User:Brian P. Josey/Notebook/2010/02/15

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Thin walls, and flow cells
Last time I got two suggestion for what I could do to see if I can visualize any movement in the ferritin. The first one came from Anthony. He suggested leaving out a flow cell on the counter top, and putting a magnet next to it, checking after a while to see if there is any change.

The second one came from Koch, and to just use thin-walled tubes for the same tube test that I did Wednesday. For this one, I created 1:10 dilution of the stock ferritin in DI water, and put it into a thin-walled tube. I am going to leave it in the magnetic yoke for an hour again today.

After taking some time to set up the yoke, I decided to add a little more ferritin. The problem was that because of the shape of the tubes, only having 50 uL of ferritin and water would settle to the bottom of the tube, which is angled in a way that I can't put it up against the magnet. The remedy this, I added 7.5 uL of the ferritin, and 67.5 uL of DI water to keep the concentration constant, but allowing the volume to grow.

With a setup that I like, I left the ferritin in the tube out for about an hour, to see if I could get anything to happen. Unfortunately, it didn't really work, and there was no obvious signs of magnetic separation. I noticed a couple of things earlier. When I originally put the extra 7.5 uL of ferritin in the tube, it settled towards the bottom, and there was a clear differentiation between the portion of the sample that had a lot of ferritin, and that which didn't. Placing the small magnet up against the side of tube, the part containing a lot of ferritin was attracted to the magnet, and removing it, the ferritin shot back into solution. However, when I held the magnet up to my earlier 1:10 dilution, and the stock solution, nothing happened.

Problems
So I'm having a couple of problems with the set up that I've been using, and a couple of solutions.
 * 1) Stability-I completely scraped the idea of holding the tube in an upside down tube holder because it is not stable enough. When I was playing with the magnet and the tube alone, I noticed that any shaking would undo any collection that I might have been able to get. My solution for this is to hold the tube containing ferritin in a scissors clamp and tape that to the top of the tube holder. I removed the yoke from the plastic base and taped it to the top of a pile of textbooks and notebooks from my backpack.
 * 2) Visualizing-Between the tube, the magnet, the yoke and the clamp that I'm using to hold it all together, it is a little hard to see the side of the tube close to the magnet. The difference between a successful separation, and an unsuccessful is not that great, and I need to be able to clearly see what is going on. However, with the current set up, it really isn't a big problem, but it is still something that I need to consider.
 * 3) Proof of concept?- I am a little confused on how I can prove that I can move the ferritin with a magnet when I have such a hard time moving it around in the tube. For comparison, I placed the magnetic beads in the yoke, the exact same way that I would have for the ferritin. After shaking it up to put the beads in solution, it took a little over four minutes and fifteen seconds for the beads to completely remove themselves from solution. In the end, they surround the point on the inside of the tube near the magnet, and to a much smaller extent, the tip of the cone.

I know that ferritin is not as magnetic as the microbeads, so I will try Ant's slide idea, to see if that helps.

Flow Cell
I tried the flow cell idea, of leaving ferritin out in a flow cell on the counter for a couple of minutes with a magnet. I created a two chamber flow cell with some of the earlier 1:10 dilutions of ferritin in both chambers. One chamber would serve as a test chamber, to see if there was any effect from the magnet, the other would serve as a control.

After placing the magnet next to one of the flow chambers for ten minutes, there was no difference between it and the control chamber. I then put the magnet directly on top of the ferritin, with the cover glass in between, and again I have no results.
 * Steve Koch 03:51, 16 February 2010 (EST): Hmm...I sense frustration? That's OK.  Here's a foothold: we know that there is some finite force on the ferritin.  It's just a question of whether it's significant.  Did you see my earlier ideas about calculations?  We should talk about those.  They'll be good things to learn, especially since some of your REUs have to do with magnetism.
 * Also: We added money to CRLS, so you should order those conical rare-earth tips, por favor

Brian P. Josey 13:27, 16 February 2010 (EST) It's a little frustrating but, I'm working though it. I did see your note on the force form last time, I'm just not a hundred percent sure yet how to calculate it out. I am going to look into it tomorrow, and start working through it. If I can learn how to do it by hand that would be awesome, if I can do it in either MATLAB or Maple, that would be doubly awesome. I had the option to take E&M this semester. It might have helped, but I decided against it, mostly to take the history class. Also, we ordered the conical magnets yesterday afternoon, so they'll come in sometime.
 * Steve Koch 22:05, 16 February 2010 (EST): I think it's best if I introduce it to you, ESPECIALLY if you haven't had E&M yet!


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