Concept of Ecological Niche Guide 2

Clinical Testing by PCR—What Makes it Good or Bad?  Sensitivity—how many virus genomes does it take to get a positive result? o Depends on:  Sample quality (RNA is easily degraded)  Efficiency of PCR amplification (dependent on primers) o Low sensitivity may lead to false negatives—infected people test negative for the virus  Specificity—will the test detect things other than the target pathogen? o Depends on:  PCR primer specificity  Sample handling procedures (PCR tests can be VERY sensitive)  Contamination of negative samples may lead to positive test results o Low specificity may lead to false positives—uninfected people test positive The Relationship Between Viruses & Disease—Myxoma virus & rabbits  British colonization brought foxes to Australia for hunting purposes o Didn’t fare well catching prey, so rabbits were introduced  Rabbits reproduced millions, creating an unpredicted ecological disaster  Biological control: o Myxoma virus (poxvirus): caused a mild skin disease in American rabbits, but killed >99% of European (Australian) rabbits o Rabbits were purposefully infected [via mosquitos & ticks] & introduced into the wild population  Year 1: mortality = 99.8%  Few years: mortality = 25% o Analysis  Did the rabbit population change? Tested for by removing rabbits from the wild population each year to expose them to the original virus.  Did the virus population change? Tested for by isolating the virus from the population, then infecting an isolated colony of rabbits. o Results  Both occurred…  Highly susceptible rabbits died, while resistant rabbits survived & reproduced  Winter causes mosquitos to go dormant, allowing time for rabbits to recover  The highly virulent viruses died off and the less virulent viruses replaced them in the population.  The winter lull in mosquito transmission meant that viruses that gave rise to milder disease (that allowed the rabbit to survive to next spring) were more successful at reproducing o Take-away: virus evolution does not necessarily favor extreme virulence; it favors evolution toward longterm survival of virus genes Immunology Overview  Must defend against… o Destruction of cell & tissues by direct invasion o Destruction of cells & tissues by products of bacterial growth o Interference w/ the function of important bodily mechanisms  Varying defense mechanisms in ways that… o Differ in degree of specificity o Operate efficiently at different times following exposure/infection o Differ in lengths of effect  Defense mechanisms come in layers—one functions until reinforcements arrive, and then another begins Level 1: Physical Barriers  Similar in that they are tough & dead  Basic types (2) o Skin  Function  Mechanical barrier & microbiota defend against invaders  Components  Epidermis: tough, highly cross-linked layer of proteins & dead cells o Tough an elastic due to keratin o Prevents access of microbes to the living cell layer at its base  Sweat glands: secrete salts & oils which inhibit growth of too many microbes o Mucus membranes (mucosa)  Functions  Line internal structures connected to the environment  Protective covering that resists penetration & traps microbial invaders  Types (2)  Mucosae: singular cells lined w/ cilia o Propel mucus toward the outside of the body, carrying potentially harmful microbes w/ it  EX: mucociliary ladder of the lungs  Mucosa epithelial layer: living cells superficial & exposed to environment o Tight junctions prevent bacteria & viruses from passing between cells o Secrete viscous mucus, limiting motility of microbes  Functions o Limit access to living cells o Limit access to interior body structures (where nutrients & living cells are concentrated) Level 2: Innate Immune System  Functions o Rapid response o Limited specificity  Effective in distinguishing self from non-self, but not in distinguishing specific types of invaders  Phagocytosis o Phagocytes: ‘eating cells’ that recognize invaders & engulf them  EX: macrophages & dendritic cells, which have differentiated from monocyte WBCs after passing out of the blood through capillary walls and entering the interstitial fluid o Summary    Pattern recognition receptors (PRRs), such as toll-like receptors (TLRs), bind pathogenassociated molecular patterns (PAMPs)  PAMPs: structures that are only found in prokaryotes/viruses & help our bodies to distinguish self from non-self  TLR = best-understood PRR, expressed on cell surfaces or on phagosomes (lipid spheres taken in from plasma membrane) Binding of PAMP to TLR causes a conformational change to the TLR part exposed to the cytoplasm The conformation change results in post-translational modifications of cytoplasmic proteins  Phosphorylation  Re-localization (to the cell membrane or to the nucleus) Signal transduction pathways result in phagocytosis or upregulation of cytokine gene expression  Results  Ideal: killing & degradation of the pathogen  Phagolysosome formation by fusion of phagosome + lysosome  Phagolysosome is excytosed  Unideal: bacteria thrive off of engulfment by macrophages  Prevention of phagosome fusion w/ lysosome, resulting in bacterial replication within the phagosome  The phagosome membrane is disrupted, allowing bacteria direct access to cytoplasm o Replication can then continue in the cytoplasm Production of cytokines o Cytokine: small peptide protein secreted by an immune cell that has an effect on functions of other cells, especially immune cells  Signaling molecule has various effects (3)  Autocrine: same cell secretes & receives cytokine signal o Inducing defensive functions within the cytokine-producing cell o    o Paracrine: cytokine signal secreted to a nearby cell o Warn nearby cells to take defensive measures Endocrine: cytokine signal secreted into circulatory system, travels to distant cells o Moving out into the bloodstream to signal distant cells & tissues  Recruit, activates, or cause death of other cells Summary (EX: Type I Interferon (IFM) synthesis—paracrine effect of cytokine release)  Cell ‘knows’ that it is being infected by sensing presence of products of infection (PAMPs) that aren’t usually present in uninfected cells  Recognition via toll-like receptors (TLRs) o Recognize structural components of virus & bacteria particles: dsRNA, ssRNA, dsRNA, & dsDNA genomes o Recognition pathways (2)  TLRs within the endosome = endocytosis: cells that are not phagocytes take in things from the environment via endocytosis, which is often an entry strategy of viruses  Causes degradation & release of the viral genome into the endosome  TLRs upon cell surface  Viruses don’t need to be endocytosed in order to be recognized Viral proteins & unusual lipids found on virus membranes, as well as cytoplasmic bacteria, are sensed in this way  Recognition via RIG-I & protein kinase R (PKR) o Recognize infection by ssRNA that are not retroviruses  Such viruses produce dsRNA, which is never present in the cytoplasm of uninfected cells o Limited specificity—recognize only that there is an RNA virus, but not what kind Signals converge on kinase TBKI/IKK-I  Kinase TBKI/IKK-I phosphorylates transcription activator protein IRF3/7—an example of post-translational modification Upon phosphorylation, IRF3/7 moves from the cytoplasm to the nucleus where it then activates type I interferon genes Type I interferon mRNA spliced & moves to the cytoplasm The spliced mRNA is translated on ribosomes at rough ER into type I interferon protein       The protein is secreted into the interstitial fluid to have an effect on surrounding cells  Protein binds to type I interferon receptor (IFNAR1)  Interferon sensitive genes (ISGs) induce an antiviral state in surrounding cells o EX: protein kinase R (PKR) Always present in some degree  High PKR activity = bad for a healthy cell  Domains (2)  Catalytic domain: transfers phosphate from ATP to recipient  Inhibitory domain: regulatory site binds to the catalytic domain or dsRNA—prefers binding dsRNA if present in the cytoplasm o Bound to dsRNA = activation & conformation change of dsRNA  Allosteric regulation  Releases catalytic domain, allowing it to become active  Antiviral state established by expression of proteins that will react to a viral infection by: o Inhibiting a virus-specific process o Inhibiting a cellular process required for viral infection o Causing death of the infected cell Type I interferon promotes recruitment of additional types of innate immune cells from the blood:  More monocytes (which differentiate into macrophages & dendritic cells)  Nature killer (NK) cells  Neutrophils o Most common WBC o Undergo extravasation (movement of WBCs from the capillary lumen into tissue) in response to cytokine recruitment o Phagocytic o Granules fuse w/ phagosomes to kill engulfed bacteria then release contents so that bacteria-killing proteins act on bacteria that haven’t been engulfed o Release their own nuclear DNA + granule contents to create viscous NET to immobilize & localize bacteria Cytokine release activates some cell types  Cause basophils (in blood) & mast cells (in resident tissues) to secrete granule contents  Contents include histamine, which causes dilation of capillaries     Acute inflammation  Combination of: o Increased blood flow resulting in redness & heat o Capillary leakage leading to fluid accumulation & swelling o Infiltration of tissue w/ neutrophils & other WBCs General themes represented in immune signaling in which this pathway illustrates:  Post-translational modification alters protein function  Addition of chemical groups (EX: phosphorylation)  Subtraction of sequences (EX: cleavage or protein via proteases)  Change in cellular location alters protein function  EX: transcription factor IRF3/7 within the cytoplasm is inactive, but IRF3/7 within the nucleus following phosphorylation by TBKI/IKK-I leads to its activation Summary (EX: compliment system—endocrine effect of cytokine release) o Nine proteins (C1-C9) present in the blood at all times o Infection leads to elevated levels in these proteins  Endocrine effects on the liver cause it to synthesize more compliment proteins  Proteins escape the blood through capillary leakage to reach inflamed tissue o Pathways to initiate the compliment system (3)  Classical pathway: requires adaptive immune response (antibodies)  Lectin pathway: requires sugar-binding proteins (lectins) to bind a pathogen  Alternative pathway: initiated spontaneously o All pathways converge to activate a central player—C3 o Activation of C3 results in a cleavage, producing two fragments—C3a & C3b  Post-translational modification regulation  C3b (an opsin) opsonizes bacteria  Binds to the surface of a pathogen + a receptor on a phagocyte to promote phagocytosis o C3b activates C5, resulting in a cleavage, producing two fragments—C5a & C5b  C5a acts like cytokines to promote inflammation  C5b recruits other compliment proteins (C6-9) to form a membrane attack complex o   Summary (EX: fever—endocrine effect of cytokine release) o Cytokines target cells that line the blood vessels o Some cytokines are pyrogens, which induce prostaglandin E2 (PGE-2) synthesis Fever thought to inhibit bacterial growth & promote function of immune cells Steps  Pyrogenic cytokine signals converge on WBCs (leukocyte = effector molecule)  More pyrogenic cytokines are produced in response, which induces PGE-2 synthesis  PGE-2 acts on the thalamus to control body temperature, resulting in fever  End-result of innate immunity o Local cells activated to resist infection o Acute inflammation (increased blood flow, capillary leakage, influx of immune cells via recruitment) o Distant tissues (liver, cells lining blood vessels) stimulated to synthesize helpful molecules o Body temperature may become elevated Level 3: Adaptive Immunity  Functions o Great specificity o o  Recognizes & reacts to small parts of individual molecules from a pathogen Breadth of response  Recognizes & distinguishes between many different types of pathogens & molecules o Tolerance  In a healthy individual, it will not develop a response to self o Memory  Response to a specific molecule is faster & stronger upon re-exposure  Primary response wains over time, w/ secondary exposure there is a more rapid & powerful immune response to the same pathogen Inducers of the adaptive immune response: antigens o Overview  Antigen: anything that will induce a specific adaptive immune response within an organism  EX: entire pathogen, a specific structure upon a pathogen  Often proteins, but may be other molecules (carbohydrates, lipids, nucleic acids)  Immune response to antigen = sum of many responses, each response developed against an epitope (sites of the antigen that bind to a specific antibody) o Mechanism  Epitope meets a lymphocyte w/ an antigen receptor on its cell surface which is able to recognize that specific epitope  Following recognition, a signal transduction pathway occurs  The cell then does one or both of the following…  Proliferates via repeated division in order to amplify the # of cells able to recognize & respond to the epitope o Amplification enhances response  Responds by acting on the antigen itself (effector cells), making effector proteins that act on the antigen, and/or make cytokines to regulate synthesis of effects or effector cell function Effectors of the adaptive immune response: antibodies o Overview  Antibody: proteins produced in response to an antigen as to counteract  Structure  2 types of polypeptide chains o Heavy chain (2): covalently linked by disulfide bonds o Light chain (2): each covalently linked to a heavy chain by disulfide bonds  Globular domains (3) o 2 identical (Fab regions) o   Formed by sequences from 1 light chain & part of 1 heavy chain Variable regions  Have different AA sequences, allowing binding to different epitopes of different antigens 1 unique (Fc region)  Formed by part of 2 heavy chains  Constant region  Doesn’t function in epitope binding Joined by flexible linker sequences—reduces rigidity & aids in recognition of antigens   o o  Classes (5)  Different heavy chain types give rise to differences in form o IgM = ‘basic’ antibody structure  o o IgA = dimer of IgM Different heavy chain types result in differences in function o Ability to localize in different places o Ability to interact w/ different cell receptors Mechanism  Neutralization: antibody binding to antigen inhibits its ability to replicate or cause disease  Binding of the antibody prevents the antigen from binding to its receptor  Binding of the antibody may result in immobility of the antigen  Opsonization: phagocytes have Fc receptors that bind to antibodies, so when a pathogen is bound by an antibody, it is prone to phagocytosis  Complement fixation: the Fc portion of the antibody recruits complement components, resulting in cleavage of C3, initiating the complement cascade, which results in lysis  Pathogen aggregation: antibodies, being multivalent (can bind 2+ epitopes at a time), are able to inhibit diffusion & movement of a pathogen from its initial site of infection  Antibody-dependent cell-mediated cytoxicity (ADCC): binding of Fc receptors to natural killer (NK) cells results in apoptosis of infected cells  NK cells kill host cells that have been recognized to be infected o Example of a cytolytic cell—kills eukaryotic cells when recognized to be foreign Death by apoptosis = release of granules that are toxic to the host cell  Inducing cell death without lysis prevents release of viruses or bacteria that already infected the cell, & prevents release of pathogen bits that will tend to amplify inflammation Thymocytes also kill cells recognized to be foreign o Release granzymes & perforins that induce the target cell to undergo apoptosis o Fragments of burst cells are contained within membranes to prevent spread o   Major histocompatibility complexes (MHC) & antigen presentation o Required in order for T-lymphocytes to recognize antigens & be activated  Presents an antigen to T-lymphocytes by binding to it o Types  Class I MHC  Proteins (2) o Alpha chain (intrinsic protein) o Beta-2 microglobulin Recognized by T cells o T cells must have 2 critical molecules on the plasma membrane…  T-cell antigen receptor (TCR)  CD8 membrane protein Class II MHC  Proteins (2) o Alpha chain (intrinsic protein) o Beta-2 microglobulin (intrinsic protein)  Recognized by T cells o T cells must have 2 critical molecules on the plasma membrane…  T-cell antigen receptor (TCR)  CD4 membrane protein   Class I MHC Class II MHC Antigen-binding Cleft All nucleated cells—not erythrocytes or platelets Made up of alpha proteins Antigen presenting cells (APCs) like phagocytes—macrophages & dendritic cells Made up of both alpha & beta proteins What it Presents Peptide epitopes (bits of protein as a result of turn-over degradation) Antigens derived from degradation within phagosome (peptide epitopes, polysaccharides, nucleic acid, etc.) Extracellular agents Where it is Found Where The Antigens it Presents Come From Cytoplasm [in which the virus is replicating] Antigen Presentation Pathway Degraded in the cytoplasm > transported into the ER > move to cell surface Cell That Recognize it End Result T cells w/ CD8 Death of presenting cell Infection it is Good For Defending Against Intracellular infections Phagolysosomes fuse w/ MHC II-containing vesicles, epitopes within phagolysosomes bind to MHC II, membrane vesicle binds w/ plasma membrane, presenting MHC II to cell surface T cells w/ CD4 Activation of cells that kill & phagocytose bacteria, stimulation of antibody production Intracellular & extracellular infections Cell killing mediated by the class I system produces apoptotic fragments of infected cells. These can be phagocytosed, degraded, & the degradation products presented by the class II system  T cells o Origin  Bone marrow (immature T cells)  Thymus (mature T cells—termed thymocytes) o Structure  Mature cells express T cell receptor (TCR)  Similar to an antibody in that it… o Has 2 chains (alpha & beta) covalently linked by disulfide bonds o Constant region—same for all TCRs  o o Variable region—different across TCRs, acts as antigen binding site Similar to a signaling receptor (MHC) in that it… o Both chains are transmembrane proteins o Oriented so that the antigen-binding site is of the outside of the cell o Recruits protein kinases to transmit signals to change the properties of the T cell in response to binding of a signal Types  CD4 helper T cell  Mechanism o Repertoire of CD4 helper T cells are naïve, having never seen antigen before o Naïve cells make only 1 kind of TCR, which is different from TCRs of all other naïve cells o Many naïve CD4 T cells cannot recognize non-self antigen-MHC II complex when presented by a dendritic cell  Lack the correct antigen-binding domain o CD4 helper T cells that can recognize it (few) will bind their TCR o Signaling occurs o Proliferation is induced as a response to signaling to amplify the response to that antigen, differentiation then allows the cell to participate in the response  Differentiation pathways  Effector cells: short-lived, immediate effect o Secrete cytokines to help other immune cells  TH1 cells: stimulate cytotoxic T cells & produce memory cells, stimulate macrophages & neutrophils for intracellular pathogen killing, & stimulate NK to kill more effectively  TH2 cells: stimulate C cell activation & differentiation into plasma cells & memory B cells, & direct antibody class switching in B cells   Memory cells: long-lived, rapid response upon re-exposure Function o Stimulation of CD4 T cells is required for:  CD8 cytolytic & memory cell differentiation  Activation of B cell memory o Stimulation of CD4 T cells improves:  Activation of V cells for antibody production  Activation of NK cell responses  Differentiation & activation of macrophages CD8 cytotoxic T cell  Mechanism  Repertoire of CD8 cytotoxic T cells are naïve, having never seen antigen before  Naïve cells make only 1 kind of TCR, which is different from TCR of all other naïve cells  Many naïve CD8 T cells cannot recognize non-self antigen-MHC I complex when presented by a dendritic cell  CD8 cytotoxic T cells that can recognize it (few) will bind their TCR  Signaling occurs  Proliferation is induced as a response to signaling to amplify the response to that antigen, activation & differentiation then allow the cell to participate in the response o Activation leads to…  Release of perforins & granzymes  Perforins perforate the target cell  Granzymes move into cell through perforins, trigger apoptosis o Differentiation leads to…  Formation of memory CD8 T cells Tolerance  Body’s ability to produce T cells & antibodies against nonself-antigens, while “tolerating” (not responding to) self-antigens T cells undergo selection processes to ensure that the repertoire is useful, but not harmful  Positive selection: ensures that TCRs are able to recognize MHCs w/ appropriate affinity  The variable region of the TCR can be so variable that some TCRs cannot recognize MHC complexes w/ or w/o antigen  Those that can interact are allowed to live & proliferate  Negative selection: removes lymphocytes that recognize self-antigens by apoptosis  T cells meet APCs that present self-antigens in the thymus  If these T cells bind well to these self-antigen MHC complexes, they are killed  o o  B cells o Structure  Actually an antibody (transmembrane)  In IgM or IgD form  Mature, naïve B cells express a cell surface antigen receptor  Each naïve B cell makes only 1 kind of antibody receptor that can bind to 1 epitope  Each naive B cell makes a different antibody receptor than other naïve B cells o Function  Requires 2 stimulus signals in order to become an active immune response  Types of paired stimulus signals:    Summary Binding of antigen to the antigen receptor + signaling from a CD4 helper T cell o Allows activated B cells to differentiate into memory cells or plasma cells (make & secrete high levels of antibodies) Binding of antigen to the antigen receptor + T cell-independent activation o Requires simultaneous engagement of many antigen receptors  Engagement of a PRR by a PAMP o Does NOT result in generation of memory B cells, only IgM antibody produced Virus Quiz 6 1) Consider the electron micrograph below of a mimivirus virion with arrows pointing to various structure. Note the scale bar in the bottom right corner of the photo equal to 200 nm. Which of the following statements is true? As far as viruses go, this one is relatively small The structure pointed to by arrow A likely assists in virus entry This capsid has helical symmetry Arrow B points to the location of the virus ribosomes EXPLAINATION: viruses do not have ribosomes. Herpes simplex is ~120 nm, which is a large virus, so this one is really large. 2) mRNA synthesis by ssRNA(+) genome viruses that are not retroviruses: Require synthesis of an ssRNA(-) template Requires cellular RNA polymerase Requires deoxynucleoside triphosphates as substrate for transcription Shows icosahedral symmetry EXPLAINATION: Plus and minus RNA genomes requires both genomes in order to use one as a template for replicating the other. 3) You want to establish a synchronous infection by a virus of a culture that contains 100,000 HeLa cells. You have a virus sample whose concentration you have just determined by doing a plaque assay. The results of the plaque assay are shown below (cells are stained w/ crystal violet). How many mL of your undiluted virus sample do you need to put onto the HeLa cells to start your infection? 0.2 mL 1.0 mL 0.025 mL 0.05 mL EXPLAINATION: 20 plaques at 1:1,000,000 dilution. 500,000 HeLa cells needed for a MOI of 5 for a synchronous infection. (500,000) / (20 plaques • 1,000,000) = 0.025. 4) Which of the following is true of the relationship of viruses to cellular organisms & to each other? The 16S RNAs encoded by viruses have diverged too far from those of cellular organisms to define a relationship The ancestor of all viruses diverged from the ancestor of cellular organisms before eukaryotes & prokaryotes diverged Viruses originated before any of the cellular organisms There is no gene that all viruses share 5) COVID-19 is an enveloped, icosahedral capsid, positive sense RNA genome virus. Given the information, which of the following statements must be true of this virus? It must carry a virus RNA polymerase protein into the virus particle Its receptor binding protein is a membrane protein It is likely to be highly resistant to drying It would probably not be inactivated by bile salts in the gut. EXPLAINATION: Virus Quiz 7 1) In a HIV-infected culture, eclipse phase ends when: When the virus protease causes maturation of the budded virus particle When the virus buds from the plasma membrane The genome is reverse transcribed When virus genomes are synthesized by host RNA polymerase EXPLANATION: Eclipse phase ends when you first begin to produce infectious virus particles. Once the HIV virus has budded, the protease has to mature the virus particle in order for it to become infectious. Often the last step is ‘when the virus buds from the plasma membrane,’ however, this is not the case for HIV, which is why protease inhibitors work. 2) Which of the following is true of the replication of the genomes of ssRNA viruses that are not retroviruses? It requires reverse transcriptase Plus & minus strand copies of the genome must be present in the cell at the same time RDRP is not required for synthesis of the template for genome synthesis Host RNA polymerase is used to synthesize the antigenome EXPLANATION: if you want to make something, you have to have a template, which is opposite to the strand you want to make. If you want to make genomes, you need the antigenome. 3) At the beginning of rolling circle replication of ssDNA virus genomes, the primer is created by: Methylase DNA polymerase Endonuclease RNA polymerase EXPLANATION: The primer is a piece of nucleic acid that provides a 3’ end for DNA polymerase to elongate off of. Endonuclease generates a 3’ end by nicking the template. 4) Consider the image that describes the varicella zoster virus (chicken pox virus) infection in humans. Based on mode of transmission, sites of virus shedding is/are likely: Skin & airway Liver Liver & kidney Nerve endings EXPLANATION: If the virus is replicating in the airway and skin, these are examples of tissues where virus is accessible to the outside world where it can be transmitted to someone else. Needle-sharing would also be an example. 5) Consider the image that describes the varicella zoster virus (chicken pox virus) infection in humans. The infection of nerve cells near the spinal cord is: Productive infection Latent infection Evidence of secondary replication Abortive infection EXPLANATION: It is latent, as opposed to abortive, because the virus become undetectable, but can come back and reactivate. Virus Quiz 8 1) Consider the life cycle for baculoviruses shown in the figure below. Caterpillars become infected with the virus by eating virus that was deposited on leaves when the previous host died of the infection. The newly infected caterpillar dies when its tissues are liquified as a result of cell destruction by the virus. The liquified remains of the host on a leaf then dry up and may be ingested by a new caterpillar to restart the cycle. Baculoviruses are very efficient at killing their caterpillar hosts. Baculovirus have been proposed as useful agents to control or eliminate agricultural pest caterpillars that destroy crops. The idea is to spray fields with baculovirus polyhedra to induce widespread infection and eradication of the caterpillars. In this scenario, which of the following would likely happen: Caterpillars would evolve to prefer different plant hosts The virus would evolve to become less efficient at killing The virus would evolve to become more efficient at killing Caterpillars would evolve to become more susceptible to virus killing 2) In the 1980s there were several reported examples of laboratory workers who infected themselves with purified HIV & developed AIDS/ Which of Koch’s postulates did these accidents fulfill? 1 2 3 4 3) Many viruses encode proteins whose function is to partially or completely prevent synthesis of type 1 interferons in the infected cell. These viral proteins can function in many different ways. Three of these strategies listed below are actually used by viruses. One is totally made up & would not be effective. Which is fake? A virus that makes a protein that binds to & coats its double stranded RNA, preventing it from binding to RIG-1 & PKR An ssRNA virus that encodes a protein to degrade dsDNA in the cytoplasm to prevent recognition by TLRs A virus that makes a protein that binds to IRF3/7 & keeps it in the cytoplasm An ssRNA virus that makes a protein that causes degradation of RIG/1 & PKR EXPLAINATION: ssRNA must make both strands, so dsRNA is going to exist in the cytoplasm. It would therefore make sense for a ssRNA virus to interfere in some way with the sensing mechanisms for dsRNA. dsDNA is not a product of virus infection, so it wouldn’t make sense for ssRNA to encode a protein to interfere w/ such mechanisms - A virus binding to IRF3/7 is a good idea because this is were signals converge (regardless of genome type) - Viruses that make dsRNA making a protein to prevent it being seen by RIG-I & PKR makes sense 4) Which of the following is a direct effect of the release of mast cell granule contents? Increased blood flow through neighboring capillaries Opsonization of bacteria Activation of complement by the lectin pathway All of the above 5) Synthesis of interferon by an infected cell, & the consequent induction of the antiviral state in neighboring cells is an example of… Endocrine function of a cytokine A positive feedback loop Paracrine function of a cytokine Cellular recruitment by cytokines