**Acknowledgements**

specifically within the study of RNATs, there is no doubt that these and other important

**cDNA library:** The collection of single-stranded DNA products generated by reverse tran‐

**Gibbs free energy: T**he thermodynamic potential of a system at a certain temperature and pressure. In this chapter, Gibbs free energy indicates the stability of a certain hairpin structure.

**Heat shock response:** The coordinated production of several proteins and other essential cellular components by a cell that work together to facilitate survival when the cell is exposed

**Hydration shell:** A shell-like structure formed by water molecules surrounding a molecule.

**Melting temperature (Tm):** The temperature at which half of the double-stranded molecules

**Quorum sensing**: The coordinated regulation of bacterial gene expression in response to a secreted signal molecule that indicates the population density. When the signal molecule

**Riboswitch:** A *cis-*encoded regulatory RNA element that functions to modulate target gene expression via switching between two mutually different secondary structures. Conforma‐ tional changes within a riboswitch are induced by binding to a metabolite or other small

**RNA thermometer**: A *cis*-encoded RNA element that represses translation via incorporation of the ribosome-binding site within an inhibitory hairpin at non-permissive temperatures. With increased temperature, the inhibitory structures within an RNA thermometer is desta‐

**Shine-Dalgarno (SD) sequence**: Also known as the ribosome-binding site, the Shine-Dalgarno sequence is a sequence on an mRNA molecule to which the ribosome binds. Binding of a ribosome to an SD sequence on a transcript is necessary for the initiation of translation.

**Sigma factor:** A protein factor that facilitates the sequence-specific binding between an RNA polymerase and specific promoter regions on the DNA. Sigma factors are necessary for

**Structurome:** The collective determination of the secondary structure of each transcript present

**Transcriptome:** The total population of RNA molecules present in a given organism or cell

to an environmental temperature that is higher than its ideal surviving temperature.

reaches a threshold amount, the cascade of signal-induced regulation occurs.

bilized, the ribosome-binding site is exposed, and translation proceeds.

scription using total RNAs isolated from an organism as templates.

within a population assume a single-stranded conformation.

molecule at a specific ligand-binding region.

transcription initiation.

type.

in a given organism or cell type.

findings will be revealed sooner than later.

176 Nucleic Acids - From Basic Aspects to Laboratory Tools

**7. Nomenclature**

The authors would like to acknowledge both the Ohio University, Ohio University Heritage College of Osteopathic Medicine, and the American Heart Association for funding their ongoing studies of bacterial RNA thermometers.
