Tuesday, May 04, 2010

Spilling sea urchin sperm, and other mishaps of biology

There's a room in our lab with three injection scopes (for shooting up sea urchin eggs with various solutions of DNA), and one fluorescent scope (for seeing where the embryos are glowing-- that tells us what genes are expressing and where). If someone's using the fluorescent scope, the lights in the room have to be off for the glow to be visible. So we've all learned to inject in the dark. It usually goes fine, but today when someone was on the fluorescent scope and I was at an injection scope, I was in a hurry. Between that and the darkness I managed to knock over my petri dish of sea urchin sperm diluted in sea water that I'd been using to fertilize the eggs I was injecting. I got sperm on the floor, the bench, my clothes... had to clean everything up by flashlight.

This inspires me to recall other incidents of my biology lab career. The first project I was given at my first real job after college was on bladder cancer. I'd look at cells from the lining of the bladder of someone being treated for cancer, and count how many cells were still cancerous. (The way to tell was to look at Chromosomes 7 and 9-- in bladder cancer cells, there's a rearrangement between those two chromosomes and you get hybrid 7/9 chromosomes.) It was part of a big ongoing project to keep tabs on the patients' progress. Pretty cool and all, but to get the cells in the first place I had to deal with something called "bladder washings". A nurse would force a bunch of saline through a catheter into the patient's bladder to encourage the cells of the lining to wash off, and then the patient would basically pee that out into a screw-top cup and I'd be the lucky recipient of the sample. I'd centrifuge this diluted urine, pipet out the cells that gathered at the bottom, fix them and drop them on a slide and incubate them with the probes for chromosomes 7 and 9, and then score them on a fluorescent scope. I explained all this to my mom. "They couldn't let you work on breast cancer instead?" she wondered.

At that same job I used to get a bunch of blood samples at the end of each day. I was working at City of Hope, a hospital that treats lots of rare cancers, and for someone who does research on rare cancer it's always a challenge to gather enough samples, so researchers coveted the blood of our patients. The patients who were already having blood drawn for tests could check a box on a consent form to allow us to keep whatever was left over and use it for our own research. I was the one who'd centrifuge the tubes of blood and save the white cell layer to be frozen for later. Every now and then, a blood sample would come through with a big fluorescent sticker: "HIV". You're supposed to treat every blood sample as if it's HIV-positive and take great care not to come in contact with it, but when you know for sure that a sample is infected with HIV, it definitely makes you concentrate a little harder!

I work with bacteria all the time-- big cultures of e. coli. It's the easiest way to get a bunch of copies of a certain DNA sequence. You take the DNA you want, mix it together with some bacteria, apply an electric shock that makes the bacteria open up their membranes and let the DNA inside, and then you just grow up the bacteria in its favorite culture medium. An e. coli bacterium can divide every twenty minutes in the right conditions, and one bacterium becomes one billion in 24 hours. Each time a bacterium divides it replicates all the DNA it's got, including whatever DNA you added to it. So you can make trillions of copies of your desired DNA sequence in 24 hours, and then there are ways to break open the e. coli cells and extract the DNA. The culture medium you grow them in smells a little bit like bread, and e. coli prefer a warm temperature, right around the average human body temperature, so in a culture room there's a smell of warm baking bread. At least, that's what I thought the first time I encountered it, back when I was a freshman biology major and didn't know what I was smelling. I remember it actually made me hungry. Now that I know what's going on and I associate the smell with billions of bacteria... yuck. I broke a flask of liquid bacteria culture once, and spilled it all over the shaker. That was fun to clean up.

Okay, but none of the above grossed me out too much. Here's what got to me (you might want to skip this paragraph.) I studied c. elegans in a genetics lab class when I was a junior. C. elegans is a microscopic worm with two sexes: males and hermaphrodites. The hermaphrodites prefer to mate with males and produce young that way, but if there are no males around they can produce their own sperm to fertilize their eggs and thus produce clones of themselves. But there's a strain of c. elegans we were studying called vulvaless because the vulva-- the orifice through which the hermaphrodite can mate and lay her eggs-- doesn't form properly. It's funny to watch males trying to mate with vulvaless hermaphrodites. They seem to get quite confused. The real problem, though, is that even though a vulvaless hermaphrodite can't mate, her eggs will still be fertilized by her own internal sperm. And the eggs start to develop into young c. elegans worms as soon as they're fertilized. But there's no vulva for the eggs to get out of the mother's body. So... can you see where this is headed? Eventually the eggs hatch inside and the young worms eat their way out. I don't have the heart to fully describe the scene, but it's pretty sad. And even sadder if you reflect that every single one of those young c. elegans is a clone of its mother, meaning they're all vulvaless hermaphrodites and destined to grow to maturity and then die in the same gruesome way, generation after generation!

If that bothers you as it did me, comfort yourself with the knowledge that these worms are tiny (only about a thousand cells each) with no brain to speak of and no capacity for consciousness like a human has. They don't know of their own horrible existence. We humans are the ones who feel sad about it because we're anthropomorphizing them.

Still unpleasant, though!


Rachel Ann said...

This is a fascinating post. Though, if I were a terrorist I'd break into your lab and steal some e. coli to spread around. I hope you keep it locked up tight! We don't want any biological warfare shenanigans going on around here.

Mary333 said...

I don't know whether to giggle or gross out :) I'm glad that God gave you the brains for this type of work and not me;)

Ashley R. said...

ohh this makes me miss bench work soo bad.. if only there were some good paying jobs around here, then i wouldn't be a professional nanny to pay of debt, but using my degree... Thanks for writing this though.. it makes me long for biology

Rachel Gray said...

Mary, I had the same reaction to some of these mishaps-- giggle or gross out? Ashley, I didn't know you were a biology type too! Rachel, the day will come when we biologists teach the world to fear us and our e. coli. :)

JimAroo said...

I can see this C. Elegans story as a major Hollywood horror movie.

Matricidal Maniacs on the March

See the never ending horror of
innocent mothers consumed
from within as a consequence
of their own
primitive passions!

A Cast of Millions!

Written and Directed
Rachel Gray

Filmed on location at
1200 East California Boulevard
Pasadena, California 91125

Rachel Gray said...

Nice! It would easily be rated R for blood and gore. In fact, didn't some horror movie have a guy eaten from inside by an alien?