Category: Proteomics

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

Symposium on Neuroproteomics in Gent

This friday, I attended the Symposium on Neuroproteomics organised at the University of Gent (B). Apart from Deborah Dumont‘s excellent talk, lectures were almost only focused on oxydative stress, neurological diseases and gel-free proteomics (like 2D-LC). One speaker even seemed to talk only to his computer or his presentation. So, it was not very interesting for me (finishing my thesis based on gel proteomics). The organisation was very “basic” and we even didn’t have any free pen + paper (fortunately, I took two pens and a notebook).

Proteom'Lux 2006

From the 11th to the 14th of October, I was at Proteom’Lux 2006, an international conference on proteomics held in Luxembourg. I presented a poster, learned quite a lot of information, met a lot of very interesting people and have now a clearer view on the directions and additional details needed in the proteomic part of my work. Some people presented some interesting new ideas (QconCat, MS-Blast, …). I am still assimilating all this information …

The conference schedule was very “tight” but, when I took some time to visit Luxembourg city a little bit, I found a place where I really wanted to enter 😉 Finally, it was also the first time I saw a biology lecture done in LaTeX Beamer (organizers also had a laptop with Ubuntu and an OpenOffice.org Impress presentation but it wasn’t apparently for a lecture).

RNA-oriented Nobel Prizes

On 6 Nobel prizes, 2 were awarded to people involved in research about RNA. The 2006 Nobel Prize in Medicine was awarded to Andrew Fire and Craig Mello “for their discovery of RNA interference – gene silencing by double-stranded RNA”. And the 2006 Nobel Prize in Chemistry was awarded to Roger Kornberg “for his studies of the molecular basis of eukaryotic transcription”.

RNA interference is a mechanism where a “double-stranded ribonucleic acid (dsRNA) interferes with the expression of a particular gene”. And transcription is basically the process through which a DNA sequence is copied to produce a complementary RNA.

Some years ago, everyone was talking about genomics, the study of genes. Now people working on RNA win Nobel Prizes. Knowing that DNA is transcripted into RNAs and that some RNAs (mRNA) are later translated into proteins, I predict that we’ll see a future Nobel Prize in proteomics, the study of proteins. 😉 Ok, Fenn, Tanaka and Wüthrich already won a Nobel Prize in 2002 for MALDI and NMR mass spectrometry, a technique used, a.o., to identify proteins. And Blobel won a Nobel Prize in 1999 for protein targeting.

Done some spot picking

Spot picker cameraToday, I did some “spot picking”. In 2D electrophoresis, you disperse proteins in a gel according to their electric charge and mass. You obtain a kind of map of proteins and, if you stain these proteins, you have a map of spots (example here). After some analysis, it could be good to identify some proteins of interest. The problem is that they are in the gel! So, today, I used a robot called “spot picker” that … picks spots representing proteins of interest out of the gel. You can see what a spot picker looks like in my proteomic set on Flickr.

A first scientific paper from the Falisse-Poirrier!

Nandini published her first paper in a scientific journal:

Falisse-Poirrier N., Ruelle V., Elmoualij B., Zorzi D., Pierard O., Heinen E., De Pauw E., Zorzi W. Advances in immunoproteomics for serological characterization of microbial antigens. J Microbiol Methods. 2006 Jul 3 (DOI access).

Congratulations! 🙂

It is still in electronic format (ahead of print) but already available on the web (but not Open Access, unfortunately ; I think Nandini will auto-archive it somewhere). Here is Nandini’s BibTex entry (will be updated for volume and pages asap).