Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate

Alternative splicing is critical for development; however, its role in the specification of the three embryonic germ layers is poorly understood. By performing RNA-Seq on human embryonic stem cells (hESCs) and derived definitive endoderm, cardiac mesoderm, and ectoderm cell lineages, we detect distinct alternative splicing programs associated with each lineage. The most prominent splicing program differences are observed between definitive endoderm and cardiac mesoderm. Integrative multi-omics analyses link each program with lineage-enriched RNA binding protein regulators, and further suggest a widespread role for Quaking (QKI) in the specification of cardiac mesoderm. Remarkably, knockout of QKI disrupts the cardiac mesoderm-associated alternative splicing program and formation of myocytes. These changes arise in part through reduced expression of BIN1 splice variants linked to cardiac development. Mechanistically, we find that QKI represses inclusion of exon 7 in BIN1 pre-mRNA via an exonic ACUAA motif, and this is concomitant with intron removal and cleavage from chromatin. Collectively, our results uncover alternative splicing programs associated with the three germ lineages and demonstrate an important role for QKI in the formation of cardiac mesoderm.

The UCSC Genome Browser Database: update 2006

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .

Volatile Constituents of Artemisia vestita Oil1

The essential oil of ARTEMISIA VESTITA (Compositae) was investigated by GLC, NMR, and mass spectrometry. Main constituents are alpha-, beta-, gamma-himachalene, caryophyllene, germacrene D, himachalol, allohimachalol, alpha-, gamma-atlantone, 1,8-cineole, yomogi alcohol, artemisia, and santolina alcohol and their acetates, and the thujones and thujanols. The characteristic oder of the oil is determined by the freshly smelling, 1, 8-cineole and thujone, and by the woody and sweet note of himachalol and atlantone.

Volatile constituents of Plectranthus rugosus leaf oil

The essential oil of Plectranthus rugosus (Labiatae) was investigated by GLC, NMR and mass spectrometry. Main constituents are caryophyllene, germacrene D, alpha-phellandrene, alpha-pinene, caryophyllene oxide, alpha-cadinol, delta-cadinene, limonene, beta-phellandrene, myrcene, and p-cymene.