Download Exam in Infection and Immunity 1BI004, November 1, 2013. Total 27

Exam in Infection and Immunity 1BI004, November 1, 2013.
Total 27 questions
Max points: 69p
Grading: F <36p; Fx ≥36p; E ≥38p (55%); D ≥44p (64%); C ≥50p (73%); B, ≥56,5p (82%);
A, ≥62,5p- (91%).
Passed half time exam gives 3p (4% of 69p).
1. What signals are provided by the dentritic cells for activation of naïve T cells, and
what is the function of these signals? (2p)
Expected answer:
Signal 1: presentation of the specific antigen via the MHC complex (MHC class I or
class II). This signal confers specificity to the T cells activation
Signal 2: costimulation via the B7-CD28 interaction, which ensures that T cells are
activated only when required
Signal 3: polarization (in case of CD4+ T cells)
2. The figure 1 below represents the changes in antibody titers of two subclasses of
immunoglobulins (IgM and IgG) during the course of a primary and secondary
infection with Dengue virus. (7p)
Figure 1. 1°Ag represents the primary infection with the pathogen X, while 2° Ag indicates a subsequent
secondary infection with the same pathogen.
Described the molecular mechanims that lead to the changes in antibody titers of the
different immunoglobulin classes over time. (3p)
What determines the switch to the specific IgG class? (1p)
Where are B lymphocytes activated? 1(p)
Why are T lymphocytes require for B cell activation? (1p)
Which are the three key events that occurs in the germinal center during the process of
B cell activation (1p)
During the intial phase of B cell activation, when the B cell encounters the cognate
antigen for the first time, the cell is activated (with the help of the appropriate T
helper lymphocyte), undergoes clonal expansion, and part of the progeny
differentiates in plasma cells, which start to secrete IgM: the default immunoglobulin
class produced (thus higher titers of IgM in the initial phase of the primary response).
Part of the clonally expanded B cells instead will form the germinal center, where they
undergo several processes, including class switch, producing a different class of
antibody and production of memory B cells (in this case IgG). After the second
encounter with the antigen, memory B cells will be immediately activated and induce a
faster and stronger response, directly producing the “switched” antibody class for
that specific antigen (IgG, thus explaining the higher titers of IgG during the
secondary infection with a shorter period of lag time compared to the primary
inefction).
Cytokines regulate the type of class switch.
B cells are activated in the B cell zone of the secondary lymphoid organs.
A pre-activated T cell delivers two signals that are require for B cell acivation: CD40CD40L interaction and secretion of IL4. The T helper step is require for the activation
of the B cells only when it is strictly required, meaning the perceived presence of a
danger (e.g. invading pathogen) that has previously induced activation of the T cell by
dendritic cells.
somatic hypermutation (random mutations within the re-arranged V region of the
immunoglobulin genes); affinity maturation (selection of the B cell clone expressing
Ab with higher affinity; class switch, induced by the interaction with the specific T cell
3. Eosinophils along with NK cells have been described as the cytotoxic cells of the
innate immune system. Describe the differences between these cells based on lineages
and modes of killing. (2p)
Expected answer:
NK cells are members of the lymphocytes and have the same cytotoxic machinery as T
cells, with granules containing perforin and granzyme B. NK cells can be triggered by
activating receptors specific for stress induced ligands on the target cells, and by
down regulation of MHC class I on the targets. NK cells do also kill target cells via
Fas/FasL and Trail/TrailL interactions.
While eosinophils are members of the granulocytes of the myeloid lineage and are
triggered by e.g. antibody coated targets via Fc receptors which leads to
degranulation of toxic proteins (major basic protein), pore forming proteins
(eosinophil cationic protein) and production of reactive oxygen species (via eosinophil
peroxidase).
4. Some species have restricted antibody- or MHC repertoire if we compare to humans.
Why do you think that these species have a restricted repertoire? E.g. cartilage fish has
three MHC and predominantly only IgM and new world monkeys which
predominantly have HLA-G MHC molecules. Speculate based on your knowledge in
immunology and microbiology. (2p)
What are the pros and cons of the expanded repertoire of MHC molecules and T and B
cell receptors in humans? (3p) (total 5p)
A good answer should contain an understanding and a discussion of the function of
the adaptive immune system, that it is partly shaped by the evolutionary pressure from
pathogens and the environment the species are inhabitants in.
Pros of an expanded repertoir of MHC molecules and T and B cell receptors can be
that the adaptive immune system is able to recognize a larger number of pathogens
that can be of benefit both on an individual and a population level. Cons are that more
T and B cell receptors (cells) will be useless and in the case of MHC that individuals
might have a less good respons to some pathogens.
5. Which mutation in which cytokine/chemokine receptor do you think gives most
clinical symptoms and problems, CXCR1 or Gamma-common chain? Why do you
think that? Why do you think that the other is not as crucial? (3p)
Expected answer:
The answer should show an understanding that a defect in the chemokine receptor
CXCR1 does not have as severe effect as a defect in the common cytokine receptor
gamma-common chain that is chared by several chemokine receptors (IL-2, IL-4, IL-7,
IL-9, IL-15 and IL-21). A defect in the chemokine receptor will lead to less good
chemotaxis in some specific instances, while a defect in the gamma-common chain will
lead to X-linked severe combined immunodeficiency since development, maturation,
activation and function of T and NK cells will be severly impaired.
6. Explain the terms dolor, rubor, calor in the context of inflammation. (2p)
Expected answer:
Dolor – pain – caused by substances released by leucocytes or dead cells that triggers
the nerves.
Rubor – redness – caused by increased blood flow and vasodilation by mediator
released by leucocytes during for example an infection.
Calor – heat – caused by the vasodilation and the increased blood flow.
7. ELISpot is a sensitive method for analyzing immune responses towards e.g. viruses.
You seed 100.000 peripheral blood mononuclear cells (PBMCs) from a patient into
duplicate wells of an ELISpot-plate with anti-IFNγ antibodies immobilized onto the
bottom of the wells. You stimulate the cells overnight with a peptide pool of a
concentration of 0.1 μg/mL from one protein (pp65) of the cytomegalovirus (CMV)
and a peptide pool of equal concentration from one protein (EBNA3) of the EpsteinBarr virus (EBV). IFNγ is secreted from the specific lymphocytes and is captured by
the immobilized antibodies. On day 2 you add a secondary antibody towards IFNγ
conjugated to an enzyme. A substrate is subsequently added which is cleaved by the
enzyme on the secondary antibodies resulting in development of visible spots. In the
duplicate wells where cells have been stimulated with CMV-peptides you count 500
and 700 spots, respectively. In the duplicate wells where cells have been stimulated
with EBV-peptides you count 0 and 0 spots, respectively. Interpret these results. (1p)
Expected answer:
Patient has cells specific for this particular CMV protein
Quantification of the CMV-response: (500+700)/2 = 600  600/100.000 cells are
specific (behöver inte räkna längre än så, men om de är duktiga på huvudräkning:
600/100.000*100 = 0,6%)
No (IFNg-secreting) specific lymphocytes for peptides from this particular EBVprotein - does not mean that the patient has no immunity versus EBV, just no response
for this particular protein.
8. Your boss wants you to test what happens if you immunize mice with a self-protein
expressed in the central nervous system (e.g. MOG) together with a strong adjuvant
(e.g. complete Freund’s adjuvance (CFA)) that contains ligands for Toll-like receptors.
After a while the mice developed symptoms that resembled multiple sclerosis, with T
cell infiltration of the brain. Give a plausible explanation why this happened, based on
what you know about activation of T cells and T cell tolerance. Why were the mice
not sick before vaccination? (3p)
Example answer: MOG is a self-protein, and as such, T cells that express a T cell
receptor specific for MOG should normally have been eliminated during T cell
selection in the thymus, where T cells that recognize self-proteins are eliminated in the
process called “negative selection”. For negative selection to work, the protein
(MOG) has to be expressed, processed and presented to thymocytes in the thymus. So,
evidently, there are T cells specific for MOG that have escaped negative selection. A
possible explanation for this is that MOG was not expressed in the thymus, why
negative selection was not able to mediate the “central tolerance”. The brain is an
immunoprivileged site, so normally (in the absence of inflammation), T cells can’t
migrate to the CNS. So the, the naïve T cells in the healthy (non-vaccinated mice) will
not encounter APCs presenting MOG peptides on MHC class I/II. However, by
vaccinating the mice together with an adjuvant, the APCs in the mouse gets activated,
start expressing co-stimulatory molecules (CD80/86), and can present the antigen to T
cells in the lymph nodes. This way, naïve T cells can become activated and migrate to
the CNS, where the antigen is expressed. In addition, vaccination with a strong
adjuvant like CFA induces inflammation, which can make the blood brain barrier
more permeable. This way the activated T cells may get increased access to the brain,
and can cause the symptoms of the mice.
9. What do we know about the etiology of rheumatoid arthritis? Please choose one risk
factor OR a specific autoantibody and discuss from an immunological point of view
which role it might play for the disease. (3p)
Expected answer:
Here, we would like the students to mention both genetic and environmental risk
factors, specifically HLA / MHC II genes (HLA-DRB1 shared epitope) and cigarette
smoking; that more women than men are affected by RA (like in many other
autoimmune diseases); that the majority of patients have autoantibodies to
citrullinated proteins (ACPA / anti-CCP antibodies), that these autoantibodies are
thought to drive disease, i.e. the chronic synovial inflammation.
10. Give an example of an autoantigen and shortly explain why it is an autoantigen. (1p)
Expected answer:
Many possible answers. The answer should countain a named autoantigen with a
description of the function of the autoantigen.
11. Describe the characteristics of viral DNA that differentiate it from cellular DNA. (1p)
Expected answer:
-Can be episomal circular DNA
-Can be ssDNA
-Poxvirus DNA replicates in the cytoplasm
-Maximal usage of coding capacity
12. Describe how IRES elements promote the initiation of translation and explain how this
is advantageous for viruses that have them. (2p)
Expected answer:
Internal Ribosome Entry sites allow cap-independent translation. = Internal initiation
of translation.
IRES containing viruses can induce host translation shut off via phosphorylation or
degradation of cap-binding complex. Thus cap dependent translation is inhibited and
the cap-independent viral mRNAs can be efficiently translated.
13. Summarize the replication steps during a lytic infection of herpes simplex virus.
Include in your answer the order and function of three types of genes expressed during
a lytic infection of HSV. (4p)
Expected answer:
Entry at the plasma membrane using viral glycoproteins gC, gD, gB and others to
mediate fusion.
Nucleocapsid transports to nucleus, DNA enters nucleus
Three types of genes:
-Immediate Early, proteins involved in protein synthesis and other cell protein
interactions
-Early: Protein synthesis and genome replication
-Late: Structural Proteins
DNA replication via rolling circle mechanism
Assembly involves scaffold proteins, tegument.
Budding at multiple sites, final site at plasma membrane
14. Describe how acyclovir achieves specificity for herpes viral DNA replication. (1p)
Expected answer:
It is first phosphorylated by viral thymidine kinase and then by cellular kinases. The
non-phosphorylated form cannot be used in DNA synthesis and thus it oly acts in
infected cells.
15. Compare two of the viruses causing the most severe forms of hemorrhagic fever, i.e.
geographical locations/sizes of outbreaks, fatality rates, and how to minimize/stop the
spread of the viruses. (4p)
Several answers possible.
16. Why is it so problematic for the immune system to control HIV-1 infection? (2p)
Expected answer:
Accumulation of mutations in viral proteins means the envelope proteins can excepae
from antibody recognition.
The virus infects and kills CH4+ T cells which are needed for antibody production.
Integration of viral DNA into host chromosomes
17. Explain the difference between dichotomous and numeric taxonomy regarding
bacteria. (2p)
Dichotomous taxonomy involves answering questions with two answers, often
arranged as keys, starting with general questions that subsequently leads to more and
more specific questions.
While numeric taxonomy is based on the idea that increasing the number of
characteristics of organisms that we observe increases the accuracy with which we
can detect similarities among them.
18. Describe advantages and disadvantages using PCR compared to grow bacterial
colonies when bacteria species should be determined from a clinical sample. (3p)
Advantages with PCR:
Sensitive, little sample needed
Good when not possible to grow the bacteria/can use dead bacteria
Fast
Specific (specific primers)
Safer (no need of culturing potential pathogens)
Disadvantages with PCR
Not possible to detect new strains/only detects the strains screened for
Not possible to derermine the morphology and characteristics of the bacterial cultures
19. Escherichia coli is part of our normal flora, without causing any symptoms. Still,
selected strains of the same bacterial species may cause a variety of infectious
diseases, such as gastrointestinal or urinary tract infections. How can this be
explained? (2p)
A: Apathogenic and pathogenic E. coli share a common “core genome”, while
pathogenic variants have received additional genetic information - virulence
determinants. This information code for virulence factors, such as bacterial adhesins
or toxins, that makes the bacterium pathogenic.
20. Bacterial adhesion is quite a prerequisite for their ability to colonize mucosal
membranes. This is usually achieved through the expression of bacterial adhesins that
bind to specific receptor structures on host cells. Apparently, optimal receptors are not
always present, and so some bacteria “induce” their own adhesion receptor on the
epithelial cell. Give an example on how this could be achieved. (2p)
A: A consequence of H. pylori-induced epithelial inflammation is that there is an
alteration in host cell carbohydrate composition. Such altered inflammation markers
could in turn act as additional adhesion receptors. Enteropathogenic E. coli uses a
bacterial protein secretion system to infect a bacterial protein into the host cell. This
protein is then phosphorylated by a host kinase. This then leads to a conformational
change in the bacterial protein to become an integral membrane protein in the host
cell. The surface-exposed proportion of the protein then acts as an adhesion receptor
for the E. coli strain.
21. Give two examples to explain why “pathogenic” enteric bacteria cause symptoms
from the gastrointestinal tract. (2p)
-Production of enterotoxins (i.e. increase in camp/cGMP, ion and water efflux)
-Induction of inflammation (through expression of PAMPS, seceretion of PAMPs,
secretion of proteins that directly activates inflammatory signaling)
-Disruption of the microhistology of the absorbtive cell
22. Give an example of a bacterial superantigen and explain how it works. (2p)
Expected answer:
Examples of superantigens: staphylococcal enterotoxin A, streptococcal pyrogenic
exotoxin. Superantigens do unspecifically activate T cells and give rise to a polyclonal
activation of a large fraction of the the T cells (15-25%) by cross-linking the MHC II
molecule with the TCR, leading to proliferation of the T-cells and release of large
amounts of pro-inflammatory cytokines, such as Il-1, TNF-α, TNF-β, INF-γ, and IL-2.
These cytokines cause a systemic inflammation.
23. Discuss pros and cons with different kinds of donors for patients undergoing allogenic
hematopoietic stem cell transplantation: (4p)
HLA-identical monozygotic twin
HLA-identical sibling
Matched unrelated donor
Cord blood unit
Answer: a) well matched, no risk for GVHD, less chance of graft-versus-leukemia
effect (increased relapse rate), genetic profile same (risk for the same disease)
b) best possible donor, ethical issues when children are sibling donors
c) takes time to identify in the registry, good match is required, higher risk for GVHD
d)low cell dose- manly used for children, more mismatches are acceptable, not
possible to use the same donor for re-transplantation or additional cell therapy,
readily available
24. Before kidney transplantation HLA-typing is performed, but different HLA-types does
not prevent transplantation between donor and recipient. Explain why HLA-match is
not required and also analyse if there is a benefit in receiving a HLA-matched organ.
(2p)
Answer: With the immunosuppressive drugs we have today, HLA is not a barrier for
transplantation if the recipient doesn’t have HLA-specific antibodies. However, a
HLA-matched organ graft has a longer graft survival.
25. Explain why vaccines are more difficult to produce than other pharmaceuticals and
why the demand for safety is higher than for other pharmaceuticals. (2p)
Answer: vaccines are biological products where the product will differ with every
batch (more resembling cooking than the chemical synthesis used for drugs where two
reagents in a known quantity will always give the same product). Drugs are usually
given to individuals that are sick and the worse the disease the more tolerance is there
for side effects. Vaccines are given to healthy individuals prophylactically so there is
in principle a zero tolerance for side effects.
26. Explain why some viral and bacterial vaccines will work without an adjuvant and give
some examples of such vaccines (2p)
Answer: Our immune system has learnt during evolution that any structure that looks
like a virus or a bacterium is dangerous for us and will therefore mount an immediate
immune response. Inactivated viral vaccines, VLPs, whole cell vaccines.
27. One of the most common infections in the world is Toxoplasma gondii infection. You
might be infected or your friend sitting next to you. However, in most cases it is not
dangerous and we do not know that we have the infection. But in some cases is it a
fatal disease and for certain humans will it be very serious. If you suspect you are
infected, what method/s would you use in your diagnose and why? (4p)
Answer should contain parts of the lifecycle where the 2 different stages are
described, acute phase detected by e.g. PCR in the blood and resting stage detected
via antibodies in the sera. Also detection with the aid of IgM/IgG ELISA and the
strength and weakness of the different methods.