Microbiology & Immunology

Microbes, the immune response to them, and how infections spread

About this course

Microbial growth, metabolism and diversity, viruses, antibiotics and resistance, then innate and adaptive immunity, vaccines, epidemic models and the microbiome.

What you will be able to do

  • Model microbial growth kinetics and describe the metabolic diversity of microbes
  • Explain how antibiotics act and how resistance evolves
  • Distinguish innate from adaptive immunity and explain clonal selection
  • Explain how vaccines produce immunological memory
  • Use the SIR model and its extensions to analyse the spread of an infection

What this course covers

  • Innate immunity overview and neutrophil budget
  • Neutrophil recruitment: rolling, adhesion, and chemotaxis
  • Complement cascade: amplification and self/non-self targeting
  • The infection race: bacterial exponential vs. immune response
  • Model robustness: evasion, exhaustion, and abscess as parameter changes
  • Fever's metabolic cost and competitive advantage
  • Worked abscess Fermi and the delivery constraint
  • Microbial size, surface-to-volume ratio, and diffusion
  • Optical resolution limit and the history of microbiology
  • The microbial census: body and Earth
  • Two genomes and two clocks: prokaryote vs. eukaryote
  • "Small is fast" as a law, not a lab artifact
  • The ATP budget of a bacterial division
  • Three-number framework and the infection exponential
  • The virion: genome in a box and one-step growth
  • Lysis versus lysogeny: two programs, one switch
  • Multiplicity of infection and Poisson landing
  • Phage–host coexistence: encounter rate and ecology
  • HIV two-phase decay and ten billion virions per day
  • Mutant counting and the three-drug rule
  • Worked example: one-step experiment arithmetic
  • Epidemic threshold and the Kermack–McKendrick result
  • SIR model: three equations and R nought
  • Final size equation and overshoot
  • Peak height, timing, and flattening the curve
  • SIR limits and heterogeneity (superspreaders)
  • Reading R nought from the doubling time
  • Capstone: worked school-outbreak example
  • Antibody binding: the dissociation constant KD
  • Antibody structure: the Y-shaped molecule
  • Combinatorial gene shuffling: V(D)J recombination
  • Self-tolerance: negative selection and its limits
  • Affinity maturation: selection in the germinal center
  • Avidity: two-armed binding on repetitive surfaces
  • ELISA: reading KD from a binding curve
  • Selective toxicity and the five antibiotic targets
  • Minimum inhibitory concentration (MIC) and breakpoint
  • The kill curve: Emax model and plateau
  • Why the MIC tube is not a simple boundary
  • Pharmacokinetics: peak, half-life, and time above MIC
  • Course length: logs killed per day and the margin day
  • Dosing regimen worked example: MIC at the breakpoint
  • Exponential growth and Monod's law
  • Ribosome speed limit on μmax
  • The batch culture curve
  • Yield and carbon accounting
  • The chemostat and steady-state growth
  • Chemostat as model for body compartments
  • Fermi estimate: one cell to a planet
  • Latency and the SEIR model
  • Generation interval and R₀ estimation
  • Branching process and extinction probability
  • Survivorship bias in pandemic emergence
  • Superspreading and the negative binomial
  • Endemic steady state, age at infection, and vaccination threshold
  • Worked example: seeds needed for outbreak under real dispersion
  • The Fluctuation Test and Jackpot Distribution
  • Mutation Rate from Empty Plates
  • Pre-existing Mutants and the Selective Sweep
  • Fitness Cost and Compensatory Mutation
  • The Mutant Selection Window
  • Plasmid Conjugation and Horizontal Gene Spread
  • Resistance as Evolution: Unifying Framework
  • The gut microbiome census
  • How the census is taken: from culture to sequencing
  • Fiber fermentation and energy contribution
  • Infectious dose: stomach acid and colonisation resistance
  • Community dynamics and the second stable state
  • Fecal microbiota transplant: trial evidence and NNT
  • Gut refill kinetics and the worked example
  • The Redox Tower: Free Energy from Electron Donors and Acceptors
  • The Biological Energy Quantum
  • ATP per Glucose and Yield by Electron Acceptor
  • Rate–Yield Trade-off and the Crabtree Effect
  • Chemolithotrophy and Syntrophy at the Tower's Margins
  • The Winogradsky Column: Tower Laid on Its Side
  • Worked Example: E. coli Switching from Oxygen to Nitrate
  • Clonal selection and clone growth
  • Lymph node anatomy and germinal centre dynamics
  • Repertoire sizing and the Poisson coverage argument
  • Why the winning clone does not take over the immune pool
  • T-cell readout: nine-residue peptides on MHC
  • Thymic selection and the blind-spot argument
  • Thymic funnel Fermi and the days memory saves
  • UPGMA tree construction from distance matrix
  • Why 16S ribosomal RNA is the universal barcode
  • The molecular clock and its saturation limit
  • Robustness of tree shape despite clock assumptions
  • Protein stability curve and extremophile adaptation
  • Horizontal gene transfer and the limits of a single tree
  • Fermi estimate of microbial diversity
  • Primary vs. secondary immune response
  • Vaccine types and what goes in the syringe
  • Antibody decay and booster scheduling
  • When circulating titre matters vs. memory alone
  • Vaccine efficacy and trial design
  • Herd immunity threshold and clustering
  • Worked example: lifetime booster schedule

Syllabus

  1. The Microbial World

    1. L1 · The Microbial World
    2. L2 · Growth Kinetics
    3. L3 · Metabolic Diversity
    4. L4 · Archaea and the Tree

  2. Viruses and Antibiotics

    1. L5 · Viruses
    2. L6 · Antibiotics
    3. L7 · Resistance as Evolution

  3. Immunity

    1. L8 · Innate Immunity
    2. L9 · Antibodies
    3. L10 · Clonal Selection
    4. L11 · Vaccines and Memory

  4. Epidemics and the Microbiome

    1. L12 · SIR
    2. L13 · Beyond SIR
    3. L14 · The Microbiome, and the Close