Since coloration is often linked to lighting, I thought I'd post a glossary. Cyan Fluorescent Proteins (CFP) - Cyan pigments are blue-green pigments with a maximum emission of up to ~500 nm. The chromophore structure of a cyan pigment is very similar to that of a green fluorescent pigment. Green Fluorescent Proteins (GFP) - This group, by far, is the most numerous of the fluorescent proteins. The structure of green fluorescent chromophores is very similar to that of cyan fluorescent chromophores. Yellow Fluorescent Proteins (YFP) - An unusual type of fluorescent protein with maximum emission in the yellow portion of the spectrum. Rare in its biological distribution, YFP is found in a zoanthid and some specimens of the stony coral Agaricia. Personally, I've noted yellow fluorescence in a very few stony corals (Porites specimens) here in Hawaii while on night dives using specialized equipment to observe such colorations (see www.nightsea.com for details on this equipment). Orange Fluorescent Protein (OFP) - I've included this protein 'type' in an attempt to avoid confusion. OFP is used to describe a pigment found in stony coral Lobophyllia hemprichii and its name suggests a rather unique sort of protein. In fact, OFP is simply a variant of the Kaede-type fluorescent proteins. Red Fluorescent Proteins (RFP) - A group of proteins including several different subtypes (Kaede, Ds-Red and Chromo-Red). Typically, fluorescent emission is in the range of ~580 nm to slightly over 600 nm. Dronpa - A green fluorescent protein that loses fluorescent when exposed to blue-green light (~490 nm) but returns when irradiated with violet light at ~400 nm. Kindling Proteins - A protein (notably from the anemone Anemonia sculata) that changes from a non-fluorescent pigment to one demonstrating fluorescence. This change is switchable/reversible and its state depends upon the spectral quality of light striking it. Chromo-Red Proteins - A new classification (Alieva et al., 2008) of a single fluorescent pigment found in the stony coral Echinophyllia. This chromo-red pigment has qualities of a non-fluorescent chromoprotein, but fluoresces at a maximum of 609 nm. Chromoproteins (CP) - This group of pigments is non-fluorescent, or has minimal fluorescence (where the quantum yield is essentially zero). Instead of relying upon fluorescence for coloration, these pigments instead absorb light most strongly in a relatively narrow portion of the visible spectrum. Most coral chromoproteins absorb light maximally at 560-593 nm. There are reports of anemones absorbing light at a maximum wavelength of 610nm, and a couple of reports of stony corals absorbing wavelengths in the 480-500nm range. Some chromoproteins are very similar in structure to the fluorescent Ds-Red proteins. In fact, genetic engineers have found that a single amino acid substitution in a protein can make the difference between non-fluorescence and fluorescence. Chromoproteins do not get much attention by researchers (relative to that of fluorescence proteins) and there are only about 40 described. Absorbance: A ratio of incident and reflected (or absorbed) light. Absorption: The process in which incident radiation is retained without reflection or transmission. Brightness: The intensity of a fluorescent emission. Extinction coefficient times Quantum Yield = Brightness. Clade: For our purposes in this article, a grouping of pigments based on similar features inherited from a common ancestor. Pigments from corals includes Clades A, B, C, and D. Clades can refer to living organisms as well (clades of Symbiodinium - zooxanthellae - are a good example.) Chromophore: The colorful portion of a pigment molecule. In some cases, chromophore refers to a granular packet containing many pigment molecules. Chromoprotein pigment: A non-fluorescent but colorful pigment. These pigments appear colorful because they reflect light. For example, a chromoprotein with a maximum absorption at 580nm might appear purple because it preferentially reflects blue and red wavelengths. Chromo-Red Pigment: A newly described type of pigment possessing characteristics of both chromoproteins and Ds-Red fluorescent proteins. Peak fluorescence is at 609nm (super red). Coloration Threshold: The point at which pigment production is sufficient to make its fluorescence (or in the case of non-fluorescent chromoproteins, it absorption) visually apparent. The term threshold generally refers pigment production, although, in some cases, it could apply to a light level where a pigment disappears (as in the cases of photobleaching, or photoconversion). Cyan Fluorescent Protein (CFP): Blue-green pigments with fluorescent emissions in the range of ~477-500nm. Cyan and green pigments share a similar chromophore structure. Cyan pigments are expressed at lower light levels than green, red or non-fluorescent pigments. Emission: That light which is fluoresced by a fluorescent pigment. Extinction Coefficient: The quantity of light absorbed by a protein under a specific set of circumstances. Excitation: That light absorbed by a fluorescent pigment. Some of the excitation light is fluoresced or emitted at a less energetic wavelength (color). Ds-Red type pigment: A type of red fluorescent pigment with a single primary emission bandwidth at 574-620nm. Originally found in the false coral Discosoma. Fluorescence: Absorption of radiation at one wavelength (or color) and emission at another wavelength (color). Absorption is also called excitation. Fluorescence ends very soon after the excitation source is removed (on the order of ~2-3 nanoseconds: Salih and Cox, 2006.) Fluorophore: The protein within the beta can that fluoresces upon exposure to proper excitation wavelengths. Green Fluorescent Protein (GFP): Fluorescent pigments with emissions of 500-525nm. ‘Hula Twist’: A bending of a fluorescent protein molecule resulting in a change of color. Molecular bonds are not broken, therefore the protein can shift back and forth, with movements reminiscent of a hula dancer. Kaede-type Protein: A type of red fluorescent pigment with a characteristic primary emission at ~574-580nm and a secondary (shoulder) emission at ~630nm. Originally found in the stony coral Trachyphyllia geoffroyi, but common in corals of suborder Faviina. Kindling Protein: A protein capable of being converted from a non-fluorescent chromoprotein to a fluorescent protein. Sometimes called a 'Kindling Fluorescent Protein', or KFP. Quantum Yield: Amount of that energy absorbed which is fluoresced. If 100 photons are absorbed, and 50 are fluoresced, the quantum yield is 0.50. Photobleaching: Some pigments, such as Dronpa, loss fluorescence if exposed to strong light (in this case, initially appearing green and bleaching to a non-fluorescent state when exposed to blue-green light). Photobleaching can obviously cause drastic changes in apparent fluorescence. In cases where multiple pigments are involved, the loss of fluorescence (or energy transfer from a donor pigment to an acceptor pigment) could also result in dramatic shifts in apparent color. Photoconversion: A rearrangement of the chemical structure of a colorful protein by light. Depending upon the protein, photoconversion can increase or decrease fluorescence (in processes called photoactivation and photobleaching, respectively). Photoconversion can break proteins' molecular bonds (as with Kaede and Eos fluorescent pigments) resulting in an irreversible color shift, or the molecule can be 'twisted' by light energy (a 'hula twist') where coloration reversal are possible depending upon the quality or quantity of light available. This process is known as photoswitching). Red Fluorescent Protein (RFP): Those pigments with an emission of ~570nm and above. Includes Ds-Red, Kaede and Chromo-Red pigments. Stokes Shift: The difference in the maximum wavelength of fluorescent pigment excitation light and the maximum wavelength of the fluoresced light (emission). For example, a pigment with an excitation wavelength of 508nm and an emission wavelength of 535nm would have a Stokes Shift of 27nm.