Mutation Patterns in the Human Genome: More Variable Than Expected

Why are some genomic positions more mutable than others? The identification of cryptic mutation hotspots in the human genome indicates that the determinants of mutation rates are more complex than anticipated

The Pan-STARRS Moving Object Processing System

We describe the Pan-STARRS Moving Object Processing System (MOPS), a modern software package that produces automatic asteroid discoveries and identifications from catalogs of transient detections from next-generation astronomical survey telescopes. MOPS achieves > 99.5% efficiency in producing orbits from a synthetic but realistic population of asteroids whose measurements were simulated for a Pan-STARRS4-class telescope. Additionally, using a non-physical grid population, we demonstrate that MOPS can detect populations of currently unknown objects such as interstellar asteroids. MOPS has been adapted successfully to the prototype Pan-STARRS1 telescope despite differences in expected false detection rates, fill-factor loss and relatively sparse observing cadence compared to a hypothetical Pan-STARRS4 telescope and survey. MOPS remains >99.5% efficient at detecting objects on a single night but drops to 80% efficiency at producing orbits for objects detected on multiple nights. This loss is primarily due to configurable MOPS processing limits that are not yet tuned for the Pan-STARRS1 mission. The core MOPS software package is the product of more than 15 person-years of software development and incorporates countless additional years of effort in third-party software to perform lower-level functions such as spatial searching or orbit determination. We describe the high-level design of MOPS and essential subcomponents, the suitability of MOPS for other survey programs, and suggest a road map for future MOPS development.Comment: 57 Pages, 26 Figures, 13 Table

Intra-Campaign Changes in Voting Preferences: The Impact of Media and Party Communication

An increasing number of citizens change and adapt their party preferences during the electoral campaign. We analyze which short-term factors explain intra-campaign changes in voting preferences, focusing on the visibility and tone of news media reporting and party canvassing. Our analyses rely on an integrative data approach, linking data from media content analysis to public opinion data. This enables us to investigate the relative impact of news media reporting as well as party communication. Inherently, we overcome previously identified methodological problems in the study of communication effects on voting behavior. Our findings reveal that campaigns matter: Especially interpersonal party canvassing increases voters’ likelihood to change their voting preferences in favor of the respective party, whereas media effects are limited to quality news outlets and depend on individual voters’ party ambivalence

Analysis of genetic systems using experimental evolution and whole-genome sequencing

The application of whole-genome sequencing to the study of microbial evolution promises to reveal the complex functional networks of mutations that underlie adaptation. A recent study of parallel evolution in populations of Escherichia coli shows how adaptation involves both functional changes to specific proteins as well as global changes in regulation

Limited Occurrence of Denitrification in Four Shallow Aquifers in Agricultural Areas of the United States

The ability of natural attenuation to mitigate agricultural nitrate contamination in recharging aquifers was investigated in four important agricultural settings in the United States. The study used laboratory analyses, field measurements, and flow and transport modeling for monitoring well transects (0.5 to 2.5 km in length) in the San Joaquin watershed, California, the Elkhorn watershed, Nebraska, the Yakima watershed, Washington, and the Chester watershed, Maryland. Ground water analyses included major ion chemistry, dissolved gases, nitrogen and oxygen stable isotopes, and estimates of recharge date. Sediment analyses included potential electron donors and stable nitrogen and carbon isotopes. Within each site and among aquifer-based medians, dissolved oxygen decreases with ground water age, and excess N2 from denitrification increases with age. Stable isotopes and excess N2 imply minimal denitrifying activity at the Maryland and Washington sites, partial denitrification at the California site, and total denitrification across portions of the Nebraska site. At all sites, recharging electron donor concentrations are not sufficient to account for the losses of dissolved oxygen and nitrate, implying that relict, solid phase electron donors drive redox reactions. Zero-order rates of denitrification range from 0 to 0.14 μmol N L−1d−1, comparable to observations of other studies using the same methods. Many values reported in the literature are, however, orders of magnitude higher, which is attributed to a combination of method limitations and bias for selection of sites with rapid denitrification. In the shallow aquifers below these agricultural fields, denitrification is limited in extent and will require residence times of decades or longer to mitigate modern nitrate contamination

Information effect on voter turnout: How campaign spending mobilises voters

We explore the impact of campaign effort on constituency-level turnout variation in Britain, under the premise that higher levels of campaign visibility stimulate electoral participation. We focus on the relationship between the competitiveness of the race and campaign effort as a provider of electoral information on the one hand, and voter turnout on the other hand. In doing so, we address the role of campaign effort and competitiveness in shaping turnout both independently as well as jointly. Further to this, we seek to add nuance to our understanding of how electoral campaigns mobilise voters by evaluating the comparative ability of different parties – based on whether or not they are ‘viable’ contenders in a particular constituency – to stimulate turnout. We find evidence that campaign effort mobilises voters and has a significant positive effect on voter turnout; this effect is independent from, and unconditioned by, the competitiveness of the race. However, we do find that this effect is mostly driven by the campaign effort of the ‘viable’ contenders in the constituency

Information effect on voter turnout: How campaign spending mobilises voters

We explore the impact of campaign effort on constituency-level turnout variation in Britain, under the premise that higher levels of campaign visibility stimulate electoral participation. We focus on the relationship between the competitiveness of the race and campaign effort as a provider of electoral information on the one hand, and voter turnout on the other hand. In doing so, we address the role of campaign effort and competitiveness in shaping turnout both independently as well as jointly. Further to this, we seek to add nuance to our understanding of how electoral campaigns mobilise voters by evaluating the comparative ability of different parties – based on whether or not they are ‘viable’ contenders in a particular constituency – to stimulate turnout. We find evidence that campaign effort mobilises voters and has a significant positive effect on voter turnout; this effect is independent from, and unconditioned by, the competitiveness of the race. However, we do find that this effect is mostly driven by the campaign effort of the ‘viable’ contenders in the constituency

Development and Disease: How Susceptibility to an Emerging Pathogen Changes through Anuran Development

Ranaviruses have caused die-offs of amphibians across the globe. In North America, these pathogens cause more amphibian mortality events than any other pathogen. Field observations suggest that ranavirus epizootics in amphibian communities are common during metamorphosis, presumably due to changes in immune function. However, few controlled studies have compared the relative susceptibility of amphibians to ranaviruses across life stages. Our objectives were to measure differences in mortality and infection prevalence following exposure to ranavirus at four developmental stages and determine whether the differences were consistent among seven anuran species. Based on previous studies, we hypothesized that susceptibility to ranavirus would be greatest at metamorphosis. Our results did not support this hypothesis, as four of the species were most susceptible to ranavirus during the larval or hatchling stages. The embryo stage had the lowest susceptibility among species probably due to the protective membranous layers of the egg. Our results indicate that generalizations should be made cautiously about patterns of susceptibility to ranaviruses among amphibian developmental stages and species. Further, if early developmental stages of amphibians are susceptible to ranaviruses, the impact of ranavirus epizootic events may be greater than realized due to the greater difficulty of detecting morbid hatchlings and larvae compared to metamorphs

Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity