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Module 1.2: Experimental workflow activity

You have worked through five stages of an omics study and ten considerations that shape what a dataset can support. Apply them to one of the scenarios below.

Activity: diagnose a study across the workflow

Choose one scenario. For the study described, answer:

  1. At which stage are the decisions most constrained, and why?

  2. Identify two considerations that pose the greatest risk to the conclusions.

  3. What would a reader need to know to reproduce the analysis and evaluate whether the findings are generalisable?

Clinical / human disease

A population of patients presents to hospital with heart failure of unknown aetiology. Echocardiography shows reduced ejection fraction and dilated ventricles, but standard clinical workup has not identified a cause. Left ventricular biopsies are collected at the time of surgical intervention and stored. A subset of patients have first-degree relatives with similar presentations, suggesting a possible heritable component; others have no family history.

Cardiomyocytes in failing hearts undergo transcriptional reprogramming, reactivating a fetal gene programme, and shift metabolic substrate preference from fatty acids toward glucose. Sarcomeric proteins may carry inherited variants that alter contractile force. Mitochondrial dysfunction is common but whether it is cause or consequence is often unclear. The same clinical endpoint can arise from fundamentally different molecular origins.

Biopsy-derived material is limiting. Matched blood samples and, for some patients, germline DNA from saliva are also available.

Aquaculture / production biology

A cohort of Atlantic salmon is reared under identical conditions — same tank, same feed formulation, same feeding schedule — yet body mass diverges substantially within a single cohort over a grow-out cycle. By harvest, the heaviest individuals may be twice the mass of the lightest, with no obvious behavioural or health explanation.

Skeletal muscle growth in fish occurs through hypertrophy and hyperplasia, both regulated by the GH/IGF-1 axis with myostatin as a negative regulator. Nutrient sensing through mTOR integrates amino acid availability with anabolic signalling. Feed conversion efficiency varies between individuals and is partly heritable. Gut microbiome composition also differs between individuals in the same tank and can alter host nutrient absorption independently of diet. Early thermal or nutritional experience during embryogenesis can programme lasting metabolic differences.

Liver, skeletal muscle, gut tissue, and blood are all accessible. Individual fish can be tagged and tracked longitudinally, allowing repeated blood sampling, though tissue biopsies are terminal.

Wildlife / infectious disease

Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), has driven amphibian population collapses globally. Exposure to the same pathogen produces markedly different outcomes across and within species: some populations suffer near-total mortality, others show subclinical infection and persist, and a small number of previously decimated populations appear to be recovering.

Bd targets keratinocytes in the skin, disrupting Na⁺/K⁺-ATPase activity and causing osmotic imbalance. Granular glands secrete antimicrobial peptides with direct antifungal activity, and skin microbiome composition varies between individuals, with some bacterial taxa producing metabolites inhibitory to Bd. MHC class II diversity has been associated with resistance in some species. Bd isolates also vary in virulence — the Global Panzootic Lineage is consistently more virulent than endemic lineages — and strains differ in protease secretion and immunomodulation of the host.

Skin swabs, skin punch biopsies, blood, and granular gland tissue are collectable. Some populations can be sampled longitudinally; others are accessible only at single time points due to rarity or access constraints.

Plant / environmental stress

A set of wheat varieties is exposed to a controlled drought stress regime in glasshouse conditions. Soil water is withheld for a defined period then restored. Physiological measurements confirm that stress was imposed and that varieties differ in response severity. Some varieties maintain photosynthetic activity and recover quickly after rewatering; others show sustained growth suppression.

Within minutes to hours of stress onset, ABA signalling drives stomatal closure and ROS accumulate. Over hours to days, stress-responsive transcription factors activate downstream genes for osmolyte synthesis, heat shock proteins, and antioxidant enzymes. Compatible solutes such as proline accumulate to maintain osmotic balance. Underlying this is the genetic architecture of the varieties — heritable differences in regulatory sequences or gene copy number affecting stress pathway components.

Leaf tissue is the primary sampling target but is metabolically dynamic; composition changes rapidly after excision. Root tissue captures a different aspect of the response. Stressed, recovering, and unstressed baseline time points are all available. The varieties differ in breeding history and are not isogenic lines.