[PSA] Biohacking FAQs #3, #4, #5

[maradydd]

3. Gel electrophoresis uses ethidium bromide, which is a dangerous chemical. How are you disposing of it safely?

I'm not using ethidium bromide. There are a number of other gel stains which are much safer and easier to work with, such as SYBR-Green and SYBR-Safe. I use GR Safe, which is similar to SYBR stains but even better, because it can be stored at room temperature.

Per standard biosafety practices, I sterilize everything before I dispose of it.

4. Why is there toilet paper sitting on your lab table?

It's absorbent and good for wiping up spills, and it wastes less paper than using full paper towels to wipe up the occasional spill of less than 2mL of liquid. (The paper towels weren't in the frame. Nor was the sharps bin, or the fire extinguisher, or any other safety equipment. It's all within reach, though.)

5. Why are there Ziploc bags sitting on your lab table?

The bacteria I work with -- Lactobacillus acidophilus, Lactobacillus bulgaricus and Streptococcus thermophilus -- are what's called "facultative anaerobes": they prefer environments where there isn't much oxygen. (They'll grow when there's O₂ around, but they won't grow as quickly.) So, when I plate them on a petri dish, I put the finished plate in a Ziploc bag. Then I put some vinegar and baking soda into an empty Coke bottle and capture the generated CO₂ gas in a balloon, squirt the gas into the Ziploc bag, and close it up.

I asked a former boss of mine (a bioinformaticist whose PhD is in population genetics) whether he had any ideas for easy ways to provide an oxygen-free environment for my plates, and he said they used the same Ziploc bag trick when he was in grad school. It's ghetto, but hey, it works.

Comments

[(Anonymous)]

As i stated in my initial post, it's the process of trading the benchtop for the kitchentop that intrigues me. You didn't inquire how she was going to clone her target, you wanted a methodology from start to finish. All I am suggesting is let her concentrate on the cloning before worrying about getting FRET to work in her recombinant bugs, validating her results, and packaging a final product!

As to how and if one can clone in their kitchen, I am certainly curious! MAKE magazine has already published plans for a homemade cycler, so if she can build a reliable electrophoresis rig, and put it all together with clean enough DNA preps, why couldn't she heat shock her vector into competent bugs? I should go make a username...

[ellameena.livejournal.com]

I'm asking fairly elementary questions, with the expectation that Meredith does indeed have answers to them. Why are you assuming that, having started her experiment, she doesn't know how to finish it?

[maradydd.livejournal.com]

They are good questions, though a little overwhelming all at once, especially since I am still at the "clone anything into L. acidophilus" stage of things. :) I'd love it if heat shock worked reliably with Gram-positive bacteria, but it is definitely not the best way of going about it; electroporation is the gold standard, and I don't have an electroporator yet. I'm building one, though. The logic to control it works great, and I have the low-voltage side optoisolated from the high-voltage side, but I'm still working the kinks out of getting the HV circuit to activate from a mere 5V in. There's a whole lot of stuff I've had to learn and am still learning, but it sure is fun!

Fundamentally I really am a software developer at heart, and a test-driven developer at that. I work by figuring out what I want a particular step of my work to do, figuring out how I'll verify that I've achieved what I wanted, then implementing and debugging till the tests succeed. It is a bit slow and plodding, but ultimately rewarding.