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This Week in Nature: Jun 18, 2009

In advanced online publication, scientists have published work looking at the evolutionary genomics of the swine flu virus. Using phylogenetic analysis, they've found that the virus was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak, they write in the abstract.

Also in early online, Robert Darnell is senior author on a paper that combined high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) and bioinformatic analysis to create miRNA-mRNA interaction maps in mouse brain.

In this week's issue, a feature article reports on the progress of the modENCODE Consortium, or the model organism ENCODE project, which is working "to generate a comprehensive annotation of the functional elements in the C. elegans and D. melanogaster genomes." The project began in 2007, and this article lays out its research methods and goals, the core of which consists of 10 groups who are using high-throughput methods to identify functional elements, they say.

Australian scientists have discovered how malaria parasites export proteins into the cytosol of the host red blood cell. Using proteomic analysis and predictive criteria, they say, they were able to find a complex of proteins that is active in the process. The "translocon of exported proteins," or PTEX, includes heat shock protein 101, a novel protein, PTEX150, and a known parasite protein, exported protein 2, and two other proteins, a new protein PTEX88 and thioredoxin 2.

CHOP's John Maris used a GWAS of CNVs in the childhood cancer neuroblastoma to look for CNVs associated with the disease. After genotyping nearly 1,000 cases and controls in Caucasians, they identified a common CNV at chromosome 1q21.1 associated with neuroblastoma. They also found a new neuroblastoma breakpoint family gene, NBPF23, associated with early tumorigenesis. "This is the first paper to really show that copy number variation – which is just another mechanism of evolution for why you and I are different – can be involved in predisposition of cancer," Maris said in a story at Boston.com.

Memorial Sloan-Kettering Cancer Center's Joan Massagué and team have identified genes that control breast cancer metastasis to the brain. Performing gene expression analysis of cells that can move into the brain in patients with advanced cancer, and then functional analysis, they found that the cyclooxygenase COX2 (also known as PTGS2), the epidermal growth factor receptor ligand HBEGF, and the 2,6-sialyltransferase ST6GALNAC5 were involved.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.