Friday, January 30, 2009

Quote of the Week--We've Made Progress Since?

... if only there were more liaison between the butterfly man, the mosquito man, the Drosophila man, and those interested in other groups.

Harold Oldroyd (1964) The Natural History of Flies. (W.W. Norton & Co. New York) 

Wednesday, January 28, 2009

Course Announcement, Wellcome Trust UK

The Wellcome Trust has announced a course for senior PhD candidates and postdocs entitled Drosophila Genetics and Genomics. Looks like a great learning opportunity, for example if you're considering or starting out a postdoc in a fly lab. Application deadline April 10, 2009.

Tuesday, January 27, 2009

Integrating Data, Prioritizing Genes

What am I reading today?
  Aerts et al. (2009) Integrating computational biology and forward genetics in Drosophila.  

Free full text from PLos Genetics.  
Associated HighFly database and software tools here.

Why am I reading it? Making the most of existing experimental evidence and computational predictions in planning new experiments, analyzing results, and integrating data sets presents interesting challenges. The authors describe a means of prioritizing genes via integrated data, and the application of the tool to predict--and then directly test using a genetic approach--genes predicted to interact with atonal.

Friday, January 23, 2009

Quote of the Week: Genes Defined

It is doubtful if we shall ever see the gene, but ... we really do not need to see it. By its work we know it.

L.C. Dunn (1932) Heredity and Variation.

Thursday, January 22, 2009

RNAi Methods Round-Up at CSH Protocols Blog

A recent blog post at Bench Marks, RNAi methods updated, provides a summary of recent publications from Cold Spring Harbor Protocols on the topic. Updated protocols include dsRNA injection into avian embryos and mouse oocytes--and more!

Tuesday, January 20, 2009

Historic Day

Impossible to ignore the U.S. political scene today. One of the things people have been abuzz about is how Obama's presidency might affect the NIH budget. Related reporting from Science here and at BBC news here. And a Google News search can point you to much, much more.

Friday, January 16, 2009

Quote of the Week: Perspective

It is no easy matter to acquire a laboratory in the open fields, when harassed by a terrible anxiety about one's daily bread.
J.H. Fabre, The Life of the Fly (1915) 
Dodd Mead & Co. New York 
Translated by A.T. De Mattos

Thursday, January 15, 2009

Big Picture

Reading today? A review article:  Lord, Martin & Ashworth (2009) RNAi interference screening demystified. J. Clin. Pathol. PubMed ID 19126568.

Why? I find myself on a fairly regular basis having to explain, to people with very different levels of understanding of relevant topics, what RNAi screening is and what it's good for. Seeing how other people explain it--in text and figures--is a help. 

And I have to admit, "demystified" caught my eye.  (The JCP editors must have realized the word is attention-getting--a "demystified" article series appears to be a regular feature of the journal.)

The first section of the article, RNA Interference (RNAi)--what, how and why? is among the most clear and concise summaries of RNAi screening I've read. Understandably, some of the in-depth bits they focus on (for example, the idea that optimization of transfection or transduction is of primary concern during assay development) are not necessarily what one would suggest for Drosophila RNAi screens. But if you're new to understanding the field, as a basic intro to RNAi screening in general, and in mammalian cells more specifically, this would be a fine place to start.

Note:  Reviews on RNAi, and high-throughput cell-based RNAi screening more specifically, abound!  Here are just a few more places to start if you're interested to read more.
Wolters & MacKeigan (2008) From sequence to function: using RNAi to elucidate mechanisms of human disease. Cell Death Differ. 15(5):809-19.
Echererri & Perrimon (2006) High-throughput RNAi screening in cultured cells: a user's guide. Nat. Rev. Genet. 7(5):373-84.
Mittal (2004) Improving the efficiency of RNA interference in mammals. Nat. Rev. Genet. 5(5):355-65.

Wednesday, January 14, 2009

Web Wednesday--NAR's Annual Database Issue

The annual Database Issue from Nucleic Acids Research is now available on-line. Free full text.

RNA biology in general seems to be prominent this year--several tools and databases dedicated to miRNAs, tRNAs and so on.

In terms of things relevant to Drosophila and/or cell-based RNAi screens, a number of things jumped out on an admittedly quick glance:

siRecords, which is cataloging effectiveness of specific siRNAs and displays them with a kind of 'heat bar' slightly reminiscence of Amazon's five-star customer ratings system. Mammalian focus. Example IDs NM_032147, NM_023662, and NM_204702. Read the NAR paper here.

FlyBase, which uses this year's issue to focus on their efforts to improve the quality of GO annotation data. Read the NAR paper here.

PIG, the Pathogen Interaction Gateway, which catalogs interactions between pathogen and host proteins. I expect this information may be useful for follow-up of the several completed, ongoing and planned screens for host-pathogen interactions done at the DRSC. Read the NAR paper here.

Cell Line Data Base or HyperCLDB, which has molecular and other information about human cell lines, and is working to apply a standard nomenclature. May be relevant to mammalian RNAi screens (and has particular relevance to researchers in Europe). Read the NAR paper here.

And as usual there are a fair share of awkward acronyms and crazy names to entertain us. My favorite for the "Yuck!" factor (although of course I recognize the scientific value) is Sys-BodyFluid (NAR paper here). And my pick for "Really?" is SysPIMP (NAR paper here) where "pimp" is for Systematic Platform for Identifying Mutated Proteins.

Monday, January 12, 2009

Breaking News--NIH requests info about Core Facilities

If you're at an NIH core facility--make use of one or more--you might be interested to respond to a recent Request for Information by the NIH.

Friday, January 9, 2009

Quote of the Week: Insect Wonders

The student of [insects] finds beauty not only in the brilliant hues of a butterfly's wing or the metallic sheen of a beetle's elytron, but also in the wonderfully adapted form of those minute organs and structures which subserve the needs of life; graceful feathered feelers that are the seat of delicate sense-organs, claws and pads on feet that ensure firm hold in walking -- all might well be acclaimed as "miracles of design." 

The Biology of Insects, George H. Carpenter, D. Sc. (1928, MacMillan & Co. New York)

Thursday, January 8, 2009

Technical Note--Making New Cell Lines

Reading today? 

Reports from A. Simcox and colleagues that describe a method for jump-starting the process of making fly cell lines:

Efficient Genetic Method for Establishing Drosophila Cell Lines Unlocks the Potential to Create Lines of Specific Genotypes (Open Access from PLoS Genetics; Figure 6 of the paper is shown here.)

Drosophila embryonic ‘fibroblasts’: Extending mutant analysis in vitro (Fly 2008, 15(2)6; PubMed ID 19077546).

The work could prove important for future screens, as it opens up new possibilities.

The authors suggest that using the approach they describe, cell lines could readily be made from a strain carrying a (non cell-lethal) marker or mutation of interest. Notably, the cells they generated and tested were transfectable and susceptible to RNAi.

Wednesday, January 7, 2009

Web Wednesday

There seems to be a mushrooming of websites or pages that are focused on various specific subject areas. 

I guess the idea is that with so much literature out there, we need someone to compile and organize it for us.

Today's Web Wednesday points out just one of these with an RNAi focus, Nature's RNAi Gateway. The site provides topic-based views of papers that have appeared in Nature, Nature Genetics or other journals under the Nature Publishing umbrella. 

In terms of Drosophila RNAi-related reports, they're likely to show up in the Arthropods section in terms of groupings by organism. One can also browse by subject area, and subjects include RNAi screens and technologies. And at the bottom of the home page you can opt to subscribe to an RSS feed.

Something in all this is reminding me of a conversation I had with a professor while I was in graduate school. I saw him in the library, holding open a copy of a journal. "Are you going to Xerox that?" I asked. "No," he said. "I'm going to neurox it.  You know, actually read it."

I've kept that conversation in my head a lot of years now. Because many times I've needed the reminder: all the copying and organizing in the world does not substitute for taking in the information itself.

Tuesday, January 6, 2009

New Protocol Chapter

Dasgupta & Gonsalves focus on Drosophila RNAi screening as a means to studying signal transduction in their chapter: High-Throughput RNAi Screen in Drosophila

From the abstract: 
This chapter discusses the application, advantages, and limitations of [high-throughput Drosophila RNAi screening] in the identification of novel modulators of cell-signaling pathways as well as its future scope and utility in designing more efficient genome-scale screens.

Appearing in the Methods in Molecular Biology series book Wnt Signaling (Humana Press). The article's PubMed ID is 19109710.

Monday, January 5, 2009

What I'm Reading Today

Like everyone else:  the backlog of emails accumulated during the winter break. Happy new year to all. Useful (or at least intended so) information will resume here tomorrow!