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.

Breaking Report: Apoptosis

Also on my desk today? Chew et al. (2009) Genome-wide silencing in Drosophila captures conserved apoptotic effectors. Nature. Primary screen in triplicate with S2R+ cells and Ambion library. Follow-up included time-lapse microscopy and siRNA in human cells.

Breaking Report: RNAi Rescue

What's on my desk today? Schulz et al. (2009) A novel method for tissue-specific RNAi rescue in Drosophila. Nucleic Acids Research. Free on-line access. The authors make use of the degeneracy of the genetic code to create rescue constructs that evade RNAi knockdown in cells or whole animals.

Breaking Report: Transgenic RNAi Flies for Neurogenetics

What's on my desk today? A report from our sister group, the Transgenic RNAi Project (TRiP), which has been funded by HHMI and NIH to produce a large-scale collection of flies for in vivo RNAi.

Ni et al. (2009) A Drosophila Resource of Transgenic RNAi Lines for Neurogenetics. Genetics. PubMed ID 19487563.

Related Links:

TRiP web pages

TRiP toolbox at Bloomington

TRiP flies at Bloomington

VDRC

'Omics & the Wnt Pathway

What's on my desk today? A pair of research reports and an accompanying opinion piece published last fall (November 2008) from R. Moon's lab. The opinion piece emphasizes the power of integrating results obtained via multiple high-throughput strategies. The research reports present examples of these types of integrated studies, with a focus on Wnt/beta-Catenin signaling.

Major et al. (2008) New regulators of Wnt/beta-Catenin signaling revealed by integrative molecular screening. Science Signaling 1:ra12.

James et al. (2008) Bruton's Tyrosine Kinase revealed as a negative regulator of Wnt-beta-Catenin signaling. Science Signaling 2:ra25.

Major & Moon (2008) "Omic" risk assessment. Science Signaling 2:eg7.

Boola Boola

About a year ago, James Rothman and Lars Branden from Yale visited the DRSC. As part of a larger tour they took of similar centers. As planned, they have now opened the doors to the Yale Center for High Throughput Cell Biology. Best wishes for success!

Cell Cyle & Fly RNAi: Methods

Two new methods papers relevant to fly RNAi are out in volume 545 of the Methods in Molecular Biology series from Humana Press (2009). Bettencourt-Dias & Goshima, RNAi in Drosophila S2 cells as a tool for studying cell cycle progression. And Pereira et al. Dissecting mitosis with laser microsurgery and RNAi in Drosophila cells.

Alas, my computer connection conspires to prevent me from taking a look at these this morning. But based on the titles alone, look like they could be of interest to those of you planning Drosophila (or other) RNAi screens that will use a plate-reader, FACS or imaging to address a cell cycle-related question.

Related Links: A few of the sub-categories we list on the DRSC's Completed Screens, By Topic publications list report the results of RNAi screens aimed at learning about cell death, division and related topics.