Bi 1: The Biology and Biophysics of Viruses

Spring 2008

This course introduces non-biologists to recent advances in our understanding of how HIV and other viruses infect and cause damage to their hosts. Because understanding and treating HIV infection involves a basic knowledge of cell and molecular biology, virology, and immunology, the course will cover fundamental concepts in these areas from a quantitative, molecular, chemical and biophysical perspective.

Where: 119 Kerckhoff
When: Mondays, Wednesdays, and Fridays at 1 pm.

News

May 16, 2008 - The solutions to the midterm have been posted. The average was 245 ± 43.8 (or ~74 ± 13 %). A histogram of the exam grades can be viewed here.

Office hour changes (permanent):

• Angela Zah -- Saturday 7PM, Lloyd room 133

May 12, 2008 - Problem Set 6 has been posted.

May 11, 2008 - Supplemental references about Molecular Dynamics (MD) for PS5 have been posted.

Interested in the bioengineering option? Come to Bioengineering Information Night on Thursday May 15th, 10:30-11:30 PM at 3rd Floor SFL Multimedia Conference Room to find out about how you can pursue Bioengineering at Caltech.

A wide range of topics will be discussed, including:
- the differences between the currently existing engineering options
- how you can combine Bioengineering courses into an existing option
- how you can create your own self-design major (as well as advantages and disadvantages of that approach
- How to get involved with Bioengineering research and what kind of backgrounds they prefer
Also provided will be the faculty's draft for what coursework would be required if a Bioengineering option were available. If you have any questions, contact Parvathy Menon (parvathy@caltech.edu).

May 9, 2008 - Want some more review of protein structure? We've posted a protein structure study guide.

Office hour changes (permanent):

• Angela Chang -- Friday 4 PM, Dabney dining hall

May 5, 2008 - Problem set 5 has been posted along with information on Swiss PDB Viewer.

Extra Credit Opportunity: Watch the movie And the Band Played On and hand in a brief discussion (<1 page) of the highlights to their TA. (For a description of the movie, see http://www.imdb.com/title/tt0106273/). You may obtain the DVD from Damien during lecture (please return it by the following lecture).
Address the following in your summary: In a dramatic scene from the movie, French scientists are seen testing for radioactivity in lymph node samples from AIDS patients. When they find a sample that has >22,000 cpm, they congratulate themselves for confirming the presence of a retrovirus. Briefly describe the scene, including which characters were present, and discuss what kind of assay involving radioactive samples could be used to detect the presence of a retrovirus.

May 4, 2008 - Office hour changes for this week only:

• Professor Bjorkman's office hours on Monday, May 5 will be from 2-2:30 PM (instead of 2-3:00 PM). Students who wish to speak with her outside of that time are welcome to make an appointment.
• Csilla Felsen's office hours on Sunday, May 4 are cancelled.
• Stephanie Johnson's office hours on Monday, May 5 are cancelled.

May 1, 2008 - The midterm and midterm resources page have been posted.

April 31, 2008 - The slides from the midterm review have been posted.

The solutions for problem set 3 and problem set 4 have been posted.

Extra credit assignment: For extra credit, attend the African health symposium held at Caltech on May 3. The GEANCO foundation symposium will focus on the health impact of HIV/AIDS and malaria in Africa. Speakers include David Baltimore and others. Saturday, May 3 from 10:00am - 1:00pm in Ramo Auditorium. Click here for more information. If you attend the symposium and send your TA a brief (~200 word) summary by May 10, you will get an extra section point.

April 27, 2008 - Problem Set 4 has been corrected and reposted. Problem 4B erroneously had the two primers used by "your friend" labeled as "forward." The two primers should have been labeled "forward" and "reverse." (The friend's error was NOT using two forward primers).

April 24, 2008 - The solutions for problem set 2 have been posted.

April 21, 2008 - Problem set 4 has been posted.

The solutions for problem set 1 have been corrected and reposted.

April 18, 2008 - The solutions for problem set 1 have been posted.

April 14, 2008 - Problem set 3 has been posted.

April 10, 2008 - The Briggs, et al. paper referenced in PS2 #4B can be found here.

Office hour changes for this week only:

• Harish Vasudevan's office hours on 4/13 have been rescheduled for Monday, 4/14 at 2 PM in the Fleming Lounge.

April 9, 2008 - The slides from the Professor Phillips's review session today have been posted.

Office hour changes (permanent):

• Peera Jaru-Ampornpan -- Sunday 6 PM, SFL Study Room 2-1

April 8, 2008 - Problem Set 2 has been corrected and reposted. (Problem 2C was corrected to say "with diameter 10µm" instead of "with radius 10µm").

April 7, 2008 - Problem Set 2 has been posted and is due Monday, April 14.

Review session - Wed, April 9: Professor Phillips will hold a review session on Wednesday, April 9 at 7 PM in 119 KRK to go over some of the basic concepts of polymer biophysics (e.g., the random walk model) and estimation. This is optional, but strongly encouraged if these concepts are new to you.

Section 3 room change - Section 3 (formerly held in 3 BBB) will now be held in 101 KRK. The time, Thursday at 2 PM, will remain the same.

Office hour changes (permanent):

• Angela Chang -- Sunday 9 PM, Ruddock Lounge
• Linda Song -- Sunday 10 PM, SFL Study Room 2-4
• Csilla Felsen -- Sunday 9 PM, SFL Study Room 2-1
• Stephanie Johnson -- Monday 10:30 AM, Broad Cafe
• Helen Lee -- Sunday 8 PM, 228 Lloyd house

April 5, 2008 - Office hour changes for this week only:

• Professor Bjorkman's office hours are cancelled on 04/07. She will be away all week.
• Angela Zah's office hours on 04/05 have been moved to 1 PM on Sunday, 04/06.

April 1, 2008 - Students may be interested to know about an African health symposium held at Caltech in May. The GEANCO foundation symposium will focus on the health impact of HIV/AIDS and malaria in Africa. Speakers include David Baltimore and others. Saturday, May 3 from 10:00am - 1:00pm in Ramo Auditorium. Click here for more information. If you attend the symposium and send your TA a brief (~200 word) summary, you will get an extra section point.

March 31, 2008 - Problem Set 1 has been posted and is due Monday, April 7.

Extra credit assignment: For extra credit, attend the seminar "Consumer Antibacterial Soaps: Effective or Just Risky" at 4 PM on April 1 in 119 KRK. If you attend the seminar and send your TA a brief (~200 word) summary, you will get an extra section point. Please turn this in by 5PM on Tuesday, April 8.