Unit three Microbiology

MEASLES VIRUS INFECTS HUMAN CELLS. -during entry of the virus into a new host cell, the envelope fuses with the host cell membrane, releasing the viral contents into the cytoplasm of the cell. -after replicating, newly formed virions become enveloped by host cell membrane as they bud out of the host cell. -the measles virus needs to bud out of a cell because it needs that part of the cell membrane to make up the virus envelope. Without that envelope, the virion couldn't infect the next cell. -remember- not all virions have that envelope and they will just destroy the cell similar to what we saw with the bacteriophages in the previous slide. Viruses like that include the ones that cause polio and common colds.

-Different viruses have different mechanisms and efficiency of TRANSMISSION. -Each species of virus infects a particular group of host species, known as the HOST RANGE. -TISSUE TROPISM refers to the range of tissue types that a virus can infect.

HOW IS A NORMAL TEMPERATURE OF 37C (98.6F) MAINTAINED? -heat sensors located throughout the skin and large organs and along the spinal cord send information about the body's temperature to the thermoregulatory center in the hypothalamus -the hypothalamus acts as a thermostat by controlling blood flow through the skin and subcutaneous areas -Vasoconstriction prevents release of heat when we are cold and vasodilation secures its quick release when we are hot 0Hypothalamus is located in the brain.

-Fever (elevated body temperature) is a natural reaction to infection and is usually accompanied by general symptoms such as sweating, chills, and the sensation of feeling cold -substances that cause fever called pyrogens -External pyrogens (such as bacterial toxins) originate outside the body, while internal pyrogens (such as interferons, tumor necrosis factor, IL-1, and IL-6) are made by the body itself. Pyrogen - pyro = fire, gen = makes, so a pyrogen is something that makes fire or in our case fever. One of the internal pyrogens missing here - once originally called Endogenous Pyrogen is Interleukin-1. It is produced by macrophages when they have engulfed an invader.

The main idea here is for the body to recognize the foreign bodies as quickly as possible to get rid of them - in addition to lacking CD-47 - bacteria and viruses have structures that can trigger additional mechanisms to deter them before the adaptive system is fully functional. That's where the Toll-like and NOD-like receptors come into play. These receptors interact with parts of bacteria (peptidoglycan, flagellin, lipoteichoic acids) or viruses (dsRNA) that are unique, but also highly repetitive (hence molecule patterns). This interaction gets the cells initially infected to produce cytokines, like interferon in viral infections, that will warn other cells to prepare for invasion and hopefully slow down the infection process until the adaptive immune system is functional.

-The cytokines made after a MAMP-TLR interaction float away, bind to receptors on various cells of the immune system, and direct them to engage the invading microbe. -TLRs are restricted to membranes, but certain intracellular proteins can also recognize MAMPs. NOD-like receptor (NLR) proteins are important intracellular sensors of MAMPs -when bound to a MAMP, NLRs trigger a signaling pathway that is different from that used by TLRs

Natural Killer Cells recognize cells that have lost expression of MHC Class I molecules. NK cells store cytotoxic molecules such as perforin in secretory lysosomes. Recognition of an infected cell triggers the release of these cytotoxic molecules (green fluorescence) which then kill the target cell. Red fluorescence indicates cytoskeleton. Perforin forms a pore in the target cell membrane (punches a hole in it or perforates it) and destroys membrane integrity. Cytotoxic proteases called granzymes are also released from the NK cell, pass through the perforin pore, and enter the target cell. The granzymes trigger apoptosis (programmed cell death) of the target cell.

-bacteria and viruses contain unique structures that immediately tag them as being foreign (peptidoglycan, flagellin, dsRNA, lipoteichoic acids) -these structures have MAMPs (microbe-associated molecular patterns) that can be recognized by Toll-like receptors (TLRs) present on various host cell types. TLRs along with NLRs can be called pattern recognition receptors (PRRs) -Once bound to a MAMP, the TLR sends a signal to the interior of the cell to start making interferon and pro-inflammatory cytokines that will speed the inflammatory response.

So the activation of the cytotoxic T cell happens in the local lymph node as all other interactions, but then the activated cell goes into the circulation, finds the infected cell and then destroys it in much the same way as a Natural Killer cell does on the innate side. It produces the proteins PERFORIN that punches a hole in the cell's membrane, then GRANZYME enters the cell and induces it to undergo apoptosis.

-once activated, cytotoxic T cells bind to and kill the target cell by inducing apoptosis -all cells have MHC I, and therefore any cell can be killed by Tc cells -Here's the killing process. Don't worry about the individual compounds that happen after Granzyme enters the cell.

With chronic inflammation - often the inflammation itself becomes part of the problem. With microbial infection, there are certain organisms that have developed strategies to evade the immune system and manage to persist in the tissues without being destroyed. The response of the immune system then is to simply wall off the invader so that it can do no more harm. Unfortunately, this isn't without consequence either. The lesions that develop in tuberculosis are in fact, the organisms being walled off because the macrophages that initially engulfed them were unable to kill them - even with the aid of the specific immune system. So the response is to form tubercles, the specific name for the granulomas, formed around the original M.tb. site of infection. We'll talk more about this later when we specifically discuss TB.

A. The fluorescent orange and yellow organisms shown here are Mycobacterium tuberculosis within macrophages in a tuberculosis abscess. A thick, waxy cell wall along with the ability to inhibit phagocyte killing mechanisms helps mycobacteria survive inside macrophages for prolonged periods. The continual stimulation of an inflammatory response leads to chronic inflammation. B. Fish tank granuloma. Mycobacterium marinum can cause tuberculosis-like infection in fish. The organism can accidentally enter the human body through an open wound or abrasion during cleaning of an aquarium containing infected fish. The infection is first noted as a lesion that heals very slowly on the hand or forearm and often forms a granuloma at the site that contains live organisms.

REGULATING COMPLEMENT ACTIVATION - the host cell surface protein, CD59 (protectin), will bind to any C5b-C8 complex trying to form and prevent C9 from polymerizing -protein factor H prevents the inadvertent activation of complement in the absence of infection. Factor H normally binds to surfaces of host cells, not pathogens, and protects cells from complement attack by inactivating C3b. -cytokines stimulate acute-phase reactant proteins such as C-reactive protein, which activates complement. -Again, as with any destructive mechanism we have described, there is always a protective mechanism for our cells. We will see this also in the adaptive immune system.

ADAPTIVE IMMUNITY VS INNATE IMMUNITY -innate immune mechanisms are present from birth -adaptive immunity develops only after exposure to an antigen. KEY PROPERTIES OF ADAPTIVE IMMUNITY: -complex and slow development - cross-regulated defense network - memory response

These divisions of the adaptive system are both likely to happen at the same time to any given antigen. While we will discuss these individually, remember that in many cases - especially viral infections, both of these arms of the immune response are triggered. They are not independent of one another for the most part. But to discuss them initially we will break them apart. HUMORAL - refers to something originally identified in the liquid portion of the blood - we now know these are antibodies, a type of protein that is made by B LYMPHOCYTES to interact with the antigen that triggered their production. Once the B cell is triggered, it begins to produce those antibodies - the cells differentiate into PLASMA CELLS - that are basically antibody factories. Some of those triggered B cells, don't become Plasma cells, but rather MEMORY B CELLS - that remain hidden in the body to be ready for the next time this same antigen enter your body. CELL-MEDIATED - here T LYMPHOCYTES are doing all the work - yes, to do it they too use chemicals, but here the cells need to be in DIRECT CONTACT with the cell that is infected or damaged, and will kill it to stop the invader. There are several types of T cells - one of which is the effector cell I just described, another one actually helps these cells as well as B cells do their jobs better, another shuts down the immune response once it has been successful, and finally a MEMORY cell so that it too can respond better and faster to this same antigen if it shows up again.

ANTIGEN -derived from the term "antibody generating" -describes anything that can elicit an immune response. EPITOPE -A specific binding site on an antigen. Antigens can have more than one epitope HAPTEN -very small molecules that, when attached to a larger carrier protein, can act as an antigen

Overview of Cell-Mediated Immunity 1) cytotoxic T cells bind antigen presented on antigen-presenting cells. 2) upon activation, the cytotoxic T cells leave the lymph node and find host cells presenting the same antigen 3) cytotoxic T cells kill the infected host cell. Most effective on: Intracellular bacteria and viruses

ANTIGENICITY- a measure of how well an antigen elicits an immune response. Strongest: proteins Medium: carbohydrates Weakest: nucleic acids and lipids Threshold dose -the amount of antigen needed to generate an optimal response -low dose does not activate enough B cells. -Too high of a dose can lead to B-cell tolerance This is what I was talking about earlier when we discussed antigens and epitopes. For the most part, we are lucky enough to usually get the right dose to trigger the response. Although, knowing how to shut certain B cells down can be important when it comes to treating abnormal reactions we'll talk about in the next chapter. Immunological specificity- the idea that antibodies generated are specific for a single antigen

WHITE BLOOD CELLS DIFFERENTIALS - clinical labs routinely count the total number of white blood cells and identify the various cell types- neutrophils, eosinophils, basophils, lymphocytes, and monocytes -this is called a white blood cell (WBC) differential and can provide the clinician with important clues about the cause of a patients illness --elevated total WBC indicates infection or allergy --elevated neutrophils suggest bacterial infection --elevated lymphocytes suggest viral infection --increased eosinophils suggest intestinal parasites or blood parasites

Again - these are the typical ranges for normal blood counts. Reference ranges for differential white blood cell count in normal adults is as follows: Neutrophils - 2.0-7.0×10^9/ l (40-80%) Lymphocytes - 1.0-3.0×10^9/ l (20-40%) Monocytes - 0.2-1.0×10^9/ l (2-10%) Eosinophils - 0.02-0.5×10^9/ l (1-6%) Basophils - 0.02-0.1×10^9/ l (< 1-2%)

there are 7 Groups of virus based just on genome structure. Note that for some of these, they require special polymerase enzymes to make a version of DNA or RNA that doesn't normally occur in the cells that they infect. These are then further divided by do they have an envelope or not, etc. Slide 21 powerpoint 12: Group 1: Double-stranded DNA is transcribed to mRNA. Group 2: Single-Stranded DNA generates a double-stranded form within the host cell, which is transcribed to mRNA. Group 3: Double-Stranded RNA makes mRNA by using RNA-dependent RNA polymerase. Group 4: Single-stranded RNA (+) makes a complementary (-) strand, which is transcribed to mRNA. Group 5: single-stranded RNA (-) is transcribed to mRNA. Group 6: Single-stranded RNA (+) is reverse-transcribed to DNA, which is transcribed to mRNA. Group 7: Double-stranded DNA is transcribed to mRNA, which is reverse-transcribed to make viral genomes for packaging into virions.

All viral replication cycles must achieve the following: -HOST RECOGNITION AND ATTACHMENT...viruses must contact and adhere to a host cell that can support their type of replication -GENOME ENTRY.... the viral genome must enter the host cell and gain access to the cell's machinery for gene expression -ASSEMBLY OF PROGENY VIRIONS....viral components must be expressed and assembled. Components usually self-assemble spontaneously. -EXIT AND TRANSMISSION... progeny virions must exit the host cell and reach new host cells and, if multicellular, new hosts to infect. It doesn't matter what virus we look at - they all do these same things in their replication cycle. However, because of envelopes or not, DNA vs. RNA, single-strand vs. double-strand, etc., they do it a little differently. BACTERIOPHAGE REPLICATION How does bacteriophage Lambda know which bacteria to infect within the mixed population in our colon? -the phage binds to the maltose porin in the outer membrane of E. coli -the maltose porin is often called the "lambda receptor protein" even though it actually is present in E.coli as a way to obtain the sugar maltose for catabolism. -natural selection maintains the maltose porin in E. coli, despite the danger of being infected by bacteriophage lambda This information is basically true for every virus as well. The first step every virus must take is to attach to the cell they are going to infect. That means there is a specific protein on the surface of the virus that is going to specifically interact with some protein on the surface of the cell. Today, for most viruses we know what each of those proteins is, like here with the Lambda phage and E. coli, but there are a few we still don't understand. It's these interactions that also controls which cells the virus infects and which organisms the virus infects.

-a normal host displays 2 types of MHC molecules on its cell membrane. MHC 1 is an indicator of "self". -When an NK cell binds to MHC 1 protein, it will not attack. However, if the host cell lacks MHC class 1 molecules, NK cells will perceive the cell as foreign and insert a pore-forming protein called perforin into the target cell membrane. -NK cells also contain antibody binding Fc receptors on their surface. Antibody-dependent cell-mediated cytotoxicity (ADCC) occurs when the Fc receptor on the NK cell links to an antibody coated host cell.

Almost every nucleated cell in the body has MHC I molecules on its surface - its how the body knows a cell belongs to you and not someone else. (These are also what needs to be "matched" when someone requires a transplant.) So when a NK cell, sees a cell that for some reason doesn't have MHC I on it - it destroys it. Cells that lack MHC I - could be infected or they could be cancerous, both can cause the loss of expression of MHC I. It's a good thing they do this for us - it has been estimated that our bodies can produce up to a million cancer cells per day - guess who destroys them before they can cause a real problem. ADCC occurs again when a cell is infected or cancerous and antibodies have been produced to an antigen that gets expressed on the cell surface - these antibodies can then bind (trust me) - so a NK cell will bind to the end of that antibody molecule and then do its thing and kill that cell.

ENDING INFLAMMATION -during the inflammatory process, neutrophils converge on an infected area (seen as pus) -what happens when the infection clears? -Neutrophils are loaded with destructive enzymes and signal molecules. Neutrophils trigger programmed cell death (apoptosis) - long-lived phagocytes such as macrophages remove the dead neutrophils by engulfing them Almost all cells have been pre-programmed to undergo apoptosis. The neutrophils that have done their job die and are engulfed by the larger macrophages and recycled to a certain degree. Debris is removed and the necessary processes to heal the damaged tissues begin.

CAN HUMAN CELLS UNDER ATTACK WARN OTHERS OF DANGER -interferons are cytokines produced by eukaryotic cells in response to intracellular infection (infection by viruses or intracellular bacterial pathogens) -Interferon action is specific to the host species, but it is virus nonspecific (meaning interferons from a mouse won't work in humans, but human interferons will protect against both poliovirus and influenza virus) -2 general types: Type 1 (high antiviral potency), including IFN-alpha, IFN-beta, IFN-omega, and Type 2 (immunomodulatory), including IFN gamma Here in the innate immune system, we are primarily talking about the Type I interferons - alpha, beta, omega. Type II interferon plays a role in the adaptive immune response.

T-cell Activation -requires antigen presented by antigen presenting cells (APCs) -antigen is presented on special surface proteins called major histocompatibility complex proteins (MHC) --Class 1 MHC proteins are found on all nucleated cells --Class 2 MHC proteins are only found on dendritic cells, macrophages, and B cells.

B cells are able of dealing with antigen all by themselves with the B cell receptors. T cells are not capable of dealing with antigen directly - they need to have antigen presented to them by specific ANTIGEN PRESENTING CELLS (APC). The nucleated cells of the body have the MHC Class I proteins on their surface - that's good, because that is what is needed, as we'll see, to present antigen to Cytotoxic T cells. And since any cell in the body may be infected, we need that interaction possible everywhere. As it says - APCs for Helper T cells are only dendritic cells, macrophages, or B cells. In order to present to the antigen, these cells have the Class II Major Histocompatibility Complex (MHC) Proteins on their surface - they are the only cells in the body to have them. There are far fewer of this cell type, but as we'll see they do most of their work in the lymph nodes and so, they don't need to be all over the body.

Sneezing will remove microbes that have been trapped within the mucosa of the nasal passages, but do little for anything trapped within the passages of the lower respiratory tract. This is where coughing comes into play (which unfortunately the book fails to mention). Again, in the trachea and bronchi - there is a mucociliary escalator to move microbes trapped in the mucus up and out, and away from the lungs. It's only when something gets past this protective mechanism and into the lungs themselves are the alveolar macrophages able to ingest and kill the invader. Hopefully....

CHEMICAL BARRIERS TO INFECTION - Acidic pH of the stomach is lethal to most bacteria -Enzymes such as lysozyme in tears will degrade the cell walls of Gram-positive bacteria -Superoxide radicals generated by host enzymes such as lactoperoxidase can kill pathogenic bacteria -Small cationic peptides, called defensins, function as important components of innate immunity --made by a variety of cells such as skin, lung, genitourinary tract, gastrointestinal tract --kill by destroying microbial cytoplasmic membrane --effective against both Gram-positive and Gram-Negative bacteria, fungi, and some viruses The defensins are interesting small peptides or sequences of amino acids. They destroy membrane - that is why they can uniquely destroy bacteria, fungi, and some viruses - as long as they are enveloped - like HIV or Influenza.

So here is the whole process put together. I'd add a few things to this diagram. The bacteria don't need to be there - the fact that the sliver alone is penetrating the skin is enough to get the process started. Macrophages release factors at this point, but so do the mast cells, the histamine is crucial to get the vasodilation going. And it's also at this stage where mediators found in the blood will begin to leak into the tissues. Certain reactants induce the vessel wall cells to begin to display the selectins that signal where the neutrophils are required. Other reactants cause the display of the integrins on the surface of the neutrophils = it's the combination of the integrins binding to the selectins that direct the neutrophils through the vessel wall to the site of the damage (extravasation). Bradykinin is both helpful - loosening cell junctions, but not by triggering prostaglandin synthesis. Finally the neutrophils can do their duty - they are at the site further directed by chemoattractants which include parts of the bacteria, cytokines released by macrophages, and components from the blood like complement (we'll talk about complement in a little bit).

CHRONIC INFLAMMATION -results from the persistent presence of a foreign body -causes permanent tissue damage, even though the body attempts repair -there are many causes of chronic inflammation: --mycobacterium tuberculosis, Actinomyces bovis, and various protozoan parasites can avoid or resist host defenses and persist at the site of infection. --as a result, they continually stimulate the basic inflammatory response. --nonliving, irritant material such as wood splinters, asbestos particles, and surgical implants can also lead to chronic inflammation. A granuloma is an attempt by the body to "wall off" the site of inflammation

Antibodies have diversity: Isotope- the types of antibodies found in all different individuals in related species -says as a human you have 5 isotopes (IgD, IgM, IgG, IgA, and IgE) Allotype- the types of antibodies found within one species --says small genetic differences in the heavy chain and light chain constant regions are found in you versus another person - your IgG vs their IgG Idiotype- the types of antibodies found within one individual --says among your IgG molecules there are small genetic differences in the variable regions of the heavy and light chains because they react to different antigens

Discuss key points of five isotypes of antibodies. IgG (don't worry about the 4 subtypes) - Primary antibody in the blood and tissues, it crosses the placenta from mother to fetus (protecting it while in utero), binds complement to trigger the Classical Pathway, aids in Opsonization (Fc binds to macrophage). Found as single Y-shaped molecule. IgA - also called secretory IgA. Primary antibody associated with mucous membranes and secretory tissues and secondarily, in the blood. Two Y-shaped molecules are held together with another protein called a J CHAIN. This gets secreted through a mucosal cell which then adds the SECRETORY PIECE - this protects the antibody molecule from digestion. Found in secretions, including breast milk to help protect the baby once it is born. Doesn't cross placenta or bind complement. IgM - found in two forms - monomeric (single Y) on the surface of B cells as a receptor for antigen, pentameric (5 Y joined by J chain) as the first antibody secreted from a B cell in response to an antigen the first time it appears. It will also bind complement to trigger the Classical Pathway, but it will not cross the placenta - it's just too big. IgD - notice there is hardly any in the serum, its primary job is as a surface receptor for antigen on a B cell, just like monomeric IgM. They share the job. IgE - even less of this is found in the serum, because as soon as it is produced it binds via the Fc region to the surface of mast cells and basophils. Remember we talked about these cells and their granules during inflammation - but when IgE is attached, these cells will degranulate once two antigens bind to the appropriate IgE. This is what happens with allergies - we'll talk about this far more in the next chapter. Note that IgG and IgD and IgE are monomers (16.7). IgM and IgD are found on the membrane of the B cell (16.9 panel C). Note that IgA is a dimer and IgM is a pentamer once secreted (16.8) See how IgE binds to a mast cell, then when antigen joins two molecule together which causes the degranulation of the cell, and we get the signs and symptoms of allergy.

Not only do the neutrophils and additional monocytes pass into the tissues at this point. Since the blood vessels are more permeable, other mediators that are the blood also pass into the tissue - such as complement proteins which aid in recruiting the neutrophils, clotting proteins which allow clots to form and keep the invader in place, and other chemokines that help get the neutrophils to where they need to be. Unfortunately, bradykinin also stimulates the production of prostaglandins which cause pain.

Extravasation is the process by which leukocytes move from the bloodstream into surrounding tissues. Signal molecules produced by damaged tissue cells induce the production of selectins (produced early in the process) on the surface of endothelial cells and integrins on the surface of the white blood cells (selectins and integrins not shown). Selectins capture leukocytes traveling through blood vessels. Leukocytes begin to roll along the vessel wall, and the integrins on the leukocyte surface lock onto endothelial cell's adhesion molecules (ICAM-1 or VCAM-1). The leukocytes are progressively activated while rolling. The neutrophil ultimately squeezes through the wall between endothelial cells (extravasation). Remember - this process occurs after the macrophages and mast cells have released their mediators to get the process started.

LYSOGENY -lysogeny occurs when the phages retain the host DNA by integrating it into the genome of the host. -Lysogenic phages may carry genes that give the host cell an advantage (ex: Shinga toxin gene in E. coli Ō57:H7) -the integrated phage genome is called a PROPHAGE -the prophage is now replicated along with the host cell DNA -the prophage may revert back to the lytic cycle by directing its own excision from the host genome and initiating lysis of the host cell The Lambda phage we just talked about is a lysogenic phage and the one used to figure out the lysogenic cycle.

FOR VIRUSES CAPABLE OF LYSOGENY -The decision between lysogeny and lysis is determined by proteins that bind the DNA and repress the transcription of genes for virus replication. -Exit from lysogeny can occur at random or it can be triggered by environmental stress such as UV light, which damages the cell's DNA. -An analogous phenomenon occurs in human viral infections such as herpes, in which environmental stress triggers reactivation of a virus that was dormant within cells. This is called a latent infection. -Reactivation of a latent herpes infection results in periodic painful outbreaks of skin lesions. As the slide mentions, animal viruses can also integrate their genome into the host genome. In human viruses, like members of the Herpes family, the process is called Latency.

COMPLEMENT -a series of 20 proteins in the blood, collectively called complement, play a huge role in preventing blood infections -several complement components are proteased that sequentially cleave each other in a cascade -Triggering the complement cascade produces a number of outcomes. Pores called membrane attack complexes (MACs) are inserted into membranes and cause cytoplasmic leaks. In addition, pieces of the complement system can attract white blood cells and facilitate phagocytosis/opsonization

I've mentioned complement a number of times - it's about time it gets explained. There are actually a total of 30 or so proteins that work together to make up the complement system. They work in one of three ways that we'll discuss. There are two main outcomes - they will either directly destroy the organism, or they will help the phagocytes to destroy the organism through opsonization that we've already talked about.

The primary problem with finding an antiviral is that viruses use the replication machinery of the cell that it infects. So any drug that we might find or develop is also going to shut down the cell- any cell, every cell. That just won't work. So we have to find drugs, just like we talked about with anti-bacterials, that are specific to something the virus has and only has. Tough job, in some cases, impossible.

ICOSAHEDRAL CAPSIDS- radial symmetry; based on an icosahedron, a polyhedron with 20 identical triangular phases. EX: Herpes simplex virus (HSV) -Each triangular face of the capsid is determined by the same genes encoding the same protein subunits. No matter what the pattern of subunits is, the structure exhibits rotational symmetry. -Some icosahedral viruses (polio-, papillomavirus) have only a protein capsid. However, others possess in addition an envelope derived from the host nucleus or ER membrane. -the space between the envelope and capsid may contain many proteins called TEGUMENT, which may help with viral replication Icosahedral capsid of herpes simplex 1 (HSV-1), envelope removed. Imaging of the capsid structure is based on computational analysis of cryo-electron microscopy (cryo-TEM). Images of 146 virus particles were combined digitally to obtain this model of the capsid at 2 nm resolution. Icosahedral symmetry includes fivefold, threefold, and twofold axes of rotation. The icosahedral capsid contains spooled DNA

Some bacteria will produce proteins that are different and are meant to get around the typical immune response. These proteins are called superantigens - because as you can see the purple superantigen on the right hand complex artificially triggers the T cell to think it's been activated and so it begins to produce a variety of cytokines. Because it is not specific, it will trigger many, many T cells resulting in far too many cytokines to be produced - making the so-called "cytokine storm". All of these cytokines will begin to cause damage to many tissues throughout the body. Two of the best known superantigens are the Toxic Shock Syndrome Toxin of Staphylococcus aureus and the Toxic Shock Syndrome-like Toxin of Streptococcus pyogenes. It's these toxins that cause the massive damage in Toxic Shock Syndrome and Necrotizing Fasciitis that these two bacteria cause.

If an organism is to survive - it needs to be able to not be destroyed by the immune system. As this slide shows, there is a variety of ways that an organism or virus can do this. This list is not complete and we will discuss more later. HIV is probably the best at this - the primary cell that HIV infects in the Helper T cell and then destroys it. Now think about that - without Helper T cells - B cells will only be able to make IgM antibodies (no isotype switching) and Cytotoxic T cells won't get the IL-2 they need to become fully activated. Basically, the immune system is lost - welcome to Acquired Immunodeficiency Syndrome (AIDS).

Use the images of the smallpox virus and the vaccinia virus to demonstrate that while immunological specificity works very well, there are examples where an immune response to one pathogen may result in protection against a similar pathogen. An example of immunological specificity working is rhinoviruses that cause the common cold. With rhinoviruses, an antibody response to one strain is unlikely to prevent infection by another strain of rhinovirus. OK - I'm going to leave this for it comes from the text - but it's a little confusing - let me try to make a little more sense. The RHINOVIRUS EXAMPLE SHOWS SPECIFICITY of the immune response. There are about 200 different, but closely related, viruses which can cause what we call the common cold. The fact that we need to mount an immune response to each of them - A DIFFERENT ANTIBODY AND CELL-MEDIATED RESPONSE FOR EACH VIRUS shows how specific the response must be. And that's why, unfortunately, you can possibly get that many colds in your lifetime. However - the response shown here - where we can use the cowpox or Vaccinia virus and use it to protect against small pox or Variola virus, DEMONSTRATES CROSS-REACTIVITY, not specificity. It shows us that both viruses share an antigen that is very similar - enough that an antibody produced to one virus will protect us from the other - this is not the norm, we got lucky here!

In 16.6 A point out the green heavy chains and yellow light chains. Also point out the sulfide bonds that hold chains together. Note the antigen in red. Panel B illustrates a three dimensional space filling model of an antibody, note the location of heavy and light chains. Use 16.7 to point out the constant and variable regions of the antibodies. So - as you see, antibody molecules are made up of a total of 4 protein chains. In DIAGRAM A - the two large identical green chains are called the HEAVY CHAINS. And the smaller yellow protein chains are the LIGHT CHAINS. They are held together by disulfide bridges (remember when we talked about proteins and I pointed out the amino acid cysteine had sulfhydryl (-SH) groups - here's one place where these are very important to hold these chains together in their quaternary structure - without them, we don't have an antibody molecule. Both the ends of the heavy and light chains combine at the ends of the arms of the Y-shaped molecule to be the ANTIGEN - BINDING SITE. It's here in a small indentation where the EPITOPE amino acids will fit and the antibody will interact with the antigen to destroy or neutralize it, dependent upon the whether its an organism, virus, or toxin. If we look at DIAGRAM C - the yellow and green coloring is different, because it now denotes function vs form. The yellow ends of both the heavy and light chains where the antigen binds are also called VARIABLE REGIONS - because it's here where the amino acid sequence changes on both chain to be able to bind to all the different epitopes - together, it is called the Fab. The remainder of both the heavy and light chains (green) are called the CONSTANT regions, because they stay pretty much the same in every antibody molecule. Overall - there are two type of light chain - KAPPA and LAMBDA. There are five types of heavy chain - DELTA, MU, GAMMA, ALPHA, and EPSILON. These heavy chains give the 5 CLASSES OF IMMUNOGLOBULINS (Ig - this is the type of serum protein where antibodies are found) - IgD, IgM, IgG, IgA, and IgE. The bottom of the molecule made of the two heavy chains are called the Fc region, it's this part of the molecule that can bind to cells like macrophages to aid in phagocytosis (remember opsonization).

VIRAL DIVERSITY AND EVOLUTION -over extended time, viral evolution generates new kinds of viruses that cause different diseases in different hosts. Herpes viruses are an ancient type of virus that has infected many types of animals. Different diseases develop over time as viruses evolve, infecting the same or different species. -Phylogeny of human and animal herpes viruses based on whole-genome sequence analysis comparing groups of genes with similar function. Numbers measure genetic divergence.

In general, viruses evolve at different levels: -WITHIN A HOST COMMUNITY... evolve to preferentially infect different species (e.g. equine herpes in horses vs murine herpes in mice). -WITHIN A VIRAL SPECIES POPULATION... strains evolve that vary in infectivity and virulence. Closely related viruses may cause diseases that are similar (herpes simplex viruses 1 and 2) or different (varicella-zoster vs cytomegalovirus) -WITHIN AN INDIVIDUAL ORGANISM... Viruses evolve variants that resist therapeutic agents (hepatitis C and HIV evolve into diverse strains that infect different tissues within the host. its difficult to say what drives the various types of evolution

How prevalent is papillomavirus? In the US, the genital strains of human papillomavirus (HPV), including those that cause cancers of the cervix, penis, and anus, infect 80% OF ADULTS The discovery that cervical cancer is caused by HPV earned German researcher Harald zur Hausen the 2008 Nobel Prize in Physiology or Medicine. The genital strains of HPV are HIGHLY INFECTIOUS through sexual contact (especially HPV-16), including oral contact leading to throat cancers. CONDOMS offer partial protection and vaccines such as GARDISIL offer greater protection from HPV. Papillomavirus generally only causes the formation of genital warts, unfortunately they are also have been found to be the cause of cervical cancer as well.

In many cases, the virus eventually is eliminated by the body's immune system. In the basal cells, however, HPV may take an alternative pathway, integrating into the genome of the host basal cells (similar to lysogeny, called latency). The integrated genome can transform host basal cells into cancer cells through increased expression of viral oncogenes E6 and E7. The process of a virus inducing CARCINOGENESIS in a host cell is called TRANSFORMATION. Be careful - here is the second definition of the term TRANSFORMATION we've seen.

WHAT IS INFLAMMATION AND HOW DOES IT DEVELOP? -inflammation is a critical innate defense system in the war between invaders and their host -it provides a way for phagocytic cells (such as neutrophils) to enter infected areas within tissues -movement of these cells out of blood vessels is called extravasation

Inflammation is a normal process that the body uses as a response to tissue damage. It doesn't matter how the damage has occurred - it could be a sprained ankle, a sliver, or a microbial invasion. It does trigger the recruitment of phagocytic cells to the damaged area to both protect against any microbe that maybe involved as well as to begin the healing process of the damaged tissue. There are five Cardinal Signs of Inflammation - think about them, you have probably experienced them all when you have hurt yourself at some point - whether a minor or more serious injury. I love the terms in Latin - for many years, we only had the first four signs - and then, they all rhymed. Redness (Rubor) - redness which comes from the vasodilation of the blood vessels Pain (Dolor) - pain which comes from the production of prostaglandins Swelling (Tumor) - swelling which comes from the infiltration of neutrophils and serum fluids Heat (Calor) - heat which is due to the increased blood flow along with the release of interleukin-1 from macrophages Loss of Function (Functio laesa)- as obvious as a sprained ankle that doesn't work or as subtle as skin that's damaged that can no longer be a protective barrier

The influenza virion is asymmetrical; it has no fixed capsid. Its genome consists of (-) sense RNA, so it is the opposite of the mRNA. The influenza genome is RNA divided among 8 chromosome segments. Each segment contains a different essential gene. When influenza infects a cell, the 8 RNA segments can reassert with segments from a coinfecting virion of a different strain of Influenza. Interspecies reassortment leads to the most virulent pandemic strains of influenza. Influenza A virus, an orthomyxovirus, is one of the most common life-threatening viruses in the U.S. The virus infects cells of the upper respiratory mucosa, causing fever, sore throat, headache, and other symptoms. Each year influenza A infects approximately 10% of the U.S. population, causing about 36,000 deaths annually. The elderly and the very young are more susceptible, but in an epidemic state, mortality rises among young people. Diagram of virion structure showing the envelope (brown), envelope proteins (HA and NA), matrix protein (yellow), RNA segments with attached polymerase, and the nuclear packing protein NS2. The inset image shows an influenza A virion. The brush-like border coating the envelope consists of glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Envelope proteins involved in receptor binding (HA and NA) are also called "spike" proteins.

Influenza strains show antigenic drift in that their envelope proteins continually mutate, evading the host immune system; thus, new strains emerge annually, the "seasonal flu." At wider intervals, extremely virulent strains emerge that cause pandemic mortality. The famous influenza pandemic of 1918 infected 20% of the world's population and killed more people than World War I did, conservative estimates make that at @30 million people, others estimate it could have been as many as 100 million since the reporting wasn't very efficient in many parts of the world. The 1918 strain arose as a mutant form of an influenza strain infecting birds. Such virulent strains usually arise through antigenic shift, in which genes from 2 or more different viruses combine. Antigenic shift says that when those two different Influenza strains meet in the same animal, during packaging of the new genomes, some from the avian strain mix with the human strain to make a new virus. The two most important genes encode the H or HA (hemagglutinin) and N (neuraminidase) proteins which are important in the infection process. If you remember a couple of years ago, we were all panicked about the H1N1 virus - now you know what that means. That was an Antigenic Shift virus and in the past we have seen severe epidemics/pandemics when this happened, like in 1918. Fortunately, that didn't happen.

An antigen is whatever triggers an immune response - not just humoral as the original name denoted - but either humoral, cell-mediated, or both. While the diagram shows that all of the macromolecules may be released after phagocytosis - the vast majority of antigens are PROTEINS. Nucleic acids and lipids are rarely antigenic, and occasionally we will see antibodies produced to polysaccharides - but not like we will see proteins as antigens. EPITOPES or antigenic determinants (old term) are small parts of the larger protein antigen that triggers and interacts with either the antibodies made by B cells or directly with the T cells via a surface receptor. If you go back to our discussion on protein structure - it's important to realize that only a few of the hundreds or thousands of amino acids that make up a protein are needed to make an epitope. Therefore, it shouldn't be surprising that a single protein can have multiple epitopes.

LOOK AT CH 16 SLIDE 7 for overview of humoral immunity Sorry they didn't put a diagram here - but this one would be a little more confusing than the humoral immunity one. This slide describes the effector T cells or cytotoxic T cells - but it doesn't explain how they get to be fully activated. COME BACK TO THIS SLIDE as well and make sure you understand what the slide says. These cells also will destroy cancer cells as well.

How bacteriophage enters bacterium: A bacteriophage attaches to the cell surface by its tail fibers and then contracts to inject its DNA. The phage injects its genome through the cell envelope into the cytoplasm, avoiding the need for the capsid to penetrate the tough cell wall. The sheath of the neck tube contracts, bringing the head near the host cell surface to insert its DNA. The pressure of the spooled DNA is released, expelling the DNA into the cell. After inserting its genome, the empty phage capsid remains on the surface of the host cell (called the "ghost"). `

LOOK AT FIGURE 12.3 The phage inserts its DNA into the cell, and phage genes are expressed by the host cell RNA polymerase and ribosomes. "Early genes" are those needed for transcribing DNA and other early steps in producing progeny. Other phage-expressed proteins and the host's cellular enzymes and ribosomes work together to replicate the phage genome and produce capsid proteins. Capsids are self assembled, each containing the phage genome. Finally, a "late gene" is expressed as an enzyme that lyses the host cell wall, releasing the mature virions. Lysis occurs when the phage genome reproduces progeny phage particles, as many as possible, and then lyses the cell to release them. Lysogeny occurs when the phage genome integrates itself into that of the host. The phage genome is replicated along with that of the host cell. The phage DNA, however, can direct its own excision. This excised phage genome then initiates a lytic cycle.

CULTURING ANIMAL VIRUSES -The host cells are usually an immortalized cell line—a line of cells from a cancer in which cells can double in culture indefinitely. -Tissue culture cells are inoculated with a virus suspension. Then, after sufficient time to allow viruses to adhere to cells, the culture fluid is removed, including unattached virions. -The fluid is then replaced by a gelatin medium which retards the dispersal of viruses from infected cells. -When host cells die, plaques are observed When growing virus in animal cells, it isn't always necessary to put the gelatin layer on. This is primarily used when doing a count of the number of virus particles. If you are just growing animal virus in cells, the fluid medium remains on the surface of the cells to keep them fed and let the viruses freely spread to other cells. When you are trying to grow virus for other uses, you want to get as many viruses as you can.

Modified plaque assay using cultured cells. The addition of gelatin medium (step 3) retards the dispersal of progeny virions from infected cells, restricting new infections to neighboring cells. The result is a visible clearing of cells (a plaque) in the monolayer. Plaque assay in which human coronavirus suspension was plated on a monolayer of colon carcinoma cells.

MONOCYTES -circulate in the blood and then migrate to tissues where they differentiate into macrophages and dendritic cells MACROPHAGES -widely distributed throughout the body and most likely to make first contact with invading pathogens -can kill invaders directly and can "present" antigens on their cell surface to T cells DENDRITIC CELLS -located in the spleen and lymph nodes, they can also take up and present small antigens on their cell surface to T cells. -different from macrophages in structure and because they can take up small soluble antigens from the surroundings as well as phagocytizing whole bacteria

MononuclearPhagocyteSystem (MPS) was previously called the reticuloendothelial system - so these cells are found in both blood and tissues - they are always found in the tissues, ever on patrol for invaders, neutrophils are only in the blood unless they are recruited to a site of damage or inflammation.

Fig 15.1 Pluripotent stem cells in bone marrow divide to form two lineages. One lineage consists of the myeloid stem cells, which develop into polymorphonuclear leukocytes (PMNs) and monocytes, which function primarily as part of innate immunity. The lymphoid stem cells ultimately form natural killer cells, B cells, and T cells. B and T cells are involved in adaptive immunity. The B cells mature in bone marrow, and T cells mature in the thymus. Colors indicate groups of differentiated cells that arise from the same progenitor. It's important to note that the Natural Killer Cells are considered part of the innate system, but they arise from the stem cell that eventually becomes the members of the adaptive system.\, B and T cells.

NEUTROPHILS- -make up nearly all WBCs in the blood -can engulf microbes by PHAGOCYTOSIS to form PHAGOSOMES (a vacuole formed around a microorganism as it is engulfed) and can kill them by fusing them with enzyme filled lysosomes. BASOPHILS & EOSINOPHILS -do not phagocytize microbes but release products that are toxic to the microbes as well as chemical mediators that affect the diameter and permeability of blood vessels MAST CELLS -contain many granules rich in histamine and heparin -reside in connective tissues and mucosa and do not circulate in the bloodstream

NATURAL KILLER CELLS -body cells that are infected or that are cancerous can be major problem for the host. -infected cells can hide a pathogenic microbe from the immune system, whereas cancer cells can take over and kill the host. -Natural Killer cells (NK cells) are able to identify and handle those situations by recognizing changes in cell surface proteins of compromised cells and then degranulate and release chemicals that kill those cells.

Natural Killer Cells are also produced from the same lineage as the lymphocytes we will talk about in Chapter 16. The difference between NK cells and some of the lymphocytes we'll talk about there is that the control here is only based on the presence or absence of a particular protein complex on the cell surface - the lymphocyte requires antigen recognition as well.

PHYSICAL BARRIERS TO INFECTION: MUCOUS MEMBRANES -selectively permeable to nutrients and waste components but a barrier against invading pathogens -secreted mucus coats surfaces and traps microbes -other secreted compounds within mucus such as lysosyme and lactoperoxide can kill organisms trapped in mucus -Microbe-associated molecular patterns (MAMPs) are recognized by cell surface receptors such as Toll-like receptors and the protein CD14 - Mucosa-associated lymphoid tissue (MALT) and gut-associated lymphoid tissue (GALT) is scattered along mucosal linings and populated with B and T cells as well as plasma cells and macrophages. MAMPs include peptidoglycan and lipopolysaccharide As you see with the skin and mucous membranes, not only are they physical barriers, but they also utilize chemicals such as sebum (fatty acids), lysozyme (which destroys peptidoglycan) and lactoperoxidase (produces reactive oxygen metabolites) along with the normal microbiota to protect us from invaders. PHYSICAL BARRIERS TO INFECTION: MUCOUS MEMBRANES -Peyer's patches are aggregations of lymphoid tissues that dot the intestinal surface, along the lower small intestine. -M cells are specialized parts of Peyer's patches that are wedged between epithelial cells. M stands for "microfold" which describes their appearance. -M cells are fixed cells that take up microbes from the intestine and release them into a pocket on the opposite side of the cell. Other cells of the innate immune system such as macrophages gather here and collect the organisms that emerge. -M cells, acting as a phagocytic filter, are extremely important for the development of mucosal immunity to pathogens. -Not only do M cells help to protect us- they may also be the entry way for some pathogens such as Salmonella and Shingella to get into the body.

PHYSICAL BARRIERS TO INFECTION: LUNGS -In addition to the respiratory mucociliary elevator, microbes larger then 100 micrometers become trapped by hairs and cilia lining the nasal cavity. -Sneezing, forceful expulsion of air from the lungs, is designed to clear the organism from the respiratory tract. -Organisms that make it to the alveoli are not easily expelled by a sneeze but are met by phagocytic cells called alveolar macrophages that ingest and kill most bacteria and send out chemical signals to attract other cells of the innate and adaptive immune systems.

The lymphatic system is a secondary circulatory system that connects with the blood circulatory system to be sure that all areas of the body are protected from invading antigens. As part of that system - we have the primary lymphoid organs - the BONE MARROW, where B cells learn what it means to be a B cell, and the THYMUS, where T cells get their education on being a T cell. To say that B cell produce antibodies and T cell modulate adaptive immunity is only the top snow flake on the tip of the iceberg. We will talk a lot more about these two cell types - what they do and how they learn to do it in Chapter 16. The secondary lymphoid organs is where the immune reactions occur. When we get to Chapter 16 - you will see that for B cells, T cells and macrophages to fight off an invader, they actually have to be in physical contact with each other - this happens in these secondary lymphoid organs. The slide mentions GALT = Gut Associated Lymphoid Tissue = you will see there is also MALT and SALT. Note the location of all of the immune tissues. Bone marrow is primarily in the long bones and hip bones. The thymus is the one that is usually mislocated - it lies just above the heart. It is largest when you are young and shrinks in size as you age. (NOT the thyroid)

PHYSICAL BARRIERS TO INFECTIONS: SKIN -protective shield covered with keratin made by keratinocytes -sebum (oily substance) also covers and protects skin -slightly acidic pH inhibits bacterial growth -competition between species limits colonization by pathogens -constant shedding removes outer epithelial layers - Skin-associated lymphoid tissue (SALT) recognizes microbes that may slip past the physical barrier -Langerhans cells (specialized dendritic cells) can phagocytize microbes. largest and most important organ of the body. Competition between species = our normal microbiota

Slide 15 ch 15 Here is another representation of a white blood cell count - part of a CBC - (complete blood cell count will also contain a count of the RBC). Note that it mentions immature forms of neutrophils called bands. If you look back at the picture of the neutrophil it has a segmented or multi-lobed nucleus. The picture shows very mature neutrophils since there are 6- 7 lobes in one - when a neutrophil is young or immature, the nucleus lacks the lobed structure and it looks more like an elongated nucleus or band. If there are a lot of bands - or a left shift - it says there is an active infection going on somewhere - the mature neutrophils have been recruited to the site and the bone marrow is producing new cells as fast as it can, so fast that it releases the immature forms.

PRIMARY LYMPHOID ORGANS -location where immature lymphoid organs mature ---bone marrow (B cells), thymus (T cells) SECONDARY LYMPHOID ORGANS - stations where lymphocytes can encounter antigens --lymph nodes, spleen, Peyer's patches, GALT, tonsils, adenoids, appendix LYMPHOCYTES - B CELLS produce antibodies - T cells modulate adaptive immunity

RECOGNIZING ALIEN CELLS AND PARTICLES -why don't phagocytes kill host cells in the absence of infection -fail-safe controls built into our immune defenses prevent this from happening -for phagocytosis to proceed, macrophages and neutrophils must first "see" the surface of a particle as being foreign -when a phagocyte surface meets with the surface of another body cell, the phagocyte becomes temporarily paralyzed so it can evaluate whether the other cell is self or non-self So if the phagocyte encounters something that has the CD-47 glycoprotein (a protein that has sugars attached) on the surface, it isn't attacked. But if it lacks CD-47 - it's fair game for phagocytosis.

RECOGNIZING ALIEN CELLS AND PARTICLES -self-recognition occurs when glycoproteins located on the white blood cell membrane bind inhibitory glycoproteins that are present on all host cell membranes. -the inhibitory glycoprotein on human cells is called CD47. Because invading bacteria lack CD47 surface molecules, they can readily be engulfed. -Many bacteria are easily recognized and engulfed by phagocytes, but others possess polysaccharide capsules that are too slippery to grab -innate and adaptive immune systems must work together in a process called opsonization in order to engulf cells enclosed by capsules

-After the specific B-cell receptor binds to the antigen, it undergoes clonal expansion. -Only the B cell that is specific for this antigen increases in number. -Some cells are kept long term in the lymph node and spleen as memory cells. -Other activated B cells become plasma cells. --First antibody that gets made is IgM --After isotype switching, IgG is then produced.

Remember - B cells have IgM and IgD as cell surface receptors for antigen. So when the appropriate antigen binds to these receptors and helps this cell to begin to grow and divide and become activated to produce antibodies. Dependent upon the type of antigen - the B cell will begin to produce IgM and that's all that may be produced. But for most other antigen, the B cell will get a signal from a T cell that we'll discuss later and stop producing IgM and now begin producing IgG or IgA or IgE - depending upon the antigen and location (remember where each isotype is found).

T-Cell Education and Deletion -T-cell education occurs in the thymus: -- positive selection: T cells that weakly recognize self MHC are allowed to live -- negative selection: T cells that bind to self MHC too strongly are destroyed. -Regulatory T cells (Tregs) are T cells that block activation of harmful self-reactive lymphocytes --Tregs prevent autoimmune disease

Remember - lymphocytes are made in the bone marrow, where B cells undergo all the genetic changes to make them ready to deal with one of those 100 Billion antigens. T cells go to the Thymus to be educated - those that are going to interact with all those antigens are kept, but the cells that will react with us will hopefully be destroyed. The same thing happens with B cells in the bone marrow - if those antigen sequences are found in our body - we don't want to keep them. Regulatory T cells play several roles - they downregulate the T cell response as it occurs so that it doesn't get out of control. They are also important in blocking any cells that make it through the thymus to be sure they don't react with us - referred to as "self". In the cases where those cells get through or B cells that produce antibodies against "self" antigens - result in causing Autoimmune Disease. This is bad and something we don't want. We'll talk about it more in the next chapter.

Neutrophils (a type of phagocyte) circulate freely through blood vessels and can squeeze between cells in the walls of a capillary (extravasation) to the site of infection. They then engulf and destroy any pathogens they encounter. But before they can do this - they must be made aware that there is a problem in the nearby tissues and that they are needed.

SIGNALS LEADING TO INFLAMMATION -in addition, macrophages secrete small protein molecules called cytokines -cytokines are made and secreted by cells as a way to communicate with other cells -these signaling peptides bind to specific membrane receptors on target cells and have powerful effects on the functions of those cells. -the cytokines diffuse to the vasculature and stimulate expression of specific receptors (called selectins) on the endothelial cells of capillaries and venules.

During phagocytosis, the intracellular phagosome is formed and subsequent phagosome-lysosome fusion (phagolysosome) permits both oxygen-independent (anaerobic) and oxygen-dependent (aerobic) killing pathways -oxygen-independent mechanisms: --lysozyme, lactoferrin, defensins -oxygen-dependent mechanisms: -- oxygen radicals such as superoxide ion and hydrogen peroxide, hydroxyl radicals, and myeloperoxidase -reactive nitrogen intermediates: -- nitric oxide, nitrite/nitrate ions The oxygen radicals include the superoxide anion (Ó-), Hydrogen peroxide (H2Ó), and hydroxyl radicals (-OH). Myeloperoxidase converts Hydrogen peroxide and chloride ions to Hypochlorous acid (HOCl). Reactive nitrogen intermediates are nitric oxide (NO), which are then further oxidized to nitrate (NǑ-) or nitrite (NÓ-) ions.

SURVIVING PHAGOCYTOSIS -phagocytosis is very effective at killing microbes -some pathogens have evolved ways to prevent being killed by phagocytosis -some bacteria become intracellular pathogens: --coxiella lives within the toxic phagolysosome --Shigella & Listeria escape from the phagosome --Salmonella stays in phagosome but secretes proteins that prevent fusion with the lysosome -- Shigella can also enter a host cell and kill it by triggering apoptosis before phagocytosis occurs Yes, phagocytosis is very efficient at killing microbes, but as we have learned before with antibiotics, bacteria and other organisms can adapt to survive in environments that would normally kill other organisms. In addition to the organisms listed here, it should be obvious that Mycobacterium tuberculosis has also developed a way to survive in the alveolar macrophages designed to kill it.

Primary B Cell Response -an antigen binds to the B-cell receptor on the surface of the B cell. Each B cell is specific for a unique epitope on an antigen. -once the antigen binds, the B cell is activated and begins to proliferate and differentiate into a high-output antibody-secreting plasma cell. The Primary B Cell Response refers to the first time an antigen encounters the B cell that has been primed to interact with it. Once this happens, the B cell is triggered to begin to make more copies of itself (proliferate) and to begin on the way to producing antibodies - differentiate into plasma cell - as well as memory cell. This doesn't happen with just antigen alone, as we will see later.

Secondary Antibody Response -After B cells have been activated, some are kept as memory cells. -When these memory B cells encounter antigen again they quickly trigger a robust secondary antibody response The Secondary Response, sometimes called the Anamnestic Response, is what happens the second and subsequent times an antigen enters the body. As you see in the diagram, the response is far faster and much more antibody is produced. IgM is always the first one secreted - even in the secondary response, because not all the B cells were triggered the first time.

Slide 21 ch 16 Here we have four different B cells - each one is pre-programmed to interact with a different antigen (epitope). When the red antigen comes along - it only binds to the appropriate B cell (4C) and triggers it to begin the antibody process.

Secondary antibody response is the basis for immunization -memory cells are created upon exposure to antigen: --Exposure through natural infection process --Exposure through vaccination with a harmless antigen This response can occur naturally - naturally through a disease process or artificially though vaccination.

Culturing Viruses Viral culture is complicated because of the need for a host cell. Any viral culture system will also include the culture of the host cells. Bacteriophages may be produced in BATCH CULTURE, a culture in an enclosed vessel of liquid medium. Culture fluid is sampled over time and assayed for phage particles. The growth pattern usually takes the form of a ONE-STEP GROWTH CURVE Actually, rarely is the fluid sampled over time with a well-known phage, since we know how long it takes the virus to replicate. Additionally, if it is a lytic phage that destroys the bacteria as it grows, the culture fluid will go from cloudy to clear once all the bacteria have been lysed by the phage - easy to see. We can also grow them on a solid phase plate and see holes develop in the bacterial lawn (solid growth of bacteria on the surface) as they bacteria are destroyed - the holes are called plaques.

Slide 30 To observe one cycle of phage reproduction, phages must be added to host cells at a multiplicity of infection (MOI or ratio of phage to cells) such that every host cell is infected. Phage particles immediately adhere to surface receptors of the host cell and inject their DNA. As a result, phages are virtually undetectable in the growth medium for a short period of time, called the eclipse period. As cells begin to lyse and liberate their progeny, the culture enters the rise period, when phage particles begin appearing in the growth medium. The burst size (the number of phages produced per infected cell) can then be calculated. After initial infection of a liquid culture of host cells, the titer of virus drops to nearly zero as all virions attach to the host. During the eclipse period, progeny phages are being assembled within the cell. As cells lyse (the rise period), phages are released until they reach the final plateau. The infectious cycle is typically complete within less than an hour. Notice that this curve looks a lot like a bacterial growth curve - only it happens MUCH faster.

CD stands for Cell Differentiation - there are numerous glycoproteins and proteins that have been discovered over the years that help us to identify specific cells within the body. CD-47 is a widespread glycoprotein since all cells have it. We will see in Chapter 16 that there are other CD cell marker proteins that we will use to specifically identify cells of the immune system. We have already discussed opsonization - where something will attach to a foreign invader and make it easier for the macrophage to engulf it. There are things on the innate side - the previously mentioned complement proteins or on the adaptive side - antibody molecules and in the best of situations, the two can work together.

Streptococcus pneumoniae surrounded by a capsule (India ink preparation). The slippery nature of the polysaccharide capsule makes phagocytosis more difficult. Think of the bacterium as having a slippery, sugar coating - I like to think of when you have a slippery watermelon seed on the countertop - you keep trying to grab it and it scoots away from you. Opsonization is a process that facilitates phagocytosis. Here, macrophage receptors bind to the Fc region of antibodies binding to bacteria. The important thing to remember here is that this won't occur immediately the first time this organism enters the body, the antibodies won't have been made yet. So this had to have happened later during the first infection or in later infections. Early in the first infection, those complement proteins I keep mentioning would do the job.

Papillomaviruses are dsDNA and do NOT have an envelope. Here you see the replication cycle of these viruses. In the affected tissues, the virus must gain access to the actively dividing cells of the basal layer, usually through a tiny wound in the tissue. Virions are endocytosed by the basal cells, but replication is inhibited until the basal cells start to differentiate into keratinocytes. As the epithelial layers slough off, progeny virions are shed. In other infected cells, however, the HPV virions become latent, persisting for months or years. The latent viral genomes may induce the host cells to form abnormal growths, such as warts or cancers.

Structurally, the papilloma- viruses are small icosahedral viruses. -The genome consists of a circular, double-stranded DNA. -The genome size is relatively small, at fewer than 8,000 base pairs encoding only 8 gene products. -The genes are expressed in overlapping reading frames to maximize the efficiency of the information content HPV virion, diameter 55 nm. Genome of HPV-16. The DNA genome is circular; the "starting" base position (base 1) is collocated with base 7906. The genome encodes 8 gene products, some of which overlap as shown.

Here is the table I mentioned earlier with some of the important cytokines that play a role in the immune response - as you can see, they can play a role on both the innate as well as the adaptive sides of the system. Some of them are very specific and have one exact, special task (IL-2, IL-3, IL-17), whereas others are very general in the action(IL-1, IL-8, TNF). TNF or tumor necrosis factor plays a variety of roles in the immune system. However, like other things a little is good, too much is bad. In diseases where chronic inflammation is seen, TNF is often the modulator of the inflammation. Most of the drugs we see advertised on TV to fight things like Rheumatoid arthritis, Psoriasis, Crohn's disease are antibodies designed to neutralize TNF.

Superantigens- bind outside of the MHC binding site and cause a massive "cytokine storm" to be released. -Is not an antigen-specific response, so many different T cells can be activated Microbial Evasion of Adaptive Immunity -examples of how pathogens escape immune action: -some viruses down-regulate MHC I or utilize a decoy MHC receptor -Many pathogens alter their surface proteins through antigenic variation -some pathogens cause cell death of T cells -Some block pro-inflammatory cytokines

B-Cell Receptors -membrane-bound antibody that includes Ig-alpha and Ig-beta components -each B cell can have up to 50000 receptors -when a large antigen with repeating epitopes bind to the B-cell receptor, the receptors cluster together. This is called capping. So antigens that have repeating epitopes are ones like polysaccharides found in the capsules of some bacteria or other similar compounds.

T-Cell-Dependent vs. Independent Antibody production -Two ways to activate a B cell to make antibody: 1) capping the receptors on a B-cell with a large repeating epitope. 2) single epitopes cannot cause capping; therefore the helper T cells bind and activate B cells. The vast majority of antibodies are produced via the T-cell dependent pathway. Remember - most antigens are small pieces of protein with varied amino acid sequences - so they do not fit the definition of a large repeating epitope.

FILAMENTOUS- Helical symmentry; a helical tube around the genome, which is wound helically within the tube. The length may extend to 50 times its width, generating a flexible filament. Ex: tobacco mosaic virus, Ebola virus. It was Rosalind Franklin who discovered the shape of TMV in research she did after she did her DNA research.

TAILED BACTERIOPHAGES- in a tailed phage, the icosahedral protein package, called the "head" is attached to an elaborate delivery device. The head contains the nucleic acid that is "injected"into the host cell envelope and DNA is released into the host cytoplasm EX: bacteriophage T4 Phage T4 particle with protein capsid containing a packaged double-stranded DNA genome. The head is attached to a neck surrounded by a tail sheath, with tail fibers that attach to the surface of the host cell. After attachment, the sheath contracts and the core penetrates the cell surface, injecting the phage's genome. If you haven't picked up on it by now, one family of bacteriophages that infect E. coli are the T-even phages. There are also T-odd bacteriophage as well.

Activated Helper T Cell Meets B Cell -Similar to T cells, B cells also need two signals to become activated: 1) antigen cross-links the BCRs on the membrane 2) during the early phase of primary response, the second signal is binding of complement factor C3 bound to pathogen 3) During the late phase of primary response, the second signal is binding to TH cell. This causes CD40 to bind to CD40 ligand on the surface of the TH cell. -Once activated by TH cell, the B cell undergoes isotype switching from IgM to IgG or IgA or IgE

TH1 cells Activate Cytotoxic T cells For cytotoxic T cells (Tc) to be activated: 1) Tc cells must bind to antigen presented on MHC 1; TCR is specific for antigen 2) CD8 on the Tc cell binds to self MHC 1 on target cell 3) IL-2, produced by TH1 cells, must bind to Tc Cell. We have finished with the humoral response and the interaction of TH2 to complete the process. Now we can look at the Cytotoxic T cells and what happens with them. These cells don't use the same APCs that Helper T cells do - any cell that is infected can display antigen along with the MHC I protein on it's surface to begin the process. So as I said before - here we will have MHC I + antigen on the infected cell - interacting with the T cell receptor + CD8 on the TC cell. Here the second signal is actually the cytokine, Interleukin 2 as well as Interferon gamma.

Innate means something you are born with - so somewhat in utero, but definitely, the second you are born these protective mechanisms are in place. One of the key things about the innate part of the system is that it will always be the same - no matter what it is reacting to or how many times it has seen the same invader or foreign substance. Two other terms are used interchangeably with adaptive immunity and I think they are better terms - adaptive immunity = acquired immunity or specific immunity. This side of your immune system must first encounter an invader or foreign substance before it will acquire the tools needed to destroy or inactivate the invader. With each encounter with the same, specific invader will cause an adaptation of the response so that it is better = stronger and faster than the previous response so it may take out the invader before you even know it was there.

THE TWO FORMS OF IMMUNITY: INNATE AND ADAPTIVE -innate and adaptive immune mechanisms intertwine in ways that support and enhance each other's effectiveness. -adaptive immunity reacts to very specific structures called antigens. -an ANTIGENS is any chemical, compound, or structure foreign to the body that will elicit an adaptive immune response (such as production of ANTIBODIES). -adaptive immune mechanisms can recognize billions of different antigenic structures and launch a directed attack against each one. -antigens are foreign to the body, the part that the body reacts to is actually a very small piece of the bacteria, virus, or chemical that may enter the body. However, it is sufficient to trigger a reaction that destroys the entire invader

HIV REPLICATION (REPLICATIVE) CYCLE The first cells infected by HIV are T lymphocytes (T cells) that possess cell surface proteins called CD4 and CCR5. You'll learn in the a couple of chapters that these are called T helper cells because the help other cells in the immune system to do their jobs better. The double-stranded DNA copy of the HIV genome enters the nucleus through a nuclear pore, where it integrates as a provirus at a random position in a host chromosome. Integration is a critical step in that it ensures permanent infection of the host. The entire length of the integrated HIV genome is transcribed to RNA by the host RNA polymerase and some RNA copies exit the nucleus to serve as mRNA for translation into proteins. Proteins are synthesized in alternative versions such as Gag-Pol. The formation of alternative versions involves cleavage by a viral protease. The viral protease breaks up the initial proteins translated from gag and pol into smaller, active proteins. Some full-length RNA transcripts exit the nucleus to be packaged as genomes for progeny virions. Meanwhile, Env (envelope) proteins are made within the endoplasmic reticulum (ER) and are exported to the cell membrane. As the HIV virion binds to CD4 and CCR5 receptors, its envelope fuses with the cell membrane of the T cell. Unlike influenza virus, the HIV core is released directly into the cytoplasm, without endocytosis. The 2 RNA genome copies are then reverse transcribed by reverse transcriptase enzyme to eventually form double-stranded DNA. At the membrane, Env proteins plug into the core particle as it forms from the RNA dimers, plus Gag-Pol peptides. The virions then bud out of the host cell, a process that requires cleavage of a host protein called TETHERIN. An alternative to budding is cell fusion, mediated by the binding of Env in the membrane to CD4 receptors on a neighboring cell. HIV particles can enter the new cell through their fused cytoplasm. The fusion of the cells can form a giant multinucleate cell called a SYNCYTIUM

THE TWO FORMS OF IMMUNITY: INNATE AND ADAPTIVE INNATE IMMUNITY: - non-adaptive, immediate response but not very specific. -buys precious time for the more specific second line of defense to engage -operates continuously from the time of infection through the INCUBATION PERIOD and until the infection ends ADAPTIVE IMMUNITY: -Takes time to develop but is highly specific to its target -becomes apparent toward the end of the prodromal phase and is maintained long after the infection clears

In this analogy, the castle plays the role of our body under attack. The castle walls form a protective barrier, like skin. The barrels of boiling oil used to douse any who attempt to climb the castle walls can be compared to chemical defenses of innate immunity. The alligators swimming in the moat represent white blood cells, such as macrophages or neutrophils, that indiscriminately drown or attack anyone who tries to enter. The archers represent our adaptive immune system (B cells and plasma cells), which must first mount the towers, see the invaders, and then specifically target them with their arrows (antibodies). Swordsmen battling invaders inside the castle can be compared to cytotoxic T cells of the adaptive immune system (discussed in the next chapter), which specifically target infected host cells. The description of the immune system has often been compared to a battle or war. So this analogy demonstrates those parts of the immune system that are defensive and those that are offensive. Protect against the invader, but if they should get through - attack and destroy. And be ready for them the next time!

THE WBC'S OF INNATE IMMUNITY: -polymorphonuclear leukocytes (PMNs) -monocytes -macrophages -dendritic cells -mast cells. This micrograph illustrates the relative sizes and shapes of these cell types. This enhanced electron micrograph - shows red blood cells and some white blood cell - we can't say which white blood cell it might be - it may be a PMN or it might be the white blood cell of the adaptive immune system - a lymphocyte. It probably isn't a monocyte, since they are characteristically 2 - 3x larger than a RBC.

Internal structure of the HIV-1 virion, color coded to match the genome in the genome sequence, the staggered levels indicate 3 different reading frames. Each virion contains two copies of the RNA genome plus multiple copies of reverse transcriptase (RT) and protease enclosed within a conical capsid (capsid subunits plus subunits of a host protein, cyclophilin A). The capsid is surrounded by matrix subunits, which reinforces the host-derived phospholipid membrane, pegged by spike proteins (SU, TM).

The genome encodes the virion proteins, as well as six accessory proteins that are expressed within the infected host cell and regulate the replicative cycle.

-External pyrogens cause fever by inducing the release of internal cytokine pyrogens, stimulating the release of phospholipase Á2, an enzyme required to make prostaglandins. -prostaglandins then change the responsiveness of neurons in the hypothalamus, making the body think it is cold. -Blood vessels are constricted and heat builds up causing the fever. Shivering and chills also generate heat.

The slides did a great job at explaining what happens how a fever is generated - but they kind of left off the most important part! We started off by saying fever is good - well, to a point. The reason we have fevers is to raise not only our temperature, but also the temperature the bacteria or virus must grow at to cause an infection. They have a much narrower temperature that they can function at than we can. So if we raise our temperature, just a little bit, it can be enough to slow down the growth or even kill the bacteria or virus and stop or at least slow down the infection. Of course, we all know that too high of a temperature is dangerous to us as well. But - if you can tolerate it and it doesn't get too high - don't take anything to bring the fever down, let it work the way it was designed. [Of course, be especially careful with small children.]

The number of each type of blood cell is highly variable in each individual, so saying neutrophils make up nearly all WBCs isn't exactly correct. They generally do make up the majority of the WBC - nearly all - no. As you can see in the levels below - someone could actually have about the same % of neutrophils as they have lymphocytes. Note - mast cells and macrophages are found in the tissues - so they won't show up in peripheral blood counts. Reference ranges for differential white blood cell count in normal adults is as follows: Neutrophils - 2.0-7.0×10^9/ l (40-80%) Lymphocytes - 1.0-3.0×10^9/ l (20-40%) Monocytes - 0.2-1.0×10^9/ l (2-10%) Eosinophils - 0.02-0.5×10^9/ l (1-6%) Basophils - 0.02-0.1×10^9/ l (< 1-2%)

There are several types of cells which can undergo phagocytosis. Because of their large number - neutrophils are the primary phagocytic cell in the blood. However, monocytes which are the precursors of macrophages can also phagocytize invading bacteria. When the monocytes leave the bloodstream and migrate into the tissues, we then refer to them as macrophages (macro = big, phage = eat, so macrophages are big eaters!) or dendritic cells. This is the process as we know it to occur in macrophages. If as described in #1 = antibody or complement aids in the binding of the macrophage to bacteria, it is called opsonization or facilitated phagocytosis. Phagocytosis is primarily meant to destroy and invading microorganism - but we will see that when macrophages or dendritic cells (another type of phagocyte in the tissues) phagocytize and breakdown an organism, they will place a small amount of it on their membrane which will serve to start the process of triggering T cells which are part of the adaptive immune system to begin doing their job. So - these cells are important to both arms of the immune response.

SIGNALS LEADING TO INFLAMMATION -the process begins with the infection itself: microorganisms grow and produce compounds that damage host cells. -resident macrophages that wander into the infected area engulf the organisms and release inflammatory mediators (chemoattractants) that "call" for more help. -these mediators include: vasoactive factors such as leukotrienes, platelet-activating factor, and prostaglandins, which act on blood vessels of the microcirculation, increasing blood volume and capillary permeability to help deliver white blood cells to the area

There generally first needs to be some tissue damage or irritation before inflammation begins, otherwise we would all be constantly inflamed just due to the presence of our microbiota. So if the damage/irritation occurs and bacteria are also present - inflammation begins. If it is in the tissues it is a combination of resident macrophages and mast cells that release the mediators of inflammation, such as histamine which causes the blood vessels to dilate - as well as other vasoactive factors such as the leukotrienes and prostaglandins. These chemicals also change the membrane of the nearby vessel wall cells and has them display molecules on their surface that attracts and attaches neutrophils as they go by the damaged/infected area.

INFLUENZA VIRUS REPLICATION 1. An influenza virion attaches to a cell when its HA envelope protein binds to a host cell receptor, a glycoprotein. 2. Some of the mRNA molecules encode envelope proteins, which are made by ribosomes attached to the endoplasmic reticulum (ER). 3. The ER will transport the envelope proteins to the Golgi and ultimately to the cell membrane, where they will coat progeny virions. 4.Other proteins needed to package the viral RNA must return to the nucleus. 5. in the nucleus, the (+) RNA strands now serve as templates for RNA-dependent RNA polymerases to make complementary (-) RNA for the progeny. 6. After the influenza virion undergoes endocytosis, the endocytic vesicle fuses with a lysosome. 7. The low pH of the lysosome contents causes hydrogen ions to leak through the virion's ion channel. 8. The lowered pH causes the virion to disassemble and fuse with the endocytic membrane. 9. The (-) viral genome segments become coated with proteins. 10. The protein coated RNA segments exit the nucleus and are transported to the cell membrane for packaging into capsids. 11. The capsids acquire envelope membrane from their host, incorporating viral envelope proteins. 12. The mature virions then bud out in a massive release of virions that destroys the host cell. 13. The final budding step requires the action of neuraminidase (NA) that cleaves the cell surface sugar molecules that bind the virion to the cell surface.

This diagram shows what happens in someone who is infected with HIV, and isn't treated with the drugs we have today, and this is the progression of the infection and disease. HIV is the causative agent of acquired immunodeficiency syndrome (AIDS) and is a member of the lentivirus family. A lentivirus is a retrovirus that causes infections that progress slowly over many years. Retroviruses are RNA viruses, but have reverse transcriptase so they quickly make DNA that then is integrated into the cells genome. Approximately 33 million people globally are estimated to be living with HIV, and 3 million people die of AIDS annually. Worldwide, HIV infects 1 in every 100 adults, equally among women and men. After the initial infection, a slow steady loss of T cells occurs (clinical latency) until a level is reached where the immune system fails, in part because B cells require T cells to produce antibodies. At this critical level, without treatment, the patient begins to experience the constitutional symptoms of AIDS, such as fever and swollen lymph nodes. When the T cell level falls below a certain level, or certain symptoms develop, it goes from being an HIV infection to full-blown AIDS. Opportunistic infections soon follow, as the immune system can no longer respond. An initial rise in virus is fought off by the immune system, while the T cell count declines and rebounds. Over years, the virus titer remains low while constitutional symptoms of AIDS appear, followed by opportunistic infections and death.

T-Cell Receptor Structure and Function: -the T-cell receptor (TCR) binds antigen on the surface of T cells. - TCR binds peptides only if bound by MHC. - The TCR is associated with the CD3 complex that helps it signal

This is most of the receptor on the surface of the T cell - it is what will interact with the appropriate MHC molecule that holds the piece of antigen for presentation. The entire complex will be stabilized with the appropriate CD molecule. Then one other signal needs to be given. Helper T cell = APC (MHC II + Antigen) + Helper T cell (TCR + CD3 + CD4) + CD28 molecule Cytotoxic T cell = infected cell (MHC I + Antigen) + Cytotoxic T cell (TCR + CD3 + CD8) + cytokines from Helper T cell

PATHWAYS OF COMPLEMENT ACTIVATION -There are 3 complement activation pathways: --Classical - depends on antibody/adaptive immune system --Alternative - does not require antibody or adaptive immunity --Lectin - requires the synthesis of mannose-binding lectin in response to cytokines released from macrophage -the major goal of the complement cascade is to insert pores into microbial membranes to destroy membrane integrity and kill the cell. -The Classical Pathway punches holes in the bacterial membranes which results in the contents of the cell leaking out and the cell dying. During the process, some of the complement proteins also helps to recruit phagocytes and aid with opsonization.

Three pathways can activate complement. The three pathways begin differently, but converge at C3. The C3b fragment (called C5 convertase) binds to bacterial surfaces (such as LPS) and cleaves C5. The C5b fragment enters the membrane and directs the assembly of the C6, C7, C8, and C9 pore, which kills the bacterial cell. The cascade from C3b to pore formation is common to all pathways. The classical pathway starts with antibody bound to a bacterial cell. The Fc tail of the antibody binds and activates the protease of C1. C1 mediates the cleavage of C4 and indirectly, C2. Parts of C2 and C4 combine to form a C3 convertase, which speeds the cleavage of C3. In the lectin pathway, lectin, made by the liver, circulates in the blood and binds mannan (polymers of mannose) on bacterial surfaces. Lectin mediates cleavage of C4 and C2. As a result C3 convertase forms and the cascade continues as before. C3a and C5a can act as chemoattractants and anaphylatoxins (this means they can trigger mast cells to degranulate and begin an inflammatory process), whereas C3b can function as an opsonin as well as a C5 convertase.

There are important differences between the adaptive or acquired immune system and the innate or non-specific system. It only develops after exposure to a SPECIFIC antigen (foreign substance, organism, or virus - or a part thereof.) It has memory - it knows that it has interacted with that SPECIFIC antigen and saves that reaction. The next time it sees that SPECIFIC antigen, it responds faster and with greater intensity than it did the first time.

Two components of Adaptive immunity: HUMORAL - ANTIBODIES -- proteins that circulate in the bloodstream and recognize foreign structures called antigens - PLASMA CELLS -- B cells that have been stimulated by antigen to produce antibodies CELL-MEDIATED - T cells -- T cells recognize antigen and can stimulate B cells or destroy infected host cells

Slide 33 ch 16 This slide not only shows the activation of a Helper TH0 cell to make a TH2 cell to help a B cell be fully activated. Note that two B cells are being activated - the one in the lymph node will get T cell help and will therefore undergo Isotype Switch from IgM to one of the others. Notice how the TH2 cell and B cell will interact just like the T cell did with the original APC - MHC II + antigen and TCR + CD4, with the second signal being the CD40 and CD40 ligand. While the one in the spleen has a different antigen, a T-independent one and so no T cell help is needed or occurs. In all these direct interactions, there are also cytokines that are being produced by these cells that help to modulate the response. SEE TABLE 16-4 on slide 40.

Two molecular signals are required for TH0 cell activation: 1)TH0 binds to APC that is presenting antigen on MHC 2 ---only the specific TH0 with the correct TCR will bind to the antigen being presented. --- CD4 receptor found only on TH0 cells must also bind to the self MHC 2 2) CD28 molecule on the T-Cell surface must also bind to a B7 protein on the APC cell surface. As I said earlier - the CD 28 which is the second signal here binds to the B7 protein on the APC.

INTERFERONS -Type 1 interferons bind to specific receptors on uninfected host cells and induce the synthesis of 2 classes of proteins: dsRNA-activated endoribonucleases and protein kinases (PKRs) that phosphorylate and inactivate elF2, which is required to translate viral RNA. Type 2 interferon functions by activating various white blood cells (macrophages, natural killer cells, T cells) to increase the number of major histocompatibility complex (MHC) antigens on their surfaces. MHC proteins are important for antigen presentation

Type I Interferons are produced by the cell initially infected with a virus that forms double-stranded RNA at some point in its replication cycle. The first cell will produce the Interferon and send it out to the neighboring cells to trigger them to produce the two enzymes that will inhibit the virus from growing in those cells. So while the initial cell will die, it will protect the neighboring cells from the infection.

Generating Antibody Diversity -We can synthesize 10^11 different antibodies. --which means 10^11 different B cells! -How does this happen? --Rearrangement of antibody genes --Random introduction of mutations --Generation of different codons during rearrangements Utilize the inSight section to discuss antibody rearrangement further - CAREFULLY READ THE inSight SECTION - PAGES 504 - 505. There are some difficult and almost unbelievable concepts when it comes to Antibody Diversity. The genetics are incredible - we all have the ability to make 1011 different antibody molecules - that's 100 BILLION!!! Basically, it's every possible combination or antigen that has every has been or ever will be. We are already set to fight against it. HINT - when a new pathogen show up, antibodies are always made against it. They aren't always made in time - but they are always made.

Types of T cells: - differentiated by CD4 or CD8 receptors -Each type has a distinct function Onto Cell-Mediated Immunity - there are a variety of T cells and each one has a different function. (B cells were only one type). There are basically 2 major types - Helper T cells and Cytotoxic T cells. We can tell the difference between these cells based on a cell membrane protein - if a cell has CD4, it's a Helper T cell and if it has CD8, it's a Cytotoxic T cell. The Helper T cells, will further differentiate into more specific cells dependent again upon the antigen, what it helps and the types of cytokines it produces. These cells are controlled by two different things antigen along with one of the Major Histocompatibility Complex Proteins we mentioned earlier and the CD molecules which are part of the T cell receptor complex. A Helper T cell that helps Cytotoxic T cells to be fully activated are called TH1, while those that play a role in the antibody class switch of a B cell are TH2. There are also Helper T cells that aid in the inflammatory process when needed called TH17 (I don't know what happened to H3-H16), they help to activate Macrophages in the tissues to destroy antigens - as with tuberculosis. And finally the Treg cells - which stands for T regulatory cells. We used to call them T suppressor cells - because that's what they do - they work to suppress the immune response once it is no longer needed - the invader has been destroyed. Cytotoxic T cells destroy cells that are infected with intracellular bacteria or viruses. They can also act similarly to Natural Killer Cells to kill cancer cells.

This is where some of the cytokines come into play. As the macrophages and mast cells release the cytokines they diffuse into the tissue and cells of the vessels and induce them to now display the receptors (selectins) on their surface that will grab onto passing neutrophils to say - Help! Come here we need you!!! Other chemicals are also released that help with other parts of the process, such as bradykinin which helps to loosen the tight junctions between the vessel walls to aid in the neutrophil being able to cross from the vessel into the tissue.

VASOACTIVE FACTORS, CYTOKINES, AND EXTRAVASATION PROCESS -the movement of neutrophils through capillary vascular walls is called extravasation -the process is initiated by vasoactive factors released by macrophages; vascular permeability is increased and vasodilation (widening of the blood vessels) is stimulated. -vasodilation slows blood flow and as a result, increases blood volume in the affected area. -the more permeable vessel allows the escape of plasma into the tissues. -both events cause localized swelling, redness, and heat. -vasoactive factors also stimulate local nerve endings, causing pain

Other viral genomes can be large, approaching the size of cellular genomes. Double-stranded DNA viral genomes tend to be especially large, encoding numerous enzymes and regulatory proteins similar to those in cells. Herpes Simplex Virus-1 (HSV-1), a cause of cold sores and genital herpes, spans 152 kilobases, encoding more than 70 gene products. These products include capsid and envelope proteins, DNA replication proteins, and accessory proteins that manage viral replication. B. The double-stranded DNA genome of herpes virus (HSV) spans 152,000 base pairs, encoding more than 70 gene products. The type of products encoded is shown by color. Regulation (green), capsid assembly (yellow), envelope proteins (orange), and DNA replication (brown) IRL and IRS are inverted repeats.

VIRAL DIVERSITY AND EVOLUTION -Viruses evolve through genome change and natural selection. Their small genome size and number of parts enable viruses to mutate 10-fold or 100-fold faster than their host cells. -rapid mutation and evolution of a virus leads to ANTIGENIC DRIFT- a population of viruses whose mutant proteins are no longer recognized by host antibodies. -Antigenetic drift generates new strains of viruses that can cause serious disease. Ex: Influenza virus continually generates new strains requiring repeated immunizations As you learned before, it only can take a single base pair change to change the protein. That small change can be enough to change the protein so it still works for the virus, but as we'll learn in the chapters to come, now the antibody molecule that was developed to fight the old virus will no longer bind and fails to neutralize the virus. As it says, Influenza is particularly good at this and the main reason why we need yearly flu shots. Influenza also under goes something called ANTIGENIC SHIFT which we'll discuss later.

VIRAL STRUCTURE -Viral genomes can be made up of either DNA or RNA, and can be either double-stranded (ds) or single-stranded (ss) -a capsid (protein coat) encloses the genetic material. -In some cases, the capsid is further encased by an envelope, derived from the host cell membrane embedded with viral proteins.

VIRUSES REPLICATE IN HOST CELLS -bacteriophages such as phage T2, are viruses that infect bacteria. -Phages insert their genome into the host cell, leaving an empty capsid outside. -within the cytoplasm, the phage genome directs the replication of progeny virions. - the virions are released when the host cells lyses Bacteriophage T2 particles form a semicrystalline array within an E. coli cell.

AMORPHOUS VIRUSES- Some viruses have no symmetrical form. The nucleic acids from these amorphous viruses are contained by a flexible "core wall" that also encloses a number of enzymes and accessory proteins, similar to a cell's cytoplasm. The core is enclosed loosely by a viral envelope studded with spike proteins. EX: vaccinia virus, smallpox viruses. in most texts, this is referred to as a complex capsid structure

Viral genomes can be surprisingly small and they evolve rapidly, enabling them to evade host defenses and to "jump" into new host species. The genome of an RNA virus can be as small as 3 genes. Avian Leukosis Virus (ALV), is a well-studied retrovirus that causes lymphoma in chickens. The ALV genome has 3 protein encoding genes: gag, pol, and env. Each gene can express 2 or 3 different products. Remember - since viruses don't have to carry all the genes to replicate themselves, they only need genes to take over the cell they infect and specific viral parts and pieces. Single-stranded RNA genome of avian leucosis virus, a retrovirus. Three genes (gag, pol, and env) encode polypeptides that are eventually cleaved to form a total of nine functional products. LTR= long terminal repeat; blue section indicates noncoding RNA. In this book, drawings of single-stranded sequences have flat edges whereas drawings of double-stranded, helical DNA are cylindrical.

Transmission: Measles = droplets of respiratory fluids, highly efficient. Human Immunodeficiency Virus (HIV) = direct contact (blood or sexual), relatively inefficient. Host Range: HIV infects only humans, while West Nile Virus (WNV) can infect many species (including humans, birds, mosquitoes). Tissue tropism: Ebola virus has a broad tropism (infects many different tissues), while rabies virus has a narrow tropism (only infects nervous tissue)

Viruses use a relatively small number of virus-encoded proteins to commandeer the metabolism of their hosts. Consequences for medical therapy: -ANTIVIRAL AGENTS ARE HARD TO DISCOVER (relatively few targets for drug design.) -ANTIVIRAL AGENTS HAVE SEVERAL SIDE EFFECTS (Disruption of viruses usually harms the host as well. ) -VIRAL GENOMES MUTATE QUICKLY, EVEN FASTER THAN BACTERIA (No one antiviral agent will work for long.)

Toll-like receptors (TLRs) bind extracellular microbe-associated molecular patterns (MAMPs) and transmit a signal through a cascade of other proteins to the nucleus. The signal cascade activates transcription of specific cytokine genes (NOTE: TLR3, TLR7, and TLR9, not shown in this figure, are located in endosomal membranes). Cytoplasmic NOD-like receptors (NLRs) bind MAMPs generated primarily by intracellular pathogens and trigger a signal cascade different from that used by TLRs.

WHAT IS FEVER AND WHY IS IT A GOOD THING -to understand fever, we must first understand how the body controls temperature (thermoregulation) -heat is produced as a consequence of metabolic reactions. The liver and muscles are major generators of heat and will warm blood that passes through them -in a healthy person, body temperature is kept constant within a very small range (36-38 C or 97-100F) Really - fever is good. We need to maintain our basic body temperature so that all of our enzymes can function at their optimal temperature = where they work the best.

Two paths for Antigen Processing and Presentation 1) PATHOGENS THAT GET ENGULFED are digested within endocytic compartments into smaller pieces. After digestion, the antigens are presented on MHC 2 2) INTRACELLULAR PATHOGENS that are found in cytoplasm of the cell, degrade and are presented on MHC 1

Whether a Helper T cell gets activated or a Cytotoxic T cell gets activated, not only depends upon the MHC, but also how the pathogen got into the cells. So it makes sense that the dendritic cells and macrophages are antigen presenting cells since they are phagocytosing extracellular pathogens. The B cells take up the antigens once they have attached to the antibody molecules, so they will be able to call for help. The cells that are infected have the antigens are inside the cells, antibodies can't get to them - so the cell needs to meet with a Cytotoxic T cell and be destroyed. BE SURE TO LOOK AT FIGURE 16.16 on PAGE 508 to see how the process occurs.

Slide 31 A suspension of bacteria in rich broth is inoculated with a low proportion of phage particles (multiplicity of infection is approximately 0.1). This means that only a few of the bacteria become infected immediately, while the rest continue to grow. Each plaque arises from a single infected bacterium that bursts, its phage particles diffusing to infect neighboring cells. Here is the process I described earlier - we can also use this procedure to count the number of phage that are produced in a liquid culture.

slide 32 Plates with individual colonies allows the isolation of a population descended from a common progenitor. In viral plate culture, viruses from a single progenitor lyse their host cells, forming a clear area called a plaque. To perform a plaque assay, phages and bacteria are mixed, plated in soft agar, and poured over an agar plate. Individual plaques can be counted and used to calculate the concentration of phage particles, or plaque-forming units (PFUs). B. Phage lambda plaques on a lawn of Escherichia coli K-12.

VIRAL CLASSIFICATION: THE BALTIMORE MODEL -the International Committee on Taxonomy of Viruses (ICTV) devised a classification scheme that includes such factors as capsid form, envelope, host range, and TYPE OF GENOME (most important!) -viruses of the same genome (such as dsDNA) are more likely to share ancestry with each other than with viruses of a different type of genome (such as RNA) This classification model was devised by David Baltimore, who, with Renato Dulbecco and Howard Temin, was awarded the Nobel Prize in Physiology or Medicine in 1975 for discovering how tumor viruses cause cancer. Classifying the different viruses is tough because of all the variables in virus structure. Just looking at the Genome is far more complex than Gram + vs. Gram - in bacteria.

the Baltimore model distinguishes classes of viruses based on the following criteria: -GENOME COMPOSITION (DNA or RNA) -whether it is SINGLE OR DOUBLE STRANDED -if single-stranded, whether the strand ENCODES PROTEIN OR REQUIRES SYNTHESIS OF A COMPLEMENT THAT ENCODES PROTEINS -There are 7 BALTIMORE GROUPS of viruses based on genome type and mRNA generation. -Within each genome type, very different viruses have evolved in hosts as different as humans and bacteria.