12/10 Crunching crunching crunching

Where an interesting prompt from Gerrit is revealed

This past week saw attention to my person as well as ideas. It got cold and rainy, suddenly, as though the weather gods turned off the furnace. I organized a nice waterproof but breathable jacket, glow-in-the-dark yellow too, some gloves with clipped fingertips, and still managed on Monday morning to get drenched through below the belt during the 15 minute cycle between East Midlands Parkway station and campus. Plastic trousers up next.

And on the science front I spent a fair amount of time crunching data. I calculated velocity profiles, like the one shown here, with some different parameters of the software, and I used curve fitting techniques of various kinds to see if I could extract some meaningful numbers. This didn’t really change anything. I could make the curves look a little different, and get a few parameters out, but all of them contained about the same band of uncertainty that my eye sees just looking at the figure.

One thing I could not try was to see what happens with shorter time intervals between images. Now, usually one might think that shorter intervals would increase the noise. And it might. But in this case, longer intervals will increase noise too because the longer the interval the more the strip used to calculate velocities changes. There is an optimum time, neither too long nor too short. Next session, I will take some sequences with shorter time intervals. By acquiring images every 30 sec, I can compare that interval with 60 and 90 second intervals and get a feeling for this. I suppose I could even do some at 15 second intervals, although that would produce a staggering number of frames if I kept it up for too long.

I did not have any wild-type roots this week because of being in France two weeks ago when the seeds would have had to have been plated. But I did have seedlings of a particular mutant, one called botero after the artist. It seems the organs of this mutant are short and squat, providing a passable allusion to the chubby people typical of Botero (see below). This mutant is of interest because it has been claimed that the cells of the mutant are impaired in mechanical sensitivity – in the shoot apex, cells appear to lose touch with one another so to speak. I thought that would be interesting to see if despite this, the root could maintain a stable velocity profile. Because the plants grow slowly, they were ready for their close ups (image sequences) only by Friday, and I look forward to further crunching this coming week. But in light of the past results, I imaged them for two hours, so that I can have a longer test of the profile’s stability.

Saint Michael by Botero

Saint Michael by Botero

A standout this week was a seminar from my former postdoc, and now full professor, Gerrit Beemster. Information about his lab is here. Perhaps not surprisingly, his work touched on what I am trying to do here in more than one way. On the one hand, he is developing an in vitro growth assay, similar to what I described wanting to do in a previous post, but using leaves. He’s gotten plenty of data already and I can see some issues I hadn’t pondered, which I will describe at that great moment when my own system starts bringing in a datum or two. On the other hand, he has been modeling the root growth zone and described how cell-autonomous rules fail to reproduce the observed behavior, particularly with respect to cell length profiles. This supports the idea that the stable velocity profile is an emergent behavior reflecting the property of the whole system. In the other extreme, let’s get rid of cells altogether and imagine the profile’s being based on standing waves. In this extreme, the importance of plasmodesmata becomes salient. To the extent that these pores are open, the root growth zone can be thought of as a single volume (or more accurately, a set of concentric volumes because plasmodesmal communication between tissues is supposed to be minimal).

The latter thought makes me want to get ahold of some mutants or probably transgenics where plasmodesmal flux has been slowed down. Happily I think I can find some in the hands of my former student Wu, working in Kim Gallagher’s lab. I am going to write and ask. It would be quite interesting to see whether closing down these pores has any impact on the stability of the velocity profile. I predict it will.

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