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[PSA] Biohacking FAQs #3, #4, #5
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.
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.
no subject
6. When you are talking about a cloned gene, expression is always controlled by the plasmid. The promoter on the plasmid controls gene expression, and it is almost always constitutive--always on. It will not "turn on" or "turn off" in response to the presence of melamine in the culture. In some biological systems, the substrate of a reaction will act as a promoter for a gene for a metabolic enzyme--but only sometimes, and only in the native organism. Once you clone the gene into another organism, there's not going to be a connection between substrate and gene expression.
7. Be careful when you heat agarose. It has a tendency to superheat and boil over. Add it to your buffer in a generously sized erlenmeyer flask, cover the flask loosely with saran, and microwave it for about 30 seconds at a time, then swirl and check to see if it's dissolved, using a heavy-duty heat-and-water proof glove (not an oven mitt).
8. What you are doing is basically 1970's technology. That is when molecular biology was just getting started and a lot of biochemists were kludging together equipment and supplies much as you are. If you check out methods manuals and seminal papers from the 1970's, you'll find pretty straightforward methods for building equipment and putting together apparatus. Even back in the early 90's, I can remember pouring my agarose gels into frames made out of tape. Acrylamide is extremely toxic. Handling it is not so bad, if you're smart enough not to eat it. But you will be generating toxic waste and you can't flush that down your drain. You will have to find an acceptable way to dispose of your toxic waste. Pouring PAGE gels is very tricky.
no subject
I know. That's exactly what I've been doing. In fact, I've referred to papers as far back as 1954 (when the nutrient medium I'm using was designed -- and it's cheap and works great!) or even 1919 (a paper on making yeast extract).