SAB Miller / University of Nottingham MRes

We have received good news that brewing company SAB Miller, together with the University of Nottingham, have agreed to fully fund a one year full time Masters by Research (MRes) into mathematical / computational analysis of phenotype data for brewers’ yeast, to be supervised by myself and Professor Katherine Smart. We will be able to offer a funded place – including all fees and a full stipend – to a home or EU student (applicants from outside the EU will need to make up difference in fees) – to start either during the summer or the next academic year. Further details will follow.


Our Japanese colleagues

We are glad to hear that all of our Japanese collaborators at the Nara Institute of Science and Technology and the University of Osaka are safe and that their families are safe. Which is not to diminish the tragedy, and our thoughts and best wishes go out to all the people of Japan.


Scientific Art – Metal E. coli

Not really work from the lab: one for fun! I spent the weekend at a metal bug making workshop in West Dean College under the superb tutelage of Mike Savage: a very generous wedding present from a friend. I made an E. coli, which raised a few eyebrows among the fellow students! The E. coli is made of copper, aluminium and steel.


The “body” is made of several plates – these represent the mosaic nature of the E. coli genome. Most of the plates are copper, with an aluminium plate representing horizontal gene transfer. There are pili and a flagellum made of steel, and the rivets represent membrane proteins: receptors, channels etc. I also like the idea that most of the bug is made of copper – essential for E. coli in small quantities, with antimicrobial effect in higher quantities. Does this bug have resistance genes?




New publication – Springer book chapter

I received today from John Herbert the pdf of our newly published book chapter:

Herbert, J.M.J., Stekel, D.J., Mura, M., Sychev, M. and Bicknell, R. 2011. Bioinformatic methods for finding differentially expressed genes in cDNA libraries, applied to the identification of tumour vascular targets. In Lu, C. et al., cDNA libraries: Methods and Applications, Methods in Molecular Biology 729. Springer.

The abstract of the chapter is:

The aim of this method is to guide a bench scientist to maximise cDNA library analyses to predict biologically relevant genes to pursue in the laboratory. Many groups have successfully utilised cDNA libraries to discover novel and/or differentially expressed genes in pathologies of interest. This is despite the high cost of cDNA library production using the Sanger method of sequencing, which produces modest numbers of expressed sequences compared to the total transcriptome. Both public and propriety cDNA libraries can be utilised in this way, and combining biologically relevant data can reveal biologically interesting genes. Pivotal to the quality of target identification are the selection of biologically relevant libraries, the accuracy of Expressed Sequence Tag to gene assignment, and the statistics used. The key steps, methods, and tools used to this end will be described using vascular targeting as an example. With the advent of next-generation sequencing, these or similar methods can be applied to find novel genes with this new source of data.