Category: Proteomics

Contamination!

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)

Would you like to visit one of my lab?

It will be possible on this Saturday March 17th, 2007! For the EDAB Brain Awareness Week, one of my lab is organizing some conferences and you’ll also have the opportunity to visit the lab and see demonstrations on experiments we do and how we do. One of my mentors, Dr. P. Leprince, will tell (and show) you how we can identify proteins and identify their roles. Other workshops include microscopy, electrophysiology, behaviour. Conference topics include stem cells, drug addiction, injuries in the brain. You can have more info on the lab website (look for our activities, in French).

Unfortunately, I may not be there since I could have some experiment to do in the other lab, at the same time.

Receiving broken vials …

Antibodies vials inside the broken cool-packI was eager to receive some new antibodies for western blotting (I was waiting for them since December 2006!). They finally arrived on Wednesday but everything was broken inside! 😦 A plastic shell was supposed to protect the precious vials (about 300US$ each) but even that was broken. I immediately phoned the company and they promised me new vials for next Wednesday. Suddenly, it’s possible to get them in one week … Well, let’s see what I’ll get on that day …

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