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Chlorophyll fluorescence terminology

A B C D E F G H I J K L M N O P Q R S T U V W XYZ, #

A

B

C

D

Dirac constant

The Dirac constant (h-bar) is equal to the Plank constant divided by 2p (h/2p). The value of h-bar is 1.054 x 10^-34 Js.

DeltaF (DF)

This term refers to the difference in fluorescence signal at two defined points. One of the many ways in which it has been used is to define the difference between F' measured immediately before a saturating pulse and Fm' measured at the peak of the same saturating pulse. Within the FluorImager program and these help files Fq' is used in this context.

E

ETR

Electron transfer rate.

F

F'

The fluorescence signal at any point between Fo' and Fm'. Within the FluorImager program and these help files, F' is used in preference to Fs and Ft, which have often been used in the same context.

Fm

The maximum fluorescence signal (when all PSII centres are in the closed state) from dark-adapted material.

Fm'

The maximum fluorescence signal (when all PSII centres are in theclosed state) from light-adapted material.

Fm/Fm' - 1

A way of quantifying changes in the level of non-photochemical quenching of chlorophyll fluorescence (NPQ).

Fo

The minimum fluorescence signal (when all PSII centres are in the open state) from dark-adapted material.

Fo'

The minimum fluorescence signal (when all PSII centres are in the open state) from light-adapted material. Within FluorImager, virtual Fo' images (which are required for the construction of Fv'/Fm' and Fq'/Fv' images) are constructed using the Fo' calculation method.

F_PSI

The contribution of PSI fluorescence to the total fluorescence signal. Expressed as a percentage of the total fluorescence signal at Fo or Fo'.

Fq'

The difference between F' measured immediately before a saturating pulse and Fm' measured at the peak of the same saturating pulse. The non-specific term DeltaF (DF) has often been used in the same context.

Fs

In most situations, this term is equivalent to F'.

Ft

In most situations, this term is equivalent to F'.

Fv

Variable fluorescence (difference between Fo and Fm) from dark-adapted material.

Fv'

Variable fluorescence (difference between Fo' and Fm'.) from light-adapted material

Fv/Fm

 Provides an estimate of the PSII maximum efficiency within dark-adapted material.

Fv'/Fm'

Provides an estimate of the PSII maximum efficiency within light-adapted material.

Fq'/Fm'

Provides an estimate of the PSII operating efficiency within light-adapted material.

Fv/(Fm.Fo)

This term is equivalent to 1/Fo – 1/Fm. When normalised to the initial value, it provides an estimate of the change in the maximum PSII photochemical efficiency that can be normally be attributed to photoinactivation of PSII centres.

Fq'/Fv'

A factor relating the PSII maximum efficiency and the PSII operating efficiency. Mathematically, Fq'/Fv' is equivalent to qP.

G

Genty factor

A term often used to describe the PSII operating efficiency (after Genty, Briantais and Baker, 1989).

H

I

Irradiance

Refers to the 'energy flux density' of light, which has the units of J m^-2 s^-1 or, more usually, W m^-2. See also; PAR, PPFD and photon irradiance.

J

K

Kautsky curve

L

M

N

Non-photochemical quenching

Quenching of variable fluorescence that can be attributed to processes other than photochemistry.

Non-radiative decay

In the context of PSII photochemistry, non-radiative decay usually refers to the transition of an electron in the outermost shell of a chlorophyll a molecule from the first excited state to the ground state that results in an increase in the overall kinetic energy of the molecule, rather than the emission of a photon as fluorescence or a charge separation event.

NPQ

The term NPQ is widely used to represent non-photochemical quenching. It is most frequently associated with the fluorescence parameter (Fm / Fm') - 1, which is a rearrangement of the Stern-Volmer equation (Bilger and Björkman, 1990). This equation simply states that the reciprocal of fluorescence yield is proportional to quencher concentration. So, for example, an increase in (Fm / Fm') - 1 from 1 to 2 could be interpreted as a doubling of quencher concentration. In reality, there is little evidence that fluorescence yield is actually modulated by quencher concentration and it should be appreciated that a change in the rate constant of a quenching mechanism, at any location within the PSII pigment bed, would be indistinguishable from a change in quencher concentration. Although (Fm / Fm') - 1 can clearly be a useful parameter, it is important to recognize that it is simply monitoring the rate constant for non-radiative decay, normalized to the dark-adapted level. Consequently, it is only valid to compare values among samples if it is known that the samples started off in the same condition: very similar initial values of Fv/Fm would be a good indication of this.

O

Open and closed PSII and PSI centres

Reaction centres are defined as being open if they are capable of stable charge separation (photochemistry) and closed if they are not. In the case of PSII, stable charge-separation results in oxidation of P680 and reduction of Q_A. Since the oxidation of Q_A^- is orders of magnitude slower than reduction of P680⁺, a PSII centre is defined as being open when Q_A is in the ground state and closed when Q_A is reduced. Conversely, a PSI centre is open when P700 is in the ground state and normally closed when P700 is oxidised (P700⁺).

P

PET

Photosynthetic electron transfer.

Photon irradiance

Photon irradiance is a term that is equivalent to PPFD and is preferred by some phycology journals. See also; PAR, PPFD and irradiance.

Planck constant

Formerly Planck's constant. The energy of a single photon (e [epsilon]) can be related to it's frequency (n [nu]) through the 'Planck constant' (h) such that:

                                    e = hn

The value of h is 6.626 x 10^-34 Js. See also Dirac constant.

PPFD (photosynthetically active photon flux density)

PPFD is the term preferred by most plant journals. The usual units are mmol m^-2 s^-1. Please note that PPFD is NOT interchangeable with irradiance or PAR. Some phycology journals prefer the term photon irradiance.

PAR (photosynthetically active radiation)

Although it is not incorrect to use PAR to refer to the photon content of light, it should be noted that "… a PAR of 250 mmol m^-2 s^-1" (for example) is incorrect because it doesn't include a reference to what is being measured. The correct statement would be "… a PAR of 250 mmol photons m^-2 s^-1". See also PPFD, irradiance and photon irradiance.

PSII maximum efficiency

The efficiency with which light absorbed by the pigment matrix associated with PSII is used to drive stable photochemistry when all PSII centres are in the open state. An estimate of the PSII maximum efficiency is provided by Fv/Fm in the dark-adapted state and Fv'/Fm' in the light-adapted state.

PSII operating efficiency

The efficiency with which light absorbed by the light-harvesting system associated with PSII is used to drive stable photochemistry, in the light-adapted state. Because a fraction of PSII centres are closed in the light-adapted state, the PSII operating efficiency is lower than the PSII maximum efficiency. It's value can be estimated through Fq'/Fm', which is equivalent to the so-called 'Genty factor'.

PSII photochemical factor

A factor relating the PSII maximum efficiency and PSII operating efficiency, which provides an estimate of the fraction of the PSII maximum efficiency that is actually realised.

Q

Quenching coefficients

The system of quenching coefficients includes one term (qP) that is related to photochemical quenching. All of the remaining quenching coefficients relate to non-photochemical quenching processes:  qN is the coefficient of total non-photochemical quenching; qE, the coefficient of energy-dependent quenching; qT, the coefficient of non-photochemical quenching associated with state-transitional changes and;  qI, the coefficient of non-photochemical quenching associated with photoinhibition. They are usually calculated as:

Where Fv is the variable fluorescence in the initial (dark-adapted) state and Fv' is the variable fluorescence at the point at which the value of a particular coefficient is being calculated. A significant problem with this method is that any change in the effective rate constant for PSII photochemistry will decrease the value of the supposedly non-photochemical quenching coefficient that is being calculated. An example of where this might occur is when a healthy plant is subjected photoinhibitory conditions (e.g. a combination of high light and low temperature). Under photoinhibitory conditions, the rate at which PSII centres are inactivated exceeds the rate at which they are replaced, with a consequent decrease in the effective rate constant for PSII photochemistry.

qN

One of two widely used quenching coefficients (the other being qP), the so-called 'co-efficient of non-photochemical quenching' is usually calculated as the change in variable fluorescence between the dark- and light-adapted states. This parameter is not calculated by FluorImager. NPQ provides similar information.

qP

 So-called 'co-efficient of photochemical quenching'. Mathematically, qP is equivalent to Fq'/Fv' (PSII photochemical factor). It has frequently been used (incorrectly) to estimate the fraction of PSII centres in the open state.

R

Reversible radical pair equilibrium model

S

Stern-Volmer quenching

A convenient way of describing the relationship between chlorophyll fluorescence yield and downregulation is to treat downregulation as a Stern-Volmer quenching process. The Stern-Volmer equation simply states that the reciprocal of fluorescence yield is proportional to quencher concentration.

Where:

F_F is the yield of chlorophyll fluorescence, A and B are Stern-Volmer quenchers and k_A and k_B are the rate constants for the quenching of the singlet excited state of chlorophyll by A and B, respectively. See NPQ for further information.

T

Trace comments

U

V

Variable fluorescence

The difference between Fo and Fm or Fo' and Fm'. Termed Fv in the dark-adapted state, Fv' in the light-adapted state. Variable fluorescence is modulated by both photochemical and non-photochemical quenching processes.

W

XYZ, #

1/Fo - 1/Fm

Originally described by Havaux et al. (1991). This parameter is equivalent (mathematically and conceptually) to Fv/(Fm.Fo), which was originally described by Baker and Dominy (1980).

1 - Fv'/Fm'

This parameter originates from a study by Demmig-Adams et al. (1986), in which it was used (incorrectly) to estimate the yield of non-radiative decay processes at PSII, in the light adapted state. This parameter actually provides an estimate of what the combined yield of non-radiative decay processes and chlorophyll fluorescence would be, if all PSII centres were in the open state at the point of measurement. Since the fraction of PSII centres in the open state tends to decrease with increasing incident PPFD, this parameter becomes an increasingly inaccurate method of estimating the yield of non-radiative decay processes at PSII.