Microbiology · Exam 1 — Study Guide

1 · Review of General Microbiology

1.1 · Objective 1 — Molecular mechanisms influencing health and disease

Environmental factors also shape transmission: temperature and humidity (influenza is more stable and transmissible at low temperature and high humidity), where vectors can flourish, and human behavior — hygiene, vaccination rates and travel patterns.

1.2 · Objective 2 — Types of infectious pathogens

Viruses sit outside both, as noncellular infectious agents.

1.3 · Objective 3 — Standard and specialized bacterial structures

1.4 · Objective 4 — Morphology and Gram staining

Three shapes, and the lecture is explicit that shape matters for identification: cocci (spherical), bacilli (rod), and spiral (helical, comma, twisted rod, spirochete).

Peptidoglycan is a polymer of alternating N-acetyl glucosamine and N-acetyl muramic acid, crosslinked by a short peptide bridge between the terminal D-alanine and the penultimate diamino-containing amino acid. Crosslinking is catalyzed by transpeptidases — the target of beta lactam antibiotics. The link can be direct, or indirect through a pentaglycine spacer as in Staphylococcus aureus.

1.5 · Objectives 5 & 6 — Identification methods and culture media

Methods of bacterial identification: microscopic morphology · macroscopic morphology (colony appearance) · physiological and biochemical characteristics · chemical analysis · serological analysis · genetic and molecular analysis (guanine plus cytosine base composition, deoxyribonucleic acid analysis with genetic probes, nucleic acid sequencing and ribosomal ribonucleic acid analysis).

Requirements for growth divide into chemical — water, energy nutrients (carbohydrates, proteins, lipids), vitamins, minerals, oxygen levels — and physical — temperature, pH, osmotic pressure.

The categories combine: blood agar is enriched and differential (gamma, beta and alpha hemolysis); mannitol salt agar is selective and differential.

1.6 · Objective 7 — The bacterial growth curve

Growth means an increase in number, not size, by binary fission — which is why it is exponential rather than arithmetic.

1.7 · Objectives 8 & 9 — Phage and animal virus replication

All viruses have capsids — protein coats enclosing and protecting the nucleic acid — which may be helical, icosahedral or complex. They contain either deoxyribonucleic acid or ribonucleic acid, and may have an envelope or spikes.

1.8 · Objective 10 — Cytopathic effects of viruses

Virus-induced damage to cells: changes in size and shape · cytoplasmic inclusion bodies · nuclear inclusion bodies · cells fusing to form multinucleated cells · cell lysis · alteration of deoxyribonucleic acid, which may activate oncogenes · transformation of cells into cancerous cells.

Radiation and chemical exposure can activate oncogenes by the same route, which is why this slide links infection to malignant transformation rather than treating them separately.

1.9 · Objective 11 — Health implications of nucleic acid mutations

A mutation is a change in the base sequence of the genome which may impact the phenotype. Mutations occur naturally at a low level but may be induced by radiation, chemicals or viruses, and may be beneficial, neutral or deleterious.

1.10 · Objectives 12 & 13 — Microbial control and the death curve

Aseptic or sterile means removal of all forms of microbial contamination; disinfection means elimination of some. Depending on circumstances, lowering numbers rather than total elimination may be good enough.

Two basic mechanisms: alteration of membrane permeability, and denaturation of proteins and nucleic acids.

Antimicrobial chemotherapeutic agents should have selective toxicity — working against the microbial agent without harming the host. Synthetic agents include the sulfa drugs, made from coal tar dyes; antibiotics are substances naturally made by one microorganism against another, such as penicillin from the Penicillium mold, active against Gram-positive bacteria.

Source: Lecture 1 — Review of General Microbiology (Dr. Webster), Slides 1–70, and the PAJ 5200 syllabus instructional objectives.

2 · Antibiotics and Resistance

2.1 · Objective 1 — Major historical events in microbial control

2.2 · Objective 2 — Criteria for drug selection

What makes a good agent — there is no perfect drug, but the lecture lists: selective toxicity · favorable pharmacokinetics (reaching the target site at an effective concentration) · appropriate spectrum of activity (broad = large range of organisms, narrow = small) · lack of side effects · low direct toxicity · low potential for hypersensitivity · good therapeutic index · little resistance development.

Choosing the agent in practice: the disk-diffusion (Kirby Bauer) method reads a zone of inhibition against a chart correcting for concentration, molecular weight and other diffusion factors. The E test (“minimal inhibitory concentration on a stick”) reads that value directly in micrograms per milliliter, where the zone of inhibition meets the strip.

2.3 · Objectives 3 & 4 — Therapeutic index and drug clearance

2.4 · Objective 5 — Drug lines and their producing organisms

2.5 · Objective 6 — Mechanisms of action

2.6 · Objective 7 — Mechanisms of drug resistance

Resistance is the ability of a microorganism to avoid an antibiotic's harmful effects by destroying it, transporting it out of the cell, or undergoing changes that block its effects — three routes that reappear below as the biochemical mechanisms.

Biofilms enhance resistance three ways: a physical and chemical barrier limiting dissemination and sequestering antibiotics; organisms within are metabolically less active and so less susceptible; and close spatial relationship enhances resistance gene transfer.

Behaviors that drive resistance: misuse or overuse · outdated or weakened antibiotics · using antibiotics for the common cold and other inappropriate conditions · failing to complete the prescribed regimen · using someone else's leftover prescription. Wider contributors include antibiotics in animal feed, environmental warming, and possible correlations with pesticide use and microplastic contamination. Tracking is via the National Antimicrobial Resistance Monitoring System — an interagency partnership monitoring humans (Centers for Disease Control and Prevention), retail meats (Food and Drug Administration) and food animals (United States Department of Agriculture).

2.7 · Objective 8 — Other problems with antimicrobial therapy

Drug combinations are one approach to resistant organisms, with three possible results: indifference (no interaction), synergism (combined effect greater than either alone) and antagonism (combined effect less than either alone).

The future: antimicrobial peptides (nisin from lactic acid bacteria, magainin from frogs, cecropin from moths) · targeting biofilm organisms · antisense agents — complementary DNA binding a pathogen's virulence genes to prevent transcription, such as fomivirsen for cytomegalovirus retinitis · phage therapy.

Source: Lecture Number 2 — Antibiotics and Resistance (Dr. Webster), Slides 1–81, and the PAJ 5200 syllabus instructional objectives.

3 · Microbe-Human Interactions

3.1 · Objective 1 — Resident flora

Resident flora includes bacteria, fungi, protozoa, viruses and arthropods. Most areas of the body in contact with the outside environment harbor resident microbes; the large intestine has the highest numbers, mainly strict or facultative anaerobes. Internal organs and tissues are a different matter.

Normally sterile sites and fluids: heart and blood vessels · kidneys and bladder · brain and spinal column · middle and inner ear · interior of the eyes · blood and cerebrospinal fluid · urine in the kidneys and bladder · amniotic fluid surrounding the fetus.

3.2 · Objective 2 — The progression of an infectious disease

The sequence the deck builds, step by step:

Infectious dose (ID) is the minimum number of microbes or viral particles required for infection, usually expressed as ID₅₀ — the dose sufficient to infect 50% of a given population. A SMALL ID₅₀ means GREATER virulence, and therefore a greater degree of pathogenicity.

3.3 · Objective 3 — Endotoxins against exotoxins

The three virulence factor groups the deck names:

3.4 · Objective 4 — The stages in the course of an infection

3.5 · Objective 5 — Clinical manifestations

Sequelae are long-term or permanent damage to tissues or organs — paralysis from polio, blindness from gonococcal conjunctivitis, sterility from syphilis or another genital infection, deafness from meningitis, arthritis from Lyme disease.

3.6 · Objective 6 — Reservoirs of disease

A reservoir is the primary habitat from which a pathogen originates. It may be living or nonliving.

Zoonosis (plural zoonoses): infections of animals may spread to humans, and vice versa. They can be bacterial, viral, fungal or protozoan in origin — the category is defined by the reservoir, not the organism. A zoonotic infection cannot be completely eliminated without also eradicating the animal reservoir.

3.7 · Objective 7 — Nosocomial infections

Nosocomial infections, also written HAI (hospital-acquired infections), are diseases acquired or developing during a hospital stay. They may prolong the stay, or end in death.

3.8 · Epidemiology and Koch's postulates

Not separate objectives, but taught in this deck and fair game. Epidemiology is the study of the frequency and distribution of disease and other health-related factors in human populations. Reportable (notifiable) diseases must be reported to public health authorities; in the United States the CDC (Centers for Disease Control and Prevention) publishes the Morbidity and Mortality Weekly Report.

Over the last hundred years the death rate from infectious disease has dropped while morbidity has remained relatively high. People stopped dying of these illnesses; they did not stop getting them.

Koch's postulates (1880s):

1. Find evidence of a particular microbe in every case of a specific disease
2. Isolate it from an infected subject and cultivate it artificially in the laboratory
3. Inoculate a susceptible healthy subject and observe the resultant disease
4. Re-isolate the agent from the newly infected subject

They do not work well for all pathogens. Mycobacterium leprae and Legionella pneumophila are the two the deck names — step 2 is the sticking point when an organism cannot be cultivated artificially. Today they are of limited use, though still applied to bacterial, fungal and protozoan pathogens.

Molecular Koch's postulates (Falkow, 1988) exist because viruses and prions routinely break all the old rules:

1. The phenotype or property under investigation should be associated with pathogenic strains or species
2. Inactivating the gene or genes associated with the virulence trait should produce a measurable loss of pathogenicity
3. Reverting the mutated gene should restore pathogenicity

4 · Transmission of Microorganisms

4.1 · The chain of infection

Six links, in order. Break any one and transmission stops — which is the whole point of infection control.

1. The infectious agent — and its traits, including whether it is already drug resistant.
2. The reservoir, known or unknown.
3. The portal of exit from the infected host.
4. The mode of transmission to other hosts.
5. The portal of entry into the new host.
6. A susceptible host — and susceptibility varies between people.

4.2 · Reservoirs, and the four carrier states

Living reservoirs: humans, animals, and — the deck marks both with a question mark — plants and fungi. Non-living reservoirs: soil, water, air, food, and fomites.

Human reservoirs come in four states, and the distinction that matters is whether the person is actually infected:

• Symptomatic and infected — the obvious case.
• Asymptomatic and infected.
• Active carriers — infected, and may or may not show symptoms. Mary Mallon, “Typhoid Mary”, carried Salmonella typhi without symptoms in the early 1900s.
• Passive carriers — NOT infected, but still transmitting. The healthcare or food-service worker with poor hand hygiene.

4.3 · Zoonoses

Infections of animals that may spread to humans, and the reverse. They can be bacterial, viral, fungal or protozoan. Humans are often the accidental host — plague and anthrax are the examples given — with the lifecycle running through primary and secondary hosts.

Why they cannot be eradicated: you would have to eradicate the animal reservoir too, which is harder still when there are several. And a pathogen that lies dormant in an intermediate host as a fungal spore or protozoan cyst outlasts any campaign against the animal.

Occupational risk is named for veterinary medicine, farm work, landscaping, gardening, zookeeping and slaughterhouse or meat processing work.

4.4 · Vectors, and how they differ from reservoirs

A vector is a living thing capable of transmitting disease — mosquitoes, fleas and ticks; flies, fruit flies and cockroaches.

4.5 · The modes of transmission

By contact. Direct splits into vertical (mother to child) and horizontal (usually mucous membrane contact — sexual contact, kissing), plus droplets from coughing, sneezing, saliva, blood, sweat and tears. Indirect contact is transmission onto inanimate surfaces first — that is fomite transmission, and it is where the rest of the lecture goes.

By vehicle. Food — gastrointestinal illness is the commonest result. Water — drinking water, and also pools, spas and water parks. Soil — contaminating produce, hands and fingernails; pinworms in children. Air — usually, though not always, an indoor phenomenon, which is why ventilation, filtration and crowding matter.

4.6 · Fomites and hospital-acquired infection

A fomite is a non-living surface or object that may transmit pathogens. Hospital-acquired infection (HAI) costs longer stays, long-term disability, preventable deaths, expense, and risk to both safety and quality of care. It is most threatening to the immunocompromised, pediatric, geriatric and HIV patients, and those with open wounds, burns or recent surgery.

Clinical fomites named: scalpels and syringes; catheters — a particular problem with biofilm-forming Staphylococcus aureus and S. epidermidis; bed rails and gurneys; telephones, remote controls, keyboards and electronic devices; floors, mops, polishers, brooms and dustpans; pillows, bedding, furniture and curtains; and stethoscopes, neckties, stuffed animals, greeting cards and flowers.

And it is not only hospitals — a public restroom, hotel room, cruise ship cabin or aeroplane tray table is a fomite-filled room too.

4.7 · The studies, and what they did not do

4.8 · Disinfection, coatings and the history

Five best practices for non-critical surfaces, in order: standardize cleaning policy; select EPA-registered hospital disinfectants; educate ALL staff including environmental services; monitor compliance with feedback; implement no-touch decontamination technology.

The history: Semmelweis in the 1840s — handwashing with chlorine solution by obstetricians. Lister in the 1860s — handwashing and wound treatment with carbolic acid.

Chemical agents — bleach, quaternary ammonium salts, phenolics — work only at the correct concentration and for adequate contact time, and they are toxic. Ozone, high-concentration hydrogen peroxide and steam require the room to be vacant, take time facilities may not have, and can damage surfaces and devices.

Coatings borrow from marine anti-fouling paint — copper, arsenic, mercury and tin compounds since the 1960s. Anti-fouling prevents attachment; antimicrobial kills. A hospital coating should be nontoxic, cost effective, commercially available, stable and durable: plastics, copper or silver alloys, photocatalytic coatings, specialized textiles, micro-patterned hydrophobic surfaces.

4.9 · Fomites and antibiotic resistance

Extensive antibiotic use has driven multi-drug resistance, and MDR, XDR and TDR strains — MRSA and carbapenem-resistant Klebsiella pneumoniae among them — are especially problematic in hospitals. Biofilms are polymicrobial networks resistant to cleaning, heat and drugs; Staphylococcus and Pseudomonas form them.

A fomite carrying a persistent pathogen cannot be told apart from a clean surface. That single sentence is the argument for the whole chapter.

5 · Host Defenses: Nonspecific Mechanisms

5.1 · Objective 1 — The lines of defense

Three categories, and three lines. The categories are barriers (physical and chemical), fixed or hard-wired mechanisms (innate), and the adaptive immune response — the one vaccination exploits, and the only one giving long-term protection.

Two of the three are nonspecific, and that is the whole subject of this lecture. Notice also that the first line includes a genetic barrier — an unusual category that becomes concrete at the defensins in 5.3.

5.2 · Objective 2 — The first line: physical, chemical and genetic

The physical list: intact skin, mucous membranes, the ciliary escalator, the lacrimal apparatus, nasal hairs, saliva, urine, sweat, defecation, the expulsion mechanisms (coughing, sneezing, vomiting), and normal flora.

Normal flora is both barriers at once, and that is the point of it. Colonization begins after birth. On the epidermis it is Staphylococcus epidermidis, other coagulase-negative staphylococci, and coryneform bacteria. They compete for living space and nutrients — a physical barrier — and they produce antimicrobial substances — a chemical one.

Gut commensals do three things beyond blocking colonization: they digest substances we cannot, they provide vitamins, and they help develop gut-associated lymphoid tissue.

The chemical list: sebum, the acid mantle of skin, lysozyme (which acts on peptidoglycan), lactic acid and electrolytes in sweat, digestive secretions, semen (spermine, lysozyme, lactoferrin, phospholipase) and vaginal secretions (lactic acid, beta defensin, hydrogen peroxide). Those last two lists are worth keeping apart — they are easy to swap.

5.3 · Objective 3 — Key factors in innate immunity

Plasma proteins that limit infection: the coagulation system, the kinin system, protease inhibitors, defensins, pentraxins, the acute-phase response, inflammation and its cytokines, and complement.

Defensins are the predominant family of antimicrobial peptides: 30 to 40 amino acids, amphipathic — hydrophobic and hydrophilic regions — which is how they damage membranes. That mechanism sets their range: bacteria, fungi, and ENVELOPED viruses, because an envelope is a membrane.

They are also the only innate components that can neutralize a broad range of microbial toxins by unfolding them, changing their three-dimensional configuration. The deck calls them antichaperones — chaperones fold proteins, these do the reverse.

Pentraxins bind pathogen surfaces and target them for phagocytosis, bridging pathogen to phagocyte much as antibody does. Short pentraxins come from hepatocytes — serum amyloid P component and C-reactive protein; long pentraxins from myeloid, endothelial and epithelial cells.

The acute-phase response runs on one signal: bacteria induce macrophages to produce interleukin 6, which tells liver cells to raise the defensive plasma proteins and lower others, including albumin. C-reactive protein and serum amyloid A rise more than a hundredfold — which is precisely why C-reactive protein is used to diagnose infection, inflammation and tissue damage. It is a pentraxin opsonin.

5.4 · Objective 4 — The recognition system

Recognition has to sort three things, not two: healthy self, non-self, and altered self — tissue damaged or changed by viruses or cancer.

Each receptor recognizes a pattern shared by a pathogen FAMILY, which is how a limited set of receptors covers a wide range of organisms. Each cell carries a unique combination, which broadens the coverage further. Macrophages are very effective at bacterial and fungal carbohydrates using lectin receptors; natural killer cells at the changed surface proteins of a virus-infected cell.

Where a receptor sits determines what it does, and the Toll-like receptors make the point best:

Effector function then runs on cytokines. Some are cached in vesicles and released fast, some must be made on demand, and some are secreted only on cell-to-cell contact. Some are pro-inflammatory and some anti-inflammatory.

5.5 · Objectives 7 and 8 — Inflammation and fever

The five cardinal signs, described by Celsus in the first century: rubor (redness), calor (heat), tumor (swelling), dolor (pain), functio laesa (loss of function).

The inflammasome starts it. When macrophages sense infection, pathogen products drive assembly of a protein structure that converts pro interleukin 1 beta into functional interleukin 1 beta in large quantities. A second cascade opens pores in the macrophage membrane to release it — and that kills the macrophage, by pyroptosis. Mutations in inflammasome genes cause autoinflammatory diseases.

Getting the leukocytes out of the blood takes two adhesion steps and a squeeze:

1. Rolling — L-selectin on the leukocyte binds vascular addressin CD34 on the endothelium. Transient, so the cell rolls along the surface.
2. Firm adhesion — integrin LFA-1 binds the immunoglobulin-like ICAM-1.
3. Diapedesis — guided by chemokines, the neutrophil squeezes between endothelial cells to reach the infection.

Endothelial cells help by upregulating adhesion molecules and loosening their tight junctions.

Tumor necrosis factor alpha is the same molecule doing opposite things at different scales, and this contrast is exam-shaped:

Containment at one site; catastrophe everywhere at once.

5.6 · Objective 11 — Complement

More than thirty proteins, ubiquitous in blood and lymph, circulating as inactive zymogens and activated by cleavage in a cascade. Its activity comes from a unique high-energy thioester bond.

The thioester bond is the mechanism. Activation cleaves C3 into C3a and C3b, exposing the bond on C3b. It then has two fates: attacked by water, it becomes soluble and does nothing; or it reacts with a hydroxyl or amino group on a pathogen surface and attaches. That is complement fixation, and it marks the pathogen for destruction. Meanwhile C3a recruits phagocytes.

All three converge on cleaving C3, which is why the deck calls C3 by far the most important molecule in the cascade — the pathways differ mainly in how they reach it. They were discovered in a different order (classical, alternative, lectin), and the system is called “complement” because it was thought to complement the specific immune system.

Regulation is what keeps it off your own cells, and the four regulators split cleanly:

C3b is the opsonin — a protein bound to a pathogen that facilitates phagocytosis. Complement receptor 1 binds it to drive phagocytosis, and does double duty protecting human cells by disrupting C3 convertase.

Then the cascade escalates. C3b binding existing C3bBb makes the alternative C5 convertase, which cleaves C5. C5a recruits neutrophils and is the most potent anaphylatoxin; C5b initiates the membrane attack complex. Human cells are protected from that too — S protein, clusterin and factor J stop C5b, C6 and C7 associating with membranes, and homologous restriction factor and CD59 (protectin) stop C9 joining a complex that has already attached.

5.7 · Objective 10 — Interferon

All are produced in response to viruses, RNA, immune products and various antigens; they bind cell surfaces and induce expression of antiviral proteins, and they inhibit expression of cancer genes and suppress tumors.

5.8 · Objectives 5 and 6 — Leukocytes and the differential

Learn the percentages — they are what the differential count is read against.

Mast cells are related to basophils but nonmotile and bound to connective tissue; whether they share a common progenitor is unsure. A macrophage is the final differentiation of a monocyte, in tissue, and takes special names in particular tissues.

The differential white count totals the number of each type and determines whether they are in normal proportion — proportion, not just total. It is used in diagnosing infection types, inflammation, allergies, immune disorders, leukemia and myelodysplastic syndrome.

Phagocytosis is done principally by macrophages and neutrophils, and the division of labor matters:

The respiratory burst: when the engulfed organism meets the neutrophil granules, NADPH oxidase produces superoxide, which picks up hydrogen ions and raises the pH so the digestive granules can break the organism down. Toxic oxygen species can diffuse out and damage host cells, so phagocytes make enzymes such as catalase to inactivate them.

Neutrophils cannot replenish their granules, so they die. Some are phagocytosed by macrophages. Dead organisms, dead neutrophils and dead tissue form pus. Others undergo netosis — bursting so their DNA and defensive proteins form a neutrophil extracellular trap that catches and kills microbes.

Dendritic cells patrol tissue, take up antigen and carry it to the nearest lymph node for T cells. Whether they arrive mature matters: an immature one fails to make a good connection for activation. Plasmacytoid dendritic cells are professional interferon producers — within six hours of activation, 60% of the cell's transcription is making type 1 interferon.

5.9 · Natural killer cells and the innate lymphoid cells

Five innate lymphoid types: natural killer cells, then ILC1 (intracellular pathogens, holding the line until natural killer cells arrive), ILC2 (mucosal, against large extracellular parasites like worms), ILC3 (extracellular bacteria and fungi, abundant in mucosa, containing gut commensals), and lymphoid tissue inducer cells, which build secondary lymphoid tissue.

Natural killer cells are large lymphocytes with cytotoxic granules, giving innate immunity against intracellular infection. Two effector functions split by subpopulation: CD56 dim kills virally infected cells; CD56 bright secretes cytokines to maintain inflammation. A special CD56 bright group in the uterus works with fetal trophoblasts to enlarge the spiral arteries and enhance blood flow to the fetus — and preeclampsia is postulated to involve abnormal killer-cell immunoglobulin-like receptor activity, more inhibitory than activating.

Their cytotoxicity rises 20 to 100 fold on exposure to interferons alpha and beta. Four cytokines activate them early; interferons favor the cytotoxic function while interleukin 12 favors cytokine production.

They cooperate in both directions. Macrophages recruit and activate natural killer cells; those return interferon gamma, which enhances macrophage phagocytosis and cytokine secretion. And if natural killer cells cannot contain the infection, they stimulate dendritic cells to migrate to secondary lymphoid tissue and start an adaptive response — control passes to T cells.

5.10 · Where it happens, and how the two systems fit

Encounters occur in the reticuloendothelial system, extracellular fluid, the bloodstream and the lymphatic system. Lymphatic capillaries reach everywhere except the central nervous system, bone, placenta and thymus, and act as the drain-off system for inflammation as well as providing surveillance.

The induced innate response fills the gap from four hours to four days. It is still nonspecific — it does not differ by invader — but uses more extensive pattern recognition by macrophages, neutrophils and dendritic cells.

6 · The Acquisition of Specific Immunity

6.1 · Objective 1 — The four kinds of acquired immunity

Specific immunity is adaptive and highly specific, acquired through contact with infectious agents — against innate immunity, which we are born with. A special type of innate immunity is species immunity: illnesses we cannot contract because we are human.

Acquired immunity sorts on two axes at once — active or passive, and natural or artificial. Four boxes, and the exam will want you to place a scenario in one:

Two numbers from this section. Children acquire 99% of natural passive immunity in utero — nursing adds beneficial microbes and maternal antibody the placenta cannot pass, but the bulk arrives before birth. And antibody titres are what tell you whether a vaccine on your record is still measurably effective, or whether a booster is needed before starting a hospital or laboratory post.

6.2 · Objective 2 — The leukocytes, in order

All five originate in the bone marrow, and are counted by manual examination of a stained blood smear or by automated hematology.

6.3 · Objectives 3 and 6 — MHC, and the genetics of self

The Major Histocompatibility Complex is also called human leukocyte antigen. Its receptors are on all cells except red blood cells, and its genes sit on chromosome 6 in a multi-gene complex of classes I, II and III. It does two jobs: recognition of self, and rejection of foreign tissue — the same system, read two ways.

Each person inherits a unique MHC profile, but it can be close enough to another's to allow transfusion or transplantation — which is also the requirement for marrow donation in 6.9.

Clonal selection is the genetic answer to objective 6, and the order of events is the part that catches people:

1. Lymphocytes use more than 500 genes to build their receptors.
2. Undifferentiated lymphocytes divide and mutate continuously in the embryo and fetus, generating millions to billions of cell types, each with a unique receptor.
3. Any clone with a specificity for self is eliminated before the fetus is harmed. A defect here gives an inherited autoimmune disorder such as severe combined immunodeficiency.
4. The surviving naive pool holds 10¹⁴ to 10¹⁸ possible variations — up to a quintillion — waiting in lymphatic tissue.

6.4 · The two receptors

The variable-region genes are locked in for the life of the cell and its progeny, including its memory cells. The first receptor on a young B cell is a small version of IgM; mature B cells carry IgD.

Maturation splits by organ. B cells are directed by bone marrow stromal cells and migrate to lymph nodes, spleen and gut-associated lymphoid tissue. T cells are directed by the thymus and its hormones — which is why the thymus unites the immune and endocrine systems. T-cell receptors are the CD markers (cluster of differentiation): CD4 on helper cells, CD8 on cytotoxic cells.

6.5 · Antigens and their special categories

An antigen is anything provoking a response in specific lymphocytes — it must be perceived as foreign and be big enough to attract attention. The antigenic determinant or epitope is the small molecular group actually recognized, and one antigen may carry many.

Size decides antigenicity. Foreign cells and complex molecules over 100,000 molecular weight are the most antigenic, and usually large proteins. Molecules under 1,000 — haptens — are generally not antigenic unless attached to a larger carrier. Drugs, metals and industrial chemicals behave this way, which is how an occupational allergy to latex or cleaning chemicals arises.

6.6 · Objective 7 — Presentation, and the two interleukins

T-cell dependent antigens must be processed by an antigen-presenting cell, which alters the antigen and attaches it to its class II MHC receptor. Presentation is a three-way collaboration: APC, T helper cell, and an antigen-specific B or T cell.

Once B cells process antigen, interact with helper cells and receive growth and differentiation factors, they undergo clonal expansion into plasma cells, which secrete antibody, and memory cells — which pause partway through mitosis. That pause is why the secondary response is so much faster.

The naming. B-cell responses are antibody-mediated immunity (or humoral-mediated in older texts); T-cell responses are cell-mediated immunity.

6.7 · Objective 4 — The five immunoglobulins

Structure first. A large Y-shaped protein of four chains. The two identical Fab ends (antigen-binding fragment) bind antigen; the Fc end (crystallizable fragment) binds cells of the immune system and allows the molecule to swivel.

Four things antibody does once bound — and each has a mechanism worth separating:

6.8 · Objective 5 — Primary against secondary response

The secondary response is also called the anamnestic response. Titre is measured in binding antibody units (BAU), and in a healthy person with robust responses it does not fall to zero between exposures.

T cells and cell-mediated immunity. T cells act directly against antigen and foreign cells but require MHC activation. All of them produce cytokines; sensitized T cells become long-lasting memory T cells. Four types:

6.9 · The applications

Passive immunization (immunotherapy) gives short-term protection — on the order of two to three months. Early use transfused horse serum antitoxins for tetanus and diphtheria; horse sera are still sometimes used for diphtheria, botulism and spider or snake bites, with serum sickness or anaphylaxis as the risks. Current pooled gamma globulin is used for hepatitis A and B, HIV, measles and generally immunodeficient patients. Convalescent plasma and monoclonal antibodies have a role in viral infection.

Vaccination is deliberate exposure to material that is antigenic but NOT pathogenic. The practice reached England through Lady Montagu; the first effective human vaccination was Jenner's, using cowpox against smallpox; Pasteur later developed one against rabies.

An effective vaccine should have low toxicity, protect against exposure, stimulate BOTH antibody-mediated and cell-mediated responses, produce lasting memory B and T cells, generally not need numerous doses or boosters, and be inexpensive, easy to give and long-lived on the shelf. A sterilizing vaccine — one leaving the target non-functioning and unable to mutate — would be best of all.

Most vaccines contain killed whole cells or inactivated viruses; live attenuated organisms; acellular or subunit antigens; toxoids from purified antigenic components; or genetically engineered organisms or antigens.

Marrow and stem cell donation requires a close class I MHC match plus further DNA compatibility testing. Marrow is harvested from the sternum, femur or iliac crest; circulating peripheral stem cells are collected by apheresis after a mobilizing drug. The recipient receives drug and radiation therapy beforehand to reduce the risk of rejecting the donor cells.