Expert-level microbiology covering bacterial and viral biology, microbial physiology, pathogenesis, antimicrobial resistance, microbiome science, and industrial microbiology.
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Cell structure: peptidoglycan wall (Gram+/Gram-), membrane, flagella, pili. Gram staining: crystal violet — Gram+ purple, Gram- pink after decolorization. Growth phases: lag, exponential, stationary, death. Metabolism: aerobic, anaerobic, fermentation, chemolithotrophy. Genetics: horizontal gene transfer (conjugation, transformation, transduction).
Structure: capsid, envelope, genome (DNA or RNA, ss or ds). Replication cycle: attachment, entry, replication, assembly, release. Lytic vs lysogenic: phage lambda as model. Reverse transcriptase: retroviruses, HIV replication. Viral evolution: mutation rates, reassortment, recombination.
Virulence factors: adhesins, toxins, capsules, immune evasion. Toxins: endotoxin (LPS), exotoxins (A-B type, pore-forming, superantigens). Biofilm formation: quorum sensing, matrix production, antibiotic tolerance. Intracellular pathogens: Mycobacterium, Listeria, Salmonella — escape mechanisms.
Mechanisms: enzymatic inactivation, target modification, efflux pumps, reduced uptake. Beta-lactamases: ESBL, carbapenemases (KPC, NDM, OXA). MRSA: mecA gene, altered PBP2a. Resistance spread: plasmids, transposons, integrons — horizontal transfer.
Gut microbiome: 38 trillion bacteria, Bacteroidetes/Firmicutes ratio. Dysbiosis: altered composition linked to IBD, obesity, mental health. 16S rRNA sequencing: V3-V4 region, OTU clustering, diversity metrics. Shotgun metagenomics: functional profiling, strain-level resolution.
| Pitfall | Fix |
|---|---|
| Contamination in cultures | Use sterile technique, include negative controls |
| Ignoring biofilm in AMR studies | Planktonic MIC underestimates biofilm tolerance |
| Misidentifying Gram reaction | Some organisms have atypical staining |
| Confusing bacteriostatic and bactericidal | Time-kill assays needed to distinguish |
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Expert-level abstract algebra knowledge. Use when working with groups, rings, fields, modules, Galois theory, representation theory, or algebraic structures. Also use when the user mentions 'group', 'ring', 'field', 'homomorphism', 'isomorphism', 'normal subgroup', 'quotient group', 'Sylow theorem', 'Galois theory', 'polynomial ring', 'ideal', 'module', 'vector space', or 'representation theory'.
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Expert-level acoustics knowledge. Use when working with sound waves, acoustic propagation, resonance, standing waves, Doppler effect, room acoustics, ultrasound, noise control, musical acoustics, or architectural acoustics. Also use when the user mentions 'sound wave', 'decibel', 'frequency', 'resonance', 'standing wave', 'Doppler effect', 'acoustic impedance', 'reverberation', 'ultrasound', 'noise control', 'harmonics', or 'sound intensity'.
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Expert-level aerodynamics covering subsonic and supersonic flow, lift and drag, airfoil theory, boundary layers, compressible flow, and CFD methods.
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Expert-level air quality engineering covering pollutant sources, atmospheric dispersion, air quality standards, emission controls, and air quality modeling.
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Expert-level aircraft structures covering structural design philosophy, wing and fuselage analysis, fatigue and damage tolerance, composite structures, and certification.
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Expert-level algorithms and complexity theory covering sorting, searching, graph algorithms, dynamic programming, greedy algorithms, NP-completeness, and algorithm design paradigms.
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