Bio322: Biophysics Labs

[2013 Edition]

Two data analysis labs will be conducted (in the interests of time):

Melting DNA: Fitting a theoretical model of DNA melting to experimental data from Salmon sperm DNA. Based on the theory, estimate T_m and compare to published work.
Lab Date: 18-Nov-2013 (in class- bring personal laptops) [PROTOCOL- click to download][Data on g-docs]
- Note: This is an individual exercise. Use Octave, MATLAB (paid), iPython or SciLab for the analysis. You only need to know how to store data in a matrix or array and plot it. In extreme cases, use Excel/OpenOffice. After plotting the data, interpolating and plotting its derivative, estimate Tm. Additionally you will need to plot the simulated curve based on the expression provided and find reasonable fits to entropy and enthalpy terms. Discuss your results.
- *No need to calculate enthalpy and entropy terms, since many of you are not familiar with the optimization techniques required.
- ** Help using octave to plot data:
  - install Octave
  - store the script and the [data file] in the same folder
  - Call the script on the command line as
    - >>plotDNAmeltOCT;
  - The plots can be saved by
    - >>print -dpdf myfigure.pdf
  - Reported DNA melting temperature in Salmon sperm DNA 87.5^oC in 0.15 M NaCl (Marmur, J. and Doty, P. (1962) J. Mol. Biol.)
- Submission date: 01-Dec-2013
Biopolymers: infer persistence length from images of thermal bending of MTs [PROTOCOL- click to download][Processed data] [Images of microtubules (MTs) (optional: actin and DNA, i.e. not part of the assignment but in case of further interest)
Lab Date: 20-Nov-2013 (in class- bring personal laptops)
- Note: Take the coordinates of contours provided (XY) from tracings done from some images of assembled tubulin from goat-brains in the presence of GTP in vitro. Calculate mean $〈 \cos θ 〉$ and use it to arrive at a $ξ_{p}$ .
- Submission date: 01-Dec-2013

How to report lab data

The analysis of lab-data needs to be done individually. The guidelines for the reports are:

I expect one lab-report per person.
Name your files as "LabNN_yyyymmdd_Yourname.pdf" where y: year, m: month, d: date, and N: lab number (01, 02) and 'Yourname' is your name with last initials.
Conclusions: Compare your results to published values. Comment on deviations if any.
Include any program code that was used to complete the lab.

More details on these labs will be posted- protocols, dates and submissions details.

Updated: 19 Nov 2013