Application of Polyelectrolyte Theory to the Study of the B-Z Transition in DNA (1)

Abstract

We have used the polyelectrolyte theory to study the ionic strength dependence of the B-Z equilibrium in DNA. A DNA molecule is molded as an infinitely long continuously charged cylinder of radius a with reduced linear charge density q. The parameters a and q for the B and Z forms were taken from X-ray data: a _B = 1nm, q _B = 4.2, a _z = 0.9 nm and q _z = 3.9. A simple theory shows that at low ionic strengths (when Debye screening length r _D>>a) the electrostatic free energy difference F ^el _Bz = F ^el _Z - F ^el _B increases with increasing ionic strength since q _B>q_z. At high ionic strengths (when r _D<<a) the F ^el _BZ would go on growing with increasing ionic strength if the inequality q _B/^a _B<q_z/a _z were valid. In the converse case when q _z/q _B<a_z/a _B the F ^el _BZ value decreases with increasing salt concentration at high ionic strength. Since X-ray data correspond to the latter case, theory predicts that the F ^el _BZ value reaches a maximum at an intermediate ionic strength of about 0.1 M (where r _D～a). We also performed rigorous calculations based on the Poisson-Boltzmann equation. These calculations have confirmed the above criterion of nonmonotonous behaviour of the F ^el _BZ value as a function of ionic strength. Different theoretical predictions for the B-Z transition in linear and superhelical molecules are discussed. Theory predicts specifically that at a very low ionic strength the Z form may prove to be more stable than the B form. Thus, one can observe the Z-B-Z transition with increasing ionic strength. In the light of our theoretical findings we discuss numerous experimental data on the B-Z transition in linear and superhelical DNA.     

Highly polar environments catalyze the unfolding of PrPC helix 1

The first α-helix (H1) likely plays an important role in the conversion of the cellular prion protein (PrP^C) into its pathogenic isoform (PrP^Sc). In this conversion, H1 may either have to unfold or may represent a site of intermolecular contact. A recent molecular dynamics simulation suggested that H1 can unfold if it is detached from the protein core (Hirschberger et al. in Biophys J 90:3908, 2006). It has been hypothesized that the high dielectric constant ε _S of the bulk water environment facilitates the unfolding of H1. To check this hypothesis, we performed a number of replica exchange molecular dynamics simulations of an H1 peptide in solvents of different ε _S . We found that the equilibrium helix fraction in water is less than 40%, in agreement with previous experimental findings, and that the helix unfolds much faster in water than in less polar solvents. The kinetically stabilizing effect of the organic solvents is largely unspecific and correlates well with their dielectric constant ε _S .     

A note on the excitation of nerve pathways

LetS denote the intensity of a stimulus, ν the frequency of discharge of a fiber, and ν _T the integral frequency of discharge of a nerve pathway. The relation between ν _T andS can be derived when the relation between ν andS, as well as the distribution function of the fiber thresholds are given. It is investigated under what conditions the functions ν _T (S) and ν(s) will be both of the same exponential form, and it is shown that this can happen only ifS exceeds the highest threshold of the pathway.     

Local Osmosis and Isotonic Transport

Osmotically driven water flow, u (cm/s), between two solutions of identical osmolarity, c_o (300 mM in mammals), has a theoretical isotonic maximum given by u = j/c_o, where j (moles/cm²/s) is the rate of salt transport. In many experimental studies, transport was found to be indistinguishable from isotonic. The purpose of this work is to investigate the conditions for u to approach isotonic. A necessary condition is that the membrane salt/water permeability ratio, ε, must be small: typical physiological values are ε = 10⁻³ to 10⁻⁵, so ε is generally small but this is not sufficient to guarantee near-isotonic transport. If we consider the simplest model of two series membranes, which secrete a tear or drop of sweat (i.e., there are no externally-imposed boundary conditions on the secretion), diffusion is negligible and the predicted osmolarities are: basal = c_o, intracellular ≈ (1 + ε)c_o, secretion ≈ (1 + 2ε)c_o, and u ≈ (1 − 2ε)j/c_o. Note that this model is also appropriate when the transported solution is experimentally collected. Thus, in the absence of external boundary conditions, transport is experimentally indistinguishable from isotonic. However, if external boundary conditions set salt concentrations to c_o on both sides of the epithelium, then fluid transport depends on distributed osmotic gradients in lateral spaces. If lateral spaces are too short and wide, diffusion dominates convection, reduces osmotic gradients and fluid flow is significantly less than isotonic. Moreover, because apical and basolateral membrane water fluxes are linked by the intracellular osmolarity, water flow is maximum when the total water permeability of basolateral membranes equals that of apical membranes. In the context of the renal proximal tubule, data suggest it is transporting at near optimal conditions. Nevertheless, typical physiological values suggest the newly filtered fluid is reabsorbed at a rate u ≈ 0.86 j/c_o, so a hypertonic solution is being reabsorbed. The osmolarity of the filtrate c_F (M) will therefore diminish with distance from the site of filtration (the glomerulus) until the solution being transported is isotonic with the filtrate, u = j/c_F.With this steady-state condition, the distributed model becomes approximately equivalent to two membranes in series. The osmolarities are now: c_F ≈ (1 − 2ε)j/c_o, intracellular ≈ (1 − ε)c_o, lateral spaces ≈ c_o, and u ≈(1 + 2ε)j/c_o. The change in c_F is predicted to occur with a length constant of about 0.3 cm. Thus, membrane transport tends to adjust transmembrane osmotic gradients toward εc_o, which induces water flow that is isotonic to within order ε. These findings provide a plausible hypothesis on how the proximal tubule or other epithelia appear to transport an isotonic solution.     

Chlorophyll fluorescence performance of sweet almond [Prunus dulcis (Miller) D. Webb] in response to salinity stress induced by NaCl

One-year old sweet almond (Prunus dulcis) seedlings were submitted to four levels of salt stress induced by NaCl, namely 0.3, 0.5, 0.7, and 1.0 S m⁻¹. Effects of salt stress on a range of chlorophyll (Chl) fluorescence parameters (Chl FPs) and Chl contents were investigated in order to establish an eco-physiological characterization of P. dulcis to salinity. Salt stress promoted an increase in F₀, F_s, and F₀/F_m and a decrease in F_m, F′_m, F_v/F_m, q_P, ΔF/F′_m, F_v/F₀, and UQF_(rel), in almost all Chl fluorescence yields (FY) and FPs due to its adverse effect on activity of photosystem 2. No significant changes were observed for quenchings q_N, NPQ, and q_N(rel). The contents of Chl a and b and their ratio were also significantly reduced at increased salt stress. In general, adverse salinity effects became significant when the electric conductivity of the nutrient solution (EC_n) exceeded 0.3 S m⁻¹. The most sensitive salt stress indicators were F_v/F₀ and Chl a content, and they are thus best used for early salt detection in P. dulcis. Monitoring of a simple Chl FY, such as F₀, also gave a good indication of induced salt stress due to the significant correlations observed between the different Chl FYs and FPs. Even essential Chl FYs, like F₀, F_m, F′_m, and F_s, and mutually independent Chl FPs, like F_v/F₀ and q_P, were strongly correlated with each other.     

Chlorophyll fluorescence in micropropagated <Emphasis Type="Italic">Rhododendron ponticum</Emphasis> subsp. <Emphasis Type="Italic">baeticum</Emphasis> plants in response to different irradiances

The aim of this study was to investigate acclimation of micropropagated plants of Rhododendron ponticum subsp. baeticum to different irradiances and recovery after exposure to high irradiance. Plants grown under high (HL) or intermediate (IL) irradiances displayed higher values of maximum electron transport rate (ETR_max) and light saturation coefficient (E_k) than plants grown under low irradiance (LL). The capacity of tolerance to photoinhibition (as assessed by the response of photochemical quenching, q_p) varied as follows: HL > IL > LL. Thermal energy dissipation (q_N) was also affected by growth irradiance, with higher saturating values being observed in HL plants. Light-response curves suggested a gradual replacement of q_p by q_N with increasing irradiance. Following exposure to irradiance higher than 1500 μmol m⁻² s⁻¹, a prolonged reduction of the maximal photochemical efficiency of PS 2 (F_v/F_m) was observed in LL plants, indicating the occurrence of chronic photoinhibition. In contrary, the decrease in F_v/F_m was quickly reverted in HL plants, pointing to a reversible photoinhibition.     

Simulation of Pulse-Amplitude-Modulated (PAM) fluorescence: Limitations of some PAM-parameters in studying environmental stress effects

Fluorescence parameters obtained during steady-state electron transport are frequently used to evaluate photosynthetic efficiency of plants. We studied the behaviour of those parameters as a function of irradiance-adapted fluorescence yields F_S and F'_M. Applied simulations showed that photochemical quenching evaluated by q_P is greatly influenced by the steady-state fluorescence level (F_S), and that its evolution is not complementary to non-photochemical quenching (q_N). On the other hand, the relative photochemical and non-photochemical quenching coefficients (q_P(rel) and q_N(rel)) proposed by Buschmann (1995) represent better the balance between the energy dissipation pathways. However, these relative parameters are also non-linearly related when the F_S level is varied. We investigated the application of a new parameter, the relative unquenched fluorescence (UQF_(rel)) which takes into account the fraction of non-quenched fluorescence yield (F_S), which is related to closed photosystem 2 reaction centres not participating in electron transport. By using computer simulations and real in vivo measurements, we found that this new parameter is complementary to q_P(rel) and q_N(rel), which may facilitate the use of PAM fluorescence as diagnostic tool in environmental studies.     

Kinetic processes initiated by a nanosecond high-current discharge in hot air

Results from numerical investigations of kinetic processes initiated by a pulsed nanosecond discharge in hot (T ₀ ≥ 1000 K) air at atmospheric pressure are presented. The calculated results on the dynamics of the electron density, the population of the N₂(B³Π _g ) and N₂(C³Π _u ) states, and the atomic oxygen density in the axial discharge region agree with experiment. The method for determining the gas temperature by measuring the rotational structure of the transitions N₂(C³Π _u , ν) → N₂(B³Π _g , ν′) of the 2⁺ nitrogen system is analyzed. It is shown that, in relatively weak reduced electric fields typical of secondary discharge pulses, the electron impact excitation of the N₂(C³Π _u ) state from the ground state N₂(X¹Σ _g ⁺) can be accompanied by its additional step population from the N₂(B³Π _g ), N₂(a′Σ _u ⁻), and other electronic states. This effect substantially influences the rotational distribution of nitrogen molecules in the N₂(C³Π _u , ν) state; moreover, the temperature determined from this distribution can be substantially higher than the true gas temperature.     

Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains

Quantitative structures are obtained at 30°C for the fully hydrated fluid phases of palmitoyloleoylphosphatidylcholine (POPC), with a double bond on the sn-2 hydrocarbon chain, and for dierucoylphosphatidylcholine (di22:1PC), with a double bond on each hydrocarbon chain. The form factors F(q _z ) for both lipids are obtained using a combination of three methods. (1) Volumetric measurements provide F(0). (2) X-ray scattering from extruded unilamellar vesicles provides ΙF(q _z )Ι for low q _z . (3) Diffuse X-ray scattering from oriented stacks of bilayers provides ΙF(q _z )Ι for high q _z . Also, data using method (2) are added to our recent data for dioleoylphosphatidylcholine (DOPC) using methods (1) and (3); the new DOPC data agree very well with the recent data and with (4) our older data obtained using a liquid crystallographic X-ray method. We used hybrid electron density models to obtain structural results from these form factors. The result for area per lipid (A) for DOPC 72.4 ± 0.5 Ų agrees well with our earlier publications, and we find A = 69.3 ± 0.5 Ų for di22:1PC and A = 68.3 ± 1.5 Ų for POPC. We obtain the values for five different average thicknesses: hydrophobic, steric, head-head, phosphate-phosphate and Luzzati. Comparison of the results for these three lipids and for our recent dimyristoylphosphatidylcholine (DMPC) determination provides quantitative measures of the effect of unsaturation on bilayer structure. Our results suggest that lipids with one monounsaturated chain have quantitative bilayer structures closer to lipids with two monounsaturated chains than to lipids with two completely saturated chains.     

Up-regulation of cyclic electron flow and down-regulation of linear electron flow in antisense-<Emphasis Type="Italic">rca</Emphasis> mutant rice

To investigate how excess excitation energy is dissipated in a ribulose-1,5-bisphospate carboxylase/oxygenase activase antisense transgenic rice with net photosynthetic rate (P _N) half of that of wild type parent, we measured the response curve of P _N to intercellular CO₂ concentration (C _i), electron transport rate (ETR), quantum yield of open photosystem 2 (PS2) reaction centres under irradiation (F_v′/F_m′), efficiency of total PS2 centres (Φ_PS2), photochemical (q_P) and non-photochemical quenching (NPQ), post-irradiation transient increase in chlorophyll (Chl) fluorescence (PITICF), and P700⁺ re-reduction. Carboxylation efficiency dependence on C _i, ETR at saturation irradiance, and F_v′/F_m′, Φ_PS2, and q_P under the irradiation were significantly lower in the mutant. However, NPQ, energy-dependent quenching (q_E), PITICF, and P700⁺ re-reduction were significantly higher in the mutant. Hence the mutant down-regulates linear ETR and stimulates cyclic electron flow around PS1, which may generate the ΔpH to support NPQ and q_E for dissipation of excess excitation energy.     

Culture–area relation in Axelrod’s model for culture dissemination

Axelrod’s model for culture dissemination offers a nontrivial answer to the question of why there is cultural diversity given that people’s beliefs have a tendency to become more similar to each other’s as they interact repeatedly. The answer depends on the two control parameters of the model, namely, the number F of cultural features that characterize each agent, and the number q of traits that each feature can take on, as well as on the size A of the territory or, equivalently, on the number of interacting agents. Here, we investigate the dependence of the number C of distinct coexisting cultures on the area A in Axelrod’s model, the culture–area relationship, through extensive Monte Carlo simulations. We find a non-monotonous culture–area relation, for which the number of cultures decreases when the area grows beyond a certain size, provided that q is smaller than a threshold value q _c = q _c (F) and F ≥ 3. In the limit of infinite area, this threshold value signals the onset of a discontinuous transition between a globalized regime marked by a uniform culture (C = 1), and a completely polarized regime where all C = q ^F possible cultures coexist. Otherwise, the culture–area relation exhibits the typical behavior of the species–area relation, i.e., a monotonically increasing curve the slope of which is steep at first and steadily levels off at some maximum diversity value.     

On the Inference of Large Phylogenies with Long Branches: How Long Is Too Long?

The accurate reconstruction of phylogenies from short molecular sequences is an important problem in computational biology. Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In Daskalakis et al. (in Probab. Theory Relat. Fields 2010), building on the work of Mossel (Trans. Am. Math. Soc. 356(6):2379–2404, 2004), a tight sequence-length requirement was obtained for the simple CFN model of substitution, that is, the case of a two-state symmetric rate matrix Q. In particular the required sequence length for high-probability reconstruction was shown to undergo a sharp transition (from O(log n) to poly(n), where n is the number of leaves) at the “critical” branch length g _ML(Q) (if it exists) of the ancestral reconstruction problem defined roughly as follows: below g _ML(Q) the sequence at the root can be accurately estimated from sequences at the leaves on deep trees, whereas above g _ML(Q) information decays exponentially quickly down the tree.     

Photosystem 2 photochemistry and pigment composition of a yellow mutant of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) under different irradiances

A yellow leaf colouration mutant (named ycm) generated from rice T-DNA insertion lines was identified with less grana lamellae and low thylakoid membrane protein contents. At weak irradiance [50 μmol(photon) m⁻² s⁻¹], chlorophyll (Chl) contents of ycm were ≈20 % of those of WT and Chl a/b ratios were 3-fold that of wild type (WT). The leaf of ycm showed lower values in the actual photosystem 2 (PS2) efficiency (Φ_PS2), photochemical quenching (q_P), and the efficiency of excitation capture by open PS2 centres 1 (F_v′/F_m′) than those of WT, except no difference in the maximal efficiency of PS2 photochemistry (F_v/F_m). With progress in irradiance [100 and 200 μmol(photon) m⁻² s⁻¹], there was a change in the photosynthetic pigment stoichiometry. In ycm, the increase of total Chl contents and the decrease in Chl a/b ratio were observed. Φ_PS2, q_P, and F_v′/F_m′ of ycm increased gradually along with the increase of irradiance but still much less than in WT. The increase of xanthophyll ratio [(Z+A)/(V+A+Z)] associated with non-photochemical quenching (q_N) was found in ycm which suggested that ycm dissipated excess energy through the turnover of xanthophylls. No significant differences in pigment composition were observed in WT under various irradiances, except Chl a/b ratio that gradually decreased. Hence the ycm mutant developed much more tardily than WT, which was caused by low photon energy utilization independent of irradiance.     

Kinetic models of photosystem II should accommodate the effect of donor side quenching on variable chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence in the microseconds time range

Quantitative data on laser flash-induced variable fluorescence in the 100 ns to 1 ms time range (Belyaeva et al. in Photosynth Res 98:105–119, 2008) confirming those of others (Steffen et al. in Biochemistry 40:173–180, 2001, Biochemistry 44:3123–3132, 2005; Belyaeva et al. in Biophysics 51(6):976–990, 2006), need a substantial correction with respect to magnitude of the normalized variable fluorescence associated with single turnover-induced charge separation in RCs of PS II. Their data are conclusive with the involvement of donor side quenching, the release of which occurs with a rate constant in the range of tens of ms⁻¹, and presumed to be associated with reduction of Y_\textz ⁺ Y_{\text{z}}^{ + } by the OEC.     

Influence of Manganese Toxicity on Photosynthesis in Ricebean (Vigna Umbellata) Seedlings

Influence of manganese (Mn) toxicity on photosynthesis in ricebean (Vigna umbellata) was studied by the measurement of gas exchange characteristics and chlorophyll fluorescence parameters. The net photosynthetic rate (P _N), transpiration rate (E), and stomatal conductance (g _s) were reduced with increasing Mn concentration in nutrient solution. The reduction in g _s and E was more pronounced at 6 d of Mn treatment. However, P _N declined at 2 d of Mn treatment implying that the reduction in photosynthesis was not due to the direct effect of Mn on stomatal regulation. Mn did not affect the maximum efficiency of photosystem 2 (PS2) photochemistry (F_v/F_m). A reduction in photochemical quenching (q_P) and excitation capture efficiency of open PS2 (F_v′/F_m′) with a concomitant increase in q_N was observed. This implies that reduced demand for ATP and NADPH due to the reduction in photosynthesis causes a down-regulation of PS2 photochemistry and thus a high pH gradient (increase in q_N) and limited electron transport (decreased q_P). This revised version was published online in August 2006 with corrections to the Cover Date.     

Dombrock blood group (DO): assignment to chromosome 12p

The Dombrock blood group system (DO) is a common polymorphism in Caucasians, represented by two red cell antigen alleles. In a linkage study in our family material of 832 families from the Copenhagen area, we found a strong indication of tight linkage with the two flanking DNA polymorphisms D12S358 (z = 7.66; at θ _M = 0.001, θ _F = 0.031) and D12S364 (z = 8.53; at θ _M = 0.068, θ _F = 0.031). DO is assigned to the region 12p13.2– 12p12.1 by physically localised markers. Received: 18 April 1996 / Revised: 4 July 1996     

The independent detection of drought stress and leaf density using hyperspectral resolution data

Measurement of vegetation drought stress or leaf density is essential in ecosystem and agronomic studies. The normalized differential vegetation index (NDVI), a widely used vegetation index in remote sensing, seems to have some limitations as it is known to be affected by both drought stress and leaf density. A field experiment was conducted, using two-year-old potted Quercus serrata (a deciduous tree) and Q. glauca (an evergreen tree), to determine the optimal indices of vegetation drought stress or leaf density that have the least a simultaneous effect, and to test if the existing vegetation indices are useful for independently detecting drought stress or leaf density. The results showed that NDVI and similar indices, which utilize the difference or ratio between the reflectance of red and near infrared bands, such as the ratio vegetation index (RVI), the difference vegetation index (DVI), the atmospherically resistant vegetation index (ARVI), the renormalized difference vegetation index (RDVI), the enhanced vegetation index (EVI), the perpendicular vegetation index (PVI), soil-adjusted vegetation index (SAVI) and the improved variants of SAVI, were effective for the independent detection of leaf density but relatively ineffective for drought stress because they were significantly affected by leaf area index (LAI). Similarly, vegetation indices developed as detectors of vegetation stress, such as the water index (WI), the stress index (SI) and the derivative chlorophyll index (DCI), showed weak correlation (r) and partial correlation (r _p) with leaf water content (LWC). The optimal hyperspectral indices were proposed as (F _502.8 − F _852.0)/(F _502.8 + F _852.0) for LWC (r = 0.847, r _p = 0.849) and R ₇₅₀/R ₅₅₀ (R750R550; Lichtenthaler et al. in J Plant Physiol 148:483–493, 1996) for LAI (r = 0.926, r _p = 0.940) where R _λ and F _λ represent reflectance and first derivatives at wavelength λ nm, respectively. A simulation of lower spectral sampling intervals (ca. 3-nm intervals of original to 10-nm intervals) indicated that it will be necessary to check the appropriateness of the derivative indices approximate to the proposed indices before application because derivative spectra are less smooth as a function of wavelength than reflectance spectra.     

Nickel(II)-substituted azurin I from Alcaligenes xylosoxidans as characterized by resonance Raman spectroscopy at cryogenic temperature

Metal-substituted blue copper proteins (cupredoxins) have been successfully used to study the effect of metal-ion identity on their active-site properties, specifically the coordination geometry and metal–ligand bond strengths. In this work, low-temperature (77 K) resonance Raman (RR) spectra of the blue copper protein Alcaligenes xylosoxidans azurin I and its Ni(II) derivative are reported. A detailed analysis of all observed bands is presented and responsiveness to metal substitution is discussed in terms of structural and bonding changes. The native cupric site exhibits a RR spectrum characteristic of a primarily trigonal planar (type 1) coordination geometry, identified by the ν(Cu–S)_Cys markers at 373, 399, 409, and 430 cm⁻¹. Replacement of Cu(II) with Ni(II) results in optical and RR spectra that reveal (1) a large hypsochromic shift in the main (Cys)S → M(II) charge-transfer absorption from 622 to 440 nm, (2) greatly reduced metal–thiolate bonding interaction, indicated by substantially lower ν(Ni–S)_Cys stretching frequencies, (3) elevation of the cysteine ν(C _β –S) stretching, amide III, and ρ _s(C _β H₂) scissors vibrational modes, and (4) primarily four-coordinated, trigonally distorted tetrahedral geometry of the Ni(II) site that is marked by characteristic ν(Ni–S)_Cys stretching RR bands at 347, 364, and 391 cm⁻¹. Comparisons of the electronic and vibrational properties between A. xylosoxidans azurin I and its closely structurally related azurin from Pseudomonas aeruginosa are made and discussed. For cupric azurins, the intensity-weighted average M(II)–S(Cys) stretching frequencies are calculated to be ν(Cu–S)_iwa = 406.3 and 407.6 cm⁻¹, respectively. These values decreased to ν(Ni–S)_iwa = 359.3 and 365.5 cm⁻¹, respectively, after Ni(II) → Cu(II) exchange, suggesting that the metal–thiolate interactions are similar in the two native proteins but are much less alike in their Ni(II)-substituted forms.     

Short-term responses of photosynthetic membrane lipids and photochemical efficiency in plants of <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> and <Emphasis Type="Italic">Vigna unguiculata</Emphasis> submitted to high irradiance

Primary leaves of young plants of common bean (Phaseolus vulgaris cv. Carioca and Negro Huasteco) and cowpea (Vigna unguiculata Walp cv. Epace 10) were exposed to high irradiance (HI) of 2 000 μmol m⁻² s⁻¹ for 10, 20, and 30 min. The initial fluorescence (F₀) was nearly constant in response to HI in each genotype except for Carioca. A distinct reduction of maximum fluorescence (F_m) was clearly observed in stressed genotypes of beans after 20 min followed by a slight recovery for the longer stress times. In common bean, the maximum quantum yield (F_v/F_m) was reduced slowly from 10 to 30 min of HI. In cowpea, only a slight reduction of F_v/F_m was observed at 20 min followed by recovery to normal values at 30 min. HI resulted in changes in the photochemical (q_P) and non-photochemical (q_N) quenching in both species, but to a different extent. In cowpea plants, more efficiency in the use of the absorbed energy under photoinhibitory conditions was related to increase in q_P and decrease in q_N. In addition, lipid peroxidation changed significantly in common bean genotypes with an evident increase after 20 min of HI. Hence the photosynthetic apparatus of cowpea was more tolerant to HI than that of common bean and the integrity of cowpea cell membranes was apparently maintained under HI.     

How to correctly determine the different chlorophyll fluorescence parameters and the chlorophyll fluorescence decrease ratio R<Subscript>Fd</Subscript> of leaves with the PAM fluorometer

This contribution is a practical guide to the measurement of the different chlorophyll (Chl) fluorescence parameters and gives examples of their development under high-irradiance stress. From the Chl fluorescence induction kinetics upon irradiation of dark-adapted leaves, measured with the PAM fluorometer, various Chl fluorescence parameters, ratios, and quenching coefficients can be determined, which provide information on the functionality of the photosystem 2 (PS2) and the photosynthetic apparatus. These are the parameters F_v, F_m, F₀, F_m′, F_v′, NF, and ΔF, the Chl fluorescence ratios F_v/F_m, F_v/F₀, ΔF/F_m′, as well as the photochemical (q_P) and non-photochemical quenching coefficients (q_N, q_CN, and NPQ). q_N consists of three components (q_N = q_E + q_T + q_I), the contribution of which can be determined via Chl fluorescence relaxation kinetics measured in the dark period after the induction kinetics. The above Chl fluorescence parameters and ratios, many of which are measured in the dark-adapted state of leaves, primarily provide information on the functionality of PS2. In fully developed green and dark-green leaves these Chl fluorescence parameters, measured at the upper adaxial leaf side, only reflect the Chl fluorescence of a small portion of the leaf chloroplasts of the green palisade parenchyma cells at the upper outer leaf half. Thus, PAM fluorometer measurements have to be performed at both leaf sides to obtain information on all chloroplasts of the whole leaf. Combined high irradiance (HI) and heat stress, applied at the upper leaf side, strongly reduced the quantum yield of the photochemical energy conversion at the upper leaf half to nearly zero, whereas the Chl fluorescence signals measured at the lower leaf side were not or only little affected. During this HL-stress treatment, q_N, q_CN, and NPQ increased in both leaf sides, but to a much higher extent at the lower compared to the upper leaf side. q_N was the best indicator for non-photochemical quenching even during a stronger HL-stress, whereas q_CN and NPQ decreased with progressive stress even though non-photochemical quenching still continued. It is strongly recommended to determine, in addition to the classical fluorescence parameters, via the PAM fluorometer also the Chl fluorescence decrease ratio R_Fd (F_d/F_s), which, when measured at saturation irradiance is directly correlated to the net CO₂ assimilation rate (_{P N}) of leaves. This R_Fd-ratio can be determined from the Chl fluorescence induction kinetics measured with the PAM fluorometer using continuous saturating light (cSL) during 4–5 min. As the R_Fd-values are fast measurable indicators correlating with the photosynthetic activity of whole leaves, they should always be determined via the PAM fluorometer parallel to the other Chl fluorescence coefficients and ratios.