The week began with a constructive meeting with Directors and representatives of our Institutes to discuss further the mechanistic detail of how the scientific and other activities of our Institutes will best be assessed as the next phase of funding is rolled out.
One of the topics that is a source of concern for the research enterprise is based on the changing computational needs of the biological community, and the increasing significance of storage and bandwidth relative to the traditional focus on floating point operations per second. Getting this e-infrastructure right is a key requirement for the future, and several ongoing reviews are seeking to address this.
One part of the e-infrastructure landscape is the UK’s contribution to the ELIXIR (European infrastructure for biological information) project, where much of the UK activity is focussed on the EBI. A capital bid is working its way through the system, led by us, and I had a very interesting meeting with the purposely independent but very well-informed representatives of the Office of Government Commerce (OGC) Gateway Team to set down why a huge community of researchers needs this new resource urgently.
Earlier in the week, we announced the appointment of Prof Dale Sanders, FRS, as the new Director of the John Innes Centre, with effect from 1 September 2010, and I attended the symposium at the JIC held in memory of his predecessor, the late Prof Chris Lamb CBE, FRS. The talks were uniformly a great mixture of first-rate science and moving and amusing memories of Chris (not least of his penchant for Latin tags and idiosyncratic but potent metaphors). Mike Bevan, who stepped up to the plate with great verve and effect following Chris’ untimely death, will continue as Acting Director.
With three of our Institutes (JIC, IFR and TGAC) on the Norwich Research Park, adjacent to UEA, the Norwich Research Park already houses a large complement of bioscientists who are working together as part of a shared intellectual vision, including a focus on diet, health and the biology of the alimentary canal. A fifth component of this consortium, that I had not previously visited, is the Norwich and Norfolk University Hospital. As well as seeing some truly impressive automated analytical kit for chemical pathology, I was briefed on a number of very exciting programmes that already, and will in the future further, interface effectively with local Institute activity.
Finally I visited TGAC for the first time since its launch last July, to see how things are progressing. Their combination of genomics and bioinformatics power is already ramping up to very significant levels, and a suite and pipeline of bioinformatics software is available. This is making it a lot easier to supplant the traditional ways of assembling genomes, so as to make them amenable to exploiting the shorter reads that are the output of the modern ‘next-generation’ sequencing machines.
Metagenomics (see a recent primer) is likely to provide a significant fraction of TGAC’s activity, and indeed the latest fruits of the Human Microbiome Project were published this week. They show that the human gut houses a gene set 150 times larger than that of the human genome, with many hundreds of prevalent strains in each individual human. The functional contribution of the microbiome to human biology is undoubtedly profound.
I blogged before about hormesis, and how the effects of toxins on cells can differ massively depending on their concentration. Now a very nice study shows how sublethal effects of antibiotics can induce resistance to their bactericidal effects by raising the natural rate of mutation. Indeed, combinations of antibiotics can interact in complex ways. As usual, unravelling these interactions is a problem of Systems Biology.
- Kohanski MA, DePristo MA, Collins JJ: Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol Cell 2010; 37:311-320
- Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010). http://dx.doi.org/10.1038/nature08821
- Wooley JC, Godzik A, Friedberg I (2010): A primer on metagenomics. PLoS Comput Biol; 6:e1000667. Free full text as pdf
- Yeh PJ, Hegreness MJ, Aiden AP, Kishony R: Drug interactions and the evolution of antibiotic resistance. Nat Rev Microbiol 2009; 7:460-466
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