PhD Interview for the Francis Crick Institute!

Despite being funded as a Cancer Research UK charity, the London Research Institute (LRI) went to considerable lengths to ensure that we interviewees were comfortable during our three-day visit to London and the institute. Firstly, our travel expenses – ranging from short intra-England train journeys to flights from across Europe and North America – were covered, as well as our accommodation at a hotel overlooking Russell Square at the heart of Bloomsbury:

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The first day was probably the most strenuous. First we listened to introductory talks given by the LRI Academic Director and the LRI’s Deputy Director who, incidentally, also quoted Donald Rumsfeld about the unknown unknowns just like at the departmental research day. Furthermore, as part of my destressing strategy I took a walk around the area during one of the breaks, inevitably stumbled into a bookshop and found this:

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The rest of the first day was filled by talks given by each of the recruiting group leaders. Eighteen times ten minutes of concentration. After that we got the chance to speak to those principal investigators (PIs) we were interested in. Lastly, we had dinner with the PIs and some of their students. And although all of this was not part of the “official” assessment procedure I think it was important to be making a good impression throughout, and therefore by the end of this first day most of us felt exhausted.

The official panel interviews were scheduled for the second day. We each had to give a presentation of a research project we were involved in, as well as a critique of a research paper. We were then asked some questions on these presentations and also had the usual questions hurtled at us, “Why do you want to do a PhD? Why do you want to do it at the LRI? What are your long-term goals?” Etc.

We were also privy to a tour of the LRI building at Lincoln’s Inn Fields. During the introductory talks they emphasised how great the facilities – DNA sequencing, flow cytometry and microscopy among others – at the LRI are. I was skeptical at first, but the tour was convincing, especially considering that probably not so much money is being invested in the upkeep of this building due to the move of the LRI into the Francis Crick Institute in 2016. At the Crick of course everything will be even better, as they didn’t fail to mention at every possible opportunity.

On the second day we had dinner together with the lab members of the recruiting labs, but without the PIs who were busy trying to work out who to invite for the third day on which one-on-one interviews would be held. We were certainly more relaxed this evening. However, the next morning between 7.15 and 8.00 am we had to come down into the reception area of the hotel to pick up a letter informing us whether we had been invited for the third and final day. It was irrational to be nervous because at this stage there was absolutely nothing to be done about the situation. Nevertheless, I, and probably many others, had difficulty sleeping that night.

Luckily, I was invited back to speak to three group leaders: Axel Behrens, Victoria Sanz-Moreno with Ilaria Malanchi, and Caroline Hill. In these sessions it became clear that I would want to work either with Axel on pancreatic cancer or with Victoria and Ilaria on melanoma. The third project was more focussed on neurodevelopment, which is interesting but my gut feeling told me to veer away from it simply because I have a stronger background in cancer biology.

At the end of the third day we had to hand in a preference list, and then all there was left to do was to go back to Cambridge and wait. But the waiting was mainly a formality since it had become clear during the day that Axel Behrens’ lab was going to make me an offer I couldn’t refuse. I am extremely excited! London, here I come!

Departmental Research Day & M. Sci. Symposium

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!

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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:

Screen Shot 2015-01-14 at 20.14.58And 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.

CRISPR Digest #3

First post of the new year, so it only makes sense to go back to one of my favourite topics: CRISPR. As you can imagine, the recent breakthrough in applying the CRISPR technology and not merely using it in basic research has sparked a large patent dispute. Although Jennifer Doudna and Emmanuelle Charpentier originally recognised the method’s potential, it is Feng Zhang who won a large patent over the technology last year (discussed in detail here). However, as far as I understand it, a legal process will be launched in which it may still be possible to reverse the patent ownership. And this would have implications for the various biotechnology start-ups, including Editas Medicine (founded by Zhang, Doudna and others; although Doudna is no longer involved with this company) and CRISPR Therapeutics (founded by Charpentier and others), that were recently launched to utilise CRISPR in therapeutic approaches. I agree with Charpentier when she says that “things are happening fast, maybe a bit too fast”, but she also seems confident that “the story is going to end up well”. According to either John Lennon, Fernando Sabino or an Indian proverb “In the end, everything will be okay. If it’s not okay, it’s not yet the end.” That must be a comforting thought when many millions of dollars are at stake.

But it is not only biotechnology start-ups that have a vested interested in CRISPR technologies. For example, the pharmaceutical company Novartis has recently released information about its attempts to use genome-editing to increase the efficacy of immunotherapy approaches – the use of immune cells, such as “killer T cells”, to treat cancers by instructing them to target malignant cells – in the treatment of haematological cancers.

Following on from the last digest (Hu et al. (2014)), more research groups are using CRISPR to investigate the interactions between HIV and human cells. In one paper (Wang et al. (2014)) they managed to disrupt CCR5, one of the main cell surface receptors of HIV-1, leading to the generation of HIV-resistant cells.

Lastly, CRISPR is being adopted as a tool by researchers in ever more diverse fields of study. For example, in addition to crop plants and HIV, a very recent paper (Peng et al. (2015)) shows the use of CRISPR in Trypanosoma cruzi, the causative agent of human Chagas disease, and a relative of Trypanosoma brucei, the causative agent of human sleeping sickness and nagana in cattle. Yet another group (Kistler et al. (2014)) used CRISPR to engineer the genome of the mosquito Aedes aegypti, the transmitter of yellow fever and dengue viruses. These advances, although at the moment “only” representing proof-of-principle experiments, may in future lead to more effective methods of interfering with the virulence of these protozoan parasites and virus vectors (both images from the Centers for  Disease Control and Prevention):

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References:

Hu WH, Kaminski R, Yang F, Zhang YG, Cosentino L, Li F, Luo BA, Alvarez-Carbonell D, Garcia-Mesa Y, Karn J, Mo XM, Khalili K (2014) RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection.Proceedings of the National Academy of Sciences of the United States of America 111: 11461-11466

Kistler KE, Vosshall LB, Matthews BJ (2014) Genome-engineering with CRISPR-Cas9 in the mosquito Aedes aegypti. 

Peng D, Kurup SP, Yao PY, Minning TA, Tarleton RL (2015) CRISPR-Cas9-Mediated Single-Gene and Gene Family Disruption in Trypanosoma cruzi. mBio 6

Wang W, Ye C, Liu J, Zhang D, Kimata JT, et al. (2014) CCR5 Gene Disruption via Lentiviral Vectors Expressing Cas9 and Single Guided RNA Renders Cells Resistant to HIV-1 Infection. PLoS ONE 9(12): e115987.