Biocurious is a weblog about biology, quantified.

The Day I See a Leaf is a Marvel of a Day*

by Andre on 20 June 2006

Yesterday, after a frustrating morning in the lab, I was walking outside with my coffee when I decided that I needed to switch gears and do something a bit different. I had sticky surfaces on the brain, so it was no surprise (at least to me) that when I saw how smooth the upper surface of a leaf on the ground looked that I decided to put it under the AFM to see what I could see.

It was nice to find that some samples are easier to prepare than others. I cut out a rectangle with a razor, stuck it to a cover slip with a piece of double sided tape, and started imaging. The first image is a topograph, 150 microns on a side, of the waxy upper side of the leaf.

Nice, as far as it goes, but the real action happens on the underside. The second image is a topograph of the same size but taken on the other side of the leaf and it was a pleasant surprise to find that the stomata are close enough together to see a few without searching. I guess they’re important for something

The last one is a close-up.

Finding unexpected intricacies in nature is one of the greatest pleasures in studying science and I find that taking the time to play a little keeps things in perspective. Of course, the pleasure is sweeter if you’re the first to observe something so as soon as I saw the stomata I checked if other people have done the same thing before and of course they have.** Is there anything that people haven’t imaged with an AFM? Suggestions are welcome. It has to be relatively flat (our instrument has a maximum height range of just over 16 microns) and should have interesting features on the nanometer to micron scale. Bonus points for transparent samples so that I can do some simultaneous optical microscopy. Double bonus points if it has features that fluoresce red. Naturally, you’ll find the results of your suggestions here in the coming weeks.

*Kenneth Patton
**On the bright side, I also found out that I’m not the first person to image crystallized buffer and put the pictures on the Internet! (see “E. coli” image)

  1. PhilipJ    4414 days ago    #

    The excitement going on in the centre of the stoma in the close-up picture.. is that just noise because the instrument can’t measure it, or is there really something there?

    What’s your ultimate resolution? Currently we coat beads with proteins, and we have no obvious way to test whether the coating worked very well except sticking them in our tweezers instrument and getting molecules tethered between them. Do you think you could resolve the difference between a ~3 micron polystyrene bead with simple carboxy groups sticking out, vs one that is meant to be covered in a layer or two of protein?

  2. Andre    4414 days ago    #

    The last image is actually an “amplitude” image, not height. That means that it’s the oscillation amplitude of the cantilever plotted at each position instead of the amount the piezo must move (the “height”) to try to keep the oscillation amplitude constant. Basically, the system tries to keep the oscillation amplitude constant as it scans the surface and the last image reflects its failure to do so as it runs into an obstacle. What’s going on in the center is that it runs into a relatively deep hole and suddenly the oscillation amplitude increases before the piezo has time to react and move closer to the sample. So, the “excitement” probably shows the small region in the center of the stomate that is open.

    The ultimate resolution depends a LOT on the type of sample. I’ve never tried to image anything on a bead before but I would be willing to try. If you have a layer or two of protein, a good strategy might be to scratch the surface with the tip and see how deep the scratch is , i.e. how many layers you have. How big is the protein you’re coating the beads with? If they’re sparse, not too small, and well attached you might be able to see individual proteins on the surface.

    But in terms of a good way to see if you have the protein you want on the surface I would try fluorescence. Do you have antibodies against your protein?

  3. maria    4413 days ago    #

    You were right,... a magnificent post… ain’t Life grand??!!

  4. Andre    4413 days ago    #

    It’s definitely not too bad!

  5. Jane Shevtsov    4413 days ago    #

    How about fungal spores and hyphae? Fungi run the world! :-)

  6. Aiden    3053 days ago    #

    could i use one of your images for a research project at school

  7. Andre    3053 days ago    #

    Aiden, sure! In fact, you don’t even have to ask. Here’s a link to the Creative Commons License we use for the site:

    Just make sure you say where you got the image.

  8. VH    1516 days ago    #

    Just curious, where did you find the Kenneth Patton quote?

  9. Andre    1491 days ago    #

    This was a long time ago, I have to admit, I don’t remember. Sorry!

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