Grain size dependent high-pressure elastic properties of ultrafine micro/nanocrystalline grossular

We have performed sound velocity and unit cell volume measurements of three synthetic, ultrafine micro/nanocrystalline grossular samples up to 50 GPa using Brillouin spectroscopy and synchrotron X-ray diffraction. The samples are characterized by average grain sizes of 90 nm, 93 nm and 179 nm (hereinafter referred to as samples Gr90, Gr93, and Gr179, respectively). The experimentally determined sound velocities and elastic properties of Gr179 sample are comparable with previous measurements, but slightly higher than those of Gr90 and Gr93 under ambient conditions. However, the differences diminish with increasing pressure, and the velocity crossover eventually takes place at approximately 20-30 GPa. The X-ray diffraction peaks of the ultrafine micro/nanocrystalline grossular samples significantly broaden between 15-40 GPa, especially for Gr179. The velocity or elasticity crossover observed at pressures over 30 GPa might be explained by different grain size reduction and/or inhomogeneous strain within the individual grains for the three grossular samples, which is supported by both the pressure-induced peak broadening observed in the X-ray diffraction experiments and transmission electron microscopy observations. The elastic behavior of ultrafine micro/nanocrystalline silicates, in this case, grossular, is both grain size and pressure dependent.

Pressure-induced phase transitions of β-type pyrochlore CsTaWO6

The β-type pyrochlore CsTaWO₆ was studied by synchrotron X-ray diffraction (XRD) and Raman scattering methods up to pressures of 43 GPa using a diamond anvil cell (DAC).

Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression

CLOCK (CLK) is a master transcriptional regulator of the circadian clock in Drosophila. To identify CLK direct target genes and address circadian transcriptional regulation in Drosophila, we performed chromatin immunoprecipitation (ChIP) tiling array assays (ChIP-chip) with a number of circadian proteins. CLK binding cycles on at least 800 sites with maximal binding in the early night. The CLK partner protein CYCLE (CYC) is on most of these sites. The CLK/CYC heterodimer is joined 4-6 h later by the transcriptional repressor PERIOD (PER), indicating that the majority of CLK targets are regulated similarly to core circadian genes. About 30% of target genes also show cycling RNA polymerase II (Pol II) binding. Many of these generate cycling RNAs despite not being documented in prior RNA cycling studies. This is due in part to different RNA isoforms and to fly head tissue heterogeneity. CLK has specific targets in different tissues, implying that important CLK partner proteins and/or mechanisms contribute to gene-specific and tissue-specific regulation.

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1 30 000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The interface is designed for clarity and ease of navigation. From the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. Searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. A few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. PyMOL and Chimera scripts that colorize reactive groups on residues that are modified can be downloaded. Features designed to facilitate proteomic analyses include downloads of modification sites, kinase–substrate data sets, sequence logo generators, a Cytoscape plugin and BioPAX download to enable pathway visualization of the kinase–substrate interactions in PhosphoSitePlus®.

The BioPAX community standard for pathway data sharing

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.