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.

The final exam resources page can be found here.

News

June 9, 2008 - A note about printing your ClustalW results for the final: certain browsers are not able to print out java applets (ClustalW uses these to display some of its results). If you are having printing issues, please read over this website.

June 6, 2008 - The final exam has been posted. The solutions to problem set 7 have also been posted.

June 2, 2008 -

Extra credit opportunity:
Want to cure HIV/AIDS? Want 20 extra credit points on your final?
Click here to find out more!

The solutions to Problem Set 6 have been posted.

May 28, 2008 - Lecture on June 6th will be given by Or Yogev, a student in Erik Antonsson's lab here at Caltech. He will discuss his research involving computational evolutionary embryogeny:

Computational Evolutionary Embryogeny
Or Yogev

Evolutionary and development processes (embryogeny) are used to evolve the configurations of three-dimensional structures to achieve specified performances. The combination of evolutionary and developmental processes is used in natural systems, but has not yet been applied to the design of continuous three-dimensional load-supporting structures.
Beginning with a single artificial cell containing information analogous to a DNA sequence, a structure is grown according to the rules encoded in the sequence which are regulated by an environment. Each artificial cell in the structure contains the same sequence of growth and development rules, and each artificial cell is an element in a finite element mesh representing the structure of the mature individual. Rule sequences are evolved over many generations through selection and survival of individuals in a population. Modularity and symmetry are visible in nearly every natural and engineered structure. Understanding of the evolution and expression of symmetry and modularity are emerging from recent biological research. Initial evidence of these attributes is present in the phenotypes that emerge from the artificial evolution, although neither characteristic is imposed nor selected-for directly.

May 27, 2008 - Problem set 8 has been posted.

May 26, 2008 - The solutions for Problem Set 5 have been posted.

May 23, 2008 - Problem Set 7 has been corrected and reposted. A glossary of immunological terms has also been posted. You may find this useful for PS7.

Office hour changes for this week only:

May 19, 2008 - Problem Set 7 has been posted. An updated midterm answer key has also been posted.

Extra credit seminar TODAY:

Molecular Choreography: Programming Nucleic Acid Self-Assembly and Disassembly Pathways
Date: Monday May 19, 2008 4:00 PM - 5:00 PM
Location: 153 Noyes, Sturdivant Lecture Hall
Niles A. Pierce, associate professor of applied and computational mathematics and bioengineering, Caltech.

Email a 200-word write-up to your TA for 1 extra credit point.

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.

AIDS/Lifecycle to support HIV/AIDS services

On June 1, 2008, Joshua Klein, one of the TAs for Bi1, will begin a 545 mile journey from San Francisco to Los Angeles to help raise funding and awareness for people living with HIV/AIDS in an event called AIDS/Lifecycle. If you'd like to sponsor him, the web link is: http://www.aidslifecycle.org/2268

Office hour changes (permanent):

Message from Pamela about clicker question answers:

You may have noticed that we haven't provided explicit answers to most of the clicker questions in the lecture material. The questions are intended as a study guide. We're hoping that it will help you learn/understand the material better if you have to think about the question without having the answer immediately available. In many cases, the answer to the question is contained in the material on the next few slides. In other cases, more than one answer is correct, or there is only a "mostly correct" answer, so providing an "answer" might be misleading. If you want to discuss any of the clicker questions, please come and see me. I'm happy to provide all of the "answers" to clicker questions or to discuss the rest of the course material.

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):

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:

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:

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

Office hour changes (permanent):

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):

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

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.

Last update: June 9, 2008 | © California Institute of Technology | Questions? soghoian@caltech.edu