Axons Weeks 2-3: Science is Beautiful

After 3 full weeks of research, I have to say that this is much better than taking classes. I’m learning a lot, it’s really fun, and I don’t have any homework when I leave! 🙂

After solving the contamination problem, we had two really busy weeks of running experiments. I got some retinal ganglion cell (RGC) explant cultures going and Karen has been working on the HEK cells and transfections.

The RGC explants are pieces of retina taken from zebra finch embryos and then stuck to a multi-well plastic plate. Once they grow axons, we can use axotomy or chemicals to cause degeneration. I got a lot of explants to stick and grow axons, which is great!

After axotomizing a plate of explants, I got images of them using the confocal microscope. This image is just a black and white version of what I actually see when I’m imaging. The stain we use causes cell membranes to fluoresce red, so the real images look even cooler.

RGC explant

Science is beautiful

After we get the images, we use a couple of software programs to analyze axon area and degeneration.

I did another experiment last week to get a taxol dose-response curve. We use taxol, a chemotherapy drug, to induce axon degeneration, but we want to make sure the degeneration isn’t from cell body death. So the idea is to use different doses and look for cell death. I’m still analyzing the data; hopefully we get some good results.

This week, we also grew some bacteria that carry the piece of DNA we need to test transfection rate. It’s a whole process I’d never done before, from actually growing the bacteria in broth, to lysing them, to collecting and purifying the DNA plasmids. My amazement at the awesomeness of science, at how much I’m learning, and at how much I still don’t know is a constant theme of my summer. I’ve almost completed a 4-year degree and it seems like I still only know the basics of biology. But honestly, I hope that’s true. This field fascinates me; I love learning about it, and you won’t hear me complain if that’s what I get to do for the rest of my life.




  1. Hey Samantha!
    First of all, I wanted to say that your post really gave me the pick-me-up I needed! Your enthusiasm for your research is so refreshing, and it reminded me of why I am also doing research. The past week I’ve kind of been in a rut and I think I lost site of the overall goal of what we do-to expand the world’s knowledge and have fun! Like I said, your enthusiasm for science just transcends through this post and definitely something I can relate to (and needed to hear).
    In regards to your project, can you explain how you are analyzing the axonal degeneration through software programs a little more?
    Xoxoxo from the 3rd floor ISC

  2. svcollins says:

    Hi! I’m sorry it took me so long to respond to your comment! I just now saw it.
    I’m so glad you enjoyed the post! Doing this much work can get exhausting, but it’s definitely worth it.
    The software program we use analyzes confocal images of the neurons. As I understand it, it traces axons, which it sees as straight lines. It also traces degenerated axons, which it sees as fragmented lines. Then it calculates degeneration index (DI), which is the fragmented axon area divided by the total axon area.