Project Update #2

After struggling slightly with the immensity of the task at hand, we (my supervisor(s) and I) have decided to delineate the project slightly more clearly: instead of studying important cancer pathways as they occur in fibroblasts (cells that mainly serve structural purposes in the body and are involved in wound healing), the research will now focus on modelling pathways involved in skin cancer. In particular, the evolution of skin cancer from initial benign states to primary and subsequently metastatic disease (melanomagenesis) will be modelled. Hopefully the work will provide some insight into how melanoma could be treated more effectively.

At the moment, although effective therapies do exist to treat melanoma, the patients almost inevitably relapse after a while, due to resistance to the drugs. The following images (from Wagle et al. (2011)) are not for the faint-hearted. This patient had advanced metastatic melanoma:

Screen Shot 2014-10-28 at 18.47.46

He was treated with a drug that inhibits one of the main “drivers” of the tumours (a protein kinase, which is constitutively activated), and the nodules entirely disappeared:

Screen Shot 2014-10-28 at 18.47.52

However, a couple of months later the tumours re-emerged and this time they were resistant to the drug. The man died a few weeks later.

Screen Shot 2014-10-28 at 18.47.59

A better understanding of the pathways involved in melanomagenesis and drug resistance mechanisms may be able to inform future therapy options. Better treatment may mean that we can pre-empt these relapses and prevent them from occurring.


Wagle N, Emery C, Berger MF, Davis MJ, Sawyer A, Pochanard P, Kehoe SM, Johannessen CM, MacConaill LE, Hahn WC, Meyerson M, Garraway LA (2011) Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling. Journal of Clinical Oncology 29: 3085-3096


Stem Cells

Stem cell biology is possibly the most controversial area of research in the life sciences, both within the research community as well as in the public eye. What exactly are stem cells? They are cells that have the choice between forming another stem cell (self-renewal) or a daughter cell which will differentiate into a specific cell type. A real stem cell has this choice every single time it divides (image from here). There are several types of stem cells: the most versatile are the pluripotent stem cells, because they can differentiate into any adult tissue, including the germ-line. The more restricted stem cells are already lineage-specific, such as haematopoietic stem cells, which form all constituent cells of the blood.

StemCellEarlier this year, a group based at the RIKEN institute in Japan claimed to be able to reprogramme differentiated, adult cells into pluripotent stem cells by simply stressing the cells using a weak acid (Obokata et al. (2014)). These cells are known as STAP (stimulus-triggered acquisition of pluripotency) cells and were an immense breakthrough – until then cells could only be reprogrammed either by transferring the nucleus of the adult cell into an enucleated oocyte (without its own nucleus) or by forcing the expression of certain proteins (transcription factors) that regulate pluripotency. Immediately scientists around the world tried to reproduce these results because it provided a much faster method of working with stem cells. However, essentially nobody could replicate the findings. A crowdsource page was set up to allow researchers to share their experiments online and eventually this led to an investigation of the lead author’s work: the RIKEN institute found that Obokata had falsified/fabricated her results, which is gross scientific misconduct. A few months after this the paper was retracted by Nature, but it is still accessible online.

I don’t claim to know what led this research group to become so desperate that they knowingly published false results, which subsequently caused hundreds of other scientists to waste their time on something that wasn’t going to work. Of course I do not think that such behaviour is justifiable. However, something that many people aren’t aware of is that Obokata’s supervisor hanged himself early this August at the RIKEN institute (press release here). I can’t even begin to imagine how many peoples’ lives have been damaged by this affair. It makes me wonder whether there is something fundamentally wrong with the way research is conducted – in a highly competitive environment! – such that it can become too much for a single person to bear and drives him/her to suicide. [I expect that East Asian scientists are probably more likely to commit suicide than American scientists, for example, due to cultural differences.]

But to end this entry on a somewhat happier note: a couple of weeks ago a group published in Cell that they could convert human pluripotent stem cells into human pancreatic beta cells, the cells which secrete insulin in the pancreas (Pagliuca et al. (2014)). After several steps of conversion in vitro they obtained cells that looked like and behaved like beta cells, which responded to glucose and could secrete insulin. To test whether they also functioned in vivo, they transplanted these cells into diabetic, immunodeficient mice (which do not reject the human cells) and they found that the mice could control blood sugar levels (image from the paper).


This finding has enormous implications because it means that patients with type I diabetes, in which beta cells are destroyed due to autoimmunity, might in future be treated with their own reprogrammed stem cells.


Obokata H, Wakayama T, Sasai Y, Kojima K, Vacanti MP, Niwa H, Yamato M, Vacanti CA (2014) Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature 505: 641-647

Pagliuca Felicia W, Millman Jeffrey R, Gürtler M, Segel M, Van Dervort A, Ryu Jennifer H, Peterson Quinn P, Greiner D, Melton Douglas A (2014) Generation of Functional Human Pancreatic β Cells In Vitro. Cell 159: 428-439

Ebola: Ape Man Hunts Bat Virus

Yesterday evening I attended a talk on ebola at the Pembroke College Stokes Society, partly because I find it shameful how little I know about this t(r)opical disease and partly because I was anxious to see whether the Society would continue to thrive this year. Peter Walsh explained his theory on the mechanism of spread of ebola, both in general and during the current outbreak in West Africa, in the crowded Nihon room in college. His main hypothesis (Walsh et al. (2005)) is that the virus (the Zaire strain specifically) is spreading in a wave-like trajectory and in a very predictable manner, at approximately 50 km per year. He said he could have predicted outbreaks with high accuracy, and that the current epidemic could have been prevented if precautionary measures had been taken. These measures would have included, among other things, educating people who live in the affected regions about the dangers of bushmeat.

In the second part of the talk Walsh explained strategies for immunising gorillas and chimpanzees: by vaccinating these apes with ebola virus-like particles (non-infectious protein fragments of ebola virus) one could try to build up herd immunity against the disease. However, it is currently impossible/forbidden to vaccinate wild apes due to various restrictions. Walsh is an ardent advocate of wildlife conservation, ape conservation in particular, because he believes that it will necessarily also have a positive impact on public health.

The talk was highly entertaining, if somewhat disheartening: it was littered with obscenities and characterised by levels of bitterness only attainable to scientists whose best theories and ideas have been cast aside by policy makers and investors. You can imagine what it was like if I tell you that Peter Walsh published an article entitled “A rant on infectious disease and ape research priorities” in 2008.

For anyone interested in ebola, Addgene has compiled additional scientific resources here.


Walsh PD, Biek R, Real LA (2005) Wave-like spread of Ebola Zaire. Plos Biology 3: 1946-1953

Walsh PD (2008) A rant on infectious disease and ape research priorities. American Journal of Primatology 70: 719-721

The Nobel Prize in Chemistry 2014

Since my knowledge and understanding of neurobiology are rudimentary at best, I thought I would write a brief entry on the Nobel Prize in Chemistry instead. This year’s prize was jointly awarded to Eric Betzig, Stefan W. Hell and William E. Moerner “for the development of super-resolved fluorescence microscopy”. [A lot of the information in this entry came from here.]

Principally, one can distinguish between two types of super-resolved fluorescence microscopy: either when an ensemble of fluorophores (those chemical entities emitting light upon appropriate irradiation) is involved or when single fluorophores are being imaged. The former technique came into use in around 2000, while the latter has only been available since 2006; there seems to be a general trend towards shorter timespans between when the scientific discoveries/developments of a technique are made and when the prizes are awarded.

Why bother with super-resolved fluorescence microscopy in the first place? It’s such a mouthful that it might not be worth the effort to develop. However, if you have a look at the following image, entitled “Untangling Neurofilaments” and submitted to the Cell Picture Show by none other than Stefan Hell, then you might realise that it is a really useful technique [image copied from the Cell Picture Show website].


The image on the left shows neuronal filaments and was acquired using confocal fluorescence microscopy, a technique that is already more advanced than standard or epifluorescence microscopy because it only allows visualisation from a single focal plane, thus increasing contrast and resolution. On the right, however, the same filaments are imaged using a super-resolved technique called stimulated emission depletion (STED). Clearly, this second micrograph shows a lot more detail and one can distinguish different filaments from one another. This can be important when trying to distinguish pre- from post-synaptic neurons, for example.

The main problem in optical microscopy, as alluded to above, is that of the diffraction limit: two objects that are closer to one another than approximately half the wavelength with which they are being visualised cannot be distinguished. For example, when imaging with blue light (the light with the shortest wavelength before it becomes UV light) two objects closer than 200 nm (400 nm divided by 2) will appear to be a single object. And this is the theoretical limit; in practice the resolution is worse. [For a more rigorous definition of the diffraction limit and a more physics-based/mathematical discussion I would recommend the “Scientific Background” provided by the Royal Swedish Academy of Sciences.]

A typical bacterial cell is about 2000 nm by 500 nm and so by conventional light/fluorescence microscopy these cells can be visualised, but their internal structure cannot be resolved. Super-resolved fluorescence microscopy relies on visualising only a subset of all fluorophores in a given sample and being able to pinpoint more precisely from where the photons are being emitted (the physical explanation of this, I’m afraid to say, is beyond my capabilities; best to check here and in the references there, if you are interested).

However, something I can explain links perfectly back to one of my favourite classes of proteins, the fluorescent proteins (FPs). When William Moerner was studying green fluorescent protein (GFP) mutants from Roger Tsien’s lab (Nobel Prize in Chemistry 2008), he noticed that some of them had to be activated before they would fluoresce at all and could be irreversibly turned off as well. This allowed the switching on of only a subset of FPs and the detection of these at super-resolution. Subsequently, this first subset is switched off and the next subset turned on, so that sequentially all FPs can be imaged and the whole picture put together. The method is called PALM (Photoactivated Localisation Microscopy).

Just like with the CRISPR Craze, I first heard about these microscopy techniques last year in a supervision: one of the M.Sci. students was presenting her project which involved PALM imaging of an enzyme as it moved along DNA; to control for the fact that the DNA itself might be moving she tracked a histone variant (histones are proteins that associate with DNA to facilitate its tight packing) and used it as a proxy for DNA movements.

Lastly, although this intellectual and technological achievement certainly deserved to be recognised by a Nobel prize (but why the Chemistry prize I’m not quite sure – Medicine/Physiology or Physics actually both seem appropriate too), I wonder how “right” or “fair” it is to award these prizes to individuals. On the one hand, yes, these three men all had great ideas about how to improve light microscopy, but on the other hand, they presumably had a tremendous amount of help from their lab members. Furthermore, science today is far more collaborative than it was when Alfred Nobel lived. I wonder whether there is a way to make sure more people are acknowledged for their hard work…

Oh, and have I mentioned that I love cells? If you do too, then maybe one of the activities at Biology Week will tickle your fancy.

Project Update #1

I’ve been back in Cambridge for four days and have already met and talked to at least four different people involved in supervising and assisting with my master’s thesis project.

Luckily, this means that I now have a somewhat clearer idea of what I’ll be doing to begin with. In essence, I think, the whole project – my project is a sub-project of the PhD student’s project in Jasmin’s lab – is an admirable undertaking. The general plan is to recreate gene and protein regulatory networks (focussing on major players in cancer) in silico by sifting through the vast amounts of published data. This should yield a simplified but useful model, which can subsequently be tested by inputting experimental data that was not used to build the model. If this works then the model can be asked to predict new outcomes when parameters are changed. Any interesting results from these simulations can then be tested in the lab, but currently that is still quite far in the future.

To begin with I will be doing a lot of literature review and model building, the prospect of which is actually very exciting because I enjoy reading papers and trying to organise data into more accessible (graphical) models.

P.S.: While I wrote this short entry the 2014 Nobel prize in Chemistry was announced. The winners are Eric Betzig, Stefan Hell and William Moerner “for the development of super-resolved fluorescence microscopy”. This means that a) both the Physics and Chemistry prizes this year were awarded for very practical, technological advances, which incidentally are both to do with visible light, and b) the Chemistry prize was once again very biological. Clearly I’m not complaining and I agree with the committee’s announcement this morning, “Biology has turned to chemistry. Chemistry has turned into biology.”