Biochimica et Biophysica Acta

The first image I made that was used on the cover of a journal was a molecular model of phospholipase D. The diagram was created using PyMOL in collaboration with my PhD supervisor, Professor Shamshad Cockcroft at University College London. The journal was a special issue on phospholipase D in Biochimica et Biophysica Acta: Molecular and Cell Biology of Lipids. It was published in September 2009. The image might easily be referred to as a diagram rather than an illustration, and sadly my name was spelt wrongly in the image credits on the first page.

BBA PLD

 

Heat map mosaic

At the beginning of December our latest research paper was accepted to the Journal of Biological Chemistry. In my research I use automated microscopy to image the movement or relative intensity of particular fluorescent signalling components in literally hundreds of single cells. This method is incredibly powerful and enables us to look at the variability between different cells in how they respond to a particular stimulus. We can monitor how they respond by looking at the activation of key signalling pathways, each of which can be considered to be a noisy communication channel. In this paper we used a statistical measure adapted from those used in the communications industry to measure signals passed down telephone lines, for example. This enabled us to see how cells use negative feedback loops to fine-tune the transmission of signals.

JBC invites authors of accepted manuscripts to submit an image for its cover. You might remember one I submitted alongside my second research paper, published in JBC in 2012. This one was also not chosen for the journal cover.

PrintHere I have fragmented one of the heat-maps from the paper that we used to describe how signal transmission is influenced by the relative strengths of slow and fast negative feedback. This is laid over some of the images of the single cells used to test the predictions of mathematical modelling. The fragments of heat map can be considered to be snippets or packets of information.

 

Lucky Socks: superstition in science

A few weeks ago our latest paper was rejected from the Journal of Biological Chemistry (‘JBC’). It had been sent to two reviewers who each felt that the paper was unsuitable for publication in its current form without further experiments. This is quite normal and is part of the peer review process. You are then given about 3 months to revise the manuscript with the new data and respond (argue politely) to the reviewers comments. If your revised manuscript is still not deemed to be acceptable by the reviewers then it is rejected from the journal and you are then able to submit it to another journal, usually lower down the pecking order.

Yesterday afternoon I made a throw-away comment: “So just two more experiments – one more week – and we’ll be all done.” I shouldn’t have said it – immediately afterwards I tried to take it back, to apologise, but it was clearly too late. Never say “Just one more experiment” or “Just one more week.”

In my current experiments I use semi-automated microscopy to analyse the dynamics of signalling pathways downstream of the Gonadotropin releasing hormone (GnRH) receptor. I use assays that have been used in the lab my me for more than a year, and by my predecessors for many years before me. These assays work.

Today’s experiment was set to be beautiful. I used all new stocks of reagents wherever possible. My mind was clear when I carried out the complicated stimulation time course. Carrying out experiments for me is a bit like drawing: if I’m tense, stressed or pre-occupied all I achieve is a little knot of pencil lines, some grainy, dead cells.

As the InCell Analyzer chugged through the imaging, one field at a time, I hovered around waiting to see the results as soon as they were ready, filling tip boxes ready to autoclave (the downside of having an entire lab to oneself is having to do all the lab chores). I couldn’t believe my eyes when the images were completely blank – well not completely blank – there was ‘background’ staining (non-specific, low-level staining) but the cells had clearly not been stimulated by GnRH.

How could this be? This has never happened before! In those last-ditch experiments one goes all out to get the perfect results, by scaling up to a larger experiment than before, by changing all the reagents in favour of nice new ones? Those fateful words stating the end is in sight.

Sadly, as I have experienced all too many times, the end is rarely as close as you think it is. My suspicion is that the new batch of hormone I made up from powder today was to blame. Perhaps it was a really old vial (and thus degraded), or there wasn’t the right amount of powder in the vial. Hopefully I will be able to make a guess at the answer next week when I run some experiments to decide which reagents I trust and which I should bin, so pushing the completion date for the revised manuscript back even further.

These experiences make us superstitious – the old stock of hormone might have lost some of its activity (it might have been thawed one too many times by the Summer lab students) but at least it works! From here it’s only a short step to using a favourite pipette for every experiment, or indeed, wearing lucky socks.