NPQ is Fm/Fm'-1? (Fm'=FmPrime; what Fm=?)
How calculate photochemical quenching (qp)? Its (FmPrime-Fs)/(FmPrime-FoPrime)?
Fluorescence decrease ratio (RFd) RFd= Fd/Fs=(Fm-Fs)/Fs. Can use RFd= Fd/Fs=(FmPrime-Fs)/Fs?
Good question... I think that David Kramer and Stefanie Tietz are soon publishing a paper about this method :) "The One" protocol includes some additional stuff to create a FoPrime, which is used in the calculation.
I'm not going to attempt to explain it here, because... we'll I'll screw it up. I'll pass this post along to Dave and perhaps he can elucidate, or at least post the journal it'll get posted to.
The ‘prime’ means that the measurements were performed in the light? And FoPrime=F0'?
This is partially right, yes it needs light but our FoPrime is actually taken from a short period in the dark after a light pulse and a short far red pulse. The far red causes PSI to open and drain the PSII PQ pool thus opening all the centers at PSII and oxidizing all of QA.
There is a paper that introduces all of the fluorescence parameters pretty nicely. It's by Neil R Baker and is called "Chlorophyll Fluorescence: A Probe of Photosynthesis in Vivo" Annu. Rev. Plant Biol. 2008. 58:89-113
Let me know if you have any more questions.
What does each of these options?
Especially Phi2MPF: and Phi2noMPF, FmPrimeMPF:FmPrimenoMPF and other from protocol The One v3.0.
Hey Herts family :)
The One v3.0 includes Tom Avenson's multi phase flash, which improves the accuracy of the maximum fluorescence (FmPrime). You can see the article here http://onlinelibrary.wiley.com/doi/10.1111/pce.12115/abstract (sorry it's paywalled but at least you can see the summary). We're still testing out this protocol, so I have included a bunch of additional output parameters which help us compare the previous The One with The One v3.0. Once complete, I'm going to remove those additional parameters.
But since they are there, I'll tell you what they mean:
Phi2MPF - that's the Phi2 produced using Tom's multi-phase flash calculation (in theory more accurate)
Phi2noMPF - the 'regular' phi2
Same is true for FmPrime and other things which have "MPF" and "noMPF" following the name.
Hope that helps -