Bi 1 Final Resources

The Bi 1 final is an open-book test. You may use your textbook, any resource on this page (including lecture slides and links), handouts from section, as well as any notes written in your own hand.

Download the Bi1 2008 final here (ZIP file).

Or, download the individual final files:

• PDF
• Fasta file for problem 1: rt.fa
• PDB files for problem 3:
  • groove.pdb
  • HLA.pdb

The final is due on Wednesday, May 11 at 5 PM in the Bi1 closet.

Resources

• BLAST

• ClustalW

• SwissPDB-related items:

  • SwissPDB Viewer for Mac OS X
    
  • SwissPDB Viewer for Windows (95/98/Me/NT/2000/XP/Vista)
    
  • Bi 1 SwissPDB Viewer tutorial and sample file

    
    

• General glossary - HTML or PDF
• Immunobiology glossary - PDF
• Problem Set 1 Solutions
• Problem Set 2 Solutions
• Problem Set 3 Solutions
• Problem Set 4 Solutions
• Midterm Solutions
• Problem Set 5 Solutions
• Problem Set 6 Solutions
• Problem Set 7 Solutions

 

Schedule

#	Lecture Topic	Lecturer	Reading 3/E	Reading 2/E	Homework & Exams	Date
1	Introduction to Bi 1	RP	Ch. 1	Ch. 1	PS 1 posted	Mon, 3/31
2	The great ideas of biology I: cell theory, unity of biochemistry, genetics	RP	Ch. 13	Ch. 13		Wed, 4/02
3	The great ideas of biology II: evolution	RP	Ch. 24, 25, 27	Ch. 23, 24, 26		Fri, 4/04
4	Eukaryotic cells and organelles	RP	Ch. 7	Ch. 7	PS 1 due PS 2 posted	Mon, 4/07
5	Parts list of a cell	RP	Ch. 3-6	Ch. 3-6		Wed, 4/09
6	Viruses and parts list of viruses	RP	Ch. 35	Ch. 34		Fri, 4/11
7	Genome science	RP	Ch. 19, 20	Ch. 19, 20	PS 2 due PS 3 posted	Mon, 4/14
8	The central dogma	RP	Ch. 15	Ch. 15		Wed, 4/16
9	Replication	RP	Ch. 14	Ch. 14		Fri, 4/18
10	Transcription and gene regulation I	RP	Ch. 16	Ch. 16	PS 3 due PS 4 posted	Mon, 4/21
11	Transcription and gene regulation II	RP	Ch. 16	Ch. 16		Wed, 4/23
12	Translation	PJB	Ch. 16-18	Ch. 16-18		Fri, 4/25
13	Molecular biology (w/ demo)	PJB/RP	Ch. 19, 20	Ch. 19, 20	PS 4 due	Mon, 4/28
14	Structural biology I: Proteins and X-ray diffraction	PJB	Ch. 3, 5, 6	Ch. 3, 5, 6		Wed, 4/30
	Midterm review, Wed 4/30, 4-6pm, 119 Kerckhoff	TAs
					Midterm posted	Thu, 5/01
15	Structural biology II: Icosahedral viruses	PJB	Ch. 35	Ch. 34		Fri, 5/02
16	HIV lifecycle and HIV evolution	PJB	Ch. 35	Ch. 34	Midterm due PS 5 posted	Mon, 5/05
17	HIV lifecycle and HIV evolution II	PJB	Ch. 35	Ch. 34		Wed, 5/07
18	Innate immunity	PJB	Ch. 49	Ch. 49		Fri, 5/09
19	Abs, B cells, VDJ recombination	PJB	Ch. 49	Ch. 49	PS 5 due PS 6 posted	Mon, 5/12
20	MHC, T-cells I	PJB	Ch. 49, 20, 35	Ch. 49, 20, 34		Wed, 5/14
21	MHC, T-cells II	PJB	Ch. 49, 20, 35	Ch. 49, 20, 34		Fri, 5/16
22	MHC, T-cells III	PJB	Ch. 49, 20, 35	Ch. 49, 20, 34	PS 6 due PS 7 posted	Mon, 5/19
	Ditch Day					Wed, 5/21
23	Stem cells	PJB	Ch. 19, 22	Ch. 19, 22		Fri, 5/23
	Memorial Day					Mon, 5/26
					PS 7 due PS 8 posted	Tue, 5/27
24	Anti-HIV drugs	PJB	Ch. 20, 35, 49	Ch. 20, 34, 49		Wed, 5/28
25	Neutralizing antibodies against HIV	PJB	Ch. 35, 49	Ch. 34, 49		Fri, 5/30
26	Vaccines I	PJB	Ch. 49	Ch. 49		Mon, 6/02
					PS 8 due	Tue, 6/03
27	Vaccines II	PJB	Ch. 49	Ch. 49		Wed, 6/04
	Final review, Wed 6/04, 4-6 pm, 119 Kerckhoff	TAs
28	"Computational Evolutionary Embryogeny" Or Yogev				Final posted	Fri, 6/06
					Final due	Wed, 6/11

Lecture 1: Introduction to Bi 1

Download: PDF (handout) - 1.6 MB | PDF (full page) - 7.8 MB | PPT - 21.7 MB

Links:

• http://www.apla.org/facts/HIV_statistics_current.pdf
  Current statistics for HIV infection and AIDS in Los Angeles County
• http://en.wikipedia.org/wiki/Image:HIV_Epidem.png
  Figure showing worldwide HIV prevalence
• http://www.kff.org/hivaids
  Fact Sheet: The Global HIV/AIDS epidemic (May 2006) from the Kaiser Family Foundation

Lecture 2: The great ideas of biology I - cell theory, the unity of biochemistry, genetics

Download: PDF (handout) - 2.4 MB | PDF (full page) - 8.2 MB | PPT - 32.1 MB

Links:

• Deciphering the Genetic Code: Marshall Nirenberg
  A beautiful and highly readable account of Nirenberg's experiments that led to understanding the genetic code (and a Nobel Prize).
• The Three Domains of Life
  This fun little article describes the three domains of life and gives a hint at the diverse lifestyles of Archaea.
• It's in the Blood! A Documentary History of Linus Pauling, Hemoglobin and Sickle Cell Anemia
  This interesting website talks about Linus Pauling's efforts in understanding hemoglobin and includes a description of his work on using molecules as clocks.
• Electron microscopy image gallery
  EM images from the Canadian Food Research and Development Centre.
• ASCB Image and Video Library
  This website has excellent images of cells so you can get a better
  feeling for cell diversity.

Lecture 3: The great ideas of biology II - evolution

Download: PDF (handout) - 1.8 MB | PDF (full page) - 9.3 MB | PPT - 14.7 MB

Suggested Reading:

• "Ancient DNA", Nat. Rev. Genetics, 2, 353, (2001) by Paabo - this article describes the use of molecular studies on extinct organisms.
• "The Beak of the Finch" by Jonathan Weiner (CLAS)- This Pulitzer prize winning book is a classic and a must read. It tells the story of studies of evolution in real time in the Galapagos, the life's work of Peter and Rosemary Grant and their students and postdocs.
• "At the Water's Edge" by Carl Zimmer - a wonderful book that tells how living organisms first left the water (fins to limbs) and how mammals went back to the sea again. Great stuff.
• "Your Inner Fish" by Neal Shubin (CLAS) - Shubin is a noted paleontologist who has found many important and celebrated transitional forms. This excellent book describes his "course" for medical students on human anatomy told from the point of view of our inner fish.
• "The Origin of Species" by Charles Darwin. Arguably the most important science book ever written. This remarkable synthetic opus is beautifully written, full of an amazing array of different ideas, observations and experiments and completely accessible to any interested reader. You must read this book.
• "Life on a Young Planet" by Andrew Knoll. (CLAS) - An amazing book that examines the evidence for life during the first four billion years of planet Earth's existence.

Links:

• Whale Evolution (YouTube)
  This is a discussion of the work of Philip Gingerich on whale fossils from the superb PBS series on evolution.
• Building Tiktaalik (YouTube)
  This video shows how models of extinct organisms like Tiktaalik are constructed.
• Evolution fish with fingers Transitional fossils (YouTube)
  A clip from the fantastic PBS series on evolution that shows Jenny Clack, discoverer of key transitional forms in the transition from fins to limbs.

Lecture 4: Eukaryotic cells and organelles

Download: PDF (handout) - 2.0 MB | PDF (full page) - 10.8 MB | PPT - 48.5 MB

Lecture 5: Parts list of a cell

Download: PDF (handout) - 10 MB | PDF (full page) - 13.1 MB | PPT - 10.7 MB

Review Session #1 - April 9

Download: PDF (handout) - 2.1 MB | PDF (full page) - 3.1 MB | PPT - 1.9 MB

Lecture 6: Viruses and parts list of viruses

Download: PDF (handout) - 11.8 MB | PDF (full page) - 15.4 MB | PPT - 14 MB

Suggested Reading:

• Structural Biology of HIV, Turner and Summers, J. Mol. Biol. 285:1 (1999)
  This article describes both the life cycle and parts list of HIV.
• Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography, Benjamin et al., J. Mol. Biol. 346:577 (2005)
  This paper uses cryo-electron microscopy to provide insights into the structure of mature HIV.
• Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells, Wright and Schooler et al., EMBO J in press (2007)
  A subsequent paper using cryo-EM to look into the structure of immature HIV particles.
• The HIV lipidome: A raft with an unusual composition, Brügger et al., PNAS 103:2641 (2006)
  This interesting paper describes measurements of the lipid content of HIV.
• Molecular Architecture of Bacteriophage T4, Mesyanzhinov et al., Biochemistry (Moscow) 69:1190 (2004)
  This paper illustrates the enormous progress that has been made on determining the parts that make up bacteriophage T4

Lecture 7: Genome science

Download: PDF (handout) - 1.9 MB | PDF (full page) - 8.2 MB | PPT - 18.9 MB

Lecture 8: The central dogma

Download: PDF (handout) - 3.6 MB | PDF (full page) - 7 MB | PPT - 2.6 MB

Lecture 9: Replication

Download: PDF (handout) - 8.6 MB | PDF (full page) - 10.3 MB | PPT - 9.6 MB

Suggested Reading:

• The DNA replication problem, 1953–1958, Frederic L. Holmes, Trends in Biochemical Sciences, Volume 23, Issue 3, 1 March 1998, Pages 117-120
  This article describes some of the intellectual challenges faced in thinking about DNA replication.

Lecture 10: Transcription and gene regulation I

Download: PDF (handout) - 6.4 MB | PDF (full page) - 8.7 MB | PPT - 10.8 MB

Lecture 11: Transcription and gene regulation II

Download: PDF (handout) - 8.2 MB | PDF (full page) - 12.4 MB | PPT - 10.2 MB

Lecture 12: Translation

Download: PDF (handout) - 3.4 MB | PDF (full page) - 3.5 MB | PPT (zip file with movies) - 32.8 MB

Links:

• The Genetic Code
  Brief description of the history of solving the genetic code.
• The RNA world: History of an idea, an idea of history
  Discusses idea that RNA was the first life-form on earth. The hypothesis is support by the facts that RNA can store, transmit and duplicate genetic information as well as function as an enzyme to catalyze reactions. See also The RNA World (nobelprize.org).
• Protein synthesis: an epic on the cellular level (YouTube) - A 1970s take on protein synthesis.
  

Lecture 13: Molecular biology

Download: PDF (handout) - 11.6 MB | PDF (full page) - 12 MB | PPT (zip file with movies) - 17.9 MB

Links:

• Plasmid cloning (YouTube) - A brief overview of DNA subcloning.
• Restriction enzymes (YouTube) - A video description of restriction enzymes.
• The test-tube synthesis of a chemical called poliovirus. Wimmer, E. EMBO Reports 7: S3-S9 (2006).
  The simple synthesis of a virus has far-reaching societal implications.
• DNA Interactive
  Many of the movies shown in class come from this site. It also includes interviews with scientists who made critical discoveries in molecular biology, biotechnology, and/or recombinant DNA research.
• genome.gov | 2003 Release: International Consortium Completes HGP
  The press release announcing the completion of the public human genome project.
• Human Genome Projects Information
  All about the Human Genome Project.
• Centre for Integrated Genomics
  "Development and application of genome science to the diagnosis and treatment of cancer"
• Commonality with other organisms
  A page exploring similarity of genomes among different species.
• Gene Expression in Cultured Cells
  This website has lots of interesting discussion of strategies for putting foreign DNA into different types of cells.
• Roche Applied Science: Cutting-Edge Transfection Reagents
  This site gives a discussion of different products that are used to transfect cells. (If you go to this URL, you may be asked to select your country. Just select "United States" and hit Go.)

Lecture 14: Structural biology I: Proteins and X-ray diffraction

Download: PDF (handout) - 7.7 MB | PDF (full page) - 8.6 MB | PPT (zip file with movies) - 25.5 MB

SwissPDB-related items:

• SwissPDB Viewer for Mac OS X
  
• SwissPDB Viewer for Windows (95/98/Me/NT/2000/XP/Vista)
  
• Bi 1 SwissPDB Viewer tutorial and sample file

Suggested reading:

• Rosalind Franklin: The Dark Lady of DNA by Brenda Maddox
  Biography of the crystallographer who obtained the diffraction image of B form DNA that led to the solution of DNA's structure.

Links:

• DNA Interactive
  Many of the movies shown in class come from this site. It also includes interviews with scientists who made critical discoveries in molecular biology, biotechnology, and/or recombinant DNA research.
• NOVA | Secret of Photo 51 | PBS
  Discusses the contributions of Rosalind Franklin to the discovery of the structure of DNA. Includes an explanation of Franklin's famous "X"-shaped diffraction pattern of DNA, which demonstrates that DNA is helical.
• Rosalind Franklin and the Double Helix, by Lynne Osman Elkin, Physics Today, March 2003
  The history of the discovery of the structure of DNA. Corrects some of the distortions about Franklin that appear in James Watson's book "The Double Helix".
• Caltech Archives Oral Histories Online - Interview with Linus Pauling
  Interview in 1984 with Linus Pauling, Caltech Professor of Chemistry, recipient of the Nobel Prize in Chemistry (1954; for "his research on the nature of the chemical bond") and the Nobel Peace Prize (1962). Pauling discusses the Biology Division at Caltech, Thomas Hunt Morgan, his work on hemoglobin in the 1930s, immunology, and his discovery of the alpha-helix.
• JenaLib: The Amino Acid Repository
  Structures and properties of the 20 amino acids in proteins
• Tangible Interfaces for Molecular Biology
  Hands-on models of proteins
• Kevin Cowtan's Picture Book of Fourier Transforms
  Nice tutorial on the use of Fourier transforms in X-ray crystallography
• The RCSB Protein Data Bank
  An archive of the coordinates of the structures of macromolecules determined by X-ray crystallography, NMR, and electron microscopy.
• The Molecular Observatory
  The Molecular Observatory provides the Caltech community with exceptional capabilities in macromolecular crystallography, including a synchrotron radiation beam line at SSRL and an on-campus crystallization laboratory providing state-of-the-art robotics for crystallization.

Midterm Review

Download: PDF (handout) - 9.8 MB | PDF (full page) - 9.8 MB | PPT - 10 MB

Lecture 15: Structrual biology II: Icosahedral viruses

Download: PDF (handout) - 10.2 MB | PDF (full page) - 11.16 MB | PPT (zip file with movies) - 65.7 MB

Reading:

• Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs, Baker et al., Microbiol Mol Biol Rev Dec 63:862 (1999)
  This gorgeous paper gives a variety of structural insights into the construction of viruses. It is also a nice review of the techniques for 3-D reconstruction of icosahedral viruses by electron microscopy.
• Geometry of Phage Head Construction, Moody, J. Mol. Biol. 293:401 (1999)
  This is a wonderful review paper discussing the architecture of phage capsids from a geometrical and physical perspective. Nanotechnology at its finest.
• Structural Biology of HIV, Turner and Summers, J. Mol. Biol. 285:1 (1999)
  This article describes both the life cycle and parts list of HIV.

Links:

• Virus Ultrastructure
  An introduction to virology, by an electron microscopist. Contains EM images of many different viruses.
• Principles of Virus Architecture
  From the Virus Ultrastructure site above, a page on the geometrical principles of virus capsid construction.
• All the Virology on the WWW
  A very large and comprehensive site with information on all aspects of virology, as well as links to course notes, tutorials, graduate programs, and more.
• The Big Picture Book of Viruses
  A massive catalog of virus pictures on the internet. Part of All the Virology on the WWW.
• Geodesic Domes
  A page on Buckminster Fuller's triangulated domes, mathematically similar to viral capsids and carbon fullerenes.
• Virus Structure
  A brief overview of virus structure, discussing HIV (incorrectly) as well as examples of helical and icosahedral viruses.
• Virus particle explorer
  Database and website for icosahedral virus structures and their analysis.

Lecture 16: HIV lifecycle and HIV evolution I

Download: PDF (handout) - 6.2 MB | PDF (full page) - 6.2 MB | PPT (zip file with movies) - 57.7 MB

Suggested Reading:

• Molecules of HIV
  This website will help you understand the parts list of HIV.
• Interactive Multimedia Textbook of HIV/AIDS
  Links to many articles about scientific and clinical aspects of HIV/AIDS.
• HIVinfosource
  Animations of various steps in the HIV lifecycle.
• HIV Lifecycle
  Allows you to step through an animation of the steps in the HIV lifecycle, with an explanation for each. Also information on mode of action of fusion inhibitors, reverse transcriptase inhibitors and protease inhibitors.

Further reading:

• Visualization of the intracellular behavior of HIV in living cells, McDonald et al., J Cell Biol 159:441 (2002)
  Live cell imaging of HIV accomplished by observing GFP-tagged viruses in infected cells.
• Unchain my heart, baby let me go—the entry and intracellular transport of HIV, Sodeik, J Cell Biol 159:393 (2002)
  Commentary on above paper.

Links:

• Structure-based drug design: From the computer to the clinic.
  Focuses on design of anti-HIV drugs and includes an overview of the HIV lifecycle.
• Attacking AIDS with a 'Cocktail' Therapy
  FDA Consumer magazine article on HAART (highly active anti-retroviral therapy)
• FDA-approved Anti-HIV Drugs
  FDA-approved anti-HIV drugs, including HIV protease inhibitors

Lecture 17: HIV lifecycle and HIV evolution II

Download: PDF (handout) - 9.1 MB | PDF (full page) - 9.3 MB | PPT (zip file with movies) - 21.3 MB

See reading for lecture 16.

Lecture 18: Innate Immunity

Download: PDF (handout) - 4.6 MB | PDF (full page) - 4.7 MB | PPT (zip file with movies) - 6.8 MB

Suggested Reading:

• Understanding the Immune System: How It Works
  A primer on immunology that introduces the cells and molecules of the immune system.
• The Health Library — Immune System
  Web resources about the immune system.
• How the Immune System Works by Lauren M. Sompayrac
  

Links:

• The Inner Life of the Cell
  This movie focuses upon leukocyte migration through blood vessel walls into inflamed tissues, which we will discuss in Lecture 16. It is highly recommended that you watch the movie in its entirety (~7 minutes), because it covers many of the processes we will discuss in class.
• Leukocyte Extravasation
  An interactive animation on leukocyte migration through blood vessel walls into inflamed tissues, as discussed in today's lecture.
• immunoanimations
  Animations from the Immunobiology textbook (Janeway et al.)
• Neutrophil Hunting
  A neutrophil hunting for a pathogen to eat.

Lecture 19: Abs, B cells, VDJ recombination

Download: PDF (handout) - 9 MB | PDF (full page) - 9 MB | PPT (zip file with movies) - 19.5 MB

Links:

• What the heck is an antibody?
  
• Mike's Immunoglobulin Structure/Function Home Page
  Pictures of antibody molecules
• The Antibody Resource Page
  Links to commercial antibody products.
• Ask Lenore ~ Breastfeeding: How Breast Milk Protects Newborns
  How breast feeding protects newborns (antibodies and other useful molecules)
• immunoanimations
  Animations from the Immunobiology textbook (Janeway et al.) Click on the orange textbook once you get to this site, then choose which animation you want to watch.
• Immunotherapy for Cancer - Monoclonal Antibodies
  Monoclonal antibodies used to treat cancer
• Medicine 1984
  The 1984 Nobel Prize in Physiology or Medicine was given to Niels Jerne, Georges Kšhler, and Cˇsar Milstein "for theories concerning the specificity in development and control of the immune system and the discovery of the principle for production of monoclonal antibodies".
• Medicine 1987
  The 1987 Nobel Prize in Physiology or Medicine was given to Susumu Tonegawa "for his discovery of the genetic principle for generation of antibody diversity" (i.e., for discovery that antibodies are made by combining different gene segments in B cells)

Lecture 20: MHC, T-cells I

Download: PDF (handout) - 15.4 MB | PDF (full page) - 15.4 MB | PPT (zip file with movies) - 29.7 MB

Reading:

• see lecture 18 for list
  

Links:

• What the heck is an MHC molecule?
  
• Body odour preferences in men and women: do they aim for specific MHC combinations or simply heterozygosity?
  Wedekind & FŸri, 1997, Proc. R. Soc. Lond. B. 264:1471-9. The T-shirt paper suggesting that MHC or linked genes influence human mate choice.
• Medicine 1996
  The 1996 Nobel Prize in Physiology or Medicine was given to Peter Doherty and Rolf Zinkernagel "for their discoveries concerning the specificity of the cell mediated immune defense" (i.e., for the discovery of MHC-restricted recognition of antigen by T cells)
• Anthony Nolan Research Institute - HLA Informatics Group
  HLA informatics web page
• MHCPEP
  Database of peptides that bind to different MHC alleles
• immunoanimations
  Animations from the Immunobiology textbook (Janeway et al.)
• Pop quiz: What is the rate of mistaken paternity?
  A web page discussing the evidence on the rates of mistaken paternity (probably not as high as 10%).
• Forget Mistletoe, What about DNA?
  An article that describes the story behind scientificmatch.com, a dating website that matches people based on MHC polymorphism.

Lecture 21: MHC, T-cells II

Download: PDF (handout) - 13.8 MB | PDF (full page) - 13.8 MB | PPT (zip file with movies) - 31.9 MB

Reading:

• see lecture 18 for list
  

Links:

• IMGT Databases at the EBI
  T cell receptor and antibody sequences
• immunoanimations
  Animations from the Immunobiology textbook (Janeway et al.) Click on the orange textbook once you get to this site, then choose which animation you want to watch.

Lecture 22: MHC, T-cells III

Download: PDF (handout) - 11.4 MB | PDF (full page) - 11.6 MB | PPT (zip file with movies) - 46.7 MB

Reading and Links:

• see lecture 20 and lecture 21

Lecture 23: Stem cells

Download: PDF (handout) - 4.9 MB | PDF (full page) - 4.9 MB | PPT - 4.8 MB

Reading:

• 5 things to know before jumping on the iPS bandwagon. David Cyranoski, Nature 452, 406-408 (2008)
  A discussion of induced pluripotent stem cells

Links:

• NIH website on stem cells
  http://stemcells.nih.gov/index.asp
• NIH glossary of stem cell terms:
  http://stemcells.nih.gov/info/glossary.asp
• Information about California's Proposition 71
  http://igs.berkeley.edu/library/htProp71StemCell.html
• California Institute for Regenerative Medicine
  http://www.cirm.ca.gov/
• Cloning fact sheet -- defines and discusses molecular cloning, reproductive cloning, therapeutic cloning
  http://www.ornl.gov/sci/techresources/Human_Genome/elsi/cloning.shtml

 

Lecture 24: Anti-HIV drugs

Download: PDF (handout) - 3.5 MB | PDF (full page) - 4 MB | PPT (zip file with movies) - 63.9 MB

Links:

• HIV Reverse Transcriptase PDB molecule of the month (September 2002)
• FDA Approved HIV and AIDS Treatments Details currently approved NRTIs, NNRTIs, protease inhibitors, entry inhibitors, integrase inhibitors, and combination medications.
  

Lecture 25: Neutralizing antibodies against HIV

Download: PDF (handout) - 6.6 MB | PDF (full page) - 6.9 MB | PPT (zip file with movies) - 8.6 MB

Reading:

• An AIDS vaccine: no time to give up. Burton et al., Lancet 364:1938 (2004).
  A one-page letter to the editor in the British medical journal Lancet, arguing for optimism in AIDS vaccine development.
• Antibody vs. HIV in a clash of evolutionary titans. Burton et al., PNAS 102:14943 (2005).
  A nice review on neutralizing antibodies against HIV. Beautifully illustrated.
• Correlates of immune protection in HIV-1 infection: what we know, what we don't know, what we should know. Pantaleo and Koup. (2004) Nat Med 10:806.
  A review on mechanisms of HIV vaccines.

Links:

• Center for HIV-AIDS Vaccine Immunology
  A description of on-going vaccine trials.

Lecture 26: Vaccines I

Download: PDF (handout) - 3.3 MB | PDF (full page) - 3.4 MB | PPT (zip file with movies) - 13.7 MB

Reading:

• Whole-Killed Vaccines, NIAID Division of AIDS, HIV Vaccine Site
  Attempts to make an HIV vaccine using a traditional approach (whole-killed viruses)
• Live-Attenuated Viruses, NIAID Division of HIV Vaccine Site
  Considerations for the use of live-attenuated viruses as vaccines against HIV
• Live attenuated HIV vaccines: pitfalls and prospects. Whitney and Ruprecht. (2004) Curr Opin Infect Dis. 17:17.
  
• Correlates of immune protection in HIV-1 infection: what we know, what we don't know, what we should know. Pantaleo and Koup. (2004) Nat Med 10:806.
  A review on mechanisms of HIV vaccines.
• Gene therapy
  The Wikipedia entry for gene therapy.
• 'Miracle' gene therapy trial halted
  Gene therapy trials to treat SCID halted because of induced cancers directly related to the treatment.
• Targeting lentiviral vectors to specific cell types in vivo. Yang et al. (2006) PNAS 103:11479
  Research done in the laboratory of David Baltimore (former Caltech President) as part of the Engineering Immunity project.
• Information on the Merck HIV vaccine trial:
  • HIV vaccine may have made people more vulnerable to infection
  • CROI: AIDS vaccine: additional infection risk restricted to uncircumcised men

Links:

• FAQs: Avian Flu
  Frequently asked questions about bird flu.
• The 1918 Spanish Flu Pandemic, and the Emerging Bird Flu Pandemic
  
• What the heck is a DNA vaccine?
  
• Center for HIV-AIDS Vaccine Immunology
  A description of on-going vaccine trials.

Lecture 27: Vaccines II

Download: PDF (handout) - 14.6 MB | PDF (full page) - 16 MB | PPT - 13.9 MB

Reading:

• See lecture 26

Final Review

Download: PDF (full page) - 20.3 MB

Lecture 28: Guest Lecture