Quote of the Week

Attempting to describe the relationship between a gene and its related phenotype is fraught with hazards.

From, X-Linked Traits: A Catalog of Loci in Nonhuman Mammals (1990) by James R. Miller (Cambridge University Press).

Web Wednesday: "Personal" Projects

Perhaps as the Church lab is in the same department as the DRSC, I've gotten used to seeing the letters PGP and thinking "Personal Genome Project" (see this link). So maybe you can understand that a quizzical look crossed my face when I saw "DPGP" and thought "Drosophila Personal Genome Project"? Really? Of course, it turns out the DPGP stands for Drosophila Population Genomics Project. But the goals are not so entirely unrelated. At least part of the DPGP plan is to sequence 50 different D. melanogaster genomes, towards understanding more about variation in a population. Visit the site to learn about the project and its goals.

Breaking Report: the modENCODE Project

Genome sequencing is one thing; understanding the sequence data is quite another. In Celniker et al. (2009) Unlocking the secrets of the genome. Nature 459: 927-930, the authors describe the NHGRI-funded modENCODE project to improve annotation of the C. elegans and Drosophila genomes. The expectation is that the data and resources generated in the consortium project will have far-reaching effects. Community input is actively sought for specific sub-projects.

Meeting Announcement: RNAi Europe

Abstract deadline for posters is Aug. 7th for the upcoming fall RNAi Europe meeting to be held in Berlin, Germany by Select Biosciences.

Breaking Report: Wnt Signaling

What's on my desk to read today? Kategaya et al. (2009) Bili Inhibits Wnt/β-Catenin Signaling by Regulating the Recruitment of Axin to LRP6. Free full text from Plos One.

Protocol Notes: Screened Clone 8 Cells (described in DasGupta R, Kaykas A, Moon RT, Perrimon N. Functional genomic analysis of the Wnt-wingless signaling pathway. Science. 2005 May 6;308(5723):826-33). Factors in defining what hits to follow up on included a look at potential off-target effects and comparison to hits identified in previous screen (the authors report that Bili was a weak or non-hit in screens in the DRSC database, suggesting specificity to the Wnt pathway). Follow-up tests included over-expression of Bili in Drosophila S2R+ and Clone 8 cells; test of shRNA directed against Bili in Drosophila embryos; tests in Zebrafish (with morpholinos); and tests in human cells (with siRNAs).

[Drawing above, very rough interpretation of part of their Figure 2.]

Quote of the Week: Independence Day

Independent assortment the random distribution of the gametes of genes located on different chromosomes. Thus, and individual of genotype Aa Bb will produce equal numbers of four types of gametes: AB, Ab, aB, and ab. See Mendel's laws.

Independent probabilities in a group of events, the occurrence of any one event having no influence on the probability of any other event. For example, the orientation of one pair of homologous chromosomes on the first meiotic metaphase plate does not influence the orientation of any other pair of homologs. See independent assortment.

From, A Dictionary of Genetics (6th Edition), R.C. King & W. D. Stansfield (2002: Oxford University Press, Inc., New York, NY).

Web Wednesday: RNAiCut

Today's Web Wednesday feature is the RNAiCut on-line tool, which--roughly speaking--lets you use available information (such as protein-protein interaction data) to 'clean up' a list of hits from a primary screen. 

See also the publication from Kaplow et al. (2009) RNAiCut: automated detection of significant genes from functional genomic screens in Nature Methods. PubMed ID 19564846.