ADDING

1. Add-Drop Instructions Immunology BICD 140 Winter 2005 ADDING 1. This class is open.  Students may add this course on a first come, first served basis via WebReg during the first two full weeks of the quarter (January 3rd- 14th). (NOTE: If this class was previously CLOSED and you were on a wait list, you will need to drop yourself from the wait list in order to add the class.) The last day to add is Friday, January 14th. 2. I cannot sign add cards for students who wish to add except if the student is a concurrent enrollment student. Concurrent Enrollment add cards will only be signed during the 3rd week of the quarter if spaces are available. Students in need of pre-requisite overrides should send an email to me including student name and PID. 3. WITHDRAWAL PROCESS The last day to drop a class without a “W” is Friday, January 28th and the last day to drop a class with a “W” is Friday, March 4th.Please direct all Add/Drop inquiries to Student Affairs at x40557.

2. Discussion Sections - Immunology BICD 140 Winter 2005Sections will discuss lectures, homework assignments, and exams. You must choose one discussion section and hand in your homework to your designated TA. SectionDayTime (50')RoomTA Email A01 TBA TBA TBA Laura lhgreen@ucsd.edu A02 Thurs 6:00 PM CENTR 217b Adam jbest@ucsd.edu A03 Thurs 5:00 PM CENTR 218 Lauren laurenannd@yahoo.com A05 Fri 08:00 AM CENTR 218 Matt jzones@ucsd.edu A06 Fri 10:00 AM CENTR 220 Hart hdengler@ucsd.edu A04 Fri 11:00 AM CENTR 218 " Note: This page will be updated to show the correspondence between TAs and Discussion Sections

3. Web Site Note: site for last year’s course: Username: bicd Password: 140 PLEASE READ “COURSE INFORMATION” If you do not check the e-mail address listed by the registrar, you will not receive course announcements http://hedricklab.ucsd.edu/BICD140

4. Grading: Two midterm exams each worth 100 points One final worth 150 points The homework grade (100 points total) will be automatically substituted for your lowest midterm! However, you must take both midterms. If you have a valid excuse to miss a midterm (e.g., death in family, severe illness, car accident on the way to school), drop off a note signed by a relevant official to Mandy Butler’s Office, York 3080. In that case, your homework will substitute for the missing midterm. Do not miss a midterm without a valid excuse. There will be no make-up midterms. You must take the final. If you have a conflict with the Final date, let me know immediately.

5. Final Exam Date (from Student Link)

6. Lecture 1 Introduction to immunology • Immunity in bacteria- there is no free lunch • Brief history of immunology • Overview of vertebrate immunity (Chapter 1) • Innate vs. Acquired Immunity- conceptual and practical difference • NEXT LECTURE • How does innate immunity work? • (Chapter 7 and 8 dealing with complement and innate immunity)

7. The word IMMUNITY Derives from the latin immunitas, meaning freedom from public service (i.e., the military draft). From Merriam-Webster dictionary: “a condition of being able to resist a particular disease especially through preventing development of a pathogenic microorganism or by counteracting the effects of its products”

8. There are two kinds of immunity HOST DEFENSE= Innate + adaptive immunity Resistance to infection can be learned or innate. It appears that many organisms lack learned immunity, but can have robust innate defenses. As we shall see, learned immunity is an evolutionary offshoot of innate immunity, and the human immune system combines both types in host defense.

9. The Triumph of Death - Pieter Brueghel the Elder ca. 1562

10. Big bugs have little bugsUpon their backs to bite ‘emLittle bugs have littler bugsAnd so on ad infinitum -Ogden Nash Every organism needs host defense Colonization of large organisms by smaller organisms or viruses is the “inverse food chain” Large complex organisms present a source of energy and a habitat for smaller organisms and viruses via colonization Colonization and defense against colonization is a fundamental principle in biology The immune system is principally and most importantly evolved to sculpt colonization to benefit the host

11. Concept 1 Every organism needs to distinguish self from non-self because everyone has a parasite Case study: bacteria

12. Bacteria have innate immunity (and tolerance) to bacteriophage Efficiency of growth 100% E. coli Strain C bacteriophage E. coli strain C is sensitive to phage grown in either strain K-12 or C. Efficiency of growth 100% Efficiency of growth 100% restriction E. coli Strain K-12 Efficiency of growth 0.02% E. coli strain K-12 is resistant to phage grown in E. coli strain C Bertani, G. & Weigle, J. J. (1953) Adapted from Murray NE. Microbiology. 2002, 148:3-20.

13. What “restricted” the phage growth? Restriction enzymes Example EcoRI target sequence 5’...GAATTC...3’ 3’...CAATTG...5’

14. A chemical difference between self and foreign is distinguished Strategy: mark “self” DNA and destroy “non-self” DNA Type 2 restriction/ modification system of bacteria EcoR1 methylase modifies host DNA EcoR1 restriction endonuclease cuts incoming bacteriophage DNA NOT methylated DNA Murray NE. Microbiology. 2002, 148:3-20.

15. Concept 2 Distinguishing self from non-self may require “marking” of self

16. Type 1 restriction/ modification enzyme complex Eco K1 TGAme(N)8 TGCT ACT(N)8 ACGA If hemimethylated methylates other strand If UN-methylated, cuts (nearby but not in sequence) Eco K1 TGA(N)8 TGCT ACT(N)8 ACGA Q: what happens during DNA synthesis?

17. Redundancy: An individual bacterium can carry multiple restriction modification enzymes with different specificities Example, E.coli strain K12 carries these two class II restriction enzymes EcoKI recognizes the sequence 5'...AAC(N)6GTGC...3' EcoBI recognizes the sequence 5'...TGA(N)8TGCT...3’ (K12 has two other restriction enzymes as well!) Q: what is the evolutionary selection for this redundancy? Probability of a particular 7 nucleotide sequence is 47=1/16,384 Genome sizes of bacteriophage range from 5,000-100,00 base pairs Bacteriophage can potentially avoid certain restriction sites.

18. Concept 3 Defense mechanisms must be redundant to reduce the likelihood of escape by the parasite. • Phage escape mechanisms • reduce genome size • eliminate certain nucleotide sequences carrying the restriction site • be single stranded, requiring replication of the second strand (and attendant methylation) prior to forming a double stranded substrate (restriction enzymes are dimers that require double stranded DNA, whereas methyltransferase work as monomers).

19. Virtually all bacteria have restriction/modification systems Recognition Sequence Enzymes AA/CGTT Acl I Arthrobacter luteus A/AGCTT Hind III Haemophilus influenzae Causitive agent of bacterial influenzae. A/CATGT Pci I Planococcus citreus A/CCGGT Age I Agrobacterium gelatinovorum ACCTGC(4/8) BspM I Bacillus sphaericas A/CGCGT Mlu I Micrococcus luteus “A bacterium that degrades the compounds in sweat into ones producing unpleasant odors.” A/GATCT Bgl II Bacillus globigii AG/CT Alu I Arthrobacter luteus AGG/CCT Stu I Streptomyces tubercidicus AGT/ACT Sca I Streptomyces caespitosus . . . .

20. Diversity Restriction enzymes have been found only within prokaryotes. Many thousands of bacteria and archae have now been screened for their presence. Analysis of sequenced prokaryotic genomes indicates that they are common--all free-living bacteria and archaea appear to code for them. Restriction enzymes 3706 ~250 different sequences seen Type I 59 Type II 3634 Methyltransferases 757 Type I 49 Type II 595 (information from a supplier of restriction enzymes, NEB) Note: Most type 2 RE see palindromic sequences and recognize 4-8 bp seque nces. There is a natural restriction enzyme for practically every conceivable such palindrome.

21. Concept 4 Defense mechanisms can force parasite specialization. Example: Phage T5 produces a protein that blocks EcoRI enzymatic activity.

22. r- m- Efficiency of growth 100% E. coli Strain C bacteriophage Q: what happens to a bacterium that loses its methylase gene? Efficiency of growth 100% Efficiency of growth 100% E. coli Strain K-12 Efficiency of growth 0.02% Carries restriction/modification system r+m+ Adapted from Murray NE. Microbiology. 2002, 148:3-20.

23. Concept 5 Defense mechanisms can be toxic to self if not properly controlled Deletion of the modification enzyme without concomiant elimination of the restriction enzyme would be lethal. Restriction and modification enzyme genes are always found closely linked in the bacterial genome. This probably minimizes the risks associated with DNA deletion.

24. Concept 6 Defense mechanisms can affect interactions with other individual of the same species Restriction enzymes also can block bacterial conjugation (between incompatible strains). Conjugation is a DNA transfer between bacteria that is analagous to sex.

25. Every organism needs host defense Example: bacteria 1. There is a need to distinguish self from non-self because everyone has a parasite. 2. Distinguishing self from non-self often requires “marking” of self. 3. Defense mechanisms must be redundant to reduce the likelihood of escape by the parasite. 4. Defense mechanisms can force parasite specialization. 5. Defense mechanisms can be toxic to self if not properly controlled. 6. Defense mechanisms can affect interactions with other individual of the same species.

26. The notion of immunity to disease is ancient Thucydides: “History of the Peloponnesian War” 5th century BCE He noted that during the plague of Athens (430 BCE) the sick were nursed by those who had recovered from the disease (caused by a bacterium, possibly Yersinia pestis) because they knew that they were safe from developing, or at least dying from, the disease a second time. It was also clear that this resistance was specific to the plague disease only. Thus the specificity and memory of immunity was recognized long ago.

27. Immunizations have been carried out for a long time Variolation was an ancient folk practice of vaccination to smallpox (infectious agent Variola major virus) practiced throughout Asia, Africa, and parts of Europe. Essentially, it followed a procedure in which blisters from diseased skin carrying virus from a smallpox victim was innoculated in the skin or nose. Variolation became a common practice in England after the Prince and Princess of Wales had their children innoculated in 1722. The precursor to the modern vaccine was based on the work of Jenner, who showed in 1798 that pustules from cows diseased with cowpox had the same smallpox protective effect. Hence vaccination (Latin vaccus, cow).

28. Germ theory and the scientific basis of immunity Jenner didn’t know why or how his vaccine worked. In the 1870s Robert Koch, Louis Pasteur, and others identified specific microbial agents of several human and animal diseases, including Anthrax (Bacillus anthracis), cholera (Vibrio cholerae), tuberculosis (Mycobacterium tuberculosis), Dyptheria (Corynebacterium diphtheriae) and the Plague (Yersinia pestis). A major breakthrough was Pasteur’s demonstration that injection of weakened pathogenic microbes of Anthrax or fowl cholera could protect animals from lethal infection of the same microbe. “Attenuated” vaccines are commonly used today. He later developed an effective rabies vaccine using ground up spinal tissue from diseased animals. However, vaccines against some microbes, such as tuberculosis, failed, and an effective vaccine is still not available for this and many other important diseases.

29. Some vaccines really work! Particulary effective are vaccines that protect from viruses that require human-to-human transmission * Smallpox * * Fig 1.1 Parham *human to human transmission Fig 1.27 Parham

30. Overview of the vertebrate immune system • Host defense is multilayered • “Innate immunity” evolves with the germline and involves receptors, enzymes and cells that detect conserved aspects of microbes and parasites. Examples: lysozyme in the eye that digests bacterial peptidoglycan, antibacterial peptides produced by epithelia, receptors for formyl-methionine or lipopolysaccharides on phagocytic cells, the complement system. • “Adaptive immunity” is provided by lymphocytes andevolves not only in the germline, but also in the soma, providing immunity with its hallmark properties of memory, specificity, and self-tolerance.

31. Cells of the immune system Bone marrow/fetal liver Thymus Naïve, resting lymphocytes in lymph nodes, spleen Adaptive Innate Fig 1.27 Parham

32. Analogies between host defense and homeland defense • Highly complex, redundant, involving overlapping responsibilities, distinct specializations, information sharing and several levels of communication between components. • Military (several types), police (several), port authorities (several), intelligence, hospitals, communications at different levels, indentification systems, central and local government coordination. Running the system is expensive, wasteful, and at any given time, many components appear to be inactive. • Lymphocytes (several types), myeloid cells (several), dendritic cells (several), pattern recognition receptors (numerous), plasma components (complement, coagulation proteins, antibacterials), cytokines (regulate cell growth and function), chemokines (regulated movement), contact dependent cell communication, central regulators (fever regulation by hypothalamus, pain sensation by nervous system).

33. Where the lymphocytes are. Yellow, primary lymphoid organs. Blue, secondary lymphoid organs. * See Fig 1.8 Parham

34. Unlike other white blood cells (leukocytes) lymphocytes are morphologically nondescript Resting lymphocyte

35. CD8+ killer T cells kill infected host cells B cells make antibodies CD4+ helper T cells sustain responses

36. 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 Antibodies Lymphocytes have unique, clonally distributed antigen receptors B cells 20 16 13 14 15 17 19 18 4 5 3 2 9 6 8 7 1 11 10 12

37. 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 T cells see “presented” antigen Antigen presenting cell CD8 T cells 20 16 13 14 15 17 19 18 4 5 3 2 9 6 8 7 1 11 12 Note: for both T and B cells antigen is a growth factor

38. Innate vs. Adaptive Immunity Figure 1.5 Memory

39. One view of animal phylogeny

40. Biological Inventionof Acquired Immunity

41. Innate Immunity • All animals have an “innate” immune system • Innate immunity is manifest in many cells of the body. The basis is the recognition of molecular patterns, that occur in microbes but not animals (e. g., unmethylated DNA sequences, dsRNA, cell wall components, etc) • This is the bedrock of immunity in all organisms--even bacteria have defense mechanisms against bacterial viruses

42. Innate Immunity, con’t • An apparent limitation is that parasitic agents have a generation time orders of magnitude less than that of their hosts • A second limitation is that there is only limited amplification of the response • A third limitation is that there is no memory

43. Adaptive Immunity • Recognizes any biochemical determinant • Provides a mechanism for immune recognition that can evolve as rapidly as the parasite (clonal selection) • There is rapid amplification of a response • There is memory

44. Origins of immunology • Distinction between innate and adaptive immunity • Cells of the vertebrate immune system • Black box overview of the adaptive immune response • Phylogeny of adaptive immunity • Next time: • Innate immunity: recognition mechanisms