The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl.

The Sol Genomics Network (SGN; http://solgenomics.net/) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. SGN is also an open source software project, continuously developing and improving a complex system for storing, integrating and analyzing data. All code and development work is publicly visible on GitHub (http://github.com). The database architecture combines SGN-specific schemas and the community-developed Chado schema (http://gmod.org/wiki/Chado) for compatibility with other genome databases. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools. Currently, over a hundred community annotators help curate the database. SGN can be accessed at http://solgenomics.net/.

An alternative splice form of Mdm2 induces p53-independent cell growth and tumorigenesis.

The Mdm2 gene is amplified in approximately one-third of human sarcomas and overexpressed in a variety of other human cancers. Mdm2 functions as an oncoprotein, in part, by acting as a negative regulator of the p53 tumor suppressor protein. Multiple spliced forms of Mdm2 transcripts have been observed in human tumors; however, the contribution of these variant transcripts to tumorigenesis is unknown. In this report, we isolate alternative splice forms of Mdm2 transcripts from sarcomas that spontaneously arise in Mdm2-overexpressing mice, including Mdm2-b, the splice form most commonly observed in human cancers. Transduction of Mdm2-b into a variety of cell types reveals that Mdm2-b promotes p53-independent cell growth, inhibits apoptosis, and up-regulates the RelA subunit of NFkappaB. Furthermore, expression of Mdm2-b induces tumor formation in transgenic mice. These results identify a p53-independent role for Mdm2 and determine that an alternate spliced form of Mdm2 can contribute to formation of cancer via a p53-independent mechanism. These findings also provide a rationale for the poorer prognosis of those patients presenting with tumors harboring multiple Mdm2 transcripts.