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.
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.
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.
P.S. Obviously I chose the time where they are in the middle of a large scale site changes and upgrades so nothing is available for now (except the screenshot).
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
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 …
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 🙂
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.
Here, the picker head is in the process of taking a part of the gel with some proteins inside. Exact positions were computed according to the fluorescent images, revealing the proteins. As you can see again: the gel is perfectly transparent for our non-bionic eyes.
Finally, you can see the spot picking robot in action. The picking head is moving following two axis thanks to the horizontal bar at the back and the perpendicular arm holding the picking head and camera. On the left, you have a pumping station: in addition to some jazz when the picking head is on the gel, the station is aspiring water through the head in order to help getting a plug out of the gel. After that the arm moves to the right of the photo where you have two 96-wells plates to collect samples. When the head is above a well, the pumping station is “blowing” water into the head in order to eject the plug into the well. Everything is under control of a computer and software that is on the right, outside of the camera angle.
This is the GE Healthcare “Typhoon 9400” scanner used to scan fluorescent gels. It’s a huge beast but it doesn’t make a lot of noise (well, I don’t want to stay the whole day next to it!). And this unit only has the red and green lasers inside. There is a second (smaller) unit below with only a blue laser source in it! You can see two gels ready to be scanned (the upper door has to be closed before!).
Other photos from my labs can be seen in my laboratory photostream.
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
“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 🙂
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)
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.