Tag: 2D

A seventh scientific paper from the Poirrier-Falisse!

Finally, a seventh scientific paper is published by the Poirrier-Falisse. After a huge batch of articles from Nandini, here is my second paper:

Poirrier J.E., Guillonneau F., Renaut J., Sergeant K., Luxen A., Maquet P. and Leprince P.: “Proteomic changes in rat hippocampus and adrenals following short-term sleep deprivation” Proteome Science, 2008, 6(1):14
doi: 10.1186/1477-5956-6-14

Very briefly, in this study we show the influence of 4 hours of prolonged wakefulness in rats hippocampus and adrenals proteome. As usual, this paper is published in an Open Access journal. Here is my updated BibTeX file (and I also updated Nandini’s BibTeX file).

Since the publication of two papers in peer-reviewed journals is a requirement, I will now be able to finish and defend my Ph.D. thesis …


Last week, our proteomic group did a 2D of a purified protein but, unfortunately, it seemed we had a contamination. So, this week-end, we performed blank tests in order to see if the contamination came from our experiment (or from the purification). We tested our fluorescent markers and different 1D strip holders. At a normal gain, the image looks fine: contamination doesn’t come from the 2D

But when I increase the gain, the image (and thus our gel) is really contaminated! 😦 We really have to look where did the contamination happen! Look at this:

In France the person fooled is known as poisson d’avril. This has been explained as arising from the fact that in April the sun quits the zodiacal sign of the fish. The French traditionally celebrated this holiday by placing dead fish on the backs of friends. Today the fish has been replaced with paper cut-out.
(Explanation from Wikipedia)

A day in front of DeCyder

The whole day, I was busy working with DeCyder, a software to analyse spots of proteins in 2D gels. I hope I won’t dream of small red/yellow/green dots tonight:

DeCyder screenshot

The software use a 3D representation of the spot. If we change this view too fast (either by moving it or by quickly browsing through spots), the graphic diplay freezes and we fall back to an ugly VGA mode (screenshot below). Since the morning, the computer crashed 7 times! I reduced the screen resolution to 1024x768pixels in 24bits colours and it seems to work correctly now. 🙂

Error when moving DeCyder 3D representation too fast

A nice 2D-DIGE difference

This week is very stressful because I am doing a 2200+ euros 2D-DIGE experiment (*) on samples from a rat organ we never studied before and from which I cannot obtain any more new samples.

We found a new pattern of proteins dispersion (compared to our previous experiments on other organs) and, more importantly, we found a clear difference in protein expression in at least 2 spots. In the image below, all the whitish spots mean proteins in these spots are found in equal amounts in the 3 conditions. But spots in red or green mean proteins expressed at different levels (even on/off) between conditions!

Difference in protein expression pattern in rat, revealed by 2D-DIGE

Now, we’ll have to perform a more mathematical/quantitative exploration of these expression patterns and hopefully identify these interesting proteins by mass spectrometry.

(*) 5nmol of Cy dyes (proteins labelling molecules) cost 2215 euros and weight something like 2.75*10-6g! I used nearly all that amount for my experiment. And I don’t take into account the 3-lasers scanner and common lab reagents