Construction of a "mutagenesis cartridge" for poliovirus genome-linked viral protein: Isolation and characterization of viable and nonviable mutants

By following a strategy of genetic analysis of poliovirus, we have constructed a synthetic "mutagenesis cartridge" spanning the genome-linked viral protein coding region and flanking cleavage sites in an infectious cDNA clone of the type 1 (Mahoney) genome. The insertion of new restriction sites within the infectious clone has allowed us to replace the wild-type sequences with short complementary pairs of synthetic oligonucleotides containing various mutations. A set of mutations have been made that create methionine codons within the genome-linked viral protein region. The resulting viruses have growth characteristics similar to wild type. Experiments that led to an alteration of the tyrosine residue responsible for the linkage to RNA have resulted in nonviable virus. In one mutant, proteolytic processing assayed in vitro appeared unimpaired by the mutation. We suggest that the position of the tyrosine residue is important for genome-linked viral protein function(s)

Possible in situ Tests of the Evolution of Elemental and Isotopic Abundances in the Solar Convection Zone

Helioseismology has shown that the chemical composition of the Sun has changed over its lifetime. The surface abundance of helium and heavy elements is believed to have decreased by up to 10% relative to their initial values. However, this reduction is too small to be tested by direct observations of the photospheric chemical composition. Here, we compare the predicted variations in the solar photospheric composition with precise measurements of abundances in meteorites and the solar wind composition. Although elemental composition ratios can vary by roughly a percent (e. g. for Ca/Mg and Ca/Fe) over the Sun's lifetime, their measurements are rife with uncertainties related to uncertainties in the interpretation of meteoritic measurements, photospheric determinations, and the complex fractionation processes occurring between the upper photosphere and lower chromosphere and the corona. On the other hand, isotopic ratios can be measured much more accurately and are not expected to be affected as much by extrasolar processes, although more work is required to quantify their effect. As the isotopic ratios evolve in the Sun proportionally to the mass ratios of the isotopes, light elements yield the highest variations in isotopic ratios. They are predicted to reach as high as 0.6% for $^{18}$O/$^{16}$O and are only slightly lower in the cases of $^{26}$Mg/$^{24}$Mg and $^{30}$Si/$^{28}$Si. Such a value should be well within the sensitivity of new missions such as Genesis.Comment: 10 pages, 6 figures, accepted for publication in Journal of geophysical Research-Space Physic

Reusable textual styles for domain-specific modeling languages

Domain-specific languages enable concise and precise formalization of domain concepts and promote direct employment by domain experts. Therefore, syntactic constructs are introduced to empower users to associate concepts and relationships with visual textual symbols. Model-based language engineering facilitates the description of concepts and relationships in an abstract manner. However, concrete representations are commonly attached to abstract domain representations, such as annotations in metamodels, or directly encoded into language grammar and thus introduce redundancy between metamodel elements and grammar elements. In this work we propose an approach that enables autonomous development and maintenance of domain concepts and textual language notations in a distinctive and metamodel-agnostic manner by employing style models containing grammar rule templates and injection-based property selection. We provide an implementation and showcase the proposed notationspecification language in a comparison with state of the art practices during the creation of notations for an executable domain-specific modeling language based on the Eclipse Modeling Framework and Xtext

Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps

<p>Abstract</p> <p>Background</p> <p>Given its sequenced genome and efficient systemic RNA interference response, the red flour beetle <it>Tribolium castaneum </it>is a model organism well suited for reverse genetics. Even so, there is a pressing need for forward genetic analysis to escape the bias inherent in candidate gene approaches.</p> <p>Results</p> <p>To produce easy-to-maintain insertional mutations and to obtain fluorescent marker lines to aid phenotypic analysis, we undertook a large-scale transposon mutagenesis screen. In this screen, we produced more than 6,500 new <it>piggyBac </it>insertions. Of these, 421 proved to be recessive lethal, 75 were semi-lethal, and eight indicated recessive sterility, while 505 showed new enhancer-trap patterns. Insertion junctions were determined for 403 lines and often appeared to be located within transcription units. Insertion sites appeared to be randomly distributed throughout the genome, with the exception of a preference for reinsertion near the donor site.</p> <p>Conclusion</p> <p>A large collection of enhancer-trap and embryonic lethal beetle lines has been made available to the research community and will foster investigations into diverse fields of insect biology, pest control, and evolution. Because the genetic elements used in this screen are species-nonspecific, and because the crossing scheme does not depend on balancer chromosomes, the methods presented herein should be broadly applicable for many insect species.</p

Does soundpeaking affect the behavior of chub (Squalius cephalus) and brown trout (Salmo trutta)? : an experimental approach

Increased turbulent flow and sediment transport during flood or hydropeaking events often induces rapid changes in underwater sound pressure levels, which is here referred to as soundpeaking. This study is the first to investigate such a change in the underwater soundscape in relation to fish behavior using an experimental approach. Trials were conducted in an experimental channel stocked with either adult chub (Squalius cephalus) or brown trout (Salmo trutta). To mimic soundpeaking, the underwater soundscape of a small alpine river was recorded during a flood event and later played back through an underwater speaker during treatment trials. Furthermore, trials were recorded with a video camera, and based on the fish position, movement variables (swimming distance, number of movement direction changes, variance of the acceleration), the aggregation of individuals, the longitudinal and the lateral position in the experimental area were compared between control (no sound played) and treatment trials. During treatment trials, brown trout changed their movement direction significantly more often, chub showed a significantly higher variation of the acceleration, and individuals from both species were significantly more aggregated. Furthermore, the soundpeaking treatment had a significant effect on the longitudinal position of brown trout in the experimental area. However, the overall results did not provide any indication for a stronger soundpeaking effect in chub despite being equipped with much more refined hearing abilities in comparison to brown trout. Based on these results and findings from other studies, soundpeaking is discussed as a behavioral trigger as well as a source of acoustic stress