The mitochondria is the powerhouse of the cell, and other scientific musings.

It occurred to me recently that I've been so busy kvetching about the drama with Andrew's family (Hi, Lily) and my own personal battle with depression that I haven't made many updates about my new job, which is actually quite exciting.

(For those who have just joined us, my new job refers to my role as the lab manager of a gnotobiotics lab.  Gnotobiotics involves the study of the microbiome and what that means is that I work with a lot of mice, their feces, and the bacteria therein.  It's not a job for people who dislike smells.  It is, however, of interest to the government right now, who just passed the "Microbiome Initiative."  Therefore our research is very well funded.)

Things are certainly doing better since the rather overwhelming November AALAS conference.  I’ve progressed from sitting at my desk trying not to look too incompetent or terrified to growing bacteria while cackling maniacally. 

I’ve also run PCRs on those bacteria, which is a special machine that replicates your parts of your bacterial DNA for you so that you have more of it, and run some electrophoresis gels, which means zapping Jell-O with electricity while forcing your bacterial DNA bits through it to see what it looks like.

Science!

But seriously, if you are wondering how this works, it’s because DNA is negatively charged and you can draw it through a gel by charging one end of the gel “positive” and the other “negative.”  Large fragments of DNA will move slower through the gel, just like how a semi moves slower on the freeway than a car and a car moves slower than a motorcycle.  You can look at the resulting “bands” and roughly estimate what sort of fragments are there based on how far the band traveled. 

This is useful if you are on NCIS and need to "match" DNA, or if you have a mouse and you want to know if the mouse has a certain gene that makes it, say, susceptible to alcoholism.  Using PCR and electrophoresis together, you can both compare DNA and check for specific genes.

Woo, genetic excuses!

To check, you take the mouse’s DNA and run it through a PCR with primers that replicate the segment of DNA that you're interested in.  Different genes have different primers.  If the mouse doesn’t have the gene, the primer won’t be able to replicate the fragment, and when you zap your DNA through a gel, no band will appear.  It's basically the difference between asking Grandma to knit you something from a pattern and not asking Grandma for anything; if the pattern exists, Grandma will knit it, and if the gene exists, the primer will replicate it.

If your gene is present and replicated in the PCR, then running the solution of PCR'ed DNA will cause a bright band to appear on your gel when you view it under UV light. 

 Pretty!

You can also use this method to genotype mice that look the same.  If you have a sample of DNA labeled “black mouse,” but you want to know whether the mouse is heterozygous (Bb) or homozygous (BB), you can check its genes using a variety of primers and seeing which ones work.  A “b” primer wouldn’t work for a homozygous mouse, and no band would appear on a gel.  This can be important for breeding.  Two homozygous mice (BB x BB) will have all black babies, but two heterozygous mice (Bb x Bb) have a 25% chance of having a non-black baby, bb, which may or may not lead the male mouse to accuse the female mouse of cheating on him.  I’m just kidding of course.  Mice don’t give a shit.

♫ ♫ Ebony and Ivory… ♫ ♫

I also recently mixed some special media for making growth gel, which is what the bacteria live and feed on in their little plates.  It had a total of 30 different ingredients, some measured in microliters and micrograms, and at least seven of which required special preparation beforehand and at least two of which smelled like sweaty cheese. 

Before mixing (a lovely peachy orange smelling of vinegary vomit):

After mixing (a frothy watermelon rose smelling of rotten eggs and meat):

As the year wraps up, I feel confident I took the right job and that everything is going to be okay, even if there is still quite a bit of a learning curve.  I'm learning more every day and the lab is shaping up nicely; I'm doing more things independently and though we still don't have any actual live mice, it's giving me the chance to catch up on basic lab techniques and other important endeavors.

Like decorating the ChemisTree.  

And now I present how science really works for all you out there who appreciate this delicate, often subtle art and the fragile line it toes between cooking, engineering, problem-solving, practicality, and magic.