Damaged? Survive!

What's on my desk to read today?  

A report from Ravi et al. (2009) A Network of Conserved Damage Survival Pathways Revealed by a Genomic RNAi Screen.  Free full text from PLoS Genetics. 

Protocol Notes: KC167 cells; full-genome screen; CellTitreGlow assay for viability as read-out. Screen data obtained at the DRSC.

Presidential Smackdown

The New York Times asks "What has 132 Rooms and Flies?"  And answers: the White House. Video clip also on YouTube.

Web Wednesday: FlyMine 17.0

FlyMine recently released their version 17.0.  View release notes here.

Breaking Reports: Bacterial and Viral Invaders and RNAi

What's on my desk to read today?

Cronin et al. (2009) Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Science. Reports the results of an in vivo screen after infection with the gut pathogen, Serratia marcescens.

Berry et al. (2009) Viral Suppressors of RNA Silencing Hinder Exogenous and Endogenous Small RNA Pathways in Drosophila. Free full text from PLoS One.

Quote of the Week: Mosquiticidal Tendencies

Invariably, advancements are accompanied by the coinage of new terms such as mosquiticidal. It joins a long series of terms including insecticide, nematicide, fungicide, larvicide, adulticide, entomicide, and even homicide, which may be convenient in indicating toxicity to or death of a target. ... The value and appropriateness of such terms remain to be seen. Certainly, in recognition of the current perception of the specificity of these agents [i.e. bacteria that kill mosquitoes or black flies], and their value, they should not be termed biocides.

in Bacterial Control of Mosquitoes & Black Flies, H. de Barjac & D.J. Sutherland, Editors. Rutgers University Press (1990; New Brunswick, NY).

Repeat, Repeat, Repeat

What's on my desk today? A report with advice on the number of replicates necessary to limit false negative and false positive results in RNAi screens--in terms of both the number of negative control wells on each plate and the total number of replicate assay plates to test in primary and secondary screening.

X.D. Zhang & J.F. Heyse (2009) Determination of sample size in genome-scale RNAi screens. Bioinformatics. 25(7):841-844.

First impressions? Their conclusions lead to advice that seems sound, practical and achievable, with different numbers of replicates suggested depending on the experimental goals.

All that and the American Wandering Spider, too

Seeing an announcement for CSHL Press's Emerging Model Organisms: A Laboratory Manual, Volume 1 (link) has made me consider adding a new feature to the blog, "Books I wish I Owned." But would just owning this book be enough? Glancing at the list of emerging models, I am taken by two things. First, I was amused to see Dictyostelium discoideum on the table of contents. PubMed records on Dicty go back as far as the 1930s. Poor Dicty, still "emerging" after all these years! And second, would someone please set up a tank of comb jellies (Ctenophora), a colony of snails (Ilyanassa), or even a small terrarium of moss (Physcomitrella patens) in my office? These sound like fun critters to have around.