Making a Manuscript

I’ve used up 75% of my PhD funding. That is to say I’m three years into my PhD with only one left to go. It’s also been nine months since I last published a post on this blog. This is partly because I’ve made time to write some other things, partly due to non-scientific commitments, and partly because I was busy in the lab working on my project.

In parallel with the experiments, we started making figures and writing the text describing and interpreting our experiments. There were several iterations of tweaking, re-tweaking, editing and re-editing, until the final piece of work didn’t resemble the first draft. Totally normal I’m told.

Last week my co-first author and I made the first submission of our manuscript to a journal of high standing. We will see what happens. As I keep telling my non-scientist friends, this is the first rather than last step of scientific publishing. But in any case, at some point we will receive reviewers’ comments  (at this journal or another) that will need to be addressed. Lab life will become busier than ever. In other words, I’m writing to find closure for this blog that has now been dormant for months anyway. I may return to it, or a new and different one, in future, but for now that’s it.

Advertisements

The halfway mark

A few days ago someone called me a “senior PhD student”. And I know it’s true. I’m just over two years, or halfway, through the official funding length of my PhD. “Official” because a lot of students in my lab end up staying for longer to publish a paper, or sometimes two. So I thought it would be a good time to take stock, take a moment to re-evaluate my life choices while trying not to fall into that abyss labelled “existential crisis”.

First, let me say this: doing a PhD is hard. Harder than you imagine it will be, even after countless people have told you that it will be challenging or difficult. It’s hard in ways I hadn’t foreseen. It tries my patience – with people, with inanimate objects, with biology itself – on a daily basis. It makes me do tasks I don’t particularly enjoy (e.g. repetitive pipetting) but that need to be done in order to accomplish those I do. (I realise that this applies to a lot of different jobs.) At the same time, especially on an intellectual level, I find it less challenging, less stimulating than I had expected or hoped for. A lot of time and energy are used to concentrate on practicalities, which leaves less of the brain’s random access memory for really thinking about science.

But it’s not only frustrating, not only bad. I have learnt a lot in the last two years. Practical skills in the lab, of course, including how to clean up centrifuges after almost breaking them, how to plan and execute experiments that take days if not weeks to complete, how to always set up experiments whose results can neatly be presented in figures, including using all the proper controls. Doing a PhD is also teaching me how to deal with the feeling of not having finished or completed something (the work never ends) as well as juggling the (natural?) highs and lows, the alternating sensations of shining confidence and utter dejection, that accompany work. [I’m pretty sure the levels of emotion elicited by work are more extreme than those caused by hormones.] Oh and then of course all the new theoretical knowledge in the forms of attending talks and conferences, as well as reading papers. Isn’t it pretty cool, for example, that using a modified version of CRISPR/Cas9 it’s now possible to precisely edit certain DNA base pairs (rather than making a cut in the DNA and hoping for the best; Gaudelli et al, 2017)? Or that reading about cancer stem cells during my degree has turned into me actually doing some of those types experiments?

Another thing that takes getting used to is that progress is slow. Improvement and success can’t simply be measured by essay feedback and exam results. It takes more effort to see and appreciate how far we, as PhD students, have come from our even humbler beginnings as school and university students. As proof of this let me show you the evolution of a scientist:

science evolution

Above: At the summer science camp of the Vienna Open Lab; Below: As a PhD student at The Francis Crick Institute

In addition to acquiring a better haircut I’ve also increased my skills when it comes to processing and taking immunofluorescence images on a fancy microscope. The Zeiss software installed on our microscopes is called Zen, which is ironic when I lose my cool after it crashes repeatedly. (The software we use to acquire data on our flow cytometers is called Diva, which is much more apt.)

IF evolution

Above: a mouse embryonic fibroblast, taken with lots of help at the MFPL in Vienna; Below: Zen screenshot of mouse pancreatic cancer tissue, taken at The Crick

The halfway mark also coincides with considerable change in our lab: several senior PhD students and post-docs are leaving for other positions (academic or as MBA students) and there are two new PhD students, one of whom is also a clinical fellow (who happens to read the London Review of Books!). This makes me one of the more seasoned members of the lab and I think it’s a good opportunity to make sure I take more responsibility, try to be more innovative, as well as being generous with my time to help others, as others were when I started.

There are several things I will focus on in the near future to make sure I don’t lose motivation: attending more conferences (such as the international PhD student cancer conference in Berlin earlier this year); focussing on one avenue of my research project more and more, really going to the depth of one small problem; going to more lectures; making more time to think; reminding myself regularly of the progress I’ve already made.


References:

Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR (2017) Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature advance online publication

PhD – 21 months in 

Do you remember my optimistic blog post about finding my bearings in the lab after a month of the PhD? I also included pictures of a failed western blot and slightly crushed centrifuge tubes.

Well, twenty months later and I’m still making mistakes. Often they’re new and different mistakes, which could almost be exciting. But today I made the same mistake and lost a lot of plasmid-growing bacteria (bacteria I am using as work horses to produce specific DNA for me) in a centrifuge (which I subsequently cleaned!)…

Photographic evidence attached.

11th International PhD Student Cancer Conference

A glorious three day bonanza of beer, brains and BRAF. — Tom Mortimer, PhD student at The Francis Crick Institute

IMG_1590

On Wednesday morning, June 14th, twenty PhD students from The Francis Crick Institute woke up early and made their way from one of London’s five airports to Berlin. Specifically to Campus Berlin-Buch – the geographic equivalent of Clare Hall Laboratories, situated right next to the M25, the London Orbital Motorway, 25 kilometres from the city centre – home to the Max Delbrück Center for Molecular Medicine (MDC).

IMG_1558

On the campus of the MDC

We were attending the 11th international PhD student cancer conference (IPSCC), which was initiated at the London Research Institute (LRI), one of the founding partners of The Crick. In fact, the opening remarks were held by Holger Gerhardt, a former group leader at the LRI. He immediately gave the meeting a political flavour by stressing how important diversity is within research, openly showing his disdain for Brexit.

The conference was organised by PhD students at the MDC for other students studying cancer across Europe, with delegates from the UK, Germany, Italy and the Netherlands. The talks were spread over three days and the topics ranged from in silico computational biology and large-scale genomics approaches to cell signalling and in vivo cancer metabolism. Strikingly, when speakers were given suggestions or asked questions they seemed sincere in their responses, especially when they didn’t know the answers. One of the talks most out of the ordinary was given by Joseph Hodgson from the CRUK Beatson Institute in Glasgow: he uses fruit flies to study the process of weight loss and muscle wasting due to cancer (also known as cachexia).

IMG_1555

Joseph Hodgson showing fluorescent images of fruit fly muscle wasting (right)

The prize for the best talk went to Rajbir Nath Batra, from the CRUK Cambridge Institute, who studies DNA methylation dynamics in breast cancer in Carlos Caldas’ group. The best poster by far was created by Cora Olpe, also at the Cambridge Institute, who is trying to understand the chemopreventive effect of aspirin on colorectal cancer in the group of Douglas Winton.

IMG_1557

Cora Olpe’s poster made use of Aspirin’s chemical formula to great effect

On the social side of things, conversation was enabled by providing generous amounts of delicious German beer as well as having us participate in career workshops, including on grant writing, conducting clinical trials, science communication and on becoming an entrepreneur. All in all it was great to get the opportunity of meeting the people who might be our future collaborators.

The keynote speakers were Mónica Bettencourt-Dias (Gulbenkian Institute, Lisbon) and Madalena Tarsounas (Institute for Radiation Oncology, Oxford). Lastly, Klaus Rajewsky (MDC, Berlin), a world-renowned immunologist, gave a lecture on his “life in science”. He ended the conference also on a political note, juxtaposing the 1975 referendum on the UK’s membership to the European common market with the Brexit referendum, also stressing how important international collaboration and diversity are within science.

Next year the 12th IPSCC will be hosted by The Francis Crick Institute. We hope to have a great turnout (especially in the face of Brexit) – see you there!

 

Behrens lab retreat 2016

Imagine spending a weekend in these idyllic surroundings in the Peak District with nothing to do but talk about and discuss science.

image1-1

The Peak Mermaid Inn – taken at sunrise on November 13th 2016

Well, that’s exactly what we, the Behrens lab, did last weekend. We invited a keynote speaker, Roland Rad, and Dieter Saur’s group from the Technical University of Munich to join us. Each of us gave a talk about the most interesting or exciting aspects of our projects and in between we drank copious amounts of coffee. In the evenings we cooked enough food to feed a small regiment, drank beer, played pool, darts or table football, all punctuated by heated debates about science. Although this wasn’t a relaxing weekend by normal standards, it was motivating and inspiring and a good reminder of why I enjoy being a scientist: a combination of rational and logical thinking, curiosity and the drive to learn new things for their own sake, all shared with people who, by and large, know more than I do and think differently.

Of the talks I just want to highlight one in particular, because my project also uses one of the techniques mentioned. Dieter Saur is a medical doctor and has his own lab group, which studies mainly gastrointestinal diseases, including pancreatic cancer. In a recently published paper (Schönhuber et al, 2014) they describe an experimental system in mice called the “dual recombinase system“. This is a genetic system that allows the study of complex diseases such as cancer. Until recently it was only possible to simultaneously switch on a gene that drives tumour progression and switch off a gene that prevents tumour formation in a cell type or organ of interest (e.g. in the pancreas). Using the dual recombinase system it is possible to make genetic alterations sequentially. For example, in the beginning of a mouse’s development one can activate a potent tumour driver called Ras and delete an important tumour suppressor called p53. And then, once a tumour has formed, one can additionally delete genes that may be important to maintain the established tumour. Alternatively, the dual system also makes it possible to make genetic changes to the normal cells surrounding the (pancreatic) tumour. If all goes well then I will be able to use these tools to conduct experiments like this in the next year or so.

15044797_10154563370871405_2126581266_o zip-line

Oh and admittedly we did have an activity scheduled that was slightly less scientific: we got all geared up and went on a GoApe outing. Secured by a harness and after some rigorous safety instructions we got to fly down zip lines, balance over gaping abysses and jump over the void below.


Lastly, the following week saw Queen Mary University London and Barts host the 11th UK cancer stem cell symposium. There were several interesting talks, including by group leaders at the Crick Institute, but the most unusual talk was given by a philosopher called Lucie Laplane. She did her PhD in philosophy and combined this with a research master’s in stem cell biology. Putting the two fields together she came up with a classification of (cancer) stem cells using definitions and guidelines borrowed from philosophy, applied to biology. [In general, researchers agree that stem cells are cells that can self-renew (i.e. generate new copies of themselves) and can produce differentiated/specialised daughter cells.] The most important point was how to pin down what kind of characteristic “stemness” is or what makes a stem cell a stem cell:

csc-table

Framework for defining (cancer) stem cells – copied from Lucie Laplane’s talk at the symposium

For instance, in some cases a stem cell might always be a stem cell no matter what the environment is like (i.e. categorical); other stem cells may be dispositional in nature, meaning that they always have the potential to act as a stem cell but only do so in a permissive environment. Alternatively, being a stem cell might not be property of a single cell at all but rather an attribute of an entire organ (i.e. systemic). Laplane argued that the way we define (cancer) stem cells has a huge impact on how we try to treat diseases such as cancer. For example, if cancer stem cells are “systemic” then even the best therapies targeted against these cells will fail because the system/the tumour will make new cancer stem cells from other tumour cells. Hans Clevers, one of the Gods in the stem cell field, wrote a glowing review of the book here.

References:

Laplane, Lucie. Cancer Stem Cells: Philosophy and Therapies. Harvard University Press, 2016.

Schonhuber N, Seidler B, Schuck K, Veltkamp C, Schachtler C, Zukowska M, Eser S, Feyerabend TB, Paul MC, Eser P, Klein S, Lowy AM, Banerjee R, Yang F, Lee C-L, Moding EJ, Kirsch DG, Scheideler A, Alessi DR, Varela I, Bradley A, Kind A, Schnieke AE, Rodewald H-R, Rad R, Schmid RM, Schneider G, Saur D (2014) A next-generation dual-recombinase system for time- and host-specific targeting of pancreatic cancer. Nat Med 20: 1340-1347