Also on my desk to read today? This report of a targeted double-knockdown screen.
Marinho J, Martins T, Neto M, Casares F, Pereira PS. The nucleolar protein Vito/Nol12 is required for the growth and differentiation progression activities
of the Dpp pathway during Drosophila eye development. Dev Biol. 2013 Feb 14. PubMed PMID: 23416177.
Thursday, March 7, 2013
Fly RNAi pathway and viral defense. Breaking reports.
On my desk to read today? These papers on RNAi as a viral defense.
Sabin LR, Zheng Q, Thekkat P, Yang J, Hannon GJ, Gregory BD, Tudor M, Cherry S. Dicer-2 processes diverse viral RNA species. PLoS One. 2013;8(2):e55458. PMID: 23424633; PMCID: PMC3570552
From the abstract: "This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi."
Goic B, Vodovar N, Mondotte JA, Monot C, Frangeul L, Blanc H, Gausson V, Vera-Otarola J, Cristofari G, Saleh MC. RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila. Nat Immunol. 2013 Feb 24. doi: 10.1038/ni.2542. PubMed PMID: 23435119.
From the abstract: "Our results identify a cooperative function for retrotransposons and antiviral RNAi in the control of lethal acute infection for the establishment of viral persistence."
Sabin LR, Zheng Q, Thekkat P, Yang J, Hannon GJ, Gregory BD, Tudor M, Cherry S. Dicer-2 processes diverse viral RNA species. PLoS One. 2013;8(2):e55458. PMID: 23424633; PMCID: PMC3570552
From the abstract: "This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi."
Goic B, Vodovar N, Mondotte JA, Monot C, Frangeul L, Blanc H, Gausson V, Vera-Otarola J, Cristofari G, Saleh MC. RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila. Nat Immunol. 2013 Feb 24. doi: 10.1038/ni.2542. PubMed PMID: 23435119.
From the abstract: "Our results identify a cooperative function for retrotransposons and antiviral RNAi in the control of lethal acute infection for the establishment of viral persistence."
Wednesday, March 6, 2013
Meeting Announcement--European Drosophila Conference--October 2013
I recently saw this announcement: "The 23rd European Drosophila Research Conference will be held in Barcelona on the 16th-19th October 2013. We encourage all of you to join us in this special event and to share with us all the latest developments in the growing community of Drosophila research.The Congress website, www.edrc2013.org, will be constantly updated to keep you informed about all the latest news regarding the scientific programme."
Monday, March 4, 2013
COMPLEAT complex enrichment tool
The DRSC is pleased to announce that we are making COMPLEAT available in our suite of online software tools.
Conceptually similar to gene set enrichment, COMPLEAT makes it possible to look for enrichment of predicted protein complexes in a large-scale RNAi data set--including those with multiple conditions or time-points. You'll see a graph (left-hand side) and can click do draw a polygon around points on the graph to view those specific complexes (right-hand side).
The online tool web pages include a Demo (narrated video) and a set of Example Files so you can test out the tool and see the data upload format. As always, your feedback is welcome!
Here's the citation and abstract from the paper, as well as a screenshot.
Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N. Protein complex-based analysis framework for high-throughput data sets. Sci Signal. 2013 Feb 26;6(264):rs5. PMID: 23443684
Abstract: Analysis of high-throughput data increasingly relies on pathway annotation and
functional information derived from Gene Ontology. This approach has limitations,
in particular for the analysis of network dynamics over time or under different
experimental conditions, in which modules within a network rather than complete
pathways might respond and change. We report an analysis framework based on
protein complexes, which are at the core of network reorganization. We generated
a protein complex resource for human, Drosophila, and yeast from the literature
and databases of protein-protein interaction networks, with each species having
thousands of complexes. We developed COMPLEAT (http://www.flyrnai.org/compleat),
a tool for data mining and visualization for complex-based analysis of
high-throughput data sets, as well as analysis and integration of heterogeneous
proteomics and gene expression data sets. With COMPLEAT, we identified
dynamically regulated protein complexes among genome-wide RNA interference data
sets that used the abundance of phosphorylated extracellular signal-regulated
kinase in cells stimulated with either insulin or epidermal growth factor as the
output. The analysis predicted that the Brahma complex participated in the
insulin response.
Conceptually similar to gene set enrichment, COMPLEAT makes it possible to look for enrichment of predicted protein complexes in a large-scale RNAi data set--including those with multiple conditions or time-points. You'll see a graph (left-hand side) and can click do draw a polygon around points on the graph to view those specific complexes (right-hand side).
The online tool web pages include a Demo (narrated video) and a set of Example Files so you can test out the tool and see the data upload format. As always, your feedback is welcome!
Here's the citation and abstract from the paper, as well as a screenshot.
Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N. Protein complex-based analysis framework for high-throughput data sets. Sci Signal. 2013 Feb 26;6(264):rs5. PMID: 23443684
Abstract: Analysis of high-throughput data increasingly relies on pathway annotation and
functional information derived from Gene Ontology. This approach has limitations,
in particular for the analysis of network dynamics over time or under different
experimental conditions, in which modules within a network rather than complete
pathways might respond and change. We report an analysis framework based on
protein complexes, which are at the core of network reorganization. We generated
a protein complex resource for human, Drosophila, and yeast from the literature
and databases of protein-protein interaction networks, with each species having
thousands of complexes. We developed COMPLEAT (http://www.flyrnai.org/compleat),
a tool for data mining and visualization for complex-based analysis of
high-throughput data sets, as well as analysis and integration of heterogeneous
proteomics and gene expression data sets. With COMPLEAT, we identified
dynamically regulated protein complexes among genome-wide RNA interference data
sets that used the abundance of phosphorylated extracellular signal-regulated
kinase in cells stimulated with either insulin or epidermal growth factor as the
output. The analysis predicted that the Brahma complex participated in the
insulin response.
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