Category: Neuroscience

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

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:

  1. 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.
  2. 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.
  3. 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

Open source animal behaviour monitoring

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”:

Some of these previous methods might have been able to meet our needs. Unfortunately, these previous programs are no longer available and all use proprietary software and/or hardware that no longer exists. The methods that we describe use only open source software tools and run interchangeably on different hardware platforms (we have used Mac OSX, Windows XP and Linux, although the data in this paper was all analyzed with a computer running Linux). Open source tools tend to have greater permanence than closed source since they are maintained by communities and they can be modified by the end user. It also is not limited to a single camera system or computer platform. It is readily available to the public, and can be modified by future users, provided that they have a general understanding of the programming language Perl.

In a second paper, Ganea and colleagues describe “a novel home cage activity counter for the recording of basal activity in rodents” [2]. It is not open source but they describe a system similar to Gemvid (my system) and they even don’t cite it! They submitted their paper after mine was published and they even cite Pasquali’s paper which describe a similar method and was published in the same journal as Gemvid. But maybe, if they would have cited my paper, their discussion about cost, limitation to light phase of circadian phase and special hardware would fizzle out 😉

In a third paper, Jonathan Peirce introduce a “Psychophysics software in Python” [3]. I must admit I didn’t know what is a “psychophysics software” until I read the paper and visited the website: http://www.psychopy.org.

So, it seems open source software slowly gain more and more attention in biomedical science … (when I started my Ph.D., nearly no one spoke about open source software, open access to scientific litterature neither, btw).

[1] R.B. Ramazani, H.R. Krishnan, S.E. Bergeson and N.S. Atkinson, “Computer automated movement detection for the analysis of behavior” Journal of Neuroscience Methods 162 (1-2): 171-179
[2] K. Ganea, C. Liebl, V. Sterlemann, M.B. Müller and M.V. Schmidt, “Pharmacological validation of a novel home cage activity counter in mice” Journal of Neuroscience Methods 162 (1-2): 180-186
[3] J.W. Peirce, “PsychoPy—Psychophysics software in Python” Journal of Neuroscience Methods 162 (1-2): 8-13

Noise level due to ventilation

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)

noise level measures

The general mean is 61.7+/-3.3dB. But if we go into the details, a Kruskall-Wallis ANOVA shows most of the rooms have the same dB levels. But there is a significant statistical difference between the room where we perform experiments and the housing unit (p < 0.05). And there is a very significant statistical difference between the experiments room and the second office (p < 0.005). A significant statistical difference is also there between the two offices (p < 0.05; now guess in which one I am …).

Although very high compared to other labs, these levels are not considered as harmfull (same level as a busy restaurant – but you don’t stay 8hours a day in a restaurant). And anyway I am alway wearing ear plugs (3M 1100). On their box, it’s written they reduce noise level by 20-30dB.

Would you like to visit one of my lab?

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.

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).