Last week saw the penultimate of our ‘roadshow’ conversations, held in Glasgow and attracting participants from both Scotland and elsewhere. As ever we had a very useful exchange of thoughts on a wide range of topics, not least about how to streamline the peer review process, where some very helpful suggestions were made. In line with an interesting recent editorial, one question elicited discussion on the extent to which funding should be concentrated on (the typically more tractable) model organisms, a question brought into focus by the comparatively little study devoted to Chalara fraxinea (the cause of ash die-back – here is a link on how to spot it) nor to thousands of other organisms. I won’t claim to have any answers here, but clearly folk may wish to give special thought to justifying the choice of organism in proposals.
I also much enjoyed a visit to the Wellcome Trust Sanger Institute, where, as well as a very useful overview from Director Mike Stratton, and astonishing statistics such as the more than 200 terabases sequenced in 2011 alone, I enjoyed a number of other discussions with a variety of senior staff. I don’t wish to pick out particular highlights, but I am always attracted to novel ‘genome-wide’ techniques being applied to complex biological problems, and four worthy of mention involved an assessment of genomic markers of drug sensitivity, a protein microarray for identifying extracellular protein interactions, an approach to assess the function of every gene in a bacterium simultaneously, and the latest version of a bioinformatics environment for high throughput sequencing data.
I see that the NIH is now to enforce its Open Access policy, and I read an interesting article on how Unilever is using Open Innovation for its sustainability agenda, as well as one on how to make the internet a safer place. An open access paper of ours has been published, discussing the utility of algorithms from evolutionary computing in molecular plant and animal breeding programmes.
I was also very intrigued by the increasing evidence for supercomplex formation in the mitochondrial respiratory chain (no mention yet of ATP synthases). Something to return to as our understanding of organellar proteomics improves.
- Bolker, J. Model organisms: There’s more to life than rats and flies. Nature 2012; 491, 31-33
- Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA: Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012; 28:464-469. Full free text
- Garnett MJ et mult al.: Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012; 483:570-575. Full free text as author ms
- Kell DB: The protonmotive force as an intermediate in electron transport-linked phosphorylation: problems and prospects. Curr Top Cell Reg 1992; 33:279-289. Full free text as ms pdf
- Laurie B, Doctorow C: Secure the internet. Nature 2012; 491:325-326
- Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L, Haase J, Charles I, Maskell DJ, Peters SE, Dougan G, Wain J, Parkhill J, Turner AK: Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome research 2009; 19:2308-2316. Full, free text
- O’Hagan S, Knowles J, Kell DB: Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing. PLoS ONE 2012; 7:e48862. Full free text
- Shoubridge EA: Supersizing the mitochondrial respiratory chain. Cell metabolism 2012; 15:271-272
- Sun Y, Gallagher-Jones M, Barker C, Wright GJ: A benchmarked protein microarray-based platform for the identification of novel low-affinity extracellular protein interactions. Anal Biochem 2012; 424:45-53. Full, free text