Topic 6 - Microbiology, Immunity and Forensics

Microbial culture requires sterile media, equipment and technique so that the organism being studied is not outcompeted or confused with contaminants. Aseptic handling protects the sample, the investigator and the environment.

Sterilise media and apparatus, disinfect the work area, minimise exposure of plates or broths, and label controls. Compare growth with a negative control to detect contamination.

If a plate exposed briefly during inoculation grows colonies outside the intended streak, those colonies may be contaminants rather than evidence about the tested organism.

A clear plate does not prove sterility, and opening a culture outside controlled conditions can create a safety hazard. Use the required containment and disposal procedure.

Microbial growth can be estimated by counting colonies, measuring turbidity or tracking another validated proxy. The method must be consistent so that differences reflect population change rather than sampling or instrument variation.

Use a known dilution or counting area, repeat measurements, keep incubation conditions constant and plot the proxy against time. A calibration is needed before converting absorbance or turbidity into cell number.

Two cultures with the same turbidity reading may contain different cell sizes or clumps, so direct colony counts or a calibration curve may be needed to compare viable cells.

Optical density measures cloudiness, not automatically living cells. Do not infer growth rate from one endpoint or compare values made with different dilution and timing conditions.

A microbial culture typically passes through lag, exponential, stationary and death phases. The rate changes as cells adapt, divide rapidly, exhaust nutrients, alter pH or accumulate toxic waste.

Growth rate is a change over time, not simply the final number of cells. A constant-rate assumption is only sensible over the relevant part of the exponential phase.

A culture may show a steep increase after adaptation, then level off when oxygen or nutrients become limiting. Changing the aeration or substrate can shift the phase boundaries.

A stationary phase does not mean cells are all dead, and an optical reading is not automatically a viable-cell count. State the measured proxy and time interval.

To investigate microbial growth, inoculate a known medium, incubate under controlled conditions and measure a consistent proxy at regular intervals. Aseptic technique prevents contaminants changing the curve.

Use replicates, a blank or negative control, calibrated dilution or turbidity measurement, and safe containment. Plot the proxy against time and identify where the rate changes.

If absorbance rises while a blank stays stable, the culture likely became more turbid; a calibration or viable count is needed before converting that reading into cell number.

A single endpoint cannot establish a growth rate, and open cultures or unsafe disposal can expose people to pathogens. Follow the specified containment level.

Bacteria are prokaryotic cells with cytoplasm, ribosomes, a circular chromosome and usually a murein wall. Viruses contain DNA or RNA in a protein capsid and may have an envelope, but no cytoplasm or ribosomes.

A bacterium can carry out its own metabolism and divide. A virus must enter a living cell and redirect host machinery to make viral components, so antibiotics that target bacterial structures do not treat viral infection.

A plasmid can carry a bacterial gene, whereas a virus attaches to a host using surface proteins and releases its genome. Both can cause disease, but their replication mechanisms differ.

Do not call a virus a cell or assume every virus has a lipid envelope. Distinguish structure, replication and treatment.

Mycobacterium tuberculosis is a bacterium transmitted in airborne droplets; HIV is an enveloped RNA retrovirus transmitted through infected body fluids. Disease outcome depends on entry route, pathogen biology and the host immune state.

TB can remain dormant inside tubercles and reactivate when immunity is weakened. HIV targets immune cells and progressively reduces immune defence, increasing susceptibility to opportunistic infections.

Overcrowding increases TB transmission through inhaled droplets, while sharing contaminated needles can transmit HIV. The prevention strategy must match the route rather than treat “infection” as one mechanism.

Infection is not identical to immediate disease, and an HIV-positive person is not defined by one opportunistic illness. State the pathogen, route and immune consequence.

Pathogens can enter through broken skin, food and drink, the respiratory tract or mucosal surfaces. Skin, clotting, gut flora, stomach acid and lysozyme reduce entry or survival before a specific immune response is needed.

Each barrier uses a different mechanism: intact skin blocks access, a clot seals damage, resident microbes compete, acid harms swallowed pathogens and lysozyme damages bacterial walls.

A cut bypasses the skin barrier, but clotting limits further entry; a swallowed pathogen must also survive stomach acid and compete with gut flora before reaching intestinal tissue.

A barrier lowers risk rather than guaranteeing protection. Do not confuse lysozyme’s bacterial-wall action with a general antiviral response.

Non-specific responses act against many pathogens and begin rapidly. Histamine-driven inflammation changes blood flow and capillary permeability; interferons limit viral replication; phagocytes engulf and digest foreign material.

During phagocytosis, a phagocyte recognises non-self antigens, encloses the pathogen in a vacuole, lysosomes fuse with it and digestive enzymes break it down. Antigen presentation can then initiate a specific response.

A splinter can trigger local swelling as histamine recruits fluid and phagocytes. A virus-infected cell can release interferons that warn nearby cells and activate immune defences.

Non-specific does not mean unregulated or ineffective, and it is not the same as antibody specificity. Keep inflammation, interferon action and phagocytosis as distinct mechanisms.

Antigens are surface markers that distinguish self from non-self. An antibody has a variable region whose binding site is complementary to a particular antigen, so the antigen–antibody complex is specific.

Specific binding can neutralise toxins, block pathogen attachment or agglutinate pathogens for easier removal. Phagocytes can present pathogen antigens to activate lymphocytes.

An antibody against a bacterial surface antigen can bind that bacterium but not a different pathogen with another epitope; the variable region, not the constant region, provides the matching site.

Antibodies do not recognise every pathogen equally, and binding alone is not the same as killing. Keep antigen recognition, antibody action and later cell-mediated responses distinct.

A T cell with the matching receptor binds antigen presented on a cell surface, then divides by mitosis to make clones. The clones differentiate into helper, killer and memory T cells.

Helper T cells release signals that activate B cells; killer T cells destroy infected cells displaying the relevant antigen; memory T cells make a later response faster.

An infected body cell can present a viral antigen and activate a matching killer T cell. A helper T cell does not itself secrete the pathogen-specific antibody; it supports the B-cell response.

T-cell receptor specificity is not the same as antibody secretion. State the antigen-presenting cell and the T-cell subtype before describing the outcome.

Active immunity follows exposure to an antigen and creates memory cells. It can be natural after infection or artificial after vaccination. Passive immunity transfers antibodies from another source and does not create memory.

Active responses are slower initially but usually longer-lasting; passive protection is immediate but temporary. Vaccination presents antigen without needing the disease itself to establish memory.

Antibodies crossing the placenta are natural passive immunity, while a vaccine is artificial active immunity. An antitoxin injection gives passive antibodies and may need repeating.

Antibody presence does not prove active immunity. A vaccine may need updating when pathogen antigens change, and passive antibodies do not train a secondary response.

An evolutionary arms race occurs when pathogen variants that evade immunity reproduce more successfully while host defences favour recognition and removal. The changing pathogen and host populations create reciprocal selection pressures.

HIV can vary its antigens, kill helper T cells and reduce antigen presentation; Mycobacterium tuberculosis can interfere with lysosome fusion and persistence inside phagocytes.

Memory cells against one viral strain may not recognise a mutated antigen, so the host faces a new primary-like response while the new strain spreads.

Co-evolution does not mean every mutation is advantageous or that immunity disappears completely. Identify the evasion mechanism and the selection consequence.

Bactericidal antibiotics kill bacterial cells, whereas bacteriostatic antibiotics inhibit growth so the immune system can remove the slowed population. At a sufficiently high dose, a bacteriostatic drug may become lethal.

Antibiotics target bacterial structures or processes such as murein-wall synthesis, ribosomes, membranes or DNA handling. Human cells and viruses lack the corresponding bacterial targets.

A drug that prevents a strong bacterial wall can cause osmotic lysis; one that binds bacterial ribosomes can halt protein synthesis without directly bursting the cell.

Antibiotics do not treat viruses, and “no growth” is not the same as “no viable cells”. The drug mechanism and target determine the outcome.

To compare antibiotics, spread a known bacterial culture on sterile agar, place equal-sized antibiotic discs and measure the clear zones after the same incubation. A larger zone suggests greater inhibition under those conditions.

Use aseptic technique, a distilled-water negative control, equal disc size and concentration where possible, replicate plates and consistent incubation. Invert plates to reduce condensation and use safe temperature/containment.

If tetracycline produces a 14 mm zone and methicillin 8 mm on the same strain, tetracycline inhibited growth more in that assay; the result does not automatically establish clinical choice.

Zone diameter depends on diffusion, concentration, agar and bacterial growth rate, not only antibiotic potency. Do not compare zones from different protocols without calibration.

Hospital-acquired infection risk is reduced by interrupting transmission: identify the pathogen and reservoir, clean or sterilise equipment, isolate cases, use hand hygiene and protect vulnerable patients.

Different controls act on different links. A disinfectant reduces environmental load, aseptic technique prevents transfer during procedures, and antibiotic stewardship reduces selection for resistant strains.

A catheter-associated infection needs both sterile insertion and ongoing site care; treating only the patient after symptoms appear leaves the route of transmission unchanged.

“Sterile” equipment and “clean” surfaces are not interchangeable, and an infection-control measure is not automatically effective without compliance and monitoring.

Bacteria and fungi secrete enzymes that digest large molecules in dead tissue into smaller molecules. They absorb and respire these products, releasing carbon dioxide and sometimes methane.

Decomposition returns carbon to the atmosphere and leaves nutrients available for reuse. Oxygen availability changes the pathway and the gases produced.

In an aerobic compost heap, decomposers release carbon dioxide while breaking down plant material; an anaerobic saturated site can produce methane instead.

Decomposers do not “destroy” carbon; they transfer it between organic matter, gases and soil. Gas output depends on conditions, not a fixed single product.

PCR copies a selected DNA sequence in vitro. Primers define the region, heat separates strands, primers anneal at a lower temperature and thermostable DNA polymerase extends complementary strands.

Each cycle can double the target, so a tiny starting sample becomes enough for profiling or analysis. The polymerase must survive the high denaturation temperature.

A 20-cycle run can produce roughly a million copies from a single target molecule under ideal doubling; a missing primer or wrong annealing condition prevents selective amplification.

PCR amplifies the chosen region; it does not identify a person by itself. Contamination can be amplified too, so controls and the target sequence matter.

DNA is negatively charged, so an electric field moves it toward the positive electrode. In an agarose gel, smaller fragments pass through pores more easily and travel farther than larger fragments.

Load samples with a known DNA standard, keep the polarity correct, run the gel consistently and compare band positions. A stain or fluorescent tag makes fragments visible.

A sample band aligning with the same-size standard indicates similar fragment length. A matching pattern across several markers is stronger evidence than one shared band.

Bands show fragment lengths, not whole-genome identity by themselves. Smearing, wrong polarity or overloaded wells can make a pattern unreliable.

DNA profiling uses PCR and gel electrophoresis to produce a pattern of fragments from a sample. Because unrelated people usually differ at variable regions, matching several bands can support an identity or relationship claim.

The conclusion depends on sample quality, contamination control, marker choice and the population frequency of the pattern. Identical twins are a special limitation because their DNA profiles are highly similar.

A crime-scene sample with bands matching a reference at every tested marker supports common source, but the strength of that inference depends on how rare the combined pattern is and whether the sample could be mixed.

A match is evidence, not absolute proof of guilt. Distinguish “same profile” from “same person” and report uncertainty and chain of custody.

Forensic time-of-death estimates combine decomposition, insect succession, body cooling and muscle stiffening. Each clue changes over time but is also affected by temperature, oxygen, clothing, humidity and location.

No single measurement gives an exact time. Independent clues can narrow an interval, while a mismatch may reveal that the environment differs from the assumed model.

A cooling body suggests time since death from the temperature difference, while blowfly larvae indicate an insect life stage; together they can constrain the estimate more than either clue alone.

Rates such as body cooling are not universal constants. State the environmental assumptions and distinguish an estimate from a precise timestamp.