MCB 4211; BASIC IMMUNOLOGY

FALL 2010

Instructor: Michael Lynes, Ph.D. phone: 486-4350; email: michael.lynes@uconn.edu

Office: Biological Sciences/Physics (BSP) room 308
Office hours: No scheduled hours. I am in my office by about 8AM, and usually stay until
about 6.
Drop by my office, phone, or email to make an appointment.
Class meetings Tuesday, Thursday room:BSP 131 (2-3:15 pm)
Teaching Assistants: Kathryn Pietrosimone (Kathryn.pietrosimon@uconn.edu) and Jamie
Rice (james.rice@uconn.edu), phone: 486-3648 Office: BSP 317/318
Course website: http://lynes.uconn.edu/Lynes_Lab/MCB4211.html

Recommended approach to studying this material:

1. skim over each assigned chapter before class, look at figures in chapter
2. take notes in class; copy notes over that night after class to ensure you understand what
you wrote. If you have trouble taking good notes, consider bringing a tape recorder to
supplement your notes. 3. following each class, read assigned chapter for comprehension
(don’t fall behind!)
4. be certain to read primary literature assignments before the assigned date! We discuss
these papers in class, and the material is fair game for the examinations.

Administrative notes:
1. please turn off your cell phone before class, do not bring cell phones, blackberry devices,
or pagers to the examinations (you may leave your bookbags with these inactivated items in
the front of the classroom during the exam if necessary).
2. randomized exam seating will be assigned at the beginning of each examination.

Grades
Examinations will focus on material presented in class, and from the supplemental assigned
readings.
The final grade will be based on two hour-long exams (30% each), and the final examination
grade (40%). Exam coverage is listed in the class schedule below.

Statement on Academic Integrity

“A fundamental tenet of all educational institutions is academic honesty; academic work
depends upon respect for and acknowledgement of the research and ideas of others.
Misrepresenting someone else's work as ones own is a serious offense in any academic
setting and it will not be condoned. Academic misconduct includes, but is not limited to,
providing or receiving assistance in a manner not authorized by the instructor in the creation
of work to be submitted for academic evaluation (e.g. papers, projects, and examinations);
any attempt to influence improperly (e.g. bribery, threats) any member of the faculty, staff, or
administration of the University in any matter pertaining to academics or research; presenting,
as one's own, the ideas or words of another for academic evaluation; doing unauthorized
academic work for which another person will receive credit or be evaluated; and presenting
the same or substantially the same papers or projects in two or more courses without the
explicit permission of the instructors involved. A student who knowingly assists another
student in committing an act of academic misconduct shall be equally accountable for the

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violation, and shall be subject to the sanctions and other remedies described in The Student
Code.”

(taken from the UCONN student handbook)

TEXTBOOK: "Janeway’s Immunobiology" by Murphy, Travers and Walport. 7th edition.

Garland Science. (2008) ISBN is 0-8153-4123-7)
Primary literature readings: see the MCB 4211 website, or upload from the e-journal site at
the UCONN library website (http://tk8nj5xn8a.search.serialssolutions.com/)
Supplemental Honors section reading
“The immortal life of Henrietta Lacks” by Rebecca Skloot ISBN 1400052173 Random House
Publishing
plus assigned readings from the primary literature
other interesting information can be found at http://rebeccaskloot.com/the-immortal-life/

Semester Schedule
Date Topic Readings
8/31 Introduction, overview of course
A. Organization of the course
1. content: lecture with associated primary literature readings
(references are noted in outline)
2. additional resource materials: assigned text readings/note additional textbook
features, websites
3. course format: lectures and discussions during class: feel free to ask
questions
in class; you may tape the lectures if you wish.
4. examination format and content
B. Historical roots of the study of Immunology
1. Immunology is a relatively young science
a. 1798 Jenner: cowpox immunization
b. 1891 Koch: DTH vs tuberculin Ag
c. 1895 Bordet: C' + Ab + bacteria = lysis
d. 1901 Landsteiner: ABO blood groups
e. 1914 Little: genetic theory of tumor transplantation
f. 1936 Gorer: identification of MHC antigens
g. 1939 Kabat and Tselius: Antibodies as gamma globulins
C. Basic components of immunological system activation
1. Signal molecule • receptor molecule • information processing•
tolerance or response
2. signal molecule = antigen; smallest unit that is recognized as non-self
3. Characteristics of the immune response
a. specificity
b. memory
D. Current trends in immunological research
1. manipulation of the response to disease
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 a. AIDS
b. cancer
c. autoimmunity
d. tissue transplantation; stem cell biology
2. antibodies as enzymes (“abzymes”)
3. antibodies as probes of biochemical/cellular structure
4. psychoneuroimmunology
5. cytokine immunotherapies
6. xenogeneic transplants of humanized tissues
7. diseases with newly recognized immunological components
8. therapeutic manipulations of disease with novel antibody constructs (single
chain, etc.)
E. Lynes laboratory research interests (http://web.uconn.edu/lyneslab/)
1. mechanisms of immunotoxicity/role of metallothionein in stress mediated
immunomodulation
2. automated measurements of chemotaxis
3. Grating-coupled surface plasmon resonance imaging (GCSPRI) and surface
plasmon enhanced fluorescence protein microarray platform applications
a. use of the GCSPRI platform for immune function characterization
arthritis and type 1 diabetes
b. GCSPRI pathogen and toxin biosensors
c. Cytometer on a chip
d. vaccine assessment in human and agricultural pathogen
immunizations
e. other optical configuration variants of GCSPRI

9/2 Basic components of the Immune Response Immunobiology, Ch 1

A. Cells
1. hematopoiesis
a. lymphoid lineage
b. other cells (erythroid and myeloid lineages)
2. structure/function of cells
3. organization of cells into tissues
4. lymphocyte traffic
B. Soluble components of the immune system
1. antibodies (structure/function)
2. complement (structure/function)
3. cytokines (structure/function)

9/7 The experimental system

A. The experimental animal
1. phylogenetic studies: interesting immune adaptations in evolutionary contexts
2. commonly used mammalian systems
a. mouse: mendelian inheritance and breeding manipulations
b. other mammalian animal systems
3. man
B. Artificial systems
1. culture techniques: in vitro
2. immunologically compromised animals (will discuss more fully on 11/9)
a. immunological mutants

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 b. radiation induced immunodeficiency
3. transgenic animals, targeted gene disruptions, chimeric animals

9/9 Antigenicity and Immunogenicity Immunobiology Appendix I,p735-745

A. Antigenicity vs. immunogenicity
B. Fundamental characteristics of antigens
C. Prototypical antigens
1. mitogens as polyclonal activators
2. T-dependent and T-independent antigens
3. the MHC as an antigenic system

9/14 Antibodies: structure and function Immunobiology, Ch 3

A. Immunoglobulin structure
1. subunit structure
2. heavy and light chains
3. Fc, Fab, and F(ab’)2
B. Antigenic determinants of immunoglobulins
1. isotypes and subclasses
2. idiotypes
3. allotypes
C. Functions associated with antibody fragments

9/16 Antibodies: structure and function (continued) Primary Literature

Reference #1
A. Antibody-antigen binding Immunobiology p 740-
756
1. parameters of binding
2. structural contributions to binding
B. Assays of antibody binding
1. Precipitation
2. Agglutination
3. Radioimmunoassay
4. ELISA
5. Fluorescent immunoassay/ Flow cytometry
6. Western immunoblot analysis
7. Immunohistochemistry/Immunoelectronmicroscopy
C. Monoclonal antibodies
1. how they are made and isolated
2. functional differences from polyclonal antisera, monospecific sera

9/21 Antibody/antigen Interactions (continued)

9/23 Sources of antibody diversity Immunology, Ch 4

(p143-155)
A. Genetics of antibody synthesis (the B cell receptor)
B. Generation of antibody diversity
1. germline vs. somatic mutation
associational, junctional and combinatorial diversity
C. Class switching

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*****sample questions that can be used to prepare for the first examination will be posted
online at the course website*****answers to the questions will be posted after an interval

9/28 Major Histocompatibility Complex (MHC) Immunology, Ch 3 p123-

138
A. Discovery as a transplantation antigen, and genetics
B. Cellular expression/tissue distribution
C. Contribution to cellular recognition (genetic restriction)
D. Structure/function

9/30 •••••••• FIRST EXAM •••••••••••will cover material through 9/23••••••••••••••

10/5 Cell biology of the MHC/protein biology of the MHC; antigen processing and
presentation Immunobiology
Ch 5
A. Mechanisms of antigen association with MHC molecules
1. endocytic pathway (exogenous antigen)
2. cytosolic pathway (endogenous antigen)
B. Interactions of antigen/MHC with the T cell antigen receptor

10/7 T cell/antigen interactions Immunobiology, Ch 2 p 123-138

A. structure of the TcR Ch 4 p154-159; Ch 6, 7
B. genetics of TcR
C. Other molecular components of the TcR
D. Signal transduction following TcR engagement

10/12 Consequences of TcR engagement Immunology, Ch 7 p273-298

A. T cell populations in the thymus and periphery
B. T cell maturation
C. Mechanisms of T cell activation
D. Products of T cell activation (see soluble mediators)

10/14 Cell mediated immunity (CMI) Immunobiology, Ch 8

A. Cytotoxicity
B. Delayed type hypersensitivity
C. Immunological protection conferred by CMI

10/19 Soluble mediators of immunity Immunobiology, Ch 2 p53-81

A. Cytokines and lymphokines: structure and function Primary literature reading #2
and #6
B. Pattern recognition receptors and lymphokine receptors Immunobiology,
Appendix III, I
C. Complement
D. Anti-idiotypic Immunoglobulins
E. Selective migration
F. Neuroendocrine regulation

10/21 Immune responses to infections agents Immunobiology, Ch2 p

82-102
A. Viral Ch 10; Ch 12 p 497-507

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 B. Bacterial
C. Protozoan
D. Invertebrate parasites

10/26 Immune responses to infections agents (continued)

10/28 Manipulation of the Immune Response Immunobiology, Ch 15

A. Vaccines (live/attenuated/killed; protein;DNA)
B. Drugs
C. Irradiation

11/2 Inappropriate immune reactions:

A. hypersensitivities Immunobiology, Ch 13
B. Immune tolerance and Autoimmune disease Immunobiology, Ch 14

1. Animal models Primary Literature

Reference #3
2. Human diseases and treatment

11/4 Inappropriate immune reactions (autoimmunity, continued)

11/9 •••••••• SECOND EXAM ••••••••• will focus on material from 9/28 through 11/4, and
will depend on material from the first section of the course. Note that you are
responsible for material in the required primary literature readings that are available on
the MCB 4211 homepage and from the e-journal site at the UConn library website.

11/11 Immunodeficiencies Immunology, Ch 12 p

507-546 A. Animal models for congenital syndromes
1. nude
2. SCID
3. beige
B. Human congenital immunodeficiencies

11/16 Immunodeficiencies (continued)

A. Acquired causes of immunodeficiencies
1. Environmental
2. Drug induced
3. Viral
B. AIDS
1. Etiology/viral replication cycle
2. symptoms/immune effects
3. epidemiology
4. current and future therapies

11/18 AIDS (continued)

11/21-11/27 No class; Fall recess!

11/30 The immune response to cancer Immunology, Ch 15

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 p 672-687
A. Mechanisms of carcinogenesis Primary Literature
Reference #4
B. Natural immune responses to neoplasia
C. Immunological diagnosis of neoplastic disease
1. tumor antigens
D. Immunotherapies for neoplasia
1. “magic bullets”: immune conjugates
a. antibody/drug conjugates
b. antibody/radionuclide conjugates
2. anti-idiotypic antibodies
3. irradiation and transplantation to reconstitute immunity
4. TILs, LAKs
5. Gene therapies
12/2 The immune response to cancer (continued)

12/7 Transplantation Biology Immunobiology, Ch14 p 637-

648
A. Immunological mechanisms of histo-incompatibility Primary Literature Reference
#5
B. Manipulation of histo-incompatibility
C. Clinical value of transplantation
D. Value of MHC polymorphism in population responses to infection; consequences to
transplant success

12/9 Overview and final comments

12/13-12/18 FINAL EXAM PERIOD; the preliminary date for the final exam is Dec 14 1-3 pm.
You can find the entire preliminary exam schedule at
http://www.registrar.uconn.edu/preliminary_fall.htm

••••••••• the final exam will emphasize material from 11/11 through 12/9, and will cover
material from the entire course. Remember that you are responsible for material in the
required primary literature readings as well as the material covered in class•••••••••

********** added at the request of the Office of Student Services and Advocacy************

Final exam week for Fall 2010 takes place from Monday, December 13th through Saturday,
December 18th. Students are required to be available for their exam during the stated time.
If you have a conflict with this time you must visit the Office of Student Services and
Advocacy to discuss the possibility of rescheduling this exam.
Please note that vacations, previously purchased tickets or reservations, graduations,
social events, misreading the exam schedule and over-sleeping are not viable excuses for
missing a final exam. If you think that your situation warrants permission to reschedule,
please contact the Office of Student Services and Advocacy with any questions. Thank you
in advance for your cooperation.
******************************************************************

Required additional reading

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(primary literature references 1-6) from the scientific literature and their web links

1. Kohler, G. and Milstein, C., Continuous cultures of fused cells secreting antibody of predefined
specificity. Nature, 1975. 256: p. 495-7.
http://www.nature.com/nature/journal/v256/n5517/pdf/256495a0.pdf

2. Rennard, B.O., et al., Chicken soup inhibits neutrophil chemotaxis in vitro. Chest, 2000. 118(4): p.
1150-7. http://www.chestjournal.org/cgi/reprint/118/4/1150

3. Youn, J., et al., Metallothionein suppresses collagen-induced arthritis via induction of TGF-beta and
down-regulation of proinflammatory mediators. Clin Exp Immunol, 2002. 129(2): p. 232-9.
http://www.blackwell-synergy.com/doi/full/10.1046/j.1365-2249.2002.01922.x

4. Dolk, E., M. van der Vaart, et al. (2005). "Isolation of llama antibody fragments for prevention of
dandruff by phage display in shampoo." Appl Environ Microbiol 71(1): 442-50.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15640220

5. Siddle, H. V., A. Kreiss, M. D. Eldridge, E. Noonan, C. J. Clarke, S. Pyecroft, G. M. Woods, and K.

Belov. 2007. Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a
threatened carnivorous marsupial. Proc Natl Acad Sci U S A 104:16221.
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1999395&blobtype=pdf

6. Schaller, M., Miller,G.E., Gervais,W.M., Yager,S., and Chen,E., (2010) Mere Visual Perception of
Others' Disease Symptoms Facilitates a More Aggressive Immune Response Psychological Sciences
doi: 10.1177/0956797610368064
http://pss.sagepub.com/content/early/2010/04/02/0956797610368064.full.pdf+html

Additional Optional Readings (not for credit)

1. You can obtain a free subscription to “Immunology in the News” published by the Dana Foundation at this
website: http://www.dana.org/news/immunologyinthenews. You can also sign up for an email alert when a
new issue posts. To set up an account go to
http://www.dana.org/MemberLogin.aspx?ReturnUrl=%2fmembership%2fsubscriptions.aspx.

2. hookworm mediated immune suppression and allergy/asthma treatment.

http://www.nytimes.com/2008/07/01/health/research/01prof.html?_r=3&pagewanted=1&sq&st=nyt&scp=2

3. local honey has no effect on seasonal allergies

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B9HC7-4YFK1VS-
C&_user=669286&_coverDate=02%2F28%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docan
chor=&view=c&_searchStrId=1356675372&_rerunOrigin=google&_acct=C000036298&_version=1&_urlV
ersion=0&_userid=669286&md5=8d142318a8eb636e5f4cfd4e796380e5

4. lack of connection between vaccination and autism

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003140

5. Some website addresses of interest to immunologists:

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 Immunology techniques, biological materials, and instrumentation websites
1. http://flowcyt.cyto.purdue.edu/flowcyt/societes/index.htm {a list of worldwide flow cytometry
associations}
2.http://www2.perkin-elmer.com/pa/340913/html/toc.html {a manufacturers guide to
immunoassays}
3. http://www.bdfacs.com/home.htm {a home page for a flow cytometer manufacturer}
4. http://www.atcc.org/ {American Type Culture Collection; a source of cell lines and genetic
resources}
5. http://www.jax.org {a resource of inbred mouse strains, transgenic and knockout mice}
6. http://biomed.nus.sg/microbio/home.html {a webpage listing for infectious disease sites on the
web}
7. http://www.elsevier.com:80/inca/homepage/sab/tto/menu.htm {technical tips for molecular
biology}

Immunology databases
1. http://www.ncbi.nlm.nih.gov/prow/cd/index_molecule.htm {a site that shows structural features of
CD molecules}
2. http://www.blacksci.co.uk/products/journals/jnltitle.htm {an HIV database hosted by Roche
pharmaceutical}
2. http://cancernet.nci.nih.gov/ord/diseases.html{the office of rare diseases at NIH; for autoimmune
diseases like Lupus, arthritis}

Genome databases
1. http://www.informatics.jax.org/userdocs/overview.shtml {mouse genome information}
2. http://www3.ncbi.nlm.nih.gov/Omim/searchomim.html{online mendelian inheritance in man}

Scientific journal websites

1.http://www.cell.com/ {the journal Cell}
2. http://www.lrpub.com/journals/j1063.htm { Journal of Acquired Immune Deficiency Syndromes
and
Human Retrovirology}
3. http://www.jimmunol.org/{ The Journal of Immunology}
4. http://flowcyt.cyto.purdue.edu/flowcyt/websites/cytsites/sitesed.htm {listing of other scientific
journal websites}
5. http://www.blacksci.co.uk/products/journals/jnltitle.htm {a host of journals from this publisher,
including Immunology and Immunology and Cell Biology}

Scientific funding websites

1. gopher://gopher.nih.gov:70/77/gopherlib/indices/crisp/index? {a site from which to search for
currently funded NIH grants}
2. http://www.nih.gov/grants/oer.htm {the National Institutes of Health website}

Scientific document search engines

1. http://www.nlm.nih.gov/databases/freemedl.html {for searching scientific journal citations
“PubMed/Medline”
2. http://sis.nlm.nih.gov/toxlinfs.htm {the National Library of Medicine’s Toxline database of toxic
chemicals}

Scientific reagent and instrumentation companies:

1. http://www.pharmingen.com/ {a supplier of monoclonal antibodies to human, mouse antigens;

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also a
subsidiary of Becton Dickinson, a flow cytometry company}

Other Links:
1. Check out these great animations!

a. Mechanisms of RNAi
http://www.nature.com/focus/rnai/animations/animation/animation.htm

b. XVIVO/Harvard's award-winning animation, "The Inner Life of a Cell" is at:

http://www.xvivo.net/press/harvard_university.htm

c. cell rolling and phagocytosis and T cell killing

http://www.xvivo.net/healing-visualization-return-to-wholeness/
2. Immunoglobulin Isotype Website
http://www.whfreeman.com/kuby/con_index.htm?04
3. Molecular basis for passive immunotherapy of Alzheimer’s disease
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994138/
4. Complement system review website
http://www.complement-genetics.uni-mainz.de/system.htm
5. The SCID Network
http://www.scid.net/
6. Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM
7. Mouse Genome Informatics (MGI)
http://www.informatics.jax.org/
8. Roche's HIV Page- Animated viral "lifecycle", HIV drug targets, and mechanisms of action
http://www.roche-hiv.com/portal/Roche-HIV/hivlifecycle
9. The history of xenotransplantation
http://www.ncbi.nlm.nih.gov/pubmed/15693840
10. Human Genome Project Information- Gene Therapy
http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml
11. Robert C. Gallo's book, "Virus Hunting: AIDS, Cancer, And the Human Retrovirus : a Story of
Scientific Discovery"
http://www.amazon.com/Virus-Hunting-Retrovirus-Scientific-Discovery/dp/0465098150/sr=1-
1/qid=1163709796/ref=sr_1_1/002-7940394-5952052?ie=UTF8&s=books
12. Animated review of PCR
http://library.thinkquest.org/24355/data/details/media/polymeraseanim.html
13. Great book about cancer by Robert Weinberg “One Renegade Cell”
http://books.google.com/books?id=r-
PsCQRE7wMC&dq=one+cell+weinberg&printsec=frontcover&source=bn&hl=en&ei=m28GTMfqIcP
38Abf2t3nCw&sa=X&oi=book_result&ct=result&resnum=4&ved=0CCAQ6AEwAw#v=onepage&q&f
=false
14. Video showing how Herceptin targets HER2 overexpressing breast cancer
http://www.youtube.com/watch?v=48VSU4AZ-L0&NR=1
15. Flash Animation- DNA Microarray Methodology
http://www.bio.davidson.edu/Courses/genomics/chip/chip.html
16. Transplantation links:
a. Whole body transplantation
http://www.nytimes.com/1998/05/05/science/essay-from-science-fiction-to-

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science-the-whole-body-transplant.html?sec=health
b. Robert Olen Butler's book "Severance"
http://www.amazon.com/Severance-Stories-Robert-Olen-Butler/dp/0811856143
c. The brain that wouldn’t die
http://www.hulu.com/watch/73925/the-brain-that-wouldnt-die

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