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Bio315/606: Cellular Biophysics

[ver.3]


Assignments, solutions and instructions for Cellular Biophysics will be posted here. (Somewhat redundantly) More material will be posted on the GoogleClassroom, with most submission in that environment. Logo
S. No. Title In class discussion Due date Form of submission Date posted Additional Information Assessment Solution
1 Critical reading and order of magnitude estimates: What is Galieo's point about giants? XX-09-2020 20-09-2018 13-August: prepare to discussbased on the previously shared slides and handout materia.

20-Agust: Upload assignment in GoogleClassroom

 19-08-2020 Use any source from the internet, published literature, books etc. 10 pts: In class responses will be separately evaluated.

10 pts: Written reports will be separately evaluated

2 Python code running examples XX-09-2020 X-09-2018 Run the example codes given and discuss any problems in class 19-08-2020 Use online help files and other resources. Should be your own work. 10 points for in class discussion
2 Simulating the flipping of a fair coin XX-09-2018 XX-09-2018 Write code in Python to simulate the flipping of a fair coin

The code should take an input from the user to determine the number of coin flips (more than 1). Then, using a random number generator the code should generate random choices between heads and tails, and store the outcome in a "list" object. Code should be uploaded before class on the classroom site.

 19-08-2020 Use the uploade example script as a help. 15 points for code running as expected. Bonus points for originality.
3 Simulating the binomial segregation of proteins into daughter cells 27-Aug-2018: discussing the problem 6-09-2018 Upload ipython code in the GoogleClassroom environment of the BIO315 course.

In class discussion with volunteer T.A. Yash Jawale yash.jawale at the rate students. iiserpune dot ac dot in

 Ref.: Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB (2005) Gene regulation at the single-cell level. Science 307:1962-1965. 1. Does the code run without an error

2. Does it perform the calculations required

3. Does it plot the variables as expected, with axes labelled

20 points
4 Critical reading: Measuring mechanics of cytoskeletal filaments 10-Sep-2018 in class figure-wise discussion of paper

13/09/2018 before 1700h: Written submission by email to <bio322@students.iiserpune.ac.in>

Reading: 10-09-2018

Written submission: 13/09/2018

(A) In class discussion 10/9/2018 Paper on torsion viscometry

of cytoskeletal proteins to understand (a) Principle of experiment,

(b) nature of setup (parts) and (c) conclusions. REF: Janmey (1991) A

torsion pendulum for measurement of the viscoelasticity of biopolymers

and its application to actin networks J. Biochem. Biophys. Meth. 22:41

(B) Written submission after class (Due: 13/09/2018 before 5pm) by

email to THIS ADDRESS (bio322@students.iiserpune.ac.in).

The title of the email should be (for example for group 1) "Group01

submission for paper reading assignment- Janmey 1991"

The report should have the following format:

(a) Title (b) Principle of experiment, (c) nature of setup (parts) and

(d) conclusions. Please write in your own words. The report will be

passed through a plagiarism checker. Marks will be awarded to the

group and become the score of each member of the group too.

The file be named as "Group01_Janmey1991.pdf" (for group 1, for

example). The group members should be clearly listed on the top of the

page

 9/9/2018 REF: Janmey (1991) A

torsion pendulum for measurement of the viscoelasticity of biopolymers

and its application to actin networks J. Biochem. Biophys. Meth. 22:41 [PDF]

 In class explanation of individual figures: 15 marks

Report submission: 15 marks
5 Critical reading & presentation (group activity) None (related to imaging, resolution and magnification) Presentations on 8-Nov-2020 Presentation with slides and board-work to demonstrate:

1) Principle of functioning of the system

2) Application of the method to specific biological problem

3) Advantages and disadvantages of the method

 19-Aug-2020
  1. Group1 [STORM] Bo Huang et al. (2008) Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy Science. 319(5864): 810–813 [LINK]
  2. Group2 [STED] Willig et al. (2007) STED microscopy with continuous wave beams. Nat Methods. 4(11):915-8. [LINK]

    Hell & Wichmann (1994) Breaking the diffraction resolution limit by stimulated emission : stimulated- emission- depletion fluorescence microscopy Opt. Lett. 19(11):780 [LINK]

  3. Group3 [PALM] Betzig et al. (2006) Imaging Intracellular Fluorescent Proteins at Nanometer Resolution Science. Vol. 313, Issue 5793, pp. 1642-1645 [LINK]

  4. Rest: Axelrod et al (1976) Mobility measurements by analysis of fluorescence photobleaching recovery kinetics. BJ [pdf] [LINK] (Monday 15/10/2018)
6

FCS Perpsective: Maiti S, Haupts U, Webb W W (1997) Proc Natl Acad Sci USA 94:11753–11757, pmid:9342306.

 15-Nov-2020 15-Nov-2020 In class discussion of figures and equations. Evaluation based on: 1) explanation of figures

2) connection with theory

3) understanding of the perpsective article

 19-Aug-2020 REF (pdf): http://www.pnas.org/content/pnas/94/22/11753.full.pdf In class explanation of individual figures: 15 marks
7 Critical reading: Affinity Chromatography 5-Dec-2020 5-Dec-2020 In class discussion of figures and equation. Evaluation based on:
  1. Understanding of figures
  2. Connection between data and equations
  3. Perspective of technique: advantages and limitations
 19-Aug-2020 Kasai and Ishii (1975) Quantitative Analysis of Affinity Chromatography of Trypsin: A New Technique for Investigation of Protein-ligand Interaction.J Biochem. 77, p261-264.

Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/805787

In class explanation of individual figures: 15 marks

Instructions for submisions

Updated: 19 Aug 2020