We briefly mentioned the idea of silent mutation in the lab meeting the other day when we discussed how DNA mutations can cause diseases. In general, a polymorphism in the wobble (3rd) position of the DNA codon often would not change the amino acid sequence. However, that doesn’t mean everything would be the same or the polymorphism would have no effect on the resulting system. It has long been known that there is codon bias, the preference of using particular codons, among different organisms. This may have implications on the fitness of the animals and evolution.
Josh Plotkin’s group at the University of Pennsylvania has recently done a very interesting study on this topic in Science magazine. They synthesized a synthetic library of 154 green fluorescent protein (GFP) with an average of 114 silent mutations between each pair. They found the expressing of these GFPs in E. Coli, as measured by fluorescence of the GFP, can vary as much as 250 fold! Further analyses revealed that this expression difference did not correlate with the codon bias but more to the secondary structures of the RNA.
As it turned out, RNA with more stable secondary structure was harder to be translated into protein and hence a lower expression level. Also, the stability near 5′ start codon explained most of the expression variation, which indicates the rate limiting step of gene expression was primarily translation initiation. They further predicted and experimentally validated GFP variants with rare codon usage, which presumably were more difficult to produce, would be highly expressed if attached with a 5′ sequence with weaker RNA secondary structure. Therefore silent mutations are not that silent after all, it depends on whether you have the right ear to hear.
Reference
Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009 Apr 10;324(5924):255-8.Click here to read [PubMed][Science]
I am proposing an outing later in the summer, and we may ask the 2nd floor people to join in. In fact I have talked to some people about this idea. We can also come to my place for movies from time to time.
I have been thinking that air hockey or table tennis would be fun. I would love to have a Wii around, but we don’t have a convenient projector system in the common room… I believe Liyun’s office would be a great location to put in the new installment.
Filed in lab discussion||Comments Off on What kind of toy should we get?
NEW YORK – The American Civil Liberties Union and the Public Patent Foundation, a not-for-profit organization affiliated with Benjamin N. Cardozo School of Law (PUBPAT), filed a lawsuit today charging that patents on two human genes associated with breast and ovarian cancer stifle research that could lead to cures and limit women’s options regarding their medical care. Mutations along the genes, known as BRCA1 and BRCA2, are responsible for most cases of hereditary breast and ovarian cancers. The lawsuit argues that the patents on these genes are unconstitutional and invalid.
Obviously genes should not be patented and should be deposited into the public domain.
A scientific research paper can start with a viral video on youtube. A while ago a cockatoo called Snowball was shown to dance to music.
Interesting questions were raised by this observation. Did the bird really dance to the music or did it mimic the human action? Dancing is a complex behaviour that requires coordination of auditory and motor responses. It has been predicted that the neural circuity evolved in vocal learning species. Motivated by this video, a group of scientists decide to test this out by observing how Snowball dances, and here is the quick result.
The short answer is Snowball can really dance to the music! The whole study was published in Current Biology.
Now the question is, why do animals and humans can both enjoy music? In other words, what is unique about music that can stimulate the nervous systems of different species the same way? What is the common neuro-architecture that underlies this behavior?
Reference
Patel AD, Iversen JR, Bregman MR, Schulz I. Experimental Evidence for Synchronization to a Musical Beat in a Nonhuman Animal. Curr Biol. 2009 Apr 29. [PubMed][Current Biology]