Friday, 27 September 2013

Quoting Donald Rumsfeld

Some of you may remember (perhaps not very fondly) Donald Rumsfeld, former US Secretary of Defense in the administration of George W. Bush. Surprisingly, the title of our latest publication actually quotes Donald Rumsfeld, whose famously said
"There are known knowns; there are things we know that we know.
There are known unknowns; that is to say, there are things that we now know we don't know.
But there are also unknown unknowns – there are things we do not know we don't know."

We've just published a paper in the journal PLoS One entitled Dead End Metabolites- Defining the Known Unknowns of the E. coli Metabolic Network. E. coli is the best model organism for studying bacteria, it is the single bacterium we know the most about after 50-60 years of study, and yet we still don't know what a quarter of it's genes do. In this paper, we use the E. coli metabolic network represented in the EcoCyc database, and try and work out what are the gaps in our knowledge about E. coli metabolism, or as Donald Rumsfeld would put it- what are the known unknowns of E. coli metabolism. Hopefully this list of known unknowns provides researchers targets for future study to enlarge our understanding of E. coli. As for the unknown unknowns, um well I guess we don't know yet.

E. coli is the one with the name tag

Tuesday, 10 September 2013

Transport Protein Workshop

I've gotten back from England, with the addition of about 4 kilos of weight from eating too many full English breakfasts. I'm going to need to need to fire up Dance Central 3 on the Xbox to work off the English sausages, bacon, black pudding, etc.

The last day in Leeds was a membrane transport workshop hosted  by Peter Henderson at the the Astbury Centre for Structural Molecular Biology, University of Leeds. Karl and I both gave talks on our groups work on characterizing multidrug efflux pumps, proteins that sit in the cell membrane, and pump out antibiotics and other drugs making the bacteria resistant.

The workshop dinner was held in the Royal Armoury in Leeds. After all of the tourists had gone home, we were able to stroll around the museum at our leisure, and see their collection of historical military and hunting artifacts, including a magnificent suit of Indian elephant armour. We then had dinner in an imitation English drawing room, whose walls were covered with leather bound books, stuffed animal heads, random weapons and other historic artifacts. A very memorable ending to an entertaining day of scientific presentations.

The Only Surviving Suit of Indian Elephant Armour in the World (dating from ~ 1600)
Here I am at dinner caught by a camera in mid-gesticulation. Also in the photo are Anne-Brit Kolsto and Ole Andreas Oksted from the University of Oslo.