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Spring 2016 Physics 131 Reminder from 4-15 Training

Page history last edited by Kim Moore 3 years, 11 months ago

Reminders from 4/15/2016 TA/LA Training (for the week of 4/18; Lab 5, Part 1)...



I hope you are enjoying your weekend. :-)  Here are the reminders from our Friday training....


1) Recitation: Estimating Capillaries & Hold the Mayo 

Hold the Mayo:  http://umdberg.pbworks.com/w/file/61771177/Hold%20the%20mayo.pdf

Estimating Capillaries: http://umdberg.pbworks.com/w/page/49226533/Estimating%20capillaries


Here are some of the course wiki pages that might help you with background info:

5.2.6 Fluid flow Quantifying fluid flow The continuity equation Internal flow -- the HP equation 


(Break--pass back graded lab 4, if it is ready)


2) Lab 5, Part 1

This is the CAPSTONE lab for 1st semester, employing all the experimental skills and physics concepts we have learned in labs 1 through 4 this semester.  We will be testing students' ability to classify motion and then using the classified motion to gain a deeper understanding of the energetic workings inside a living cell.


a) For TAs keeping track of students' Lab Roles: Organizing lab groups for this 5th lab may be a little tricky.  If a student has not yet taken a turn at all of the roles, they need to complete the jobs' list during this lab.  I usually let the students try organizing themselves during the break between recitation and lab, and then step in and do it for them if they can't figure it out in a timely fashion.


b) I never wrote the equipment list in the lab document (mea culpa!).  Spare supplies are in the plastic bins of the center-right cabinet at the back of the room.  Here it is:

For the TA: One onion, one knife (figure that out. :-)  [And please do not let the students handle the knife!]

Per group:

    • 1 microscope
    • 1 slide with 1 cover slip  (You, the TA/LA, can dole out a second slide and cover slip if needed, but have them try with 1 of each first....)
    • 1 vial of saline solution
    • 1 eyedropper pipette
    • 1/6 of a fresh onion


c) Safety precaution: the cover slips are VERY thin glass and are VERY sharp (especially if they shatter).  The cover slips should be treated very gently at all times.  The glass slides are a little sturdier, but they can also be dangerous if broken.  Also, when the students are preparing their slides, they should blot the excess fluid before placing the slide on the microscope--no fluids IN the microscope, please!  (If the onion odor becomes too much, open the window.)


d) Disposal: At the end of the lab, dispose of all used paper towels, all pipettes, and all onion chunks in a trash receptacle.  Place all USED slides and cover slips in the sharps container by the refrigerator at the back of the room (do NOT slide the plastic door shut--very hard to re-open).  Place all vials of saline back in the fridge.  Sort and stack all lab/recitation documents.


e) In order to get a good video (like the sample onion cell video on their computers in the "My Documents" folder--no, they can't track this--it is compressed (missing data chunks) and they do not know the timing between frames), students may need to do 2 or even 3 different slide preps.  Tell them to be patient and not to give up before they get a good video.  Share with them how many slide preps it took YOU to get a good video (or your LA from 131/132 last year).  Also point out that this is a place where they, as students, generally surpass you, the 'masters'--so they should try and likely they will succeed on the first sample!  Encourage students to use the lateral movement options on the microscope in order to hunt through a slide for a better cell sample.  When they think they have a good video, the TA/LA should visually check it.  You should be looking for a well-focused image with clear vesicle movement and no signs of 'broken' cell membrane (free-floating vesicles crossing cell boundaries).


f) We have, at most, 1 onion per lab section.  DO NOT cut into a second onion.  Instead, ask students to borrow from their neighboring lab group's chunk.  (In the past, some sections have thought that they didn't have a 'good' onion, but they eventually got good videos from all!)  Students need to handle the onion skin VERY gently (no pulling, squeezing, or tugging)!  If the refresh rate of VirtualDub is too low (~1-2 fps), students may find it difficult to focus the video by looking at the computer screen.  Point out that they could use the eyepieces to focus the video and then use VirtualDub to capture it.  They can also usually fix the frame rate back to a better value (~10 fps) by setting all the 'capture filter' settings back to 'default.'  If that doesn't fix it, rebooting the program or the computer may help, or just switching the microscope to the other computer.  If you have no success and a group needs to 'borrow' a video, then check the TA computer at the front of the room.  There is a copy of the video TAs took during our Friday lab training.  (These are all 40x with medium resolution.)


g) Due to the varying background intensity, students will have to harvest data from these video using MANUAL tracking.  (~20 objects that look 'random' and ~20 objects that look 'directed' in their motion, tracked on different computers.  Try to get close to 10 different time points in the video, spread out over the entire video, making sure that each new bead is tracked in the same set of frames.)  We are interested in testing students' skills in visually separating the types of motion, now that they have had some practice with these motions in Labs 2, 3, and 4.  Students are expected to complete the following in the lab period: take an appropriate video of the motion in an onion cell, track the random and directed motion within the video using ImageJ, determine the vesicle size (they will need this for the viscous force), and analyze the data from tracking using Excel to produce log <r^2> vs. log (t) plots for both the random and the directed motion.


h) We haven't been having trouble with this issue this semester, but just in case it crops up: John Giannini has a suggestion for getting VirtualDub to behave itself.  If the microscope is connected to a USB port but VirtualDub is still giving you the 'black screen of Death,' try opening "ToupView" (icon on desktop).  This is the video software that originally came with the microscope cameras.  Once the camera is recognized through ToupView, you can close the program, open VirtualDub, and take a video.  John G. says that this usually fixes most problems for him.  (Do not take the video IN ToupView, as it is even harder to work with than VirtualDub.)


i) At the end of the lab, in addition to cleaning up after themselves and saving their data files, remind students that there will be a "pre-reading" for Lab 5, Part 2--the Kinesin Walking video (doesn't play well on the classroom computers, as they have no sound card).  Also, ask them to try to figure out how to use what they know to find the rate of ATP hydrolization (R) and the effective viscosity of the cytosol.  (Doing some 'thinking ahead' will make the 2nd week go faster/more smoothly.)  Also, the data files they are using should be WELL-LABELED (including frame rate and distance-to-pixel conversions from the video).


3) Other Logistics


a) Start organizing your list of which students need a make-up lab (see below).  If there are sufficient students needing a make-up in your lab section, you can run the make-up lab at their normal time.  If you have too few students, we will need to pool them together, set a limited number of make-up slots, and ask the students to commit to a time and day (which may or may not match their normal lab time).  Getting your ELMS gradebook up-to-date (with both Lab scores and Recitation/Lab Participation scores) will help you get organized.  Check back through your previous score entries to ensure you have not made any mistakes or missed entering any scores.  I need your list by Saturday, April 23rd--and you should update the list and email me immediately if any students miss Lab 5, Part 2.  The make-up lab (which will take place during the week of May 2nd).  I need the following information for EACH student in your sections who has missed any week of lab:

    • Student's full name
    • Student's section number
    • Student's email address (find this via UMEG)
    • Number of weeks of lab missed--and which parts of which labs were missed

Once I have this information, I will coordinate with these students to arrange the make-up lab days/times.  Please send me the above information by Saturday, April 23rd.


I think that covers it!  Please let me know if you have any questions or concerns.

Good luck to you this week!




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