Tag: biochemistry

  • Carbon, metabolism and management

    Uncategorized | Douglas Kell

    Since I had almost no external visits in last week’s Bank Holiday-truncated schedule – although I did have one of my regular 1:1 meetings with Sir Mark Walport of the Wellcome Trust – I shall ruminate a little on the relationships between biochemistry and management. This is partly, of course, because both involve an understanding of systems and how they adapt to external inputs, a rather nice example from this perspective (IMHO) being an analysis that I have just co-authored. As I have remarked before, biological systems have tended to select for robustness over immediate efficiency; one way that this can achieved is via a substantial elasticity of individual biochemical steps to changes in inputs. In the study cited, we looked at the rather extensive changes in gene expression and metabolism consequent upon a pulsed change in nutrient status. Some, such as changes in inosine metabolism, were rather striking and not necessarily expected, which is why it is best not to start with hypotheses for this kind of experiment. [...]

  • Cheminformatics, e-science and agroecology

    Uncategorized | Douglas Kell

    My first and very interesting appointment of last week was to attend and speak at a wonderful symposium – Visions of a (Semantic) Molecular Future – held in Cambridge to celebrate the visionary activities of Peter Murray-Rust. Peter long ago recognized the power of computers in helping us to attack complex biochemical problems in drug discovery, and therefore started developing e-science long before it became known as such. The symposium was streamed and will be available online in due time, though since it was tweeted pretty effectively, it is easy to get a feel for events by following the hashtag #pmrsymp. Inspection of the programme suggests that this is probably the first occasion in which both the Chair and Chief Executive of BBSRC have given scientific talks at the same symposium! My own talk focused on the use of semantic technologies to describe biochemical networks in a principled manner, and how such knowledge could assist our understanding of how pharmaceutical drugs get into cells and how this can explain the very clear drug-metabolite similarities that exist. [...]

  • Chemical biology, biocatalysis, industrial biotechnology, Cheltenham, farming and PhDs

    Uncategorized | Douglas Kell

    I have remarked before that events or intellectual activities often seem to cluster, and last week was no exception, with bio-chemistry (purposely hyphenated) and industrial biotechnology probably being the main themes. Chemical biology is an important part of our activities (witness for instance the Selective Chemical Intervention in Biological Systems initiative), and last week we ran (with MRC and EPSRC) an event (with many industry speakers as well as those from academia) to explore the relevant research agenda and how it might best be addressed. Clearly Industrial Biotechnology is mainly about making molecules (chemistry), and depending upon the complexity of the activities required involves finding and improving biocatalysts and (for whole cells) optimising the organisms and pathways in which they are embedded. To this end, I also attended a separate but intellectually related event (PDF) on the interface between Biocatalysis and Industrial Biotechnology, again with a good mixture of academia and industry. In both cases, it was easy to celebrate the fact that we have some very high-class communities who are able and willing to take forward our Industrial Biotechnology agenda. Not for the first time (PDF) one can recognise that investment in the UK’s excellence in basic biology and biotechnology translates more or less readily into the industries of the future. A number of strands in Biofuels have been based on producing oil or oil substitutes for the future, but comparatively few have as yet been based on using (or engineering) microbes to remove it, as in the necessary clean-up of the Deepwater Horizon oil spill in the Gulf of Mexico. Given that natural microbial activities removed at least the lighter fractions of crude oil much more quickly than was anticipated following previous disasters of this type (e.g. Exxon Valdez, Torrey Canyon), this would seem an important programme worth pursuing with urgency. [...]