Bi 1 “The Biology and Biophysics of Viruses”

1. Bi 1“The Biology and Biophysics of Viruses” Lecture 1 Monday March 28, 2011 Organization of the Course

2. Topic for Bi 1 since 2007:“The Biology and Biophysics of Viruses” Goal: Introduce biological concepts from a quantitative, molecular, chemical and biophysical perspective. No memorization (open book problem sets, exams). Focus on a topic critical to human health: viruses (HIV in particular). An opportunity to use what you’ve learned to address a real world problem. Important to ask questions (PJB Office hours Wednesday after class or by appointment).

3. By the end of the course, students will gain a basic understanding of many issues affecting today’s world; e.g., Evolution Recombinant DNA technology, biotechnology Stem Cell Research Gene therapy Viral outbreaks (e.g., swine flu) Why biology needs physics, math, chemistry, computer science, engineering, etc. and why these fields needs biology Possible careers in fields that use biology

4. What we will NOT cover Clinical aspects of AIDS and other viral diseases, social/political issues surrounding HIV/AIDS Many interesting fields of biology

5. Head TA: Linda Song Office Hours:Tuesdays 2:30 pm; 153 Broad

6. The Bi 1 homepage: http://www.its.caltech.edu/~bi1 Includes: List of TAs, office hours A glossary Links to relevant websites Lecture notes, lecture recordings, problem sets Course information, announcements, policies

7. Moodle • Weekly homework surveys courses.caltech.edu • To join Bi1 class, you’ll need the codeword: jenner

8. Clickers We will use “clickers” (interactive response pads) to assess success in conveying key concepts. We will NOT use clickers to take attendance. Your responses are anonymous -- will not affect your grade.

9. Clicker question: My major is (or will probably be) 1. Chemistry 2. Math 3. Physics 4. Engineering 5. Geology 6. Computer Science

10. Clicker question: I have had taken one or more Biology courses in high school. 1. YES, ≥2 years in high school including AP Biology. YES, 1 year in high school. NO, but I took Biology in junior high. NO.

11. Clicker question: Which is correct? 1. RNA --> DNA --> Protein 2. Protein --> RNA --> DNA 3. DNA --> RNA --> Protein 4. DNA <--> RNA --> Protein

12. Clicker question: HIV and other viruses are susceptible to antibiotics. 1. True 2. False

13. Plagues and pestilence History shaped by epidemics Bubonic plague in 14th century killed 1/3 of Asian and 1/2 of European population (20 million deaths). 16th century Conquistadors conquered America with measles and small pox. 1700s: European navigators introduce syphilis, tuberculosis and whooping cough to South Pacific Islands. Population of Hawaii reduced by almost 90% by 1860. Flu epidemic in 1918-19 killed 20-40 million (more than died in WWI).

14. Ignorance/blame about disease is nothing new… Christians blamed Jews for bubonic plague outbreaks in 14th century. 15-16th centuries: Italians called syphilis “The French Disease”. French called it “The Italian Disease”. 1930s: Cholera in New York was blamed on the Irish. Early 20th century: Polio in US said to be caused by Italian immigrants.

15. CDC* definition of AIDS A = Acquired = a virus received from someone else I = Immune = an individual’s natural protection against disease-causing microorganisms D = Deficiency = a deterioration of the immune system S = Syndrome = a group of signs and symptoms that together define AIDS as a human disease * (Centers for Disease Control and Prevention; Atlanta, GA)

16. What is AIDS? HIV infection is not AIDS (is “HIV disease”) AIDS is umbrella term for 26 known diseases and symptoms AIDS diagnosis if meet three conditions: Have one or more of known diseases/symptoms CD4 T cell count <200/µL What is CD4? What are T cells? Test positive for HIVWhat do HIV tests detect?

17. HIVs (there are many) are related to Simian Immunodeficiency Viruses (SIV) SIVsm • Three groups of HIV-1 M = Main O = Outlier N = New • Group M HIV-1 is responsible for 99% of AIDS cases worldwide. M is divided into ~10 clades. • HIV-2 (related to SIVsm): less prevalent than HIV-1. • We will concentrate on Group M HIV-1. • HIV-1 is related to SIVcpz. SIV is relatively benign, whereas HIV is lethal. HIV-2 O SIVcpz M

18. HIV-1, HIV-2, and SIVsIn nature:HIV-1 and HIV-2 infect humans.HIV-1-related CPZ viruses infect chimps.SIVs infect African monkeys. In laboratories:HIV-1 infects chimpanzees, but does not cause disease. HIV-1 does not infect old world monkeys.Asian macaques infected by some SIV and HIV-2 strains develop AIDS-like disease.

19. World-wide prevalence of HIV (July 2008) People living with HIV/AIDS: ~33 million http://en.wikipedia.org/wiki/Image:HIV_Epidem.png

20. Estimated number of adult and child deaths due to AIDS globally, 1990–2007 3.0 Millions 2.5 2.0 1.5 1.0 0.5 0 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 Year This bar indicates the range around the estimate 5.3

21. Early history of HIV/AIDS 1884-1924 -- (New) estimate for when SIVcpz crossed into humans 1959 -- Earliest known AIDS case: a Bantu man in the Republic of Congo 1981 -- first AIDS cases reported among homosexual males in US 1982 -- AIDS in hemophiliacs, transfusion patients, IV drug users 1983 -- AIDS in US heterosexuals; majority of AIDS in Central Africa affects heterosexuals 1983 -- Virus causing AIDS isolated by groups led by Luc Montagnier (France) and Robert Gallo (US)(SARS virus isolated in 2 weeks in 2003 by international consortium of 13 labs) 1985 -- Blood test to detect HIV 1987 -- AZT licensed for use in AIDS patients 1996 -- anti-HIV drugs (HAART*) reduce AIDS death rates *Highly Active Anti-Retroviral Therapy

22. 10 leading causes of death in US in adults 25-44 years old

23. Impact of AIDS on life expectancy in five African countries, 1970–2010 70 65 60 Botswana 55 South Africa Life expectancy at birth (years) 50 45 Swaziland 40 35 Zambia 30 Zimbabwe 25 20 1970–1975 1980–1985 1990–1995 2000–2005 1975–1980 1985–1990 1995–2000 2005–2010 Source: United Nations Population Division (2004). World Population Prospects: The 2004 Revision, database. 4.1

24. 75 50 Percent testing positive 25 0 0 8 16 24 32 40 48 52 Age HIV Prevalence by Age Pregnant women, Durban, South Africa Fundiswe Chonco, Mopo Leshwedi, Thumbi Ndung’u et al, unpublished

25. What is a virus? Viruses are small* (compared with bacteria) infectious replicating objects that can cause disease in plants, animals, humans. [*5x108 rhinoviruses (common cold) will fit on the head of a pin.] Viruses are parasites -- they live inside cells of their host animal or plant and reproduce by forcing their host to make new viruses. Newly-made viruses leave host cell and infect similar cells. All viruses have a protein coat that encloses genetic material (DNA or RNA). Some also have a membrane (envelope) around the protein coat. Viruses use host cell machinery to make their components (proteins, carbohydrates, membranes), so they are harder to target with drugs than such as bacteria or fungi (self-sufficient pathogens).

26. The genetic material in a virus can be DNA or RNA

28. Why don’t antibiotics work against viruses? • Antibiotics interfere with metabolic processes in bacteria. Metabolic processes in bacteria (prokaryotes) and in us (eukaryotes) are different. • Example: penicillin interferes with the production of bacterial cell walls. Eukaryotic cells don’t have cell walls (neither do viruses). • Viruses use host cell machinery to undergo metabolic processes -- hard to specifically target a viral metabolic process.

29. DNA viruses follow the “Central Dogma” DNA --> RNA --> Protein transcription translation Most RNA viruses also follow part of the Central Dogma RNA --> Protein

30. HIV is a RetrovirusRetroviruses do NOT follow the Central Dogma Retroviruses: a subset of RNA viruses that reverse usual flow of genetic information within host cell Reverse transcription of viral RNA into viral DNA RNA --> DNA --> RNA --> Protein Three subfamilies of retroviruses Oncoviruses (cause cancer) Feline leukemia virus, Rous Sarcoma Virus, Mouse Mammary Tumor Virus Lentiviruses (slow viruses) HIV-1 & HIV-2, Feline Immunodeficiency Virus (cats), Visna virus (sheep), caprine arthritis-encephalitis virus (goats), SIV (nonhuman primates) Spumavirus (not associated with human disease)

32. Some believe that HIV does not cause AIDS ~1987 to present: Peter Duesberg (UC Berkeley) believes there is no single causative agent of AIDS, but disease is a collection of non-infectious deficiencies associated with drug use, malnutrition, parasitic infections, other specific risks. (www.duesberg.com) ~2000-2002: South African President Thabo Mbeki made statements that HIV does not cause AIDS, and that AIDS does not exist (>5 million people in South Africa are HIV-positive).

33. HIV causes AIDS http://www.meds.com/hiv/hivindex3.html See also Durban declaration (signed by >5000 HIV/AIDS scientists and physicians, released in July 2000) for evidence that HIV causes AIDS: http://www.thebody.com/atn/346/declaration.htmlA few compelling facts: Data from matched groups of homosexual males and hemophiliacs shows that only those infected with HIV develop AIDS. Only HIV-positive mothers transmit HIV to fetuses and only HIV-positive newborns develop AIDS. HIV-negative newborns from HIV-positive mothers do not develop AIDS. Laboratory and health-care workers with no known risk factors have developed AIDS after exposure to HIV.

34. Koch’s postulates have been satisfied Causative agent must be found in all cases of the disease. It must be isolated from the host and grown in pure culture. It must reproduce the original disease when introduced into a susceptible host. It must be found in the experimental host so infected.

35. You will need to fill out an add card if: • you register late • want to change sections • want to switch to P/F grading • must be done before Drop Day (5/18/11) • Either Linda or I can sign this.

36. Extra slides

37. Why study HIV? “The Human Immunodeficiency Virus (HIV) epidemic has spawned a scientific effort unprecedented in the history of infectious disease research. This effort has merged aspects of clinical research, basic molecular biology, immunology, cell biology, epidemiology, and mathematical modeling in ways that have not been seen before. The ever unfolding discoveries of novel aspects of HIV-host interaction have been accompanied by (and often have resulted from) novel interactions among researchers in the disparate disciplines.” Coffin, J.M. 1999. Molecular Biology of HIV. In The Evolution of HIV, ed. K.A. Crandall. Baltimore: Johns Hopkins University Press.

39. New AIDS cases and deaths due to AIDS have been reduced in the US

40. Figure 9-12 Number of HIV cases worldwide at end of 2002

41. Worldwide, HIV has spread to 70 million people, killed 30 million and is estimated to infect 40 million more in the next decade. Consider Africa…. Sub-Saharan Africa has ~67% of world’s HIV/AIDS cases but only 10-11% of world’s population -- home to 87% of 2.3 million children living with HIV/AIDS. South Africa has highest number of people living with HIV/AIDS in the world (5.5 million in May 2006) and almost one in five South African adults are HIV positive. National HIV prevalence rate in Swaziland is 33%, the highest in the world. Fact Sheet: The Global HIV/AIDS epidemic (May 2006) Kaiser Family Foundation; www.kff.org/hivaids

42. Figure 9-22 Opportunistic infections and malignancies in AIDS patients

43. Symptoms of AIDS(each symptom can be caused by another disease; can’t rely on symptoms to diagnose AIDS) Rapid weight loss Dry cough Recurring fevers, night sweats Unexplained fatigue Swollen lymph glands Diarrhea that lasts more than a month White spots on tongue, in mouth, or throat (thrush) Pneumonia Red, brown, pink or purplish blotches on skin or inside mouth, nose, or eyelids (Kaposi Sarcoma) Memory loss, depression, other neurological disorders

44. Killing viruses • Can inactivate viruses using physical and chemical agents • Heat (e.g., boiling water) alters structures of proteins and nucleic acids • UV radiation crosslinks thymines in nucleic acids (more in problem set 1) • Formaldehyde combines with free amino groups on nucleic acids • Metals and phenol react with proteins in the viral capsid • Chlorine combines chemically with viral nucleic acid • Detergents denature viral proteins • Antiviral drugs (rare because they can interfere with essential chemical reactions in the host)