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Immunology

Purpose of Course  showclose

Immunology is the study of our immune system, a highly sophisticated system that defends us against all disease-causing invaders by identifying and neutralizing such threats. Even though we might get sick every now and then, the immune system does an incredible job of warding off infection given how many infectious agents (thousands!) we come into contact with every day. This becomes most apparent when a healthy individual compares himself or herself to an individual with little or no immune response who cannot survive in a normal environment and must rely on specialized rooms much cleaner than even a surgery room. Before the discovery of immunity, we used to associate sickness and disease with various superstitions and beliefs. Only with the discovery of bacteria, viruses, and our own cells did scientists slowly piece together the modern theory of our immune system. Our overall system can be broken down into two sub-systems, each with its own unique cells, molecules, and functions. Our cells are in turn capable of recognizing billions of different patterns of molecules, all of them alien to ourselves, which helps us identify foreign invaders. It is important to recognize that, as with any system in our body, when the immune system malfunctions, disease can result. In this course we will take a look at what happens when an inappropriate immune response takes place.

Course Requirements  showclose

In order to take this course you must:

√    Have access to a computer.

√    Have continuous broadband Internet access.

√    Have the ability/permission to install plug-ins or software (e.g., Adobe Reader or Flash).

√    Have the ability to download and save files and documents to a computer.

√    Have the ability to open Microsoft files and documents (.doc, .ppt,.xls, etc.).

√    Be competent in the English language.

√    Have read the Saylor Student Handbook.

Unit Outline show close


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  • Unit 1: An Introduction to the Immune System  

    In this first unit, we will cover the core concepts of immunology and identify the components of the innate (non-specific) and adaptive (specific) immune systems.

    Both the innate and the adaptive immune systems help distinguish between what is “self” and what is “non-self” and subsequently protect against non-self.  Although this is an easy statement to say and read, stop for a moment and think of the complexity of this feat.  It takes so many different molecules to make you, and so many other molecules are on potential pathogens, how does the immune system know the difference, and react quickly enough to protect you? That question will be answered throughout this course. 

    The innate immune system is available quickly and thus it is the first line of defense.  However, the innate immune system recognizes general patterns in pathogens so it is not specific for the individual pathogen. In addition, the innate immune response has no memory so there is no improvement in the innate immune response with repeat infection with the same pathogen.  The adaptive immune response takes time to respond, it is specific to the pathogen, it has memory so the subsequent response to the same pathogen occurs more quickly and is greater in magnitude.   In this unit, you will be introduced to the cells, proteins, structures and fluids involved in the innate and adaptive immune responses.

     

     

    Unit 1 Time Advisory   show close
    Unit 1 Learning Outcomes   show close
  • 1.1 Basic Components of Immune System  
    • Reading: National Institutes of Health: Professor Charles Janeway et al.’s Immunobiology: “The Components of the Immune System”

      Link: National Institutes of Health: Professor Charles Janeway et al.’s Immunobiology: “The Components of the Immune System” (HTML)
       
      Instructions: Read this page in its entirety, along with all associated figures.  It will cover the material in 1.1.
       
      This resource will take approximately 30 minutes to complete.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      Note: The cells of the immune system are broadly classified as being of the innate or the adaptive immune systems, but as you learn about these cells you will see that a complex system of interactions occur so that the cells of the innate immune system interact with the cells of the adaptive immune response to form the system that helps protect you from infection. The cells of the immune system, wheter of the innate or the adaptive immune system, are all white blood cells. Most of the cells of the innate immune system are of myeloid lineage and are granulocytes (subclassified as neutrophils, eosinophils and basophils), monocytes that mature to macrophages, dendritic cells, and mast cells. One ocell of lymphoid lineage is in the group of cells of the innate immune response and that is the Natural Killer cell also know as the NK cell. The other cells of lymphoid lineage, T cells, and B cells are the cells of the adaptive immune system. 

      The cells of the adaptive immune system have the important assignment of being able to recognize and specifically react to non-self, while leaving self alone. This function is directed by the time that these cells spend maturing in their respective primary lymphatic organ, the bone marrow for B cells and the thymus for T cells.  The next part of the assignment for T and B cells is to meet and respond to antigens.  This takes place in the organs that are called secondary lymphatic organs and include the lymph nodes, the spleen, mucosal associated lymphoid tissue (MALT) and skin associated lymphoid tissue (SALT). Here the cells of the adaptive immune system interact with the cells of the innate immune system and the optimum response is formed.

      See a broken link? Please let us know!

  • 1.1.1 Myeloid-Progenitor Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.1.1 Granulocytes  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.1.2 Macrophages  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.1.3 Dendritic Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.1.4 Mast Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.2 Lymphoid-Progenitor Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.2.1 B Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.2.2 T Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.2.3 Natural Killer (NK) Cells  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.3 Central (Primary) Lymphoid Organs  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.3.1 Bone Marrow  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.3.2 Thymus  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.4 Peripheral (Secondary) Lymphoid Organs  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.4.1 Lymph Nodes  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.4.2 Spleen  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.1.4.3 Mucosal-Associated Lymphoid Tissues (MALT)  

    Note: This subunit is covered by the reading for subunit 1.1.

  • 1.2 Basic Concepts of Innate and Adaptive Immunity  
    • Reading: National Institutes of Health: Professor Charles Janeway et al.’s Immunobiology: “Principles of Innate and Adaptive Immunity”

      National Institutes of Health: Professor Charles Janeway et al.’s Immunobiology: “Principles of Innate and Adaptive Immunity” (HTML)

      Instructions: Read this page in its entirety along with all associated figures.  It will cover the material in 1.2.
       
      This resource will take approximately 45 minutes to complete.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      Note: The inflammatory response and innate immunity is the first line of defense, but its role extends to helping begin the adaptive immune response as well.  The hallmarks of inflammation are redness, heat, pain, and swelling. These hallmarks are due to the actions of the chemicals and cells of the innate immune system which will briefly be described here. The adaptive immune response is further separated into humoral and cellular immunity. 

      Humoral immunity originates with the term humours which means body fluid, however the term humoral immunity is generally used to describe the adaptive immune response that occurs in the fluid of the blood, which more simply put, is antibody based immunity. Cell-mediated immunity is defense specifically created by the direct actions of immune T cells. Theories are available concerning how lymphocytes can respond to many different antigens  how specific responss are initiated when needed, and how reaction with self-antigens is prevented were developed and tested in experiments that illuminated these important and elegant traits. The theories began with Burnet’s clonal selection theory, and were advanced with Medawar’s understanding of tolerance to self, and then final elucidation of these traits came with Tonegawa’s data concerning the inheritance of immunoglobulin genes as gene segments that recombined to form the intact gene. These theories and data are described in this chapter and will help you realize what a remarkable system protects you.

      See a broken link? Please let us know!

  • 1.2.1 The Inflammatory Response and Innate Immunity  

    Note: This subunit is covered by the reading for subunit 1.2.

  • 1.2.2 Initiation of Adaptive Immunity  

    Note: This subunit is covered by the reading for subunit 1.2.

  • 1.2.3 Lymphocyte Specificity  

    Note: This subunit is covered by the reading for subunit 1.2.

  • 1.2.4 Antibody Formation  

    Note: This subunit is covered by the reading for subunit 1.2.

  • 1.2.5 Antigen Receptors  

    Note: This subunit is covered by the reading for subunit 1.2.

  • 1.3 Recognition and Signaling in Immune Systems  
  • 1.3.1 Extracellular Antigen Recognition  

    Note: This subunit is covered by the reading for subunit 1.3.

  • 1.3.2 Intracellular Recognition – T Cells  

    Note: This subunit is covered by the reading for subunit 1.3.

  • 1.3.3 The MHC (Major Histocompatibility Complex) and Antigen Recognition  

    Note: This subunit is covered by the reading for subunit 1.3.

  • Unit 1 Assessment  
  • Unit 2: Innate Immunity  

    In order to understand the processes of the immune system, you must first understand how infection occurs.  Infections begin where the inside of us has contact with the outside world. Individuals can acquire an infection via an airway, the skin, the digestive tract, or the reproductive tract.  Our innate immunity thus naturally begins in those areas.  Our first line of defense is the skin, which is an impenetrable barrier to almost all foreign invaders.  Infections often begin with a break in the skin.  We can also ingest or inhale an infectious agent or acquire it through sexual contact.  Innate defenses, however, are not just skin deep; we have many strong internal innate defenses as well.  Do remember, however, that since the innate immune system is non-specific, it reacts in the same way to every type of foreign invader.  Also remember that the innate response is available instantly but does not improve with a repeat infection with the same organism, as there is no memory in the innate immune system.

    Unit 2 Time Advisory   show close
    Unit 2 Learning Outcomes   show close
    • Lecture: The University of South Carolina School of Medicine: Dr. Jennifer Nyland’s “Innate Immune Response”

      Link: The University of South Carolina School of Medicine: Dr.  Jennifer Nyland’s “Innate Immune Response” (Adobe Flash, MP3 or Quicktime)
       
      Instructions: Click on the arrow of the Immunology folder to open, then click on the “Innate Immune Response” lecture.  You have the choice of watching this on your computer with audio and slideshow or downloading the lecture to an MP3 player.  This lecture will cover the entirety of Unit 2 (in conjunction with the other resources listed below).
       
      This resource will take you approximately 30 minutes to complete.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      See a broken link? Please let us know!

  • 2.1 Routes of Infection  
  • 2.1.1 Mucosal Routes  

    Note: This subunit is covered by the reading for subunit 2.1.

  • 2.1.2 External-Epithelia Routes  

    Note: This subunit is covered by the reading for subunit 2.1.

  • 2.2 First Encounter: Phagocytes  

    Note: This subunit is covered by the reading for subunit 2.1.

  • 2.3 The Inflammatory Response  

    Note: This subunit is covered by the reading for subunit 2.1.

  • 2.3.1 Inflammatory Cytokines  

    Note: This subunit is covered by the reading for subunit 2.1.

  • 2.3.2 Leukocyte Localization  

    Note: This subunit is covered by the reading for subunit 2.1.

  • 2.4 The Complement System  
  • 2.4.1 Classic Pathway  

    Note: This subunit is covered by the reading for subunit 2.4.

  • 2.4.2 Mannan-Binding Lectin Pathway  

    Note: This subunit is covered by the reading for subunit 2.4.

  • 2.4.3 Alternative Pathway  

    Note: This subunit is covered by the reading for subunit 2.4.

  • 2.4.4 Opsonization and Inflammation mediated by complement  

    Note: This subunit is covered by the reading for subunit 2.4.

  • 2.4.5 Lysis mediated by complement  

    Note: This subunit is covered by the reading for subunit 2.4.

  • 2.4.6 Regulation of complement  

    Note: This subunit is covered by the reading for subunit 2.4.

  • 2.5 Receptors of the Innate Immune System  

    Note: The general name now used for all the receptors of the innate immune system that recognize patterns on pathogens is pattern recognition receptors (PRR).  PRR include TLRs, mannan binding lectin, the chemotactic receptors, among others. The innate immune system, although not specific for the pathogen, recognizes patterns that occur in many pathogens to differentiate non-self from self. Please review the last five slides of Dr. Jennifer Nyland’s "Innate Immune Response” lecture to begin your studies of the receptors of the innate immune response.

  • 2.5.1 Pattern Recognition Receptors  

    Note: This subunit is covered by the reading for subunit 2.5.

  • 2.5.2 Pathogen Associated Molecular Patterns  

    Note: This subunit is covered by the reading for subunit 2.5.

  • 2.5.3 Receptor Involvement in Phagocytosis  

    Note: This subunit is covered by the reading for subunit 2.5.

  • 2.5.4 Toll-Like Receptors (TLRs)  

    Note: This subunit is covered by the reading for subunit 2.5.

  • 2.6 Induced Responses  
  • 2.6.1 Cytokines  

    Note: This subunit is covered by the reading for subunit 2.6.

  • 2.6.2 Chemokines  

    Note: This subunit is covered by the reading for subunit 2.6.

  • 2.6.3 Cell-Adhesion Molecules  

    Note: This subunit is covered by the reading for subunit 2.6.

  • 2.6.4 Neutrophils  

    Note: This subunit is covered by the reading for subunit 2.6.

  • 2.6.5 Tumor-Necrosis Factor Alpha (TNF-?)  

    Note: This subunit is covered by the reading for subunit 2.6.

  • 2.6.6 Interferons  

    Note: This subunit is covered by the reading for subunit 2.6.

  • 2.6.7 Natural-Killer Cells  

    Note: This subunit is covered by the reading for subunit 2.6.

  • Unit 2 Assessment  
  • Unit 3: Immunoglobulins  

    Units 1 and 2 introduced you to many of the important components of the immune system, but some molecules, such as immunoglobulins, require more in-depth investigation.  Immunoglobulins (also known as antibodies) are critical to the immune response.  They bind to antigens and to various other immune-system molecules in order to stimulate defensive function.  All immunoglobulins have the same general, Y-shaped structure, but they can vary in aspects of their structure and function.  There are five classes, or isotypes, of immunoglobulins, and each plays a different role in the immune system.  This unit will cover the general structure and function of immunoglobulins as well as the more specific roles of each class of immunoglobulins. It will also address the genetic mechanisms that help create the wide diversity of immunoglobulin types. 

    Unit 3 Time Advisory   show close
    Unit 3 Learning Outcomes   show close
  • 3.1 Immunoglobulins  
  • 3.1.1 Structure  

    Note: This subunit is covered by the reading for subunit 3.1. 

  • 3.1.2 Light and Heavy Chains  

    Note: This subunit is covered by the reading for subunit 3.1. 

  • 3.1.3 Fab Fragments  

    Note: This subunit is covered by the reading for subunit 3.1. 

  • 3.2 Ig Classes: Structures, Properties, and Clinical Implications  
  • 3.2.1 IgG  

    Note: This subunit is covered by the reading for subunit 3.2.

  • 3.2.2 IgA  

    Note: This subunit is covered by the reading for subunit 3.2.

  • 3.2.3 IgM  

    Note: This subunit is covered by the reading for subunit 3.2.

  • 3.2.4 IgE  

    Note: This subunit is covered by the reading for subunit 3.2.

  • 3.2.5 IgD  

    Note: This subunit is covered by the reading for subunit 3.2.

  • 3.3 Immunoglobulins in Adaptive Immunity  
  • 3.3.1 Distribution of Ig Isotypes  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.3.2 Anti-Bacterial Functions  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.3.3 Neutralization of Bacterial Toxins  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.3.4 Reduction of Viral Infectivity  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.3.5 Induction of Classical Complement System  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.3.6 Immune Complex Formation  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.3.7 Opsonization  

    Note: This subunit is covered by the reading for subunit 3.3.

  • 3.4 Genetics and Genetic Regulation  

    Note: A person’s immune repertoire refers to all of the different antigens that the person can react to. From the first lessons you might recall that there is exquisite specificity in each reaction. There is an enormous number of different reactions, perhaps 10 11, or more. How can this be when only about 20,000 genes make up the human genome?  The readings in this section answer this question. By the way, when there is an antigen that you don’t respond to, it is called a hole in your repertoire.

  • 3.4.1 Genetics  

    Note: This subunit is covered by the reading for subunit 3.4.

  • 3.4.2 Rearrangement and Ig Diversity  

    Note: This subunit is covered by the reading for subunit 3.4.

  • 3.4.3 RAG Proteins  

    Note: This subunit is covered by the reading for subunit 3.4.

  • 3.4.4 Somatic Mutation  

    Note: This subunit is covered by the reading for subunit 3.4.

  • Unit 3 Assessment  
  • Unit 4: Antigen Presentation  

    The immune system can combat individual threats, but in order to do so, it must be able to identify these threats.  Immunogenicity, that is, whether a compound causes an immune response or not, is related to how foreign the compound is, as well as its molecular weight, complexity, chemical composition, and physical form. In general, the more foreign, the more immunogenic a compound is. Compounds of larger molecular weight are more immunogenic. Because complexity increases immunogenicity, homopolymers are unlikely to be immunogenic. In terms of composition, proteins are more immunogenic than carbohydrates while lipids and nucleic acids are rarely immunogenic. In terms of physical form, particulates are more immunogenic than soluble compounds while denatured compounds are more immunogenic than native structures. Immunogenicity is also influenced by how much of a compound enters the body and the manner in which it enters.

    B cells can recognize soluble antigens, but T cells only react to antigens presented to them. Antigen presentation is the process through which immune system cells (such as dendritic cells, B cells and macrophages) identify antigens and “present” them to T cells in a form that T cells can recognize.  Once antigens have been presented, the T cells can begin to eliminate these invaders from the body.  This unit will cover how antigens are recognized by immune-system cells and presented to T cells.

    Unit 4 Time Advisory   show close
    Unit 4 Learning Outcomes   show close
    • Lecture: The University of South Carolina School of Medicine: Dr. Jennifer Nyland’s “Antigens”

      Link:  The University of South Carolina School of Medicine: Dr. Jennifer Nyland’s “Antigens” (Adobe Flash, MP3 or Quicktime)
       
      Instructions: Click on the arrow of the Immunology folder to open it, then click on the “Antigens” lecture.  You have the choice of watching this on your computer with audio and slideshow or downloading the lectures to an MP3 player.  This will cover the material in Unit 4.
       
      This resource will take approximately 45 minutes to complete.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      See a broken link? Please let us know!

  • 4.1 Immunogenicity  
  • 4.2 Antigen Recognition by B and T Cells  
  • 4.2.1 Recognition by Immunoglobulins (Antibodies)  

    Note: An epitope is the portion of the immunogen that binds with the antibody molecule, the part that fits in the paratope of the antibody. Conformation is often found to be important in the recognition of an epitope by an antibody molecule because an antibody can react to soluble, unprocessed antigens. 

  • 4.2.2 Recognition by T Cells  

    Note: T cells recognize antigens as peptides presented in the major histocompatibility molecules on the surface of an antigen-presenting cell. These molecules were termed major histocompatibility for their discovery during transplantation reactions, so the name comes from the major role of these molecules in tissue (histo) compatibility. CD8+ T cells (cytotoxic T cells) recognize antigens presented by antigen presenting cells in MHC Class I molecules, and CD4+ T cells (helper T cells) recognize antigens presented in MHC Class II molecules.  The CD4 molecule binds to the MHC Class II molecule and the CD8 molecule binds to the MHC Class I molecule. These are required co-receptors of the interaction. MHC Class I molecules are on all nucleated cells in our body, whereas MHC Class II molecules are on antigen-presenting cells. Because of the requirement for antigen-presenting cell presentation, T cells recognize processed antigens.
     
    The T cell receptors of most T cells are composed of an alpha chain and a beta chain. A small set of T cells have T cell receptors that have gamma delta chains. Unlike immunoglobulin, the B cell receptor, T cell receptors are not secreted. 

  • 4.2.2.1 TCR? and TCR? (T-cell Receptor)  

    Note: This subunit is covered by the reading for subunit 4.2.2.

  • 4.2.2.2 CD4 and MHC II  

    Note: This subunit is covered by the reading for subunit 4.2.2.

  • 4.2.2.3 CD8 and MHC I  

    Note: This subunit is covered by the reading for subunit 4.2.2.

  • 4.3 Recognition  
  • 4.3.1 Dendritic Cell and MHC II  

    Note: This subunit is covered by the reading for subunit 4.3.

  • 4.3.2 Macrophage Activation  

    Note: This subunit is covered by the reading for subunit 4.3.

  • 4.3.3 T Lymphocyte Activation  

    Note: This subunit is covered by the reading for subunit 4.3.

  • 4.4 Antigen Presentation of MHC I  
    • Reading: National Institutes of Health: Professor Charles Janeway et al.’s Immunobiology: “The Generation of T-Cell Receptor Ligands”

      Link: National Institutes of Health: Professor Charles Janeway et al.’s Immunobiology: “The Generation of T-Cell Receptor Ligands” (HTML)
       
      Instructions: Read sections 5-2 through 5-4 along with all associated figures.  This will cover the material in subunit 4.4.
       
      This resource will take approximately 30 minutes to complete. 

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      See a broken link? Please let us know!

    • Lecture: The University of South Carolina School of Medicine: Dr. Jennifer Nyland’s “Major Histocompatibility Complex and T-Cell Receptors”

      Link: The University of South Carolina School of Medicine: Dr.  Jennifer Nyland’s “Major Histocompatibility Complex and T-Cell Receptors” (Adobe Flash, MP3 or Quicktime)
       
      Instructions: Click on the arrow of the Immunology folder to open it, then click on the first “MHC” lecture.  You have the choice of watching this on your computer with audio and slideshow or downloading the lectures to an MP3 player.  This will cover the material in subunits 4.4-4.5. Please don't be confused by a slight mistake at time 5:27 when the speaker accidentally says that Clas I molecules bind to T helper cells, although she means that Class I molecules bind to cytotoxic T cells. Also listen to her second file with the same title but with II in the title. 

      This resource will take approximately 45 minutes to complete.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      Note: It is important to keep in mind that recognition of non-self and not self is key to understanding immunity. Recognition controls how an MHC Class I or MHC Class II molecule is loaded with the peptides that will be presented to T cells. While Class I molecules present antigens on the surface of the infected cells (endogenous antigens), Class II molecules present antigens taken up by phagocytosis. The method that loads Class I molecules is critically different from the method which loads Class II molecules.  helps  

      See a broken link? Please let us know!

  • 4.4.1 Ubiquitination and Proteasome Degradation  

    Note: This subunit is covered by the reading for subunit 4.4.

  • 4.4.2 TAP (Transporter associated with Antigen Processing) Transport  

    Note: This subunit is covered by the reading for subunit 4.4.

  • 4.4.3 Binding to MHC I  

    Note: This subunit is covered by the reading for subunit 4.4.

  • 4.4.4 Vesicular Presentation  

    Note: This subunit is covered by the reading for subunit 4.4.

  • 4.5 Antigen Presentation of MHC II  
  • 4.5.1 MHC II Invariant Chain  

    Note: This subunit is covered by the reading for subunits 4.4 and 4.5. 

  • 4.5.2 Acidified Endocytic Vesicles  

    Note: This subunit is covered by the reading for subunits 4.4 and 4.5. 

  • 4.5.3 MHC II Loading  

    Note: This subunit is covered by the reading for subunits 4.4 and 4.5. 

  • Unit 4 Assessment  
  • Unit 5: Cell Signaling and Maturation  

    The immune system (especially the adaptive immune system) relies upon many distinct pathways of communication all acting in synergy.  This unit will introduce the signaling processes that occur immediately after antigen recognition in order to initiate adaptive immunity.

    The adaptive immune system relies not only on signaling, but also on cells’ ability to recognize and respond to an extraordinary number of different kinds of pathogens.  The body is able to produce cells that recognize a vast number of foreign objects through the process of lymphocyte maturation.  Most biologists explain this process through the clonal selection theory (covered in the reading for subunit 1.2 and revisited in this unit).  Although there are alternative explanations for the process of lymphocyte maturation, this unit will focus on the clonal selection theory to explain this phenomenon.   

    Unit 5 Time Advisory   show close
    Unit 5 Learning Outcomes   show close
  • 5.1 Antigen Recognition Signaling  
  • 5.1.1 Invariant Chain  

    Note: This subunit is covered by the reading for subunit 5.1.

  • 5.1.2 ITAMs (Immunoreceptor Tyrosine-based Activation Motifs)  

    Note: This subunit is covered by the reading for subunit 5.1.

  • 5.1.3 Co-Receptors  

    Note: This subunit is covered by the reading for subunit 5.1.

  • 5.1.4 Downstream Phosphorylation  

    Note: This subunit is covered by the reading for subunit 5.1.

  • 5.1.5 NFAT (Nuclear Factor of Activated T Cells)  

    Note: This subunit is covered by the reading for subunit 5.1.

  • 5.1.6 Agonist and Antagonist Peptides  

    Note: This subunit is covered by the reading for subunit 5.1.

  • 5.2 Main Signaling Pathways  
  • 5.2.1 NF-?B (Nuclear Factor ?B)  

    Note: This subunit is covered by the reading for subunit 5.2.

  • 5.2.2 GPCR (G Protein Coupled Receptor) Family  

    Note: This subunit is covered by the reading for subunit 5.2.

  • 5.2.3 JAKs (Janus Kinases) and STATs (Signal Transducers and Activators of Transcription)  

    Note: This subunit is covered by the reading for subunit 5.2.

  • 5.2.4 TNF (Tumor Necrosis Factor) Family  

    Note: This subunit is covered by the reading for subunit 5.2. Please disregard what this chapter says about TNF and listen to the following web resource:

  • 5.3 Common Origin of B and T Lymphocytes  
  • 5.3.1 Hematopoietic Stem Cell  

    Note: This subunit is covered by the reading for subunit 5.3.

  • 5.3.2 Bone Marrow Development  

    Note: This subunit is covered by the reading for subunit 5.3.

  • 5.3.3 Lymphocyte Progenitor  

    Note: This subunit is covered by the reading for subunit 5.3.

  • 5.3.4 Stromal Cell Interaction  

    Note: This subunit is covered by the reading for subunit 5.3.

  • 5.4 B Lymphocyte Development  
  • 5.4.1 CXCL12 (Stromal cell-derived factor-1) and IL-7  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.4.2 Peripheral Lymphoid Organs  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.4.3 Pro-B Cell  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.4.4 Pre-B Cell  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.4.5 Immature B Cell  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.4.6 Mature B Cell  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.4.7 B Cell Surface Markers  

    Note: This subunit is covered by the reading for subunit 5.4.

  • 5.5 T Lymphocyte Development  
  • 5.5.1 Maturation in Thymus  

    Note: This subunit is covered by the reading for subunit 5.5.

  • 5.5.2 T Cell Surface Markers  

    Note: This subunit is covered by the reading for subunit 5.5.

  • 5.5.3 Double-Negative Thymocytes  

    Note: This subunit is covered by the reading for subunit 5.5.

  • 5.5.4 Natural Killer T Cell Development  

    Note: This subunit is covered by the reading for subunit 5.5.

  • 5.5.5 Double Positive Thymocytes  

    Note: This subunit is covered by the reading for subunit 5.5.

  • 5.5.6 Single Positive Thymocytes  

    Note: This subunit is covered by the reading for subunit 5.5.

  • 5.6 Antigen-Receptor Gene Rearrangement  
  • 5.6.1 Control of Lymphocyte Development  

    Note: This subunit is covered by the reading for subunit 5.6.

  • 5.6.2 V, D, and J Genetic Segments  

    Note: This subunit is covered by the reading for subunit 5.6.

  • 5.6.3 V(D)J Recombination in B Cell Receptor  

    Note: This subunit is covered by the reading for subunit 5.6.

  • 5.6.4 T Cell Receptor Gene Recombination  

    Note: This subunit is covered by the reading for subunit 5.6.

  • 5.7 Positive and Negative Selection  
  • 5.7.1 Positive Selection for CD4/CD8 T Cells  
  • 5.7.2 Positive Selection for Specificity  

    Note: This subunit is covered by the reading for subunit 5.7.1.

  • 5.7.3 Self Antigen Reaction and Negative Selection  
  • 5.7.4 Order and Specificity of Positive vs. Negative Selection  
  • Unit 5 Assessment  
  • Unit 6: Adaptive Immunity  

    Adaptive immunity is our last and most potent line of defense.  If it fails, we will inevitably succumb to infection.  Much of adaptive immunity relies upon two main processes: antibody production and cytotoxic cells.  If a given pathogen is so destructive that it requires the activation of adaptive immunity, it is important that our bodies remember it and are capable of recognizing it in case of future attack.  For this reason, we have memory cells that “remember” the same pathogen and, should that pathogen invade again, are able to mount a much faster defense against it.  Vaccines make use of this memory process in order to provide us with protection against many infections that we might not otherwise successfully fight.  

    Unit 6 Time Advisory   show close
    Unit 6 Learning Outcomes   show close
  • 6.1 T Lymphocyte Activation  
  • 6.1.1 Naive T Lymphocyte  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.1.2 APC Interaction  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.1.3 Co-stimulatory Molecules  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.1.4 CD8 and CD4 Differentiation  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.1.5 Clonal Expansion  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.2 Cytotoxic T Lymphocytes  
  • 6.2.1 Apoptosis Induction  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.2.2 Fas Ligand  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.2.3 TNF- ? (Tumor Necrosis Factor-?)  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.2.4 Cytokine Release  

    Note: This subunit is covered by the reading for subunit 6.1.

  • 6.3 TH1 CD4+ T Lymphocyte  
  • 6.3.1 Macrophage Activation  

    Note: This subunit is covered by the reading for subunit 6.3.

  • 6.3.2 Macrophage Differentiation  

    Note: This subunit is covered by the reading for subunit 6.3.

  • 6.3.3 TNF-? and IFN-?  

    Note: This subunit is covered by the reading for subunit 6.3.

  • 6.3.4 Infected Cell Destruction  

    Note: This subunit is covered by the reading for subunit 6.3.

  • 6.4 TH2 CD4+ T Lymphocyte  
  • 6.4.1 B Lymphocyte Activation  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.4.2 Interleukin Production  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.4.3 Ig Isotype Switching  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.5 B Lymphocytes and Adaptive Immunity  
  • 6.5.1 Activation of B Lymphocytes  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.5.2 T Cell Dependent Activation  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.5.3 T Cell Independent Activation  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.5.4 Plasma B Cells  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.5.5 Memory B Cells  

    Note: This subunit is covered by the reading for subunit 6.4.

  • 6.6 Immunological Memory  
  • 6.6.1 Memory in B and T Lymphocytes  

    Note: This subunit is covered by the reading for subunit 6.6.

  • 6.6.2 Somatic Hypermutation  

    Note: This subunit is covered by the reading for subunit 6.6.

  • 6.6.3 Primary vs. Secondary Response  

    Note: This subunit is covered by the reading for subunit 6.6.

  • 6.6.4 Isotype Switch  

    Note: This subunit is covered by the reading for subunit 6.6.

  • Unit 6 Assessment  
  • Unit 7: Failures of the Immune System  

    Even as the human immune system has evolved and developed complex defensive mechanisms against pathogens, pathogens themselves have evolved and developed new means of evading the immune system.  In some cases, the adaptations of pathogens are such that they are extremely infectious, virulent, and sometimes even fatal. 

    We are also threatened by health hazards posed by our own immune system.  The immune system can, for example, respond inappropriately to its own cells (as in the case of autoimmune diseases) or to innocuous foreign cells (as in the case of allergies and other hypersensitivity diseases).  This unit will cover some clinical and medical aspects of the immune system as it relates to immune-system dysfunction. 

    Unit 7 Time Advisory   show close
    Unit 7 Learning Outcomes   show close
  • 7.1 Pathogenic Evasion of Immune System  
  • 7.1.1 Antigenic Drift and Shift  

    Note: This subunit is covered by the reading for subunit 7.1.

  • 7.1.2 Latency  

    Note: This subunit is covered by the reading for subunit 7.1.

  • 7.1.3 Resistance to Effector Mechanisms  

    Note: This subunit is covered by the reading for subunit 7.1.

  • 7.2 Immunodeficiency  
  • 7.2.1 Inherited Immunodeficiency  
  • 7.2.2 Acquired Immunodeficiency  
  • 7.3 Allergy and Hypersensitivity  
  • 7.3.1 Antigen vs. Allergen  
  • 7.3.2 IgE-mediated Allergy  

    Note: This subunit is covered by the reading for subunit 7.3.1.

  • 7.3.3 Four Types of Allergies  
  • 7.3.4 Allergic Response Phases  

    Note: This subunit is covered by the reading for subunit 7.3.3.

  • 7.3.5 Treatment of Allergic Reaction  

    Note: This subunit is covered by the reading for subunit 7.3.3.

  • 7.3.6 Type II and III Hypersensitivity  
  • 7.4 Autoimmunity  
  • 7.4.1 Self Antigens  
  • 7.4.2 Systemic vs. Organ-specific Diseases  

    Note: This subunit is covered by the reading for subunit 7.4.1.

  • 7.4.3 Epitope Spreading  

    Note: This subunit is covered by the reading for subunit 7.4.1.

  • 7.4.4 Immunologically Privileged Sites  

    Note: This subunit is covered by the reading for subunit 7.4.1.

  • 7.4.5 Genetic Basis  

    Note: This subunit is covered by the reading for subunit 7.4.1.

  • 7.4.6 Environmental Basis  

    Note: This subunit is covered by the reading for subunit 7.4.1.

  • 7.4.7 Tolerance Loss  
  • 7.4.8 Transplantation and Graft Rejection  
  • Unit 7 Assessment  
  • Unit 8: Regulation of Immune Response  

    This last unit will cover the major methods that scientists and researchers use to manipulate the immune system in our favor, including vaccination (to boost immune responses) and immunosuppression (to temper immune responses to allergens or transplantations).  We will also discuss the development of new treatments that promise to direct our immune system to recognize and attack tumor cells.

    Unit 8 Time Advisory   show close
    Unit 8 Learning Outcomes   show close
  • 8.1 Immunosuppression  
  • 8.1.1 Corticosteroids  

    Note: This subunit is covered by the reading for subunit 8.1.

  • 8.1.2 Cytotoxic Drugs  

    Note: This subunit is covered by the reading for subunit 8.1.

  • 8.1.3 T-cell Intereference Drugs  

    Note: This subunit is covered by the reading for subunit 8.1.

  • 8.2 Biological Therapy  

    Note: This subunit is covered by the reading for subunit 8.1.

  • 8.3 Cancer Treatment  
  • 8.3.1 Tumor Rejection Antigens  

    Note: This subunit is covered by the reading for subunit 8.3.

  • 8.3.2 Monoclonal Antibodies  

    Note: This subunit is covered by the reading for subunit 8.3.

  • 8.3.3 Immunogenicity of Tumors  

    Note: This subunit is covered by the reading for subunit 8.3.

  • 8.4 Vaccination  
  • 8.4.1 Attenuated Organisms  

    Note: This subunit is covered by the reading for subunit 8.4.

  • 8.4.2 Whole cell and acellular or sub-unit vaccines  

    Note: This subunit is covered by the reading for subunit 8.4.

  • 8.4.3 Conjugate Vaccines  

    Note: This subunit is covered by the reading for subunit 8.4.

  • 8.4.4 Adjuvants  

    Note: This subunit is covered by the reading for subunit 8.4.

  • 8.4.5 Live-Attenuated Vaccines  

    Note: This subunit is covered by the reading for subunit 8.4.

  • 8.4.6 Routes of Vaccines  

    Note: This subunit is covered by the reading for subunit 8.4.

  • Unit 8 Assessment  
  • Final Exam  

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