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.

Cancer Research UK – PhD Student Meeting

Cancer Research UK (CRUK) is the world’s largest independent cancer charity (according to Wikipedia)  and funds thousands of scientists across the UK. In the latest annual report they state that more than £340 million were spent on research. Take a look at the fancy infographic here to see a break-down of how that money was spent:

annual report

The reason for writing this post on CRUK is that today the charity held its first-ever first year PhD students’ meeting in London, at the Quaker Friends House near Euston station. The attendees came from all over the UK: from as far afield as Aberdeen and Manchester to Oxford and Cambridge and finally us lazy Londoners who could afford to get up later than on a normal lab day.

The main aims of the meeting were to get to know some of the people working at CRUK’s head office in London and how, in future, we might apply for their funding. One of the first things I learnt today was that CRUK has made four cancer types – brain, lung, pancreatic (!) and oesophageal – “strategic priorities”, because the survival rates for these are still low and lagging behind those of, say, breast and prostate cancer. We also heard, from the senior research funding manager, Richard Oakley, how CRUK spends its money and what we can and are meant to do to help. Among other things this involves wearing branded t-shirts and participating in fundraising events. So tomorrow morning I will wear this to run in the park in preparation for the 10 km Race for Life happening at the end of June – please feel free to fund me and/or the maybe pink team and/or join the run! [We can start a separate conversation on the topic of the martial language used by CRUK, and other charities, to help raise the money. N.B. The back of the t-shirt reads, “Ask me about my life-saving research.”]

cruk

Since doing a PhD is all about the learning experience, most of the morning was filled with one of three workshops on either a) assertiveness, b) time management, or c) having an effective working relationship with your supervisor. I chose the first option, and although some people (especially in my lab) will argue that it would be better if I were a bit more quiet on occasion, I thought it would be interesting to see what it could offer. The basic message was, of course, quite clear: effectively communicate your needs whilst appreciating other people’s needs. Easier said than done for sure. The only thing that helps is practising being in potentially awkward situations and putting oneself outside one’s comfort zone, which is where learning can happen. Possibly the most helpful information was to realise what isn’t assertive behaviour (e.g. being too passive, or too (indirectly) aggressive) and making sure to recognise those behaviours in oneself and learning to avoid them in future. We’ll see how that goes.

Over lunch we got to browse a few posters. I particularly enjoyed the ones on intestinal stem cells and a potential preventative treatment for breast cancer using the diabetes drug Metformin. And lastly, we were politely, with the help of beer and/or wine, coerced into networking…

Inducing PhD Students

What a feat of architecture and design: the new Francis Crick Institute on Brill Place right next to (West of) St. Pancras Station in London. Apparently the ground floor was built first and then extended up and down simultaneously; I didn’t know that was possible. If you decide to watch the video, I recommend turning off the sound and ignoring the spectres and shadows of people.

Now, sadly, I don’t have a picture of us new PhD students posing outside or inside the building because it isn’t finished yet. As far as I am aware, there have been issues with the air conditioning and parts of the basement vibrate too much for sensitive instruments, such as microscopes, to be set up. The latter is perhaps not surprising considering that the Crick is wedged right between St. Pancras and Euston stations…

Last week we were induced/introduced/inducted to the life of being PhD students. The CEO of the Crick, Paul Nurse, who happens to have won a Nobel Prize, talked to us about how we shouldn’t work too much, try to step out of our projects from time to time to gain an overview, and remember that it is a privilege and not an entitlement to be doing a PhD at the Crick. He also said that leaving academia after this four-year PhD should not be regarded as a failure and that we would receive support in doing other things. I’m a bit sceptical because he also heavily implied that we were not to disappoint the institute, but we’ll see.

As part of the degree we will also have to complete ten days of training per year, which should cover all our bases (according to the Researcher Development Framework; gone are the days of the solitary, uncommunicative, mad scientist):

RDF

In between the serious talks there were plenty of opportunities to get to know – or schmooze with, as one of the students put it – the other students over coffee/tea/beer/wine/pizza/sandwiches. During the first icebreaker session we introduced ourselves and had to provide a memorable fact: they ranged from having started a cupcake business, to being fond of planes, teaching children the piano, appearing in a television series as a child and even being Austrian (!).

We also had a lecture on scientific integrity and ethics (in research). The take-home message was, as always, to be honest. We were shown how not to manipulate or massage data. Luckily, we will be given training in Photoshop and Illustrator so that we can handle our images correctly.

Two half-days were spent listening to the leaders of the so-called Science & Technology Platforms (STPs). These are specialised labs that usually do not have their own projects, but rather lend their equipment and expertise to the other research groups in the institute to enable them to perform experiments they would not be able to do on their own. The STPs include, among others, advanced microscopy facilities (both light and electron microscopy), flow cytometry (to analyse cells at the single-cell level and even sort them), bioinformatics and statistics, DNA/RNA sequencing and peptide chemistry/synthesis. However, the one I was most surprised by was the “scientific instrument prototyping” group – they basically create new scientific machines that no company has made before. They probably conform to the crazy inventor stereotype the most. Overall, the services offered by the STPs seem absolutely incredible and hopefully many of us will actually get to work with them.

After a week of what I thought would be a relaxed introduction to the next four years I am asking myself the question how I used to be able to sit through and concentrate during lectures?! It’s really not that long ago. And also, how have I never really reflected upon the fact that most speakers/lecturers are white middle-aged men? With the exception of the administration team, the communications/engagement team, the scientists in charge of the animal facilities and the professor who gave the talk on ethics, all of the speakers were men. Bear in mind that in our year women make up almost 70% of all students.

The last activity was organised by current PhD students and called “What Mad Pursuits“, after a book by Francis Crick. A few students from each year outlined their take on scientific discovery, told us a bit about their research, gave us refreshing examples of how and how often they’ve made mistakes (e.g. putting the microscope slide the wrong way up for two weeks before figuring out why there was no image; setting gloves on fire etc.) and gave us some advice. One student recommended reading this paper (Schwartz, 2008) – The importance of stupidity in scientific research:

Productive stupidity means being ignorant by choice. Focusing on important questions puts us in the awkward position of being ignorant. One of the beautiful things about science is that it allows us to bumble along, getting it wrong time after time, and feel perfectly fine as long as we learn something each time. No doubt, this can be difficult for students who are accustomed to getting the answers right. […] The more comfortable we become with being stupid, the deeper we will wade into the unknown and the more likely we are to make big discoveries.

References:

Medawar PB (1979) Advice to a Young Scientist. Basic Books, New York.

Schwartz MA (2008) The importance of stupidity in scientific research. Journal of Cell Science 121: 1771

An Introduction to the Pancreas and its Cancer(s)

Given that the four-year PhD I am about to embark on is being partly funded by Cancer Research UK (CRUK), why not start with a short video they have put together containing ten things about that pancreatic cancer that you may (not) have known:

Firstly, is there anything more to its anatomy than “being a small organ in the abdomen”? Why yes, funny you should ask. The pancreas reaches up to 15 cm in length in humans and is a J-shaped structure, apparently a bit like a hockey stick. The organ is not symmetric, rather it is made of a head (left), body (middle) and tail (right), as shown below. In the head the main pancreatic duct merges with the common bile duct before they join into the duodenum, where food is further digested after it leaves the stomach.

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Cartoon illustration of a human pancreas – copied directly from Hezel et al, 2006

As is often the case in biology – and this applies from the level of individual proteins to a whole organism – there is an intricate relationship between structure and function. The pancreas has two main functions: firstly, it contains endocrine cells that produce hormones, such as insulin, to regulate glucose balance (or homeostasis). Secondly, it contains exocrine cells, which make up the majority of the organ, that produce enzymes to aid food digestion. These two categories of cells therefore work together and coordinate the body’s metabolic response to food consumption.

Not all animals have pancreases as complex as those found in mammals since they have evolved over time. Worms, for instance, have some specialised gut cells that produce a substance similar to insulin. Ancient sharks and some fish contain organs in which the exo- and endocrine cells are found together. Fruit flies astonishingly produce insulin in their brains and, in particular, those cells develop from a completely different tissue in the embryo – called the ectoderm – than in other animals, where the pancreas stems from the endoderm. In amphibians and mammals the anatomy becomes more complex with characteristic “islets” of endocrine cells. (See Stanger & Hebrok, 2013 for more details.)

Since I am the daughter of two doctors I am usually interested in the pathological side of human biology. What sort of diseases befall the pancreas? Possibly the first that comes to mind is (type I, auto-immune type) diabetes in which the pancreas fails to make enough insulin because the body is attacking its own beta cells that normally produce insulin. Other than that the pancreas can of course become inflamed like any other organ and this is known as pancreatitis. It is caused, among other things, by high doses of alcohol. Lastly, the pancreas can become cancerous.

Although there are a few different types of pancreatic cancer the focus will lie on pancreatic ductal adenocarcinoma (PDAC) since it is both the most frequent and also the best understood type. It is one of the deadliest types of cancer because it often goes unnoticed until the tumour has disseminated (or metastasised) in the body – fewer than 10% of people who are diagnosed survive for longer than five years.

Therefore it is important to find out more about PDAC. But for the moment there is a lot we do know, decades of hard work that are often frustratingly glossed over. For instance, the genetic mutations that start and maintain PDACs are well known. Among them are activating mutations in a famous oncogene – a gene whose overactivation contributes to cell proliferation and cancer – called KRAS, and deletions of tumour suppressors – those genes/proteins that act as checks and balances and stop cells from overproliferating – such as p16 and p53. Moreover, it is well known when these mutations occur during the development of the cancer. The following image shows how some PDACs form: from healthy tissue to slightly abnormal tissue until it invades into the rest of the body.

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Histology of normal (left), dysplastic (middle) and malignant (right) pancreatic tissue – copied directly from Bardeesy & DePinho, 2002

As for treatment, the most effective method, if successful, is surgery. However, this often involves removing the head of the pancreas as well as parts of the duodenum and this, in turn, means that the stomach has to be surgically joined directly to subsequent parts of the digestive tract, making it a complex procedure. In addition, patients receive radio- and/or chemotherapy, which “targets” most proliferating cells. Targeted therapies that are specific to the cancer cells, as opposed to healthily dividing cells, are, as far as I am aware, not particularly established yet for pancreatic cancer.

For surgery to be effective the cancer needs to be detected at earlier stages. In other words, better diagnosis procedures need to be developed. Recently, two papers attracted some attention because they uncovered methods that could potentially make diagnoses easier using either blood (Melo et al, 2015) or urine (Radon et al, 2015) samples. However, as CRUK rightly point out, these techniques need to be refined for them to be able to tell true cancers from chronic pancreas infections.

And on that cheery note… Next time you can look forward to learning a bit more about how PDAC is studied in the lab and pancreatic anatomy in slightly more detail.

References:

Bardeesy N, DePinho RA (2002) Pancreatic cancer biology and genetics. Nat Rev Cancer 2: 897-909

Hezel AF, Kimmelman AC, Stanger BZ, Bardeesy N, DePinho RA (2006) Genetics and biology of pancreatic ductal adenocarcinoma. Genes & Development 20: 1218-1249

Melo SA, Luecke LB, Kahlert C, Fernandez AF, Gammon ST, Kaye J, LeBleu VS, Mittendorf EA, Weitz J, Rahbari N, Reissfelder C, Pilarsky C, Fraga MF, Piwnica-Worms D, Kalluri R (2015) Glypican-1 identifies cancer exosomes and detects early pancreatic cancer. Nature 523: 177-182

Radon TP, Massat NJ, Jones R, Alrawashdeh W, Dumartin L, Ennis D, Duffy SW, Kocher HM, Pereira SP, Guarner  L, Murta-Nascimento C, Real FX, Malats N, Neoptolemos J, Costello E, Greenhalf W, Lemoine NR, Crnogorac-Jurcevic T (2015) Identification of a Three-Biomarker Panel in Urine for Early Detection of Pancreatic Adenocarcinoma. Clinical Cancer Research 21: 3512-3521

Stanger BZ, Hebrok M (2013) Control of Cell Identity in Pancreas Development and Regeneration. Gastroenterology 144: 1170-1179

A Fledgling PhD Student

Here I am standing in front of the gigantic Francis Crick Institute in London, which is situated right next to St. Pancras railway station and just behind the British Library. I’m not actually saluting, just shielding my eyes from the sun. [Photo courtesy: Kai Wang]

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As you can see, even a wide-angle lens cannot quite capture all of the building in a single shot. A recent News article in Nature described the institute as “Sir Paul’s Cathedral”. It will be the biggest biomedical research centre in Europe – it’s bigger than Buckingham Palace – and will become populated with scientists early next year. The building costs came to a whopping £700 million. Additionally, its annual budget will be £150 million, which is more than the School of Biological Sciences at the University of Cambridge received in the academic year 2013/14 according to this report (if I am interpreting it correctly). The charity Cancer Research UK (CRUK) is one of the Crick’s main funders and this summer they are launching an art campaign to raise money for the Crick: CRUK is setting up 21 DNA sculptures across London so that you can go on a DNAtrail and at the end of the exhibit the “sculptures will be auctioned in September 2015 to raise funds to help complete the construction of the Francis Crick Institute”. Makes it sound slightly like they won’t be able to complete the building unless the auction goes really well… As far as I’m aware the Crick already has a roof and is currently being furnished. [Picture copied from the CRUK website.]

dna_trail_02

Sir Paul Nurse’s “Crick project” was/is daring and the numbers above are certainly impressive. But with this grandeur come great expectations. Sceptics of the project will be awaiting great results, results even better (and by that I probably mean more translatable into medicine and the real world) than those already being produced by the research groups moving into the Crick. Although I have no doubt that it will be an exciting place to work, with excellent facilities and support staff, I can imagine it will also be a high pressure environment. We shall see.

At the moment it’s barely been a week since I graduated with my undergraduate degree (woohoooo!) and part of my brain is already getting a little bit impatient for something new to think about and to work on. Another, perhaps more calculating, part of my brain is saying, “Are you mad? Enjoy these weeks of freedom. You’ll never have holidays like these again!” In any case, the PhD doesn’t start until September but in the mean time I’m scheduled to join a lab meeting of my future lab in late July. That means that I should do a bit of preparatory reading beforehand, including the lab’s most recent publications (see below).

References:

Behrens A, van Deursen JM, Rudolph KL, Schumacher B (2014) Impact of genomic damage and ageing on stem cell function. Nature Cell Biology 16: 201-207

Chakraborty A, Diefenbacher ME, Mylona A, Kassel O, Behrens A (2015) The E3 ubiquitin ligase Trim7 mediates c-Jun/AP-1 activation by Ras signalling. Nat Commun 6: 6782

Diefenbacher ME, Chakraborty A, Blake SM, Mitter R, Popov N, Eilers M, Behrens A (2015) Usp28 Counteracts Fbw7 in Intestinal Homeostasis and Cancer. Cancer Research 75: 1181-1186

Sancho R, Gruber R, Gu G, Behrens A (2014) Loss of Fbw7 reprograms adult pancreatic ductal cells into alpha, delta, and beta cells. Cell Stem Cell 15: 139-153

Sancho R, Cremona CA, Behrens A (2015) Stem cell and progenitor fate in the mammalian intestine: Notch and lateral inhibition in homeostasis and disease. EMBO Reports 16: 571-581

Schulein-Volk C, Wolf E, Zhu J, Xu W, Taranets L, Hellmann A, Janicke LA, Diefenbacher ME, Behrens A, Eilers M, Popov N (2014) Dual regulation of Fbw7 function and oncogenic transformation by Usp28. Cell Rep 9: 1099-1109