Neuroscience on Jean-Etienne's blog

Idea shared #1 - measure your sleep

Sat, 22 Sep 2012 21:48:32 +0000

I don’t consider having more or better ideas than others. But I gradually realized I have less and less time for some activities like programming, electronics etc. Maybe that’s how we realize we are getting older now adults. So I decided to share these ideas rather than fueling the illusory idea that I will implement them one day.

So idea 1 is about measuring sleep. I recorded animals’sleep during my Ph.D. - but it was thanks to an EEG device. I think that if you want to understand or improve something you have to first measure it in a way or another. So I started to try to measure my own sleep with an app ( Sleep Cycle). But despite its good reviews it doesn’t work, at least for me.

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

Frequently Asked Questions about the Morris Water Maze

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!

FOSDEM 2009, Gemvid video

Sun, 29 Mar 2009 23:05:23 +0000

Along with all the videos of all FOSDEM editions, the FOSDEM team put the 2009 videos on YouTube. So here is the video about Gemvid:

[youtube

&hl=en&fs=1]

The presentation in PDF is still available from the Gemvid webpage (and in live here).

Baby movements during sleep

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.

var s1 = new SWFObject("../videos/player.swf",“ply”,“360”,“240”,“9”,"#FFFFFF"); s1.addParam(“allowfullscreen”,“false”); s1.addParam(“allowscriptaccess”,“sameDomain”); s1.addParam(“flashvars”,“file=../videos/081129-night.flv&image=../videos/081129-night.jpg”); s1.write(“container”);

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).

Published in Nature!

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

Where are the neurosciences?

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

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 :-)

Open source animal behaviour monitoring

Fri, 06 Apr 2007 22:25:32 +0000

In the last issue of the Journal of Neuroscience Methods (impact factor: 1.5), 3 papers deal with animal behaviour monitoring and 2 of them introduce open source software.

Roseanna Ramazani and her colleagues “designed an automated system for the collection and analysis of locomotor behavior data, using the IEEE 1394 acquisition program dvgrab, the image toolkit ImageMagick and the programming language Perl” [1]. What is interesting is that they highlight the longevity and reliability of open source software, leaving behing the simplistic view “open source = free as in free beer”:

Noise level due to ventilation

Fri, 16 Mar 2007 12:02:59 +0000

Since a few days, I am back to my previous laboratory to collect some more samples. While looking after my rats, I measured the noise level with a dBmeter. The conditions are:

8.30 am
doors are left open (except in the housing unit) as it is usually the case
five samples per room: one in each corner of the room (without moving any furniture) and one in the middle
measures taken at ear height
device: YF-20 (YFE)

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).

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).

Dasher: where do you want to write today?

Wed, 18 Oct 2006 23:14:34 +0000

Hannah Wallash put their slides about Dasher on the web (quite the same as these ones from her mentor). Dasher is an “information-efficient text-entry interface”.

What made me interested in Dasher is her introduction about the way we communicate with computers and how they help us to communicate with them. There are keyboards (even reduced ones), gesture alphabets, text entry prediction, etc. I am interested in the ways people can enter text on a touch-screen, without physical keyboard. Usually, people use a virtual keyboard (like in kiosks for tourists or in handheld devices). But they are apparently not the best solutions.

EURON Ph.D. days in Maastricht

Sat, 23 Sep 2006 00:29:48 +0000

These last 1.5 days, I was in Maastricht (NL) for the 10th Euron PhD days. Euron is the “European graduate school of neuroscience”. I presented a poster and did an 15 minutes oral presentation of my last results. It was a good meeting in its 1st meaning: I met interesting people. I also enjoyed listening to other Ph.D. students’presentations since it always gives you i) a glimpse at what other people (in other universities) are interested in (by other means that paper/digital articles) and ii) the impression that you are not the only one to have problems with your protocol, your animals, your proteins, … The location was great ( Fort Sint Pieter), sun was there. The ULg team was very small (only 4 Ph.D. students and 2 senior scientists on a total of about 100 participants) but this gave an occasion to know other students better.

Recognition

Tue, 19 Sep 2006 01:50:26 +0000

A media looked for someone with experience in scientific mazes. They contacted Rudy D’Hooge, from the Laboratory of Neurochemistry & Behaviour, University of Antwerp (with Prof. De Deyn, he wrote an authoritative review on the subject). He gave my name and my lab as a reference for the Morris water maze (*). Maybe he gave other names and labs but …

Nearly 4 years ago, I took the train to visit his laboratory in order to see how we could install a water maze in our lab, what protocol we need to use, pittfalls to avoid, … We were nowhere, I learned from them (**) and now they cited us as a reference lab. After so much toil and trouble, it is heart warming. Thank you.

Neuroscience = pseudoscience?

Wed, 13 Sep 2006 17:40:41 +0000

At least, that’s what the Thunderbird speller found ;-)

OK, it was also associated with “bioscience” and “omniscience”. I just thought it was fun after a day full of experiments and reading interesting articles ( neuroscience is a real science).

Another scientific paper from the Poirrier-Falisse!

Fri, 25 Aug 2006 11:24:32 +0000

Finally, a second scientific paper is published by the Poirrier-Falisse (a first paper for me):

Poirrier JE., Poirrier L., Leprince P., Maquet P. " Gemvid, an open source, modular, automated activity recording system for rats using digital video". Journal of Circadian Rhythms 2006, 4:10 ( full text, doi)

It is still in a provisional PDF version but already available on the web and Open Access (of course)! Here is my BibTex entry. I will upload source code tonight on the project website.

Associative memory

Mon, 05 Jun 2006 10:01:06 +0000

Sunday, we went to a restaurant with my in-laws. They used to go there since a long time and they personally know the restaurant owner. Each time they eat there, it’s an opportunity to chat about the respective families ; so, when my wife is with her parents, the owner remembers what my wife is doing in life. But, since a few months, we went there three or four times alone (i.e. just my wife and me) and the owner never recognised my wife.

Again, some toys for geeks

Thu, 02 Feb 2006 16:43:07 +0000

After the IR camera, I bought a dB meter and a light meter for the laboratory. They were the cheapest ones available (but they are still costly, around 150 euros, knowing money is coming from my own pocket).

The dB meter measures noise level. In my office, it measured 62 dB (approximately). According to the Wikipedia article on Decibel, it’s between “Office or restaurant inside” and “Busy traffic at 5 meters”. The problem is that I am exposed to this continuous environmental noise everyday, at least 8 hours a day. Now I can put a number on the reason why I appreciate silence and calm. Fortunately, I only have a few months left, here.

Scientists find a "sweet tooth" in the (rat) brain

Fri, 23 Dec 2005 16:39:29 +0000

Researchers at the University of Michigan have found a “pleasure spot” in the brains of rats that may shed light on how food translates into pleasure for humans. The spot in rats’ brains makes sweet tastes more “liked” than other tastes. So now I know what’s going on when I am eating sweet Indian pastries :-p

Reference: PeciÃ±a, S. and Berridge, K.C. " Hedonic hot spot in nucleus accumbens shell: where do mu-opioids cause increased hedonic impact of sweetness?" in J. Neurosci., 25: 11777-11786 (2005). On Berridge’s web page, you can also view a cool video illustrating this subject.

Caffeine enhances short-term memory

Thu, 08 Dec 2005 15:14:04 +0000

Caffeine is currently the most widely used stimulant in the world (it can be found in coffee, tea, soft drinks and chocolate, e.g.). For the first time, researchers have directly demonstrated that caffeine modulates short-term working memory.

Using functional magnetic resonance imaging ( fMRI), Florian Koppelstatter (Medical University Innsbruck, Austria) and his colleagues determined the effects of caffeine consumption on brain activation in a network of modules subserving short-term memory of healthy adult volunteers during a working memory task (working memory represents brain activity required to remember things for a short period of time). When given caffeine (approximately the amount in two cups of coffee), the volunteers demonstrated a tendency towards improved short-term memory skills and reaction times during the given task. The fMRI showed increased activity in brain regions located in the frontal lobe and the anterior cingulum. This shows that caffeine modulates a higher brain function through its effects on distinct areas of the brain. What is exciting is that by means of fMRI, they were able to see increases in neuronal activity along with changes in behaviour.