Stellar hydrodynamics caught in the act: Asteroseismology with CoRoT and Kepler

Asteroseismic investigations, particularly based on data on stellar oscillations from the CoRoT and Kepler space missions, are providing unique possibilities for investigating the properties of stellar interiors. This constitutes entirely new ways to study the effects of dynamic phenomena on stellar structure and evolution. Important examples are the extent of convection zones and the associated mixing and the direct and indirect effects of stellar rotation. In addition, the stellar oscillations themselves show very interesting dynamic behaviour. Here we discuss examples of the results obtained from such investigations, across the Hertzsprung-Russell diagram.Comment: Proc. IAU Symposium 271, Astrophysical Dynamics: From stars to galaxies, eds N. Brummell, A. S. Brun, M. S. Miesch, Y. Ponty, IAU and Cambridge University Press, in the pres

Long-wavelength observations of debris discs around sun-like stars

[Abridged] We present two deep surveys of circumstellar discs around solar-type stars at different ages carried out at 350 micron with the CSO and at 1.2 mm with the IRAM 30-m telescope. The aim of this study is to understand the evolution timescale of circumstellar debris discs, and the physical mechanisms responsible for such evolution around solar-type stars. In addition, we perform a detailed characterisation of the detected debris discs. Theoretically, the mass of the disc is expected to decrease with time. In order to test this hypothesis, we performed the generalised Kendall's tau correlation and three different two-sample tests. A characterisation of the detected debris discs has been obtained by computing the collision and Poynting-Robertson timescales and by modelling the spectral energy distribution. The Kendall's tau correlation yields a probability of 76% that the mass of debris discs and their age are correlated. Similarly, the three two-sample tests give a probability between 70 and 83% that younger and older debris systems belong to different parent populations in terms of dust mass. We detected submillimetre/millimetre emission from six debris discs, enabling a detailed SED modelling. Our results on the correlation and evolution of dust mass as a function of age are conditioned by the sensitivity limit of our survey. Deeper millimetre observations are needed to confirm the evolution of debris material around solar-like stars. In the case of the detected discs, the comparison between collision and Poynting-Robertson timescales supports the hypothesis that these discs are collision dominated. All detected debris disc systems show the inner part evacuated from small micron-sized grains.Comment: Accepted by A&

A genome-scale shRNA resource for transgenic RNAi in Drosophila

Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource. © 2011 Nature America, Inc. All rights reserved

Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals

Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin-binding patterns, likely due to interactions with various specificity factors. Previously, we showed that the chromatin-binding pattern of the HP1 protein Rhino, a crucial factor of the Drosophila PIWI-interacting RNA (piRNA) pathway, is largely defined by a DNA sequence-specific C2H2 zinc finger protein named Kipferl (Baumgartner et al., 2022). Here, we elucidate the molecular basis of the interaction between Rhino and its guidance factor Kipferl. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino’s chromodomain, G31D, that does not affect H3K9me2/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the rhinoG31D mutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhino’s chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein

A universal method for the rapid isolation of all known classes of functional silencing small RNAs

International audienceDiverse classes of silencing small (s)RNAs operate via ARGONAUTE-family proteins within RNA-induced-silencing-complexes (RISCs). Here, we have streamlined various embodiments of a Q-sepharose-based RISC-purification method that relies on conserved biochemical properties of all ARGONAUTEs. We show, in multiple benchmarking assays, that the resulting 15-min benchtop extraction procedure allows simultaneous purification of all known classes of RISC-associated sRNAs without prior knowledge of the samples-intrinsic ARGONAUTE repertoires. Optimized under a user-friendly format, the method-coined 'TraPR' for Trans-kingdom, rapid, affordable Purification of RISCs-operates irrespectively of the organism, tissue, cell type or bio-fluid of interest , and scales to minute amounts of input material. The method is highly suited for direct profiling of silencing sRNAs, with TraPR-generated sequenc-ing libraries outperforming those obtained via gold-standard procedures that require immunoprecipita-tions and/or lengthy polyacrylamide gel-selection. TraPR considerably improves the quality and consistency of silencing sRNA sample preparation including from notoriously difficult-to-handle tissues/bio-fluids such as starchy storage roots or mammalian plasma, and regardless of RNA contaminants or RNA degradation status of samples

Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi\u27s genomic targets still not identified

Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors\u27 genome-wide conclusions

Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified

Summary Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors’ genome-wide conclusions

Analysis of Vestibular Labyrinthine Geometry and Variation in the Human Temporal Bone

Stable posture and body movement in humans is dictated by the precise functioning of the ampulla organs in the semi-circular canals. Statistical analysis of the interrelationship between bony and membranous compartments within the semi-circular canals is dependent on the visualization of soft tissue structures. Thirty-one human inner ears were prepared, post-fixed with osmium tetroxide and decalcified for soft tissue contrast enhancement. High resolution X-ray microtomography images at 15 μm voxel-size were manually segmented. This data served as templates for centerline generation and cross-sectional area extraction. Our estimates demonstrate the variability of individual specimens from averaged centerlines of both bony and membranous labyrinth. Centerline lengths and cross-sectional areas along these lines were identified from segmented data. Using centerlines weighted by the inverse squares of the cross-sectional areas, plane angles could be quantified. The fit planes indicate that the bony labyrinth resembles a Cartesian coordinate system more closely than the membranous labyrinth. A widening in the membranous labyrinth of the lateral semi-circular canal was observed in some of the specimens. Likewise, the cross-sectional areas in the perilymphatic spaces of the lateral canal differed from the other canals. For the first time we could precisely describe the geometry of the human membranous labyrinth based on a large sample size. Awareness of the variations in the canal geometry of the membranous and bony labyrinth would be a helpful reference in designing electrodes for future vestibular prosthesis and simulating fluid dynamics more precisely