Because of the Queen’s Jubilee celebrations, the blog had a week off. Among many other meetings was a very useful one with Sir John Beddington, the Government Chief Scientific Adviser, and other Departmental Chief Scientists. These meetings provide excellent fora for developing scientific thinking across Government Departments, and certainly expose me to issues broader than those that I typically contemplate.
We were pleased to note the announcement (amid a welter of bad puns such as ‘tomato genome project bears fruit’, ‘sauce code’, and the like) of the sequences of two tomato genomes. Given the very widespread consumption of tomatoes, and their perceived health benefits, it will be most exciting to see how quickly this knowledge translates into strains with improved traits such as taste, anti-oxidant content, post-harvest longevity, disease resistance, and so on. (Incidentally, growing tomatoes in saline conditions can improve their taste, but not yield, considerably!)
I greatly enjoyed speaking at and attending part of a New Phytologist Workshop on Synthetic Biology, where as well as highlighting BBSRC’s enthusiastic support for the field I was able to rehearse a couple of syn bio studies – on aptamers and on quantitative proteomics – in which I had been involved.
Examples of useful products emerging from the applications of synthetic biology continue apace; an excellent recent example is the production at 40g.L-1 of amorpha-4,11-diene (a precursor of the antimalarial artemisinin) using baker’s yeast.
We had one of our very useful annual meetings with Heads of Department, where I was able to hear a range of views of areas that need development, those that merely need tweaking, and indeed those that are going particularly well.
In the 3 months since acquiring an electronic pedometer, I note that the range between my most and least active days is ca 3.5-fold (~4,000 to ~14,500 steps) – albeit the interquartile range is much narrower as that ignores my occasional air travel. I am not sure whether that range is a lot or a little, but it encourages one to move to the upper end more regularly – which presumably is precisely the point of using a recording pedometer whose results are accessible online. I see ambulatory physiology (and maybe even physiological computing) as an interesting area for doing important kinds of crowd sourcing science in the future.
Other papers I enjoyed reading included one on DNA self assembly (and commentary), a preprint deconstructing further an implausible claim of the chemical role of arsenate in bacterial DNA (implausible given the extreme lability of the phospho-arsenate bond, which is well known to explain why arsenate is a toxic uncoupler…), an important new method for epigeneomic sequencing, an analysis of the physiological benefits of high kcat values, and an analysis – as may happen on biological membranes – of water-mediated proton hopping.
As part of some developing thinking on small molecule promiscuity, not least in the context of cellular drug uptake, I also enjoyed reading a paper (and commentary) about a novel target for salicylate.
Finally, I also enjoyed a splendidly inventive spoof biotechnology website (that clearly fooled a number of newspapers…).
- Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S: Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012; 336:934-937
- Carroll, K. M. et mult al. (2011). Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Mol Cell Proteomics 10, M111 007633
- Eames M, Kortemme T: Cost-benefit tradeoffs in engineered lac operons. Science 2012; 336:911-915
- Hawley SA et mult al. The ancient drug salicylate directly activates AMP-activated protein kinase. Science 2012; 336:918-922
- Johnson HE, Gilbert RJ, Winson MK, Goodacre R, Smith AR, Rowland JJ, Hall MA, Kell DB: Explanatory analysis of the metabolome using genetic programming of simple, interpretable rules. Genetic Progr Evolvable Machines 2000; 1:243-258
- Kell DB: On the functional proton current pathway of electron transport phosphorylation: an electrodic view. Biochim Biophys Acta 1979; 549:55-99
- Kell DB: Metabolites do social networking. Nat Chem Biol 2011; 7:7-8
- Kell DB, Dobson PD, Oliver SG: Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only. Drug Disc Today 2011; 16:704-714
- Knight, C. G., Platt, M., Rowe, W., Wedge, D. C., Khan, F., Day, P., McShea, A., Knowles, J. & Kell, D. B. (2009). Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape. Nucleic Acids Res 37, e6. Full free text
- Merte LR, Peng G, Bechstein R, Rieboldt F, Farberow CA, Grabow LC, Kudernatsch W, Wendt S, Laegsgaard E, Mavrikakis M, Besenbacher F: Water-mediated proton hopping on an iron oxide surface. Science 2012; 336:889-893
- Reaves, M. L., Sinha, S., Rabinowitz, J. D., Kruglyak, L. and Redfield, R.J. (2012) Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Preprint as pdf at ArXiV.org
- Rothemund PWK, Andersen ES: The importance of being modular. Nature 2012; 485:584-585
- Shaw RJ, Cantley LC: Ancient sensor for ancient drug. Science 2012; 336:813-814
- The Tomato Genome Consortium: The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012; 485:635-641. Full free text
- Wei B, Dai M, Yin P: Complex shapes self-assembled from single-stranded DNA tiles. Nature 2012; 485:623-626
- Westfall PJ et mult al.: Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci U S A 2012; 109:E111-118
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