Environmental sensing and response genes in cnidaria : the chemical defensome in the sea anemone Nematostella vectensis

Author Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Cell Biology and Toxicology 24 (2008): 483-502, doi:10.1007/s10565-008-9107-5.The starlet sea anemone Nematostella vectensis has been recently established as a new model system for the study of the evolution of developmental processes, as cnidaria occupy a key evolutionary position at the base of the bilateria. Cnidaria play important roles in estuarine and reef communities, but are exposed to many environmental stressors. Here I describe the genetic components of a ‘chemical defensome’ in the genome of N. vectensis, and review cnidarian molecular toxicology. Gene families that defend against chemical stressors and the transcription factors that regulate these genes have been termed a ‘chemical defensome,’ and include the cytochromes P450 and other oxidases, various conjugating enyzymes, the ATP-dependent efflux transporters, oxidative detoxification proteins, as well as various transcription factors. These genes account for about 1% (266/27200) of the predicted genes in the sea anemone genome, similar to the proportion observed in tunicates and humans, but lower than that observed in sea urchins. While there are comparable numbers of stress-response genes, the stress sensor genes appear to be reduced in N. vectensis relative to many model protostomes and deuterostomes. Cnidarian toxicology is understudied, especially given the important ecological roles of many cnidarian species. New genomic resources should stimulate the study of chemical stress sensing and response mechanisms in cnidaria, and allow us to further illuminate the evolution of chemical defense gene networks.WHOI Ocean Life Institute and NIH R01-ES01591

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

BackgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.ResultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.ConclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.Peer reviewe

Evolution of cuticular hydrocarbons in the hymenoptera : a meta-analysis

Chemical communication is the oldest form of communication, spreading across all organisms of life. In insects, cuticular hydrocarbons (CHC) function as the chemical recognition cues for the recognition of mates, species and nest-mates in social insects. Although much is known about the function of individual hydrocarbons and their biosynthesis, a phylogenetic overview is lacking. Here we review the CHC profiles of 241 species of hymenoptera, one of the largest and important insect orders, including the Symphyta (sawflies), the polyphyletic Parasitica (parasitoid wasps) and the Aculeata (wasps, bees and ants). We investigated whether these five major taxonomic groups differed in the presence and absence of CHC classes and whether the sociality of a species (solitarily vs. social) had an effect on CHC profile complexity. We found that the main CHC classes (i.e., n-alkanes, alkenes and methylalkanes) were all present early in the evolutionary history of the hymenoptera, as evidenced by their presence in ancient Symphyta and primitive Parasitica wasps. Throughout all groups within the Hymenoptera the more complex a CHC the fewer species that produce it, which may reflect the Occam's razor principle that insects’ only biosynthesize the most simple compound that fulfil its needs. Surprisingly there was no difference in the complexity of CHC profiles between social and solitary species, with some of the most complex CHC profiles belonging to the Parasitica. This profile complexity has been maintained in the ants, but some specialisation in biosynthetic pathways has led to a simplification of profiles in the aculeate wasps and bees. The absence of CHC classes in some taxa or species may be due to gene silencing or down-regulation rather than gene loss, as evidenced by sister species having highly divergent CHC profiles, and cannot be predicted by their phylogenetic history. The presence of highly complex CHC profiles prior to the vast radiation of the social hymenoptera indicates a 'spring-loaded' system where the diverse CHC needed for the complex communication systems of social insects, were already present for natural selection to act upon rather than evolve independently. This would greatly aid the multiple evolution of sociality in the Aculeata

Volatile Organic Compounds Emitted by Fungal Associates of Conifer Bark Beetles and their Potential in Bark Beetle Control

Conifer bark beetles attack and kill mature spruce and pine trees, especially during hot and dry conditions. These beetles are closely associated with ophiostomatoid fungi of the Ascomycetes, including the genera Ophiostoma, Grosmannia, and Endoconidiophora, which enhance beetle success by improving nutrition and modifying their substrate, but also have negative impacts on beetles by attracting predators and parasites. A survey of the literature and our own data revealed that ophiostomatoid fungi emit a variety of volatile organic compounds under laboratory conditions including fusel alcohols, terpenoids, aromatic compounds, and aliphatic alcohols. Many of these compounds already have been shown to elicit behavioral responses from bark beetles, functioning as attractants or repellents, often as synergists to compounds currently used in bark beetle control. Thus, these compounds could serve as valuable new agents for bark beetle management. However, bark beetle associations with fungi are very complex. Beetle behavior varies with the species of fungus, the stage of the beetle life cycle, the host tree quality, and probably with changes in the emission rate of fungal volatiles. Additional research on bark beetles and their symbiotic associates is necessary before the basic significance of ophiostomatoid fungal volatiles can be understood and their applied potential realized

Growth of ultrathin ZrO2 films on Si(100): Film-thickness-dependent band alignment

The band alignment of ultrathin ZrO2 films of different thickness formed on Si(100) have been monitored with synchrotron radiation photoelectron spectroscopy and x-ray absorption spectroscopy. The films were deposited sequentially by way of metal-organic chemical-vapor deposition in ultrahigh vacuum. A significant decrease in the conduction band offset is found for increasing film thickness. It is accompanied by a corresponding increase of the valence band offset. The variations originate in the formation of an interfacial layer characterized by a lower degree of Zr-O interaction than in bulk ZrO2 but with no clear evidence for partially occupied Zr 4d dangling bonds. (c) 2006 American Institute of Physics