Science topic

Chlorophyll Fluorescence - Science topic

Chlorophyll fluorescence is light that has been re-emitted after being absorbed by chlorophyll molecules of plant leaves. By measuring the intensity and nature of this fluorescence, plant ecophysiology can be investigated.
Questions related to Chlorophyll Fluorescence
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
Sample Number Date Time O T100 K J I P S M T tFm Fo Fm Fv/Fm. Can anyone help me explain the J, Fo, and Fm parameters on the Chlorophyll Fluorescence measure and its significance to drought stress? I used a portable, pulse-modulated OS-30p+ chlorophyll fluorimeter (Opti Sciences). I am working on the effect of Alectra vogelii on Bambara groundnut.
Relevant answer
Answer
Thank you very much.
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
Hi everyone
I need some good papers which can explain the above-asked question. I need to know what exactly LRCs tell about the photosynthesis in plants which is not covered by chlorophyll fluorescence alone. If anyone can explain in simple words (with some references), it would be highly appreciable.
Relevant answer
Answer
Light response curves can be based on either gas exchange or chlorophyll fluorescence parameters (including ETR and NPQ). In LRCs, we analyze a photosynthetic parameter relative to light intensity instead of time. This allows us to understand the dynamics of the photosynthetic apparatus relative to light intensity and understand such things as optimal light intensities, define light limiting environments, and more.
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
The question is in another way.
What is the relationship between SPAD chlorophyll value and Chlorophyll a, b and total Chl?
For example, if the lettuce plant has high SAPD content value that means the Chlorophyll must be high?? or any relationship with other chlorophyll components??
Relevant answer
Answer
SPAD ​​index and chlorophyll content are directly related.
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
Hello. I've been working on photosynthesis pigment content in in vitro grown trees and was examining the formulas for determining the concentration of chlorophyll a and b and carotenoids based on absorbance, i.e. using a spectrophotometer. I've found various formulas, and even though they all share the same general design: concentration=coefficient1*adsorbance1-coeficeint2*adsorbance2, the coefficients differ among sources. I was curious as to the reason behind this. Is it due to the use of different equipment, i.e. every spectrophotometer is different, or something else? I'm new to this field, thus any help, directions to relevant introductory literature, articles, would be great.
Relevant answer
Answer
Philipp Girr Thanks, you made my day.
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
  • Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !
Relevant answer
Answer
ThankYou Dear Salah Uddin Xuhua Wang
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
Hi
I'm currently using a FluorCAM 800MF along with FluorCam 7- software to measure fvfm in some macroalgae. The problem I'm facing is that some dead zones from the algae athough they have f0 lower than 100, they end up having fvfm sometimes greater that 0.7, which creates a false ilusion of well being the the algae. The software allows the creation of protocols to customize the readings, but I can't seem to find a way to create a threshold for this low f0 values.
Has anyone tried doing this?
Thank you.
Cheers, Luís Pereira.
Relevant answer
Answer
Hey Luis, have you tried to increase the sensitivity and the shutter settings, rather than trying to cut of Fo lower than 100?
If that is not possible go to the last tab "results", lowest window right side. There you will find the option "value range" right in the middle. There you will find the option to set a minimum value. Hope I could help. Silja
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
As both Chlorophyll semi-synthetic derivative and methylene blue organic dye has been widely used as a potential photosensitizer in applications like PDT but I want to know that; a chlorophyll derivative can photodegrade methylene blue by Type II photosensitization process or not?
Please provide me some reason if it is feasible then. thank you
Relevant answer
Answer
I did an experiment at the lab concerning KMnO4 to check this point. I prepared an initial concentration of KMnO4 then I left the solution under visible light for 3 hours but when I measured it concentration again I found it decreased. hope my experience help you
  • asked a question related to Chlorophyll Fluorescence
Question
8 answers
I do not have the PAR data. Fluorescence can be detected from dead particles too, but can it be utilized to get an idea about the euphotic depth.
Relevant answer
Answer
Have a look at our paper, "Resolving the Euphotic Zone," Deep-Sea Research I, vol. 83, pp. 45-50. We propose that the biological compensation depth is roughly equivalent to the depth of the base of the fluorescence maximum.
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
Hello, I hope somebody could help in clarifying this point.
I am following an experiment on young olive plants in southern Italy, and I will take chlorophyll fluorescence measurements using a Fluorpen (PSI).
I will use the OJIP protocol and I am in the process of setting the saturating light intensity: I understand that in order to obtain proper Fmax measurements in dark adapted samples, one should make sure that the intensity of the initial flash of high intensity light is strong enough to temporarily close all Reaction Centers.
My questions is: which is the procedure to find the saturating light intensity ?
I already performed a series of OJIP measurements setting the light intensity from 300 to 3000 micromoles of PAR but it is not clear for me which value I should choose.
According to the Fluorpen instruction manual, one should choose the light intensity which results in the maximum Fv/Fmax ratio.
In my case this occurs at 1200 micromoles of PAR, while this ratio decreases at higher sat pulse intensities.
I also found a different suggestion in a recent review by M. Tsimilli-Michael (Revisiting JIP-test, Photosynthetic 57, 90.107, 2019): to test different light intensities (I) and to select the value for which Fpeak/I gets saturated. In my case this ratio reaches a peak at 1200 micro moles of PAR after which it starts decreasing, but I cannot see it reaching a steady value.
Am I following the right procedure ? Actually, I am not sure that 1200 micro moles could actually be a strong enough light to close all RCs in olive plants, since the “midday" PAR intensity can be over 2000 in this season.
I am looking forward to reading your comments.
Thank you
Relevant answer
Answer
Dear Stefano,
On the one hand, the manufacturer should provide the PAR value emitted by the diode. On the other hand, you can visit colleague at the nearest physics / optics department and ask for an exact measurement for your instrument. You can also try to measure with an ordinary PAR meter, although the measurement will be probably burdened with a significant error. Either way, if you measure a value above 3000 everything is ok.
Plants have evolved in sunlight (~2000 PAR), so 3000 and more are likely to saturate the photosynthetic apparatus.
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
I am using SIMPSON to simulate DQ signals generated by the pulse sequence SPC5. The input file of my simulation is modified from the input file of Post-C7, which is written in the original SIMPSON paper (Bak, M.; Rasmussen, J. T.; Nielsen, N. C. Journal of Magnetic Resonance 2011, 213 (2), 366–400.) My input file is as followed:
#Cb, Ca, C' in order
#parameters from Journal of Magnetic Resonance 164 (2003) 270–285 (for alanine)
spinsys {
channels 13C
nuclei 13C 13C 13C
dipole 1 2 -2147 0 69 111
dipole 2 3 -2117 0 0 0
dipole 1 3 -475 0 34 111
}
par {
spin_rate 25000
sw spin_rate/2.0
np 64
crystal_file rep100
gamma_angles 40
start_operator Inz
detect_operator -Inz
verbose 1101
}
proc pulseq {} {
global par
maxdt 1
#matrix set detect totalcoherence {2}
set rf [expr 5.0*$par(spin_rate)]
set t90 [expr 0.25e6/$rf]
set t270 [expr 0.75e6/$rf]
set t360 [expr 1e6/$rf]
reset
for {set i 0} {$i < 5} {incr i} {
set ph [expr $i*360.0/5.0]
pulse $t90 $rf $ph
pulse $t360 $rf [expr $ph+180]
pulse $t270 $rf $ph
}
store 1
acq $par(np) 1
}
proc main {} {
global par
fsave [fsimpson] $par(name).fid
}
I used "-Inz" first for detect_operator as in the original paper and got a build-up curve with intensity ~0.75 (as attached). But I want to obtain DQ signals so I change the detect_operator to be "–(I1p*I2p+I1m*I2m)", which stands for DQx. However I got a build-up curve with intensity ~0.0007, too low for the DQ conversion efficiency (as attached). I also tried "matrix set detect totalcoherence {2}" in the proc pulseq part to obtain DQ signals but had the intensity with similar intensity.
Does anyone know what’s wrong with my coding? Thanks in advance.
Relevant answer
Answer
Hi!
Did you get a chance to solve your problem ? I am struggling with the simulation of DQ-DRAWS experimental results myself ... I would be thrilled if you could give me some insight if you managed to obtain good fits.
Thanks,
Ben
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
I need to image cyanobacteria using fluorescent microscopy, I have easily done this before with good results using the fluorescence of chlorophyl on a traditional fluorescent microscope. However, when I attempted to do this on a confocal system I had very poor results when imaging Cy5.5 along side the chlorophyl.
What excitation and emission wavelengths should I use for chlorophyl, specifically for cyanobacteria?
Should I use a different second dye like NBD or rhodamine instead of Cy5.5?
Relevant answer
Answer
It seems that it would depend on the species of cyanobacteria.
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
I grew Podocarpus seedlings at elevated temperatures for 16 weeks after which I ran temperature response curves using a Licor 6400 IRGA.
The optimum temperature for photosynthesis remained roughly the same for heat acclimated and none-heat acclimated plants, however, max photosynthesis decreased in the heat acclimated plants. The graph is attached!
Does anyone have an explanation for this?
Relevant answer
Answer
Besides other parameters mentioned by Kathryn, did you look at stomatal density?
  • asked a question related to Chlorophyll Fluorescence
Question
7 answers
I've run multiple RLC's (6 reps for each of; 3 seagrass species, 5 time periods and 6 treatments). I'm am looking for a R script that can pull out the slope, ETRmax and saturating irradiance parameters.
Thank you for your help.
Relevant answer
Answer
Hi, here is R code for building a loop which fits a light curve model (Platt et al. 1980) to the data, extracts the coefficients into a data frame and plots the results into tiff files (one file for each fitted curve) using "phytotools" package mentioned above. This is largely based on the code examples provided by the authors of the phytotools package. One should be able to fit the other models in the package also by modifying the plot and fitting sections of the script (model equations I think are specified in phytotools documentation). This is a bit late answer but I'll upload it in any case if someone still finds this useful.
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
Using a chlorophyll fluorometer (Mini-PAM; Walz; Effeltrich, Germany) I plotted ETR vs PPFD curves. What software / r package/excel sheet can I used to fit this data to a rectangular hyperbola model or other models.
Most literature focuses on fitting gas exchange data, not fluorescence.
Can the same models/excel sheets as created in Lobo et al. 2013 (Fitting net photosynthetic light-response curves with Microsoft Excel - a critical look at the models work?)
Suggestions are welcomed!
Thank you.
Relevant answer
Answer
Dear Joshua,
If you are fluent in R use (not my case unfortunately):
The Ritchie paper is really woth reading for your very initial question:
You will need to have at least some real measurements of dioxygen evolution and / or CO2 incorporation to translate rETR as true production values.
And in my own experience, @Raymond J Ritchie in Researchgate is certainly able to give you precises answers.
Hope this will help,
Christophe
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
Dear colleagues,
I would like to ask for your advice regarding NPQ determination through the use of a PAM.
Looking at the manual, it seems to me that for NPQ calculations we need to use the same part of the leaf. So, and after dark adaptation for Fm determination, the same leaf part is light-adapted in order to get Fm´.
I wonder if we can make use of different parts of the same leaf specifically, to use the Fm value obtained after dark adaptation in one part of the leaf and the Fm´ value obtained in another leaf part.
Additionally, I wonder if adaptation under FR light and actinic light is required for the light-adapted measurements or normally illuminated leaves are ok.
Thank you so much for your help
Best Regards
Relevant answer
Answer
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
What is the correlation between Chl a/ b ratio, Fv/Fm and ETR? please help me to understand.
Relevant answer
Answer
Dear Darshan,
under deep shade you may expect plants to undergo a reorganization of their photosynthetic apparatus at many levels, from the morphological one to the biomolecular one. The extent of this response may depend also on the time during which the plant has undergone low light. However, regarding your question, a general response of plants to shade is a lower Chl a/ b ratio, which is indicative of a higher investment in antenna complexes (or, at least, a lower disinvestment in antenna complexes, if the resources are scarce), where chl B is located. A shade-acclimated plant should also display high values of Fv/Fm, because its potential photochemical efficiency is not affected by those processes that may be generally considered the cause of chronic photoinhibition, which may be induced under prolonged exposure to high photon flux density. Last: obviously, in shaded environments ETR is limited by the low light energy.
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
I am trying to use paraquat (methyl viologen) to test a hypothesis related to my research on chlorophyll fluorescence. Most of the literature on paraquat that I've seen (at least to study photosynthesis) uses thylakoid suspensions. I'm not having much luck using it on whole diatom cells and I was wondering if anyone had any advice.
Relevant answer
Answer
So after some experimenting I discovered that an incubation time of at least one hour was necessary to see results. After that, fluorescence didn't show any further change. I'm leaving this answer for any who has the same question I did.
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
I am trying to make a benzoxazole compound.
Is it possible to carry out the condensation with acetic acid?
Relevant answer
Answer
There are a few patents as mentioned below which talks of similar methods. The feasibility part is for you to decide.
EP0031296B1
CN102070627A
US3641044A
  • asked a question related to Chlorophyll Fluorescence
Question
29 answers
Dear Colleagues,
I am relatively a newcomer to the amazing fields of photophysics and photochemistry.
From the available scientific literature, we may read that induced chlorophyll a fluorescence is mainly emitted by chlorophyll a molecules, located in Photosystem II (PSII), upon illumination onset. It has been reported about 300-500 chlorophyll a molecules in a single Photosystem II.
PSI fluorescence is constant and much lower than fluorescence from PSII. Its contribution to emitted plant fluorescence is considered negligible.
Some authors speak about P680 (a pigment named P680, located in Photosystem II), the reaction center RC or the special pair or the special chlorophyll dimers pigments PD1 or PD2, as the only source of fluorescence. I have a bit of confusion because it is not clear what chemical species is emitting the fluorescence that we can sense with our portable fluorometers.
1) If the Special Pair or RC is closed (it has been chemically switched to its reduced state), during the time that the Special pair is in that state, is the full bunch of chlorophyll a molecules in PSII going to dissipate their excitonic energy as fluorescence?
2) Why fluorescence emitted from PSI is not variable but constant? Does it has this fact something to do with the ratio [Chl a] to [Chl b] ???
Thank you so much in advance for your precious and kind help!
Relevant answer
Answer
Howdy Stancho,
First Chlrorphyll fluorescence is not a photophysical or photochemical phenomenon, but a photobiological one.
Chlorophyll fluorescence is light re-emitted by chlorophyll molecules (yes
chlorophyll!) during return from excited to non-excited states. It is used as an indicator of photosynthetic energy conversion in higher plants, algae and bacteria. Excited chlorophyll dissipates the absorbed light energy by driving photosynthesis (photochemical energy conversion), as heat in non-photochemical quenching or by emission as fluorescence radiation. As these processes are complementary processes, the analysis of chlorophyll fluorescence is an important tool in plant research with a wide spectra of applications.
The Kautsky effect
Upon illumination of a dark-adapted leaf, there is a rapid rise in fluorescence from Photosystem II (PSII), followed by a slow decline. First observed by Kautsky et al., 1960, this is called the Kautsky Effect. This variable rise in chlorophyll fluorescence rise is due to photosystem II. Fluorescence from photosystem I is not variable, but constant.
The increase in fluorescence is due to PSII reaction centers being in a "closed" or chemically reduced state. Reaction centers are "closed" when unable to accept further electrons. This occurs when electron acceptors downstream of PSII have not yet passed their electrons to a subsequent electron carrier, so are unable to accept another electron. Closed reaction centres reduce the overall photochemical efficiency, and so increases the level of fluorescence. Transferring a leaf from dark into light increases the proportion of closed PSII reaction centres, so fluorescence levels increase for 1–2 seconds. Subsequently, fluorescence decreases over a few minutes. This is due to; 1. more "photochemical quenching" in which electrons are transported away from PSII due to enzymes involved in carbon fixation; and 2. more "non-photochemical quenching" in which more energy is converted to heat.
PSII yield as a measure of photosynthesis
Chlorophyll fluorescence appears to be a measure of photosynthesis, but this is an over-simplification. Fluorescence can measure the efficiency of PSII photochemistry, which can be used to estimate the rate of linear electron transport by multiplying with light intensity. However, researchers generally mean carbon fixation when they refer to photosynthesis. Electron transport and CO2 fixation correlate well, but may not correlate in the field due to processes such as photorespiration, nitrogen metabolism and the Mehler reaction.
Relating electron transport to carbon fixation
A powerful research technique is to simultaneously measure chlorophyll fluorescence and gas exchange to obtain a full picture of the response of plants to their environment. One technique is to simultaneously measure CO2 fixation and PSII photochemistry at different light intensities, in non-photorespiratory conditions. A plot of CO2 fixation and PSII photochemistry indicates the electron requirement per molecule CO2 fixed. From this estimation, the extent of photorespiration may be estimated. This has been used to explore the significance of photorespiration as a photoprotective mechanism during drought.
Fluorescence analysis can also be applied to understanding the effects of low and high temperatures.
  • Sobrado (2008) investigated gas exchange and chlorophyll a fluorescence responses to high intensity light, of pioneer species and forest species. Midday leaf gas exchange was measured using a photosynthesis system, which measured net photosynthetic rate, gs, and intercellular CO2 concentration. His results show that despite pioneer species and forest species occupying different habitats, both showed similar vulnerability to midday photoinhibition in sun-exposed leaves.
Measuring stress and stress tolerance
Chlorophyll fluorescence can measure most types of plant stress. Chlorophyll fluorescence can be used as a proxy of plant stress because environmental stresses, e.g. extremes of temperature, light and water availability, can reduce the ability of a plant to metabolise normally. This can mean an imbalance between the absorption of light energy by chlorophyll and the use of energy in photosynthesis.
  • Favaretto et al. (2010) investigated adaptation to a strong light environment in pioneer and late successional species, grown under 100% and 10% light. Numerous parameters, including chlorophyll a fluorescence, were measured. Overall, their results show that pioneer species perform better under high-sun light than late- successional species, suggesting that pioneer plants have more potential tolerance to photo-oxidative damage.
  • Neocleous and Vasilakakis (2009) investigated the response of raspberry to Boron and salt stress. Leaf chlorophyll fluorescence was not significantly affected by NaCl concentration when Boron concentration was low. When Boron was increased, leaf chlorophyll fluorescence was reduced under saline conditions. They be concluded that the combined effect of Boron and NaCl on raspberries induces a toxic effect in photochemical parameters.
  • Lu and Zhang (1999) studied heat stress in wheat plants and found that temperature stability in Photosystem II of water-stressed leaves correlates positively and well, to the resistance in metabolism during photosynthesis.
Nitrogen Balance Index
A portable multiparametric fluorometer using the ratio between chlorophyll and flavonols can be applied to detect nitrogen deficiency in plants Because of the link between chlorophyll content and nitrogen content in leaves, chlorophyll fluorometers can be used to detect nitrogen deficiency in plants, by several methods.
Based on several years of research and experimentation, polyphenols can be assigned as indicators of the nitrogen status of a plant. For instance, when a plant is under optimal conditions, it favours its primary metabolism and synthesises the proteins (nitrogen molecules) containing chlorophyll, and few flavonols (carbon-based secondary compounds). On the other hand, in case of lack of nitrogen, we will observe an increased production of flavonols by the plant.
The NBI (Nitrogen Balance Index), allows the assessment of nitrogen conditions of a plant by calculating the ratio between Chlorophyll and Flavonols (related to Nitrogen/Carbon allocation) .
Hence Stancho,
I hope this short summary elucidates soma aspects of the photobiology of plant chlorophyll fluorescence. A lot more information is available. For example models to simulate plant fluorescence. An interesting one can be found at:
Success with your studies,
Frank
  • asked a question related to Chlorophyll Fluorescence
Question
7 answers
Dear Community,
I am currently working on a project envolving the data extraction of the spectral charateristics of plants under artifical light for quality optimisation in PFAL Systems.
Therefore I have to access the Chlorophyll Fluorescence Yield (ChlFY) without the possibility of PAM AC signal filtering.
My tool is a simple spectrometer, with which I can acess the Raw Readings, the absolute PPFD readings and the Calibrated relative Reflection from 400 to 880nm. The sample speed is 1,2Hz. So short pulse modulation (PAM) is not possible.
But the system is designed to work with artificial light sorces (white LEDs + RGB LED) only. Therefore light intensity and spectra can be adjusted.
How can I acess Information abouth The ChlFY with this setup? Should I modulate some low frequency AC Light intensity change and check the ChlF change? Or is there some Index like NDVI/PRI to acess ChlFY?
Or did I missunderstand the Concept or difference between ChlF and ChlFY?
Thank you for your Help!
Relevant answer
Answer
Chlorophyll fluorescence is measured by a fluorimeter .
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
We are measuring the chlorophyll fluorescence of trees in Namibia. Their Fv/Fm values average at around 0.86, light intensity 3500, gain 1, dark offset ON. Recently we started getting Fm high warnings for some of our measurements. Autogain recommends a gain setting of 1.1. The Fm values then go in excess of 4000. I would like to understand the gain setting a little better - what exactly does it do?
To compare the different data sets, I understand that the values must be normalised. How is this achieved manually?
Thanks!
Relevant answer
Answer
Gain setting basically is adjusted so as to get the optimum signal before the detector saturates
In order to compare data, the measurement has to be done at identical gain settings. First use "auto gain" to find a good gain value, then afterwards use manual gain setting found during optimal gain procedure, and then use the same gain setting for all the data sets
  • asked a question related to Chlorophyll Fluorescence
Question
7 answers
In general, parameters such as Fo, Fm, ... (Chlorophyll fluorescence parameters in darkness) are extracted from this machine.
Relevant answer
Answer
Hello,
yes. unfortunately I don't have any data about Fo', Fm' (Chlorophyll fluorescence parameters in lightness). My data is in the attached file.
Thanks for your attention.
  • asked a question related to Chlorophyll Fluorescence
Question
8 answers
Are there tools or parameters ? what treatment use to enhance of chlorophyll response to radiation ?
Relevant answer
Answer
Dear Dr. Nabil,
I would like to tell you that I measured chlorophyll fluorescence by using two instruments: (I) The MONITORING-PAM (Walz, Effeltrich, Germany) and (LI-6400 XT; Li-Cor, Lincoln, NE, U.S.A.). That's mean you need this equipment.
Please do not hesitate to contact me should you need any other information or help !
Kind regards,
ALAA M. ISSA
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
LHCB genes encode for the chlorophyll a/b binding proteins which form the apoprotein of PSII in the thylakoid membrane. LHCB genes are light-regulated (through phytochromes). Now if under low light stress, the expression of LHCB genes are downregulated, it is obvious that the PS II would be deficient in Chlorophyll a/b binding proteins. Also, it has been reported that the density of PSII under low light decreases, total chlorophyll concentration increases and chlorophyll a/b ratio decreases. Following the above points, we get a specific type of PSII under low light(ll PS-II) having more of pigments and less of apoproteins( chlorophyll a/b binding proteins).What is the impact of this low light formed PS II(ll PS-II), deficient in chl a/b binding proteins and rich in photosynthetic pigments, on the photochemistry and fluorescence under low light stress?
Relevant answer
Answer
Every parameter in the environment of your system may influence more or less the behavior of the system. You have to be an expert to know already before what and how the changes will be. To come to that point you have to repeat the experiments or doing other experiments and read the findings of other colleagues. If you only trust your good guesses, you may be lucky and right, but mostly Nature goes other ways than what your predictions predict. That's why we still have to do experiments and accept situations where Nature does not follow our way of logic thinking. By accepting tha.t we are learning and proposing new questions.
Good luck
Reto J. Strasser strasserreto(at)bluewin.ch
  • asked a question related to Chlorophyll Fluorescence
Question
7 answers
Dear all,
We are going to use the Maxi-Pam (Imaging) to measure chlorophyll fluorescence and measure classic parameters in Arabidopsis leave or in potted plants (plant-pathogens interaction), and I'm looking for a reliable method to use this system in routine or some help to start. There are so many possibilities...And also, does anyone use green light in work room when you need to transfer your dark adapted plants? Do you wear some protection from blue light like glasses, when you don't use the red perspex hood? Many thanks, Alina
Relevant answer
Answer
Attention, plants absorb also green light!
Regards,
Michele
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
Is the data obtained from simultaneous gas exchange & chlorophyll fluorescence measurement using LI-COR reliable to study photosynthesis & chlorophyll fluorescence in plants? The photosynthesis, stomatal conductance and Ci values I obtained from simultaneous measurement are noisy and as well the values are quite different from the independent measurement.
Relevant answer
Answer
Yes, i have used in my experiments.... The data is more than 90% reliable
  • asked a question related to Chlorophyll Fluorescence
Question
14 answers
For ornamental plants and shrubs growing in the open field and in the shade (close to big buildings).
Relevant answer
Answer
Dear Mr. Hussain,
For planning your experiment, specifically, the time at which you would like to make the fluorescence sampling, well, the answer depends actually on several factors:
Are you planning to make a diurnal changes experiment? You want to observe how the photosynthetic machinery of your plants works along a full sunny day? or along a full week or a full month? Then you will have to measure periodically, every hour? every two hours? Do you want to establish a relationship between stomatal aperture and primary photochemistry events monitored with Chl a fluorescence? are you following the evolution of drought stress in a big or small field? What exactly are you trying to observe? The precise time of the day, it's important for you? why? Do you need only one single measurement per day? why? If you need to measure along a full day, then the interval in between the diurnal variations measurements depends on the the time scale resolution you want to have. Do you want to observe rapid changes after application of a specific stressor (herbicide, heavy metal, heat, cold, salt, any other plant stressing condition) or simply you want to observe diurnal photosynthetic behavior of your plants? Are those changes expected to occur fast or it can takes several hours to evolve? OK, let's say, you make a diurnal changes sampling for studying diurnal variations in leaf temperature, stomatal aperture, chlorophyll fluorescence, gas exchange photosynthesis, protein expression, induced levels of abcisic acid, or any, and you start at 6:00 AM, preparing a tea or a coffee and your plants for dark adaptation, and after 30 minutes you are ready for measuring fluorescence and depending upon the amount of plants to measure and the time it takes for each measurement, then you could run your first sampling campaign of the day for about 30 minutes to 1 hour... or more... how many plants do you have to measure? How long are you going to invest in measuring each plant? How many leaves are you going to measure in one plant? how easy it is to reach the leaves? What about sampling the other parameters? In a word, do you have a clearly defined measuring protocol? have you already done a series of measurements for knowing how long does it take to sample fluorescence in one leaf? in a whole plant? in one full plant, shrub, bush? Is one leaf from one plant enough representative for you? are the leaves enough big to measure? to sample a full plant (if several leaves are going to be measured), how many plants are you going to measure? You need to know all that before planning an experiment, any experiment, in order to optimize sampling time, and the experiment itself. OK, let's say, you plan to make a diurnal changes experiment to observe how the plant behaves along a full day, and you start your sampling campaign, now once that you have collected your fist set of data, can you immediately transfer all the collected data to your portable computer? or do you have to go back to the lab to do that? How long does it takes to transfer the data? can it wait until you have finished all of your measurements? Does your Fluorometer machine has enough memory to keep all of the measured data in it until the end of the day? That takes time also. And here is another important question to answer> are you going to measure ONLY fluorescence or do you plan to measure other parameters? Do you plan to measure plant spectral reflectance, chlorophyll content, CO2/O2 evolution photosynthesis, or any other kind of measurements beside fluorescence? OK, let's assume you collect and prepare next sampling in a short time, 30 minutes for example, remember that you need to put your plants in darkness (dark adaptation for at least 30 minutes) before measuring Chlorophyll a fluorescence. What it is your own personal time availability? Do you have to attend lectures in between? Do you have technical staff in charge of the experimental sampling ?  And another important question to answer is: In order to have comparable data, you need to optimize the speed of sampling time, the amount of plant individuals to measure. it has to be as closest as possible in time. So, many questions to be answered before you can get the optimal answer to the one simple question. In a word, the best moment of the day to measure fluorescence depends upon many factors.
For comparing the photosynthetic behavior of two groups ornamental shrubs same species same variety, growing in two different light regimes: in shade and in open light conditions, and assuming any other conditions are kept the same (soil humidity, soil chemistry, wind speed, atmosphere chemistry, etc), I would recommend a diurnal changes experiment.
So, you measure Chl fluorescence every 2 hours from 6 AM until 8 PM. Each 2 hours, you should measure also (at least) : ambient light, air temperature, soil temperature, soil pH, soil humidity. You may repeat this measurements, once in a full sunny day  and once in a cloudy day. You could repeat it also along once per week during several weeks. Preferably, take your measurements before flowering, as flowering introduce a lot of "noise" in fluorescence measurements. This way, you can see how plants behave in shade and open field light conditions . Then, after that, you could add some changes in controllable factors, you can change humidity (irrigation frequency, soil type, or any other type of factor that you could be interested in to study its influence on your plants).
  • asked a question related to Chlorophyll Fluorescence
Question
9 answers
Hello,
I just read about your project that I find amazing and absolutely interesting.
Do you have any plans for adding Chl a Fluorescence as a complementary technique for investigating heavy metal induced stress in plants/trees ?
Ronald
Relevant answer
Answer
Hello Dr. Ronald ...I am retired but style alive. Yes, there are some grasses, Brachypodium sp. , cariologically related with the cereals for human consumption (wheet , barley , corn). Would be very interesting to research their performance on heavy metal soils.
  • asked a question related to Chlorophyll Fluorescence
Question
7 answers
fluorometer, drought stress.
Relevant answer
Answer
Any fluorescence signal emitted from excited chlorophyll of any plant we are measuring, is based on 6 parameters answering the following questions (all starting with a W):
1) Who is fluorescing?.....................describe your plant or your fluorescing sample
2) Where is it fluorescing?...............Indicate the wavelength or filter where you                                                                      measure the fluorescence signal
3) Why is it fluorescing?                   Because the sample is excited: indicate the
                                                         wavelengths of your excitation light (nm or used                                                              filter)                                                                         4) What kind of fluorescence?         direct, prompt or modulated or delayed                                                                            fluorescence kinetics you are measuring (e.g. an                                                            OJIP fluorescence transient: see internet: JIP-                                                                test Strasser) describe the shape of the curve                                                                you see.
5) What amount?                              of fluorescence you see? This is the measured                                                              fluorescence intensity emitted by your sample per                                                          measured sample cross-section.                             6) When?                                          are you measuring the fluorescence intensity (the                                                          time-point of your OJIP-prompt fluorescence trace
                                                     e,g. as Fo to Fm or Fo to F(I) to Fm or Fo to F(J)                                                                    to FI) to Fm or Fo to F(K) to F(J) to F(I) to F(m) 
The JIP-test STRASSER (see internet) will give you some explanations of what these Fluorescence SHAPES may represent on the classical basis which states that: if all RCs are open (open is understood that the reaction center complex has an oxidized Qa and closed is understood that Qa is in the reduced state as Qa-. Therefore the fluorescence transient with high excitation light, of a dark adapted leaf, is going from Fo to Fm passing the intermediate step-phases Fk then Fj then Fi to Fm  (seen as inflection points or often partially as steps (on a log time scale) seen at: labelled K (at 300 us) then labelled J (at 2 to 3 ms) then labelled I at 30 ms ( labelled this way as I for INTERMEDIATE step between Fo and Fm, measured in the past with mechanical shutter instruments, not having safe recordings of faster signals (below 1 ms). Fp as the highest fluorescence intensity measured within the time segment of 1 second emitted by a dark adapted sample of a leaf or algae. With fast shutterless optoelectronics, much faster prompt-fluorescence-kinetics than 1ms for going from darkness to full light intensity reviled intermediate steps in the fast fluorescence kinetics of about the following steps:
from O(? ns) to L(30 us) to K(300 us) to J(3ms) to I(30ms) to H(300ms) (H for Highest or P forPpeak) P(300ms) under saturating light intensity.
Named as kinetic steps or bands in
alphabetical order from longer to shorter time units: O--(N)..(M)--L--K--J--I--H--G--F(t)
Depending on the experimental conditions all these steps can be visualized more or less clearly. A kind of general agreement exists that at time zero of the fluorescence kinetics Fo all reducible RCs are in the oxidized state with Qa and at Fm all reducible RCs are in the reduced state with Qa-.
Below this phenomenologically described fast fluorescence rise-kinetics OKJIP are hidden a succession of redox states of the oxidised RCII.QaQb complex which gets fully reduced as reducedRCII.Qa-Qb= etc.
The Qa to Qa- reduction is therefore called in the literature as PRIMARY PHOTOCHEMISTRY (even so the word "primary" is always questionable.) Nevertheless the reduction of Qa to Qa- is a classical stable reduction. The fluorescence yield of Qa- is higher than the fluorescence yield of the oxidized form Qa. Therefore the phenomenon of variable fluorescence kinetics is a measure of the reduction kinetics of Qa to Qa-.            
Therefore the variable fluorescence kinetics (in vivo or in vitro) is a measure of the reduction within the mixture of  all Qa complexes of different unit types (e.g. small units without Chl b, big units with chl b, non exciton exchanging units (separate pack units) and cooperative units getting reduced to Qa- within a group (grouped pack units). All forms of complexes do exist in green mature samples of leaves and algae. This mixture of heterogeneity of the energy distribution within the photosynthetic apparatus leads morphologically to different types of stroma- and grana-thylakoid formations, leading to different structures and functions of  chloroplasts thylakoids in plants and algae. 
Any questions or comments welcome to:
Reto J. Strasser,  strasserreto@bluewin.ch
Hofgutweg 51B
CH 3400 BURGDORF
Switzerland 
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
Among gas exchange parameters indicating the efficiency of plant photosynthetic machinery; Pn, A and CER abbreviations are commonly used. Net assimilation rate (Pn) and photosynthetic rate (A) both refer to the same parameter  indicated by umol carbon dioxide per m2 of the leaf area per second. The question is about CER (carbon dioxide exchange rate); does it refer to the same parameter, and is it logic to be measured with positive and negative values?
Relevant answer
Answer
Pn and A are the same.  CER can also come from individual gas exchange measurements and can be negative if the leaf is respiring more than fixing C.  CER can also be derived from eddy flux measurements and will be negative at time (for example, at night).
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
Dear researchers,
Can anyone provide articles on the effects of plant density and cultivar on cotton leaf chlorophyll fluorescence?
Thanks
Relevant answer
Answer
It is a tricky question , literature  on this issue is really very limited . But you can have a look at these PDFs to get some clues..
  • asked a question related to Chlorophyll Fluorescence
Question
26 answers
The options: Photosynthetic Yield, Rapid Light Response Curves, or ETRmax?
Or some other measurement that I haven't thought of for measuring photosynthesis in kleptoplasts.
Relevant answer
Answer
Dear Samantha Ann,
A research group from Portugal working on keptoplasts have already used the  PAM technique and have chosen the ETR method for studying that particular and enigmatic endosymbiotic association, please, see
Philos Trans Royal Soc London B Biol Sci. 2014 Mar 3;369(1640):20130242.
doi: 10.1098/rstb.2013.0242.
Photophysiology of kleptoplasts: photosynthetic use of light by chloroplasts living in animal cells.
Serôdio J1, Cruz S, Cartaxana P, Calado R.
My recommendation for you is using a safe and well established method for measuring oxygen evolution (to measure whole chain PET as well as PSII and PSI activities on isolated thylakoids), for example, using oxygen electrodes in parallel to ANY kind of fluorescence measurements, just as Bryan Green did, please  see:
Mollusc-Algal Chloroplast Endosymbiosis. Photosynthesis, Thylakoid Protein Maintenance, and Chloroplast Gene Expression Continue for Many Months in the Absence of the Algal Nucleus
Brian J. Green, Wei-Ye Li, James R. Manhart, Theodore C. Fox, Elizabeth J. Summer, Robert A. Kennedy, Sidney K. Pierce, Mary E. Rumpho
Plant Physiology Sep 2000, 124 (1) 331-342; DOI: 10.1104/pp.124.1.331
PSI and PSII in kleptoplasts is different. You will see that along a several months screning, the evolution of PSI keeps up while PSII activity is
By the way, Martin Pecheux shared a nice experiment with Merope Tsimili Michel and Reto Strasser and measured fluorescence from foraminifers  (another  kind of kleptoplastic association) using the PEA (HANSATECH UK) machine that measures fast fluorescence induction curves (1 to 255 seconds). Their results are very interesting. See
Tsimilli-Michael, Merope, Martin Pêcheux and Reto J. Strasser. 2014. Light and Heat Stress Adaptation of the Symbionts of Temperate and Coral Reef Foraminifers Probed in Hospite by the Chlorophyll a Fluorescence Kinetics. Zeitschrift für Naturforschung C. 54(9-10): 671-680. Retrieved 23 Jul. 2017, from doi:10.1515/znc-1999-9-1009
Good luck!
Ronald
  • asked a question related to Chlorophyll Fluorescence
Question
9 answers
The biggest challenge to agriculture scientists today  is  abiotic stresses like drought, salinity and flood . As a result of these stresses, a  huge quantum  of economic productivity  is lost.  Every year one or two new varieties are released in cash crops for either drought or salinity tolerance or sometimes in rice   for flooding tolerance as well.   At times the induction of stress tolerance in these plants is comparatively marginal only.  Therefore, it may be of interest to note whether  the quality chlorophyll fluorescence could be taken as a marker  of stress tolerance
Relevant answer
Answer
I think , in any cases the quality  depends the linear relationship with the applied stress
  • asked a question related to Chlorophyll Fluorescence
Question
15 answers
Please suggest to me how to measure chlorophyll fluorescence in needle type of leaves in casuarina or such species. If there are any references available please suggest them.
Relevant answer
Answer
Thank you sir 
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
I have purchased Chl C2 standrad from DHI. This standrad was dissolved in acetone 90%.  I injected this standard to make calibration curve, however it could not be detected with the methods. I used Kraay et al. 1992 methods. Does any one can help e to solve the problem. 
Relevant answer
Answer
Thank you very much munusamy vivekanandan And guido bongi
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
Hello Everyone,
I have been thinking of the reason for placing plants under low light intensities when exposed to low-temperature stress. I assume it has something to do with photooxidative damage but I am not sure how!
Does someone have any idea!
Thanks much.
Relevant answer
Answer
Good points Duran.Your  last statement has great relevance in the context of the question.
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
The SCOPE model integrated in the ARTMO software is reported to be used to simulate canopy radiances comprising reflected solar radiation and emitted chlorophyll fluorescence (SIF). Does anyone know about the specific procedure I should follow to complete this simulation? I have already get the software installed.
Relevant answer
Answer
Dear Siheng Wang
first you have to collect required inputs for SCOPE.
lint for Incoming Shortwave radiation: http://clearskycalculator.com
follow this paper i will solve all your problems.
i simulated SIF using SCOPE.
if any required help i am here.
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
I haven´t seen negative values of driving force (DF) anywhere in the literature. I have measurements of some severly stressed plant samples with negative DF. Since DF is on a log scale negative values can happen. What would negative value mean?
Relevant answer
Answer
Maybe this would help: Krüger, G. H. J., De Villiers, M. F., Strauss, A. J., De Beer, M., Van Heerden, P. D. R., Maldonado, R., & Strasser, R. J. (2014). Inhibition of photosystem II activities in soybean (Glycine max) genotypes differing in chilling sensitivity. South African Journal of Botany, 95, 85-96.
  • asked a question related to Chlorophyll Fluorescence
Question
12 answers
I'm trying to use the fluorescence level at the J phase of the OJIP transient to roughly determine the redox state of the plastoquinone pool in darkness in Arabidopsis leaves. I compare the values from fully dark-adapted (>20 min) leaves to leaves pre-illuminated with far red light to fully oxidize the PQ pool, like described in Toth et al. (2007) Photosynthesis Res. 93, 193-203. I use a Walz MultiColor PAM with a 440 nm measuring light and max intensity 440 nm MT flash to do the measurements.
I'm having trouble with deciding the time point from which to take the value. Literature suggests 2 ms or ms, which is fine for WT, as that is where the signal plateaus. In my mutant line, however, the FJ peaks at around 1 ms, then declines slightly at 2-3 ms before rising again in the J-I phase. Now, if I take the values from 2 or 3 ms, there is no difference between WT and my mutant line. If I however calculate (FJ-FJ ox)/ (Fm- FJ ox) using the values at 1 ms, I get significantly larger values for the mutant line. My question is, does this "bump" at 1 ms actually reflect a more reduced PQ pool at al, or is it caused by something else entirely?
Relevant answer
Answer
Dear Lauri,
The dip you observed is due to a transient peak of P680+ in the S3 state. Reducing the light intensity broadens and lowers this peak making the dip disappear.
I do not agree with Sandra though that those in active centers affect the determination of the PQ-redox state in darkness. The idea of Toth et al. was to place the measured J-step between a minimum and a maximum value, showing that the PQ-redox state changes more or less linear with the J-step between these values. Those inactive centers are then in the off set (the fluorescence rise below J) which does not affect the calculation.
In 2005 (Schansker and Strasser Photosynth Res 2005) I published a paper in which I proposed a method to determine amount of those inactive centers. Lavergne and Leci in the nineties had listed all the problems with the quantification and I showed that by using far-red light to excite PSII you could reduce this to two factors and solve the problem. However since you use a modulated system with measuring light that is more actinic than far-red light we may assume that already at your F0 all inactive centers are closed.
You wrote that the literature suggests 2 ms for the J-step. I think we used consistently 3 ms and in Khalaji et al. (PRES in press) an argument is made why from a kinetic point of view the 3 ms point is better than the 2 ms point, but of course with a P680+ dip that gets complicated.
Best regards,
Gert Schansker
  • asked a question related to Chlorophyll Fluorescence
Question
14 answers
Photolysis is one of the critical step for photosynthesis as an electron source.Do you know any plant that undergoes photosynthesis by passing PSII, photosystem II,  (or without it), generating alternative electron source apart from water splitting.
Relevant answer
Answer
When the excess amount of NAPH is produced and more ATP is required, PSII is by-passed and cyclic photosynthesis take place where electrons are travelled through PS I to Q. This is a well-known phonemenon in plants. 
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
I am growing Chlamydomonas (wild type) on 24 well plates and wanting to test its growth rate using chlorophyll fluorescence. The literature says testing every 30 mins for 80 hours will provide a high throughput growth curve. I am looking for any other suggestions on a decent time frame
  • asked a question related to Chlorophyll Fluorescence
Question
4 answers
It is required apply some factor to the obtained data? The equations to calculate chl a, chl b and carotenoids could be the same as used for the determination of photosynthetic pigments in spectrophotometer?
Relevant answer
Answer
Hi Maehdi, 
I think you question is technical. You are asking if it is possible to use the microplate reader to quantify chlorophyll a, chlorophyll b and carotenoids based on the formula given for 1 cm pathlengh cuvettes (for example, Wellburn method, Vol. 144, No. 3, 1994, p. 307-313)?? 
The answer is YES, and you need to use a constant factor to get the final corrected data equivalent to what you will get in a 1 cm pathlength cuvette. This depends on the amount of liquid used (well length, lightpathlength). In my case, the plate reader and plate I use, I need to multiply the data with 3.5 constant factor when I use 100 ul extracts per well. but this factor will change if I use 200 or 250 ul.
Hope this helps.
Thanks
Sushanta
  • asked a question related to Chlorophyll Fluorescence
Question
8 answers
I would like to measure photosynthesis rate using PAM-210 Chlorophyll Fluorometer but I don't know how to operate it. It would be a great help if someone share your experience.
Relevant answer
Answer
Yes PAM 210 is an outdated model, but it is still useful and can give you lot of information. 
  • asked a question related to Chlorophyll Fluorescence
  • asked a question related to Chlorophyll Fluorescence
Question
12 answers
I want to know how to correlate the OJIP curve with the efficiency of PSII. In the file attached( Panda,Sirkar 2011), Polyphasic Chlorophyll fluorescence transients of Swarna and Swarna Sub1 under non-submerged control (1) and after 1 (2), 3 (3), 5 (4) and 7 (5) d of complete submergence. The first, second, third, fourth and fifth lines from left position demonstrate the fluorescence intensity at 50 μs, 100 μs, 300 μs, 2 ms, and 30 ms, respectively. The lines meet at the fluorescence curve at 50 μs, 2 ms and 30 ms are known as O-, J- and I-phase, respectively. The highest peak in the curve was designated
as maximum fluorescence (P=Fm). A= Swarna, B= Swarna Sub 1. I want to know how to correlate this data with the PSII efficiency. 
Relevant answer
Answer
Dear Darshan,
I am answering from a practical point of view only, using my own expertise in the field and many years analysing hundreds of thousands fluorescence curves... I will avoid scientific polemics and technical terms as much as possible, to help you understand what's going on with those curves, and what they tell you about your plants... ok?
From the Kautsky curves you've measured (OJIP fluorescence induction kinetics) on Swarna varieties (A, swarna control or SC) and Swarna Sub1 (B or SS), after 1, 3, 5 and 7 days of full submergence we can observe:
1) no differences between SC0 and SS0 (0 means Chl a fluorescence measured at  start of submergence experiment or day 0),
2) no differences between SC1 and SS1 (day 1),
3) Slightly differences between SC3 and SS3 start to appear... (day 3),
4) Chl a Fluorescence of the SS5 plants shows a SS plant doing better than the control SC5 (day 5),
5) Chl a Fluorescence of the SS7 shows a plant doing much better than the control SC7 (day 7).
I suggest to use Biolyzer software for making a double normalisation plot of fluorescence between F=20 us and F=Fmax for each group of curves. You can calculate the JIP test parameters in order to compare PI(ABS) for each case. Usually, those curves represented in your figure should correspond to an average curve for each case. The average curve should be estimated in advance, after doing a pre-evaluation of statistical variability of Kautsky curves.
Ideally, in order to compare both samples, light, temperature and any other conditions should be the same for both populations. Well, I assume, it is difficult to keep same temperature and light conditions on both, control and submerged Swarna plants. Possibly, a slightly more "optimal" photosynthesis in SS plants can be explained by differences in the ambient temperature, because, from what I see in those curves, light/temperature conditions were higher in control plants compared to submerged plants. Possibly foliage in control plants is less than in submerged plants? In any case, it seems like SS submerged plants were able to cope better with light/temperature changes than control plants. Also, seems like submerged plants are more "green" and happy than control plants. You should measure Chlorophyll content using a SPAD machine for example... I would not be surprised if you tell me that SS is a genetically modified variety of plants developed for coping with flooding... we can see that also from those curves...
Please, check the double normalisation and show us the pictures. Then we can talk about PSII efficiency. But in any case, when using JIP test ideas  and OJIP curves, PSII efficiency is a relative, steady and overall parameter. It is like energy, an absolute magnitude, but we can not measure absolute energy, nobody did until now, however we can measure changes in temperature and then we can calculate state changes in energetic content... beside that, PSII efficiency is by definition a ratio, therefore, it is a relative magnitude, that's why we speak of comparing the "efficiency" of a plant with the efficiency of a "reference" control plant... 
Kind regards,
Ronald
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
Dear all,
we are going to use the PAM-2500 to measure chlorophyll fluorescence parameters in grapevine. The measurements will be conducted outside, therefore we want to keep it simple, but of course efficient in data aquisition. Therefore dark adaptation is no option for us, bu the instrument has many different functions to circumvent this problem.
I have the following questions:
1. the field screen with the Y(II) measurment provides no light acclimation step with standard actinic light, just a light puls. do you think a standardized acclimations to actinic light is necessary?
2. Fo´is measured under field sceen after the light sat puls and a short period of FR. Is this similar to the FR+Y option?
3. do you use default light intensities? we are working with grapevine
many thanks
Michaela
Relevant answer
Answer
http://www.walz.com/products/chl_p700/pam-2500/downloads.html, YII will vary with light intensity and a step curve can be made with portions of the leaf shaded by a net or a filter 5 min before taking reads. Clips with a frame holder can be made from spare. Further questions are on manual, care in recording temperature water status and chl density, with the best
  • asked a question related to Chlorophyll Fluorescence
Question
12 answers
We are measuring Photosynthetic Index (PI) with a Hansatech Pocket PEA on various trials on potatoes infield whilst applying various carbons with fertilizer. The soils are intensively farmed. The measurements are taken weekly.
  • When the Carbon is fulvic acid based, we see a spike in PI above the control immediately after application, which then steadily declines (correlating with the control as nutrients are depleted)
  • When the carbon is humic acid the PI drops immediately after application (below the control) and then gradually increases.
On both trials the average over time is higher than the control.This trend seems to be replicating in ongoing further trials
Relevant answer
Answer
Hello,
I recommend you to very cautious about your PI measurements. As mentioned above PI is a derivation of the JIP-Test model publish by Reto. It was designed mostly as a parameter to help you elucidate differences when other “more standard” parameters (such as Fv/Fm) do not show differences. The problem with it is that is very sensitive (too sensitive) and without solid statistic is very difficult to establish how valid are your differences.
Furthermore, I do not recommend you just average individual PI and estimate the STD. What you need to do is calculate the statistical significance of the individual PI components [(RC/ABS)*(ABS/TR)*(ET/TR)]. Only then you can be sure that the PI changes have a physiological meaning.
Do not get me wrong, I’m a strong believer of the JIP-Test. But because the JIP-Test is dependent of several assumptions (12 to 18), you have to be very cautious. In fact, due to abuse of parameters such as PI(abs) by many groups, you will find that most reviewers would not trust in your measurement. An over- simplification of an increase PI is that light reactions of PSII are more efficient, and a decrease would mean less efficient. But in my opinion, PI does not have a meaning unless you know what happens to FV/FM, ET/TR and RC/ABS. Remember that chl a fluorescence is sensitive to a bunch of things such as temperature and formation of other quenchers that will alter your measurement.  Additionally, you need to support your data with O2 evolution or even better Gas exchange at least. Why don’t you try ETR(II) measurements instead?
I recommend you to read a paper of Stirbet and Govindjee where they criticize the JIP-Test, that way you can test the validity of your measurements. Here is the link:
Cheers,
Alonso
(not proofread, so typos may be included
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
This year, we are going to use fluorpen for the first time to measure chlorophyll and quantum yield. But does anybody have precise protocol or teaching guide for this? For example, I pressed Ft measure and it was running continuously until 6859...I dont understand that why it is not stopped and what measurement I have to use..
Relevant answer
Answer
You can take  the manual from fluorpen site and follow the procedure. The instrument is used for fluorescence kinetics under different light and principles are described in one of the many refs, as in http://jxb.oxfordjournals.org/content/51/345/659.full.pdf, the manual is at http://www.psi.cz/download/document/manuals/fluorpen/FluorPen_Series_Manual.pdf and probably Ft is a continous recording of chl fluorescence used in thermal stress in the dark,
  • asked a question related to Chlorophyll Fluorescence
Question
9 answers
I'm shopping for field photosynthesis measuring systems.  The LiCOR 6400 and PP Systems CIRAS-3 both have the option of estimating apparent electron transport rate (ETR) and PSII yield based on fluorometry: basically looking at Chlorophyll fluorescence. The WALZ PAM 2500 is exclusively a fluorometer.  In contrast, the LiCOR 6400 and PP SYSTEMS CIRAS-3 are mainly estimating photosynthetic rate based on differences in CO2 and H2O vapor.  
Have people tried both fluorometry and gas exchange approaches to estimating photosynthesis? What are the relative advantages of both approaches?  Do you really need both systems to get an estimate of photosynthetic rates?  What are the relative errors?
Relevant answer
Answer
Marcin is mostly right, but you should note that fluorometry can treat more leaves per time. So it might be the method of choice for screening of larger number of plants. 
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
We are using a PAM fluorometer to measure the quantum yield of chlorophyll fluorescence in an intact microalga culture. When the culture is dark-adapted for 20-30 minutes, the quantum yield is rather low (0.4), while if it's measured under low light (~50uM quanta) the yield will increase to about 0.6. The alga medium is not agitated and the cells form a biofilm on the bottom of the flask. Could this be a result of a low-oxygen layer forming around the biofilm after being in the dark, inhibiting PQ pool oxidation? Is there another explanation?
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
chlorophyll fluorescence, remote sensing of vegetation, plant science 
Relevant answer
Answer
I have used differential equations and kinetic Monte Carlo model to simulate ChlF.
  • asked a question related to Chlorophyll Fluorescence
Question
14 answers
I'm using the Walz Diving PAM to measure Fv/Fm (after 30 min darkness) and F'/Fm' (light-adapted) in the same algae samples. Fv/Fm values are consistently lower than F'/Fm'. Any ideas would be greatly appreciated!
Relevant answer
Answer
Just to add some details to the first comment of Dieter Hanelt: Also in diatoms the highest Fv/Fm is often only obtained after low light acclimation but not after dark acclimation. It has been shown that in darkness a significant amount of diatoxanthin can be produced, which may induce some NPQ, thus lowering Fv/Fm (Jakob et al. 1999, Plant Biology). This has been interpreted in terms of chlororespiration involving the PQ-pool, as described in Dieters' comment. However, recent results of Bailleul et al. (2015, Nature) explain this by a backwards reaction of the plastidic ATPase, using mitochondrial produced ATP, which then generates a proton gradient over the thylakoid membrane.
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
I am interested in marking a number of different things with antibodies and fluorophores, but all of the standard protocols cause chlorophyll to leak out of the cells. I have had no luck finding a method that preserves chl a and still perforates the membranes to get an antibody in. Any/all help is greatly appreciated!
Relevant answer
Answer
Hi Elise,
     My experience with labeling plant cells is exactly zero, but I have a couple questions for you.
1)   Are you fixing the cells? If so, how?  We routinely use freshly made 4% paraformaldehyde to fix our animal cells, which does not create autofluorescence problems. (Don't use old paraformaldehyde or formalin- they can polymerize to form autofluorescent complexes). If you can fix your cells, you should be able to retain the chlorophyll. Paraformaldehyde will create some tiny pores in the cell membrane but I wouldn't think they should allow the chlorophyll to escape. For our cells, we fix for 15-30 minutes at 4 degrees C, but plant cells may require a longer fixation due to the cell wall. I would specifically recommend against using glutaraldehyde as a fixative as it generates alot of autofluorescence in the green channel.
   If paraformaldehyde is problematic, have you tried fixing using methanol fixation? 
2) Once the the cells are fixed, you should be able to use buffers that contain gentle detergents (such as Triton X-100 at 0.5%) to create some pores to allow your antibodies and other reagents to penetrate into the cells.
3) If you need immunolabeling protocols, I'll be happy to send you ours so you can see what we do for comparison. (Just send me an e-mail if you need them: david-sherry@ouhsc.edu)
Just out of curiosity, what color is chlorophyll fluorescence? Red?
I hope this helps.
Dave Sherry
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
In order simulate some satellite observations of solar-induced chlorophyll fluorescence (SIF, ground-emitted), which is coupled with reflected sunlight, what is the most convenient RT model to obtain the solar irradiance at ground, TOA (Top of atmosphere) radiances, and BOA (bottom of atmosphere) radiances at the same time? What about MODTRAN5 model?
Relevant answer
Answer
Basic infos are on the fluormod site http://www.ias.csic.es/fluormod/ Probably as far performances you should ask their desk
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
I have a chlorophyll data. estimated by 80% acetone method. how can i predict / calculate / derive / chlorophyll content to N content. Plz... give me your suggestion and references.
Relevant answer
Answer
Maybe the following publication which showed relationship between chlorophyll content and nitrogen applications can help
  • asked a question related to Chlorophyll Fluorescence
Question
14 answers
New instruments 
Relevant answer
Answer
Dear Habib
You can use the portable SPAD-502 chlorophyll meter after correlating the SPAD 
readings with actual chlorophyll content. Firstly, you have to construct a calibration curve for the plant species you are interested.
You have to record the SPAD measurements from leaves of different greenness (I think that 30 leaf samples are quite enough) and then you have to estimate their chlorophyll content with a biochemical method.
Then, the calibration curve of SPAD readings versus leaf chlorophyll content can be used for chlorophyll content estimation using only the respective SPAD readings of the unknown samples of the certain plant species.
According to the certain biochemical method that you will use, you must convert the spectrophotometric measurements to chlorophyll concentration (for example mgr/gr fresh weight, mgr/cm2, mgr/gr dry weight) in order to construct the calibration curve.
In the attached paper you can see one of these methods.
  • asked a question related to Chlorophyll Fluorescence
Question
9 answers
Is it possible to measure clorophyll fluorescence in the night? Just to avoid the wasteful process of shading each leaf with a little piece of black cardboard during 30 minutes. Thank you.
  • asked a question related to Chlorophyll Fluorescence
Question
11 answers
The measurement of in vitro or in vivo chlorophyll fluorescence is an accepted alternative to the measurement of algal biomass in algal growth inhibition testing (see OECD guideline 201). 
The prerequisites are (1) satisfactory correlation of fluorescence with biomass over the range of biomass occurring in the test, and (2) knowledge on the conversion factor between the fluorescence.
I am wondering what might generally compromise the correlation between fluorescence signal and biomass. In particular, which chemicals might do so and can certain mechanisms of action of chemicals be identified which compromise the correlation during testing (especially during the recommended test duration of 72 h.).
I would be happy to be reminded in case this has been discussed already.
Many thanks in advance
Relevant answer
Answer
I think that generally you can use raw florescence as a robust indicator of biomass if you first calibrate your fluorescence readings to cell densities/chl. a concentrations.  It will vary from species to species and will be highly affected by the physiological state of the cell.  For example when cells are iron limited their chl a content and subsequent fluorescence decreases dramatically.  It would therefore not be advisable to use fluorescence to compare the biomass of iron limited and iron replete cultures.  Fluorescence also has a strong diel signal and this its important to samples at the same time of day in order to get consistent and reliable results. Generally I throw my cells into the fluorometer first, then add DCMU which kills photosystem 2 and allows for the determination of a Fv/Fm ratio, then I do a cell count.  This gives me the relative health of the cells and allows for a nice regression of fluorescence and biomass…..then i can later use just the fluorescence as a biomass indicator…..again its important that this regression is done for every species and every treatment.
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
The instrument is for for measuring photosynthesis, chlorophyll fluorescence, soil respiration and net canopy flux
Relevant answer
Answer
There are available a lot of this kind of instruments to measure net photosynthetic rate and stomatal conductance (CIRAS, Licor, Waltz). check their accuracy before spend a lot of money!
Cheers
  • asked a question related to Chlorophyll Fluorescence
Question
1 answer
Chlorophyll Fluorescence mission of NASA initiated at 1999  
Relevant answer
Answer
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
I am looking to obtain SCOPE chlorophyll fluorescence Model code for my work. Can anyone suggest how to obtain it? I tried to contact van der Tol for the same and have received no communication in this regard.
Relevant answer
Answer
Hi, You can obtain the SCOPE model from this website:  http://ipl.uv.es/artmo/
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
This is causing an error on the curves and the REG values cannot be calculated.
Relevant answer
Answer
You should reproduce fig. 2b of http://link.springer.com/article/10.1023%2FA%3A1006188004189#page-1, leaves should be kept flat, and conditioned for 6 h at growing light. exposure times and saturating light intensity should be kept under control.
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
How does one calculate benthic chlorophyll a concentrations using a fluorometer? I am familiar with the methods described/summarized by Aminot and Rey (2000) for calculating chl a for phytoplankton, but how would does one adapt the equation to estimate chlorophyll a content of the surface area of a rock (in units of micrograms chl a/cm-2, for example)?
Any help would be greatly appreciated!
Relevant answer
Answer
Isabella --
the "classic" method for measuring the surface area of rocks for periphyton research has been to use aluminum foil. In short, you cover the rock or portion of the rock (if subsampled) with a single layer of aluminum foil -- cut off the creases - and then calculate surface area from a standard curve of foil area and mass. A good review article on this and some other methods is :
Bergey and Getty. 2006. A review of methods for measuring the surface area of stream substrates. Hydrobiologia, 556:7–16. DOI 10.1007/s10750-005-1042-3. (link attached)
They found very high r2 values (>0.95) on the regression curves for all the methods that they evaluated, including foil.
Additionally you can simply do a google (or bing) search on:
"periphyton rock surface area aluminum foil"
for a bunch of other references (including USGS/NAWQA) using the foil, but they are all essentially doing the same thing.
When I was doing this type of research, I would always do a new regression curve for each new roll of foil.
  • asked a question related to Chlorophyll Fluorescence
Question
3 answers
I read a paper where the heat stability of thylakoid membranes and loss chlorophyll in heat stress in winter wheat has a strong correlation. I was wondering if I could use the SPAD to screen several accessions of quinoa in my heat experiments. Because, if I use the chlorophyll fluorescence I will take me long time, due to the leaf needs dark adaptation.
Relevant answer
Answer
Clearly, chlorophyll fluorescence is more reliable indicator in this situation. Dark adaptation only takes 20 min, and one can use a whole batch of leaf clips for that purpose, so, the delay would not be considerable. SPAD measurement also takes some time...
  • asked a question related to Chlorophyll Fluorescence
Question
6 answers
I want to measure chlorophyll fluorescence in relation to the Cadmium stress in rice plants by using above mentioned leaf fluorometer. What is the correct way of doing this in order to take a better measurement? Is dark pulse compulsory to do this? Can't I use full flashed condition to measure this?
Relevant answer
Answer
Dear Salman,
Thank you very much. I followed suggestions.
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
Is it necessary that when Fv/Fm is high, PI is also high?
Relevant answer
Answer
Analysis of chlorophyll a fluorescence is appreciated as widely used method in research of photosynthetic efficiency in higher plants (8). One of the most often employed parameters is maximum quantum yield of PSII (Fv/Fm) or so called Genty’s parameter , which gives the information about the proportion of the light absorbed by chlorophyll in PSII that is used in photochemical processes. Further advances in chlorophyll fluorescence techniques as well as development of new apparatuses for its measurement allowed the introduction a plenty parameters that describe PSII photochemistry in detail. One of the most powerful and most comprehensive parameter is performance index (PIABS). This is a multiparametric
expression that takes into account all of the main photochemical processes, such as absorption and trapping of excitation energy, electron transport further than primary plastoquinone (QA) and dissipation of excess excitation energy. Unlike Fv/Fm which utilizes only extreme values of chlorophyll fluorescence, namely minimal (F0) and maximal (Fm) fluorescence, very fast and accurate measurement
of fluorescence transient between these two extremes is necessary for PIABS calculation. Therefore, PIABS appeared to be very suitable and sensitive parameter
to investigate plant overall photosynthetic performance under different abiotic and biotic stresses .
  • asked a question related to Chlorophyll Fluorescence
Question
13 answers
I request you all to let me know what will be the nature of fluorescence under low light conditions. Some paper say that Fv/Fm increases under low light conditions ( 25% of natural light) in comparison to 100% natural light. 
Relevant answer
Answer
This clearly suggests that the photosynthetic machinery (in particular PS II) of this specific rice cultivar is sensitive to high photon flux density (high light intensity). You will be able to confirm the same by plotting light saturation curve (you can use PAM, PEA or any photosynthetic systems that has provision for such measurements). You findings make me believe that PS II (of rice cultivar that is being tested by you) is getting photodamaged at high light intensity. This could be due to generation of superoxide anion radicals, singlet oxygen and hydrogen peroxide at elevated levels (this would automatically promote generation of hydroxyl radicals etc.) and lack of desired degree of antioxidant capacity (you may look for carotenoids levels and other non-enzymatic antioxidants as well as enzymatic antioxidants).
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
I am hoping to find a procedure for analyzing lyophilized algal samples. I want to determine the fraction of algal biomass (based on the chlorophyll fluorescence) within a co-culture with other organisms.  I worry that the freezing and desiccation may negatively impact the chlorophyll readings.  
Relevant answer
Answer
 This may be tricky. Unfortunately, Phaeophytin is not necessarily the only, nor the main mode of degradation of chlorophyll within the cells.  
  • asked a question related to Chlorophyll Fluorescence
Question
2 answers
Dear, I take a experiment about arabidopsis
And I want to get potochlorophyllide fluorescence spectrum under total dark conditions. But my plants were grown in MS plate, and when I trying to sampling that plants, light must be penetrated. So, I take fluorescence intensity, chlides that converted from pChlide intensity was measured. But many researchers detected only pchlides. But there were no specific method how they sampling the plants.
Relevant answer
Answer
Hi,
There is not many possibilities. You must go with your plants in a dark room and prepare your samples there. To make the preparation easier, you can bring with you a weak green light. Of course, you must verify thatit does not trigger the transformation of protochlorophyllide to chlorophyllide. This is the procedure for recording 77K fluorescence spectra. For romm temperature fluorescence spectra, it is more delicate.
Of course, you cannot get a fluorescence spectrum under total dark conditions! I you are interested, I can give you access to a dropbox where are stored many papers about fluorescence measurements of protochlorophyllide. I just need your e-mail address.
Sincerely yours,
Benoît Schoefs
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
There is sufficient literature related to inhibition of PS II activity, but very few on blocking PS I activity in leaves. Kindly enlighten me on the blocking of PS I ETR and/or CEF of electrons around PS I.
Relevant answer
Answer
Plus 1 for DBMIB.
  • asked a question related to Chlorophyll Fluorescence
Question
5 answers
I would like to get an idea of the depth of light penetration using calibrated chl fluorescence (and transmittance if necessary) depth profiles. Casts were performed before dawn yielding poor PAR profiles.
Is there an up to date version of the Morel 1988 equation: Ctot = 4910*Ze-1.34?
Relevant answer
Answer
Hi Nicolas,
you can use the model of morel (1988) and take a look to Morel and Maritorrena (2001) for updated parameterizations.
Besides, you can use standard models for IOPs in case 1 waters, see for instance this publication by André morel which give a good summary of all these relationships (MOrel, 2009), and then calculate Kd as a function of IOPs using MOrel and Loisel (1998) pour each wavelenghts to get Ed at each wavelenght, and integrate over the visible domain.
hope it helps
hubert
Morel, A., and S. Maritorena (2001). Bio-optical properties of oceanic waters: A reappraisal. Journal of Geophysical research, 106, 7763-7780
Morel, A. and J.F. Berthon (1989). Surface pigments, algal biomass profiles, and potential production of the euphotic layer: Relationships reinvestigated in view of remote-sensing applications, Limnology and Oceanography, 34, 1545-1562.
Morel, A. (1988). Optical modeling of the upper ocean in relation to its biogenous matter content (case 1 water), Journal of Geophysical Research, 93, 10,749-10,768.
Morel, A. and H. Loisel (1998). Apparent optical properties of oceanic water: Dependence on the molecular scattering contribution. Applied Optics, 37, 4765-4774.
Morel, A. (2009). Are the empirical relationships describing the bio-optical properties of case 1 waters consistent and internally compatible? Journal of Geophysical Research, 114, C01016, doi:10.1029/2008JC004803.
  • asked a question related to Chlorophyll Fluorescence
Question
13 answers
Please let me know in terms of F0, Fm , Fv/Fm.
Relevant answer
Answer
Thanks a lot for this guidance. I am growing two types of plants under low light stress. One is japonica variety Akitokomachi and its Phytochrome A mutant, A0410. I am seeing the total chlorophyll content of A0410 is increasing than Akitokomachi under shade( having 25% natural light). Can you please let me know the expected result for Fv/Fm for Akitokomachi ( wild type) and its Phytochrome A mutant ( A0410).
Please guide me :)