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Lab Protocols

Protocols for benchwork in the lab (e.g. RNA isolation), for commonly used instruments and software (e.g. proteomics data analysis in Skyline), and for commonly performed hatchery practices and tissue sampling.

Foundational protocols can be found here. As they become prominent, they will be migrated here for posterity.

Common Physiological Assays of Interest

Assay Measurement Reference
Oxygen consumption (OC) Volume of O2 consumed animal-1 hour-1 (J. Widdows and Johnson 1988)
Clearance rate (CR) Volume of water cleared of particles animal-1 hour-1 (Pernet et al. 2007)
Filtration rate (FR) (weight of faeces + pseudofaeces h-1) x [(weight total particulates per volume seawater) ÷ (weight inorganic matter per volume seawater)] (Hawkins et al. 1996)
Excretion rate (ER) Ammonia excreted hour-1 (John Widdows, Donkin, and Evans 1985)
Net organic ingestion rate (NOIR) FR x (organic fraction within total particulates available) (Hawkins et al. 1996)
Net organic absorption rate (NOAR) NOIR - [(weight of total faeces egested h-1) x (organic fraction of faces)] (Hawkins et al. 1996)
Total carbohydrates Total carbohydrate content of oyster meat (Dubois et al. 1956)
Total lipids Total lipid content of oyster meat (Bligh and Dyer 1959)
Total protein Total protein content of oyster meat (Jeung et al. 2016)
Glycogen content Total glycogen content as a fraction of total protein (Krisman 1962)
Condition index (CI) Dry meat weight (internal shell cavity volume)-1 x 100 (Lawrence and Scott 1982)
Reproductive status Stage of gonadal development determined through histological observation (Matt and Allen 2021)
Ash free dry weight (AFDW) Dry weight of oyster meat after incineration at 500℃ (Ricciardi and Bourget 1998)

Associated Calculations

Parameter Calculation Reference
Protein synthesis rate (PR) Mass of protein synthesized individual-1 hour-1 (Pace and Manahan 2006)
Protein turnover rate protein synthesis rate ÷ (total protein content)-1 x 100 (Pan, Applebaum, and Manahan 2015)
Net absorption efficiency (AE) NOAR ÷ NOIR (Hawkins et al. 1996)
Standard metabolic rate (SMR) OC hour-1 mass-1
Consumption (C) CR (l g-1 h-1) x POM (mg l-1) x 23 J mg-1 ash-free dry weight (J. Widdows and Johnson 1988)
Respiration (R) VO2 (ml 02 g-1 h-1) x 20.33 J ml-1O2 (J. Widdows and Johnson 1988)
Energy lost to excreta (U) mg NH4 g-1 h-1 x 19.4 J mg-1 NH4 (J. Widdows and Johnson 1988)
Absorbed ration (A) C x AE (J. Widdows and Johnson 1988)
Production (P) A - (R + U) (J. Widdows and Johnson 1988)
Scope for growth (SFG) SFG = A - (R + U), where A = energy absorbed; R = respiratory energy expenditure; U = energy lost through excreta (J. Widdows and Johnson 1988)