Jean-Etienne's blog » Neuroscience

Ph.D. thesis

Jean-Etienne — 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

View more presentations from Jean-Etienne Poirrier.

Frequently Asked Questions about the Morris Water Maze

Jean-Etienne — Wed, 06 May 2009 22:24:10 +0000

Since I published some videos of Morris Water Maze (MWM) experiments, I received questions about the set-up of the maze and its concept in general. I tried my best to answer them. I collected them and here are the Frequently Asked Questions about the Morris Water Maze. If you have some more questions, don’t hesitate to ask!

Baby movements during sleep

Jean-Etienne — Tue, 27 Jan 2009 23:39:11 +0000

After a while, here is why I got a TV tuner for my Linux laptop, took screen captures and wrote a script to add a timestamp on pictures … I wanted to know how my (then 5-month-old) son was sleeping (his mom can be reassured: I was not planning to put electrodes on his scalp ).

Get the Flash Player to see this player.

Following this, I had interesting discussions with my dad about sleep patterns in babies. It could also be interesting to hybridize what we did for Gemvid and this simple solution in order to be able to quantify human/baby movements during sleep. My little knowledge of OpenCV can then come in handy for the motion and pattern detection …

Some additional technical details : Video was made from 321 TV screen captures (1 every 2 minutes) and played back at 1 frame per second. It was converted with FFmpeg (LGPL) and the Flash player is JW FLV Media Player (CC by-nc-sa). Ok: Flash is not free.

A seventh scientific paper from the Poirrier-Falisse!

Jean-Etienne — 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).

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 …

Published in Nature!

Jean-Etienne — Sat, 18 Aug 2007 14:49:32 +0000

I was very pleased to see my first publication in Nature ⁽¹⁾, the scientific journal with an impact factor of 26! Well, it’s not really what you can expect (especially if you are one of my two mentors): one of my photos on Flickr, representing a rat eating (or praying?), was chosen to illustrate a summary of UK Academy of Medical Sciences report on animal-human chimeras

Click on the thumbnail above to see the full screenshot

Here is the article full reference: DeWitt, N. “Animal-human chimeras: Summary of UK Academy of Medical Sciences Report” Nature Reports Stem Cells, published online on August, 2nd, 2007.

Note that I don’t know if they completely comply with the photo license since the Creative Commons Attribution-ShareAlike 2.0 allows them to re-use the photo and do the modifications, provided they give credit (ok) and distribute the resulting work only under a licence identical to the CC-by-sa. They are not clearly stating to others the licence terms of their new work …

⁽¹⁾ As Jan Schoones wrote in his comment, it’s not published in Nature itself but in Nature Reports Stem Cells, a journal published by the same company as Nature but which does not have an impact factor! (Edited on August, 20th)

Where are the neurosciences?

Jean-Etienne — Mon, 09 Jul 2007 10:40:50 +0000

Since I already posted a lot about IT here, I decided not to mix everything, not to confuse some readers and to start another blog dedicated to neurosciences on the Nature Network. So, here is the branching-plot novel choice:

You want to read more entries on IT? Stay here.
You want to read more entries on neurosciences? Go there.

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

Jean-Etienne — 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 …

In this figure, two monomers (squares) forms a hypothetical protein
highly involved in a memory process at the synapse level. Each monomer can be in two states: active (plus sign) or inactive (minus sign). Activation of the monomer could be done by phosphorylation (in this example ; any other modification could be applied here). The hypothetical protein can either be active (plus plus) or inactive. The key point in Crick’s hypothesis is an enzyme which will phosphorylate a monomer if the protein is in state (plus minus), giving an active (plus plus) protein, but not if it is in state (minus minus). This will counteract the molecular turnover which transform an active (plus plus) protein into an inactive (plus minus) one.

Of course, Crick’s hypothesis can be extended to proteins that are trimers, tetramers, … other process than phosphorylation could be used (methylation, glycosylation, …) and more conditions could also be added (anchoring, maturity, …).

What do you think of this hypothesis?

¹ Crick F. “Neurobiology: Memory and molecular turnover” in Nature 312:101 (1984) – read the PDF

Pure happiness

Jean-Etienne — Sat, 12 May 2007 17:14:37 +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!

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

A small post from Luxembourg

Jean-Etienne — Fri, 11 May 2007 20:47:31 +0000

A small post from the Benelux Sleep Congress 2007 (where they left two unprotected wifi networks near and in the congress hall ). It’s mainly a medical congress but I had very interesting discussions with, a.o., Prof. Peter Meerlo and Dr. Michel Cramer Bornemann, mainly about Gemvid and the proteomic aspect of my Ph.D. Let’s see what can I do with all these contacts …

Otherwise, the Domaine Thermal of Mondorf-les-Bains is a beautiful place (ok, it’s not as natural as landscapes aroung the highway and national roads going to Luxembourg). Unfortunately, I left my camera at home (and it’s really a stupid decision taken in this morning rush).

Disappointed by BSN meeting

Jean-Etienne — Mon, 07 May 2007 20:38:58 +0000

I’m very disappointed by this BSN meeting. This event is organised every 2 years so you might expect some quality standards. Well, don’t expect too much … (don’t expect anything, in fact).

Morning talks were ok, nothing more: it was not better nor worse than any other congress. But the poster session was not organised at all and there was no support from senior scientists … Moreover, authors of about 1/3 of posters didn’t even deign to come and hang a poster! Most of senior scientists left before the afternoon poster sessions (usually, questions from seniors are more useful than other students’ questions); maybe 2-3 seniors were left (for the whole Belgium!!!). And the final touch, lunch was not free (not even sandwiches!) although we paid 45€ for registration (free for members – membership is 12€ per year for students). Instead we were redirected to the UAntwerp canteen … Are they not smart enough to find a sponsor? I think it would have been better to attend the Neuroinformatics Meeting only.

We decided to leave at 16.00: on the 200 people there at 14.00, approximately 20 were left, most of the posters were already removed and no one was there anymore 1) from my lab 2) to have interesting discussions (apart from the weather topic). It’s sad for the last speaker but, hey, if the meeting organising committee is treating us like s..t, what do you expect? We spent at least one day designing our posters (I know people who spent the whole week on it!) and no one is there to discuss about it? We spent hours on highways and traffic jams trying to enter Antwerp at 9.00 to be at the same level as inept people not even coming to hang their poster? I’m sure they even didn’t designed their posters. And the result is the same for everyone: 1 line on the cv. I’m really disappointed.

Note: Alexandre Dulaunoy already left a comment on one of my photos of the meeting on Flickr.