Pathogens in Crassostrea ariakensis and other Asian oyster species: implications for non-native oyster introduction to Chesapeake Bay

With the drastic decline of eastern oyster Crassostrea virginica populations in the Chesapeake Bay due to over-fishing, diseases and habitat destruction, there is interest in Maryland and Virginia in utilizing the non-native oyster species Crassostrea ariakensis for aquaculture, fishery resource enhancement, and ecological restoration. The International Council for the Exploration of the Sea (ICES) recommends that non-native species be examined for ecological, genetic and disease relationships in the native range prior to a deliberate introduction to a new region. Therefore, a pathogen survey of C. ariakensis and other sympatric oyster species was conducted on samples collected in the PR China, Japan and Korea using molecular diagnostics and histopathology. Molecular assays focused on 2 types of pathogens: protistan parasites in the genus Perkinsus and herpesviruses, both with known impacts on commercially important molluscan species around the world, including Asia. PCR amplification and DNA sequence data from the internal transcribed spacer region of the rRNA gene complex revealed the presence of 2 Perkinsus species not currently found in USA waters: P. olseni and an undescribed species. In addition, 3 genetic strains of molluscan herpesviruses were detected in oysters from several potential C. ariakensis broodstock acquisition sites in Asia. Viral gametocytic hypertrophy, Chlamydia-like organisms, a Steinhausia-like microsporidian, Perkinsus sp., Nematopsis sp., ciliates, and cestodes were also detected by histopathology.     

Acetylene functionalized BODIPY dyes and their application in the synthesis of activity based proteasome probes

The synthesis of three acetylene functionalized BODIPY dyes is described. These dyes are used to fluorescently modify an azido functionalized epoxomicin analogue employing the Huisgen 1,3-dipolar cycloaddition, resulting in a panel of fluorescent epoxomicin derived proteasome probes.     

Knockout of cGAS and STING Rescues Virus Infection of Plasmid DNA-Transfected Cells

It is well known that plasmid DNA transfection, prior to virus infection, negatively affects infection efficiency. Here, we show that cytosolic plasmid DNA activates the cGAS/STING signaling pathway, which ultimately leads to the induction of an antiviral state of the cells. Using a transient one-plasmid clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, we generated cGAS/STING-knockout cells and show that these cells can be infected after plasmid DNA transfection as efficiently as nontransfected cells.     

Ecological contrasts drive responses of wintering farmland birds to conservation management

In the past decades, large‐scale conservation programs have been implemented to halt the decline of farmland species. The mechanisms explaining the effectiveness of these programs remain poorly understood. Here we test the recent hypothesis that the effects of conservation management are determined by the ecological contrasts in limiting resources they create relative to the baseline situation. We examine responses of wintering seed‐eating farmland birds to the experimental establishment of winter food plots in areas with contrasting food availability. We found that farmland bird abundance and species richness were strongly positively related to seed availability, regardless of compositional differences between agricultural landscapes. In line with the ecological contrast hypothesis, the responses of wintering farmland birds increased with increasing conservation induced contrast in a key limiting resource. Both contrasts and relative responses were negatively related to baseline food availability, but the absolute bird density in food plots was unrelated to baseline food availability. This indicates that both relative and absolute effects of conservation management need to be considered to properly evaluate the effectiveness of conservation management.     

Evolution of risk‐taking during conspicuous mating displays

In many species, males possess conspicuous characteristics to attract females. These traits often attract predators as well, and males thus may have to balance the conspicuousness of their signals in relation to the prevailing predation risk. Here we develop a theoretical model of optimal signaling and risk‐taking behavior for males differing in the attractiveness of their signals. All else being equal, more attractive males should behave more cautiously. Yet this prediction may drastically change if males differ in any additional characteristic, especially if basal mortality rate or signaling costs are higher or if the vulnerability to predators is lower for attractive males. A key insight from our model is that male competition will create a positive feedback so that selection on male risk‐taking strategies is acting in opposite directions. If selection acts on one male type to behave more cautiously, this will strengthen selection on males of the other types to take higher risks and vice versa. Our results further demonstrate that the asset‐protection principle, which states that individuals with higher future expectations should behave more cautiously, may often be violated. We also offer an alternative to the handicap principle explaining the often found positive association between male ornamentation and viability: attractive males may simply behave more cautiously.     

Optimized design and assessment of whole genome tiling arrays

MOTIVATION: Recent advances in microarray technologies have made it feasible to interrogate whole genomes with tiling arrays and this technique is rapidly becoming one of the most important high-throughput functional genomics assays. For large mammalian genomes, analyzing oligonucleotide tiling array data is complicated by the presence of non-unique sequences on the array, which increases the overall noise in the data and may lead to false positive results due to cross-hybridization. The ability to create custom microarrays using maskless array synthesis has led us to consider ways to optimize array design characteristics for improving data quality and analysis. We have identified a number of design parameters to be optimized including uniqueness of the probe sequences within the whole genome, melting temperature and self-hybridization potential. RESULTS: We introduce the uniqueness score, U, a novel quality measure for oligonucleotide probes and present a method to quickly compute it. We show that U is equivalent to the number of shortest unique substrings in the probe and describe an efficient greedy algorithm to design mammalian whole genome tiling arrays using probes that maximize U. Using the mouse genome, we demonstrate how several optimizations influence the tiling array design characteristics. With a sensible set of parameters, our designs cover 78% of the mouse genome including many regions previously considered 'untilable' due to the presence of repetitive sequence. Finally, we compare our whole genome tiling array designs with commercially available designs. AVAILABILITY: Source code is available under an open source license from http://www.ebi.ac.uk/~graef/arraydesign/.