Quote of the Week: Comparing Screen and Array Datasets

Cells respond to stimuli by changes in various processes, including signaling pathways and gene expression. Efforts to identify components of these responses increasingly depend on mRNA profiling and genetic library screens. By comparing the results of these two assays [in yeast] across various stimuli, we found that genetic screens tend to identify response regulators, whereas mRNA profiling frequently detects metabolic responses.

Yeger-Lotem et al. (2009) Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nature Genetics. 41(3):316-323. PubMed ID: 19234470.

A Look at the DRSC: Main Lab

Breaking Paper--Control of Cell Size

On my desk today? Sims et al. (2009) PDGF/VEGF signalling controls cell size in Drosophila. Genome Biology. PubMed ID 19216764.  As of this posting, abstract viewable on-line and free full text downloadable as provisional PDF.

The paper focuses on cell size-related results from a genome-wide screen performed at the DRSC (see also Boutros et al. 2004 Science 303:832-835). 

Protocol Notes:  Screen done with S2R+ cells. Image data were put through an automated image analysis to determine average cell size (total monolayer cell area divided by the number of DAPI-positive nuclei counts). With by-eye follow up to check for phenotypes like cell adhesion effects that were not of interest for this study but might also score as positives. Network analysis using FLIGHT. Hit validation using two independent amplicons and a related but different image-based analysis.

Quote of the Week--Act III, Scene 2

Poor harmless fly,

That with his pretty buzzing melody

Came here to make us merry!

William Shakespeare, Titus Andronicus

Web Wednesday--50th ADRC Abstracts On-Line

Today's web feature is the Abstract Planner, now on-line in advance of the upcoming 50th Annual Drosophila Research Conference in Chicago, IL, USA.  Search away!  And remember, in an effort to go green, this year's conference booklets will not have full abstracts.

Breaking Report--Ecdysone & Death

On my desktop today?  

A report from Chittaranjan et al. (2009) Steroid Hormone Control of Cell Death and Cell Survival: Molecular Insights Using RNAi. Free online access from PLoS Genetics. (Figure show is from this report.)

Like the report from Rogers et al. that I blogged about in a previous post (Little Screens, Big Results), these authors focused their screen on a set of candidate genes. In this case, a set of 460 candidates. To do this, the authors generated dsRNAs for each candidate and followed up with a second dsRNA for screen hits.

Chitteranjan et al. performed what is essentially two screens. One focused on identification of pro-death and pro-surivival factors. And the other on "death related effects" dependent upon or independent of ecdysone treatment.

Protocol notes:  Their screen was done on ecdysone-treated l(2)mbn cells. Death and survival monitored with what I think of as an old-school (but reliable) approach, a trypan blue exclusion assay. And they took a closer look at cell death with DAPI staining and TUNEL analysis.

Some thoughts:  Reading another report like this focused on a defined set of candidate genes has me excited for something the DRSC has just begun to offer:  synthesis of custom sets of dsRNAs in 96-well format (based on existing amplicons).  

This made sense as (1) we're expert at doing IVTs at high-throughput, including quality analysis and troubleshooting, and have ready access to our collections of PCR amplicons used as templates for the dsRNA. And (2) the increasing interest in the community to screen a custom-curated sets of genes.  

We just successfully completed a pilot project and given the right lead-time, can now accommodate more requests. 

Please contact me if you're interested to learn more about the service. 

Quote of the Week--Looking Forward

Today's quote comes from a recent News & Views on two papers that describe multiple, simultaneous disruption of gene functions. We here at the DRSC are seeing an increase in the number of studies that combine multiple high-throughput approaches and/or disruption under multiple contexts, working towards understanding networks at a systems level.

The authors conclude in their review of the work that:

The analysis of multiple mutants and multiply perturbed cells provides crucial information for reconstructing the ‘wiring diagram’ of the cell.

Quote from:  Giaever & Nislow (2009) Knocking sense into regulatory pathways. Nature Biotechnology 27(2):149-150.

Papers discussed in this News & Views:

Bakal, C. et al.  (2008) Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science 322, 453–456.  Featuring work performed at the DRSC.

Capaldi, A.P. et al. (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet. 40, 1300–1306.