Lab-Life

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! ...

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.

I’ve just written some “search plugins” for Firefox (1.x and 2.x) that allow you to quickly look for a specific Digital Object Identifier ( DOI). These DOI are more and more used in biomedical sciences. One of their interesting features is that they allow direct linking to the scientific article. The plugins are availble here. If you already have Firefox 2, the installation procedure is very easy: all you have to do is go to the plugins page, click on the small arrow near your Firefox search box and choose the “Add DOI lookup” option; it will then automatically be installed for you. ...

GGGRRrrrrrrr … I was quietly using R to analyse my data when, suddently, I wasn’t able to open the file containing these data anymore. It’s just a plain text file! How can it be corrupted? Here is the error message: t < - read.table('ratsdata.csv', header=TRUE, sep=",") Warning message: incomplete final line found by readTableHeader on 'ratsdata.csv' For hours, I tried everything: I counted the number of separators on each line, I counted the number of decimal points on each line, I removed double quotes around factors, I examined in details the final line, etc. (well, Python scripts did the job for me because my file already has > 700 lines). Finally, the solution was so dumb: I mistakenly deleted one double quote before a header. My first line looked like (1) and should look like (2): ...

I really like this kind of application: a person used an old hard disk to bevel micropipettes for electrophysiology [1]. It’s fast, simple, easy and the author got an article published at an impact factor 1.784. [1] Canfield, J.G. " Dry beveling micropipettes using a computer hard drive" Journal of Neuroscience Methods 158 (1):19-21.

In biology, we often need to use PubMed, a biomedical articles search engine for citations from MEDLINE and other life science journals. In the MS-Windows world, you have nice, proprietary tools (like Reference Manager or Endnote) that retrieves citations from PubMed, store them in a database and allow you to use them in proprietary word processing software (in fact, in MS-Word only since nor Wordperfect nor OpenOffice.org are supported). If you are using BibTeX (for LaTeX) as your citations repository, there isn’t a lot of tools. The best one, imho, is JabRef, a free reference manager written in Java (for me, the only “problem” is that it adds custom, non-BibTeX tags). Or you can edit the BibTeX file by yourself with any text editor. ...

I went to Gent, last Friday, to the BASS Autumn Meeting. With “New drugs for sleep” as a title and mainly physicians and psychatrists in the audience, I didn’t expected to have a lot of “basic science” presentations but the University of Liege was well represented by T. Dang-Vu, P. Peigneux, C. Schmidt and me in the free communications section (btw, we are all four from the Cyclotron Research Center). I outlined some recent findings on proteins differentially expressed after a short-term sleep deprivation. I had a nice question from Prof. Verbraecken ( UZA) and, next time, I’ll focus more on pathways and physiological implications of proteins found rather than on functions only.

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. ...

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. ...

Although the University of Liege ( ULg) network of libraries webpage is very old and ugly, the network is starting to use new, technologically advanced tools to allow digital access to its content (articles, books, thesis and other media). Three tools are available since a short time: Source gives access to all media currently available in libraries (it replaces the Telnet-based Liber, for those who used it before). Source is based on Aleph from ExLibris, a proprietary software. PoPuPS is a publication platform for scientific journals from the ULg and the FSAGx. PoPuPS is based on Lodel CMS, a free (GPL) web publishing software. Articles in this database seem to be Open Access although no precise licence is defined (and some articles look strange : see the second picture in this geological article). BICTEL/e is an institutional repository of Ph.D. thesis. It seems to be developed internally by the UCL With these tools, the ULg try to catch the Open Access movement. Source is already connected to other types of databases but it seems that PoPuPS and BICTEL are not (yet) connected to cross-references systems like DOI nor using standardised metadata like in Eprints. ...