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Gee Research Blog

It Pays to Be Different:Evolutionary Distinctiveness and Conservation Priorities

Tue, 15 Jul 2014 13:15:25 +0000

The world is currently experiencing an extinction crisis. A mass extinction on a scale not seen since the dinosaurs. While conservationists work tirelessly to try and protect the World’s biodiversity, it will not be possible to save everything, and it is important to focus conservation efforts intelligently. Evolutionary distinctiveness is a measure of how isolated [...]

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Synthetic Biology and Conservation

Mon, 07 Jul 2014 16:20:18 +0000

Synthetic biology, a hybrid between Engineering and Biology, is an emerging field of research promising to change the way we think about manufacturing, medicine, food production, and even conservation and sustainability. A review paper released this month in Oryx, authored by Dr Kent Redford, Professor William Adams, Dr Rob Carlson, Bertina Ceccarelli and CBER’s Professor [...]

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Measure Twice, Cut Once: Quantifying Biases in Sexual Selection Studies

Wed, 25 Jun 2014 10:44:30 +0000

Bateman’s principles are conceptually quite simple, but form the basis of our understanding of sexual selection across the animal kingdom. First proposed in 1948, Bateman’s three principles posit that sexual selection is more intense in males than in females for three reasons: 1) males show more variability in the number of mates they have (mating [...]

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Technology for Nature?

Mon, 16 Jun 2014 13:23:54 +0000

Many of our greatest technological advances have tended to mark disaster for nature. Cars guzzle fossil fuels and contribute to global warming; industrialised farming practices cause habitat loss and pollution; computers and mobile phones require harmful mining procedures to harvest rare metals. But increasingly, ecologists and conservation biologists are asking whether we can use technology [...]

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Nice Flies Don’t Finish Last: Meiotic Drive and Sexual Selection in Stalk-Eyed Flies

Thu, 12 Jun 2014 15:54:47 +0000

While it might seem as though our genes are all working together for our own good, some of them are actually rather selfish. Scientists have known about ‘selfish genetic elements’ for nearly a century, but research to understand their behaviour and effects is ongoing. Recent research in GEE reveals how sexually selected traits are signalling [...]

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13 May 2013

"Why does selection care about codon usage (or what really determines ribosome velocity)"


Speaker:

Laurence Hurst
(Bath)
Date & Time:
Wednesday, 22 May at 5pm
Venue: Medical Sciences AV Hill Lecture Theatre (map)
Host: Jurg Bahler (51602)


Abstract
Owing to the structure of the genetic code more than one codon can specify the same amino acid.  At first sight natural selection should not care which of the multiple synonymous codons is employed as the translated protein will be the same regardless.  That we see selection on codon usage is thus intruiging.  Understanding why selection cares about codon usage is important for understanding how cells work and, in turn, for understanding how to intelligently engineer transgenes.  I provide evidence that selection cares about codon usage because it minimizes errors: it ensures translation is accurate and, in mammals, it ensures splicing is accurate. It is also commonly assumed that, because common codons match common tRNAs, codon usage must affect ribosomal velocity. Using ribosome protection data I find no evidence that in normal conditions codon usage has any effect on ribosomal velocity.  In retrospect this result makes sense as the original logic was flawed - it considered only tRNA supply, not codon driven tRNA demand.  We expect evolution to drive towards supply:demand equilibrium at which point rare codons specified by rare tRNAs wait as long to be translated as common codons specified by common tRNAs.  More generally, we see little or no evidence for RNA mediated effects on translational velocity (either codon usage or mRNA structure). This leaves the problem of what does actually determine ribosomal velocity.  I show that positively charged amino acids entering into the negatively charged ribosome exit tunnel have a profound effect on ribosome velocity.   This can explain the evolution of the polyA tail.  Methods to improve transgenes are suggested by these results.

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