Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expressionComment: 7 figures, 20 supplementary figures, 6 supplementary tables Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, et al. (2013) Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression. PLoS Genet 9(9): e1003748. doi:10.1371/journal.pgen.100374

Deceit: A flexible distributed file system

Deceit, a distributed file system (DFS) being developed at Cornell, focuses on flexible file semantics in relation to efficiency, scalability, and reliability. Deceit servers are interchangeable and collectively provide the illusion of a single, large server machine to any clients of the Deceit service. Non-volatile replicas of each file are stored on a subset of the file servers. The user is able to set parameters on a file to achieve different levels of availability, performance, and one-copy serializability. Deceit also supports a file version control mechanism. In contrast with many recent DFS efforts, Deceit can behave like a plain Sun Network File System (NFS) server and can be used by any NFS client without modifying any client software. The current Deceit prototype uses the ISIS Distributed Programming Environment for all communication and process group management, an approach that reduces system complexity and increases system robustness

Exploring Halo Substructure with Giant Stars IV: The Extended Structure of the Ursa Minor Dwarf Spheroidal

We present a large area photometric survey of the Ursa Minor dSph. We identify UMi giant star candidates extending to ~3 deg from the center of the dSph. Comparison to previous catalogues of stars within the tidal radius of UMi suggests that our photometric luminosity classification is 100% accurate. Over a large fraction of the survey area, blue horizontal branch stars associated with UMi can also be identified. The spatial distribution of both the UMi giant stars and the BHB stars are remarkably similar, and a large fraction of both samples of stars are found outside the tidal radius of UMi. An isodensity contour map of the stars within the tidal radius of UMi reveals two morphological peculiarities: (1) The highest density of dSph stars is offset from the center of symmetry of the outer isodensity contours. (2) The overall shape of the outer contours appear S-shaped. We find that previously determined King profiles with ~50' tidal radii do not fit well the distribution of our UMi stars. A King profile with a larger tidal radius produces a reasonable fit, however a power law with index -3 provides a better fit for radii > 20'. The existence of UMi stars at large distances from the core of the galaxy, the peculiar morphology of the dSph within its tidal radius, and the shape of its surface density profile all suggest that UMi is evolving significantly due to the tidal influence of the Milky Way. However, the photometric data on UMi stars alone does not allow us to determine if the candidate extratidal stars are now unbound or if they remain bound to the dSph within an extended dark matter halo. (Abridged)Comment: accepted by AJ, 32 pages, 15 figures, emulateapj5 styl

Modélisation des paramètres de pénétrance incomplète et de phénocopie d'une méthode de cartographie fine d'une maladie complexe

Les méthodes de cartographie fine sont des modèles qui estiment la position d'un allèle mutant pouvant causer une maladie dans un groupe d'individus. Le travail de Larribe et al. (2002, 2003), MapArg, n'a pas tenu compte des paramètres de pénétrance jusqu'à maintenant. Ce mémoire démontre les effets de ces paramètres, soit la pénétrance et la phénocopie, sur la performance de MapArg, dans des populations haploïdes. De plus, deux méthodes que nous avons développées seront ensuite incorporées à MapArg dans le but d'améliorer son efficacité si il y a pénétrance et/ou phénocopie. Les résultats démontrent que la phénocopie peut avoir une influence négative sur l'efficacité de MapArg. La pénétrance ne semble pas avoir d'effet majeur sur MapArg. La première méthode développée est un modèle simple qui n'apporte pas d'amélioration majeure de MapArg par rapport à ce même modèle sans ajustement. Par contre, cela procure un point de départ pour les développements futurs dans les populations diploïdes. La deuxieme méthode améliore l'efficacité de MapArg sous certaines conditions,\ud en particulier, si la taille de l'échantillon est assez grande. La deuxieme méthode fonctionne également très bien pour les données réelles de la Fibrose Kystique (Kerem et al., 1989). ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Phénocopie, Pénétrance, Pénétrance incomplète, Cartographie fine

Co-Evolution of Transcriptional Silencing Proteins and the DNA Elements Specifying Their Assembly

Co-evolution of transcriptional regulatory proteins and their sites of action has been often hypothesized but rarely demonstrated. Here we provide experimental evidence of such co-evolution in yeast silent chromatin, a finding that emerged from studies of hybrids formed between two closely related Saccharomyces species. A unidirectional silencing incompatibility between S. cerevisiae and S. bayanus led to a key discovery: asymmetrical complementation of divergent orthologs of the silent chromatin component Sir4. In S. cerevisiae/S. bayanus interspecies hybrids, ChIP-Seq analysis revealed a restriction against S. cerevisiae Sir4 associating with most S. bayanus silenced regions; in contrast, S. bayanus Sir4 associated with S. cerevisiae silenced loci to an even greater degree than did S. cerevisiae's own Sir4. Functional changes in silencer sequences paralleled changes in Sir4 sequence and a reduction in Sir1 family members in S. cerevisiae. Critically, species-specific silencing of the S. bayanus HMR locus could be reconstituted in S. cerevisiae by co-transfer of the S. bayanus Sir4 and Kos3 (the ancestral relative of Sir1) proteins. As Sir1/Kos3 and Sir4 bind conserved silencer-binding proteins, but not specific DNA sequences, these rapidly evolving proteins served to interpret differences in the two species' silencers presumably involving emergent features created by the regulatory proteins that bind sequences within silencers. The results presented here, and in particular the high resolution ChIP-Seq localization of the Sir4 protein, provided unanticipated insights into the mechanism of silent chromatin assembly in yeast.National Science Foundation (U.S.) (GM31105)National Science Foundation (U.S.) (Predoctoral Fellowships