Science Caturday: One Code, Two Code…

Like a DNA nucleotide, this LOLcat is capable of playing multiple roles. It is good for creation vs. evolution, and so much more. Global warming vs. something else? You are covered. Homeopathy vs. physics? Done. Duons vs. the genetic code? In the bag.

Duons vs. the genetic code? What is a duon?

Good question. A duon is a DNA nucleotide that can do two roles. This perhaps makes it a rather lame nucleotide. DNA nucleotides have a lot of potential tasks they can do (eg, help encode an amino acid, be part of a protein binding site, indicate a splice site, etc) as part of their role storing information in our cells. The idea that a nucleotide might be subject to evolutionary pressure from several different tasks simultaneously is nothing new.

There is, as Emily Willingham points out at Forbes, no real “duon” controversy outside the minds of the folks that wrote the press release (and, perhaps, John Stamatoyannopoulos, if the press release quote is accurate, which I suspect it might be based on his advocacy for the ENCODE Consortium’s “junk DNA is functional” boondoggle). These researchers have provided some evidence to support the hypothesis that evolutionarily conserved codon bias (using one codon, of the several possible for an amino acid, in the genetic code more than expected by chance) is due to selection to maintain transcription factor binding sites.

This is not an unreasonable hypothesis, but it is hardly shocking, hardly requires a new term, and is hardly a controversy.

Single cell gene expression linkfest

Gene regulation is an old field, but gene regulation at the single cell level is a whole new ball of wax. Some of us in the lab are trying to get up to speed in this field, and I need to pick out five good papers for consideration.

The place to begin is with this great review, and then work through the references:

Central dogma at the single-molecule level in living cells, Gene-Wei Li and X. Sunney Xie, Nature 475, 308–315 (21 July 2011)

Picking selectively, I ended up with the list below, and unfortunately I need to somehow narrow this down to five… and preferably all five won’t be from Sunney Xie’s group. Any suggestions?

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells, Yuichi Taniguchi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu, Jeremy Hearn, Andrew Emili and X. Sunney Xie, Science 30 July 2010: Vol. 329 no. 5991 pp. 533-538 Continue reading “Single cell gene expression linkfest”

Coming to news stands. . .


Needless to say (but I’m going to anyway), I am pleased as punch that my lab’s most recent offering unto the body of scientific literature (“Analysis of alternative splicing associated with aging and neurodegeneration in the human brain”) was put on the cover of the current issue of Genome Research. In this paper, we investigated the connections between alternative splicing profiles in the aging brain and in brains suffering from neurodegenerative disorders, like Alzheimer’s disease. It is important to note that we were characterizing the alternative splicing differences associated with aging and disease, not identifying splicing changes that cause the diseases or the symptoms. Such questions will require ongoing work, which this study will, hopefully, help guide. Continue reading “Coming to news stands. . .”