First Online EMBL PhD Symposium

This looks interesting … the First Online EMBL PhD Symposium, a sort of ‘online’ conference for the life sciences. Everybody with a scientific background is invited to participate. Registration is free.

The programme (Career Development Session, Omics Session / Systems Biology, Scientific Communication 2.0 and Participant’s Contributions) and speakers list makes it look sort of like a “Biology 2.0” conference.

Apart from the (possible) IRC sessions, hopefully the fact that everything is stored as video/audio + comments on their content managment system means the ‘inconvenient’ timezone in Australia won’t limit my participation too much.

(via the worldwide bioinformatics cabal :), Neil via Pedro, Roland and Stew)

International Genetically Engineered Machine competition videos

The 2006 iGEM Jamboree (International Genetically Engineered Machine competition) happened at the start of this month. This is a synthetic biology ‘competition’ where teams of talented undergraduates from around the world engineer an organism for a specific purpose … like E. coli that produce mint or banana smell, or form simple logic gates the could potentially be used to make a ‘biological computer’.

They are encouraged to use BioBricks from the Registry of Standard Biological Parts, which at the moment is essentially comprised of series many well-characterized DNA constructs (promoters, repressors, selection markers, lots of fluorescence protein coding sequences, etc) with standardized restriction site that can be mixed and matched to produce new and interesting behaviours in bacteria, yeast or mammalian cells. BioBricks are sent out to teams in in 96-well format, so everyone has a good basic set of starting components.

Videos of the student presentations have finally turned up on Google Video. (Unfortunately, the videos only show the speakers, not the slides for the presentation … which makes some parts pretty hard to follow).

I watched the presentation by the University of Arizona team. They printed bacteria onto paper using a stock-standard inkjet printer, with the ink simply removed from the cartridges and replaced with a solution of bacteria. They could then tranfer this to agar plates to grow in whatever pattern they printed. Very simple, but inkjet hardware hacking crossed with molecular biology is just plain cool. As a side discovery, they noticed some weird fractal patterns in colonies under the confocal microscope, apparently based on variation in the fluorescent protein expression level of cells in a single colony.

I wonder how much interest there would be from undergrads (and their supervising acedemics) to start an Australian iGEM team for 2007 ? Funding would also be a tricky issue, as always.

Protein structure sculpture

Check out these amazing protein structure sculptures by Julian Voss-Andreae. The GFP (Green Fluorescent Protein) in shiny steel is particularly striking.

He has even provided instructions on how to construct your own [pdf] … Before the advent of molecular graphics on computers, making physical models similar to this was what crystallographers (and Linus Pauling) did to build protein models.

I’ve gotta find time to make one of these … the question is, do I make something of personal significance, or a choose a structure that is actually a little more challenging ?

Sheik Taj Din al-Hilaly compares men to puddy cats …

Okay, okay, so this news is a few days stale, but the outrage has only just hit me ….

In a sermon delivered in Arabic (but thankfully translated by The Australian for the sake of some racial-hatred-arousing journalism) Sheik Taj Din al-Hilaly has compared men to cats which have no free will and cannot help but eat uncovered meat left out on the street.

As a red-blooded Aussie male, I’m extremely offended at being compared to such a prissy weak rotting-meat-on-the-street eating animal. Maybe something more masculine like a rhinoceros or a Great White Shark may have been a more thoughtful comparison on the Sheiks part … even a “big cat” such as a lion wouldn’t be so bad.

But a feral flea bitten moggy eating uncovered meat on the street ! This guy should aim to improve on his metaphors.

The SDS-PAGE Hall of Shame

For the uninitiated .. SDS-PAGE is a method that biochemists use to separate mixtures of proteins (and sometimes other biomolecules, like short pieces of DNA). It’s a really useful technique, and most of the time it works perfectly, giving a nice little ‘ladder’ of bands with large proteins at the top and the smallest ones at the bottom.

Occasionally, something goes wrong … enter the SDS-PAGE “Hall of Shame”.

This is a hilarious gallery of botched SDS-PAGE gels, which doubles as a useful trouble-shooting guide.

Over the years, despite trying my best to avoid it, I’ve occasionally run gels which have suffered from most of these problems. This one resembles the gel I ran yesterday … I was in a hurry and turned the voltage up too high. Normally I’d get away with it, but this time the cooling wasn’t adequate enough. It doesn’t pay to rush these things.

(For the non-scientists: SDS-PAGE is an acronym for for sodium dodecyl sulphate polyacrylamide gel electrophoresis … sorry you asked ?)