Proteomics on Jean-Etienne's blog

Ph.D. thesis

Thu, 25 Mar 2010 22:43:03 +0000

As I promised before, you’ll find here the text and slides of my Ph.D. thesis (btw text and slides are in French). The oral presentation was on March 24th, 2010 and everything was fine :-) Slides can be watched below.

Effets du sommeil et de la privation de sommeil sur le protéome hippocampique de rat après apprentissage topographique http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=3557617&stripped_title=effets-du-sommeil-et-de-la-privation-de-sommeil-sur-le-protome-hippocampique-de-rat-aprs-apprentissage-topographique-3557617

2.54

Thu, 08 Oct 2009 22:18:51 +0000

It’s the impact factor of the Open Access journal Proteome Science where I published my last article, last year.

I didn’t see that before but came to know when I downloaded the 453 remaining e-mails from an old account (3 months without fetching them). The announcement of this new impact factor was in one of the three interesting e-mails.

A new home for IPGphor2reader

Thu, 02 Jul 2009 21:46:09 +0000

IPGphor2reader is a software meant to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. I previously hosted it on my personal website and just moved it to Sourceforge, here. Amongst the various reasons for this move, I wanted the possibility for anyone to participate in the project and no hassle to manage this.

Slowly, slowly, most software on my website will be hosted on Sourceforge or Bioinformatics.net.

A seventh scientific paper from the Poirrier-Falisse!

Thu, 22 May 2008 20:25:38 +0000

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).

Picklist Editor 0.2

Sat, 28 Jul 2007 02:08:45 +0000

I’ve just released the version 0.2 of Picklist Editor. Now you have a table of all the proteins on the right of the gel. If you double-click on a cell, you can edit it (note this is not a recommended behaviour). After revalidating the table, your new spot will be included in the gel (and saved to your picklist if you like it). For me, this version is stable and fully functional :-)

The hardware side of Picklist Editor 0.1

Thu, 26 Jul 2007 20:34:42 +0000

This morning, I released Picklist Editor 0.1 with a text introduction … Hmmm … on my photos on Flickr you can see the hardware side of the picking process … (click on pictures to see details).

On the photo on the left, you can see a gel on a low-fluorescent glass plate. This plate is in part in a tray that firmly holds it when the robot is doing its job. The holes everywhere result from the picking process but there are proteins everywhere and you can’t see them in visible light since they are labelled with fluorescent Cy dyes. You can see two white round stickers on each side of the gel: these are the picking references.

Francis Crick and the long-term storage of the memory trace

Mon, 09 Jul 2007 08:32:20 +0000

Since my Ph.D. is related to memory consolidation, I was interested in a strange idea from Francis Crick. He asked the question of long-term storage of the memory trace 1. How is this memory trace stored in our brain? And, more importantly, how is it protected against molecular turnover? In his view, Crick suggested three hypothesis:

Memory could be encoded in alterations of some part of the cell DNA. This will imply that each neuron synapse would be represented by a part of the neuron DNA since the actual paradigm states that memory is encoded in the strength of individual synapse. This first hypothesis seems unlikely.
Memory could otherwise be stored in a local piece of DNA or RNA, at the synapse (a bit like the mitochondrion has its own DNA). This piece would be immune to the molecular turnover. Although more logical, this hypothesis seems unlikely too.
Finally, Crick’s last hypothesis states that molecules at the synapse level would interact in such a way they could be replaced by new ones, one at a time, without altering the general status (strength). The figure below shows a working example of this hypothesis …

Pure happiness

Sat, 12 May 2007 19:14:37 +0000

“Que du bonheur” (French) can be translated into “Pure Happiness”. I found this ad for a hotel/casino on the way back from Luxembourg where I won the best poster award at the Benelux Sleep Congress 2007. So, I’m really happy! :-D

The winning poster is the one on the left, on the photo above. The poster on the right was about Gemvid and was ranked second :-)

Contamination!

Sun, 01 Apr 2007 22:59:35 +0000

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:

Would you like to visit one of my lab?

Wed, 14 Mar 2007 21:42:34 +0000

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).

Colourful western blots

Fri, 09 Mar 2007 19:24:02 +0000

Last week, I received broken vials with(out) my antibodies. This week, as the company promised, I received new ones (not broken, this time). Thanks to our technician, I was able to get colourful western blots (using the ECL Plex system) :-)

Receiving broken vials ...

Fri, 02 Mar 2007 23:53:57 +0000

I 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

Tue, 19 Dec 2006 19:49:39 +0000

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:

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. :-)

A nice 2D-DIGE difference

Fri, 08 Dec 2006 01:03:26 +0000

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!

Some websites to find antibodies

Mon, 27 Nov 2006 13:03:50 +0000

Just to remember, here are some websites to find antibodies:

abcam, the largest one, apparently
Biocompare antibody search (links to many vendors websites)
Invitrogen search engine (never found any antibodies there but, in case it could useful, …)

Links to information and protocols about antibodies on IHC World and the antibody resource page.

Symposium on Neuroproteomics in Gent

Sun, 22 Oct 2006 11:50:46 +0000

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

Sun, 15 Oct 2006 22:42:43 +0000

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 …

RNA-oriented Nobel Prizes

Wed, 04 Oct 2006 17:19:02 +0000

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.

Done some spot picking

Wed, 23 Aug 2006 23:24:33 +0000

Today, 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!

Fri, 14 Jul 2006 14:07:40 +0000

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).

The "bioinformatic effort"

Fri, 07 Jul 2006 11:14:39 +0000

In the June 2006 issue of BioTechniques, Thomas Conrads and colleagues wrote an article about mass spectrometry used in biomarker discovery [1]. It is part of a “Special Section” devoted to mass spectrometry for proteomics analysis that is worth reading in itself. But one figure caught my attention. In this figure (reproduced below), they plot the mass spectrometry data acquisition effort and bioinformatic effort -vs- the experimental focus. In the few past years, people relied too much on the increasing power of mass spectrometry and bioinformatic tools in their experimental design. The authors criticise the fact that people “are overly dependent on technology and suffer from lack of imaginative sample preparation”. It’s not because analysis power is available downstream that sample collection and processing could be neglected.

Bioforum 2006, ISAL cultural evening, experiments ... A very busy week!

Sat, 20 May 2006 22:18:18 +0000

This week was quite busy … In the proteomic lab, I released the first version of IPGPhor2 Reader (see also the previous post). Of course, since we didn’t fail any recent experiment ;-) we don’t see the immediate usefullness of this software. The main purpose of this software is that it allows to see where and when an experiment failed, how the current was given during the IEF and when it was not correctly supplied.

Release of IPGPhor2Reader

Sun, 14 May 2006 01:45:13 +0000

IPGPhor is a device from GE Healthcare (formerly Amersham Biosciences) that performs an isoelectrofocusing of proteins. Version 2 of IPGPhor can be connected to any computer via a serial cable. GE Healthcare provides a monitoring software but no post-hoc analysis software. This gap is efficiently filled by IPGPhor 2 Reader.

Today, I wrote “IPGPhor 2 Reader”. Its goal is to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. This software (for MS-Windows, since IPGPhor logs are collected on a MS-Windows computer) is available here.

First thoughts about the Open2Dprot project

Tue, 19 Jul 2005 20:28:52 +0000

The Open2Dprot project is “a community effort to create an open source n-dimensional (n-D) protein expression data analysis system”. It looks very promising and has a lot of interesting thoughts about how a 2D (nD) gel analysis should be done. It has a modular approach (each step will be caried by a specific tool or “subproject”; I think this is a good thing, à-la-Unix), it’s based on an old but functional version of Gellab-II and will be using Java (for the disponibility of the proprietary-JVMs under many operating systems), R (for the stats), SVG for graphics and MySQL/PostgreSQL for storing data. They even have plans to extend the use of Open2Dprot to n dimensions, incorporating tools for microarrays, liquid chromatography, mass spectrometry. When it will be finished, it will be a cool and useful tool, from the beginning of the proteome(s) analysis to its end. And we won’t be dependent on proprietary - and costly - software from big companies anymore.