Tuesday, August 19, 2014

Integer linear optimization approach to signaling network construction based on protein-protein interaction and RNAi data sets

Ozsoy OE, Can T. A divide and conquer approach for construction of large-scale signaling networks from PPI and RNAi data using linear programming. IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):869-83. PMID: 24334382.

From the abstract: "... In this paper, we propose an integer linear optimization (ILP) model for reconstruction of signaling networks from RNAi data and a reference network. ..."

Related approaches available as online tools at the DRSC include COMPLEAT and SignedPPI

Monday, August 18, 2014

New report--CRISPR-Cas9 nickase system in Drosophila

Ren X, Yang Z, Mao D, Chang Z, Qiao HH, Wang X, Sun J, Hu Q, Cui Y, Liu LP, Ji JY, Xu J, Ni JQ. Performance of the Cas9 Nickase System in Drosophila melanogaster. G3 (Bethesda). 2014 Aug 15. pii: g3.114.013821. PMID: 25128437.

Monday, August 11, 2014

in vivo fly RNAi screen uses live imaging assay

Mauri F, Reichardt I, Mummery-Widmer JL, Yamazaki M, Knoblich JA. The Conserved Discs-large Binding Partner Banderuola Regulates Asymmetric Cell Division in Drosophila. Curr Biol. 2014 Jul 30. pii: S0960-9822(14)00775-1. PMID: 25088559.

Thursday, August 7, 2014

Study explores culture media for Drosophila cells

Burnette M, Brito-Robinson T, Li J, Zartman J. An inverse small molecule screen to design a chemically defined medium supporting long-term growth of Drosophila cell lines. Mol Biosyst. 2014 Aug 6. PMID: 25096480.

From the abstract: "Drosophila cell culture is used as a model system with multiple applications ...  To characterize the minimal requirements for long-term maintenance of Drosophila cell lines, we developed an inverse screening strategy to identify small molecules and synergies stimulating proliferation in a chemically defined medium. ... Validated factors were investigated for their ability to maintain cell growth over multiple passages in the chemically defined medium (CDM). The polyamine spermidine proved to be the critical component that enables the CDM to support long-term maintenance of Cl.8 cells. Spermidine supplementation upregulates DNA synthesis for Cl.8 and S2 cells and increases MAPK signaling for Cl.8 cells. The CDM also supports the long-term growth of Kc167 cells. Our target scoring approach validated the importance of polyamines ... Future iterations of the screen will enable the identification of compound combinations optimized for specific applications ... thus increasing the versatility of Drosophila cell culture as both a genetic and biochemical model system. ..."

Tuesday, August 5, 2014

Planning Gal4-UAS studies in the larval CNS, such as with in vivo RNAi? Report of >6,000 Gal4 lines

Li HH, Kroll JR, Lennox SM, Ogundeyi O, Jeter J, Depasquale G, Truman JW. A GAL4 Driver Resource for Developmental and Behavioral Studies on the Larval CNS of Drosophila. Cell Rep. 2014 Jul 30. pii: S2211-1247(14)00569-5. PMID: 25088417.

Monday, July 28, 2014

Genome-wide, high-content image-based screen preformed at DRSC--identification of regulators of organization of polycomb foci

Gonzalez I, Mateos-Langerak J, Thomas A, Cheutin T, Cavalli G. Identification of regulators of the three-dimensional polycomb organization by a microscopy-based genome-wide RNAi screen. Mol Cell. 2014 May 8;54(3):485-99. PMID: 24703951.  

From the abstract: "... Here, we report the results of a high-resolution microscopy genome-wide RNAi screen that identifies 129 genes that regulate the nuclear organization of Pc foci. Candidate genes include PcG components and chromatin factors, as well as many protein-modifying enzymes, including components of the SUMOylation pathway. ... suggesting that the dynamic regulation of Pc SUMOylation regulates PcG-mediated silencing by modulating the kinetics of Pc binding to chromatin as well as its ability to form Polycomb foci."

Thursday, July 24, 2014

Cell-based assays related to Notch signaling

Xu A, Irvine KD. Notch-ligand binding assays in Drosophila cells. Methods Mol Biol. 2014;1187:277-84. PMID: 25053497.

 Li J, Housden BE, Bray SJ. Notch signaling assays in Drosophila cultured cell lines. Methods Mol Biol. 2014;1187:131-41. PMID: 25053486.