Shaken not stirred: a global research cocktail served in Hinxton

A report of the 2007 Cold Spring Harbor Laboratory/Wellcome Trust Conference on Functional Genomics and Systems Biology, Hinxton, UK, 10-13 October 2007

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

BACKGROUND: The generation of mature mRNAs involves interconnected processes, including transcription by RNA polymerase II (Pol II), modification of histones, and processing of pre-mRNAs through capping, intron splicing, and polyadenylation. These processes are thought to be integrated, both spatially and temporally, but it is unclear how these connections manifest at a global level with respect to chromatin patterns and transcription kinetics. We sought to clarify the relationships between chromatin, transcription and splicing using multiple genome-wide approaches in fission yeast. RESULTS: To investigate these functional interdependencies, we determined Pol II occupancy across all genes using high-density tiling arrays. We also performed ChIP-chip on the same array platform to globally map histone H3 and its H3K36me3 modification, complemented by formaldehyde-assisted isolation of regulatory elements (FAIRE). Surprisingly, Pol II occupancy was higher in introns than in exons, and this difference was inversely correlated with gene expression levels at a global level. Moreover, introns showed distinct distributions of histone H3, H3K36me3 and FAIRE signals, similar to those at promoters and terminators. These distinct transcription and chromatin patterns of intronic regions were most pronounced in poorly expressed genes. CONCLUSIONS: Our findings suggest that Pol II accumulates at the 3 ends of introns, leading to substantial transcriptional delays in weakly transcribed genes. We propose that the global relationship between transcription, chromatin remodeling, and splicing may reflect differences in local nuclear environments, with highly expressed genes being associated with abundant processing factors that promote effective intron splicing and transcriptional elongation

Broadband UBVRI Photometry of Horizontal-Branch and Metal-Poor Candidates from the HK and Hamburg/ESO Surveys. I

We report broadband UBV and/or BVRI CCD photometry for a total of 1857 stars in the thick-disk and halo populations of the Galaxy. The majority of our targets were selected as candidate field horizontal-branch or other A-type stars (FHB/A, N = 576), or candidate low-metallicity stars (N = 1221), from the HK and Hamburg/ESO objective-prism surveys. Similar data for a small number of additional stars from other samples are also reported. These data are being used for several purposes. In the case of the FHB/A candidates they are used to accurately separate the lower-gravity FHB stars from various higher-gravity A-type stars, a subsample that includes the so-called Blue Metal Poor stars, halo and thick-disk blue stragglers, main-sequence A-type dwarfs, and Am and Ap stars. These data are also being used to derive photometric distance estimates to high-velocity hydrogen clouds in the Galaxy and for improved measurements of the mass of the Galaxy. Photometric data for the metal-poor candidates are being used to refine estimates of stellar metallicity for objects with available medium-resolution spectroscopy, to obtain distance estimates for kinematic analyses, and to establish initial estimates of effective temperature for analysis of high-resolution spectroscopy of the stars for which this information now exists.Comment: 22 pages, including 3 figures, 5 tables, and two ascii files of full data, accepted for publication in the Astrophysical Journal (Supplements

Broadband UBVR_CI_C Photometry of Horizontal-Branch and Metal-poor Candidates from the HK and Hamburg/ESO Surveys. I.

We report broadband UBV and/or BVR_CI_C CCD photometry for a total of 1857 stars in the thick-disk and halo populations of the Galaxy. The majority of our targets were selected as candidate field horizontal-branch or other A-type stars (FHB/A, N = 576), or candidate low-metallicity stars (N = 1221), from the HK and Hamburg/ESO objective-prism surveys. Similar data for a small number of additional stars from other samples are also reported. These data are being used for several purposes. In the case of the FHB/A candidates they are used to accurately separate the lower gravity FHB stars from various higher gravity A-type stars, a subsample that includes the so-called blue metal poor stars, halo and thick-disk blue stragglers, main-sequence A-type dwarfs, and Am and Ap stars. These data are also being used to derive photometric distance estimates to high-velocity hydrogen clouds in the Galaxy and for improved measurements of the mass of the Galaxy. Photometric data for the metal-poor candidates are being used to refine estimates of stellar metallicity for objects with available medium-resolution spectroscopy, to obtain distance estimates for kinematic analyses, and to establish initial estimates of effective temperature for analysis of high-resolution spectroscopy of the stars for which this information now exists

Broadband UBVR C I C Photometry of Horizontal-branch and Metal-poor Candidates from the HK and Hamburg/ESO Surveys. I

We report broadband UBVand/or BVRCIC CCD photometry for a total of 1857 stars in the thick-disk and halo populations of the Galaxy. The majority of our targets were selected as candidate field horizontal-branch or other A-type stars (FHB/A, N = 576), or candidate low-metallicity stars (N =1221), from the HK and Hamburg/ESO objective-prism surveys. Similar data for a small number of additional stars from other samples are also reported. These data are being used for several purposes. In the case of the FHB/A candidates they are used to accurately separate the lower gravity FHB stars from various higher gravity A-type stars, a subsample that includes the so-called blue metal poor stars, halo and thick-disk blue stragglers, main-sequence A-type dwarfs, and Am and Ap stars. These data are also being used to derive photometric distance estimates to high-velocity hydrogen clouds in the Galaxy and for improved measurements of the mass of the Galaxy. Photometric data for the metal-poor candidates are being used to refine estimates of stellar metallicity for objects with available medium-resolution spectroscopy, to obtain distance estimates for kinematic analyses, and to establish initial estimates of effective temperature for analysis of high-resolution spectroscopy of the stars for which this information now exists

Protein and lipid kinase inhibitors as targeted anticancer agents of the Ras/Raf/MEK and PI3K/PKB pathways

The identification and characterization of the components of individual signal transduction cascades, and advances in our understanding on how these biological signals are integrated in cancer initiation and progression, have provided new strategies for therapeutic intervention in solid tumors and hematological malignancies. To this end, pharmaceutical efforts have been directed to target different components of the Ras/Raf/MEK and PI3K/PKB pathways. This review article covers recent salient achievements in the identification and development of Raf, MEK, and PI3K inhibitors

Long-Distance Three-Color Neuronal Tracing in Fixed Tissue Using NeuroVue Dyes

Dissecting development of neuronal connections is critical for understanding neuronal function in both normal and diseased states. Charting the development of the multitude of connections is a monumental task, since a given neuron typically receives hundreds of convergent inputs from other neurons and provides divergent outputs for hundreds of other neurons. Although progress is being made utilizing various mutants and/or genetic constructs expressing fluorescent proteins like GFP, substantial work remains before a database documenting the development and final location of the neuronal pathways in an adult animal is completed. The vast majority of developing neurons cannot be specifically labeled with antibodies and making specific GFP-expressing constructs to tag each of them is an overwhelming task. Fortunately, fluorescent lipophilic dyes have emerged as very useful tools to systematically compare changes in neuronal networks between wild-type and mutant mice. These dyes diffuse laterally along nerve cell membranes in fixed preparations, allowing tracing of the position of a given neuron within the neuronal network in murine mutants fixed at various stages of development. Until recently, however, most evaluations have been limited to one, or at most, two color analyses. We have previously reported three color neuronal profiling using the novel lipophilic dyes NeuroVue (NV) Green, Red and Maroon (Fritzsch et al., Brain. Res. Bull. 66:249–258, 2005). Unfortunately such three color experiments have been limited by the fact that NV Green and its brighter successor, NV Emerald, both exhibit substantially decreased signal intensities when times greater than 48 hours at 37°C are required to achieve neuronal profile filling (unpublished observations). Here we describe a standardized test system developed to allow comparison of candidate dyes and its use to evaluate a series of 488 nm-excited green-emitting lipophilic dyes. The best of these, NV Jade, has spectral properties well matched to NV Red and NV Maroon, better solubility in DMF than DiO or DiA, improved thermostability compared with NV Emerald, and the ability to fill neuronal profiles at rates of 1 mm per day for periods of at least 5 days. Use of NV Jade in combination with NV Red and NV Maroon substantially improves the efficiency of connectional analysis in complex mutants and transgenic models where limited numbers of specimens are available

The Milky Way Tomography with SDSS: II. Stellar Metallicity

Using effective temperature and metallicity derived from SDSS spectra for ~60,000 F and G type main sequence stars (0.2<g-r<0.6), we develop polynomial models for estimating these parameters from the SDSS u-g and g-r colors. We apply this method to SDSS photometric data for about 2 million F/G stars and measure the unbiased metallicity distribution for a complete volume-limited sample of stars at distances between 500 pc and 8 kpc. The metallicity distribution can be exquisitely modeled using two components with a spatially varying number ratio, that correspond to disk and halo. The two components also possess the kinematics expected for disk and halo stars. The metallicity of the halo component is spatially invariant, while the median disk metallicity smoothly decreases with distance from the Galactic plane from -0.6 at 500 pc to -0.8 beyond several kpc. The absence of a correlation between metallicity and kinematics for disk stars is in a conflict with the traditional decomposition in terms of thin and thick disks. We detect coherent substructures in the kinematics--metallicity space, such as the Monoceros stream, which rotates faster than the LSR, and has a median metallicity of [Fe/H]=-0.96, with an rms scatter of only ~0.15 dex. We extrapolate our results to the performance expected from the Large Synoptic Survey Telescope (LSST) and estimate that the LSST will obtain metallicity measurements accurate to 0.2 dex or better, with proper motion measurements accurate to ~0.2 mas/yr, for about 200 million F/G dwarf stars within a distance limit of ~100 kpc (g<23.5). [abridged]Comment: 40 pages, 21 figures, emulateApJ style, accepted to ApJ, high resolution figures are available from http://www.astro.washington.edu/ivezic/sdss/mw/astroph0804.385

The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback

The regulation of the G1- to S-phase transition is critical for cell-cycle progression. This transition is driven by a transient transcriptional wave regulated by transcription factor complexes termed MBF/SBF in yeast and E2F-DP in mammals. Here we apply genomic, genetic, and biochemical approaches to show that the Yox1p homeodomain protein of fission yeast plays a critical role in confining MBF-dependent transcription to the G1/S transition of the cell cycle. The yox1 gene is an MBF target, and Yox1p accumulates and preferentially binds to MBF-regulated promoters, via the MBF components Res2p and Nrm1p, when they are transcriptionally repressed during the cell cycle. Deletion of yox1 results in constitutively high transcription of MBF target genes and loss of their cell cycle–regulated expression, similar to deletion of nrm1. Genome-wide location analyses of Yox1p and the MBF component Cdc10p reveal dozens of genes whose promoters are bound by both factors, including their own genes and histone genes. In addition, Cdc10p shows promiscuous binding to other sites, most notably close to replication origins. This study establishes Yox1p as a new regulatory MBF component in fission yeast, which is transcriptionally induced by MBF and in turn inhibits MBF-dependent transcription. Yox1p may function together with Nrm1p to confine MBF-dependent transcription to the G1/S transition of the cell cycle via negative feedback. Compared to the orthologous budding yeast Yox1p, which indirectly functions in a negative feedback loop for cell-cycle transcription, similarities but also notable differences in the wiring of the regulatory circuits are evident