IMMUNITY.
IMMUNODIAGNOSTICS
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 prerequisite 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.
Discussion Sections - Immunology BICD 140 Winter 2005
Sections will discuss lectures, homework assignments, and
exams. You must choose one discussion section and hand in
your homework to your designated TA.
Section
Day
Time (50')
Room
TA
Email
A01
A02
A03
A05
A06
A04
TBA
Thurs
Thurs
Fri
Fri
Fri
TBA
6:00 PM
5:00 PM
08:00 AM
10:00 AM
11:00 AM
TBA
CENTR 217b
CENTR 218
CENTR 218
CENTR 220
CENTR 218
Laura
Adam
Lauren
Matt
Hart
"
lhgreen@ucsd.edu
jbest@ucsd.edu
laurenannd@yahoo.com
jzones@ucsd.edu
hdengler@ucsd.edu
Note: This page will be updated to show the correspondence between TAs
and Discussion Sections
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.
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)
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”
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.
The Triumph of Death - Pieter Brueghel the Elder ca. 1562
Big bugs have little bugs
Upon their backs to bite ‘em
Little bugs have littler bugs
And 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
Concept 1
Every organism needs to distinguish self from
non-self because everyone has a parasite
Case study: bacteria
Bacteria have innate immunity (and tolerance) to bacteriophage
bacteriophage
Efficiency of growth
100%
Efficiency of growth
100%
E. coli
Strain C
E. coli strain C is
sensitive to phage
grown in either
strain K-12 or C.
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.
What “restricted” the phage growth?
Restriction enzymes
Example EcoRI
target sequence
5’...GAATTC...3’
3’...CAATTG...5’
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
Murray NE. Microbiology. 2002, 148:3-20.
EcoR1 restriction
endonuclease
cuts incoming
bacteriophage DNA
NOT methylated DNA
Concept 2
Distinguishing self from
non-self may require “marking” of self
Type 1 restriction/ modification enzyme complex
Eco K1
TGAme(N)8 TGCT
ACT (N)8 ACGA
Eco K1
If UN-methylated, cuts
TGA(N)8 TGCT
ACT(N)8 ACGA (nearby but not in sequence)
If hemimethylated
methylates other strand
Q: what happens during DNA synthesis?
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.
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).
Virtually all bacteria have restriction/modification systems
Recognition Sequence
AA/CGTT
A/AGCTT
A/CATGT
A/CCGGT
ACCTGC(4/8)
A/CGCGT
Enzymes
Acl I
Hind III
Pci I
Age I
BspM I
Mlu I
Arthrobacter luteus
Haemophilus influenzae
Causitive agent of bacterial influenzae.
Planococcus citreus
Agrobacterium gelatinovorum
Bacillus sphaericas
Micrococcus luteus
“A bacterium that degrades the compounds in sweat into ones producing unpleasant odors.”
A/GATCT
AG/CT
AGG/CCT
AGT/ACT
.
.
Bgl II
Alu I
Stu I
Sca I
.
.
Bacillus globigii
Arthrobacter luteus
Streptomyces tubercidicus
Streptomyces caespitosus
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
Type I
Type II
3706
59
3634
Methyltransferases
Type I
Type II
757
49
595
~250 different sequences seen
(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.
Concept 4
Defense mechanisms can force parasite specialization.
Example:
Phage T5 produces a protein that blocks EcoRI
enzymatic activity.
r- m bacteriophage
Efficiency of growth
100%
Efficiency of growth
100%
E. coli
Strain C
Q: what happens
to a bacterium
that loses its
methylase gene?
E. coli
Strain K-12
Carries restriction/modification system
r+m+
Efficiency of growth
100%
Efficiency of growth
0.02%
Adapted from Murray NE. Microbiology. 2002, 148:3-20.
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.
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.
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.
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.
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).
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.
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
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 and
evolves not only in the germline, but also in the soma,
providing immunity with its hallmark properties of
memory, specificity, and self-tolerance.
Cells of the immune system
Bone marrow/fetal liver
Thymus
Naïve, resting
lymphocytes in
lymph nodes,
spleen
Adaptive
Innate
Fig 1.27 Parham
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).
Where the
lymphocytes are.
*
Yellow, primary
lymphoid organs.
Blue, secondary
lymphoid organs.
See Fig 1.8 Parham
Unlike other white blood cells (leukocytes)
lymphocytes are morphologically nondescript
Resting lymphocyte
B cells
make
antibodies
CD4+ helper
T cells
sustain responses
CD8+ killer
T cells
kill infected
host cells
Lymphocytes have unique, clonally distributed antigen receptors
13 14
1
2
16
15
3
4
17
5
6
20
19
18
7
B cells
8
9
10
11
12
10 10
Antibodies
10 10 10 10
10 10 10 10 10 10
10 10
10 10
10 10
T cells see “presented” antigen
Antigen presenting cell
13 14
1
2
16
15
3
4
17
5
6
20
19
18
7
8
10
9
CD8 T cells
11
12
10 10
10 10 10 10
10 10 10 10 10 10
10 10
10 10
10 10
Note: for both T and B cells antigen is a growth factor
Innate vs. Adaptive Immunity
Figure 1.5
Memory
One view of
animal phylogeny
Biological Invention
of Acquired Immunity
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
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
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
•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