Thursday, January 29, 2015

CRISPR-based gene photoactivation system

Nihongaki Y, Yamamoto S, Kawano F, Suzuki H, Sato M. CRISPR-Cas9-based Photoactivatable Transcription System. Chem Biol. 2015 Jan 20. pii: S1074-5521(14)00459-1. PMID: 25619936.

From the abstract: "... Here we created a light-inducible, user-defined, endogenous gene activation system based on CRISPR-Cas9. ... this ... system can allow rapid and reversible targeted gene activation by light."

Friday, January 9, 2015

Over-expression of transcription factors--resource and screen paper from Deplancke lab

Early online at Genome Research:  A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Claus Schertel, Monica Albarca, Claudia Rockel-Bauer, Nicholas W Kelley, Johannes Bischof, Korneel Hens, Erik van Nimwegen, Konrad Basler and Bart Deplancke. 2015.

From the abstract: "... We generated 596 site-directed transgenic Drosophila lines that contain integrations of individual UAS-TF constructs to facilitate spatio-temporally controlled misexpression in vivo. All transgenes were expressed in the developing wing and two thirds induced specific phenotypic defects. In vivo knock-down of the same genes yielded a phenotype for 50%, with both methods indicating a great potential for misexpression to characterize novel functions in wing growth, patterning and development. Thus, our UAS-TF library provides an important addition to the genetic toolbox of Drosophila research ..."

Thursday, January 8, 2015

SignedPPI included in list of "Signaling Breakthroughs of the Year"

How cool is this? SignedPPI, which was developed by the Perrimon lab and DRSC, made it onto the Signaling Breakthroughs of the Year list at Science Signaling!

Here's the paper that describes SignedPPI (free in PubMed Central): Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, Samsonova AA, Neumüller RA, Mohr SE, Perrimon N. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods. 2014 Jan;11(1):94-9. PMID: 24240319; PMCID: PMC3877743.

NIH funding announcement--basic research in neuroscience

NIH FOA PAS-15-029 is specifically slated for basic research R01 applications and thus, might be of special interest to some of you. NINDS, NIA, NIDA and NIMH are participating. 

From the Purpose Statement:  "The goal of this Funding Opportunity Announcement (FOA) is to stimulate research addressing fundamental questions in basic neuroscience. Proposed projects can address any area of neuroscience within the missions of the participating institutes and should focus on understanding the structure and/or function of the normal nervous system."

Tuesday, January 6, 2015

Sorting by size--with automation

In the "posting this because it looks cool" department:  
The FlyCatwalk: A High Throughput Feature-Based Sorting System for Artificial Selection in Drosophila. Vasco Medici, Sibylle Chantal Vonesch, Steven N. Fry, and Ernst Hafen G3 early online January 2, 2015, doi:10.1534/g3.114.013664 http://www.g3journal.org/content/early/2015/01/02/g3.114.013664.abstract

Fig. 1 includes a photo of their device, "a fully automated, high throughput system to sort live fruit flies ... based on morphometric traits."

Monday, December 15, 2014

Thinking ahead--What could custom CRISPR engineered cell lines do for your research?

Open call to the Drosophila research community from the DRSC:

Since it was founded in 2003 by Prof. N. Perrimon, the Drosophila RNAi Screening Center (DRSC) has served as a technology transfer center, helping the Drosophila community-at-large gain access to leading-edge technologies such as genome-wide RNAi.

As readers of this blog are likely aware, we have been working to support technology transfer in many areas additional to RNAi, including in the area of CRISPR-Cas9 engineering. For example, we developed and made freely available a database of short guide RNAs, accompanying genome browser-based online user interface, and sgRNA efficiency prediction tool to help support sgRNA selection for CRISPR-Cas9 engineering in flies (see www.flyrnai.org/crispr2).

The DRSC will apply early next year (end of February 2015) for renewal of our NIH R01 grant funding, which makes it possible for us to provide all we do to the community.

One of the things we are beginning to do with community members, and would like to propose to expand and continue in the next funding cycle, is to build custom CRISPR-Cas9-modified cell lines. These can be of value for a wide range of studies, including but not limited to RNAi screens using custom engineered cells (e.g. knockout mutant cells for sensitized screens, endogenously tagged loci for reporter assays or to screen for disruption of sub-cellular localization).

In short, we need your help!

If custom engineered cells would help your research--i.e. if you can imagine turning to the DRSC to help support making and/or screening of specific custom lines for your research within the next, say, 1-3 years, and particularly if you're a US-based lab, we would appreciate if you'd please get in touch and be willing to write a letter of support for our renewal application. We are of course also interested to hear from folks who are planning to use our library resources for other types of screens in the next few years, and from others who are depending on continuity of online resources and/or research services at the DRSC. Ideas for additional tools or resources are also welcome.

Please contact, or have your PI contact, DRSC Director (and blog author) Dr. Stephanie Mohr.

Wednesday, November 19, 2014

Review and detailed protocols--CRISPR-Cas9 in flies and fly cells

Housden BE, Lin S, Perrimon N. Cas9-based genome editing in Drosophila. Methods Enzymol. 2014;546:415-39. PMID: 25398351.  

From the abstract: "... we first discuss some general design principles for genome engineering experiments in Drosophila and then present detailed protocols for the production of CRISPR reagents and screening strategies to detect successful genome modification events in both tissue culture cells and animals."

Includes helpful tables listing sgRNA design tools, relevant fly stocks and plasmids.