Count IT (Big Bad Bonus Bacillus Edition)

I’m doing double duty today! Posting twice! I realized that my morning meditation didn’t include my weekly training round-up so I thought I’d do a post on that. I’m also going to include a special look into the strange and wonderful things I think about for my work. Get ready everyone, it’s Saturday afternoon, and it’s time for some numbers. (You all know I love counting)

My research concerns the processes that lead to mutations in specific genes in bacterial genomes. I have a lot of different techniques to address this question, but I am about to get an exciting new trick up my sleeve. I will be using a very fancy next-generation sequencing method to identify exactly which mutations are occurring on which strand of the genome for a gene that I am interested in. This technique is called “duplex sequencing” and it lets you detect super-rare mutations. Here’s a link to a pretty good article explaining the technique: Duplex Sequencing. This method lets you detect mutations that are as rare as one in one MILLION per cell, which is WAY below the error rate for conventional techniques. So that’s great….but I’m running into a stumbling block. The mutations I’m interested in happen at a rate of two to five mutations per one hundred million cells per generation…which still 100 times below the detection limit. 

OK, so I’m a clever scientist. You may have noticed that the numbers I gave you are expressed as rates per cell per generation…I’m 100 times below the detection limit, but what if I just grow my cells for 100 generations? Then I’ll have two to five mutations per one million cells. Hell, if I grow these bad boys for 1000 generations, I’ll have ten times the number of mutations that I need. Bacillus doubles in 20 minutes, growing them for 100 generations would take me 33 hours…a day. Easy-peasy, right?
Science is NEVER easy
Wrong. The way bacteria grow is they double exponentially. Even if I started with a SINGLE Bacillus cell, after 100 generations I would end up with 1030 cells after that day. If that sounds like a lot: it is. Bacteria are pretty tiny, but they start to run out of food after they reach a density of around a billion cells per milliliter. I did the back of the envelope calculation, and in order to grow that many cells without them starving, I would need 1018liters of media. That is six thousand times the volume of Lake Tahoe. Our lab manager is really good, but that is a LOT of Luria Bertani broth….
 

Imagine if Lake Tahoe in the Background was FILLED with bacteria…then imagine 6,000 of that

So growing these guys in liquid is clearly not super-practical. Luckily there are other (and better) ways to propogate cells long-term and have them accumulate mutations. The strategy I’m going to use is called “Mutation accumulation” (link to a figure from an excellent review laying all this out) and it’s a simple as streaking colonies out on a plate over and over and over again. The idea is each plate represents a bottleneck event, so every single mutation that happens comes along for the ride. It’s a relief to have figured out a realistic strategy, but a small part of me is disappointed that I wont be growing the BIGGEST BACTERIAL CULTURE EVER.
And after all that, here is
Training for the week of 2.08.14 by the numbers:
Miles ran: 35.3
Yards swam: 2400
Problems solved: 1
Selfies taken: 9 (sometimes it takes a few tries)

Bowls of oatmeal consumed: 8 (I may or may not have had oatmeal for breakfast and lunch today…marathon training requires a lot of carbohydrates…I REALLY like oatmeal…please don’t judge me)

2 thoughts on “Count IT (Big Bad Bonus Bacillus Edition)

  1. So THAT”S what the heck you are doing up there. I'm sure your swim buddies are glad you aren't eyeing the pool for more bacteria growing space. But, although I am judging you about the oatmeal, I still want to know how you eat that much oatmeal and not get sick of it. I often put butter and salt on mine — I hate sweet stuff in the morning. Do you have any ideas for savory oatmeal?

    Like

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