immunology: erica's cytokine chart

made by the undisputed master of chartmaking in our class, erica zelfand

immunology: class notes 3/10/09- psychoneuroimmunology

this lecture was about psychoneuroimmunology, the study of how the mindset can influence and be influenced by the interplay between the nervous and immune systems. contrast this with neuroimmunomodulation, which is the study of how the central nervous system can produce changes in the immune system. we looked mainly at the interplay between stress (actually defined as the perception of the inadequacy to cope to a situation that compromises one's physiological or psychological well being), the neuropeptides that it produces in the CNS, and the ultimate effect that it has on the immune system.

the HPA axis, hypothalamus / pituitary / adrenal cortex releases cortisol in response to stress: stress causes the hypothalmus to release cortitropin releaseing hormone and arginine vasopressin, which triggers the pituitary to make adrenocorticotropic hormone, which triggers the adrenal cortex to make cortisol. in addition, glucocorticoids are secreted by the adrenal cortex. both of these substances produce a wide variety of effects within the immune system, including mediation of cytokine production, chemokine production, adhesion molecules, cell trafficking, proliferation. in particular, glucocorticoids can bind to "transcription receptors" on cytokine producing cells, which are then endocytosed and bind to "response elements" which up or downregulate the transcription of cytokines.

the SAM axis is the sympathetic adrenal medullary axis, and produces norepinephrine and epinephrine (catecholamines) alongside the HPA's production of cortisol and glucocorticoids in response to stress. adrenergic receptors for catecholamines are present on macrophages in two forms; alpha adrenergic receptors have a high affinity for catecholamines and therefore are active during low stress levels. beta adrenergic receptors have a low affinity, and therefore are active during high stress levels. the alpha adrenergic receptors act to stimulate the immune response by increasing phagocytosis, TNF-alpha production, IL-6 production. in contrast, binding to the beta adrenergic receptors decreases phagocytosis, decreases antigen processing and presentation, and decreases IL-12 production.

questions
neuroimmunomodulation...
1. what is the difference between psychoneuroimmunology and neuroimmunomodulation?
2. what was a "historical" example of neuroimmunomodulation?
3. what is an example of evidence of how the immune system affects the brain?
4. what is an example of how the central nervous system affects the immune system?

stress and the HPA axis...
5. describe how stress can trigger events in the HPA axis.
6. what is adrenal fatigue?
7. what are glucocorticoids and what are their role in the immune system?
8. how do glucocorticoids affect cytokine levels?
9. what is the theory for how cortisol affects the immune system?

SAM axis and opiods...
10. what is the SAM axis and what is its role in the immune system?
11. what is the effect of catecholamines on the immune system?
12. what are the two types of adrenergic receptors on macrophage and how do they relate to stress levels?
13. what are the effects of binding to the alpha adrenergic receptor?
14. what are the effects of binding to the beta adrenergic receptor?
15. how do opioids affect the immune system?

answers
1. neuroimmunomodulation is based on the premise that the nervous system can affect the immune system and vice versa. psychoneuroimmunology is the study of how the nervous and immune system interact with mood as well.
2. injecting LPS into someone can cause a fever- this implies that the immune response activates the HPA axis to secrete cortisol. we now know that the mechanism is related to macrophage's secretion of IL-1 that crosses the blood brain barrier.
3. the presence of IL-1 receptors in the brain; IL-1 makes you sleepy.
4. the innervation of lymph nodes, receptors on lymph nodes for certain neurotransmitters.

5. stress causes hypothalamus to release corticotropin releasing hormone and arginine vasopressin, which triggers the pituitary to make adrenocoricotropic hormone, which triggers adrenal cortex to make cortisol.
6. adrenal fatigue is the idea that chronic stress can eventually deplete cortisol levels, after an initial increase. the idea also states that cortisol and DHEA are similar hormones made from the same precursor, and that as cortisol levels increase, DHEA decreases; but that DHEA levels are maintained while cortisol levels eventually fall.
7. a hormone produced by the adrenal cortex that has diverse effects in the immune system, including mediation of cytokines, chemokines, adhesion molecules, cell trafficking, proliferation.
8. glucocorticoids bind to transcription receptors which are endocytosed upon binding and attach to "response elements" in front of cytokine genes, allowing it to upregulate or downregulate transcription of cytokine genes.
9. cortisol might play a role in preventing the immune system from being overstimulated. this has been evidenced in some rheumatoid arthritis patients who had increased disease activity when cortisol levels were blocked.

10. the sympathetic adrenal medullary axis; works in concert with the HPA axis by producing catecholamines.
11. similar to glucocorticoids produced by the HPA axis; cell proliferation, cytokine production, antibody production, cell trafficking. in general, catecholamines mediate the "fight or flight" response.
12. alpha adrenergic has a high affinity for catecholamines and therefore is active during low stress levels; beta adrenergic has a low affinity for catecholamines and therefore is active during high stress levels.
13. increases phagocytosis, increases TNF-alpha, increases IL-6.
14. decreases phagocytosis, decreases antigen processing and presentation, decreases production of IL-12.
15. decreases IL-12 production by macrophages, favoring a Th2 response.

immunology: class notes 3/8/9- cancer

this lecture focused on cancer from an immunological perspective. tumors appear in the body on a somewhat regular basis due to viral infection. because these tumors are virally induced, the APC's that bind to tumor cells will also express co-stimulatory molecules (viral elements will bind to toll like receptors). however, in cancerous tumors, this is not necessarily the case, and tumors can subvert the surveillance of the immune system by the absence of these co-stimulatory molecules. in this case, macrophages can go so far as to eat the dead tumor cells (cells on the center of the tumor die because of the lack of blood supply) and present them in MHC class II; but since there is no CD86, an immune response will not be mounted.

there are several approaches to cancer treatment. first is a historical approach with "coley's toxin", which is basically ground up, heat killed gram negative bacteria that is injected at the tumor site. the bacteria signals an infection and the APC's that are presenting the tumor peptide are able to express the co-stimulatory molecules required to mount an immune response (note- this method also induces a high fever in its patients). a more modern approach is the dendritic cell treatment, which isolates dendritic cells outside of the body, stimulates them to differentiate with GMCSF and IL-4, exposes them to heat killed tumor, and injects them back into the body to mount an immune response. this method is effective but as it is completely individualized, is prohibitively expensive and hard to access.

some ways that the presence of a tumor can be identified: the abnormal or over expression of proteins, high telomerase activity (telomerase is an enzyme that adds base pairs to the end telomeres of genes during DNA replication), and other tumor specific antigens. some of these include MAGE and MART in melanoma, BRCA 1-5, MUC 1-3 in breast cancer, prostate specific antigen in prostate cancer.

questions
treatment strategies...
1. describe the studies performed in mice that lead to the conclusion that injecting dead tumors can confer protectivity.
2. how does protectivity of the dead tumor cells depend on the method used to kill the tumor?
3. how are non-cancerous tumors normally destroyed by the body?
4. what is the idea behind IL-2 treatment and what are its pitfalls?
5. what is the dendritic cell cancer treatment and what are its pitfalls?
6. what is "coley's toxin"?

tumor specific antigens...
7. what is the relationship of tumors and telomeres?
8. what is the problem with mounting an immune response against cells with high levels of telomerase?
9. what are three ways that protein expression can indicate presence of tumors?
10. what are the tumor specific antigens in melanoma?
11. what are the tumor specific antigens in breast cancer?
12. what are the tumor specific antigens in prostate cancer?
13. how do most tumors escape immunosurveillance?

14. what are the different ways that cells of the immune system could potentially kill tumor cells?
15. what is the relationship between severe burns and cancer treatment?

answers
1. in one study, two mice were injected with dead tumor A, and then one mouse with live tumor A and the other with live tumor B. the mouse injected with tumor A survived and the other died. in another study, two mice were injected with dead tumor A, then had their t cells depleted. one mouse was then injected with tumor A and the other with tumor B; both of them died. these studies showed that injecting a dead tumor can confer protectivity against its live counterpart as long as t cells are in healthy supply.
2. the tumor cells must be killed via necrotic cell death (generally by freeze-thawing twice)- necrosis causes CD86 expression which mimics infection and can provoke an immune response.
3. most of these tumors are virally caused and therefore express CD86; the immune system can mount a response to them immediately.
4. IL-2 is the cytokine involved in t cell proliferation and thus might be able to intensify the t cell population's response to the tumor. however, it can cause t cells not specific for the tumor to divide, and also cause systemic shock simply because of the presence of high cytokines levels in the blood.
5. similar to the HIV DC treatment; removing DC cells, putting them in a dish with GMCSF and IL-4 to induce differentiation, then adding necrotically killed tumor cells- this causes DC's to secrete IL-12, CD86. DC's are them put back into the host and migrate to the lymph nodes where they mount an immune response agains the live tumor; the downside is that this is a completely individualized treatment and prohibitively expensive. also, treatment depends on the individual having a functioning immune system and thus chemotherapy patients must wait 2-6 years before receiving the treatment.
6. ground up, heat killed, gram negative bacteria that is injected in cancer patients at tumor sites; binds to TLR's and induces expression of co-stimulatory molecules so that CD8 t cells can be activated. treatment also causes high fever.

7. most tumor cells have overactive telomerase activity, which normally add base pairs to the end of genes during DNA replication.
8. stem cells also have high levels of telomerase.
9. presence of mutant proteins, abnormal expression of protein (foot protein being expressed in head), over-expression of proteins.
10. MAGE, MART
11. BRCA 1-5, MUC-1,3
12. prostate specific antigen
13. the absence of CD86 expression, the fact that the cells originate from the self, the expression of low levels of MHC (sometimes the tumor cells make their own MHC molecules), and cytokine production such as TGF-beta which can inhibit t cell activity.

14. CD8 t cell mediated immunity, macrophage production of reactive oxygen species, NK cell response (?).
15. burn victims express high levels of TNF-alpha, which aids in the protection against cancer.

immunology: class notes 3/2-3/3- autoimmunity

autoimmunity is the phenomenon of the immune system attacking host cells, including immune system cells. it arises either from "spontaneous" factors, or from infection, or from various environmental triggers. autoimmunity can be viewed in the same framework as the four types of hypersensitivity in that the mechanisms are the same. the exception is type I hypersensitivity, which involves a class switch to IgE- this mechanism is not seen in autoimmunity. type II autoimmunity involves a class switch to IgG, which binds to different self-antigens.

the first example of type II autoimmunity is autoimmune hemolytic anemia, in which b cells specific for red blood cells start proliferating and producing antibodies, which bind to red blood cells. in this case, the b cells can proliferate using a "antibody crosslinking" mechanism, bypassing the need for IFN-gamma. the antibodies opsinize red blood cells and leave them primed for phagocytosis and destruction by macrophages and natural killer cells. myesthenia gravis is another example of type II autoimmunity, in which antibodies bind to acetylcholine receptors at the neuromuscular junction and thus prevent neural conduction. grave's disease is the third example, where antibody binds to thyroid stimulating hormone receptors, this time stimulating the receptor, resulting in hyperthyroidism.

type III autoimmunity involves a class switch to IgA. this often induces formation of antibody/antigen complexes which block blood vessels or nephritic tubules and cause macrophages to come and secrete reactive oxygen species and damage surrounding tissue. lupus is an example of type III autoimmunity- where the self antigens are all contained within the nucleus of cells: histones, nucleosomes, spliceosomes, transcription factors. these self antigens are thus attacked only in places of high cell turnover or division; such as the skin and joints.

type IV autoimmunity involves a t cell mediated response against self antigens. the first main example is type I diabetes, where pancreatic beta cells are attacked by CD8 t cells specific for insulin, which are activated by dendritic cells which express co-stimulatory molecules by means of a simulaneous infection (or other "spontaneous" means). in multiple sclerosis, the self antigen is the myelin basic protein which coats neurons-- in this case CD4 t cells are activated to produce antibody which opsinize the myelin sheath and cause macrophages to attack. at this point the myelin sheath can be regenerated from oligodendrocytes, but eventually CD8 t cells are activated to attack the oligodendrocytes as well. finally, rheumatoid arthritis is an autoimmune disease in which the antigen is not clearly defined; either collagen or heat shock proteins, which end up with macrophages being recruited to joints and causing damage by reactive oxygen species, etc. rheumatoid factor is also present in the disease, which acts as an antibody to antibodies and can form antibody complexes which can exacerbate disease by damage by macrophages.

questions
1. what is autoimmunity?
2. how does autoimmunity arise?
3. what are some factors involved in development of autoimmune disease?
4. what percentage of monozygotic twins and dizygotic twins show autoimmune disease concordance?
5. what disease occurs when an autoimmune response to myelin basic protein is mounted?
6. what disease occurs when an autoimmune response to insulin is mounted?

7. what is type I hypersensitivity and how is it related to autoimmunity?
8. what is type II hypersensitivity and how is it related to autoimmunity?
9. what are the two ways in which IgM normally class switches to IgG?
10. describe the mechanism of autoimmune hemolytic anemia.
11. describe the mechanism of myesthenia gravis.
12. describe the mechanism of grave's disease.
13. how would one test for the presence of an autoimmune disease in which host cells are being killed (as in question 10)?
14. how would one test for the presence of an autoimmune disease in which host cell receptors are being blocked? (question 11)?
15. how would one test for the presence of an autoimmune disease in which host cell receptors are being overstimulated (as in question 12)?

16. what is the class switching that occurs in type III autoimmunity?
17. how is damage caused by self-specific IgA in type III autoimmunity?
18. what are the self antigens in lupus?
19. why does lupus cause joint pain and skin problems?
20. what is the difference in the autoimmune response to apoptosis vs. necrosis?

21. what is type IV autoimmunity? what are some examples?
22. why does type I diabetes result in hyperglycemia?
23. what is the hereditary component to type I diabetes?
24. which immune system cells "escape tolerance" in type I diabetes?
25. describe the mechanism of autoimmunity in type I diabetes.
26. how are CD8 t cells activated in type I diabetes?
27. what is glutamine acid decarboxylase and how is it related to type I diabetes?

28. what is MS?
29. what is the relative prevalance of MS in males compared to females?
30. what is the average age of onset in MS?
31. what are some epidemiological trends of MS?
32. what is the mechanism to the autoimmune response in MS?
33. what is the role of oligodendricytes in MS?

34. what is rheumatoid arthritis?
35. what is the relative prevalance of rheumatoid arhritis in women vs. men? why?
36. what is the self antigen in rheumatoid arthritis?
37. what are heat shock proteins and what do they do?
38. what are gamma delta t cells and how might they be involved in rheumatoid arthritis?
39. how are joints damaged in rheumatoid arthiritis?
40. what is it that recruits macrophages and neutrophils to the joint areas?
41. what is rheumatoid factor? how does it exacerbate disease?


answers
1. an immune response to self-tissue.
2. either by spontaneous/unknown causes, or in response to extreme childhood stress or trauma, or by infection.
3. environmental (including nutrition), hereditary, the tissues involved, the mechanism of the autoimmune response.
4. mono: 20%, di: 5%
5. multiple sclerosis.
6. diabetes.

7. an allergic response which involves a class switch to IgE. this type of mechanism is not found in autoimmunity.
8. a cytotoxic/antibody dependent response which involves a class switch to IgG. this type of mechanism is the main response used against self tissues in autoimmunity.
9. via IFN-gamma or CD40/CD40L.
10. b cells which are specific to host blood cells are not destroyed during development as they should be and begin proliferating and class switching to IgG (subverting the normal mechanism in question 9 by "cross linking antibodies"). IgG binds to red blood cells and are either opsinized by macrophages or destroyed by NK cells.
11. b cells secrete antibodies which are specific for the host's nicotinic acetylcholine receptors- which blocks acetyl choline binding and results in muscle weakness.
12. b cells secrete antibodies which are specific for thyroid stimulating hormone receptors- which stimulate the receptors, resulting in hyperthyroidism and a downregulation of the TSH receptors on the affected cells.
13. in the case of autoimmune hemolytic anemia, one could look for an abnormally low red blood cell count or an abnormally high b/t cell count in a blood sample.
14. one could test for elevated amounts of the ligand which can no longer bind to the receptor.
15. one could test for elevated levels of the product of the stimulation of the particular host cell, or test for presence of phosphorylated proteins (indicating that the receptor has been bound to and endocytosed).

16. a class switching of IgG or IgM to IgA.
17. IgA can form large complexes with self antigen in vessels or nephritic tubules and block them. additionally, macrophages will bind to the antibodies using Fc receptors and produce reactive oxygen species, which will damage nearby tissues.
18. histone, nucleosome, spliceosome, transcription factors: Ro, La.
19. the self antigens are contained in the nucleus of cells; thus they are primarily exposed to the autoimmune response at places of high apoptosis and necrosis, which would expose nuclear contents during degradation. the joints and skin are two such places.
20. apoptosis is considered "silent" compared to necrosis because only necrosis initiates the inflammatory response.

21. t-cell mediated autoimmunity: multiple sclerosis, type I diabetes, rheumatoid arthritis.
22. because the insulin producing beta-islet cells in the pancreas are destroyed and thus cells can not take in glucose from the blood.
23. the passing down of HLA molecules which are predisposed for diabetes: HLA DR3, DR4, DQ, DQB1*0302.
24. CD8 t cells, CD4 t cells, b cells.
25. a dendritic cell phagocytoses and presents insulin on its surface in both MHC classes. normally, this does not provoke a response from the immune system; however, if this occurs simultaneously with an infection, co-stimulatory molecules will be expressed and t cells specific to insulin will be stimulated to destroy pancreatic beta cells.
26. APC's will stimulate CD4 t cells, which will differentiate into Th1 cells, which will produce IFN-gamma, which will activate CD8 t cells.
27. another antigen that can invoke a similar autoimmune response against the pancreas.

28. an autoimmune disorder which results in multiple sites of demyelination in the brain, spinal cord without axonal degeneration.
29. 7:1 more common in females.
30. 25-35
31. high prevalence in far northern and far southern locales: might be vitamin D related. also very dependent on residence during the first 15 years of life. higher prevalance in high socioeconomic groups and among caucasians.
32. dendritic cells ingest and present myelin basic protein in both MHC classes, causing CD4 t cells to differentiate into Th1 cells, which secrete IFN-gamma, which cause a class switch in MBP specific b cells to produce IgG. IgG binds to myelin and opsinizes, priming myelin for opsinization by macrophages (by way of Fc receptors).
33. oligodendrocytes produce MBP and as such can counter the effects of MS-- until the CD8 t cells are stimulated to attack the oligodendrocytes.

34. an autoimmune disease that leads to destruction of cartilage, bone, and joint deformities.
35. 3:1 prevalence in women as compared to men-- estrogen triggers higher TNF-production via macrophages.
36. unknown; possibly collagen, or heat shock
37. bind to denatured proteins and prevent them from being degraded; activated by excess heat or cold.
38. a special type of t cell that makes high levels of IFN-gamma, causing a class switch to IgG, and also is involved in the production of RF factor.
39. by macrophages which produce reactive oxygen species, IL-1, TNF-alpha.
40. Th17 cells, cytokines such as IL-1, TNF-alpha, IL-6, IL-17.
41. antibody for antibodies which can bind to all antibodies within one isotype. they exacerbate disease when forming antibody "complexes", the accumulation of antibody and RF factor, which blocks vessels and causes macrophages to come and produce ROS, etc.

immunology: class notes 2/23,2/24- vaccines

this unit dealt with vaccination in all its glory; all the immunological, biochemical, ethical, developmental issues that sprout forth from it. vaccination is basically the act of injecting a small amount of inactive or inactivated antigen into the body in order to purposely create an immune response and develop immunological memory so as to be better prepared for the next encounter with that antigen. in a population, vaccination is effective because of the principle of "herd immunity"- the unvaccinated individual still has good chances of not being infected because everyone else is vaccinated. vaccines can be designed to invoke responses against different types of antigens; a b cell response would be desired for extracellular pathogen or toxins, while a t cell response would be desired for intracellular pathogen.

some developmental considerations: up until 1 year, infants can't invoke a Th1 response due to the inability of the antigen presenting cells to make IL-12, and the inability of their t cells to make IFN-gamma (they receive their IFN-gamma from breastmilk up until this point). thus, infants younger than 1 year will only invoke a Th2 (antibody) response when vaccinated. even though this is the case, it is routine to vaccinate infants within 12 hours of birth for hepatitis B, mainly due to logistical factors (cheaper, more convenient, next checkup might not be for a while).

vaccine design has to take many factors into account, such as safety, timing of administration, cost, mechanism of action, type of antigen involved, etc. there are several different ways to kill or inactivate antigen-- note that "inactivated" antigen means that the antigen can never again be pathogenic, whereas "inactive" or attenuated refers to antigen that is at the moment not pathogenic, but has the potential to be. the old method for producing inactive antigen was to simply boil the antigen- the downside to this being that immune response to these denatured proteins might be different than to the original antigen. now the conventional method is "formalyn inactivation"- a chemical inactivation.

there are other ways to prepare vaccines besides the killing / inactivation route, each with their own advantages and disadvantages. the "protein subunit" method uses just a piece of the toxin as the antigen- while this guarantees that the antigen will not be pathogenic, it also requires multiple doses to get an adequate immune response. some vaccines use just the DNA of the antigenic protein instead of the protein itself-- while this method is cheap, it doesn't work too well with humans. another method tries to make antigenic peptides that fit directly into MHC (as opposed to antigen being processed into peptides in the cell and presented in MHC)-- unfortunately, because of the lack of expression of co-stimulatory molecules, this method produces tolerance rather than immunity. finally, DC vaccines are currently in development- dendritic cells are isolated outside of the host, exposed to the antigen, then put back into the host, where they can go to the lymph nodes and initiate an immune response.


questions
definitions...
1. what is contained in a vaccine?
2. what is the difference between inactive and inactivated pathogens?
3. what is the purpose of a vaccine?
4. what is meant by "herd immunity"?
5. what are some considerations required for the design of vaccines?
6. what sort of immune response would be appropriate for an extracellular pathogen?
7. what sort of immune response would be appropriate for intracellular pathogens?
8. what sort of immune response would be appropriate against toxins?
9. what is thimersol and why was thimersol used in vaccines up until recently?
10. why is aluminum added to vaccines?

developmental issues...
11. why can't infants younger than 1 year old invoke a Th1 response?
12. what is the response to vaccination of an 6 month old infant?
13. where do infants get their IFN-gamma?
14. when is the hepatitis B vaccine generally administered and why?

vaccine preparation...
15. what is a conjugate vaccine?
16. what is an attenuated vaccine?
17. what is the CDC recommendation for the timing of the measles mumps ruebella vaccine?
18. what was the old way for killing viruses for vaccine preparation and what was its downfall?
19. what is the new way for killing viruses for vaccine preparation?
20. how is the flu vaccine formulated?

what are these types of vaccines and what are their advantages and disadvantages:
21. protein subunit
22. DNA
23. peptide
24. DC vaccines

answers
1. an inactive or inactivated form of antigen.
2. inactive can potentially still be activated (also called attenuated), whereas inactivated pathogens will never be harmful again.
3. to increase numbers of T, B cells specific for the injected antigen so as to provide immunological memory to protect against future infection.
4. the idea that the effectiveness of vaccination is proportional to how much of the population is vaccinated- or that the unvaccinated individual has less of a chance of infection because everyone else has been vaccinated.
5. type of antigen / pathway of infection, safety / toxicity, timing of administration, cost.
6. a b cell response.
7. a t cell response
8. an antibody (b cell) response.
9. it is a mercury containing component of vaccines that was used to protect against contamination of the vaccine itself- due to repeated usage of the same bottle for multiple vaccinations by doctors.
10. it enhances the antibody response.

11. their APC's can't make IL-12, and their t cells can't make IFN-gamma; CD8 t cells won't be activated.
12. this infant will produce a Th2 response.
13. breastmilk.
14. within 12 hours, mainly due to convenience, and the fact that before 2 years old the infants have a much higher susceptibility for infection by the Hep B virus.

15. conjugate vaccine is an non-protein antigen (hapten) that is combined with a protein ("carrier") in order to ellicit an immune response.
16. an inactive form of antigen which has been passed through several different animals, usually including a bird, in order to make it non-tropic for humans.
17. 18 months.
18. boil a protein to denature it- but the new protein has might produce a different immune response than the original.
19. "formalyn inactivation"
20. 3 strains of the flu are combined into one vaccine based on what strains are expected to be virulent for the upcoming season.

21. using only a piece of toxin to initiate the immune response; don't get a big immune response, so need multiple doses.
22. injecting the DNA instead of the antigenic protein; cheap but doesn't work well in humans.
23. make the peptide that fits directly into the MHC molecules; instead of creating immunity creates tolerance because doesn't cause co-stimulatory molecule expression.
24. isolating dendritic cells, exposing them to antibody outside of the body, putting them back into the body, where they can travel back to lymph nodes and initiate immune response; is still in development and very expensive.

immunology: HIV lecture

during this class we talked about the HIV virus and the particular way in which it infects host cells. the structure of the HIV virus was described; a viral "particle" which contains a nucleocapsid core in its center, which contains 3 genes's worth of RNA and 3 proteins. on the surface of the particle is the GP120 receptor, a highly mutagenic receptor which binds to host cells, and the GP40 receptor, which aids in fusion of the viral particle with the host cell.

HIV most commonly binds to the CD4 t cell but can also infect macrophages and dendritic cells. the viral life cycle for HIV infecting a macrophage: GP120 binds to the CCR5 and CD4 receptors on the surface of the macrophage, which stimulates viral fusion with the macrophage. the nucleocapsid core dissolves, releasing the contents into the host cell cytoplasm. the three proteins contained in the core, integrase, protease, and reverse transcriptase, are set into action.

reverse transcriptase produces fragments of cDNA from the viral RNA. integrase caps off the ends of the cDNA and incorporates it into the host cell genome. at this point the host cell is officially a "provirus". the host cell transcribes the viral DNA as its own and produces 3 long viral proteins (hence the 3 genes contained in the nucleocapsid core), which are activated and cleaved by protease into 13 smaller proteins. 10 of these proteins are left in the provirus to aid in replication and 3 are packaged into a new viral bud, which uses for its membrane the membrane of the host cell. one consequence of this is "viral tropism"- a virus that buds off from a macrophage will have the macrophage surface receptors for t cells and thus will be more likely to infect t cells, and vice versa.

the immune response to HIV depends on the pathway of infection and the type of cell it infects. if HIV exists extracellularly, the immune response will be to produce antibodies against it- at first IgM, before t cells are involved. HIV can also reside intracellularly in host cells- either through infection or phagocytosis. in the case of phagocytosis, the APC will present the viral peptides through the MHC class II peptides, and the co-stimulatory molecules will also be expressed (by virtue of the antigen being phagocytosed), thus ultimately provoking the CD8 response against the infected cell. this would occur through activation of CD4 cells that are specific for HIV, which would then secrete IFN-gamma, which would: upregulate MHC's, stimulate the CD8 response, and cause an antibody class switch to IgG.

in the case of infection, the response against HIV gets complicated and potentially dangerous. if HIV infects a macrophage, the GP120 binding to the CCR5 and CD4 jointly will stimulate expression of the co-stimulatory molecules, leading to the CD8 response. however, if it infects a CD4 t cell, there will be no expression of co-stimulatory molecule and therefore no response from the CD8 cells. furthermore, a CD8 response could potentially be triggered by other cells, as described above, which would then begin attacking all of the infected CD4 cells. it is this mechanism which lowers the CD4 count in HIV infected individuals and leads to AIDS.

a few extra notes: a follicular dendritic cell is a special APC which resides in the lymph notes and serves as a "catalogue" for all the antibodies the body has been exposed to- by way of extremely long dendrites that are covered in Fc receptors. unfortunately, this means that in HIV infected individuals, the Fc receptors will bind to antibody which have HIV viral particles bound to it. thus follicular dendritic cells can function as a reservoir for HIV particles, which are then released during the stress response.

the current HIV treatment is a "triple cocktail" of 2 protease inhibitors and 1 reverse transcriptase inhibitor. most single drugs are rendered ineffective because of HIV's high mutagenicity. two HIV tests are the ELISA test and the PCR test. the ELISA test measures for the presence of antibody specific for HIV by using a second, fluorescent-ly labeled antibody specific for the viral antibody. the PCR test tests for the presence of viral DNA by using a primer specific for the infected DNA, which can then be amplified and detected using the PCR technique.

questions
surface receptors...
1. what is GP 120 and what does it do?
2. what is GP 40 and what does it do?
3. what are the two receptors on macrophages that HIV binds to? what are they receptors for?
4. what are the two receptors on t cells that HIV binds to?
5. what is viral tropism?
6. what is the nucleocapsid core and what is inside it?

viral proteins...
7. what does reverse transcriptase do?
8. what does integrase do?
9. what does protease do?
10. what is meant by a "provirus"?

treatments...
11. what are some drugs that can aid in preventing HIV infection?
12. what are the disadvantages to these drugs?
13. what is currently the conventional drug treatment plan for HIV?
14. what is the difference between a lytic virus and a budding virus?

FDC's...
15. what is a follicular dendritic cell (FDC)?
16. what is the "job" of an FDC?
17. how can FDC's function as a reservoir for HIV?
18. what is a condition that releases the antibodies from FDC's?

immune response...
19. in general, what are the two pathways of HIV infection?
20. what is the immune response against an extracellular HIV infection?
21. what are the two ways in which HIV can exist intracellularly?
22. describe the immune response when HIV infects a macrophage.
23. describe the immune response when HIV infects a CD4 t-cell.
24. describe the immune response to phagocytose-d HIV in a macrophage.
25. what is the main cytokine that CD4 t cells secrete in response to viral infection and what are its effects?
26. how is the CD4 population depleted by HIV? is this autoimmunity?

testing...
27. what is the ELISA test? how does it work?
28. what is the PCR test? how does it work?


answers
1. GP 120 is a surface protein on the HIV virus particle which facilitates its binding to host cells.
2. GP 40 is the membrane protein on the HIV virus particle which facilitates fusion with the host cells.
3. CD4, CCR5. CD4 is the same receptor on t cells. CCR5 is a chemokine receptor.
4. CD4, CXCR4- another chemokine receptor.
5. the attraction of the viral particle for other host cells depending on what cell the viral particle "buds off" from.
6. the central compartment inside a viral particle that contains 3 genes and 3 proteins. genes: GAG, POL, ENV. proteins: integrase, reverse transcriptase, protease.

7. it transcribes the viral mRNA into cDNA.
8. integrase caps the end of the cDNA, then integrates the DNA fragment into the host genome, where it will be transcribed into proteins.
9. protease cleaves the proteins created by transcription of the cDNA- it cleaves the 3 long proteins into 13 small, active proteins.
10. a provirus is an infected host cell that has had viral cDNA incorporated into its genome.

11. drugs that inhibit or block the action of: reverse transcriptase, integrase, envelope proteins, proteases.
12. HIV mutates at such a fast rate that they are rendered ineffective on the order of months, or even days.
13. a "triple cocktail" of 2 protease inhibitors and 1 reverse transcriptase inhibitor.
14. a lytic virus kills the infected host cell whereas a budding virus simply uses the host cells machinery to replicate itself.

15. a dendritic cell in the lymph nodes with extremely long dendrites which are covered in Fc receptors.
16. to keep a "catalogue" of all the antibodies that the host has been exposed to.
17. the Fc receptors on the dendrites might bind antibodies that have virus particles bound to them.
18. stress.

19. intracellular and extracellular.
20. antibody production- IgM at first, before helper t cells are enlisted.
21. through infection and phagocytosis.
22. HIV infects the macrophage and some of the viral protein is degraded and presented by the MHC class I pathway. CD86 is expressed on the surface due to the joint binding of CCR5 and CD4 with the viral GP120- this stimulates the production of IL-12 and potentially activates a CD-8 t cell response.
23. viral peptide still expressed on MHC class I, but no co-stimulatory molecule is expressed; thus immune response is subverted.
24. the MHC class II pathway is activated, as well as co-stimulatory molecules (which are generally expressed with phagocytosis of antigens). the macrophages can then activate CD4 t cells specific to HIV, which will secrete cytokines to provoke the immune response against it.
25. IFN-gamma, which increases MHC expression, activates CD8 t cells, and causes a class switch from IgM to IgG.
26. this is not autoimmunity. the CD8 t cells that are activated against HIV begin killing the CD4 t cells that have also been infected with HIV (this happens in particular when the virus buds off a macrophage)

27. ELISA is a test for the presence of antibody specific for HIV in the blood. it works by using a secondary antibody which binds to the first- the secondary antibody is labeled with fluorescent material which shows up during spectrophotometry tests.
28. PCR test tests for the presence of infected DNA by using a primer specific for this DNA, which then aids in the "amplification" of this DNA using the PCR (polymerase chain reaction) technique, allowing for its detection.

immunology: hypersensitivity

hypersensitivity is the phenomenon where the immune system's cells overreact against non-pathogenic antigen. there are four classifications based on the mechanism of the immune response. type I hypersensitivity is the allergic response; involves a class switch from IgM to IgE and a Th2 based response. an example is an allergy to corn: corn particles are ingested by dendritic cells and macrophages in the intestinal lymph tissue and presented to a CD4 cell. if co-stimulatory molecules are expressed, and the cytokines IL-10 and IL-15 are secreted, the CD4 cell differentiates into a Th2 cell, secreting IL-4,5,13. IL-4 causes a class switch from IgM to IgE, which causes binds to mast cells and causes degranulation and also secretion of TNF-alpha (TNF-alpha damages intestinal epithelium, contributing to leaky gut, potentially worsening the allergic response).

type II hypersensitivity is characterized by release of antibodies specific for molecules on cell surface. an example is the hypersensitivity to penicillin, which can occur when penicillin binds to a glycosylated protein on red blood cells. antibodies specific for the penicillin then bind to the redbloodcell/penicillin and are subsequently attacked by macrophages, resulting in hemolytic anemia (note that this is not an autoimmune response because the macrophages are targeting the penicillin primarily).

type III hypersensitivity is characterized by antibodies that are specific for soluble proteins- generally only occurs with high levels of soluble proteins. this often results in the formation of large antibody-soluble antigen complexes which can grow to block vessels or tubules. when this occurs macrophages and neutrophils are recruit to phagocytose the complexes and often damage the peripheral tissue by way of ROS production.

type IV hypersensitivity is a t-cell mediated response against antigen. the example given to us is celiac disease, which is a hypersensitivity to a peptide in wheat, gliadin. wheat is transported in from the lumen of the gut into the peyer's patches by microfold cells, where it can be ingested by macrophages and dendritic cell. these cells present the wheat peptide in an MHC to a CD4 t cell; if there is no co-stimulatory molecule expressed as well, this leads to a state of anergy and peripheral tolerance in the t cell. if there is co-stimulatory molecule expression (note that the increased microflora that enters the intestinal layers due to leaky gut can increase the likelihood of expression of co-stimulatory molecules) the CD4 t cell will be differentiated into a Th3 cell, which will proliferate and secrete TGF beta, resulting in a state of tolerance.

questions
different hypersensitivity mechanisms...
1. what is type I hypersensitivity characterized by?
2. what is type II hypersensitivity characterized by?
3. what is type III hypersensitivity characterized by?
4. what is type IV hypersensitivity characterized by?
5. what does an immune response dominated by Th2 result in? Th1?
6. what type of hypersensitivity is a penicillin hypersensitivity? describe the immune response.
7. why is a penicillin hypersensitivity not considered an autoimmune disease considering that red blood cells die in the process?
8. describe a typical type III hypersensitivity immune response.
9. describe a typical type IV hypersensitivity immune response.

celiac disease...
10. why is celiac disease not technically an allergic response?
11. what is the antigen in celiac disease?
12. describe the class switching mechanism in celiac disease.
13. what are microfold cells?
14. describe the activation of CD4 t cells in celiac disease.
15. when is a Th2 response employed in celiac's disease as opposed to a Th3 response?

other food allergies...
16. what are some characteristics of foods that commonly yield allergies?
17. describe how an allergic reaction to corn can lead to leaky gut.
18. what are some foods that typically create an allergic response?

answers
1. allergies, class switch to IgE
2. IgG against a surface protein
3. IgG against a soluble protein
4. t-cell mediated response
5. Th2 dominance is an allergic response, Th1 dominance is autoimmune disease.
6. type II hypersensitivity. glycosylated protein on RBC binds to penicillin, which is then opsinized by antibody, priming it for destruction by macrophages- resulting in hemolytic anemia.
7. because the immune response is against the penicillin, not the RBC’s- they are just a casualty.
8. antibody is released in response to soluble antigen; large antibody/antigen complexes form that can clog vessels. macrophages and neutrophils phagocytose complexes and create ROS which can damage the periphery.
9. the tuberculosis test is a typical type IV hypersensitivity response. purified protein derivative (PPD) is injected into the body- macrophages or dendritic cells ingest, carry to lymph nodes, and activate a Th1 response- T cells return to the infection site.

10. because there is no IgE class switch or a Th2 response- this is a Th1 response mediated by CD4 and CD8.
11. gliadin- resembles transglutaminase.
12. instead of being caused by a cytokine, it is caused by a the CD40/CD40L on B cell.
13. cells on the intestinal epithelium that transports whole antigen to the peyer’s patches.
14. dendritic cells or macrophages will ingest the wheat and produce one of two responses in T cells: if there is no co-stimulatory molecule, the T cell will go into the anergic state. if there is a co-stimulatory molecule (can be due to microflora entering from leaky gut caused by wheat), this causes IL-10 secretion and differentiation into Th3 cells, which secrete TGF beta, producing tolerance.
15. when IL-10 is secreted alongside IL-15.

16. high concentrations of hard to digest proteins, they make it far down the GI tract before being absorbed.
17. corn particles are ingested by macrophages in the peyer’s patches, and presented alongside CD86 (which is expressed for unknown reasons) to a CD4 t cell. the t cell differentiates into a Th2 cell by way of IL-10 and IL-15 cytokines, and secretes IL-4,5, and 13. IL-4 causes a class switch to IgE, which causes mast cells to degranulate and secrete TNF-alpha, which breaks down gut barrier and causes leaky gut.
18. dairy, soy, wheat, shellfish, nuts, corn, eggs, potatoes.

immunology: parham's the immune system chapter 6- t cell mediated immunity

this chapter talked about the activation and actions of the three different types of t cells: CD8 t cells, CD4 TH1 cells, and CD4 TH2 cells.

naive t cells are formed in the thymus and are constantly in circulation and are activated only when they encounter antigen presenting cells (APC's) in the lymph. there are three "professional" antigen presenting cells- dendritic cells, macrophages, and b cells. out of these three, dendritic cells are most involved in activating t cells, because they migrate from peripheral tissues, where the infection occurs, into the lymph nodes where they can encounter naive t cells- whereas macrophages stay in the infected tissues to combat the infection.

activating a t cell requires several factors to be in place: first the expression of cell adhesion molecules such as LFA's on the surface of the t cells and APC's will transiently bind the two together, allowing the t cell receptors to have a chance to bind to the MHC:peptide complex on the APC. to be fully activated, the t cell receptor needs to be specific for that particular MHC:peptide, and co-stimulation also needs to occur. costimulation is the expression of the CD80 or CD86 ligand on the APC surface in response to binding of common microbial constituents such as lipoproteinsaccharide. CD80/86 binds to CD28 on the t cell, which causes the release of the cytokine IL-2, which causes proliferation and differentiation of the t cell.

thus, costimulation acts as a confirmation of the presence of an infection. if no costimulation occurs, this generally means that the t cell is being presented with a self-antigen. this leads to no IL-2 being secreted, and the t cell goes into the state of "anergy", where the t cell receptors are actually less receptive to the (self) antigen next time it encounters it.

t cells can then differentiate into cytotoxic CD8 t cells, which migrate to the site of infection and release cytokines and cytotoxins into the virus infected cells. when the CD8 cells are activated in the lymph tissue, they form "lytic granules" which are then released in close proximity to the infected cells. these granules contain perforin, granulysin, and granzymes- the first two perforate the cell membrane and allow granzymes to enter the infected cell, which activates proteases and enzymes which trigger apoptosis.

t cells can also differentiate into CD4 TH1 cells, which are involved in macrophage activation. these cells also migrate to the site of infection in peripheral tissues. they secrete a number of cytokines such as IFN-gamma, TNF-alpha, IL-2, IL-3, GMCSF, the chemokine CXCL2, and the ligand CD40, which have various effects on the macrophage. IL-3 and GMCSF cause increased macrophage production in the bone marrow. IL-2 causes the TH1 cells to proliferate. TNF-alpha facilitate diapedesis of macrophages into sites of infection. but perhaps most importantly, the cytokine IFN-gamma and the CD40 ligand on TH1 cells stimulate macrophages to increase microbicidal activity, such as increased fusion of phagosomes with lysosomes, or creating more reactive oxygen species. this helps the fight against pathogens which reside within the macrophages themselves.

finally, t cells can differentiate into CD4 TH2 cells, which are involved in activating b cells. t cells might come into contact with a dendritic cell in the lymph tissue and then differentiate into a TH2 cell; in contrast to the other t cells which migrate to the infected tissues, the TH2 cell remains in the lymph tissue to await an encounter with the circulating b cells. in order to activate a b cell, it needs to recognize the MHC:peptide from the same antigen that it is specific for. this causes the t cell to express the CD40 ligand and secrete cytokines IL4,5 and 6, which cause b cell proliferation and differentiation into plasma cells.

questions
1. why are dendritic cells better suited to activate naive t-cells in the peripheral lymph tissues compared to macrophages?
2. for any given infection, a naive t cell specific for the pathogen will represent 1 in ... of the total population of circulation t cells.
3. how long does it take for naive t cells to differentiate into effector t cells?
4. how do t cells move from circulation into the lymph tissues?
5. what is an LFA and how is it related to the maturation of a t lymphocyte?
6. what is costimulation and what molecules are required in this process?
7. what is CTLA4 and what does it do?

8. what are the three types of professional antigen producing cells and where do they reside in the lymph node?
9. describe the maturation of a dendritic cell.
10. what do macrophages do in the lymph node?
11. how are macrophages activated to professional APC status?
12. how does listeria subvert the body's immune defenses?
13. describe how b cells act as APC's.
14. what are adjuvants?

15. what is ZAP-70?
16. what does the tyrosine kinase pathway ultimately induce?
17. how is IL-2 produced?
18. what effect does IL-2 have on t cells?
19. what is the state of anergy?

20. what is Th1 and Th2 activation called?
21. describe the development of a bias of Th1 vs. Th2 cells.
22. which is the only APC cell that can stimulate CD8 activation and why?
23. what are the three ways in which CD8 cells can be activated?

24. describe the difference in costimulation requirements for effector CD8 and CD4 cells.
25. what are lytic granules?
26. describe the formation and release of lytic granules by cytotoxic CD8 cells.
27. what is the cytokine that CD8 secretes and what does it do?
28. what are the cytotoxins that CD8 cells release and what do they do?
29. what are Fas ligands and how do CD8 cells use them?

30. what is macrophage activation?
31. what are the cytokines required for macrophage activation?
32. how do CD-8 t cells also contribute to macrophage activation?
33. how do TH2 cells inhibit macrophage activation?
34. what are the different cytokines produced by TH1 cells and how do they contribute to macrophage activation?

35. describe the activation of B cells via TH2 cells.
36. what are the cytokines involved in activation of B cells? what effect do they have?


answers
1. because dendritic cells are migratory cells which travel from the site of infection to the lymph tissues, whereas macrophages reside in the tissues to combat infection.
2. 1 in 106.
3. a few days.
4. via cell adhesion molecules and chemokines.
5. LFA is lymphocyte functioning associated antigen, an integrin on the surface of the t cells which aids in the transient connection to dendritic cells, so that the t cell receptors might bind to a MHC/peptide complex, thereby beginning the maturation process.
6. in order for the t cell to differentiate, two things must occur: the MHC/peptide has to bind to the t cell receptor, and the CD28 receptor on the t cell must bind to either the CD86 or CD80 ligand on the dendritic cell. this is called co-stimulation.
7. it binds to CD86 or CD80 20 times as strongly as CD28 and acts as an antagonist, inactivating t cells.

8. dendritic cells are in the cortex, macrophages are throughout the cortex and medulla, b cells are in the germinal centers.
9. once dendritic cells bind to antigens in the peripheral tissues they migrate to the cortex of lymph nodes and undergo several changes: they display costimulatory molecules on their surface, secrete chemokines which attract naive t cells, and increase their cell adhesion molecules to facilitate the transient connections described in question 5.
10. they phagocytose circulating pathogens - for the purposes of stimulating t cells as well as preventing the infection from reaching into the blood and becoming systemic. they also kill lymphocytes.
11. through binding of one of their germline encoded surface receptors: mannose receptor, scavenger receptor, complement receptors, toll like receptors.
12. once phagocytosed by macrophages, it resides in the cytosol instead of being destroyed in a phagolysosome.
13. b cells bind antigen via their surface immunoglobulins, which are then endocytosed and presented on class II MHC's. costimulatory molecules are expressed in response to binding of certain microbial components (such as LPS).
14. adjuvants are bacterial components that are used to stimulate costimulatory molecules in APC's.

15. ZAP-70 is a tyrosine kinase that is activated when the t cell receptor binds to a MHC/peptide complex, which is involved in initiating the intracellular signalling pathway.
16. the production of transcription factors which initiate the profileration and differentiation of t cells, and also the upregulation of cytokine production, such as IL-2.
17. IL-2 is upregulated when a t cell binds to both MHC/peptide as well as costimulatory molecule. IL-2 high affinity receptors are also upregulated upon t cell activation.
18. IL-2 induces proliferation of the antigen specific t cells.
19. anergy is when a t cell does not produce IL-2 and therefore cannot proliferate. this occurs when a naive t cell binds to self antigen (which therefore does not produce co-stimulation)

20. Th1 helper cells activate macrophage's microbicial activity and thus is called cell mediated immunity. Th2 activates b cells secretion of antibodies and thus is referred to as humoral immunity.
21. once Th1 or Th2 cells begin proliferating they suppress the other type.
22. dendritic cell, because they are the only APC that can provide sufficient costimulation.
23. dendritic cells can activate via costimulation, CD4 cells can secrete cytokines which stimulate APC's to express costimulatory molecules, and CD4 cells can also secrete IL-2 which binds to IL-2 receptors on CD8 cells, thereby activating them.

24. when CD8 and CD4 t cells proliferate and become effector cells, they can be stimulated to their effector functions without the need for costimulation by the CD80 or CD86 which is found only on professional APC's. this means that cytotoxic CD8 cells can destroy all infected cells it encounters and CD4 can better activate b cells in the lymph tissues.
25. modified lysosomes in CD8 t cells that contain cytotoxins.
26. lytic granules are formed in CD8 cells in response to activation by antigen in the lymph tissues. the CD8 cells then migrate to the site of infection and release the lytic granules upon binding to the antigen/MHC complex of infected cells. when the cell begins to die, the CD8 cell releases, forms new lytic granules, and attaches to another infected cell to repeat the process.
27. IFN-gamma, which upregulates the expression of MHC I, inhibits viral DNA replication, and activates nearby macrophages.
28. perforin and granulysin make pores in the cell membrane through which granzymes can enter, which then activate nucleases and enzymes that lead to apoptosis.
29. Fas ligands are expressed on cytotoxic CD8 t cells, which bind to the Fas molecules on infected cells, triggering apoptosis (a secondary route, although a primary route for disposing of old lymphocytes).

30. macrophage activation is the activation by CD4 TH1 cells whereby macrophage's antimicrobial activities are increased; phagosome fusion with lysosome is increased, microbicial molecules are produced, and antigen presentating to t cells is increased.
31. TH1 cells secrete IFN-gamma, TNF-alpha, and express the CD-40 ligand, all of which activate the macrophage.
32. CD-8 secretes IFN-gamma, which contributes to macrophage activation.
33. by the cytokines TGF-alpha, IL-4, IL-10, IL-13, which inhibit macrophage activation.
34. IL-2 promotes proliferation of t cells, IL-3 and GMCSF promote macrophage differentiation in the bone marrow, TNF-alpha and beta contribute to macrophage diapedesis into the site of infection, and CCL2 acts as a chemokine to guide the phagocytes to the infected area.

35. infected dendritic cells travel to the t cell areas of peripheral lymph tissues and activate naive t cells into TH2 helper cells. circulating b cells then come into contact with these TH2 cells and become activated.
36. IL-4, IL-5, IL-6 and CD40 ligand, which causes proliferation of b cells and differentiation into plasma cells.

immunology: parham's the immune system chapter 3- antigen recognition by t lymphocytes

this chapter talked about t-cell receptors and the ligand that they bind, MHC molecules. MHC's are surface molecules expressed on host cells that display peptide fragments derived from antigen. MHC's are differentiated by two classes: class 1 MHC's bind to intracellular peptide fragments, from antigen which has been degraded by proteosomes in the cytosol. class 2 MHC's bind to peptides in extracellular vescicles which have been degraded by lysosomes or acidification.

t cells are also divided into two families based on the type of antigen they are responding to. CD8 t cells respond to intracellular antigen (such as viral infection) and accordingly bind to MHC class 1 molecules, which trap intracellular antigen. CD4 t cells respond to extracellular antigen (such as bacterial infection) and therefore bind to MHC class 2 molecules. within CD4 t cells, TH1 cells stimulate macrophages to release cytokines and TH2 cells stimulate b cells to release antibodies.

the t cell receptor is similar in structure to one Fab arm of the b cell immunoglobulin, in that it is made out of two chains with 4 domains and an antigen binding site on the extended end. the diversity of the variable domain is also created in a similar way to the immunoglobulins in that it uses somatic recombination of varied gene segments. one main difference between t cell receptors and immunoglobulins is that while immunoglobulins are modified after contact with antigen, either to class switch to a different effector function or to enhance binding specificity for the antigen, t cell receptors remain the same.

MHC molecules, as mentioned above, bind to peptides in host cells and present them to t cells to provoke an immune response. whereas all host cells have class 1 MHC's, only professional antigen presenting cells have class 2 MHC's: dendritic cells, macrophages, and b-cells. although MHC's are binding a diverse array of peptide from antigen, the source of diversity of the binding site is much different than that of immunoglobulins or t cell receptors. instead of random rearrangement of gene segments, MHC binding sites achieve high diversity by the polymorphism present in the genes that encode them.


questions
1. what are the similarities between immunoglobulins and t cell receptors?
2. what are the two chains in a t cell receptor?
3. what are CDR's and how many does each t cell receptor have?
4. what is the context in which antigen binds to t cell receptors?
5. why are t cell receptors not further modified after encountering antigen, as immunoglobulins are?
6. what gene segments do the alpha and beta chain locuses contain?
7. where does t cell receptor gene rearrangment occur?
8. what is SCID?
9. what is Omenn syndrome?
10. what is the CD3 complex?
11. what are gamma-mu t-cells?
12. what type of t cell receptor do t cells that reside in epithelial tissue have?

13. what are the different subdivisions of t cells?
14. HIV exploits which receptor on t cells?
15. what are the divisions within MHC molecules and what type of T cells do they bind to?
16. describe the structure of MHC class 1 and class 2 molecules.
17. how does the structure of MHC molecules allow for simultaneous binding of t cell receptors and coreceptors?
18. compare the length of peptides pinned down by MHC class 1 and class 2's.

19. what are TAP's?
20. what are chaperones?
21. the MHC class I molecules cannot leave the endoplasmic reticulum unless..
22. how do MHC's relate to autoimmunity?
23. describe the intracellular path by which MHC class II molecules bind to peptides in extracellular vesicles.
24. what are the two functions of invariant chains?
25. what is HLA-DM and what does it do?

26. what is a common cell that lacks MHC class I molecules?
27. describe the difference between the body's expression of MHC class I and II molecules.
28. what are professional antigen presenting cells?
29. what effect does the cytokine IFN-gamma have on professional antigen presenting cells?

30. what is it that makes MHC's highly polymorphic?
31. what are the class 1 MHC isotypes?
32. what are the class 2 MHC isotypes?
33. what are anchor residues?

answers
1. t cell receptors are like the Fab portion of an immunoglobulin in that they are made up of two different chains and have a variable region on the outside. t cell receptors are also formed by somatic recombination of gene segments just like immunoglobulins as well.
2. TCR-alpha and TCR-beta.
3. complementarity determining regions, each chain has three; each t cell receptor has 6.
4. only via opposing cell surfaces when binding to antigen peptides presented by MHC's on the surface of other cell (as opposed to soluble immunoglobulins binding to antigen in solution).
5. because immunoglobulins act as effectors which need to increase their efficiency of binding to the particular antigen; whereas t cell receptors are simply receptors.
6. the alpha chain contains V and J gene segments and thus is analogous to the immunoglobulin's light chain whereas the beta chain contains V,J, and D, and is analogous to the heavy chain.
7. in the thymus
8. severe combined immunodeficiency disease, in which the RAG gene complex is dysfunctional, leading to absence of functional B and T (hence the "combined") cells.
9. immunodeficiency syndrome caused from a partially defective RAG gene.
10. the four invariant membrane proteins that t cell receptors associate with in the ER, which facilitate expression of the receptor on the cell surface.
11. a set of t cells that express t cell receptors with gamma-mu chains instead of alpha-beta chains.
12. mostly the gamma-mu t cell receptors.

13. CD4 and CD8 t cells, based on a specific glycoprotein present on the t cell's surface. CD4 t cells are cytotoxic, killing infected cells. CD8 t cells are further subdivided into TH1 cells, which activate macrophages, and TH2 cells, which stimulate antibody release from b cells.
14. the CD4 receptor.
15. MHC class 1 molecules bind intracellular antigens and therefore to the cytotoxic CD8 cells, and MHC class 2 molecules bind antigen in extracellular vescicles, therefore binding to CD4 helper cells.
16. MHC class 1 is made up of 4 extracellular units, 2 layers of 2 domains. the closest layer has one transmembrane alpha domain and a beta protein (which is not encoded by the MHC), while the outer layer has two alpha domains that make up the peptide binding site. MHC class 2 is made up of 4 extracellular units as well, where the first layer is made up of an alpha and beta domain, and the outer layer is made up of another alpha and beta domain.
17. the t cell receptor and peptide binds to the outer domains and the coreceptors bind to the inner layer.
18. the length is limited in class 1 MHC to about 9 amino acid long peptides, because both sides of the peptide are pinned down to the peptide binding pocket, whereas in class 2 MHC's the can extend beyond the pocket and can thus be longer.

19. TAP's are "transporters associated with antigen presentation" which transport peptides that result from antigen breakdown in proteosomes, into the ER to meet with MHC class 1 molecules.
20. chaperones are proteins that aid in the folding and the binding of peptides for MHC class 1 molecules.
21. they have bound a peptide.
22. in the absence of an infection, MHC's present peptides derived from the host rather than from antigens. if the t cells respond to these self antigens, this produces autoimmunity.
23. in this pathway, antigen is phagocytosed/endocytosed into phagosomes, which combine with lysosomes to form phagolysosomes, which degrade the antigen into peptides. the MHC class II molecules then travel to these vesicles and bind to peptide, and then are expressed on the cell surface.
24. invariant chains bind to MHC class II's in the ER, preventing them from binding to the peptides destined for class II MHC's. they also aid in transport to the extracellular vesicles which contain peptides that they will eventually bind to.
25. HLA-DM is the molecule that removes the CLIP (the last bit of the invariant chain that is not removed by proteases in the extracellular vesicles) from the MHC class II, allowing it to bind peptide.

26. erythrocytes.
27. all cells have MHC class I molecules and are thus under total surveillance via t cells for viral infection. only certain cells have MHC class II molecules, and are called professional antigen presenting cells.
28. macrophages, dendritic cells, b cells; can present peptide derived from extracellular vesicles to the CD4 T cells.
29. it upregulates the MHC class II molecules and therefore aids in response to infection or inflammation.

30. the presence of many alleles within the gene families that code for MHC's.
31. the class 1 MHC isotypes are HLA-A,B,C,E,F,G
32. HLA-DM, DO, DP, DQ, DR
33. residues on the peptide that have side chains that bind to pockets within the binding groove of MHC's

main ideas:
t cell receptor structure and synthesis
subdivisions of function among t cells

differences in MHC classes between:
structure of molecule
function
peptides bound
cells which express them
invariant chains

source of MHC polymorphism

immunology: parham's the immune system chapter 2- antibodies and b cell diversity

note: i switched from janeway's "immunobiology" to parham's "the immune system" for its conciseness (30 pages per chapter vs. 50 pages)

this chapter introduces b cells and antibodies and the way that they are produced before encountering antigen, and the way that they are modified after encountering antigen. antibodies are y-shaped molecules which are made up of 2 "heavy" chains and 2 "light chains". each of these chains has a constant region, all 4 of which make up the stem of the y, and a variable region, which make up the two arms of the y (one light chain variable region and one heavy chain variable region per arm). the variable region at the arms of the y contain 3 hypervariable regions that are the binding sites for antigen. antibodies are expressed either on the surface of b cells, where they are bound with a hydrophobic anchor at the carboxy terminus of the constant region, or as free floating molecules.

the production of antibodies in naive b cells is designed to make an incredible diversity of structure in the variable regions of the antibody. the more diverse the antibody repertoire is, the more likely it will bind to a antigen, and thus the process of producing variability is introduced in the production of antibodies in several different places: initially during random recombination of gene segments, also in junctional diversity, then through somatic hypermutation.

while genes for other proteins are transcribed from continuous sections of DNA (loci) from which DNA might be spliced out, the DNA for antibody molecules is represented in gene segments, in which there are multiple varied choices for each section of the gene. for example, for each light chain there are two gene segments required to make the variable region; a V segment and a J segment. there are 30 such V segments and 5 J segments to choose from, resulting in 180 possible combinations of the variable region for the light chain. the heavy chain has more possible segments and yet another segment, D, which adds more variability and results in about 10,000 possible configurations. furthermore, the unique combination of light chain plus heavy chain variable regions represent another source for variability.

when the junctions between these gene segments are formed during recombination, further variability is added by enzymes that add palindromic sequences as well as random nucleotides between the gene segments. the antibody can then be produced and expressed on the b cell surface. the first antibodies that are produced are IgG and IgM- classifications of antibodies based on their constant region.

somatic hypermutation occurs after the b cell has encountered antigen- this involves both a proliferation of b cells, and random mutation / nucleotide substitution in the variable region of the antibody. this produces large quantities of b cells with slightly different variable regions, some of which have a higher affinity for the antigen than the original b cell antibody. this b cell is positively selected for in a process called affinity maturation and the higher affinity antibody is produced in greater quantities.

a b cell can receive signals from cytokines to "class switch" its antibodies, which refers to changing the "constant" region of the antibody (the stem of the y). the variable region is the same, which means the antibody still has the same antigen specificity; however the effector actions and role in the body can be different. for example, IgM is the first antibody produced, is relatively inflexible and forms a pentameric ring. IgA is present in epithelial linings and secretions and the lumen of the gut. IgG is the most common antibody present in the blood and acts directly on antigens to neutralize or opsonize for phagocytosis. IgE is specialized to stimulate mast cells during inflammation or infection.

questions
1. what are the five classes of antibodies?
2. what is the most common antibody?
3. the chains in immunoglobulins are linked by...
4. describe the middle portion of an IgG molecule.
5. what are the kappa and lambda isotypes?
6. what are hypervariable regions?
7. how many hypervariable regions are there per variable domain?
8. what is the antigen binding site composed of? what else are they called?
9. what is an antigenic determinant or epitope?
10. what is a multivalent antigen?
11. what is the difference between a linear and discontinuous epitope?
12. what sort of forces does binding of antigen to antibody depend on?

13. where and when in a b cell's development does rearrangment of gene segments for antibody production occur?
14. what are the types of gene segments that encode the variable regions of the light and heavy chains?
15. what are the main differences between the gene segments that code for the variable sections of the antibody?
16. what is somatic recombination?
17. describe the difference between somatic recombination of a light chain vs. a heavy chain.
18. approximately how many different arrangements of gene segments are possible for light vs. heavy chains?
19. what are RSS's?
20. what is the 12/23 rule for RSS's?
21. what is the RAG?
22. what is the difference between the coding joint and the signal joint?
23. what is meant by "junctional diversity"?
24. what is unique about IgM and IgD?
25. what is allelic exclusion?
26. what are Ig-alpha and Ig-beta?

27. what happens to IgM and IgD upon the b cell's encounter with antigen?
28. what is the main difference between membrane bound and secreted immunoglobulins?
29. what is somatic hypermutation?
30. what is the frequency of mutation/nucelotide substitution in somatic hypermutation?
31. what is affinity maturation?

32. what are the characteristics of IgM?
33. what are the characteristics of IgG?
34. what are the characteristics of IgA?
35. what are the characteristics of IgE?

answers
1. IgA, IgD, IgE, IgG, IgM
2. IgG
3. disulfide bonds.
4. it is a relatively flexible "hinge" region that can be cleaved proteolytically.
5. a the class of immunoglobulin based on the light chain classification in the constant region.
6. regions on the exposed tip of variable domains that have a particularly diverse expression of amino acids.
7. 3
8. the combining of the hypervariable region from the variable domains of both the light and heavy chains. also called complementary determining regions (CDR).
9. the part of an antigen that the antibody binds to
10. an antigen that has more than one epitope.
11. linear is when the CDR binds to adjacent amino acids and discontinuous is when the CDR binds to amino acids that have been brought together by the antigen's chain folding.
12. noncovalent bonds such as hydrogen bonding, van der waal's forces, salt bridges, etc

13. in the bone marrow, early in b cell development.
14. for light chain: variable and joining gene segments. for heavy chain: variable, joining, and diversity gene segments.
15. the sequences that encode the first and second hypervariable regions.
16. the joining of gene segments to form the heavy or light chains.
17. for a light chain only one recombination is required; between the V and the J segments. for a heavy chain two recombinations are required: between the J and D, then the J/D to the V segment.
18. about 300 for light and 10,000 for heavy.
19. recombinant signal sequences, the gene sequences that flank the gene segments.
20. an RSS has either a 12 or 23 long base pair spacer in its middle; a 12 RSS can only be combined with a 23 RSS- this allows the different gene segments to be joined correctly to each other, in the right order and sequence.
21. the recombinant activating genes
22. after recombination, the coding joint is the joint between the adjoined gene segments whereas the signal joint is the loop of base pairs that was excised out between the gene segments.
23. junctional diversity is introduced in the "hairpin" that is formed when gene segments are combined by the RAG complex. the hairpin is then spliced and P (palindromic) and N nucleotides (added randomly) are added in, increasing the diversity of gene sequence in the third hypervariable region.
24. these are immunoglobulins that are produced and expressed first and simultaenously by the naive b cell before encountering antigen.
25. every B cell has two copies, or alleles, of the heavy or light chain locus which can be rearranged to produce a particular immunoglobulin. instead of drawing from both alleles, each B cell only uses one.
26. the transmembrane proteins that freshly produced immunoglobulins associate with in the endoplasmic reticulum which form a complex that bind to the b cell membrane surface. the Ig-alpha and beta proteins have longer tails which extend into the cytoplasm which are involved in intracellular signalling during antigen binding.

27. they are expressed in the secreted form instead of the membrane bound form.
28. the membrane bound form has a hydrophobic anchor on the carboxy terminus of the heavy chains, allowing it to stay on the cell membrane.
29. a process that the b cells undergo after encountering antigen where random nucleotide mutations occur in the variable regions of both the light and heavy chains, producing a great diversity of "mutant" immunoglobulin molecules, some of which have an even higher affinity for antigen than the original.
30. one mutation per cell division, more than a million times the normal mutation rate for a gene.
31. the process by which the b cells which bear mutant immunoglobulins produced by hypermutation which have a higher affinity for antigen are selected for and proliferate.

32. IgM is the first antibody produced by the b cells in response to pathogen and is often in the pentameric form, where it has less flexibility but more binding sites for antigen.
33. IgG is the most common antibody found in circulation and tissues. it is smaller than IgM and has a flexible hinge region, allowing the Fab regions to move indepently. it also has more effector actions than IgM, such as opsonization and activating the complement system. it can also pass through the placenta.
34. IgA is the principal antibody secreted by the lymph tissue into the lumen of the gut, as well as other secretions such as tears and sweat. it is often in the dimeric form.
35. IgE is the antibody which is highly specialized to stimulate mast cells during inflammation, causing it to release its histamine and heparine granules.

immunology: janeway's immunobiology chapter 2

this chapter introduced the mechanisms used by the innate immune system to ward off early infection and also trigger an adaptive immune response.

the first means of defense employed by the innate immune system are in the epithelial surfaces. this includes the tight junctions and thick layers in the epithelia that prevent microorganisms from entering, the mucosal layers and cilia in the lungs that constantly trap and remove microorganisms, antimicrobial agents in tears, and the chemically hazardous environment in the GI tract from gastric and pancreatic enzymes.

if pathogens penetrate this epithelial layer, they then encounter the cells of the innate immune system: macrophages and neutrophils. macrophages are derived from monocytes that circulate in the blood that reside in tissues, and are long lived. neutrophils circulate in the blood and are called into the tissues in large numbers in response to infection and are short lived. both cells have "germline-encoded" receptors that have evolved to recognize common membrane constituents of bacteria. some common receptors on the cells of the innate immune system are mannose binding lectin and scavenger receptors.

pathogen binding to these receptors can stimulate phagocytosis: the pathogen is enveloped in the cell membrane and forms an intracellular vesicle called a phagosome which can then become acidic or fuse with a lysosome, killing the pathogen via lysosomal enzymes. secondly, it can trigger the release of cytokines and chemokines, which can mediate the inflammatory response.

the inflammatory response is a local vasodilation, redness, pain, and heating, caused by release of cytokines and chemokines. it can also trigger blood clotting, which prevents the infection from spreading systemically. these changes promote recruitment of leukocytes from the bloodstream to aid in infection: cytokines act on the endothelium of the nearby blood vessels, causing vasodilation, while chemokines act on the cell-adhesion molecules (CAM) of the endothelium, changing their conformation and affinity for the integrins on the circulating leukocytes. this causes the leukocytes in circulation to bind with selectins, then ICAM's, arresting their flow. they then bore holes through the basement membrane via enzymes that break down the extracellular matrix and enter into peripheral tissues. here, they are guided by increasing concentration gradients of chemokines to the site of infection.

toll like receptors are another pathogen binding receptor on innate immunity cells that also trigger the release of chemokines and cytokines, as well as stimulating the surface expression of co-stimulatory molecules, which trigger the maturation of naive lymphocytes and thus help initiate the adaptive immune response. this is an example of how the innate immune system triggers the adaptive immune response.

the complement system is also used by the innate immune system to aid in the phagocytosis of pathogens. there are three pathways, the classical, MB-lectin, and alternative, all of which are zymogenic cascades which are initiated by protein complexes in the plasma. the classical pathway is initiated by pathogen binding, which triggers a cascade which creates a C3 convertase, which opsonizes the pathogen's surface with C3b, leaving it susceptible to phagocytosis. the MB-lectin pathway is similar except is initiated by a different protein complex. the alternative pathway is initiated by spontaneous cleavage of a complement protein C3, as opposed to pathogen binding, which then also forms a C3 convertase. the alternative pathway can be used by the other two pathways to greatly amplify the complement process, since C3b created by the convertase can then be used to initiate another alternative pathway.

the complement pathway also releases small protein fragments (denoted by the small "a" after the protein as opposed to the membrane bound "b") which are weak mediators of inflammation or can signal other molecules. another mechanism that the complement pathway uses to destroy pathogens is the membrane attack complex, which is the formation of membrane pores on a pathogen's surface that disrupt the concentration gradients and kill the cells. however this is a relatively limited mechanism and only used against certain pathogens.

interferons are used in the innate immune system to fight off against infection. cells infected with viruses release interferons, which then act on itself and its uninfected neighbors, triggering transcription of proteins which act intracellularly to destroy viral RNA and halt transcription. they also induce expression of class 1 MHC molecules, which signal natural killer cells to release cytotoxic granules which trigger cell death in these infected cells.

questions
1. how quickly can the innate immune system respond to infection?
2. what are some of the mechanisms that the innate immune system uses?
3. what are some of the microorganisms that cause disease?
4. what are obligate vs. facultative intracellular pathogens?
5. what is a zoonotic infection?
6. what is the first barrier which prevents infection?
7. what goes on in the epithelial layer of the lung to prevent infection?
8. what goes on in the epithelial layer of the gut to prevent infection?
9. what is secreted in the tears that prevents infection?
10. what are commensal bacteria and how do they aid in preventing infection?

11. what are the two types of phagocytic cells in the innate immune system?
12. describe how a macrophage can use phagocytosis to kill a pathogen.
13. what are some of the toxic chemicals that the macrophages and neutrophils can produce?
14. what is the respiratory burst?
15. major differences between neutrophils and macrophages...


16. what are two strategies that bacteria have evolved to evade the innate immune system?
17. what do cytokines and chemokines do?
18. what is the inflammation response?
19. what two enzymatic cascades can be triggered by activated endothelium during the inflammation response?

20. what is the difference between the receptors on the cells of the innate immune system vs. that of the adaptive immune system?
21. what are some common molecular patterns of bacteria and viruses that can be recognized by the cells of the innate immune system?
22. what is the mannose binding lectin and the macrophage mannose receptor?
23. what are scavenger receptors?
24. what are toll like receptors and what do they do?
25. describe the recognition of bacterial LPS and how it relates to toll like receptors.

complement...
26. what is the complement system?
27. what are the three pathways to the complement system?
28. describe the main differences between the three pathways.
29. the complement fragments C3a, C4a, and C5a acts as...
30. what can the terminal fragments of the complement system also do?

31. what are the two families of cytokines released from phagocytic cells in the innate immune system?
32. what are the ways in which chemokines help fight infection?
33. what are selectins?
34. what are ICAM's?
35. what is p-selectin and what is it expressed in response to?
36. describe the first step in extravasation.
37. describe the second step in extravasation.
38. what is diapedesis?
39. what is the fourth and final step in extravasation?

40. how does TNF-alpha help contain infection to a local area?
41. what is septic shock and what role does TNF-alpha play in it?
42. what are endogenous pyrogens and what are some examples?
43. what is the "acute phase response?"
44. what are the acute phase proteins and how do they work?
45. what is leukocytosis?
46. what are interferons and what do they do?
47. what is the signalling system that interferons use to recruit natural killer cells?
48. what are natural killer cells? what do they do? what are they activated by?

answers
1. within minutes/hours
2. physical barrier of the epithelia, phacocytic cells beneath epithelia, inflammation response, recruiting other leukocytes from the blood stream, the complement system, chemokines/cytokines, natural killer cells.
3. viruses, bacteria, fungus, protozoa, worms
4. obligate intracellular pathogens can only proliferate inside of a host cell, whereas facultative intracellular pathogens can proliferate outside as well.
5. when an infection migrates from animals to humans.
6. tight junctions of the epithelial layer
7. the respiratory airways secrete mucus and have cilia which are constantly moving trapped particulates and pathogens out of the body cavity.
8. the gut has mucus as well, as well as a corrosive chemical environment, as well as peristaltic action which constantly moves microorganisms outward.
9. anti microbial chemicals such as lyzozyme and phospholipase A.
10. the bacteria that lives symbiotically in the gut, which competes with harmful microorganisms for nutrients and space.

11. macrophages and neutrophils.
12. pathogens that bind to the receptors on the macrophage are then enveloped in the membrane of the macrophage and ingested into the cell, where it forms a phagosome. it then fuses with a lysosome to form a phagolysosome, which exposes the pathogen to the harmful lysomal enzymes and kills it. alternatively, the phagosome can turn acidic, which also kills pathogens.
13. hydrogen peroxide, nitric oxide, superoxide anion .
14. the process of forming superoxide anion from hydrogen peroxide; so called because it demands an extra burst of oxygen consumption.
15. macrophages are long lived, reside in tissues (after differentiation from monocytes), while neutrophils reside in the circulatory system and are called upon to fight infection in the tissues, after which they die.

16. forming a thick polysaccharide capsule covering the molecules that would be recognized by the receptors on macrophages and neutrophils. also, inhibiting acidification in phagosomes after phagocytosis, or preventing fusion with lysosomes.
17. cytokines act to produce different changes in other cells or tissues, and chemokines are chemical attractants that cause chemotaxis in effector cells. they also help mediate the inflammation response.
18. a series of local events triggered by release of cytokines and chemokines that includes swelling, redness, pain, vasodilation, recruitment of effector cells such as neutrophils.
19. the kinin system and the blood clotting cascade.

20. on the cells of the innate immune system, each cell has a variety of "germline- coded" receptors that have evolved to recognize common bacterial membrane components. on the cells of the adaptive, each cell has only one type of receptor on its membrane which was created by the clonal selection mechanism described in the previous chapter.
21. bacteria have unmethylated repeats of the dinucelotide CpG, viruses express double stranded RNA.
22. the mannose binding lectin is a free floating molecule receptor that binds to the a particular arrangement and spacing of mannose molecules on bacteria. the macrophage mannose receptor is the membrane bound version of this receptor.
23. another type of phagocytic receptor that binds various anionic polymers and acetylated (modified) LDL's.
24. another type of receptor that acts as a "danger signal" and produces several effects such as release of cytokines, chemokines, and display of co-stimulatory molecules which activate naive lymphocytes.
25. LPS is recognized by the phagocytic cell's CD14 surface receptor, which then associates with the toll like receptor 4, which is then activated to produce cytokines, chemokines, and display costimulatory molecules.

26. the complement system is a system of proteins (activated using a zymogenic cascade) that opsinizes pathogens and aids in their phagocytosis.
27. the classical, MB-lectin, and alternative
28. the classical pathway is activated by binding to pathogen and the pivotal step is the production of C3 convertase which coats the pathogen with C3b molecules, aiding phagocytes' destruction of the pathogen. the MB-lectin pathway is similar but uses a different pathogen-binding complex to initiate the zymogenic cascade. the alternative pathway is initiated by spontaneous hydrolysis of C3 as opposed to pathogen binding, and it can be amplified (the pathway produces C3b, which can be used to initiate a new cycle)
29. weak mediators of inflammation, causing vasodilation, upregulation of CAM's in endothelium, and inducing smooth muscle contraction.
30. form a membrane attack complex, which creates pores in the pathogen and disrupts concentration gradients, ultimately killing the pathogen.

31. hematopoeitin and TNF
32. they work to recruit effector cells from the circulation by causing conformation change in the CAM's and also by attracting effector cells to places of infection in the tissue by means of increasing concentration gradients. finally, they can also activate the macrophages and neutrophils to fight the infection; producing the respiratory burst or releasing lysosomal contents.
33. selectins are a family of CAM's that initiate leukocyte-endothelium interaction.
34. intercellular cell adhesion molecules are the second CAM that cause extravasation of effector cells
35. p-selectin is a CAM that is expressed in response to the complement protein C5a, leukotriene B4, or histamine from mast cells. it can also be induced by bacterial LPS or the cytokine TNF-alpha.
36. rolling adhesion is the first step of extravasation in which effector cells are loosely bound to p-selectins and e-selectins on the endothelial surface.
37. chemokines induce upregulation of integrins on leukocytes, which then bind to ICAM's on the endothelium, arresting their movement
38. the process in extravasation by which leukocytes cross through the basement membrane of the endothelium by way of enzymes that break down the extracellular matrix.
39. migration of the effector cell towards the site of infection by means of a extracellular matrix-bound concentration gradient of chemokines which were produced by phagocytic cells.

40. by stimulating vasodilation (decreased perfusion) and blood clotting in the endothelium, it prevents the spread of the pathogen to other parts of the body.
41. in an infection reaches the bloodstream ("sepsis"), TNF-alpha is released by macrophages in the bloodstream, which causes systemic vasodilation (and therefore systemic edema) and clotting, which causes multiple organ failure, the eventual loss of blood clotting ability, and a high mortality rate.
42. molecules produced by the host that stimulate an increase in body temperature, such as TNF-alpha, IL-1beta, and IL-6.
43. the stimulation of hepatocytes by cytokines to produce acute phase proteins.
44. SP-A, SP-D, MB-lectin, C-reactive protein. these are all molecular receptors for common components on bacterial membranes.
45. the stimulation by cytokines of increased production of leukocytes, either by release from the bone marrow or from endothelial walls
46. interferons are molecules that are secreted from host cells that have been infected with a virus. they have autocrine and paracrine actions, acting on the infected cell itself and the neighboring uninfected cells. the receptors that they bind to signal intracellular pathways that block viral RNA transcription and destroy RNA fragments.
47. interferons also upregulate expression of MHC class I molecules, which are then used to signal natural killer cells, which destroy the infected cell.
48. natural killer cells are derived from the lymphoid lineage and resides in circulation. they release cytotoxic granules which induce cell death, and are stimulated in response to cytokines or interferons.

immunology: janeway's immunobiology chapter 1

bear with me while i try a few different formats for this class... my usual question/answer/summary format didn't work for me for this chapter for some reason.

this chapter introduced the innate and adaptive immune systems and introduced the dynamics of the cells involved, as well as the interaction between the two systems.

the history of immunology
edward jenner discovered smallpox vaccination in 1796. robert koch discovered that microorganisms are the source of pathologies. louis pasteur devised a vaccine against chickens. antibodies discovered 1890.

cells involved
all cells derived from pluripotent, hematopoetic stem cells. these differentiate into two lineages, myeloid and lymphoid. the myeloid lineage creates red blood cells, platelets, dendritic cells, macrophages and granulocytes (the key players in the innate immune system). the lymphoid lineage creates lymphocytes, which are the main players in the adaptive immune system.

lymphoid organs and tissues
primary/central lymphoid organs such as bone marrow and thymus produce lymphocytes and peripheral/secondary lymphoid organs such as the spleen and lymph nodes maintain lymphocytes. in the peripheral lymph organs, antigen-bearing cells from infected tissues meet naive lymphocytes and initiate the adaptive immune response.

innate immune system
the innate immune system is the body's first defense which is non specific and uses mainly the phagocytic cells such as the macrophage and the dendritic cell which reside in the peripheral tissues.

inflammation response
macrophages that encounter antigens in tissues secrete chemokines and cytokines, which vasodilate the nearby blood vessels and cause fluid leakage, allowing lymphocytes to enter the tissues and fight the infection. this is accompanied by redness, swelling, heating.

clonal selection theory
each lymphocyte in the adaptive immune system has a different specificity for a particular antigen- resulting in a portfolio of millions of potential antigens it can guard against. this diversity is created during the production of lymphocytes via a random recombination of varied "gene segments" which rearranges and recombines the sections of DNA that code for the antigen specific proteins.

the so called "naive" lymphocytes then go through a selection process where if they encounter antigen on a regular basis, they will survive (the cells need regular "survival signals from peripheral lymphatic tissues in order to halt apoptosis). if they are receptive to too much antigen (meaning, sensitive to self), they will be deleted, and likewise if they do not bind to any antigen.

antibodies- structure and strategies
antibodies are y shaped molecules found on b and t lymphocytes. the stem of the y is called the constant region of the antibody and is representative of the functional class of antibody. the branched tip of the antibody is called the variable region and differs from antibody to antibody.

free antibodies can bind directly to toxins, preventing them from infecting cells- called neutralization. they can also bind to infected cells and be better recognized by macrophages and other phagocytic cells, called opsonization. finally, they can initiate a "complement" system which aids in phagocytosis and also creates membrane complexes on infected cells which facilitates their destruction.

b cells vs t cells
b and t lymphocytes are the main cells in the adaptive immune system. b cells' sole contribution is the antibody, while t cells have a variety of effector actions. t cells can be further differentiated into cytotoxic t cells, which bind to and destroy virus infected cells, and t-helper cells. within t-helper cells, there are two subclasses: first is TH1 cells, which fight cells infected by pathogens residing in vesicles (thereby remaining undetected) by causing fusion of lysosomes and the vesicles. second is TH2 cells, which signal B-cells to become mature effector cells, as a sort of confirmation of infection.

MHC's
MHC's (major histocompatibility complex) are membrane protein complexes that bind to antigen during their formation in the cytosol and mount themselves on the outside of the plasma membrane, displaying peptide fragments from the particular antigen that the cell has encountered.

there are two classes of MHC molecules based on what they bind to. MHC class 1 molecules bind to viral peptides and therefore are involved in recognition from cytotoxic t cells (see above) and MHC class 2 molecules bind to intracellular vesicles and therefore are involved in recognition from t-helper cells.

allergies and autoimmune diseases
allergies are caused when the immune system mounts a response against a foreign, but innocuous substance. autoimmune diseases are when the immune system begins to recognize itself as an antigen.




page by page summaries:

p. 1
the beginning of immunology lie in the discovery of the smallpox vaccine by edward jenner in 1796. robert koch discovered that pathologies are caused by microorganisms, of four types: bacteria, viruses, fungi, and parasites.
based on these two discoveries, louis pasteur devised a vaccine against cholera in chickens. emil von behring and shibasaburo kitasato discovered antibodies, substances that bind to pathogens.

p.2
the innate immune system was discovered mainly by elie metchnikoff, who observed the microorganism-consuming properties of macrophages and how the body comes pre-prepared to combat a wide variety of pathogens. contrast this with adaptive immunity, which is the body's specific response against an unknown antigen. the term antigen is used to describe any substance that produces an immune response (which might or might not involve antibody production). both immune systems involve the leukocyte, or white blood cells. the innate immune system involves granulocytes (most importantly, neutrophils) and macrophages. the adaptive immune system uses mainly leukocytes. both systems complement each other and work together to provide a remarkably effective form of defense against antigens.

this book will mostly talk about the adaptive immune system, but the innate immune system often participates in adaptive immune responses as well.

p.3
all the cellular elements of blood are formed by pluripotent hematopoetic stem cells in the bone marrow. these produce two lineages: myeloid and lymphoid. the myeloid "progenitor" gives rise to granulocytes, dendritic cells, and macrophages. macrophages are huge phagocytic cells which reside in tissues and are derived from monocytes that circulate in the blood. dendritic cells also migrate from the blood to tissues; immature cells are phagocytic cells that reside in the tissues and upon encountering an antigen, mature and travel to the lymph, where they present the antigen to lymphocytes. mast cells also differentiate in the tissues and involved in both allergic responses and also some immune functions.

three types of granulocytes: neutrophils, eosinophils, basophils. neutrophils are phagocytic cells that play the most important role in the immune response of granulocytes. eosinophils are thought to be involved in protection against parasitic infection. the function of basophils is complementary and similar to eosinophils and mast cells.

the lymphoid progenitor produces two types of lymphocytes- b cells and t cells. b cells differentiate into plasma cells when activated, which secrete antibodies. t cells differentiate into two types: cytotoxic t cells which combats virus infection, and another type that activates other B cells and macrophages.

p.4
lymphocytes appear to be inactive because of the lack of cytoplasm, ER, and condensed chromatin- and in fact they are inactive until encountering an antigen. lymphocytes have a huge portfolio of antigen receptors which enables them to ward off attacks from virtually any foreign antigen. natural killer cells are the third cell from the lymphoid lineage and are non-specific, and part of the innate immune system.

p.5
the lymphoid organs are masses of tissue where lymphocytes are created and maintained. the primary/central lymphoid organs produce lymphocytes, including the bone marrow and thymus, and the secondary/peripheral lymphoid organs maintain the lymphocytes, such as the spleen and lymph nodes. t and b cells both originate in bone marrow, but t cells then migrate to the thymus for maturation. both then enter the bloodstream.

peripheral lymphoid organs are the places where antigens and lymphocytes meet.

p.6
lymph is extracellular fluid that is collected from tissues and recirculated into the blood. on the way, they are filtered into lymph nodes, where antigens are trapped and where b and t cells congregate. b cells are mainly in the follicles, sometimes with germinal centers, and t cells are mainly in the paracortical areas.

p.8
the spleen is a large lymph organ which is made up of mainly "red pulp", which is responsible for disposing of old red blood cells. the white pulp is the section that deals with antigens; through which antigen containing blood flows from trabecular arteries, through a "periarteriolar lymphoid sheath" made up of T cells, and a B cell "follicle" made up of germinal centers and a "corona", then back out to the trabecular veins. the interactions between the b and t cells in an immune response will be discussed later.

p.9
the gut associated lymphatic tissues: tonsils, appendix, adenoid, and peyer's patches, collect antigen from epithelial surfaces of the GI tract. the peyer's patch in the gut is the most highly organized and dense; they are formed from aggregations of mainly b cells into follicles, surrounded by smaller numbers of T cells.

p.10
all of these lymphoid organs have the same basic formula: trap antigen from site of infection and initiate an immune response. also, they provide signals to circulating lymph which sustain them and keep them prepared to fight off antigens.

lymphocytes circulate back and forth between the blood and lymph. during infection, lymphocytes are trapped in the lymphoid tissues and differentiate into effector cells that can combat the infection.

p.11
lymphoid organs are dynamic and ever adapting in response to infection; for example, in lymph nodes, expanding b cell germinal centers during infection can cause the entire lymph node to enlarge. also, the diffuse mucus associated lymphoid tissue can appear and reappear according to local need.

p.12
the innate immune system is the body's front line, general defense against antigens via phagocytic macrophages and neutrophils. when the infectious microorganism can not be overcome, or if the pathogen is not recognized, the adaptive immune system is then enlisted.

when macrophages encounter bacteria, they release molecules known as chemokines and cytokines, which initiate the inflammation response. part of the inflammation response involves vasodilation, which increases blood flow to the area, causing swelling, fluid leakage, and heating. the cytokines act on the endothelial walls, causing circulating leukocyte to adhere and squeeze out into the tissues, where they are attracted to the chemokines that have been secreted. the transport and actions of the leukocytes account for the pain during inflammation.

p.13
neutrophils and macrophages are the main cells involved in the inflammatory response. they are both phagocytic and both have surface receptor molecules specific to certain common constituents of bacteria.

dendritic cells are the cells that initiate the adaptive immune response. they are created in bone marrow and sent to peripheral tissues, where they reside in preparation for encountering pathogens. during infection, they phagocytose pathogens and travel to the lymph system and interact with naive lymphocytes.

although dendritic cells have the same mechanism for recognizing and phagocytosis, their primary job is to circulate to the peripheral lymphoid tissues and interact with T-lymphocytes. they employ a second strategy to take up antigens which is not receptor dependent- macropinocytosis.

p.14
the receptors of the cells in the innate immune system are designed to sense certain bacterial components that have been constant over the course of evolution. in this way they are limited and are unable to recognize new strains or bacteria that have evolved with a protective shell which hides those molecules. furthermore, viruses have no such common markers. however, dendritic cells are constantly taking in extracellular fluid via macropinocytosis, where any viruses or cloaked bacteria will be unmasked and the immune response will be activated.

lymphocytes, in contrast to the innate immune system cells, each have receptors with a specificity for only one particular pathogen.

p.15
the wide variety of lymphocytes undergoes a sort of natural selection in which the cells that encounter antigen proliferate and differentiate.

clonal selection theory is the theory that elucidates this idea which explains why we only produce antibodies for antigens that we have been exposed to: the body has a huge diversity of potentially anti-body producing cells, with different specificities. a lymphocyte's encounter and successful recognition with a particular antigen via a membrane bound version of the antibody causes it to clone itself and produce many antibodies of the same type.

james gowans discovered that lymphocytes are directly related to the adaptive immune response by removing them in mice and observing that the adaptive immune response disappeared.

clonal deletion is the idea that the immature lymphocytes that have receptors for the self are destroyed before maturation.

p.16
four postulates of the clonal selection hypothesis:
each lymphocyte has a receptor of unique specificity
when a foreign molecule binds to the receptor of a lymphocyte, it is activated
the differentiated effector cells from an activated lymphocyte will have the same receptor specificity as the parent
lymphocytes with receptors specific to the self will be deleted in early stages of lymphocyte development

antibodies are the free form of the receptors on lymphocytes. they have two portions; the constant region which is the same for all antibodies, and the variable region which has a unique structure. both regions are made up of two identical light chains and two heavy chains.

p.17
the diversity of lymphocyte receptors is produced by recombination of "gene segments" that code for the variable region of the antibody.

b cell receptors are detachable and have two different variable regions, whereas t cell receptors are bound to the membrane and have only one variable region.

p.18
the pool of maturing lymphocytes with the huge diversity of receptors is then selected for based upon the signals that the receptors receive. in order to proliferate, naive lymphocytes need to receive signals periodically. if they receive too many signals this indicates that they are self-reactive and if they don't receive any, that means that the receptors are not useful for sensing commonly encountered antigens.

this maintenance of useful lymphocytes depends on a system of "survival-signalling", where the body provides periodic signals to useful lymphocytes, for them to continue to proliferate by inhibiting apoptosis. the implication here is that if the lymphocyte dies, the particular specificity that its receptor had is now removed from the receptor portfolio of the immune system.

p.19
when the naive lymphocyte encounters the particular antigen it is receptive for in the peripheral lymph tissues, it stops circulating and enlarges, forming a lymphoblast. a lymphoblast has a larger cytoplasm and nucleus, visible chromatin, and new RNA's and proteins are synthesized. the lymphoblast then divide, creating thousands of copies of themselves within a few days. the lymphoblasts then differentiate into b cells and t cells- b cells secrete antibodies and t cells can destroy infected cells. the whole process takes 4-5 days.

after the infection has been cleared, most of the effector cells undergo apoptosis; the ones that don't are memory cells and allow the body to be better prepared against a recurrent attack from that particular antigen, an idea called immunological memory.

p.20
peripheral lymphoid tissues, in particular the spleen and lymph nodes, are organized to both trap antigen presenting cells / naive lymphocytes, and also designed to allow them to interact efficiently.

p.21
in order to be fully activated, lymphocytes need to be signalled twice; once by the antigen itself and once by a cell in the immune system which confirms the presence of the antigen. in the case of t-lymphocytes, the second signal is from the antigen presenting dendritic cell. for the b-lymphocytes, the second signal is from an activated t-cell.

p.23
the receptors on b cells are adapted to detect antigen from outside the body; ie bacteria. the receptors on t cells are adapted to detect antigen generated inside infected cells; ie from viruses.

p.24
as described before, antibodies have two parts, the constant region and the variable region, and are y-shaped. the "stem" of the y determines the class of the antibody, which corresponds to the type of effector action that will be produced.

the simplest strategy for antibodies is to bind to the pathogens, preventing them from entering cells they are trying to infect. this is called neutralization.

another strategy that antibodies are used for is opsonization, where they bind to pathogens and allow macrophages to phagocytose the pathogen (after recognizing the constant region of the antibody)

a third strategy that antibodies are used for is called "complementing"; where antibodies can initiate a series of complement proteins on the pathogen's surface which allow phagocytic cells to recognize and aid in the attack against the pathogen.

p.25
all of the cells marked by antibodies have the same fate; digestion and removal via phagocytes.

the complement system and phagocytes are non-specific and depend on antibodies for recognizing antigens.

b cell's only contribution to the immune system is the antibody, whereas t cells have a variety of effector actions.

p.26
t-cells are involved in the "cell mediated immune response" where pathogens are generated intracellularly (mostly via viruses).

a virally infected cell has antigens on its surface which cytotoxic t-cells can recognize, enabling them to destroy the cell before the virus uses the cell's machinery to replicate itself.

p.27
the second class of t-cells are called CD-4 t cells because of a particular molecule (co-receptor) that is present on the membrane. there are two subclasses of CD-4 t cells; first is TH1 cells. these cells stimulate macrophages to destroy intracellular pathogens, oftentimes from bacteria, by fusing the pathogen-destroying lysosomes with the intracellular vesicles in which the pathogens are being protected.

the second class is TH2 cells, cells which activate b-cells. b-cells in general need a confirmation signal from a helper t-cell in order to mature into an effector cell.

p.28
MHC's are membrane glycoprotein complexes that hold ("present") antigen for recognition by t-cells.

there are two classes of MHC based on the type of antigen peptide that they capture and present. MHC class 1 molecules collect intracellular peptides and thus are able to display antigens from virus infected cells. MHC class 2 molecules collect peptides that are contained within the intracellular vescicles and therefore are able to display antigens from infected macrophages.

p.29
accordingly, class 1 MHC's are recognized by cytotoxic T cells, which combat virus-infected cells, and class 2 MHC's are recognized by TH1 cells, which combat infected macrophages.

p.30
when recognizing the infected cells, t cells can either release various effector molecules or enlist the help of other cells.

AIDS is an autoimmune disease in which the TH1 cells are destroyed, leaving macrophages susceptible to infection.

p.31
allergic reactions manifest when the immune system responds against an innocuous foreign substance.

immuosuppresants are used in some auto-immune diseases or grafting procedures to stop the immune system's response against the body or the transplanted tissue. these immunosuppresants are not antigen specific and therefore suppress more lymphocytes than needed.