we show the ability to better visualize patterns of fluorescent transgenic reporters in Hps5 mutant fish. Thus, Hps5 mutations present an opportunity to study pigmented LROs in the emerging stickleback model system, as well as a tool to aid in assaying genome editing and visualizing enhancer activity in transgenic fish

Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.

Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis

Parallel developmental genetic features underlie stickleback gill raker evolution.

BackgroundConvergent evolution, the repeated evolution of similar phenotypes in independent lineages, provides natural replicates to study mechanisms of evolution. Cases of convergent evolution might have the same underlying developmental and genetic bases, implying that some evolutionary trajectories might be predictable. In a classic example of convergent evolution, most freshwater populations of threespine stickleback fish have independently evolved a reduction of gill raker number to adapt to novel diets. Gill rakers are a segmentally reiterated set of dermal bones important for fish feeding. A previous large quantitative trait locus (QTL) mapping study using a marine × freshwater F2 cross identified QTL on chromosomes 4 and 20 with large effects on evolved gill raker reduction.ResultsBy examining skeletal morphology in adult and developing sticklebacks, we find heritable marine/freshwater differences in gill raker number and spacing that are specified early in development. Using the expression of the Ectodysplasin receptor (Edar) gene as a marker of raker primordia, we find that the differences are present before the budding of gill rakers occurs, suggesting an early change to a lateral inhibition process controlling raker primordia spacing. Through linkage mapping in F2 fish from crosses with three independently derived freshwater populations, we find in all three crosses QTL overlapping both previously identified QTL on chromosomes 4 and 20 that control raker number. These two QTL affect the early spacing of gill raker buds.ConclusionsCollectively, these data demonstrate that parallel developmental genetic features underlie the convergent evolution of gill raker reduction in freshwater sticklebacks, suggesting that even highly polygenic adaptive traits can have a predictable developmental genetic basis

Attitudes of Students in a Wildlife Damage Management Class Towards Nuisance Wildlife Control

Students majoring in wildlife management at the University of Georgia have the option of enrolling in our Wildlife Damage Management course. Students participate in a variety of field activities associated with the laboratory portion of the class while also attending twice-weekly lectures on wildlife damage topics. Each spring at the beginning of the semester, students participate in a short survey to assess their opinions on various topics related to wildlife damage management. The same students participate in the same survey at the end of the semester. We have been collecting pre-and post-course data since 1994. Significantly more students agreed with a variety of coyote (Canis latrans) control activities in the post-class survey except when asked about paying farmers and ranchers for livestock losses. They disagreed with this practice and did not change their view. Students generally agreed with the practice of using poison to control selected species except eagles but there were fewer significant attitude shifts pre-and post-class. As expected, students scored high on knowledge questions related to coyotes. The statement that producers had the right to protect property saw a significant change in attitude (\u3e percentage agreed post-class)

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni

<p>Abstract</p> <p>Background</p> <p><it>Campylobacter jejuni </it>has been divided into two subspecies: <it>C. jejuni </it>subsp. <it>jejuni </it>(<it>Cjj</it>) and <it>C. jejuni </it>subsp. <it>doylei </it>(<it>Cjd</it>). Nearly all of the <it>C. jejuni </it>strains isolated are <it>Cjj</it>; nevertheless, although <it>Cjd </it>strains are isolated infrequently, they differ from <it>Cjj </it>in two key aspects: they are obtained primarily from human clinical samples and are associated often with bacteremia, in addition to gastroenteritis. In this study, we utilized multilocus sequence typing (MLST) and a DNA microarray-based comparative genomic indexing (CGI) approach to examine the genomic diversity and gene content of <it>Cjd </it>strains.</p> <p>Results</p> <p>A geographically diverse collection of eight <it>Cjd </it>strains was examined by MLST and determined to be phylogenetically distinct from <it>Cjj </it>strains. Microarray-based CGI approach also supported this. We were able to demonstrate that <it>Cjd </it>strains exhibited divergence from <it>Cjj </it>strains NCTC 11168 and RM1221 in many of the intraspecies hypervariable regions. Moreover, multiple metabolic, transport and virulence functions (e.g. cytolethal distending toxin) were shown to be absent in the <it>Cjd </it>strains examined.</p> <p>Conclusion</p> <p>Our data demonstrate that <it>Cjd </it>are phylogenetically distinct from <it>Cjj </it>strains. Using the CGI approach, we identified subsets of absent genes from amongst the <it>C. jejuni </it>genes that provide clues as to the potential evolutionary origin and unusual pathogenicity of <it>Cjd</it>.</p

The Exceptionally Luminous Type Ia Supernova 2007If

SN 2007if was the third over-luminous Type Ia supernova (SN Ia) detected after 2003fg and 2006gz. We present the photometric and spectroscopic observations of the SN and its host by ROTSE-III, HET, and Keck. From the H a line identified in the host spectra, we determine a redshift of 0.0736. At this distance, the SN reached an absolute magnitude of -20.4, brighter than any other SNe Ia ever observed. If the source of luminosity is radioactive decay, a large amount of radioactive nickel (similar to 1.5 M(circle dot)) is required to power the peak luminosity, more than can be produced realistically in a Chandrasekhar mass progenitor. Low expansion velocity, similar to that of 2003fg, is also measured around the maximum light. The observations may suggest that SN 2007if was from a massive white dwarf progenitor, plausibly exploding with mass well beyond 1.4 M(circle dot). Alternatively, we investigate circumstellar interaction that may contribute to the excess luminosity.NASA NNX-08AN25G, NNX-08AV63GNSF AST-0707769, PHY-0801007Australian Research CouncilUniversity of New South WalesUniversity of TexasUniversity of MichiganAstronom

X-ray variability during the quiescent state of the neutron-star X-ray transient in the globular cluster NGC 6440

The globular cluster NGC 6440 is known to harbor a bright neutron-star X-ray transient. We observed the globular cluster with Chandra on two occasions when the bright transient was in its quiescent state in July 2000 and June 2003 (both observations were made nearly 2 years after the end of their preceding outbursts). The quiescent spectrum during the first observation is well represented by a two component model (a neutron-star atmosphere model plus a power-law component which dominates at energies above 2 keV). During the second observation (which was roughly of equal duration to the first observation) we found that the power-law component could no longer be detected. Our spectral fits indicate that the effective temperature of the neutron-star surface was consistent between the two observations. We conclude that the effect of the change in power-law component caused the 0.5-10 keV flux to be a factor of ~2 lower during the second observation compared to the first observation. We discuss plausible explanations for the variations, including variable residual accretion onto the neutron star magnetosphere or some variation in the interaction of the pulsar wind with the matter still outflowing from the companion star.Comment: 18 pages, 3 color figs, 1 b&w figures, 3 tables; discussion expanded; accepted for publication in Ap

cis-Regulatory Changes in Kit Ligand Expression and Parallel Evolution of Pigmentation in Sticklebacks and Humans

SummaryDramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans

NuSTAR Observations of the Black Hole GS 1354-645: Evidence of Rapid Black Hole Spin

We present the results of a NuSTAR study of the dynamically confirmed stellar-mass black hole GS 1354-645. The source was observed during its 2015 "hard" state outburst; we concentrate on spectra from two relatively bright phases. In the higher-flux observation, the broadband NuSTAR spectra reveal a clear, strong disk reflection spectrum, blurred by a degree that requires a black hole spin of a = cJ/GM^2 > 0.98 (1 sigma statistical limits only). The fits also require a high inclination: theta = 75(2) degrees. Strong "dips" are sometimes observed in the X-ray light curves of sources viewed at such an angle; these are absent, perhaps indicating that dips correspond to flared disk structures that only manifest at higher accretion rates. In the lower-flux observation, there is evidence of radial truncation of the thin accretion disk. We discuss these results in the context of spin in stellar-mass black holes, and inner accretion flow geometries at moderate accretion rates.Comment: Accepted for publication in ApJ Letter

Amazonian Hydrothermal Alteration Comparing Nakhlite Secondary Mineralogy to Water Rock Reaction Experiments

We report on results from experiments with Mars analog materials under diagenetic conditions. The mineralogical results of our experiments suggest that an important type of fluid alteration in the Amazonian may be short duration (e.g. less than 1 year) events from near neutral, dilute brines, that were able to exchange CO2 either directly, or via ice reservoirs, with the atmosphere