Sunday, September 7, 2014

UAS system combined with CRISPR-Cas9 in Drosophila

Zhaoyu Xue, Menghua Wu, Kejia Wen, Menda Ren, Li Long, Xuedi Zhang and Guanjun Gao. CRISPR/Cas9 Mediates Efficient Conditional Mutagenesis in Drosophila. G3. Available as early online content.

From the abstract:  "... tissue-specific expression of Cas9 driven by the Gal4/upstream activating site (UAS) system with various ubiquitously expressed gRNA transgenes to effectively inactivate gene expression in a temporally and spatially controlled manner. ... by including multiple gRNAs in a transgenic vector to target a single gene, we achieved a high degree of gene mutagenesis in specific tissues. ..."

Thursday, September 4, 2014

Genome editing--design tools

On my desk to read today--another paper related to CRISPRs.

Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W401-7. PMID: 24861617.

This report describes the ChopChop suite of tools, which includes support for Drosophila sgRNA design.

The DRSC offers our CRISPR2 sgRNA design tool, which provides a genome-browse view and includes efficiency scores (or you can run any designs through a 'calculator').

Additional tools are listed at AddGene.

The DRSC offers support for sgRNA and donor construct building through the Genome Engineering Production Group.

Wednesday, September 3, 2014

RNAi screening in fly cells to investigate Brucella infection

Pandey A, Ding SL, Ficht TA, de Figueiredo P. siRNA Screens Using Drosophila Cells to Identify Host Factors Required for Infection. Methods Mol Biol. 2014;1197:229-44. PMID: 25172284.

Tuesday, August 26, 2014

Fly CRISPR -- fluorescent tag and RMCE approach

Learned about this pre-print online from the Insect Genetic Technologies Research Coordination Network (see "technology tips" section).

Describes use of fluorescent tagging to more efficiently identify successful knock-ins, then RMCE to change the knocked-in cassette.

Xu Zhang, Wouter Koolhaas, Frank Schnorrer. A versatile two-step CRISPR- and RMCE-based strategy for efficient genome engineering in Drosophila. doi: http://dx.doi.org/10.1101/007864

Pre-print is available online:
http://biorxiv.org/content/early/2014/08/11/007864

Friday, August 22, 2014

Anti-Cas9 antibody

If an anti-Cas9 antibody would be useful to your CRISPR-related projects--at least one company now reports availability of an anti-Cas9 monoclonal.

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.