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In 'open system' (or 'continuous flow') respirometry, a measured flow of gas -- usually air -- is moved through the metabolism chamber containing the organism in question.   When dealing with a big animal, or with a small one with a high metabolic rate, the flow rate needs to be kept high to prevent undue depletion of O₂ or buildup of CO₂ in the chamber.   Also, at high temperatures, a high flow rate may be needed to keep relative humidity low enough for an endotherm to effectively use evaporative cooling (sweating, panting, gular flutter).   High flow rates also help to mix air in large chambers and keep the system response time reasonable.   However, these flows can be larger than you want -- or need -- to send through the analyzers and scrubbing systems.  For example, most gas analyzers are not designed to handle flows more than a few hundred ml/min and some can be damaged or destroyed at high flow rates.

The solution is to subsample the excurrent gas stream coming out of the animal chamber.   The main flow is 'spilled' into the atmosphere and a subsample (perhaps 50-200 ml/min) is passed through the analysis plumbing.   Not only does this greatly reduce the amount of scrubber chemicals needed (to remove water vapor and/or CO₂), it also solves the problem of keeping analyzer flow rate and pressure constant when switching between animal and reference gas, which is needed to account for analyzer drift (almost unavoidable, especially for oxygen analyzers).

This diagram shows a simple respirometry system with subsampling (this one is for oxygen consumption, but the same arrangement works for CO₂ production, water vapor measurement, etc.):

The idea is that two large gas flows -- reference gas (identical to what enters the animal chamber) and excurrent gas from the chamber -- are subsampled one at a time.   The large flows spill into the atmosphere through two 'sipping' chambers. I've shown hypodermic syringe barrels here; they're very convenient for this purpose.   It's crucial that the large end is open to the atmosphere.   This ensures that when subsampling is switched between animal and reference flows (by an automated valve, or simply by moving the small tube connected to scrubber chemicals from one syringe to the other), there is no change in either the pressure or flow rate within the analyzer subsystem.   Most gas analyzers are sensitive to pressure and some to flow.

For this kind of setup, it's crucial that the flow into the 'sippers' (reference or animal gas) is much larger than the subsample flow.   Otherwise there is a risk that the subsampled gas can be contaminated with room air, by diffusion and/or small air currents.   You can put some lose-fitting cotton in the syringe barrels to help prevent this, but do not make it gas-tight!

This page shows the animal and reference gas flows provided by an air pump (incidentally, aquarium air pumps work quite well for this purpose, as long as you don't need really large flows or high pressures).   It's also possible to supply gas from some other pressure source, such as high-pressure air from a lab utility or a cylinder of compressed air or other gas mixture.  In either case, if the gas is dry (little or no water vapor) you may not need the scrubber canister shown here, between pump and flowmeter.  However, for extremely sensitive CO2 measurements it may be desirable to scrub out the small amount (~0.04%) of CO2 in ambient air, and then re-dry the air stream (since CO2 scrubbers produce water as a byproduct).