Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals. This includes humans, where hepatitis B viruses (HBVs) are prevalent pathogens in considerable parts of the global population. Recently, endogenized sequences of HBVs (eHBVs) have been discovered in bird genomes where they constitute direct evidence for the coexistence of these viruses and their hosts from the late Mesozoic until present. Nevertheless, virtually nothing is known about the ancient host range of this virus family in other animals. Here we report the first eHBVs from crocodilian, snake, and turtle genomes, including a turtle eHBV that endogenized >207 million years ago. This genomic “fossil” is >125 million years older than the oldest avian eHBV and provides the first direct evidence that Hepadnaviridae already existed during the Early Mesozoic. This implies that the Mesozoic fossil record of HBV infection spans three of the five major groups of land vertebrates, namely birds, crocodilians, and turtles. We show that the deep phylogenetic relationships of HBVs are largely congruent with the deep phylogeny of their amniote hosts, which suggests an ancient amniote–HBV coexistence and codivergence, at least since the Early Mesozoic. Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene. We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs. Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.     

Unravelling the Scent of Vetiver: Identification of Character‐Impact Compounds

Vetiver oil is a highly esteemed basic ingredient of modern perfumery, but the nature of the constituents that really impart its typical and most sought woody‐earthy scent has remained controversial. Indeed, vetiver oil is considered as one of the most complex essential oils, being mostly composed of several hundreds of sesquiterpene derivatives with a large structural diversity. Its complexity has hindered the direct identification of its odoriferous components. We thus aimed at using a combination of GC×GC/MS and GC‐Olfactometry in order to identify most of its odor‐impact constituents. The olfactory analysis of vetiver oil and vetiveryl acetate revealed a huge variety of odors in both products. While khusimone has almost unanimously been recognized as the most characteristic vetiver odorant, we have identified several even more important contributors to the typical vetiver character.     

pyOpenMS: A Python‐based interface to the OpenMS mass‐spectrometry algorithm library

pyOpenMS is an open‐source, Python‐based interface to the C++ OpenMS library, providing facile access to a feature‐rich, open‐source algorithm library for MS‐based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de‐isotoping, and peak‐picking) and complex data analysis (including label‐free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open‐source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3‐clause BSD licence).     

The Avian Head Induces Cues for Sound Localization in Elevation

Accurate sound source localization in three-dimensional space is essential for an animal’s orientation and survival. While the horizontal position can be determined by interaural time and intensity differences, localization in elevation was thought to require external structures that modify sound before it reaches the tympanum. Here we show that in birds even without external structures like pinnae or feather ruffs, the simple shape of their head induces sound modifications that depend on the elevation of the source. Based on a model of localization errors, we show that these cues are sufficient to locate sounds in the vertical plane. These results suggest that the head of all birds induces acoustic cues for sound localization in the vertical plane, even in the absence of external ears.     

How Do Stomata Sense Reductions in Atmospheric Relative Humidity？

Dear Editor, It has been known since the work of Francis Darwin that, in response to a reduction in atmospheric relative humidity （rh）, stomatal aperture decreases. Screening for Arabidopsis mutants compromised in stomatal responses to reduced rh resulted in the identification of two genes, OST1 and ABA2, that are involved in stomatal response to low rh conditions. Interestingly both encode proteins previously known to be involved in ABA signaling （Xie et al., 2006, and references therein）. These findings strongly suggested that, at least in part, the stomatal response to low rh is mediated by ABA and the intracellular ABA signaling pathway. Our most recent data show that low rh-induced stomatal closure can pro- ceed by guard cell autonomous ABA synthesis （Bauer et al., 2013）,     

Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics

Growth factor receptor mediated signaling is meanwhile recognized as a complex signaling network, which is initiated by recruiting specific patterns of adaptor proteins to the intracellular domain of epidermal growth factor receptor (EGFR). Approaches to globally identify EGFR‐binding proteins are required to elucidate this network. We affinity‐purified EGFR with its interacting proteins by coprecipitation from lysates of A431 cells. A total of 183 proteins were repeatedly detected in high‐resolution MS measurements. For 15 of these, direct interactions with EGFR were listed in the iRefIndex interaction database, including Grb2, shc‐1, SOS1 and 2, STAT 1 and 3, AP2, UBS3B, and ERRFI. The newly developed Cytoscape plugin ModuleGraph allowed retrieving and visualizing 93 well‐described protein complexes that contained at least one of the proteins found to interact with EGFR in our experiments. Abundances of 14 proteins were modulated more than twofold upon EGFR activation whereof clathrin‐associated adaptor complex AP‐2 showed 4.6‐fold enrichment. These proteins were further annotated with different cellular compartments. Finally, interactions of AP‐2 proteins and the newly discovered interaction of CIP2A could be verified. In conclusion, a powerful technique is presented that allowed identification and quantitative assessment of the EGFR interactome to provide further insight into EGFR signaling.     

Synthesis and Application of Isosteric Purine 2′-Deoxyribofuranosides

Abstract

The diastereoselective synthesis of several pyrrolo[2,3-d]- and pyrazolo[3,4-d]pyrimidine 2′-deoxy-ribofuranosides employing l-chloro-2-deoxy-3,5-di-0-(p-tolu-oyl)-a-D-erythropentofuranose and the nucleobase anion, generated by liquid-liquid or solid-liquid phase-transfer catalysis, is described. Appropriately protected phosphoramidites of 8-aza-7-deaza-2′-deoxyadenosine and 2′-deoxytubercidin were prepared and employed in solid-phase synthesis of palindromic DNA-fragments. The replacement of dA residues by deoxytubercidin within the Eco RI recognition site d(GAATTC) of the dodecamer d(GTAGAATTCTAC) gave evidence for purine N-7 binding to the endodeoxyribonuclease. The interpretation of similar experiments carried out on d(CGCGAATTCGCG) was obscured because of hairpin formation.