The beginning of Lent term was far from gentle. For three days I have been sitting in lecture theatres and seminar rooms. Firstly, for a full day we listened to several professors/group leaders of the biochemistry department describing their research. And secondly, we had two days of the so-called Part III symposium, that is a twenty-minute research update from each of the 31 biochemistry M. Sci. students in the department. (Since then I have started working in a lab again and I have to admit I had forgotten how strenuous it can be.)
First things first. The “departmental research day” was hosted at Robinson College, because the lecture theatre within the department is actually too small to seat all the members of staff and students. The introduction was given by Chris Smith and his most interesting point was probably that the department received an Athena SWAN bronze award last year, which “recognises and celebrates good practice in recruiting, retaining and promoting women in Science, Technology, Engineering, Mathematics and Medicine (STEMM) within Higher Education”. So three cheers for the department!
The actual research talks by the various professors ranged from mildly piquing to downright riveting. There were several talks on cancer (the head of the department, Gerard Evan, is a cancer biologist so this is hardly surprising): at one end for example, Helen Mott explained how basic biology, crystallography and peptide chemistry are being exploited to research a new class of drugs based on alpha-helical peptides, which are meant to block activity of some small GTPases (sometimes known as cellular switches because they can turn signalling pathways on and off). At the more clinical end, Kevin Brindle demonstrated how techniques such as dynamic nuclear polarisation magnetic resonance imaging (MRI) are progressing to better image biology/cancer in (live) patients. However, the department is also strong in the field of structural biology, since the crystallographer Tom Blundell used to be the head of the department. Furthermore, there is an increasing number of lab groups working on single-celled eukaryotes such as trypanosomes and Toxoplasma.
Additionally, there were at least two overt political references to keep us on our toes. The first one was this:
And I have to say that I wholeheartedly agree. Perhaps unsurprisingly, the professor who used this image in her slides is originally from the Czech Republic and probably quite vehemently opposes the idea of having an in/out referendum in the UK. [Eukaryotes, by the way, are organisms whose cells contain a nucleus and would include plants, animals and fungi, but also single-celled eukaryotes such as trypanosomes and Toxoplasma.]
The second political reference was a quote by Donald Rumsfeld: “As we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns – the ones we don’t know we don’t know.” He said this in response to questions about Iraq’s involvement in the supply of weapons to terrorist groups. In the context of science this was a comment on the inherent difficulties of modelling biological processes: Steve Oliver uses yeast as a model organism to study metabolic pathways, and in contrast to the qualitative modelling I have been doing, his models are quantitative (i.e. use differential equations and enzyme kinetic data). Interestingly however, both types of model can suffer from similar problems; for example they can be plain wrong, or incomplete, or based on faulty assumptions. And sometimes when we know they are wrong that doesn’t mean we know how to improve them. Not knowing that they are wrong/incomplete (i.e. the unknown unknown) is arguably the most comfortable position to be in.
The following two days were filled with project reports of all the biochemistry M. Sci. students. It is worth noting that several of these talks were possibly more interesting and of better quality than some of those given by the professors. There was an extremely wide variety of topics including: cancer research, developmental biology, disease biology (including the rare lysosomal storage disease called Krabbe disease), in vitro enzyme evolution, structural biology (including taking trips to the x-ray source near Oxford, the Diamond Light Source), stem cell biology and research into the origins of life. This latter research project is investigating how the first RNA molecules may have come together to form larger, catalytic molecules of RNA (“RNA world hypothesis”), and to do this the reactions are carried out at -9ºC in the eutectic phase of water-ice, a condition thought to mimic prebiotic chemistry.
Lastly, what would a blog post be without the mention of CRISPR. At least two of the M. Sci. projects involve the use of this genome-editing technology. In one case it will be used to knock-out a microRNA that may be involved in the regulation of bicoid mRNA during Drosophila (fruit fly) development. And in the other case it is being used to target a transcription factor that is implicated in the regulation of stem cell fate. Interestingly, the strategy here involves using two guide RNAs simultaneously, both targeted to within the gene of interest, with the aim of creating a large deletion rather than just a small insertion/deletion.
Needless to say, the progress of all our projects is far slower than we (and probably our supervisors) would have hoped.