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A plant hormone involved in water-stress responses, seed dormancy and other processes. In guard cells, ABA-dependent receptor inhibition of phosphatases permits kinase activation and stomatal closure.

An auxin response element is a cis-regulatory element involved in auxin-responsive transcription. It is a DNA sequence recognized by regulatory proteins, including auxin response factors. The element, its binding protein and the plant hormone are different participants in the response.^[ref]

A motivating experiment compared the sequence requirements for factor binding in vitro with those associated with a transcriptional response in living cells. Agreement linked molecular recognition to regulation, rather than merely identifying a sequence that happened to lie near an expressed gene.^[ref]

The synthetic element used in the DR5 auxin response reporter supplies a concrete example. It can drive a measurable reporter gene response, but its output also depends on the regulatory state of the cell. In the original experiments, Aux/IAA proteins could repress reporter expression. Thus a response element is part of a control system: the same regulatory DNA does not guarantee the same output under every cellular condition.^[ref]

Indole-3-acetic acid is a naturally occurring auxin and plant hormone. Its structure combines an indole ring system with an acetic acid side chain; the neutral molecule has formula ${\mathrm{C}}_{10}{\mathrm{H}}_9\mathrm{N}{\mathrm{O}}_2$. Its chemical identity is more specific than the functional class auxin, which also includes other compounds.^[ref]

A transport experiment illustrates the difference between applying a signal and delivering it to the responsive cells. Work on Arabidopsis thaliana localized AUX1 within the root apex and connected its function to uptake and redistribution of indole-3-acetic acid. A membrane-permeable synthetic analogue, naphthaleneacetic acid, could bypass the mutant's uptake defect in a gravitropism assay.^[ref]

Concentration and total amount must also be distinguished. In an illustrative homogeneous solution, $1\mathrm{mL}$ at $1\mu \mathrm{mol}{\mathrm{L}}^{-1}$ contains $1\mathrm{nmol}$ of solute by $n=cV$. That calculation specifies an inventory; it does not establish the intracellular concentration, spatial distribution or growth response. Those require measurements of transport and biological activity.

Juliane K. Ishida is the first-listed author of a 2016 study connecting local auxin production to haustorium development in the parasitic plant Phtheirospermum japonicum. A haustorium connects a parasitic plant with its host. The study investigated how a localized developmental response arises, rather than treating the plant hormone as a uniform signal throughout the whole root.^[ref]

The researchers observed localized gene expression of an auxin-biosynthesis enzyme, measured increased auxin near a developing haustorium, and tested changes in the enzyme's expression. Reduced expression impaired development, while ectopic expression produced haustorium-like features. These comparisons illustrate the difference between a marker that accompanies organ formation and a biochemical process that contributes to it. The result concerns initiation and morphology: a haustorium-like swelling alone does not establish that every later connection to a host has formed.^[ref]

In auxin experiments, naphthaleneacetic acid usually denotes the synthetic plant hormone analogue 1-NAA. It can enter plant cells without the same dependence on an auxin influx carrier as indole-3-acetic acid. That difference makes it a useful experimental probe of membrane transport, rather than simply another interchangeable way to apply auxin.^[ref]

In a 2001 study of Arabidopsis thaliana, a mutant affecting AUX1 showed defective root gravitropism. Treatment with $10^{-7}\mathrm{mol}{\mathrm{L}}^{-1}$ 1-NAA restored the response, while the comparison auxin treatment in the same figure did not. The authors also examined a reporter of auxin-responsive expression.^[ref]

The illuminating feature is the bypass: changing how a signal enters a biological cell can restore a response despite a transport defect. Chemical identity, delivery and measured response must be distinguished when interpreting polar auxin transport.

S. F. Yang studied the biosynthesis of Ethylene, a plant hormone involved in fruit ripening. A 1979 study with D. O. Adams established 1-aminocyclopropane-1-carboxylate as an intermediate between methionine and Ethylene.^[ref]

In apple tissue, labelled methionine produced Ethylene in air but accumulated the cyclic intermediate under nitrogen. Supplying labelled 1-aminocyclopropane-1-carboxylate and comparing responses to an inhibitor helped establish the order of the reactions. The design used both precursor tracing and bypass of a blocked upstream step, rather than assuming that correlated concentrations reveal pathway order.^[ref]