Friday, May 29, 2009

Quote of the Week: Making Friends

In rural sections of the southern United States, many people believe that if one removes a fly from a spider's web he will gain a friend.

from Wonders of the Fly World, Sigmund A. Lane (1970) Dodd, Mead & Co. New York.

Thursday, May 28, 2009

Breaking Reports: Tools for Fly Recombineering

Following up on a Web Wednesday post, the paper from Venken et al. is now out in Nature Methods. Along with another report on fly tools from Ejsmont et al. in the same issue.

Friday, May 22, 2009

Quote of the Week: Beach Colors

The insect-species confined to the sea-coasts, as every collector knows, are often brassy or lurid.
from Charles Darwin's The Origin of Species.

Wednesday, May 20, 2009

Web Wednesday: Image Analysis

Today's Web Wednesday feature, CellProfiler

It's a freely available, open-source software suite for high-throughput image analysis. 

Associated Carpenter et al. (2006) paper at Genome Biology.

Monday, May 18, 2009

Breaking Report: Comparing DRSC Screen Data to PPI Data

What's on my desk today? 

Wang, Tu & Sun (2009) A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics, 10:220.

Why this paper? 

Among other reasons, as it's based on results of 24 screens performed at the DRSC (full citations of these and more here), which the authors downloaded from our openly accessible website and database. It's great to see that our data sharing policies are facilitating this type of work. 

Also, at the DRSC we are interested in computational and experimental approaches that lead to integration of large datasets. It's becoming clear that analysis of integrated results can improve our understanding and interpretation of individual results. Indeed, Wang et al. conclude in their study that integrating the RNAi results with protein-protein interaction data informs the understanding of false positive and false negative results.

Friday, May 15, 2009

Quote of the Week

If genius is the ability to reduce the complicated to the simple, then the study of p53 makes fools of us all.

Voudsden & Prives (2009) in the review, Blinded by the Light: the Growing Complexity of p53. Cell 137(3):413-431

Wednesday, May 13, 2009

Meeting Announcement: Arthropod Genomics

Just saw an announcement for the 3rd Annual Arthropod Genomics Symposium: Frontiers in Arthropod Genomics. Registration & Poster abstract deadline is May 15, 2009. From ticks to aphids, flies to mosquitoes--looks like an interesting line-up.

Tuesday, May 12, 2009

Breaking Report: Tissue-Specific RNA Preps

What am I reading today? A report on tissue-specific isolation of RNA from whole flies. Sounds like a method that could be quite useful as part of in vivo follow-up to cell-based screens.

Miller MR, Robinson KJ, Cleary MD, Doe CQ (2009) TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nat Methods. May 10. PMID: 19430475.

Related post: Report of Single-Cell RNAseq.

Friday, May 8, 2009

Quote of the Week: Diversity in Development

If morphological diversity is all about development, and development results from genetic regulatory programs, then is the evolution of diversity directly related to the evolution of genetic regulatory programs? Simply put, yes. But to understand how diversity evolves, we must first understand the genetic regulatory mechanisms that operate in development. In other words, what is the genetic toolkit of development and how does it operate to build animals?

In, From DNA to Diversity
Carroll, Grenier and Weatherbee (2001, Blackwell Science; p.13).

Thursday, May 7, 2009

Breaking Report: Divisions Gone Wrong

What's on my desk today? A paper on a Drosophila kinase RNAi screen and a very recent report that extends the results to a specific topic in human disease.

Bettencourt-Dias et al. (2004) Genome-wide survey of protein kinases required for cell cycle progression. Nature 432:980-987. At PubMed.

Wang et al. (2009) Association of genetic variation in mitotic kinases with breast cancer risk. Breast Cancer Res. Treat. DOI 10.1007/s10549-009-0404-3. At PubMed.

Related Links:
DRSC Kinase & Phosphatase Sub-Library (on- or off-site screening).
Transgenic RNAi Project (TRiP) stock list (click to expand the current list, download the xls file, open in Excel, and see Column H on the spreadsheet to view which hairpin lines target kinase-encoding genes).

Wednesday, May 6, 2009

Web Wednesday: On-Line Forums for Screen Imaging

For today's Web Wednesday, I'm going to share a link to the newly-created Opera High Content Imaging google group, which was co-founded by a colleague of ours in the HMS Department of Genetics. 

Their stated purpose is "for the users of the Opera platform to exchange tips and tricks when dealing with the Instrument," as well as to exchange Acapella scripts. From the Opera google group page (or this link) you can also get to an on-line group for high-content imaging more generally.

Tuesday, May 5, 2009

Make Way for Ducklings

It's not all research, all the time here at the DRSC. Thanks to all who joined us for spring fun on Friday.

Monday, May 4, 2009

At HMS or Affiliated? Proteomics Nanocourse

An upcoming half-day course on proteomics offered by Harvard Catalyst might be of interest. Check it out if you're in the area. May 18th 1 to 5 pm at the BIDMC. Registration is required.

Friday, May 1, 2009

Quote of the Week: Flu & Flying

What I recommend people [in airplanes] do is turn the overhead air releaser on to a low stream and position it so the flow goes in front of your face. That will increase the ventilation, at minimal, create a turbulence of air in front of your face. If a particle is coming by, that might be enough to push it out of the way.

M. Gendreau, Tufts University & Lahey Clinic
in When Flu Flies (Newsweek) April 27, 2009

Flies & Flu

With today's news on my mind, I searched for "Drosophila" and "flu" today at PubMed and that led me to: Hao et al. (2008) Drosophila RNAi screen indentifies host genes important for influenza virus replication. Nature 454:890-893. Protocol Notes: Screened in D-Mel2 cells with Ambion dsRNAs. Follow-up in mammalian cells using siRNAs.