[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

[siliconshaman.livejournal.com]

Hi there, read the article and came on over after a friend of mine pointed me this way... once, many years ago [in '88] I graduated with a degree in molecular genetics myself, and promptly found myself unemployable as the industry here in the uk suffered a downturn in the wake of a whole slew of regulations introduced by good folks afraid of a 'Frankenstein bug' ...

Anyway, it's never really occurred to be that one could 'biohack' like you're doing... I mean, sure, I've often thought what I could do with a few thousand and some second-hand lab gear... but doing it ghetto style like you are... nah. [the trick with the ziplocs being a case in point] I guess that's the fault of having an excess of resources at Uni.

I'm guessing that's why you're using yoghurt bacterium, cheap and available, right?

Incidentally, is there a guide to biohacking, or compendium of tips? The FAQ's are useful, but a novice like myself needs someplace to start.

[kejlina.livejournal.com]

I thought it was a little weird that people in various comments threads were getting so hung up on ethidium bromide. I mean, if someone knows enough about electrophoresis to know what ethidium bromide is and how dangerous it is, they should also know that there's different types of electrophoresis and different dyes available, right?

[(Anonymous)]

You are so inspiring. I always thought that I'm a fan genetics engineering, but this is real enthusiasm. Really nice to see it is possible to have a high tech lab in the basement :D

[unixfan.livejournal.com]

I must say.. what you're doing is.. awesome. :)

Also; You're hot! :D

CO2

[jncline.livejournal.com]

Interesting regarding the CO2. A couple ways of easily getting milliliter CO2-on-tap come to mind. Easiest these days might be to buy a CO2 bicycle pump which use CO2 cartridges, then you've also got CO2 on tap from the pump valve. For liters of CO2, most common source these days for the big canisters seems to be anywhere that sells paintball or airgun sporting equipment; have to create a dispenser though. Whichever is cheaper of course.

Cheers

do try this at home!

[(Anonymous)]

Hi Meredith:

I love this stuff. I have done some moderately serious science in my time and I reckon that 90% of useful experiments need at least one household item. No, this is not a joke. Household items are very cheap 'cos they are made in volume, very precise and/or accurate for the same reason and they have been tested, tested, tested. I do, however, include things like BluRay disc players as household items! I would have given - in fact I did give - a lot for a deep violet diode laser 10 years ago.

My ancestors, who were blacksmiths, had a deep understanding of the physical world that they used to manipulate matter. The gentry might have thought it was just a peasant pounding hot iron until something useful happens. Crap - those ancestors were engineering materials, optimizing processes and so on. I am afraid that people young enough to be my grandchildren will lose that ability to understand reality - to manipulate the real world - in favour of low-information-content digital simulations.

Rant over.

Please keep blogging

John Hennessy

I like your blog

[(Anonymous)]

A good biologist, you know how to take care of your work and health (GR Safe is great, I like it).

Dr. P. Shaw

[hkneale.livejournal.com]

Ohmigosh! I love the CO₂ tip. Before, when I've needed to create a low-oxygen environment (usually for the purpose of long-term food storage), I've either popped in one of those oxygen absorber packets or used dry ice. Only one problem: sourcing either one takes a bit of a song-and-dance.

But the baking soda and vinegar trick? Nifty and ultra-convenient. Will have to use that one next time.

[ellameena.livejournal.com]

Are you aware of NIH RAC guidelines for recombinant DNA research?

http://oba.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm

Your vitamin C project most definitely falls under their jurisdiction. I am not so sure about the melamine detecting bacteria. Glowgurt certainly would because it's intended to be eaten. Also, anything with medical applications is subject to FDA approval (and may also apply to a food safety test.)

An ELISA test kit can be as easy and as cheap as a home pregnancy test, no recombinant DNA necessary.

ColE1 origin

[(Anonymous)]

Hello Meredith,

As a professional science geek that does molecular biology for a living (as long as the funding holds up, anyway) I think what you're doing a absolutely fantastic.

Quick hint: I noticed that the the plasmid you're using has a ColE1 origin of replication that is, I believe, specific for E. coli. I don't think it'll work in your bugs. Prokaryotic DNA replication isn't my speciality (not even close) so I could be wrong, but you might want to look into it.

Best of luck...