Allergy and Immunology

Allergy and Immunology is a medical specialty, rooted in the biological study of the immune system, that focuses on diagnosing and treating diseases caused by immune system dysregulation. This field encompasses conditions of immune system overactivity, such as allergies, where the body mounts an exaggerated response to normally harmless substances (allergens), and autoimmune diseases, where the immune system mistakenly attacks the body's own tissues. It also covers immunodeficiency disorders, in which parts of the immune system are missing or functioning inadequately, leading to increased susceptibility to infections.

1. Fundamentals of the Immune System
   1. Overview of Immunity
      1. Definitions and Basic Concepts
         1. Immunity Definition
         2. Antigen and Antibody Concepts
         3. Self vs Non-self Recognition
         4. Immune Response Overview
      2. Innate Immunity
         1. Physical Barriers
            1. Skin Structure and Function
            2. Mucous Membranes
            3. Ciliary Action
         2. Chemical Barriers
            1. Antimicrobial Peptides
            2. Complement Proteins
            3. pH and Enzyme Barriers
         3. Cellular Components
            1. Neutrophils
            2. Macrophages
            3. Dendritic Cells
            4. Natural Killer Cells
         4. Pattern Recognition Receptors
            1. Toll-like Receptors
            2. NOD-like Receptors
            3. RIG-I-like Receptors
            4. C-type Lectin Receptors
      3. Adaptive Immunity
         1. Antigen Specificity
            1. Antigen Recognition Mechanisms
            2. Specificity vs Cross-reactivity
         2. Clonal Selection Theory
            1. Lymphocyte Activation
            2. Clonal Expansion
         3. Memory Formation
            1. Memory Cell Development
            2. Long-term Protection
      4. Comparison of Innate vs Adaptive Immunity
         1. Speed of Response
         2. Specificity Differences
         3. Memory Characteristics
         4. Evolutionary Conservation
      5. Cellular Immunity
         1. T-cell Mediated Responses
            1. CD4+ T Helper Cells
            2. CD8+ Cytotoxic T Cells
            3. Regulatory T Cells
         2. Cell-mediated Cytotoxicity
         3. Delayed-type Hypersensitivity
      6. Humoral Immunity
         1. B-cell Mediated Responses
            1. B-cell Activation
            2. Plasma Cell Differentiation
         2. Antibody Production
            1. Immunoglobulin Structure
            2. Antibody Functions
         3. Complement Activation
      7. Primary Immune Response
         1. Lag Phase Characteristics
         2. Initial Antibody Production
         3. Antibody Isotype Switching
            1. Class Switch Recombination
            2. Cytokine Influence
      8. Secondary Immune Response
         1. Memory Cell Activation
         2. Enhanced Response Kinetics
         3. Affinity Maturation
         4. Increased Antibody Levels
   2. Organs and Tissues of the Immune System
      1. Primary Lymphoid Organs
         1. Bone Marrow
            1. Hematopoiesis Process
            2. B-cell Development
            3. Stem Cell Niches
         2. Thymus
            1. T-cell Development
            2. Positive Selection
            3. Negative Selection
            4. Thymic Involution
      2. Secondary Lymphoid Organs
         1. Spleen
            1. White Pulp Structure
            2. Red Pulp Function
            3. Blood-borne Antigen Response
            4. Splenic Marginal Zone
         2. Lymph Nodes
            1. Anatomical Structure
            2. Lymphatic Circulation
            3. Antigen Filtration
            4. Germinal Center Formation
         3. Mucosa-Associated Lymphoid Tissue
            1. Gut-Associated Lymphoid Tissue
               1. Peyer's Patches
               2. Isolated Lymphoid Follicles
            2. Bronchus-Associated Lymphoid Tissue
            3. Nasal-Associated Lymphoid Tissue
            4. Tonsils and Adenoids
   3. Cells of the Immune System
      1. Myeloid Lineage
         1. Phagocytes
            1. Neutrophils
               1. Morphology and Identification
               2. Antimicrobial Functions
               3. Role in Acute Inflammation
               4. Neutrophil Extracellular Traps
            2. Macrophages
               1. Tissue Distribution
               2. Phagocytic Function
               3. Antigen Presentation
               4. Cytokine Production
               5. M1 vs M2 Polarization
            3. Monocytes
               1. Circulating Precursors
               2. Differentiation Pathways
         2. Granulocytes
            1. Eosinophils
               1. Morphology and Identification
               2. Role in Parasitic Infections
               3. Involvement in Allergic Reactions
               4. Tissue Damage Mechanisms
            2. Basophils
               1. Morphology and Identification
               2. Mediator Release
               3. Role in Hypersensitivity
               4. Relationship to Mast Cells
         3. Mast Cells
            1. Tissue Localization
            2. Degranulation Mechanisms
            3. Mediator Release
            4. Role in Allergic Reactions
         4. Dendritic Cells
            1. Subtypes and Distribution
            2. Antigen Uptake and Processing
            3. Migration to Lymph Nodes
            4. T-cell Activation
            5. Cross-presentation
      2. Lymphoid Lineage
         1. T Lymphocytes
            1. T-cell Development
            2. T-cell Receptor Structure
            3. Helper T Cells
               1. Th1 Subset
               2. Th2 Subset
               3. Th17 Subset
               4. Tfh Subset
               5. Regulatory T Cells
            4. Cytotoxic T Cells
               1. Perforin-Granzyme Pathway
               2. Fas-FasL Pathway
               3. Target Cell Recognition
         2. B Lymphocytes
            1. B-cell Development
            2. B-cell Receptor Structure
            3. Naive B Cells
            4. Plasma Cells
               1. Antibody Secretion
               2. Lifespan and Function
            5. Memory B Cells
               1. Long-term Immunity
               2. Rapid Recall Response
         3. Natural Killer Cells
            1. Activating Receptors
            2. Inhibitory Receptors
            3. Missing Self Recognition
            4. Cytotoxic Mechanisms
   4. Molecules of the Immune System
      1. Antibodies
         1. Structure and Function
            1. Heavy Chains
            2. Light Chains
            3. Variable Regions
            4. Constant Regions
            5. Antigen Binding Sites
            6. Fc Region Functions
         2. Antibody Isotypes
            1. IgG
               1. IgG1 Subclass
               2. IgG2 Subclass
               3. IgG3 Subclass
               4. IgG4 Subclass
            2. IgA
               1. Serum IgA
               2. Secretory IgA
               3. Mucosal Protection
            3. IgM
               1. Pentameric Structure
               2. Primary Response
               3. Complement Activation
            4. IgE
               1. Role in Allergy
               2. Parasitic Infection Response
               3. Mast Cell Binding
            5. IgD
               1. B-cell Surface Expression
               2. Function in Activation
      2. Cytokines
         1. Interleukins
            1. IL-1 Family
            2. IL-2 and T-cell Growth
            3. IL-4 and Th2 Responses
            4. IL-5 and Eosinophils
            5. IL-6 and Acute Phase Response
            6. IL-10 and Immunoregulation
            7. IL-12 and Th1 Responses
            8. IL-17 and Inflammation
         2. Interferons
            1. Type I Interferons
               1. IFN-α
               2. IFN-β
               3. Antiviral Responses
            2. Type II Interferon
               1. IFN-γ
               2. Macrophage Activation
         3. Tumor Necrosis Factor
            1. TNF-α Structure and Function
            2. Inflammation Induction
            3. Apoptosis Mechanisms
         4. Chemokines
            1. CC Chemokines
            2. CXC Chemokines
            3. Chemotaxis Mechanisms
            4. Cell Recruitment
      3. Complement System
         1. Components and Functions
            1. C1 through C9 Components
            2. Regulatory Proteins
         2. Classical Pathway
            1. C1 Complex Activation
            2. Antibody-dependent Activation
            3. C3 Convertase Formation
         3. Alternative Pathway
            1. Spontaneous Activation
            2. Pathogen Surface Recognition
            3. Properdin Stabilization
         4. Lectin Pathway
            1. Mannose-binding Lectin
            2. Ficolin Recognition
            3. MASP Activation
         5. Effector Functions
            1. Opsonization Mechanisms
            2. Membrane Attack Complex
            3. Inflammatory Mediator Release
            4. Immune Complex Clearance
      4. Major Histocompatibility Complex
         1. MHC Class I
            1. Structure and Components
            2. Tissue Distribution
            3. Endogenous Antigen Presentation
            4. CD8+ T-cell Recognition
         2. MHC Class II
            1. Structure and Components
            2. Tissue Distribution
            3. Exogenous Antigen Presentation
            4. CD4+ T-cell Recognition
         3. Antigen Processing Pathways
            1. Proteasomal Degradation
            2. TAP Transport
            3. Endosomal Processing
            4. CLIP Removal
   5. Key Immunological Processes
      1. Antigen Recognition
         1. Molecular Patterns
         2. Epitope Recognition
         3. Cross-reactivity
      2. Antigen Presentation
         1. Antigen-Presenting Cells
         2. MHC Restriction
         3. Co-stimulatory Signals
         4. Immunological Synapse
      3. T-cell Activation and Differentiation
         1. Signal 1 Requirements
         2. Signal 2 Co-stimulation
         3. Signal 3 Cytokine Influence
         4. Differentiation Pathways
         5. Effector Function Development
      4. B-cell Activation and Antibody Production
         1. T-dependent Activation
         2. T-independent Activation
         3. Germinal Center Reactions
         4. Class Switch Recombination
         5. Somatic Hypermutation
         6. Affinity Maturation
      5. Immunological Memory
         1. Memory T-cell Formation
         2. Memory B-cell Formation
         3. Central Memory Cells
         4. Effector Memory Cells
         5. Longevity Mechanisms
         6. Recall Response Characteristics
      6. Self-Tolerance
         1. Central Tolerance
            1. Thymic Selection
            2. Bone Marrow Tolerance
         2. Peripheral Tolerance
            1. Anergy Induction
            2. Regulatory T-cell Function
            3. Immune Privilege
         3. Tolerance Breakdown
            1. Autoimmunity Development