4 Groups of Pathogens:

Bacteria

Most have a Cell Wall: Peptidoglycan Layer

Gram +

Thick Peptidoglycan Layer

Teichoic Acid, Lipotechoic Acid

Single Membrane

Example: Staphaureus

Gram

Cell Wall is in the Periplasmic Space

LPS (binds to TLR4/CD14)

Two Membranes Inner and Outer

Example: E. Coli

Capsule: Conjugated Vaccines

Influenza Type B

Streptococcus Pneumonia

Acid Fast:

Example: Mycobacterium

Acid-Fast organisms have wax-like, nearly impermeable cell walls.

Cell walls contain Mycolic Acid, Fatty Acids, Waxes, and Lipids

No Cell Wall:

Mycoplasma

Gene Transfers:

Transposition: Transposons, Jumping Genes

Transformation: Naked DNA

Conjugation: Donor Bacteria Recipient Bacteria

Uses Sex Pilus

HFR or Plasmid Transfer

Always happens at the OriT Break

Normal Plasmid Exchange:

F+A+ x F-A- = F+A-

Recipient becomes donor.

HFR Exchange:

F is in the actual Chromosome

HfrA+ x F-A- = F-A+/A-

Recipient never becomes donor.

The pore breaks down before the F+ is transferred.

A+ or A- depends on if there was recombination with the Recipient DNA.

Transduction: Viruses infect Bacteria (Bacteriophages)

Generalized: Lytic Phages

Specialized: Lysogenic (Temperate) Phages

Lysogenic Conversion:

Site-Specific Recombination into the chromosome of the bacterium Lysogen

Viruses:

Genome:

DNA

Linear or Circular

Single-Stranded or Double-Stranded

RNA:

Linear or Segmented

Segmented RNA: Influenza

Single Stranded or Double Stranded

Single Stranded:

+ Sense (like mRNA)

Must encode, but not package RNA-Dependent RNA Polymerase

Sense

Must encode and package RNA-Dependent RNA Polymerase

Ambisense (+ and -)

Capsid:

Helical

Icosahedral

Nucleocapsid = Genome + Capsid

The basic structure for any virus (naked)

Additional Extras:

Envelope: for budding, lipid bilayer from host cell.

Susceptible to MAC of Complement

Peplomers: Viral Glycoprotein Spikes

Targets for Neutralizing Antibodies

Packaged Enzymes:

Replicases, Proteases

Types of Proteins:

Structural (Part of Virion)

Non-Structural (Enzymes)

Not always packaged in the virion.

Viral Replication Pathways: Only differ in Extracellular Phase.

Naked:

Lytic (burst the cell)

Antibody

Better with CTL

Enveloped:

Budding, Fusion

Antibody

HAVE TO HAVE CTL

Fusion:

pH-Independent Fusion:

Neutral pH

At the Plasma Membrane

Syncytia

Example: HIV

pH-Dependent Fusion:

Acidic pH

At the Endosome

No Syncytia

Example: Influenza

Transforming:

Host Cell Transformation

Types of Genomic Replication in Viruses:

Exceptions to the Rule:

Most DNA Viruses replicate in Nucleus

DNA Virus that replicates in the Cytoplasm:

Pox Viruses

Needs RNA Polymerase because it replicates in the Cytoplasm.

Most RNA Viruses replicate in the Cytoplasm

RNA Viruses that replicates in the Nucleus:

Orthomycoviruses (Influenza)

Replicate in both Compartments:

Retroviruses (HIV)

Hepadnaviruses (Hepatitis B)

These can cause Intranuclear and Cytoplasmic Inclusion Bodies

This depends on where they replicate.

Innate Immunity:

PAMP

PAMP Location

PRR

PRR Location

Chitin

Fungi Cell Wall

TLR-2

Extracellular

LPS

Gram - Bacteria

TLR-4

Extracellular

Flagellin

Extracellular Bacteria

TLR-5

Extracellular

B-Glucan

Fungi Cell Wall

Dectin-1

Extracellular

Viral Nucleic Acid

Virus

TLR-3, TLR-7, RIG-1

Intracellular

Bacterial DNA

Intracellular Bacteria

TLR-9

Intracellular

Lipids of Intracellular Bacteria

Intracellular Bacteria

NOD-1, NOD-2

Intracellular

Lectin Pathway:

Detection: MBL/Ficolins

Activation of Protease: MASP

Classical Pathway:

Detection: C1Q binding to Antibody that has bound to the pathogen.

C-Reactive Protein/C1q can bind to Phosphocholine independent of Antibody.

Activation of Protease: C1S

Alternative Pathway:

Detection: Spontaneous C3B

Complement:

Innate Cells:

Mast Cells are already in the tissue tissue resident cells.

Neutrophils make up the first wave of cells that cross the blood vessel and enter inflamed tissues.

Extravasation:

Rolling:

E-Selection on Endothelium

Sialyl Lewis Leukocyte

Tight Binding:

ICAM on Endothelium

LFA1 on Leukocyte

Diapedesis: squeeze between cells

Migration: Follow Chemokine Gradient

IL-8

During Acute Inflammation, Professional APCs go into the infected tissue and carry it to the closest Lymph Node. (DCs)

By the time they get there, the MHC I or II will be loaded with the processed antigen to show antigen.

RECAPS:

TCR:

_______________________________________________________________________________________________________________

Maturation of T-Cells:

Common Lymphoid Progenitors enter the Thymus.

Pre-TCR = Expression of CD4 and CD8

TCR = Expression of CD3

IL-7 induces rearrangement of the TCR Gene (gamma, delta, beta)

If Gamma, Delta wins = leaves as a Double Negative Thymocyte

If Beta wins out, we get the Surrogate Alpha Chain expressed, the CD4/CD8 expressed, CD3 expressed, Beta rearrangement shuts down, and cell proliferation is induced.

All of the proliferated cells then go through Alpha and Gamma/Delta arrangement. Once Alpha is rearranged, this cuts out the Delta Locus permanently.

If at this stage, if the double positive cell recognizes the (MHC Class 1-Like Molecule) CD1 NK T-Cell.

Positive Selection: Some cells that do not interact with MHC die. Other cells will go on to be a CD4 or a CD8 as long as they interact with something.

Negative Selection: Central Tolerance

AIRE is expressed in MEC, which turns on MHC-Self-Antigens. If the thymocytes bind to these antigens with high affinity, they die.

If TCR interacts with MHC Class II CD4

If TCR interacts with MHC Class I CD8

If the binding is high affinity Apoptosis

If binding is intermediate, Foxp3 will be transcribed and the cells will become natural Tregs (CD25, CD4, Foxp3)

Use TGFb and IL-10

When T-Cells Meet Antigen:

Nave T-Cells migrates through the peripheral lymphoid tissue (using HEVs), sampling MHC complexes on Dendritic Cells.

Spleen does not have HEV.

The same rolling/sticking family proteins are needed for adhesion of the T-Cells through the HEV.

If they encounter something, they proliferation (Signal 1 and Signal 2)

If they do not bind, they continue going from Lymph Node to Lymph Node.

Clonal Selection:

Binding of APC by an antigen specific T-Cell, primarily in peripheral lymph organs

Signal 1: APCs present peptide-MHC (CD3) to TCR on CD4 T-Cells

Signal 2: APCs present co-stimulatory molecules to CD28 on T-Cell, leading to IL-2 production and IL-2R (CD25) expression.

Binds to CD80 or CD86 on the APC

Clonal Expression:

T-Cells are now receptive to autocrine (CD4) and paracrine (CD8) stimulation by IL-2 leading to proliferation.

Th1 helps CD8

Differentiation: T-Cells respond to Cytokines to become Effector and/or Memory T-Cells

Inducers of T-Cell Activation:

Allogenic MHC

Superantigens

Bacterial Exotoxins

Bind and Cross-Linked MHC Class II

Th0

Dendritic Cell presents Antigen to Th0

IL-12 and IFN-y T-Bet Th1 IFN-y Cell-Mediated Immunity, Type IV HSR (DTH) CD40L on T-Cells bind to CD40 on Macrophages

Th1 Cells also help for CTL Differentiation using Paracrine IL-2

Causes proliferation of Perforin and Granzymes in Granules.

IL-4 GATA 3 Th2 Il-4, IL-5, IL-13 Humoral Immunity, Type I HSR

TGF-B Foxp3 induced Treg TGFB, IL-10 Suppression of Immune Responses.

1st T-B Interaction: IgM, Somatic Hypermutation, Affinity Maturation

2nd T-B Interaction: Isotype Switching

IgM IgG1

TGFB and IL-6 RORyt Th17 IL-17 Inflammation (IL-8)

Types of Pathogens/Responses

Measuring CD4 T-Cell Activity:

Antigen-Induced Proliferation: Thymidine

Lymphocyte Proliferation (stimulation assay)

Mixed Lymphocyte Reaction (MLR) against Allogenic HLA-DR, -DP.

Amount of Cytokine Produced:

ELISA (soluble)

Numbers of Cytokine Secreting CD4 Cells:

ELISPOT (insoluble)

CTL or NK Cell Killing Activity

Cytotoxicity Assay

Immunization:

Passive:

Natural: IgG trans-placentally

Artificial: IgA Colostrum Secretory

Active:

Natural Infection

Artificial Vaccination

Graft Rejections:

TSA and TAA: