3.2.1.P4
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The listeria bacterium infects mammalian cells and moves through the cell by co-opting the fundamental mechanism of motion inside the cell -- the growth of chains of polymers of actin. One end of the actin chain attaches to the cytoskeleton and the other end to the bacterium. The end attached to the bacterium disconnects, adds an actin molecule to the chain, and reattaches, pushing the bacterium forward. (For how it does this, see Yang, Sept, & Carlson.) This is shown in a simulation created by Yang and Zhu Click on the picture to see the animation in action, then press the back arrow to return to this page.
There are many videos showing the motion of listeria bacteria through a cell. In this problem, we will take data from one of those videos, measure the speed of the bacterium, and from that, infer the rate at which actin molecules are added. (Since this is a random process, this only gives us the average rate.)
In order to extract this information from the video of the actual listeria moving in a cell, we will use the program LoggerPro.
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From a Brownian dynamics
simulation by Le Yang and Jie Zhu.
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We will study the motion of the bacteria in the video at the right using LoggerPro. You can view the full video (with commentary) for the infection of a cell by listeria on YouTube. To carry out this assignment, you should have LoggerPro installed on your computer. If it is not, come see the TA to get it installed, or install the 30 day trial version. If you do not have a computer on which you can do this, you may use one of the campus computers.
Then, download the following documents to the same folder on your computer (or to your desktop if you prefer). For some browsers you may have to right-click on the link and choose "save as". The names to save the files with are given in parentheses.
If you have done this all correctly, launch LoggerPro and then from the File menu, choose open and open the file Listeria.cmbl. When it opens, it should have the imbedded video clip and the columns for all the calculations that need to be done. The window should look like this:
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Fliqz has shut down their service. To access this video, email support with this video id: ecffb08127e14980b2fffffd940f7e34 Listeria infection: Garlandscience on YouTube
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If you don't have the vertical bar with the little buttons on the right of the videoclip, click on the "take video data" button at the right under the videoclip. It looks like this: 
. Clicking it will toggle the column of buttons on the right of the video on and off.
Watch the video through a few times and pick a bacterium that you choose to follow. Since the bacteria are moving in 3D and we are only seeing them projected in 2D, some of the time they might be moving up and down -- perpendicular to the screen. And since the mechanism is random rather than continuous, the motion may be a bit herky-jerky. Pick one bacterium to follow that seems to be moving in a straight line.
A. Take data from the video by first picking an origin and coordinate axes and then setting the distance scale. The width of a typical mammalian cell is approximately 30 microns across. The video frames are taken every 2 s (and the cmbl is set up for that time step). The graph is set up to plot x vs t and y vs t.
From your data, use the curve fitting to fit a straight line to each of the graphs you generated. Read off the x and y components of the velocity from the fit and construct the average speed of the bacterium you have chosen. Include a printout of your screen with your data and the fit with your homework. (You can do this using the File/Print... command in LoggerPro. It will look better if you print it landscape. Or you can just maximize the window and let your computer print the entire screen.)
B. Now click on the x-y symbols on the left of the graph's vertical axis and choose "More". Turn off the x and y plotting and turn on vx, vy, and v (velocity components and speed). Fitting these each with a straight line, which of the parameters of your straight line fit should match what you found in part A? Why? How good is the agreement between the two methods? Which one do you trust most and why?
C. Now let's take our best speed and use us to give information about the actin polymerization taking place. There is evidence that many actin chains are attached to the "actin comet tail" connected to the bacterium. But for now, let's model this as just a single chain with actin being added. From your data on the speed at which the bacterium moves and the size of an actin molecule (diameter about 5.4 nm), estimate the number of actins being added to the chain per second.
Joe Redish and W. Losert 8/9/11
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