Monday, February 1, 2010

Megafuge, yeah baby!

Today, I finally got my first piece of serious lab equipment, a Heraeus Megafuge 1.0R thermal centrifuge. This machine is massive (about the size of your average dishwasher, but half its height) and weighs a lot.

The machine can generate close to 18,000 g and spin 4 tubes of up to 400ml or a whole bunch of well plates. Its thermal range is between 0C and 40C. The specs are way beyond what I will need, so this is awesome.

I m a bigger geek than the lady in the picture below, because she doesn't have the thermal model, and hers only does just over 6,000 g. Yawn.

The equipment was being discarded at work, because it was evaluated as "unsafe" about two years ago, but was still being used until last week. So, it still works, but I should be cautioned not to use it at maximum capacity. For the projects I have in mind, the specs of this machine are far out anyway, but I can still do most of the basic centrifuge jobs I'll have in my lab. The machine will have to be used with caution, I don't want a centrifuge explosion in my house, it shatters windows and parts flung from an exploding machine can easily fly through walls (that's what close to 18,000g will do to you).

Since the centrifuge is also thermally controlled, I can use it as an incubator as well and limit my usage of the centrifuge components to a few thousand RPM to spare the machinery.

This machine was bought new 8 years ago by our department for (probably) over 6000 euros, so saving this working (but unsafe ...) machine from the trash was definitely worth it. If I manage to break it (gently), there's still plenty of components in the machine that could be useful elsewhere.

It has taken a few months for my first equipment to appear in my garage, I'm sure it'll take much, much longer before I have a fully equipped lab. But this first step is great. Thanks, work!

Thursday, August 20, 2009

Can I haz lab?

Since March 2008, I'm working as a bioinformatician at the Department of Molecular Genetics of the Flemish Institute for Biotechnology, at the University of Antwerp. Before I came here, I had never done any wet lab work, but dove right in, following my colleagues' efforts around the lab, and trying to participate in lab work where possible. Now, I'm confident enough to conduct my own genetic screening and sequencing experiments at work, getting the hang of some elementary genetics techniques along the way.

Learning these elementary techniques of a genetics laboratory, I'm also growing some confidence that many of these experiments should be possible to do at home, in a little laboratory built in one's garage. Doing biological experimentation at home is one of the latest fads in hacker land (see, e.g., DIYBio), and I don't want to miss out on such an interesting opportunity to do something completely new as a hobby project. The opportunities to do mind boggling biological projects seem endless.

As one example, it should be possible to discover and detect genetic markers in plants, for various features. One experiment could be to find markers to determine the sex of plants (e.g., Cannabis Sativa) or to discover markers for special properties of flowering plants. My father-in-law grows his own varieties of hellebores, but it often takes 4 years before the flowering of the plant starts so he can see whether the plants have acquired new properties (e.g., he created doubly flowering hellebores). Genetic screening of his plants may help in finding the responsible genes and determining interesting flowering features many years ahead in the lab. With techniques such as Random Amplification of Polymorphic DNA, these marker tests could be designed at home, given that equipment for doing PCR and gel electrophoresis are at hand. Most of the steps involved in protocols for such experiments can be done safely, in a home environment, without requiring much safety procedures.

Another example of what can be done in a home laboratory is to genetically engineer microorganisms. One example could be to insert green fluorescent protein into bacteria, as in this YouTube video. The engineering of bacteria again opens up a whole range of possible experiments, as shown by the International Genetically Engineered Machine competition (iGEM). Many genetic constructs are available as so-called BioBricks, and genetic components can be clicked together and be inserted into little organisms such as harmless cultivated laboratory strains of e.g. E. coli (e.g., K12). These kinds of experiments would require my laboratory to agree with Biosafety Level 1 requirements, but this is quite doable.

So, I'm sure that there's many interesing studies that can be done in a molecular genetics lab in my garage, and I'm slowly collecting all the necessary information (protocols, safety issues, where to get cheap equipment, pricing of reagents, ...) so I can start thinking of budget friendly ways to build my own biochemical laboratory.

This will surely be a process that will take a long time, with many pauses in between, but the project is feasible, it can be done. Now I just have to do it. I hope that more details about my progress in building my own garage lab will soon appear here. Here we go! Let's haz a lab!